1
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Ortiz D, Pekár S, Dianat M. A consequential one-night stand: Episodic historical hybridization leads to mitochondrial takeover in sympatric desert ant-eating spiders. Mol Phylogenet Evol 2024; 199:108167. [PMID: 39103025 DOI: 10.1016/j.ympev.2024.108167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 07/03/2024] [Accepted: 08/01/2024] [Indexed: 08/07/2024]
Abstract
Disentangling the genomic intricacies underlying speciation and the causes of discordance between sources of evidence can offer remarkable insights into evolutionary dynamics. The ant-eating spider Zodarion nitidum, found across the Middle East and Egypt, displays yellowish and blackish morphs that co-occur sympatrically. These morphs additionally differ in behavioral and physiological features and show complete pre-mating reproductive isolation. In contrast, they possess similar sexual features and lack distinct differences in their mitochondrial DNA. We analyzed both Z. nitidum morphs and outgroups using genome-wide and additional mitochondrial DNA data. The genomic evidence indicated that Yellow and Black are reciprocally independent lineages without signs of recent admixture. Interestingly, the sister group of Yellow is not Black but Z. luctuosum, a morphologically distinct species. Genomic gene flow analyses pinpointed an asymmetric nuclear introgression event, with Yellow contributing nearly 5 % of its genome to Black roughly 320,000 years ago, intriguingly aligning with the independently estimated origin of the mitochondrial DNA of Black. We conclude that the blackish and yellowish morphs of Z. nitidum are long-diverged distinct species, and that the ancient and modest genomic introgression event registered resulted in a complete mitochondrial takeover of Black by Yellow. This investigation underscores the profound long-term effects that even modest hybridization events can have on the genome of organisms. It also exemplifies the utility of phylogenetic networks for estimating historical events and how integrating independent lines of evidence can increase the reliability of such estimations.
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Affiliation(s)
- David Ortiz
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czechia.
| | - Stano Pekár
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Malahat Dianat
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czechia; Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czechia
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2
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Preiss R, Fletcher E, Garshol LM, Foster B, Ozsahin E, Lubberts M, van der Merwe G, Krogerus K. European farmhouse brewing yeasts form a distinct genetic group. Appl Microbiol Biotechnol 2024; 108:430. [PMID: 39093468 PMCID: PMC11297104 DOI: 10.1007/s00253-024-13267-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 07/22/2024] [Accepted: 07/24/2024] [Indexed: 08/04/2024]
Abstract
The brewing industry is constantly evolving, driven by the quest for novel flavours and fermentation characteristics that cater to evolving consumer preferences. This study explores the genetic and phenotypic diversity of European farmhouse yeasts, traditionally used in rural brewing practices and maintained outside of pure culture industrial yeast selection. We isolated landrace brewing yeast strains from diverse geographical locations across Europe, including Norway, Lithuania, Latvia, and Russia, and also included African farmhouse brewing strains from Ghana. Our genomic analysis using long-read and short-read whole genome sequencing uncovered a genetically distinct group that diverges from industrial brewing yeasts. This group, which is closely related to ale brewing strains, is preliminarily named the 'European Farmhouse' group and shows greater predicted admixture from Asian fermentation strains. Through genomic and phenotypic analyses, including flavour metabolite analysis via headspace gas chromatography-mass spectrometry, sugar metabolite analysis via high-performance liquid chromatography, and wort fermentation analysis, we found a broad spectrum of fermentation capabilities, from rapid and efficient fermentation to unique aroma and flavour compound profiles, potentially offering novel traits for brewing applications. This study highlights the importance of preservation of brewing cultural heritage knowledge and resources including yeast cultures. KEY POINTS: • A large set of geographically diverse farmhouse brewing strains were characterized • Norwegian and Baltic farmhouse brewing strains form a distinct genetic group • Farmhouse strains show considerable diversity in fermentation and flavour formation.
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Affiliation(s)
| | - Eugene Fletcher
- Escarpment Laboratories, Guelph, ON, Canada
- Carleton University, Ottawa, Canada
| | | | - Barret Foster
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Emine Ozsahin
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Mark Lubberts
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - George van der Merwe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Kristoffer Krogerus
- VTT Technical Research Centre of Finland, Tekniikantie 21, 02150, Espoo, Finland.
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3
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Beer MA, Trumbo DR, Rautsaw RM, Kozakiewicz CP, Epstein B, Hohenlohe PA, Alford RA, Schwarzkopf L, Storfer A. Spatial variation in genomic signatures of local adaptation during the cane toad invasion of Australia. Mol Ecol 2024; 33:e17464. [PMID: 38994885 DOI: 10.1111/mec.17464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 06/09/2024] [Accepted: 07/01/2024] [Indexed: 07/13/2024]
Abstract
Adaptive evolution can facilitate species' range expansions across environmentally heterogeneous landscapes. However, serial founder effects can limit the efficacy of selection, and the evolution of increased dispersal during range expansions may result in gene flow swamping local adaptation. Here, we study how genetic drift, gene flow and selection interact during the cane toad's (Rhinella marina) invasion across the heterogeneous landscape of Australia. Following its introduction in 1935, the cane toad colonised eastern Australia and established several stable range edges. The ongoing, more rapid range expansion in north-central Australia has occurred concomitant with an evolved increase in dispersal capacity. Using reduced representation genomic data of Australian cane toads from the expansion front and from two areas of their established range, we test the hypothesis that high gene flow constrains local adaptation at the expansion front relative to established areas. Genetic analyses indicate the three study areas are genetically distinct but show similar levels of allelic richness, heterozygosity and inbreeding. Markedly higher gene flow or recency of colonisation at the expansion front have likely hindered local adaptation at the time of sampling, as indicated by reduced slopes of genetic-environment associations (GEAs) estimated using a novel application of geographically weighted regression that accounts for allele surfing; GEA slopes are significantly steeper in established parts of the range. Our work bolsters evidence supporting adaptation of invasive species post-introduction and adds novel evidence for differing strengths of evolutionary forces among geographic areas with different invasion histories.
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Affiliation(s)
- Marc A Beer
- School of Biological Sciences, Washington State University, Pullman, Washington, USA
| | - Daryl R Trumbo
- Department of Biology, Colorado State University Pueblo, Pueblo, Colorado, USA
| | - Rhett M Rautsaw
- School of Biological Sciences, Washington State University, Pullman, Washington, USA
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - Christopher P Kozakiewicz
- W.K. Kellogg Biological Station, Department of Integrative Biology, Michigan State University, Hickory Corners, Michigan, USA
| | - Brendan Epstein
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, Minnesota, USA
| | - Paul A Hohenlohe
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
| | - Ross A Alford
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Lin Schwarzkopf
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, Washington, USA
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4
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Wróbel A, Klichowska E, Nowak A, Nobis M. Alpine Extremophytes in Evolutionary Turmoil: Complex Diversification Patterns and Demographic Responses of a Halophilic Grass in a Central Asian Biodiversity Hotspot. Syst Biol 2024; 73:263-278. [PMID: 38141222 PMCID: PMC11282368 DOI: 10.1093/sysbio/syad073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 11/23/2023] [Accepted: 12/19/2023] [Indexed: 12/25/2023] Open
Abstract
Diversification and demographic responses are key processes shaping species evolutionary history. Yet we still lack a full understanding of ecological mechanisms that shape genetic diversity at different spatial scales upon rapid environmental changes. In this study, we examined genetic differentiation in an extremophilic grass Puccinellia pamirica and factors affecting its population dynamics among the occupied hypersaline alpine wetlands on the arid Pamir Plateau in Central Asia. Using genomic data, we found evidence of fine-scale population structure and gene flow among the localities established across the high-elevation plateau as well as fingerprints of historical demographic expansion. We showed that an increase in the effective population size could coincide with the Last Glacial Period, which was followed by the species demographic decline during the Holocene. Geographic distance plays a vital role in shaping the spatial genetic structure of P. pamirica alongside with isolation-by-environment and habitat fragmentation. Our results highlight a complex history of divergence and gene flow in this species-poor alpine region during the Late Quaternary. We demonstrate that regional climate specificity and a shortage of nonclimate data largely impede predictions of future range changes of the alpine extremophile using ecological niche modeling. This study emphasizes the importance of fine-scale environmental heterogeneity for population dynamics and species distribution shifts.
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Affiliation(s)
- Anna Wróbel
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387 Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Prof. St. Łojasiewicza 11, 30-348 Kraków, Poland
| | - Ewelina Klichowska
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387 Kraków, Poland
| | - Arkadiusz Nowak
- Botanical Garden, Center for Biological Diversity Conservation, Polish Academy of Sciences, Prawdziwka 2, 02-973 Warszawa, Poland
- Botanical Garden of the Wrocław University, Sienkiewicza 23, 50-335 Wrocław, Poland
| | - Marcin Nobis
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387 Kraków, Poland
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Cho MS, Kim Y, Kim SH, Jeon JH, Yang J, Kim SC. Phylogenetic relationships and genetic diversity of the Korean endemic Phedimus latiovalifolius (Crassulaceae) and its close relatives. Sci Rep 2024; 14:16255. [PMID: 39009598 PMCID: PMC11251145 DOI: 10.1038/s41598-024-63272-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/27/2024] [Indexed: 07/17/2024] Open
Abstract
Phedimus latiovalifolius (Y.N.Lee) D.C.Son & H.J.Kim is exclusively distributed in the high mountains in the Korean Peninsula, mainly along the Baekdudaegan mountain range. Despite its morphological and distributional distinction from other Phedimus Raf. species, its taxonomic identity and phylogenetic relationship with congeneric species remain unclear. This study employs genotyping-by-sequencing-derived genome-wide single nucleotide polymorphisms to establish the monophyly of P. latiovalifolius and its relationship with closely related species. Genetic diversity and population differentiation of P. latiovalifolius are also assessed to provide baseline genetic information for future conservation and management strategies. Our phylogenetic analyses robustly demonstrate the monophyletic nature of P. latiovalifolius, with P. aizoon (L.) 't Hart identified as its closest sister lineage. There is no genetic evidence supporting a hybrid origin of P. latiovalifolius from P. aizoon involving either P. ellacombeanus (Praeger) 't Hart or P. kamtschaticus (Fisch.) 't Hart. Population genetic analyses reveal two major groups within P. latiovalifolius. A higher genetic variation is observed in P. ellacombeanus than in the congeneric species. Notably, most of the genetic variation exists within P. latiovalifolius populations. Given its distribution and the potential role of Baekdudaegan as an East Asian Pleistocene refugia, P. latiovalifolius could be considered rare and endemic, persisting in the refugium across glacial/interglacial cycles.
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Affiliation(s)
- Myong-Suk Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Yongsung Kim
- Honam National Institute of Biological Resources, Mokpo, 58762, Korea
| | - Seon-Hee Kim
- Department of Botany, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Ji-Hyeon Jeon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - JiYoung Yang
- Institute for Dok-Do and Ulleung-Do Island, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
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6
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Wang SZ, Yan Y, Widlund M, Qian CC, Zhang LL, Zhang SJ, Li ZM, Cao P, Dai QY, Feng XT, Liu F, Wang L, Gao C, Fu QM, Hytönen MK, Lohi H, Savolainen P, Wang GD. Historic dog Furs Unravel the Origin and Artificial Selection of Modern Nordic Lapphund and Elkhound dog Breeds. Mol Biol Evol 2024; 41:msae108. [PMID: 38842255 PMCID: PMC11226788 DOI: 10.1093/molbev/msae108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/28/2024] [Accepted: 05/31/2024] [Indexed: 06/07/2024] Open
Abstract
The origins and extreme morphological evolution of the modern dog breeds are poorly studied because the founder populations are extinct. Here, we analyse eight 100 to 200 years old dog fur samples obtained from traditional North Swedish clothing, to explore the origin and artificial selection of the modern Nordic Lapphund and Elkhound dog breeds. Population genomic analysis confirmed the Lapphund and Elkhound breeds to originate from the local dog population, and showed a distinct decrease in genetic diversity in agreement with intense breeding. We identified eleven genes under positive selection during the breed development. In particular, the MSRB3 gene, associated with breed-related ear morphology, was selected in all Lapphund and Elkhound breeds, and functional assays showed that a SNP mutation in the 3'UTR region suppresses its expression through miRNA regulation. Our findings demonstrate analysis of near-modern dog artifacts as an effective tool for interpreting the origin and artificial selection of the modern dog breeds.
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Affiliation(s)
- Shi-Zhi Wang
- Key Laboratory of Genetic Evolution & Animal Models, Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Yu Yan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Malin Widlund
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Chen-Chang Qian
- Key Laboratory of Genetic Evolution & Animal Models, Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | | | - Shao-Jie Zhang
- Key Laboratory of Genetic Evolution & Animal Models, Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Zi-Mai Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Qing-Yan Dai
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Xiao-Tian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Feng Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Lu Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Chao Gao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Qiao-Mei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Marjo K Hytönen
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Hannes Lohi
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Peter Savolainen
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Guo-Dong Wang
- Key Laboratory of Genetic Evolution & Animal Models, Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
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7
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Tian R, Zhang Y, Kang H, Zhang F, Jin Z, Wang J, Zhang P, Zhou X, Lanyon JM, Sneath HL, Woolford L, Fan G, Li S, Seim I. Sirenian genomes illuminate the evolution of fully aquatic species within the mammalian superorder afrotheria. Nat Commun 2024; 15:5568. [PMID: 38956050 PMCID: PMC11219930 DOI: 10.1038/s41467-024-49769-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 06/12/2024] [Indexed: 07/04/2024] Open
Abstract
Sirenians of the superorder Afrotheria were the first mammals to transition from land to water and are the only herbivorous marine mammals. Here, we generated a chromosome-level dugong (Dugong dugon) genome. A comparison of our assembly with other afrotherian genomes reveals possible molecular adaptations to aquatic life by sirenians, including a shift in daily activity patterns (circadian clock) and tolerance to a high-iodine plant diet mediated through changes in the iodide transporter NIS (SLC5A5) and its co-transporters. Functional in vitro assays confirm that sirenian amino acid substitutions alter the properties of the circadian clock protein PER2 and NIS. Sirenians show evidence of convergent regression of integumentary system (skin and its appendages) genes with cetaceans. Our analysis also uncovers gene losses that may be maladaptive in a modern environment, including a candidate gene (KCNK18) for sirenian cold stress syndrome likely lost during their evolutionary shift in daily activity patterns. Genomes from nine Australian locations and the functionally extinct Okinawan population confirm and date a genetic break ~10.7 thousand years ago on the Australian east coast and provide evidence of an associated ecotype, and highlight the need for whole-genome resequencing data from dugong populations worldwide for conservation and genetic management.
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Affiliation(s)
- Ran Tian
- Integrative Biology Laboratory, Nanjing Normal University, Nanjing, 210023, China
| | - Yaolei Zhang
- BGI Research, Qingdao, 266555, China
- BGI Research, Shenzhen, 518083, China
- Qingdao Key Laboratory of Marine Genomics BGI Research, Qingdao, 266555, China
| | - Hui Kang
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
- The Innovation Research Center for Aquatic Mammals, and Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Fan Zhang
- Integrative Biology Laboratory, Nanjing Normal University, Nanjing, 210023, China
| | - Zhihong Jin
- Integrative Biology Laboratory, Nanjing Normal University, Nanjing, 210023, China
| | - Jiahao Wang
- BGI Research, Qingdao, 266555, China
- BGI Research, Shenzhen, 518083, China
| | - Peijun Zhang
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
| | - Xuming Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Janet M Lanyon
- School of the Environment, The University of Queensland, Lucia, 4072, Australia
| | - Helen L Sneath
- School of the Environment, The University of Queensland, Lucia, 4072, Australia
| | - Lucy Woolford
- School of Veterinary Sciences, The University of Adelaide, Roseworthy, 5371, Australia
| | - Guangyi Fan
- BGI Research, Qingdao, 266555, China.
