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Yu Y, Yang X, Liu D, Du P, Meng H, Huang Z, Xiong J, Ding Y, Ren X, Allen E, Wang H, Han S, Jin L, Wang CC, Wen S. Ancient genomic analysis of a Chinese hereditary elite from the Northern and Southern Dynasties. J Genet Genomics 2024:S1673-8527(24)00184-X. [PMID: 39009302 DOI: 10.1016/j.jgg.2024.07.009] [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: 12/05/2023] [Revised: 07/01/2024] [Accepted: 07/04/2024] [Indexed: 07/17/2024]
Abstract
China's Northern and Southern Dynasties period (3rd-6th centuries AD) marked a significant era of ethnic integration in northern China. However, previous ancient DNA studies have primarily focused on northern ethnic groups, with limited research on the genetic formation of the hereditary elite family, especially considering their abundant archaeological record and clear material identity. In this study, we obtained the ancient genome of a hereditary elite family, Gao Bin (, 503-572 AD), at 0.6473-fold coverage with 475132 single-nucleotide polymorphisms (SNPs) on the 1240k panel. His mitochondrial haplogroup belonged to Z4 and Y-haplogroup to O1a1a2b-F2444*. The genetic profile of Gao Bin was most similar to that of the northern Han Chinese. He could be modelled as deriving all his ancestry from Late Neolithic to Iron Age Yellow River farmers without influence from Northeast Asia, Korea, or the Mongolian Plateau. Our study sheds light on the genetic formation of hereditary elite families in the context of the Southern and Northern Dynasties ethnic integration.
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Affiliation(s)
- Yao Yu
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China; Department of History, Fudan University, Shanghai 200433, China
| | - Xiaomin Yang
- Department of Anthropology and Ethnology, Institute of Anthropology, Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, Fujian 361005, China
| | - Daiyun Liu
- Shaanxi Academy of Archaeology, Xi'an, Shaanxi 710054, China
| | - Panxin Du
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China; State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China
| | - Hailiang Meng
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Zixiao Huang
- Department of History, Fudan University, Shanghai 200433, China
| | - Jianxue Xiong
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China
| | - Yi Ding
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China
| | - Xiaoying Ren
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China
| | - Edward Allen
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China
| | - Hui Wang
- Center for the Belt and Road Archaeology and Ancient Civilizations, Shanghai 200433, China
| | - Sheng Han
- Department of History, Fudan University, Shanghai 200433, China
| | - Li Jin
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China.
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, Fujian 361005, China; State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian 361102, China; Institute of Artificial Intelligence, Xiamen University, Xiamen, Fujian 361005, China.
| | - Shaoqing Wen
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China; Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China; Center for the Belt and Road Archaeology and Ancient Civilizations, Shanghai 200433, China; MOE Laboratory for National Development and Intelligent Governance, Fudan University, Shanghai 200433, China.
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Luo JJ, Shang H, Xue ZQ, Wang Y, Dai XL, Shen H, Yan YH. Genome-wide data reveal bi-direction and asymmetrical hybridization origin of a fern species Microlepia matthewii. FRONTIERS IN PLANT SCIENCE 2024; 15:1392990. [PMID: 39040506 PMCID: PMC11260791 DOI: 10.3389/fpls.2024.1392990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 06/20/2024] [Indexed: 07/24/2024]
Abstract
Introduction Natural hybridization is common and plays a crucial role in driving biodiversity in nature. Despite its significance, the understanding of hybridization in ferns remains inadequate. Therefore, it is imperative to study fern hybridization to gain a more comprehensive understanding of fern biodiversity. Our study delves into the role of hybridization in shaping fern species, employing Microlepia matthewii as a case study to investigate its origins of hybridization. Methods We performed double digest Genotyping-by-sequencing (dd-GBS) on M. matthewii and its potential parent species, identifying nuclear and chloroplast SNPs. Initially, nuclear SNPs were employed to construct the three cluster analysis: phylogenetic tree, principal component analysis, and population structure analysis. Subsequently, to confirm whether the observed genetic mixture pattern resulted from hybridization, we utilized two methods: ABBA-BABA statistical values in the D-suite program and gene frequency covariance in the Treemix software to detect gene flow. Finally, we employed chloroplast SNPs to construct a phylogenetic tree, tracing the maternal origin. Results and discussion The analysis of the nuclear SNP cluster revealed that M. matthewii possesses a genetic composition that is a combination of M. hancei and M. calvescens. Furthermore, the analysis provided strong evidence of significant gene flow signatures from the parental species to the hybrid, as indicated by the two gene flow analyses. The samples of M. matthewii cluster separately with M. hancei or M. calvescens on the chloroplast systematic tree. However, the parentage ratio significantly differs from 1:1, suggesting that M. matthewii is a bidirectional and asymmetrical hybrid offspring of M. hancei and M. calvescens.
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Affiliation(s)
- Jun-Jie Luo
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
- College of Life Sciences, Shanghai Normal University, Shanghai, China
- Middle School Department, Songjiang Experimental School Affiliated To Shanghai University of International Business and Economics (SUIBE), Shanghai, China
| | - Hui Shang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Zhi-Qing Xue
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Ying Wang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Xi-Ling Dai
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Hui Shen
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
- Shanghai Chenshan Science Research Center, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yue-Hong Yan
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation& Research Center of