- BGI Research, Shenzhen, 518083, China.
- Qingdao Key Laboratory of Marine Genomics BGI Research, Qingdao, 266555, China.
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, 518083, China.
| | - Songhai Li
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China.
- The Innovation Research Center for Aquatic Mammals, and Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Inge Seim
- Integrative Biology Laboratory, Nanjing Normal University, Nanjing, 210023, China.
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China.
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8
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Choi TY, Son DC, Oh A, Lee SR. Unveiling a potential threat to forest ecosystems: molecular diagnosis of Alliaria petiolata, a newly introduced alien plant in Korea. FRONTIERS IN PLANT SCIENCE 2024; 15:1395676. [PMID: 39011305 PMCID: PMC11246967 DOI: 10.3389/fpls.2024.1395676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 06/14/2024] [Indexed: 07/17/2024]
Abstract
Identifying stages of a species invasion in a new habitat (i.e., colonization, establishment, and landscape spread) and their primary determinants in biological invasion warrants attention, as it provides vital insights for preventing non-native species from becoming pervasive invaders. However, delineating invasion stages and their associated factors can pose significant challenges due to the ambiguous distinctions between these stages. Alliaria petiolata, one of the most noxious weeds in woodland habitats, has recently been introduced to Korea and observed in a few distant locations. Although the plant's spread has been relatively slow thus far, rapid spread is highly likely in the future, given the high invasive potential reported elsewhere. We indirectly diagnose the current status of A. petiolata invasion in Korea through the assessment of genetic diversity and phylogenetic inferences using genome-wide molecular markers and cytological data. We analyzed 86 individual samples collected from two native and six introduced populations, employing 1,172 SNPs. Our analysis estimated within- and among-population genetic diversity and included two clustering analyses. Furthermore, we investigated potential gene flow and reticulation events among the sampled populations. Our data unraveled that Korean garlic mustard exhibits a hexaploid ploidy level with two distinct chromosome numbers, 2n = 36 and 42. The extent of genetic diversity measured in Korean populations was comparable to that of native populations. Using genome-wide SNP data, we identified three distinct clusters with minor gene flow, while failing to detect indications of reticulation among Korean populations. Based on the multifaceted analyses, our study provides valuable insights into the colonization process and stressed the importance of closely monitoring A. petiolata populations in Korea.
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Affiliation(s)
- Tae-Young Choi
- Department of Biology Education, College of Education, Chosun University, Gwangju, Republic of Korea
| | - Dong Chan Son
- Division of Forest Biodiversity and Herbarium, Korea National Arboretum, Pocheon, Republic of Korea
| | - Ami Oh
- Department of Biology Education, College of Education, Chosun University, Gwangju, Republic of Korea
| | - Soo-Rang Lee
- Department of Biology Education, College of Education, Chosun University, Gwangju, Republic of Korea
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9
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Zhang T, Peng W, Xiao H, Cao S, Chen Z, Su X, Luo Y, Liu Z, Peng Y, Yang X, Jiang GF, Xu X, Ma Z, Zhou Y. Population genomics highlights structural variations in local adaptation to saline coastal environments in woolly grape. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1408-1426. [PMID: 38578160 DOI: 10.1111/jipb.13653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 03/04/2024] [Indexed: 04/06/2024]
Abstract
Structural variations (SVs) are a feature of plant genomes that has been largely unexplored despite their significant impact on plant phenotypic traits and local adaptation to abiotic and biotic stress. In this study, we employed woolly grape (Vitis retordii), a species native to the tropical and subtropical regions of East Asia with both coastal and inland habitats, as a valuable model for examining the impact of SVs on local adaptation. We assembled a haplotype-resolved chromosomal reference genome for woolly grape, and conducted population genetic analyses based on whole-genome sequencing (WGS) data from coastal and inland populations. The demographic analyses revealed recent bottlenecks in all populations and asymmetric gene flow from the inland to the coastal population. In total, 1,035 genes associated with plant adaptive regulation for salt stress, radiation, and environmental adaptation were detected underlying local selection by SVs and SNPs in the coastal population, of which 37.29% and 65.26% were detected by SVs and SNPs, respectively. Candidate genes such as FSD2, RGA1, and AAP8 associated with salt tolerance were found to be highly differentiated and selected during the process of local adaptation to coastal habitats in SV regions. Our study highlights the importance of SVs in local adaptation; candidate genes related to salt stress and climatic adaptation to tropical and subtropical environments are important genomic resources for future breeding programs of grapevine and its rootstocks.
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Affiliation(s)
- Tianhao Zhang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Forest Ecology and Conservation, Guangxi Colleges and Universities Key Laboratory for Cultivation and Utilization of Subtropical Forest Plantation, College of Forestry, Guangxi University, Nanning, 530004, China
- College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenjing Peng
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Hua Xiao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Shuo Cao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- Key Laboratory of Horticultural Plant Biology Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhuyifu Chen
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Xiangnian Su
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Forest Ecology and Conservation, Guangxi Colleges and Universities Key Laboratory for Cultivation and Utilization of Subtropical Forest Plantation, College of Forestry, Guangxi University, Nanning, 530004, China
| | - Yuanyuan Luo
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Zhongjie Liu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Yanling Peng
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Xiping Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Guo-Feng Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Forest Ecology and Conservation, Guangxi Colleges and Universities Key Laboratory for Cultivation and Utilization of Subtropical Forest Plantation, College of Forestry, Guangxi University, Nanning, 530004, China
| | - Xiaodong Xu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Zhiyao Ma
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Yongfeng Zhou
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- National Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
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10
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Geng FD, Liu MQ, Zhang XD, Wang LZ, Lei MF. Genomics of hybrid parallel origin in Aquilegia ecalcarata. BMC Ecol Evol 2024; 24:75. [PMID: 38844857 PMCID: PMC11155106 DOI: 10.1186/s12862-024-02266-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND The parallel evolution of similar traits or species provides strong evidence for the role of natural selection in evolution. Traits or species that evolved repeatedly can be driven by separate de novo mutations or interspecific gene flow. Although parallel evolution has been reported in many studies, documented cases of parallel evolution caused by gene flow are scarce by comparison. Aquilegia ecalcarata and A. kansuensis belong to the genus of Aquilegia, and are the closest related sister species. Mutiple origins of A. ecalcarata have been reported in previous studies, but whether they have been driven by separate de novo mutations or gene flow remains unclear. RESULTS In this study, We conducted genomic analysis from 158 individuals of two repeatedly evolving pairs of A. ecalcarata and A. kansuensis. All samples were divided into two distinct clades with obvious geographical distribution based on phylogeny and population structure. Demographic modeling revealed that the origin of the A. ecalcarata in the Eastern of China was caused by gene flow, and the Eastern A. ecalcarata occurred following introgression from Western A. ecalcarata population. Analysis of Treemix and D-statistic also revealed that a strong signal of gene flow was detected from Western A. ecalcarata to Eastern A. ecalcarata. Genetic divergence and selective sweep analyses inferred parallel regions of genomic divergence and identified many candidate genes associated with ecologically adaptive divergence between species pair. Comparative analysis of parallel diverged regions and gene introgression confirms that gene flow contributed to the parallel evolution of A. ecalcarata. CONCLUSIONS Our results further confirmed the multiple origins of A. ecalcarata and highlighted the roles of gene flow. These findings provide new evidence for parallel origin after hybridization as well as insights into the ecological adaptation mechanisms underlying the parallel origins of species.
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Affiliation(s)
- Fang-Dong Geng
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China.
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.
| | - Miao-Qing Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Xue-Dong Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Lu-Zhen Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Meng-Fan Lei
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
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11
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Xu L, Zhang Y, Guo Y, Chen Q, Zhang M, Chen H, Geng J, Huang X. Whole-genome resequencing uncovers diversity and selective sweep in Kazakh cattle. Anim Genet 2024; 55:377-386. [PMID: 38561945 DOI: 10.1111/age.13425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 03/07/2024] [Accepted: 03/22/2024] [Indexed: 04/04/2024]
Abstract
The Kazakh cattle in the Xinjiang Uygur Autonomous Region of China are highly adaptable and have multiple uses, including milk and meat production, and use as draft animals. They are an excellent original breed that could be enhanced by breeding and hybrid improvement. However, the genomic diversity and signature of selection underlying the germplasm characteristics require further elucidation. Herein, we evaluated 26 Kazakh cattle genomes in comparison with 103 genomes of seven other cattle breeds from regions around the world to assess the Kazakh cattle genetic variability. We revealed that the relatively low linkage disequilibrium at large SNP distances was strongly correlated with the largest effective population size among Kazakh cattle. Using population structural analysis, we next demonstrated a taurine lineage with restricted Bos indicus introgression among Kazakh cattle. Notably, we identified putative selected genes associated with resistance to disease and body size within Kazakh cattle. Together, our findings shed light on the evolutionary history and breeding profile of Kazakh cattle, as well as offering indispensable resources for germplasm resource conservation and crossbreeding program implementation.
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Affiliation(s)
- Lei Xu
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Yunyun Zhang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Yang Guo
- Xinjiang Uygur Autonomous Region Animal Husbandry Station, Urumqi, China
| | - Qiuming Chen
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Menghua Zhang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Hong Chen
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Juan Geng
- Xinjiang Uygur Autonomous Region Animal Husbandry Station, Urumqi, China
| | - Xixia Huang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
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12
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Nguyen-Hoang A, Sandell FL, Himmelbauer H, Dohm JC. Spinach genomes reveal migration history and candidate genes for important crop traits. NAR Genom Bioinform 2024; 6:lqae034. [PMID: 38633427 PMCID: PMC11023180 DOI: 10.1093/nargab/lqae034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 03/14/2024] [Accepted: 03/28/2024] [Indexed: 04/19/2024] Open
Abstract
Spinach (Spinacia oleracea) is an important leafy crop possessing notable economic value and health benefits. Current genomic resources include reference genomes and genome-wide association studies. However, the worldwide genetic relationships and the migration history of the crop remained uncertain, and genome-wide association studies have produced extensive gene lists related to agronomic traits. Here, we re-analysed the sequenced genomes of 305 cultivated and wild spinach accessions to unveil the phylogeny and history of cultivated spinach and to explore genetic variation in relation to phenotypes. In contrast to previous studies, we employed machine learning methods (based on Extreme Gradient Boosting, XGBoost) to detect variants that are collectively associated with agronomic traits. Variant-based cluster analyses revealed three primary spinach groups in the Middle East, Asia and Europe/US. Combining admixture analysis and allele-sharing statistics, migration routes of spinach from the Middle East to Europe and Asia are presented. Using XGBoost machine learning models we predict genomic variants influencing bolting time, flowering time, petiole color, and leaf surface texture and propose candidate genes for each trait. This study enhances our understanding of the history and phylogeny of domesticated spinach and provides valuable information on candidate genes for future genetic improvement of the crop.
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Affiliation(s)
- An Nguyen-Hoang
- Institute of Computational Biology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Felix L Sandell
- Institute of Computational Biology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Heinz Himmelbauer
- Institute of Computational Biology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Juliane C Dohm
- Institute of Computational Biology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
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13
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Wang Y, Gou Y, Yuan R, Zou Q, Zhang X, Zheng T, Fei K, Shi R, Zhang M, Li Y, Gong Z, Luo C, Xiong Y, Shan D, Wei C, Shen L, Tang G, Li M, Zhu L, Li X, Jiang Y. A chromosome-level genome of Chenghua pig provides new insights into the domestication and local adaptation of pigs. Int J Biol Macromol 2024; 270:131796. [PMID: 38677688 DOI: 10.1016/j.ijbiomac.2024.131796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 03/24/2024] [Accepted: 04/04/2024] [Indexed: 04/29/2024]
Abstract
As a country with abundant genetic resources of pigs, the domestication history of pigs in China and the adaptive evolution of Chinese pig breeds at different latitudes have rarely been elucidated at the genome-wide level. To fill this gap, we first assembled a high-quality chromosome-level genome of the Chenghua pig and used it as a benchmark to analyse the genomes of 272 samples from three genera of three continents. The divergence of the three species belonging to three genera, Phacochoerus africanus, Potamochoerus porcus, and Sus scrofa, was assessed. The introgression of pig breeds redefined that the migration routes were basically from southern China to central and southwestern China, then spread to eastern China, arrived in northern China, and finally reached Europe. The domestication of pigs in China occurred ∼12,000 years ago, earlier than the available Chinese archaeological domestication evidence. In addition, FBN1 and NR6A1 were identified in our study as candidate genes related to extreme skin thickness differences in Eurasian pig breeds and adaptive evolution at different latitudes in Chinese pig breeds, respectively. Our study provides a new resource for the pig genomic pool and refines our understanding of pig genetic diversity, domestication, migration, and adaptive evolution at different latitudes.
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Affiliation(s)
- Yifei Wang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Yuwei Gou
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Rong Yuan
- Chengdu Livestock and Poultry Genetic Resources Protection Center, Chengdu, Sichuan 610081, China
| | - Qin Zou
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Xukun Zhang
- Academy for Engineering and Technology, Fudan University, Shanghai 200433, China
| | - Ting Zheng
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Kaixin Fei
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Rui Shi
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Mei Zhang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Yujing Li
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Zhengyin Gong
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Chenggang Luo
- Chengdu Livestock and Poultry Genetic Resources Protection Center, Chengdu, Sichuan 610081, China
| | - Ying Xiong
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Dai Shan
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Chenyang Wei
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Linyuan Shen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Guoqing Tang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Mingzhou Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Li Zhu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Xuewei Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Yanzhi Jiang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China.
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14
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Abdelmanova AA, Deniskova TE, Kharzinova VR, Chinarov RY, Boronetskaya OI, Sölkner J, Brem G, Ai H, Huang L, Trukhachev VI, Zinovieva NA. Tracing the Dynamical Genetic Diversity Changes of Russian Livni Pigs during the Last 50 Years with the Museum, Old, and Modern Samples. Animals (Basel) 2024; 14:1629. [PMID: 38891676 PMCID: PMC11171240 DOI: 10.3390/ani14111629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/27/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
The pig industry is usually considered an intensive livestock industry, mainly supported by hybrid breeding between commercial pig breeds. However, people's pursuit of a more natural environment and higher meat quality has led to an increasing demand for eco-friendly and diverse pig feeding systems. Therefore, the importance of rearing and conserving local pig breeds is increasing. The Livni pig is a local breed with good adaptability to the environmental and fodder conditions in central Russia. In this study, we aimed to analyze the genetic diversity and population structure of Livni pigs using whole-genome single nucleotide polymorphism (SNP) data. We utilized the Porcine GGP HD BeadChip on genotype samples from old (n = 32, 2004) and modern (n = 32, 2019) populations of Livni pigs. For the museum samples of Livni pigs (n = 3), we extracted DNA from their teeth, performed genomic sequencing, and obtained SNP genotypes from the whole-genome sequences. SNP genotypes of Landrace (n = 32) and Large White (n = 32) pigs were included for comparative analysis. We observed that the allelic richness of Livni pigs was higher than those of Landrace and Large White pigs (AR = 1.775-1.798 vs. 1.703 and 1.668, respectively). The effective population size estimates (NE5 = 108 for Livni pigs, NE5 = 59 for Landrace and Large White pigs) confirmed their genetic diversity tendency. This was further supported by the length and number of runs of homozygosity, as well as the genomic inbreeding coefficient (almost twofold lower in Livni pigs compared to Landrace and Large White pigs). These findings suggest that the Livni pig population exhibits higher genetic diversity and experiences lower selection pressure compared to commercial pig populations. Furthermore, both principal component and network tree analyses demonstrated a clear differentiation between Livni pigs and transboundary commercial pigs. The TreeMix results indicated gene flow from Landrace ancestors to Livni pigs (2019) and from Large White ancestors to Livni pigs (2004), which was consistent with their respective historical breeding backgrounds. The comparative analysis of museum, old, and modern Livni pigs indicated that the modern Livni pig populations have preserved their historical genomic components, suggesting their potential suitability for future design selection programs.
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Affiliation(s)
- Alexandra A. Abdelmanova
- L.K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk Municipal District, Moscow Region, Podolsk 142132, Russia; (A.A.A.); (V.R.K.); (R.Y.C.)
| | - Tatiana E. Deniskova
- L.K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk Municipal District, Moscow Region, Podolsk 142132, Russia; (A.A.A.); (V.R.K.); (R.Y.C.)
| | - Veronika R. Kharzinova
- L.K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk Municipal District, Moscow Region, Podolsk 142132, Russia; (A.A.A.); (V.R.K.); (R.Y.C.)
| | - Roman Yu Chinarov
- L.K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk Municipal District, Moscow Region, Podolsk 142132, Russia; (A.A.A.); (V.R.K.); (R.Y.C.)
| | - Oksana I. Boronetskaya
- Museum of Livestock, Timiryazev Russian State Agrarian University—Moscow Agrarian Academy, 49, ul. Timiryazevskaya, Moscow 127550, Russia; (O.I.B.); (V.I.T.)
| | - Johann Sölkner
- Division of Livestock Sciences, University of Natural Resources and Life Sciences, 1180 Vienna, Austria;
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine (VMU), Veterinärplatz, 1210 Vienna, Austria;
| | - Huashui Ai
- National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation, Ministry of Science and Technology of China, Jiangxi Agricultural University, Nanchang 330045, China; (H.A.); (L.H.)
| | - Lusheng Huang
- National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation, Ministry of Science and Technology of China, Jiangxi Agricultural University, Nanchang 330045, China; (H.A.); (L.H.)
| | - Vladimir I. Trukhachev
- Museum of Livestock, Timiryazev Russian State Agrarian University—Moscow Agrarian Academy, 49, ul. Timiryazevskaya, Moscow 127550, Russia; (O.I.B.); (V.I.T.)
| | - Natalia A. Zinovieva
- L.K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk Municipal District, Moscow Region, Podolsk 142132, Russia; (A.A.A.); (V.R.K.); (R.Y.C.)
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15
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Gutiérrez-Valencia J, Zervakis PI, Postel Z, Fracassetti M, Losvik A, Mehrabi S, Bunikis I, Soler L, Hughes PW, Désamoré A, Laenen B, Abdelaziz M, Pettersson OV, Arroyo J, Slotte T. Genetic Causes and Genomic Consequences of Breakdown of Distyly in Linum trigynum. Mol Biol Evol 2024; 41:msae087. [PMID: 38709782 PMCID: PMC11114476 DOI: 10.1093/molbev/msae087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/22/2024] [Accepted: 04/29/2024] [Indexed: 05/08/2024] Open
Abstract
Distyly is an iconic floral polymorphism governed by a supergene, which promotes efficient pollen transfer and outcrossing through reciprocal differences in the position of sexual organs in flowers, often coupled with heteromorphic self-incompatibility. Distyly has evolved convergently in multiple flowering plant lineages, but has also broken down repeatedly, often resulting in homostylous, self-compatible populations with elevated rates of self-fertilization. Here, we aimed to study the genetic causes and genomic consequences of the shift to homostyly in Linum trigynum, which is closely related to distylous Linum tenue. Building on a high-quality genome assembly, we show that L. trigynum harbors a genomic region homologous to the dominant haplotype of the distyly supergene conferring long stamens and short styles in L. tenue, suggesting that loss of distyly first occurred in a short-styled individual. In contrast to homostylous Primula and Fagopyrum, L. trigynum harbors no fixed loss-of-function mutations in coding sequences of S-linked distyly candidate genes. Instead, floral gene expression analyses and controlled crosses suggest that mutations downregulating the S-linked LtWDR-44 candidate gene for male self-incompatibility and/or anther height could underlie homostyly and self-compatibility in L. trigynum. Population genomic analyses of 224 whole-genome sequences further demonstrate that L. trigynum is highly self-fertilizing, exhibits significantly lower genetic diversity genome-wide, and is experiencing relaxed purifying selection and less frequent positive selection on nonsynonymous mutations relative to L. tenue. Our analyses shed light on the loss of distyly in L. trigynum, and advance our understanding of a common evolutionary transition in flowering plants.
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Affiliation(s)
- Juanita Gutiérrez-Valencia
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Panagiotis-Ioannis Zervakis
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Zoé Postel
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Marco Fracassetti
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Aleksandra Losvik
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Sara Mehrabi
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Ignas Bunikis
- Department of Immunology, Genetics and Pathology, Uppsala Genome Center, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lucile Soler
- Department of Medical Biochemistry and Microbiology, Uppsala University, National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - P William Hughes
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Aurélie Désamoré
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Benjamin Laenen
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | | | - Olga Vinnere Pettersson
- Department of Immunology, Genetics and Pathology, Uppsala Genome Center, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Juan Arroyo
- Department of Plant Biology and Ecology, University of Seville, Seville, Spain
| | - Tanja Slotte
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
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16
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Liu B, Li J, Peng Y, Zhang K, Liu Q, Jin X, Zheng S, Wang Y, Gong L, Liu L, Lü Z, Liu Y. Chromosome-level genome assembly and population genomic analysis reveal evolution and local adaptation in common hairfin anchovy (Setipinna tenuifilis). Mol Ecol 2024; 33:e17067. [PMID: 37434292 DOI: 10.1111/mec.17067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 04/23/2023] [Accepted: 06/19/2023] [Indexed: 07/13/2023]
Abstract
Understanding the genetic structure and the factors associated with adaptive diversity has significant implications for the effective management of wild populations under threat from overfishing and climate change. The common hairfin anchovy (Setipinna tenuifilis) is an economically and ecologically important pelagic fish species, spanning a broad latitudinal gradient along marginal seas of the Northwest Pacific. In this study, we constructed the first reference genome of S. tenuifilis using PacBio long reads and high-resolution chromosome conformation capture (Hi-C) technology. The assembled genome was 798.38 Mb with a contig N50 of 1.43 Mb and a scaffold N50 of 32.42 Mb, which were anchored onto 24 pseudochromosomes. A total of 22,019 genes were functionally annotated, which accounted for 95.27% of the predicted protein-coding genes. Chromosomal collinearity analysis revealed chromosome fusion or fission events in Clupeiformes species. Three genetic groups of S. tenuifilis were revealed along the Chinese coast using restriction site-associated DNA sequencing (RADseq). We investigated the influence of four bioclimatic variables as potential drivers of adaptive divergence in S. tenuifilis, suggesting that these environmental variables, especially sea surface temperature, may play important roles as drivers of spatially varying selection for S. tenuifilis. We also identified candidate functional genes underlying adaptive mechanisms and ecological tradeoffs using redundancy analysis (RDA) and BayeScan analysis. In summary, this study sheds light on the evolution and spatial patterns of genetic variation of S. tenuifilis, providing a valuable genomic resource for further biological and genetic studies on this species and other closely related Clupeiformes.
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Affiliation(s)
- Bingjian Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Jiasheng Li
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Ying Peng
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Kun Zhang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Qi Liu
- Wuhan Onemore-tech Co., Ltd., Wuhan, China
| | - Xun Jin
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Sixu Zheng
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Yunpeng Wang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Li Gong
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Liqin Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Zhenming Lü
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Yifan Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
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17
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Dai JX, Cao LJ, Chen JC, Yang F, Shen XJ, Ma LJ, Hoffmann AA, Chen M, Wei SJ. Testing for adaptive changes linked to range expansion following a single introduction of the fall webworm. Mol Ecol 2024; 33:e17038. [PMID: 37277936 DOI: 10.1111/mec.17038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 05/24/2023] [Indexed: 06/07/2023]
Abstract
Adaptive evolution following colonization can affect the impact of invasive species. The fall webworm (FWW) invaded China 40 years ago through a single introduction event involving a severe bottleneck and subsequently diverged into two genetic groups. The well-recorded invasion history of FWW, coupled with a clear pattern of genetic divergence, provides an opportunity to investigate whether there is any sign of adaptive evolution following the invasion. Based on genome-wide SNPs, we identified genetically separated western and eastern groups of FWW and correlated spatial variation in SNPs with geographical and climatic factors. Geographical factors explained a similar proportion of the genetic variation across all populations compared with climatic factors. However, when the two population groups were analysed separately, environmental factors explained more variation than geographical factors. SNP outliers in populations of the western group had relatively stronger response to precipitation than temperature-related variables. Functional annotation of SNP outliers identified genes associated with insect cuticle protein potentially related to desiccation adaptation in the western group and genes associated with lipase biosynthesis potentially related to temperature adaptation in the eastern group. Our study suggests that invasive species may maintain the evolutionary potential to adapt to heterogeneous environments despite a single invasion event. The molecular data suggest that quantitative trait comparisons across environments would be worthwhile.
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Affiliation(s)
- Jin-Xu Dai
- Beijing Key Laboratory for Forest Pests Control, Beijing Forestry University, Beijing, China
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Li-Jun Cao
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jin-Cui Chen
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Fangyuan Yang
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xiu-Jing Shen
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Li-Jun Ma
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Ary Anthony Hoffmann
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Min Chen
- Beijing Key Laboratory for Forest Pests Control, Beijing Forestry University, Beijing, China
| | - Shu-Jun Wei
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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18
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Otalora K, Riera JL, Tavecchia G, Rotger A, Igual JM, Trotta JP, Baldo L. Population genetics and phylogeographic history of the insular lizard Podarcis lilfordi (Gunther, 1874) from the Balearic Islands based on genome-wide polymorphic data. Ecol Evol 2024; 14:e11407. [PMID: 38799398 PMCID: PMC11116764 DOI: 10.1002/ece3.11407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/12/2024] [Accepted: 04/30/2024] [Indexed: 05/29/2024] Open
Abstract
Islands provide a great system to explore the processes that maintain genetic diversity and promote local adaptation. We explored the genomic diversity of the Balearic lizard Podarcis lilfordi, an endemic species characterized by numerous small insular populations with large phenotypic diversity. Using the newly available genome for this species, we characterized more than 300,000 SNPs, merging genotyping-by-sequencing (GBS) data with previously published restriction site-associated DNA sequencing (RAD-Seq) data, providing a dataset of 16 island populations (191 individuals) across the range of species distribution (Menorca, Mallorca, and Cabrera). Results indicate that each islet hosts a well-differentiated population (F ST = 0.247 ± 0.09), with no recent immigration/translocation events. Contrary to expectations, most populations harbor a considerable genetic diversity (mean nucleotide diversity, P i = 0.144 ± 0.021), characterized by overall low inbreeding values (F IS < 0.1). While the genetic diversity significantly decreased with decreasing islet surface, maintenance of substantial genetic diversity even in tiny islets suggests variable selection or other mechanisms that buffer genetic drift. Maximum-likelihood tree based on concatenated SNP data confirmed the existence of the two major independent lineages of Menorca and Mallorca/Cabrera. Multiple lines of evidence, including admixture and root testing, robustly placed the origin of the species in the Mallorca Island, rather than in Menorca. Outlier analysis mainly retrieved a strong signature of genome differentiation between the two major archipelagos, especially in the sexual chromosome Z. A set of proteins were target of multiple outliers and primarily associated with binding and catalytic activity, providing interesting candidates for future selection studies. This study provides the framework to explore crucial aspects of the genetic basis of phenotypic divergence and insular adaptation.
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Affiliation(s)
- Katherin Otalora
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Biology FacultyUniversity of Barcelona (UB)BarcelonaSpain
- Fundación FUNMAJO, EBA, RAIEC, Biodiversity BranchTunjaBoyacáColombia
| | - Joan Lluís Riera
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Biology FacultyUniversity of Barcelona (UB)BarcelonaSpain
| | - Giacomo Tavecchia
- Animal Demography and Ecology Unit (GEDA‐IMEDEA, CSIC‐UIB)EsporlesSpain
| | - Andreu Rotger
- Animal Demography and Ecology Unit (GEDA‐IMEDEA, CSIC‐UIB)EsporlesSpain
| | - José Manuel Igual
- Animal Demography and Ecology Unit (GEDA‐IMEDEA, CSIC‐UIB)EsporlesSpain
| | - Jean‐Remi Paul Trotta
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
| | - Laura Baldo
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Biology FacultyUniversity of Barcelona (UB)BarcelonaSpain
- Institute for Research on Biodiversity (IRBio)University of Barcelona (UB)BarcelonaSpain
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19
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Tengstedt ANB, Liu S, Jacobsen MW, Gundlund C, Møller PR, Berg S, Bekkevold D, Hansen MM. Genomic insights on conservation priorities for North Sea houting and European lake whitefish (Coregonus spp.). Mol Ecol 2024:e17367. [PMID: 38686435 DOI: 10.1111/mec.17367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/08/2024] [Accepted: 04/12/2024] [Indexed: 05/02/2024]
Abstract
Population genomics analysis holds great potential for informing conservation of endangered populations. We focused on a controversial case of European whitefish (Coregonus spp.) populations. The endangered North Sea houting is the only coregonid fish that tolerates oceanic salinities and was previously considered a species (C. oxyrhinchus) distinct from European lake whitefish (C. lavaretus). However, no firm evidence for genetic-based salinity adaptation has been available. Also, studies based on microsatellite and mitogenome data suggested surprisingly recent divergence (c. 2500 years bp) between houting and lake whitefish. These data types furthermore have provided no evidence for possible inbreeding. Finally, a controversial taxonomic revision recently classified all whitefish in the region as C. maraena, calling conservation priorities of houting into question. We used whole-genome and ddRAD sequencing to analyse six lake whitefish populations and the only extant indigenous houting population. Demographic inference indicated post-glacial expansion and divergence between lake whitefish and houting occurring not long after the Last Glaciation, implying deeper population histories than previous analyses. Runs of homozygosity analysis suggested not only high inbreeding (FROH up to 30.6%) in some freshwater populations but also FROH up to 10.6% in the houting prompting conservation concerns. Finally, outlier scans provided evidence for adaptation to high salinities in the houting. Applying a framework for defining conservation units based on current and historical reproductive isolation and adaptive divergence led us to recommend that the houting be treated as a separate conservation unit regardless of species status. In total, the results underscore the potential of genomics to inform conservation practices, in this case clarifying conservation units and highlighting populations of concern.
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Affiliation(s)
| | - Shenglin Liu
- Department of Biology, Aarhus University, Aarhus C, Denmark
| | - Magnus W Jacobsen
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | | | - Peter Rask Møller
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Søren Berg
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | - Dorte Bekkevold
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
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20
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Chen J, Liu C, Li W, Zhang W, Wang Y, Clark AG, Lu J. From sub-Saharan Africa to China: Evolutionary history and adaptation of Drosophila melanogaster revealed by population genomics. SCIENCE ADVANCES 2024; 10:eadh3425. [PMID: 38630810 PMCID: PMC11023512 DOI: 10.1126/sciadv.adh3425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 03/13/2024] [Indexed: 04/19/2024]
Abstract
Drosophila melanogaster is a widely used model organism for studying environmental adaptation. However, the genetic diversity of populations in Asia is poorly understood, leaving a notable gap in our knowledge of the global evolution and adaptation of this species. We sequenced genomes of 292 D. melanogaster strains from various ecological settings in China and analyzed them along with previously published genome sequences. We have identified six global genetic ancestry groups, despite the presence of widespread genetic admixture. The strains from China represent a unique ancestry group, although detectable differentiation exists among populations within China. We deciphered the global migration and demography of D. melanogaster, and identified widespread signals of adaptation, including genetic changes in response to insecticides. We validated the effects of insecticide resistance variants using population cage trials and deep sequencing. This work highlights the importance of population genomics in understanding the genetic underpinnings of adaptation, an effort that is particularly relevant given the deterioration of ecosystems.
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Affiliation(s)
- Junhao Chen
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Chenlu Liu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Weixuan Li
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Wenxia Zhang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yirong Wang
- College of Biology, Hunan University, Changsha 410082, China
| | - Andrew G. Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
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21
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Wróbel A, Klichowska E, Nobis M. Hybrids as mirrors of the past: genomic footprints reveal spatio-temporal dynamics and extinction risk of alpine extremophytes in the mountains of Central Asia. FRONTIERS IN PLANT SCIENCE 2024; 15:1369732. [PMID: 38693932 PMCID: PMC11061500 DOI: 10.3389/fpls.2024.1369732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/02/2024] [Indexed: 05/03/2024]
Abstract
Hybridization is one of the key processes shaping lineage diversification, particularly in regions that experienced strong climate oscillations. The alpine biome with its rich history of glacial-interglacial cycles and complex patterns of species distribution shifts offers an excellent system to investigate the impact of gene flow on population dynamics and speciation, important issues for evolutionary biology and biodiversity conservation. In this study, we combined genomic data (DArTseq), chloroplast markers, and morphology to examine phylogenetic relationships and the permeability of species boundaries and their evolutionary outcomes among the alpine extremophilic species of Puccinellia (Poaceae) in the Pamir Mountains, a part of the Mountains of Central Asia biodiversity hotspot. We determined the occurrence of interspecific hybrids between P. himalaica and P. pamirica, which demonstrated almost symmetric ancestry from their parental species and did not show signals of introgression. According to our integrative revision, the natural hybrids between P. himalaica and P. pamirica should be classified as Puccinellia ×vachanica (pro species). Using approximate Bayesian computation for population history inference, we uncovered that P. himalaica hybridized with P. pamirica independently in multiple localities over the Holocene. Hybrids inherited the fine-scale genetic structure from their parental species, which developed these patterns earlier, during the Late Pleistocene. Hybridization had different consequences for the involved parental lineages, likely playing an important role in a continuing decline of P. himalaica in the Pamir Mountains over the Holocene. Our results show that P. himalaica should be considered a critically endangered species in the Pamir Mountains and could also be retreating across its entire range of distribution in High Mountain Asia. Using a comparative phylogeographic framework, we revealed the risk of extinction of a cold-adapted alpine species in a global biodiversity hotspot. This study highlights that genomics could unravel diversity trends under climate change and provides valuable evidence for conservation management.
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Affiliation(s)
- Anna Wróbel
- Institute of Botany, Faculty of Biology, Jagiellonian University, Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Kraków, Poland
| | - Ewelina Klichowska
- Institute of Botany, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Marcin Nobis
- Institute of Botany, Faculty of Biology, Jagiellonian University, Kraków, Poland
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22
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Upadhyay M, Pogorevc N, Medugorac I. scalepopgen: Bioinformatic Workflow Resources Implemented in Nextflow for Comprehensive Population Genomic Analyses. Mol Biol Evol 2024; 41:msae057. [PMID: 38507648 PMCID: PMC10994858 DOI: 10.1093/molbev/msae057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 02/07/2024] [Accepted: 03/04/2024] [Indexed: 03/22/2024] Open
Abstract
Population genomic analyses such as inference of population structure and identifying signatures of selection usually involve the application of a plethora of tools. The installation of tools and their dependencies, data transformation, or series of data preprocessing in a particular order sometimes makes the analyses challenging. While the usage of container-based technologies has significantly resolved the problems associated with the installation of tools and their dependencies, population genomic analyses requiring multistep pipelines or complex data transformation can greatly be facilitated by the application of workflow management systems such as Nextflow and Snakemake. Here, we present scalepopgen, a collection of fully automated workflows that can carry out widely used population genomic analyses on the biallelic single nucleotide polymorphism data stored in either variant calling format files or the plink-generated binary files. scalepopgen is developed in Nextflow and can be run locally or on high-performance computing systems using either Conda, Singularity, or Docker. The automated workflow includes procedures such as (i) filtering of individuals and genotypes; (ii) principal component analysis, admixture with identifying optimal K-values; (iii) running TreeMix analysis with or without bootstrapping and migration edges, followed by identification of an optimal number of migration edges; (iv) implementing single-population and pair-wise population comparison-based procedures to identify genomic signatures of selection. The pipeline uses various open-source tools; additionally, several Python and R scripts are also provided to collect and visualize the results. The tool is freely available at https://github.com/Popgen48/scalepopgen.
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Affiliation(s)
- Maulik Upadhyay
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Martinsried 82152, Germany
| | - Neža Pogorevc
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Martinsried 82152, Germany
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Martinsried 82152, Germany
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23
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Jin M, Wang H, Liu G, Lu J, Yuan Z, Li T, Liu E, Lu Z, Du L, Wei C. Whole-genome resequencing of Chinese indigenous sheep provides insight into the genetic basis underlying climate adaptation. Genet Sel Evol 2024; 56:26. [PMID: 38565986 PMCID: PMC10988870 DOI: 10.1186/s12711-024-00880-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/31/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Chinese indigenous sheep are valuable resources with unique features and characteristics. They are distributed across regions with different climates in mainland China; however, few reports have analyzed the environmental adaptability of sheep based on their genome. We examined the variants and signatures of selection involved in adaptation to extreme humidity, altitude, and temperature conditions in 173 sheep genomes from 41 phenotypically and geographically representative Chinese indigenous sheep breeds to characterize the genetic basis underlying environmental adaptation in these populations. RESULTS Based on the analysis of population structure, we inferred that Chinese indigenous sheep are divided into four groups: Kazakh (KAZ), Mongolian (MON), Tibetan (TIB), and Yunnan (YUN). We also detected a set of candidate genes that are relevant to adaptation to extreme environmental conditions, such as drought-prone regions (TBXT, TG, and HOXA1), high-altitude regions (DYSF, EPAS1, JAZF1, PDGFD, and NF1) and warm-temperature regions (TSHR, ABCD4, and TEX11). Among all these candidate genes, eight ABCD4, CNTN4, DOCK10, LOC105608545, LOC121816479, SEM3A, SVIL, and TSHR overlap between extreme environmental conditions. The TSHR gene shows a strong signature for positive selection in the warm-temperature group and harbors a single nucleotide polymorphism (SNP) missense mutation located between positions 90,600,001 and 90,650,001 on chromosome 7, which leads to a change in the protein structure of TSHR and influences its stability. CONCLUSIONS Analysis of the signatures of selection uncovered genes that are likely related to environmental adaptation and a SNP missense mutation in the TSHR gene that affects the protein structure and stability. It also provides information on the evolution of the phylogeographic structure of Chinese indigenous sheep populations. These results provide important genetic resources for future breeding studies and new perspectives on how animals can adapt to climate change.
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Affiliation(s)
- Meilin Jin
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huihua Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Gang Liu
- National Animal Husbandry Service, National Center of Preservation and Utilization of Animal Genetic Resources, Beijing, China
| | - Jian Lu
- National Animal Husbandry Service, National Center of Preservation and Utilization of Animal Genetic Resources, Beijing, China
| | - Zehu Yuan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Taotao Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Engming Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zengkui Lu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lan-Zhou, China
| | - Lixin Du
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Caihong Wei
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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24
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Roycroft E, Ford F, Ramm T, Schembri R, Breed WG, Burns PA, Rowe KC, Moritz C. Speciation across biomes: Rapid diversification with reproductive isolation in the Australian delicate mice. Mol Ecol 2024; 33:e17301. [PMID: 38385302 DOI: 10.1111/mec.17301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/25/2024] [Accepted: 01/30/2024] [Indexed: 02/23/2024]
Abstract
Phylogeographic studies of continental clades, especially when combined with palaeoclimate modelling, provide powerful insight into how environment drives speciation across climatic contexts. Australia, a continent characterized by disparate modern biomes and dynamic climate change, provides diverse opportunity to reconstruct the impact of past and present environments on diversification. Here, we use genomic-scale data (1310 exons and whole mitogenomes from 111 samples) to investigate Pleistocene diversification, cryptic diversity, and secondary contact in the Australian delicate mice (Hydromyini: Pseudomys), a recent radiation spanning almost all Australian environments. Across northern Australia, we find no evidence for introgression between cryptic lineages within Pseudomys delicatulus sensu lato, with palaeoclimate models supporting contraction and expansion of suitable habitat since the last glacial maximum. Despite multiple contact zones, we also find little evidence of introgression at a continental scale, with the exception of a potential hybrid zone in the mesic biome. In the arid zone, combined insights from genetic data and palaeomodels support a recent expansion in the arid specialist P. hermannsburgensis and contraction in the semi-arid P. bolami. In the face of repeated secondary contact, differences in sperm morphology and chromosomal rearrangements are potential mechanisms that maintain species boundaries in these recently diverged species. Additionally, we describe the western delicate mouse as a new species and recommend taxonomic reinstatement of the eastern delicate mouse. Overall, we show that speciation in an evolutionarily young and widespread clade has been driven by environmental change, and potentially maintained by divergence in reproductive morphology and chromosome rearrangements.
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Affiliation(s)
- Emily Roycroft
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, Australian Capital Territory, Australia
| | - Fred Ford
- Biodiversity Conservation and Science, New South Wales Department of Planning and Environment, Queanbeyan, New South Wales, Australia
- Australian National Wildlife Collection, National Research Collections Australia, CSIRO, Canberra, Australian Capital Territory, Australia
| | - Till Ramm
- Zoo Leipzig, Leipzig, Germany
- Museum für Naturkunde Berlin, Berlin, Germany
| | - Rhiannon Schembri
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, Australian Capital Territory, Australia
- School of Natural Sciences, Macquarie University, Macquarie Park, New South Wales, Australia
| | - William G Breed
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Phoebe A Burns
- Wildlife Conservation and Science, Zoos Victoria, Parkville, Victoria, Australia
| | - Kevin C Rowe
- Sciences Department, Museums Victoria, Melbourne, Victoria, Australia
- School of Biosciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Craig Moritz
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, Australian Capital Territory, Australia
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25
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Marques V, Hinojosa JC, Dapporto L, Talavera G, Stefanescu C, Gutiérrez D, Vila R. The opposed forces of differentiation and admixture across glacial cycles in the butterfly Aglais urticae. Mol Ecol 2024; 33:e17304. [PMID: 38421113 DOI: 10.1111/mec.17304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 02/13/2024] [Accepted: 02/15/2024] [Indexed: 03/02/2024]
Abstract
Glacial cycles lead to periodic population interbreeding and isolation in warm-adapted species, which impact genetic structure and evolution. However, the effects of these processes on highly mobile and more cold-tolerant species are not well understood. This study aims to shed light on the phylogeographic history of Aglais urticae, a butterfly species with considerable dispersal ability, and a wide Palearctic distribution reaching the Arctic. Through the analysis of genomic data, four main genetic lineages are identified: European, Sierra Nevada, Sicily/Calabria/Peloponnese, and Eastern. The results indicate that the Sardo-Corsican endemic taxon ichnusa is a distinct species. The split between the relict lineages in southern Europe and the main European lineage is estimated to have happened 400-450 thousand years ago, with admixture observed during the Quaternary glacial cycles, and still ongoing, albeit to a much smaller extent. These results suggest that these lineages may be better treated as subspecific parapatric taxa. Ecological niche modelling supported the existence of both Mediterranean and extra-Mediterranean refugia during the glacial periods, with the main one located on the Atlantic coast. Nevertheless, gene flow between populations was possible, indicating that both differentiation and admixture have acted continuously across glacial cycles in this cold-tolerant butterfly, generally balancing each other but producing differentiated lineages in the southern peninsulas. We conclude that the population dynamics and the processes shaping the population genetic structure of cold-adapted species during the Quaternary ice ages may be different than those classically accepted for warm-adapted species.
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Affiliation(s)
- Valéria Marques
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Joan Carles Hinojosa
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Leonardo Dapporto
- Dipartimento di Biologia, Università degli Studi di Firenze, Sesto Fiorentino, Italy
| | - Gerard Talavera
- Institut Botànic de Barcelona (IBB), CSIC-CMCNB, Barcelona, Spain
| | - Constantí Stefanescu
- Natural Sciences Museum of Granollers, Granollers, Spain
- CREAF, Cerdanyola del Vallès, Spain
| | - David Gutiérrez
- Instituto de Investigación en Cambio Global (IICG), Universidad Rey Juan Carlos, Madrid, Spain
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, Madrid, Spain
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
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26
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Le SV, de Las Heras-Saldana S, Alexandri P, Olmo L, Walkden-Brown SW, van der Werf JHJ. Genetic diversity, population structure and origin of the native goats in Central Laos. J Anim Breed Genet 2024. [PMID: 38520124 DOI: 10.1111/jbg.12862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 02/14/2024] [Accepted: 03/10/2024] [Indexed: 03/25/2024]
Abstract
Maintaining genetic diversity and variation in livestock populations is critical for natural and artificial selection promoting genetic improvement while avoiding problems due to inbreeding. In Laos, there are concerns that there has been a decline in genetic diversity and a rise in inbreeding among native goats in their village-based smallholder system. In this study, we investigated the genetic diversity of Lao native goats in Phin, Songkhone and Sepon districts in Central Laos for the first time using Illumina's Goat SNP50 BeadChip. We also explored the genetic relationships between Lao goats with 163 global goat populations from 36 countries. Our results revealled a close genetic relationship between Lao native goats and Chinese, Mongolian and Pakistani goats, sharing ancestries with Guangfen, Jining Grey and Luoping Yellow breeds (China) and Teddi goats (Pakistan). The observed (Ho) and expected (He) heterozygosity were 0.292 and 0.303 (Laos), 0.288 and 0.288 (Sepon), 0.299 and 0.308 (Phin) and 0.289 and 0.305 (Songkhone), respectively. There was low to moderate genetic differentiation (FST: 0.011-0.043) and negligible inbreeding coefficients (FIS: -0.001 to 0.052) between goat districts. The runs of homozygosity (ROH) had an average length of 5.92-6.85 Mb, with short ROH segments (1-5 Mb length) being the most prevalent (66.34%). Longer ROH segments (20-40 and >40 Mb length categories) were less common, comprising only 4.81% and 1.01%, respectively. Lao goats exhibit moderate genetic diversity, low-inbreeding levels and adequate effective population size. Some genetic distinctions between Lao goats may be explained by geographic and cultural features.
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Affiliation(s)
- Sang V Le
- School of Rural & Environmental Science, University of New England, Armidale, New South Wales, Australia
| | - Sara de Las Heras-Saldana
- AGBU, a Joint Venture of the NSW Department of Primary Industries and the University of New England, Armidale, New South Wales, Australia
| | - Panoraia Alexandri
- AGBU, a Joint Venture of the NSW Department of Primary Industries and the University of New England, Armidale, New South Wales, Australia
| | - Luisa Olmo
- School of Rural & Environmental Science, University of New England, Armidale, New South Wales, Australia
| | - Stephen W Walkden-Brown
- School of Rural & Environmental Science, University of New England, Armidale, New South Wales, Australia
| | - Julius H J van der Werf
- School of Rural & Environmental Science, University of New England, Armidale, New South Wales, Australia
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Caputo B, De Marco CM, Pichler V, Bottà G, Bennett KL, Clarkson CS, Tennessen JA, Weetman D, Miles A, Torre AD. Speciation within the Anopheles gambiae complex: high-throughput whole genome sequencing reveals evidence of a putative new cryptic taxon in 'far-west' Africa. RESEARCH SQUARE 2024:rs.3.rs-3914444. [PMID: 38562903 PMCID: PMC10984024 DOI: 10.21203/rs.3.rs-3914444/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The two main Afrotropical malaria vectors - Anopheles coluzzii and An. gambiae - are genetically distinct and reproductively isolated across West Africa. However, populations at the western extreme of their range are assigned as "intermediate" between the two species by whole genome sequence (WGS) data, and as hybrid forms by conventional molecular diagnostics. By exploiting WGS data from 1,190 specimens collected across west Africa via the Anopheles gambiae 1000 Genomes network, we identify a novel putative taxon in the far-west (provisionally named Bissau molecular form), which did not arise by admixture but rather originated at the same time as the split between An. coluzzii and An. gambiae. Intriguingly, these populations lack insecticide resistance mechanisms commonly observed in the two main species. These findings lead to a change of perspective on malaria vector species in the far-west region with potential for epidemiological implications, and a new challenge for genetic-based mosquito control approaches.
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Affiliation(s)
- B Caputo
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "Sapienza", Rome Italy
| | - C M De Marco
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "Sapienza", Rome Italy
| | - V Pichler
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "Sapienza", Rome Italy
| | - G Bottà
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "Sapienza", Rome Italy
| | - K L Bennett
- Wellcome Sanger Genomic Surveillance Unit, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - C S Clarkson
- Wellcome Sanger Genomic Surveillance Unit, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - J A Tennessen
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - D Weetman
- Liverpool School of Tropical Medicine, Liverpool, UK
| | - A Miles
- Wellcome Sanger Genomic Surveillance Unit, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - A Della Torre
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "Sapienza", Rome Italy
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He Y, Zhang K, Shi Y, Lin H, Huang X, Lu X, Wang Z, Li W, Feng X, Shi T, Chen Q, Wang J, Tang Y, Chapman MA, Germ M, Luthar Z, Kreft I, Janovská D, Meglič V, Woo SH, Quinet M, Fernie AR, Liu X, Zhou M. Genomic insight into the origin, domestication, dispersal, diversification and human selection of Tartary buckwheat. Genome Biol 2024; 25:61. [PMID: 38414075 PMCID: PMC10898187 DOI: 10.1186/s13059-024-03203-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 02/21/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Tartary buckwheat, Fagopyrum tataricum, is a pseudocereal crop with worldwide distribution and high nutritional value. However, the origin and domestication history of this crop remain to be elucidated. RESULTS Here, by analyzing the population genomics of 567 accessions collected worldwide and reviewing historical documents, we find that Tartary buckwheat originated in the Himalayan region and then spread southwest possibly along with the migration of the Yi people, a minority in Southwestern China that has a long history of planting Tartary buckwheat. Along with the expansion of the Mongol Empire, Tartary buckwheat dispersed to Europe and ultimately to the rest of the world. The different natural growth environments resulted in adaptation, especially significant differences in salt tolerance between northern and southern Chinese Tartary buckwheat populations. By scanning for selective sweeps and using a genome-wide association study, we identify genes responsible for Tartary buckwheat domestication and differentiation, which we then experimentally validate. Comparative genomics and QTL analysis further shed light on the genetic foundation of the easily dehulled trait in a particular variety that was artificially selected by the Wa people, a minority group in Southwestern China known for cultivating Tartary buckwheat specifically for steaming as a staple food to prevent lysine deficiency. CONCLUSIONS This study provides both comprehensive insights into the origin and domestication of, and a foundation for molecular breeding for, Tartary buckwheat.
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Affiliation(s)
- Yuqi He
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Kaixuan Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yaliang Shi
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hao Lin
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xu Huang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiang Lu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhirong Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wei Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xibo Feng
- Tibet Key Experiments of Crop Cultivation and Farming/College of Plant Science, Tibet Agriculture and Animal Husbandry University, Linzhi, 860000, China
| | - Taoxiong Shi
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, China
| | - Qingfu Chen
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, China
| | - Junzhen Wang
- Xichang Institute of Agricultural Science, Liangshan Yi People Autonomous Prefecture, Liangshan, Sichuan, 615000, China
| | - Yu Tang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Life Sciences Building 85, Highfield Campus, Southampton, SO17 1BJ, UK
| | - Mateja Germ
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia
| | - Zlata Luthar
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia
| | - Ivan Kreft
- Nutrition Institute, Koprska Ulica 98, SI-1000, Ljubljana, Slovenia
| | - Dagmar Janovská
- Gene Bank, Crop Research Institute, Drnovská 507, Prague 6, Czech Republic
| | - Vladimir Meglič
- Agricultural Institute of Slovenia, Hacquetova ulica 17, SI-1000, Ljubljana, Slovenia
| | - Sun-Hee Woo
- Department of Crop Science, Chungbuk National University, Cheong-ju, Republic of Korea
| | - Muriel Quinet
- Groupe de Recherche en Physiologie Végétale (GRPV), Earth and Life Institute-Agronomy (ELI-A), Université catholique de Louvain, Croix du Sud 45, boîte L7.07.13, B-1348, Louvain-la-Neuve, Belgium
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Xu Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Meiliang Zhou
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Zhou Y, Song R, Nevo E, Fu X, Wang X, Wang Y, Wang C, Chen J, Sun G, Sun D, Ren X. Genomic evidence for climate-linked diversity loss and increased vulnerability of wild barley spanning 28 years of climate warming. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 913:169679. [PMID: 38163608 DOI: 10.1016/j.scitotenv.2023.169679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/19/2023] [Accepted: 12/23/2023] [Indexed: 01/03/2024]
Abstract
The information on how plant populations respond genetically to climate warming is scarce. Here, landscape genomic and machine learning approaches were integrated to assess genetic response of 10 wild barley (Hordeum vulgare ssp. spontaneum; WB) populations in the past and future, using whole genomic sequencing (WGS) data. The WB populations were sampled in 1980 and again in 2008. Phylogeny of accessions was roughly in conformity with sampling sites, which accompanied by admixture/introgressions. The 28-y climate warming resulted in decreased genetic diversity, increased selection pressure, and an increase in deleterious single nucleotide polymorphism (dSNP) numbers, heterozygous deleterious and total deleterious burdens for WB. Genome-environment associations identified some candidate genes belonging to peroxidase family (HORVU2Hr1G057450, HORVU4Hr1G052060 and HORVU4Hr1G057210) and heat shock protein 70 family (HORVU2Hr1G112630). The gene HORVU2Hr1G120170 identified by selective sweep analysis was under strong selection during the climate warming of the 28-y, and its derived haplotypes were fixed by WB when faced with the 28-y increasingly severe environment. Temperature variables were found to be more important than precipitation variables in influencing genomic variation, with an eco-physiological index gdd5 (growing degree-days at the baseline threshold temperature of 5 °C) being the most important determinant. Gradient forest modelling revealed higher predicted genomic vulnerability in Sede Boqer under future climate scenarios at 2041-2070 and 2071-2100. Additionally, estimates of effective population size (Ne) tracing back to 250 years indicated a forward decline in all populations over time. Our assessment about past genetic response and future vulnerability of WB under climate warming is crucial for informing conservation efforts for wild cereals and rational use strategies.
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Affiliation(s)
- Yu Zhou
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ruilian Song
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Eviator Nevo
- Institute of Evolution, University of Haifa, Mount Carmel, 31905 Haifa, Israel
| | - Xiaoqin Fu
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiaofang Wang
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yixiang Wang
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chengyang Wang
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Junpeng Chen
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Genlou Sun
- Saint Mary's University, Halifax, NS B3H 3C3, Canada
| | - Dongfa Sun
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xifeng Ren
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
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Hu Z, Su Y, Zong W, Niu N, Zhao R, Liang R, Wang L, Zhang Y, Zhang L. Unveiling the Genetic Secrets of Chinese Indigenous Pigs from Guizhou Province: Diversity, Evolution and Candidate Genes Affecting Pig Coat Color. Animals (Basel) 2024; 14:699. [PMID: 38473084 DOI: 10.3390/ani14050699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 01/27/2024] [Accepted: 02/10/2024] [Indexed: 03/14/2024] Open
Abstract
The local pig breeds in Guizhou possess exceptional meat quality, robust adaptability, and resilience to harsh feeding conditions, making them ideal for producing high-quality pork. With over 10 local pig breeds in the region, we focused on 7 specific breeds: Baixi pigs (BX), Congjiang Xiang pigs (CJX), Guanling pigs (GL), Jianhe White Xiang pigs (JHBX), Jiangkou Luobo pigs (JKLB), Kele pigs (KL), and Qiandong Hua pigs (QDH). Unfortunately, these breeds face threats such as introduced species and inbreeding, resulting in a decline in population size and numbers. To better protect and utilize these breeds, we employed genome-wide single-nucleotide polymorphism (SNP) markers to investigate the population structure, genetic diversity, and selection characteristics of 283 pigs across these seven breeds. Our findings revealed distinct ancestral sources between Chinese and Western pig breeds, as demonstrated by principal component analysis, adjacent tree analysis, and ADMIXTURE analysis. Notably, JHBX exhibited a distant genetic relationship from the other six local pig breeds in Guizhou province, showcasing unique genetic characteristics. While the genetic diversity of the six Chinese native pig populations, excluding JHBX, was generally moderate in Guizhou province, the JHBX population displayed low genetic diversity. Therefore, it is imperative to intensify selection efforts to prevent inbreeding decline in JHBX while further enhancing the protection measures for the other six pig populations. Additionally, we identified candidate genes influencing the size disparity among pigs in Guizhou province through signal selection. Our study outcomes serve as a reference for developing effective conservation and utilization plans for pig breeds in Guizhou province and deepen our understanding of the genetic mechanisms underlying pig body size.
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Affiliation(s)
- Ziping Hu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China
| | - Yanfang Su
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Wencheng Zong
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Naiqi Niu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Runze Zhao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Ruiping Liang
- Beijing Changping District Center for Animal Disease Prevention and Control, Beijing 102200, China
| | - Lixian Wang
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China
| | - Yiyu Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Longchao Zhang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
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31
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Soares LS, Freitas LB. The phylogeographic journey of a plant species from lowland to highlands during the Pleistocene. Sci Rep 2024; 14:3825. [PMID: 38360894 PMCID: PMC10869790 DOI: 10.1038/s41598-024-53414-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/31/2024] [Indexed: 02/17/2024] Open
Abstract
Phylogeographic history refers to how species evolve and diversify in response to historical, ecological, and demographic factors. The climate fluctuation during the Pleistocene period marked a crucial time in shaping many species' distribution and genetic structure, particularly those from southern South American grasslands. This work investigated the phylogeographic history of a highland grassland, Petunia altiplana T. Ando & Hashim. (Solanaceae), its diversity, and geographic distribution using a population genomic approach based on RAD-seq data. Our results indicated that, during the Pleistocene, when the grasslands expanded to highlands, the lowland populations of P. altiplana reached the higher open fields, enlarging their geographic distribution. We found that the P. altiplana genetic diversity followed the geographic division into eastern (E) and western (WE) population groups, with a subtle division in the E group regarding the Pelotas River headwater. The results also showed that isolation by distance was the main divergence pattern, with elevation playing a pivotal role in shaping WE and E groups. Our findings indicated that lowland-adapted populations quickly colonized highlands during the late Pleistocene.
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Affiliation(s)
- Luana Sousa Soares
- Department of Genetics, Universidade Federal do Rio Grande do Sul, PoBox 15053, Porto Alegre, 91501-970, Brazil
| | - Loreta B Freitas
- Department of Genetics, Universidade Federal do Rio Grande do Sul, PoBox 15053, Porto Alegre, 91501-970, Brazil.
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32
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Xu L, Zhou K, Huang X, Chen H, Dong H, Chen Q. Whole-genome resequencing provides insights into the diversity and adaptation to desert environment in Xinjiang Mongolian cattle. BMC Genomics 2024; 25:176. [PMID: 38355434 PMCID: PMC10865613 DOI: 10.1186/s12864-024-10084-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 02/02/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Xinjiang Mongolian cattle is an indigenous breed that inhabits the Taklimakan Desert and is characterized by its small body size. However, the genomic diversity, origin, and genetic basis underlying the adaptation to the desert environment have been poorly studied. RESULTS We analyzed patterns of Xinjiang Mongolian cattle genetic variation by sequencing 20 genomes together with seven previously sequenced genomes and comparing them to the 134 genomes of nine representative breeds worldwide. Among the breeds of Bos taurus, we found the highest nucleotide diversity (0.0024) associated with the lower inbreeding coefficient (2.0110-6), the lowest linkage disequilibrium (r2 = 0.3889 at distance of 10 kb), and the highest effective population size (181 at 20 generations ago) in Xinjiang Mongolian cattle. The genomic diversity pattern could be explained by a limited introgression of Bos indicus genes. More importantly, similarly to desert-adapted camel and same-habitat sheep, we also identified signatures of selection including genes, GO terms, and/or KEGG pathways controlling water reabsorption and osmoregulation, metabolic regulation and energy balance, as well as small body size in Xinjiang Mongolian cattle. CONCLUSIONS Our results imply that Xinjiang Mongolian cattle might have acquired distinct genomic diversity by virtue of the introgression of Bos indicus, which helps understand the demographic history. The identification of selection signatures can provide novel insights into the genomic basis underlying the adaptation of Xinjiang Mongolian cattle to the desert environment.
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Affiliation(s)
- Lei Xu
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Kaiqing Zhou
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Xixia Huang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Hong Chen
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Hong Dong
- Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, China.
| | - Qiuming Chen
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang, China.
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Peng Y, Liu Y, Li J, Zhang K, Jin X, Zheng S, Wang Y, Lü Z, Liu L, Gong L, Liu B. New perspectives on the genetic structure of dotted gizzard shad ( Konosirus punctatus) based on RAD-seq. MARINE LIFE SCIENCE & TECHNOLOGY 2024; 6:50-67. [PMID: 38433959 PMCID: PMC10901767 DOI: 10.1007/s42995-024-00216-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 01/19/2024] [Indexed: 03/05/2024]
Abstract
To maintain, develop and rationally utilize marine organisms, understanding their genetic structure and habitat adaptation pattern is necessary. Konosirus punctatus, which is a commercial fish species inhabiting the Indo-west Pacific Ocean, has shown an obvious annual global capture and aquaculture production decline due to climate changes and human activities. In the present study, restriction-site associated DNA sequencing (RAD-seq) was used to describe its genome-wide single nucleotide polymorphisms panel (SNPs). Among 146 individuals collected at nine locations scattered in China, Korea and Japan, a set of 632,090 SNPs were identified. Population genetic analysis showed that K. punctatus individuals were divided into two significant genetic clusters. Meanwhile, potential genetic differentiation between northern and southern population of K. punctatus was found. Treemix results indicated that gene flow existed among sampling locations of K. punctatus, especially from southern Japan to others. Moreover, candidate genes associated with habitat adaptations of K. punctatus were identified, which are involved in diverse physiological processes of K. punctatus including growth and development (e.g., KIDINS220, PAN3), substance metabolism (e.g., PGM5) and immune response (e.g., VAV3, CCT7, HSPA12B). Our findings may aid in understanding the possible mechanisms for the population genetic structure and local adaptation of K. punctatus, which is beneficial to establish the management and conservation units of K. punctatus, guiding the rational use of resources, with reference significance for a profound understanding of the adaptative mechanisms of other marine organisms to the environment. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-024-00216-2.
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Affiliation(s)
- Ying Peng
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022 China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 China
| | - Yifan Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022 China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 China
| | - Jiasheng Li
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022 China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 China
| | - Kun Zhang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022 China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 China
| | - Xun Jin
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022 China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 China
| | - Sixu Zheng
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022 China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 China
| | - Yunpeng Wang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022 China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 China
| | - Zhenming Lü
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022 China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 China
| | - Liqin Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022 China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 China
| | - Li Gong
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022 China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 China
| | - Bingjian Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022 China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 China
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Zhou W, Zhang N, Huang K, Lin H, Tu J, Zheng C, Que P, Chiang CY, Martinez J, Naerhulan H, Székely T, Zhang Z, Liu Y. Divergent Selection in Low Recombination Regions Shapes the Genomic Islands in Two Incipient Shorebird Species. Mol Biol Evol 2024; 41:msae006. [PMID: 38225175 PMCID: PMC10835341 DOI: 10.1093/molbev/msae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 01/02/2024] [Accepted: 01/08/2024] [Indexed: 01/17/2024] Open
Abstract
Speciation in the face of gene flow is usually associated with a heterogeneous genomic landscape of divergence in nascent species pairs. However, multiple factors, such as divergent selection and local recombination rate variation, can influence the formation of these genomic islands. Examination of the genomic landscapes of species pairs that are still in the early stages of speciation provides an insight into this conundrum. In this study, population genomic analyses were undertaken using a wide range of sampling and whole-genome resequencing data from 96 unrelated individuals of Kentish plover (Charadrius alexandrinus) and white-faced plover (Charadrius dealbatus). We suggest that the two species exhibit varying levels of population admixture along the Chinese coast and on the Taiwan Island. Genome-wide analyses for introgression indicate that ancient introgression had occurred in Taiwan population, and gene flow is still ongoing in mainland coastal populations. Furthermore, we identified a few genomic regions with significant levels of interspecific differentiation and local recombination suppression, which contain several genes potentially associated with disease resistance, coloration, and regulation of plumage molting and thus may be relevant to the phenotypic and ecological divergence of the two nascent species. Overall, our findings suggest that divergent selection in low recombination regions may be a main force in shaping the genomic islands in two incipient shorebird species.
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Affiliation(s)
- Wenjun Zhou
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Nan Zhang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
| | - Kaichi Huang
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, Bc, Canada
| | - Hongzhou Lin
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
| | - Jie Tu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
| | - Chenqing Zheng
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
| | - Pinjia Que
- Ministry of Education Key Laboratory for Biodiversity Sciences and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan Academy of Giant Panda, Chengdu, China
| | - Chung-Yu Chiang
- Department of Environmental Science, Tunghai University, Taichung, Taiwan, China
| | | | - Halimubieke Naerhulan
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Tamás Székely
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
- Ministry of Education Key Laboratory for Biodiversity Sciences and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Zhengwang Zhang
- Ministry of Education Key Laboratory for Biodiversity Sciences and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yang Liu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
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Wagner S, Seguin-Orlando A, Leplé JC, Leroy T, Lalanne C, Labadie K, Aury JM, Poirier S, Wincker P, Plomion C, Kremer A, Orlando L. Tracking population structure and phenology through time using ancient genomes from waterlogged white oak wood. Mol Ecol 2024; 33:e16859. [PMID: 36748324 PMCID: PMC7615563 DOI: 10.1111/mec.16859] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 12/08/2022] [Accepted: 01/16/2023] [Indexed: 02/08/2023]
Abstract
Whole genome characterizations of crop plants based on ancient DNA have provided unique keys for a better understanding of the evolutionary origins of modern cultivars, the pace and mode of selection underlying their adaptation to new environments and the production of phenotypes of interest. Although forests are among the most biologically rich ecosystems on earth and represent a fundamental resource for human societies, no ancient genome sequences have been generated for trees. This contrasts with the generation of multiple ancient reference genomes for important crops. Here, we sequenced the first ancient tree genomes using two white oak wood remains from Germany dating to the Last Little Ice Age (15th century CE, 7.3× and 4.0×) and one from France dating to the Bronze Age (1700 BCE, 3.4×). We assessed the underlying species and identified one medieval remains as a hybrid between two common oak species (Quercus robur and Q. petraea) and the other two remains as Q. robur. We found that diversity at the global genome level had not changed over time. However, exploratory analyses suggested that a reduction of diversity took place at different time periods. Finally, we determined the timing of leaf unfolding for ancient trees for the first time. The study extends the application of ancient wood beyond the classical proxies of dendroclimatology, dendrochronology, dendroarchaeology and dendroecology, thereby enhancing resolution of inferences on the responses of forest ecosystems to past environmental changes, epidemics and silvicultural practices.
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Affiliation(s)
- Stefanie Wagner
- Plant Genomic Resources Center (CNRGV), INRAE, Castanet-Tolosan, France
- Centre for Anthropobiology and Genomics of Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse, France
| | - Andaine Seguin-Orlando
- Centre for Anthropobiology and Genomics of Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse, France
| | | | - Thibault Leroy
- IRHS UMR1345, Université d’Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, Beaucouzé, France
| | | | - Karine Labadie
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Jean-Marc Aury
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | | | - Patrick Wincker
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | | | | | - Ludovic Orlando
- Centre for Anthropobiology and Genomics of Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse, France
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Lin L, Cai L, Huang H, Ming S, Sun W. Transcriptome data reveals the conservation genetics of Cypripedium forrestii, a plant species with extremely small populations endemic to Yunnan, China. FRONTIERS IN PLANT SCIENCE 2024; 15:1303625. [PMID: 38357270 PMCID: PMC10864665 DOI: 10.3389/fpls.2024.1303625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/08/2024] [Indexed: 02/16/2024]
Abstract
The Cypripedium forrestii is an orchid species with extremely small populations (PSESP) in Yunnan, China. C. forrestii is range-restricted and less-studied than many orchid species, and it is exposed to various threats to its survival. We investigated its potential habitats and collected 52 samples from eight locations, as well as two outgroup species for reference. We developed genetic markers (SNPs) for C. forrestii based on transcriptome sequencing (RNA-seq) data, and analyzed the genetic diversity, population structure, gene flow and demographic history of C. forrestii in detail. C. forrestii is a taxonomically independent species to protect. We found that the genetic diversity of C. forrestii was very low (1.7e-4) compared with other endangered species. We identified three genetic clusters, and several populations with distinct genetic backgrounds. Most genetic diversity was found within sampling sites (87.87%) and genetic clusters (91.39%). Gene flow has been greatly limited over the most recent generations, probably due to geographical distance, historical climate change and habitat fragmentation. We also detected a severe bottleneck event brought about by the recent population constraints. These factors, together with its reproductive characteristics, contribute to the population fragmentation and low genetic diversity of C. forrestii. Based on our findings, we suggest an integrative conservation strategy to protect and recover the genetic diversity of C. forrestii and a further comprehensive study of its ecological traits in the future.
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Affiliation(s)
- Liewen Lin
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Lei Cai
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Hua Huang
- Lijiang Alpine Botanic Garden/ Kunming Botanical Garden, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Shengping Ming
- Lijiang Alpine Botanic Garden/ Kunming Botanical Garden, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Weibang Sun
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Lijiang Alpine Botanic Garden/ Kunming Botanical Garden, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
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Zunino L, Cubry P, Sarah G, Mournet P, El Bakkali A, Aqbouch L, Sidibé-Bocs S, Costes E, Khadari B. Genomic evidence of genuine wild versus admixed olive populations evolving in the same natural environments in western Mediterranean Basin. PLoS One 2024; 19:e0295043. [PMID: 38232071 DOI: 10.1371/journal.pone.0295043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 11/14/2023] [Indexed: 01/19/2024] Open
Abstract
Crop-to-wild gene flow is a mechanism process widely documented, both in plants and animals. This can have positive or negative impacts on the evolution of admixed populations in natural environments, yet the phenomenon is still misunderstood in long-lived woody species, contrary to short-lived crops. Wild olive Olea europaea L. occurs in the same eco-geographical range as domesticated olive, i.e. the Mediterranean Basin (MB). Moreover, it is an allogamous and anemophilous species whose seeds are disseminated by birds, i.e. factors that drive gene flow between crops and their wild relatives. Here we investigated the genetic structure of western MB wild olive populations in natural environments assuming a homogenous gene pool with limited impact of cultivated alleles, as previously suggested. We used a target sequencing method based on annotated genes from the Farga reference genome to analyze 27 western MB olive tree populations sampled in natural environments in France, Spain and Morocco. We also target sequenced cultivated olive tree accessions from the Worldwide Olive Germplasm Bank of Marrakech and Porquerolles and from an eastern MB wild olive tree population. We combined PCA, sNMF, pairwise FST and TreeMix and clearly identified genuine wild olive trees throughout their natural distribution range along a north-south gradient including, for the first time, in southern France. However, contrary to our assumption, we highlighted more admixed than genuine wild olive trees. Our results raise questions regarding the admixed population evolution pattern in this environment, which might be facilitated by crop-to-wild gene flow.
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Affiliation(s)
- Lison Zunino
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- DIADE, University of Montpellier, CIRAD, IRD, Montpellier, France
| | - Philippe Cubry
- DIADE, University of Montpellier, CIRAD, IRD, Montpellier, France
| | - Gautier Sarah
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Pierre Mournet
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR AGAP Institut, Montpellier, France
| | - Ahmed El Bakkali
- INRA, UR Amélioration des Plantes et Conservation des Ressources Phytogénétiques, Meknes, Morocco
| | - Laila Aqbouch
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Stéphanie Sidibé-Bocs
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR AGAP Institut, Montpellier, France
| | - Evelyne Costes
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Bouchaib Khadari
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- Conservatoire Botanique National Méditerranéen (CBNMed), UMR AGAP Institut, Montpellier, France
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Criscione A, Chessari G, Cesarani A, Ablondi M, Asti V, Bigi D, Bordonaro S, Ciampolini R, Cipolat-Gotet C, Congiu M, De Palo P, Landi V, Macciotta NPP, Matassino D, Portolano B, Riggio S, Sabbioni A, Sardina MT, Senczuk G, Tumino S, Vasini M, Ciani E, Mastrangelo S. Analysis of ddRAD-seq data provides new insights into the genomic structure and patterns of diversity in Italian donkey populations. J Anim Sci 2024; 102:skae165. [PMID: 38874306 PMCID: PMC11214105 DOI: 10.1093/jas/skae165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 06/13/2024] [Indexed: 06/15/2024] Open
Abstract
With more than 150 recognized breeds, donkeys assume relevant economic importance, especially in developing countries. Even if the estimated number of heads worldwide is 53M, this species received less attention than other livestock species. Italy has traditionally been considered one of the cradles of European donkey breeding, and despite a considerable loss of biodiversity, today still counts nine autochthonous populations. A total of 220 animals belonging to nine different populations were genotyped using the double-digest restriction site associated DNA (ddRAD) sequencing to investigate the pattern of diversity using a multi-technique approach. A total of 418,602,730 reads were generated and successfully demultiplexed to obtain a medium-density SNP genotypes panel with about 27K markers. The diversity indices showed moderate levels of variability. The genetic distances and relationships, largely agree with the breeding history of the donkey populations under investigation. The results highlighted the separation of populations based on their genetic origin or geographical proximity between breeding areas, showed low to moderate levels of admixture, and indicated a clear genetic difference in some cases. For some breeds, the results also validate the success of proper management conservation plans. Identified runs of homozygosity islands, mapped within genomic regions related to immune response and local adaptation, are consistent with the characteristics of the species known for its rusticity and adaptability. This study is the first exhaustive genome-wide analysis of the diversity of Italian donkey populations. The results emphasized the high informativeness of genome-wide markers retrieved through the ddRAD approach. The findings take on great significance in designing and implementing conservation strategies. Standardized genotype arrays for donkey species would make it possible to combine worldwide datasets to provide further insights into the evolution of the genomic structure and origin of this important genetic resource.
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Affiliation(s)
- Andrea Criscione
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | - Giorgio Chessari
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
- Department of Animal Sciences, Georg-August-University Göttingen, Göttingen, Germany
| | - Alberto Cesarani
- Dipartimento di Agraria, University of Sassari, Sassari, Italy
- Department of Animal and Dairy Science, University of Georgia, Athens, USA
| | - Michela Ablondi
- Dipartimento di Scienze Medico-Veterinarie, University of Parma, Parma, Italy
| | - Vittoria Asti
- Dipartimento di Scienze Medico-Veterinarie, University of Parma, Parma, Italy
| | - Daniele Bigi
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, University of Bologna, Bologna, Italy
| | - Salvatore Bordonaro
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | | | | | - Michele Congiu
- Dipartimento di Agraria, University of Sassari, Sassari, Italy
| | - Pasquale De Palo
- Dipartimento di Medicina Veterinaria, University of Bari Aldo Moro, Valenzano, Italy
| | - Vincenzo Landi
- Dipartimento di Medicina Veterinaria, University of Bari Aldo Moro, Valenzano, Italy
| | | | - Donato Matassino
- Consorzio per la Sperimentazione, Divulgazione e Applicazione di Biotecniche Innovative, Benevento, Italy
| | - Baldassare Portolano
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Silvia Riggio
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Alberto Sabbioni
- Dipartimento di Scienze Medico-Veterinarie, University of Parma, Parma, Italy
| | - Maria Teresa Sardina
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Gabriele Senczuk
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, Campobasso, Italy
| | - Serena Tumino
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | - Matteo Vasini
- Associazione Nazionale Allevatori delle Razze Equine ed Asinine Italiane, ANAREAI, Roma, Italy
| | - Elena Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, University of Bari Aldo Moro, Bari, Italy
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
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Senczuk G, Macrì M, Di Civita M, Mastrangelo S, Del Rosario Fresno M, Capote J, Pilla F, Delgado JV, Amills M, Martínez A. The demographic history and adaptation of Canarian goat breeds to environmental conditions through the use of genome-wide SNP data. Genet Sel Evol 2024; 56:2. [PMID: 38172652 PMCID: PMC10763158 DOI: 10.1186/s12711-023-00869-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND The presence of goats in the Canary Islands dates back to the late 1st millennium BC, which coincides with the colonization by the Amazigh settlers. However, the exact geographic origin of Canarian goats is uncertain since the Amazigh peoples were distributed over a wide spatial range. Nowadays, three Canarian breeds (Palmera, Majorera and Tinerfeña) are officially recognized, along with two distinct South and North Tinerfeña ecotypes, with the South Tinerfeña and Majorera goats thriving in arid and dry semi-desertic environments and the Palmera and North Tinerfeña goats are adapted to humid and temperate areas that are influenced by trade winds. Genotypes for 224 Canarian goats were generated using the Illumina Goat single nucleotide polymorphism (SNP)50 BeadChip. By merging these data with the genotypes from 1007 individuals of African and Southern European ancestry, our aim was to ascertain the geographic origin of the Canarian goats and identify genes associated with adaptation to diverse environmental conditions. RESULTS The diversity indices of the Canarian breeds align with most of those of the analyzed local breeds from Africa and Europe, except for the Palmera goats that showed lower levels of genetic variation. The Canarian breeds demonstrate a significant genetic differentiation compared to other populations, which indicates a history of prolonged geographic isolation. Moreover, the phylogenetic reconstruction indicated that the ancestry of the Canarian goats is fundamentally North African rather than West African. The ADMIXTURE and the TreeMix analyses showed no evidence of gene flow between Canarian goats and other continental breeds. The analysis of runs of homozygosity (ROH) identified 13 ROH islands while the window-based FST method detected 25 genomic regions under selection. Major signals of selection were found on Capra hircus (CHI) chromosomes 6, 7, and 10 using various comparisons and methods. CONCLUSIONS This genome-wide analysis sheds new light on the evolutionary history of the four breeds that inhabit the Canary Islands. Our findings suggest a North African origin of the Canarian goats. In addition, within the genomic regions highlighted by the ROH and FST approaches, several genes related to body size and heat tolerance were identified.
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Affiliation(s)
- Gabriele Senczuk
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, Italy.
| | - Martina Macrì
- Animal Breeding Consulting S.L., 14014, Córdoba, Spain
- Universidad de Córdoba, 14071, Córdoba, Spain
| | - Marika Di Civita
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, Italy
| | - Salvatore Mastrangelo
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128, Palermo, Italy
| | | | - Juan Capote
- Instituto Canario de Investigaciones Científicas, 38260, Tenerife, Spain
| | - Fabio Pilla
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, Italy
| | | | - Marcel Amills
- CRAG, CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
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Shi YJ, Huang JL, Mi JX, Li J, Meng FY, Zhong Y, He F, Tian FF, Zhang F, Chen LH, Yang HB, Hu HL, Wan XQ. A model of hybrid speciation process drawn from three new poplar species originating from distant hybridization between sections. Mol Phylogenet Evol 2024; 190:107966. [PMID: 37981264 DOI: 10.1016/j.ympev.2023.107966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 11/11/2023] [Accepted: 11/16/2023] [Indexed: 11/21/2023]
Abstract
Although numerous studies have been conducted on hybrid speciation, our understanding of this process remains limited. Through an 18-year systematic investigation of all taxa of Populus on the Qinghai-Tibet Plateau, we discovered three new taxa with clear characteristics of sect. Leucoides. Further evidence was gathered from morphology, whole-genome bioinformatics, biogeography, and breeding to demonstrate synthetically that they all originated from distant hybridization between sect. Leucoides and sect. Tacamahaca. P. gonggaensis originated from the hybridization of P. lasiocarpa with P. cathayana, P. butuoensis from the hybridization of P. wilsonii with P. szechuanica, and P. dafengensis from the hybridization of P. lasiocarpa with P. szechuanica. Due to heterosis, the three hybrid taxa possess greater ecological adaptability than their ancestral species. We propose a hybrid speciation process model that incorporates orthogonal, reverse, and backcrossing events. This model can adequately explain some crucial evolutionary concerns, such as the nuclear-cytoplasmic conflict on phylogeny and the extinction of ancestral species within the distribution range of hybrid species.
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Affiliation(s)
- Yu-Jie Shi
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China; Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou 318000, China
| | - Jin-Liang Huang
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Jia-Xuan Mi
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Jing Li
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Fan-Yu Meng
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Yu Zhong
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China; Sichuan Province Key Laboratory of Ecological Forestry Engineering on the Upper Reaches of the Yangtze River, Chengdu 611130, China
| | - Fang He
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Fei-Fei Tian
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Fan Zhang
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu 611130, China
| | - Liang-Hua Chen
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China; Sichuan Province Key Laboratory of Ecological Forestry Engineering on the Upper Reaches of the Yangtze River, Chengdu 611130, China
| | - Han-Bo Yang
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China; Sichuan Province Key Laboratory of Ecological Forestry Engineering on the Upper Reaches of the Yangtze River, Chengdu 611130, China
| | - Hong-Lin Hu
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Xue-Qin Wan
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China; Sichuan Province Key Laboratory of Ecological Forestry Engineering on the Upper Reaches of the Yangtze River, Chengdu 611130, China.
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Pogorevc N, Dotsev A, Upadhyay M, Sandoval-Castellanos E, Hannemann E, Simčič M, Antoniou A, Papachristou D, Koutsouli P, Rahmatalla S, Brockmann G, Sölkner J, Burger P, Lymberakis P, Poulakakis N, Bizelis I, Zinovieva N, Horvat S, Medugorac I. Whole-genome SNP genotyping unveils ancestral and recent introgression in wild and domestic goats. Mol Ecol 2024; 33:e17190. [PMID: 37909668 DOI: 10.1111/mec.17190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/04/2023] [Accepted: 10/16/2023] [Indexed: 11/03/2023]
Abstract
After the domestication of goats around 10,000 years before the present (BP), humans transported goats far beyond the range of their wild ancestor, the bezoar goat. This brought domestic goats into contact with many wild goat species such as ibex and markhor, enabling introgression between domestic and wild goats. To investigate this, while shedding light on the taxonomic status of wild and domestic goats, we analysed genome-wide SNP data of 613 specimens from 14 taxonomic units, including Capra hircus, C. pyrenaica, C. ibex (from Switzerland, Austria, Germany and Slovenia), C. aegagrus aegagrus, C. a. cretica, C. h. dorcas, C. caucasica caucasica, C. c. severtzovi, C. c. cylindricornis, C. falconeri, C. sibirica sibirica, C. s. alaiana and C. nubiana, as well as Oreamnos americanus (mountain goat) as an outgroup. To trace gene flow between domestic and wild goats, we integrated genotype data of local goat breeds from the Alps as well as from countries such as Spain, Greece, Türkiye, Egypt, Sudan, Iran, Russia (Caucasus and Altai) and Pakistan. Our phylogenetic analyses displayed a clear separation between bezoar-type and ibex-type clades with wild goats from the Greek islands of Crete and Youra clustered within domestic goats, confirming their feral origin. Our analyses also revealed gene flow between the lineages of Caucasian tur and domestic goats that most likely occurred before or during early domestication. Within the clade of domestic goats, analyses inferred gene flow between African and Iberian goats. The detected events of introgression were consistent with previous reports and offered interesting insights into the historical relationships among domestic and wild goats.
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Affiliation(s)
- Neža Pogorevc
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
- Population Genomics Group, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-University of Munich, Martinsried/Planegg, Germany
| | - Arsen Dotsev
- L.K. Ernst Federal Research Center for Animal Husbandry, Podolsk, Russia
| | - Maulik Upadhyay
- Population Genomics Group, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-University of Munich, Martinsried/Planegg, Germany
| | - Edson Sandoval-Castellanos
- Population Genomics Group, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-University of Munich, Martinsried/Planegg, Germany
| | - Elisabeth Hannemann
- Population Genomics Group, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-University of Munich, Martinsried/Planegg, Germany
| | - Mojca Simčič
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Aglaia Antoniou
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Crete, Greece
| | - Dimitris Papachristou
- Laboratory of Animal Breeding and Husbandry, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, Athens, Greece
| | - Panagiota Koutsouli
- Laboratory of Animal Breeding and Husbandry, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, Athens, Greece
| | - Siham Rahmatalla
- Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Animal Breeding and Molecular Genetics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Gudrun Brockmann
- Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Animal Breeding and Molecular Genetics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Johann Sölkner
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Pamela Burger
- Department of Interdisciplinary Life Sciences, Research Institute of Wildlife Ecology, Vetmeduni Vienna, Vienna, Austria
| | - Petros Lymberakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Irakleio, Greece
| | - Nikos Poulakakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Irakleio, Greece
- Biology Department, School of Sciences and Engineering, University of Crete, Irakleio, Greece
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Irakleio, Greece
| | - Iosif Bizelis
- Laboratory of Animal Breeding and Husbandry, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, Athens, Greece
| | - Natalia Zinovieva
- L.K. Ernst Federal Research Center for Animal Husbandry, Podolsk, Russia
| | - Simon Horvat
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-University of Munich, Martinsried/Planegg, Germany
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Gao Y, Dai D, Wang H, Wu W, Xiao P, Wu L, Wei X, Yin S. Genomic insights into differentiation and adaptation of Amorphophallus yunnanensis in the mountainous region of Southwest China. Ecol Evol 2024; 14:e10861. [PMID: 38264337 PMCID: PMC10805605 DOI: 10.1002/ece3.10861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 01/25/2024] Open
Abstract
The role of geographical isolation and environmental adaptation in driving the differentiation and radiation of species has been a hotspot in evolutionary biology. The extremely complicated and fragmented geography of the mountainous region of Southwest China provides an excellent system for investigating the process of species divergence in heterogeneous habitats. Amorphophallus yunnanensis is a species of extreme habitat preference that resides mainly in the mountainous region of Southwest China. Here, we used restriction site-associated DNA sequencing (RAD-seq) to characterize the geographic pattern of genetic variation among 19 populations of A. yunnanensis as well as the genomic basis of environmental adaptation. A pattern of low population genetic diversity and high level of genetic differentiation was observed. The genomic data revealed a clear east-west genetic differentiation, with two distinct genetic lineages corresponding to the Guizhou plateau and Yunnan plateau, respectively. However, we discovered demographic expansion of the Guizhou Plateau lineage and recent hybridization in populations at the contact region. Significant levels of isolation by distance along with isolation by environment were detected. Outlier tests and genome-environment association analyses identified 89 putatively adaptive loci that might play a role in environmental adaptation. Our results suggest that the genetic divergence of A. yunnanensis is attributed to geographical isolation together with divergent selection in the mountainous region of Southwest China.
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Affiliation(s)
- Yong Gao
- College of Biological Resource and Food EngineeringQujing Normal UniversityQujingYunnanChina
| | - Dongqin Dai
- College of Biological Resource and Food EngineeringQujing Normal UniversityQujingYunnanChina
| | - Haibo Wang
- College of Biological Resource and Food EngineeringQujing Normal UniversityQujingYunnanChina
| | - Weijia Wu
- College of Biological Resource and Food EngineeringQujing Normal UniversityQujingYunnanChina
| | - Penghui Xiao
- College of Biological Resource and Food EngineeringQujing Normal UniversityQujingYunnanChina
| | - Lifang Wu
- College of Biological Resource and Food EngineeringQujing Normal UniversityQujingYunnanChina
| | - Xiaomei Wei
- College of Biological Resource and Food EngineeringQujing Normal UniversityQujingYunnanChina
| | - Si Yin
- College of Biological Resource and Food EngineeringQujing Normal UniversityQujingYunnanChina
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Lau SCY, Wilson NG, Golledge NR, Naish TR, Watts PC, Silva CNS, Cooke IR, Allcock AL, Mark FC, Linse K, Strugnell JM. Genomic evidence for West Antarctic Ice Sheet collapse during the Last Interglacial. Science 2023; 382:1384-1389. [PMID: 38127761 DOI: 10.1126/science.ade0664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 10/30/2023] [Indexed: 12/23/2023]
Abstract
The marine-based West Antarctic Ice Sheet (WAIS) is considered vulnerable to irreversible collapse under future climate trajectories, and its tipping point may lie within the mitigated warming scenarios of 1.5° to 2°C of the United Nations Paris Agreement. Knowledge of ice loss during similarly warm past climates could resolve this uncertainty, including the Last Interglacial when global sea levels were 5 to 10 meters higher than today and global average temperatures were 0.5° to 1.5°C warmer than preindustrial levels. Using a panel of genome-wide, single-nucleotide polymorphisms of a circum-Antarctic octopus, we show persistent, historic signals of gene flow only possible with complete WAIS collapse. Our results provide the first empirical evidence that the tipping point of WAIS loss could be reached even under stringent climate mitigation scenarios.
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Affiliation(s)
- Sally C Y Lau
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, Townsville, Qld, Australia
- Securing Antarctica's Environmental Future, James Cook University, Townsville, Qld, Australia
| | - Nerida G Wilson
- Collections & Research, Western Australian Museum, Welshpool, WA, Australia
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
- Securing Antarctica's Environmental Future, Western Australian Museum, Welshpool, WA, Australia
| | - Nicholas R Golledge
- Antarctic Research Centre, Victoria University of Wellington, Wellington, New Zealand
| | - Tim R Naish
- Antarctic Research Centre, Victoria University of Wellington, Wellington, New Zealand
| | - Phillip C Watts
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Catarina N S Silva
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, Townsville, Qld, Australia
- Centre for Functional Ecology - Science for People & the Planet (CFE), Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra, Portugal
| | - Ira R Cooke
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Qld, Australia
| | - A Louise Allcock
- School of Natural Sciences and Ryan Institute, University of Galway, Galway, Ireland
| | - Felix C Mark
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | | | - Jan M Strugnell
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, Townsville, Qld, Australia
- Securing Antarctica's Environmental Future, James Cook University, Townsville, Qld, Australia
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Zhang CL, Zhang J, Tuersuntuoheti M, Zhou W, Han Z, Li X, Yang R, Zhang L, Zheng L, Liu S. Landscape genomics reveals adaptive divergence of indigenous sheep in different ecological environments of Xinjiang, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166698. [PMID: 37683864 DOI: 10.1016/j.scitotenv.2023.166698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 08/22/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023]
Abstract
Sheep are important livestock animals that have evolved under various ecological pressures. Xinjiang is a region with diverse and harsh environments that have shaped many local sheep breeds with unique characteristics and environmental adaptability. However, these breeds are losing ecological flexibility due to the promotion of intensive farming practices. Here we sequenced 14 local sheep breeds from Xinjiang and analyzed their genetic structure and gene flow with other sheep breeds from neighboring regions. The Tibetan Plateau was the geographic origin of Xinjiang native sheep evolution. We performed genome-environment association analysis and identified Bio9: Mean Temperature of Driest Quarter and Bio15: Precipitation Seasonality as the key environmental factors affecting Xinjiang local sheep and the key genes involved in their survival and adaptation. We classified Xinjiang native sheep breeds into six groups based on their differential genes by pairwise selective sweep analysis and Community Network Analysis. We analyzed transcriptome expression data of 832 sheep tissues and detected tissue-specific enrichment of six group-specific genes in different biological systems. Our results revealed the genetic basis of year-round estrus, drought tolerance, hypoxia resistance, and cold tolerance traits of Xinjiang sheep breeds. Moreover, we proposed conservation strategies for Xinjiang local sheep breeds and provided theoretical guidance for breeding new sheep breeds under global extreme environments.
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Affiliation(s)
- Cheng-Long Zhang
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Jihu Zhang
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Mirenisa Tuersuntuoheti
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Wen Zhou
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Zhipeng Han
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Xiaopeng Li
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Ruizhi Yang
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Lulu Zhang
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Langman Zheng
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Shudong Liu
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China.
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45
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Kishino H, Nakamichi R, Kitada S. Genetic adaptations in the population history of Arabidopsis thaliana. G3 (BETHESDA, MD.) 2023; 13:jkad218. [PMID: 37748020 PMCID: PMC10700115 DOI: 10.1093/g3journal/jkad218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 05/26/2023] [Accepted: 09/14/2023] [Indexed: 09/27/2023]
Abstract
A population encounters a variety of environmental stresses, so the full source of its resilience can only be captured by collecting all the signatures of adaptation to the selection of the local environment in its population history. Based on the multiomic data of Arabidopsis thaliana, we constructed a database of phenotypic adaptations (p-adaptations) and gene expression (e-adaptations) adaptations in the population. Through the enrichment analysis of the identified adaptations, we inferred a likely scenario of adaptation that is consistent with the biological evidence from experimental work. We analyzed the dynamics of the allele frequencies at the 23,880 QTLs of 174 traits and 8,618 eQTLs of 1,829 genes with respect to the total SNPs in the genomes and identified 650 p-adaptations and 3,925 e-adaptations [false discovery rate (FDR) = 0.05]. The population underwent large-scale p-adaptations and e-adaptations along 4 lineages. Extremely cold winters and short summers prolonged seed dormancy and expanded the root system architecture. Low temperatures prolonged the growing season, and low light intensity required the increased chloroplast activity. The subtropical and humid environment enhanced phytohormone signaling pathways in response to the biotic and abiotic stresses. Exposure to heavy metals selected alleles for lower heavy metal uptake from soil, lower growth rate, lower resistance to bacteria, and higher expression of photosynthetic genes were selected. The p-adaptations are directly interpretable, while the coadapted gene expressions reflect the physiological requirements for the adaptation. The integration of this information characterizes when and where the population has experienced environmental stress and how the population responded at the molecular level.
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Affiliation(s)
- Hirohisa Kishino
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Research and Development Initiative, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan
| | - Reiichiro Nakamichi
- Fisheries Resources Institute, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan
| | - Shuichi Kitada
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
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Tourvas N, Ganopoulos I, Koubouris G, Kostelenos G, Manthos I, Bazakos C, Stournaras V, Molassiotis A, Aravanopoulos F. Wild and cultivated olive tree genetic diversity in Greece: a diverse resource in danger of erosion. Front Genet 2023; 14:1298565. [PMID: 38111682 PMCID: PMC10725918 DOI: 10.3389/fgene.2023.1298565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 11/20/2023] [Indexed: 12/20/2023] Open
Abstract
The genetic relationships between Greek wild olive tree populations and cultivars were investigated. A total of 219 wild genotypes and 67 cultivar genotypes were analyzed by employing 10 SSR markers. Data evidenced that the wild populations exhibited high levels of genetic diversity and exclusively host 40% of the total number of alleles detected. Inbreeding was observed within populations, probably as a consequence of their fragmented spatial distribution. The genetic differentiation between cultivars and wild individuals, as well as within wild populations, was low. Nevertheless, three gene pools of wild trees were detected, corresponding to the geographical areas of Northeastern Greece, Peloponnese-Crete and Epirus. Most cultivars clustered in a separate group, while the rest of them formed a heterogenous group with membership coefficients akin to the three wild olive clusters. Regarding the history of olive cultivation in Greece, bidirectional gene flow was detected between populations of Peloponnese-Crete and the gene pool that composes some of Greece's most important cultivars, such as "Koroneiki" and "Mastoidis", which is inferred as an indication of a minor domestication event in the area. A strategy for the protection of Greek-oriented olive genetic resources is proposed, along with suggestions for the utilization of the genetically diverse wild resources with regard to the introgression of traits of agronomical interest to cultivars.
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Affiliation(s)
- Nikolaos Tourvas
- Laboratory of Forest Genetics, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization (ELGO) DIMITRA, Thessaloniki-Thermi, Greece
| | - Georgios Koubouris
- Institute of Olive Tree, Subtropical Crops and Viticulture, Hellenic Agricultural Organization (ELGO) DIMITRA, Chania, Greece
| | | | - Ioannis Manthos
- Department of Nut Trees, Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization (ELGO) DIMITRA, Neo Krikello-Lamia, Greece
| | - Christos Bazakos
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization (ELGO) DIMITRA, Thessaloniki-Thermi, Greece
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Vasileios Stournaras
- Department of Olive and Horticultural Crops, Institute of Olive Tree, Subtropical Crops and Viticulture, Hellenic Agricultural Organization (ELGO) DIMITRA, Kalamata, Greece
| | - Athanassios Molassiotis
- Laboratory of Pomology, Department of Horticulture, Aristotle University of Thessaloniki, Thessaloniki-Thermi, Greece
| | - Filippos Aravanopoulos
- Laboratory of Forest Genetics, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, Greece
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Barchi L, Aprea G, Rabanus-Wallace MT, Toppino L, Alonso D, Portis E, Lanteri S, Gaccione L, Omondi E, van Zonneveld M, Schafleitner R, Ferrante P, Börner A, Stein N, Díez MJ, Lefebvre V, Salinier J, Boyaci HF, Finkers R, Brouwer M, Bovy AG, Rotino GL, Prohens J, Giuliano G. Analysis of >3400 worldwide eggplant accessions reveals two independent domestication events and multiple migration-diversification routes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1667-1680. [PMID: 37682777 DOI: 10.1111/tpj.16455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 08/26/2023] [Indexed: 09/10/2023]
Abstract
Eggplant (Solanum melongena) is an important Solanaceous crop, widely cultivated and consumed in Asia, the Mediterranean basin, and Southeast Europe. Its domestication centers and migration and diversification routes are still a matter of debate. We report the largest georeferenced and genotyped collection to this date for eggplant and its wild relatives, consisting of 3499 accessions from seven worldwide genebanks, originating from 105 countries in five continents. The combination of genotypic and passport data points to the existence of at least two main centers of domestication, in Southeast Asia and the Indian subcontinent, with limited genetic exchange between them. The wild and weedy eggplant ancestor S. insanum shows admixture with domesticated S. melongena, similar to what was described for other fruit-bearing Solanaceous crops such as tomato and pepper and their wild ancestors. After domestication, migration and admixture of eggplant populations from different regions have been less conspicuous with respect to tomato and pepper, thus better preserving 'local' phenotypic characteristics. The data allowed the identification of misclassified and putatively duplicated accessions, facilitating genebank management. All the genetic, phenotypic, and passport data have been deposited in the Open Access G2P-SOL database, and constitute an invaluable resource for understanding the domestication, migration and diversification of this cosmopolitan vegetable.
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Affiliation(s)
- Lorenzo Barchi
- DISAFA - Plant Genetics, University of Turin, Grugliasco, Torino, 10095, Italy
| | - Giuseppe Aprea
- ENEA, Casaccia Res Ctr, Via Anguillarese 301, Rome, 00123, Italy
| | - M Timothy Rabanus-Wallace
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Seeland, OT Gatersleben, 06466, Germany
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Australia
| | - Laura Toppino
- CREA, Research Centre for Genomics and Bioinformatics, Via Paullese 28, Montanaso Lombardo, LO 26836, Italy
| | - David Alonso
- Universitat Politècnica de València, Camino de Vera 14, Valencia, 46022, Spain
| | - Ezio Portis
- DISAFA - Plant Genetics, University of Turin, Grugliasco, Torino, 10095, Italy
| | - Sergio Lanteri
- DISAFA - Plant Genetics, University of Turin, Grugliasco, Torino, 10095, Italy
| | - Luciana Gaccione
- DISAFA - Plant Genetics, University of Turin, Grugliasco, Torino, 10095, Italy
| | | | | | | | - Paola Ferrante
- ENEA, Casaccia Res Ctr, Via Anguillarese 301, Rome, 00123, Italy
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Seeland, OT Gatersleben, 06466, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Seeland, OT Gatersleben, 06466, Germany
- Department of Crop Sciences, Center for Integrated Breeding Research (CiBreed), Georg-August-University, Von Siebold Str. 8, Göttingen, 37075, Germany
| | - Maria José Díez
- Universitat Politècnica de València, Camino de Vera 14, Valencia, 46022, Spain
| | | | - Jérémy Salinier
- INRAE, GAFL, Montfavet, F-84140, France
- CIRAD La Réunion et Mayotte, UMR PVBMT Saint-Pierre, La Réunion, France
| | - Hatice Filiz Boyaci
- Department of Horticulture, Faculty of Agriculture, University of Recep Tayyip Erdogan, Rize, Turkey
| | - Richard Finkers
- Wageningen University & Research WUR, Wageningen, The Netherlands
- GenNovation B.V., Wageningen, The Netherlands
| | - Matthijs Brouwer
- Wageningen University & Research WUR, Wageningen, The Netherlands
| | - Arnaud G Bovy
- Wageningen University & Research WUR, Wageningen, The Netherlands
| | - Giuseppe Leonardo Rotino
- CREA, Research Centre for Genomics and Bioinformatics, Via Paullese 28, Montanaso Lombardo, LO 26836, Italy
| | - Jaime Prohens
- Universitat Politècnica de València, Camino de Vera 14, Valencia, 46022, Spain
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Muniz AC, de Oliveira Buzatti RS, de Lemos-Filho JP, Heuertz M, Nazareno AG, Lovato MB. Genomic signatures of ecological divergence between savanna and forest populations of a Neotropical tree. ANNALS OF BOTANY 2023; 132:523-540. [PMID: 37642427 PMCID: PMC10667007 DOI: 10.1093/aob/mcad120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 08/25/2023] [Indexed: 08/31/2023]
Abstract
BACKGROUND AND AIMS In eastern Neotropical South America, the Cerrado, a large savanna vegetation, and the Atlantic Forest harbour high biodiversity levels, and their habitats are rather different from each other. The biomes have intrinsic evolutionary relationships, with high lineage exchange that can be attributed, in part, to a large contact zone between them. The genomic study of ecotypes, i.e. populations adapted to divergent habitats, can be a model to study the genomic signatures of ecological divergence. Here, we investigated two ecotypes of the tree Plathymenia reticulata, one from the Cerrado and the other from the Atlantic Forest, which have a hybrid zone in the ecotonal zone of Atlantic Forest-Cerrado. METHODS The ecotypes were sampled in the two biomes and their ecotone. The evolutionary history of the divergence of the species was analysed with double-digest restriction site-associated DNA sequencing. The genetic structure and the genotypic composition of the hybrid zone were determined. Genotype-association analyses were performed, and the loci under putative selection and their functions were investigated. KEY RESULTS High divergence between the two ecotypes was found, and only early-generation hybrids were found in the hybrid zone, suggesting a partial reproductive barrier. Ancient introgression between the Cerrado and Atlantic Forest was not detected. The soil and climate were associated with genetic divergence in Plathymenia ecotypes and outlier loci were found to be associated with the stress response, with stomatal and root development and with reproduction. CONCLUSIONS The high genomic, ecological and morphophysiological divergence between ecotypes, coupled with partial reproductive isolation, indicate that the ecotypes represent two species and should be managed as different evolutionary lineages. We advise that the forest species should be re-evaluated and restated as vulnerable. Our results provide insights into the genomic mechanisms underlying the diversification of species across savanna and forest habitats and the evolutionary forces acting in the species diversification in the Neotropics.
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Affiliation(s)
- André Carneiro Muniz
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, CP 486, Belo Horizonte, MG 31270-901, Brazil
| | | | - José Pires de Lemos-Filho
- Departamento de Botânica, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Myriam Heuertz
- Biogeco, INRAE, Univ. Bordeaux, 69 route d’Arcachon, 33610 Cestas, France
| | - Alison Gonçalves Nazareno
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, CP 486, Belo Horizonte, MG 31270-901, Brazil
| | - Maria Bernadete Lovato
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, CP 486, Belo Horizonte, MG 31270-901, Brazil
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49
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Volkova NA, Romanov MN, Abdelmanova AS, Larionova PV, German NY, Vetokh AN, Shakhin AV, Volkova LA, Anshakov DV, Fisinin VI, Narushin VG, Griffin DK, Sölkner J, Brem G, McEwan JC, Brauning R, Zinovieva NA. Genotyping-by-Sequencing Strategy for Integrating Genomic Structure, Diversity and Performance of Various Japanese Quail ( Coturnix japonica) Breeds. Animals (Basel) 2023; 13:3439. [PMID: 38003057 PMCID: PMC10668688 DOI: 10.3390/ani13223439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/23/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Traces of long-term artificial selection can be detected in genomes of domesticated birds via whole-genome screening using single-nucleotide polymorphism (SNP) markers. This study thus examined putative genomic regions under selection that are relevant to the development history, divergence and phylogeny among Japanese quails of various breeds and utility types. We sampled 99 birds from eight breeds (11% of the global gene pool) of egg (Japanese, English White, English Black, Tuxedo and Manchurian Golden), meat (Texas White and Pharaoh) and dual-purpose (Estonian) types. The genotyping-by-sequencing analysis was performed for the first time in domestic quails, providing 62,935 SNPs. Using principal component analysis, Neighbor-Net and Admixture algorithms, the studied breeds were characterized according to their genomic architecture, ancestry and direction of selective breeding. Japanese and Pharaoh breeds had the smallest number and length of homozygous segments indicating a lower selective pressure. Tuxedo and Texas White breeds showed the highest values of these indicators and genomic inbreeding suggesting a greater homozygosity. We revealed evidence for the integration of genomic and performance data, and our findings are applicable for elucidating the history of creation and genomic variability in quail breeds that, in turn, will be useful for future breeding improvement strategies.
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Affiliation(s)
- Natalia A. Volkova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Michael N. Romanov
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK;
| | - Alexandra S. Abdelmanova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Polina V. Larionova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Nadezhda Yu. German
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Anastasia N. Vetokh
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Alexey V. Shakhin
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Ludmila A. Volkova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Dmitry V. Anshakov
- Breeding and Genetic Center Zagorsk Experimental Breeding Farm—Branch of the Federal Research Centre, All-Russian Poultry Research and Technological Institute, Russian Academy of Sciences, Sergiev Posad 141311, Moscow Oblast, Russia;
| | - Vladimir I. Fisinin
- Federal Research Center “All-Russian Poultry Research and Technological Institute” of the Russian Academy of Sciences, Sergiev Posad 141311, Moscow Oblast, Russia;
| | - Valeriy G. Narushin
- Research Institute for Environment Treatment, 69032 Zaporizhya, Ukraine;
- Vita-Market Co., Ltd., 69032 Zaporizhya, Ukraine
| | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK;
| | - Johann Sölkner
- Institute of Livestock Sciences (NUWI), University of Natural Resources and Life Sciences Vienna, 1180 Vienna, Austria;
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, 1210 Vienna, Austria;
| | - John C. McEwan
- AgResearch, Invermay Agricultural Centre, Mosgiel 9053, New Zealand; (J.C.M.); (R.B.)
| | - Rudiger Brauning
- AgResearch, Invermay Agricultural Centre, Mosgiel 9053, New Zealand; (J.C.M.); (R.B.)
| | - Natalia A. Zinovieva
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
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Yuan R, Li J, Ma X, Feng Z, Xing R, Chen S, Gao Q. Investigation of phylogenetic relationships within Saxifraga diversifolia complex (Saxifragaceae) based on restriction-site associated DNA sequence markers. Ecol Evol 2023; 13:e10675. [PMID: 37928197 PMCID: PMC10620575 DOI: 10.1002/ece3.10675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 09/28/2023] [Accepted: 10/16/2023] [Indexed: 11/07/2023] Open
Abstract
Subsect. Hirculoideae Engl. & Irmsch., belonging to Saxifraga sect. Ciliatae Haw., has high species richness. It can be divided into S. diversifolia, S. pseudohirculus, and S. sinomontana complexes based on morphological characteristics. The species with prominent leaf veins on the posterior leaf edge were placed in the S. diversifolia complex, which is mainly distributed on the eastern and southern margins of the Qinghai-Tibetan Plateau. In this study, 53 samples, representing 15 of the 33 described species in the S. diversifolia complex, were sequenced using the Restriction-site Associated DNA Sequence (RAD-seq) technique. A total of 111,938 high-quality SNP loci were screened to investigate the phylogenetic relationships within the S. diversifolia complex. The result of the neighbor-joining (NJ) tree shows that the S. diversifolia complex is a paraphyletic group. Despite of some inconsistencies as revealed by genetic structural analysis, clustering results of representative species reconstructed by both NJ and principal component analysis analyses support previous biogeographic and morphological evidences. In addition, long-distance gene flow events for 11 taxa were detected in the S. diversifolia complex, respectively from S. implicans 1 to S. implicans 2, S. diversifolia and S. maxionggouensis, and from S. maxionggouensis to S. nigroglandulifera. These findings may improve our comprehension of the phylogeny, classification, and evolution of the S. diversifolia complex.
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Affiliation(s)
- Rui Yuan
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National Park Chinese Academy of Sciences Xining China
- University of Chinese Academy of Sciences Beijing China
| | - Jiaxin Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National Park Chinese Academy of Sciences Xining China
- University of Chinese Academy of Sciences Beijing China
| | - Xiaolei Ma
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National Park Chinese Academy of Sciences Xining China
- University of Chinese Academy of Sciences Beijing China
| | - Zhilin Feng
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National Park Chinese Academy of Sciences Xining China
- University of Chinese Academy of Sciences Beijing China
| | - Rui Xing
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National Park Chinese Academy of Sciences Xining China
| | - Shilong Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National Park Chinese Academy of Sciences Xining China
| | - Qingbo Gao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National Park Chinese Academy of Sciences Xining China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology Chinese Academy of Sciences Xining China
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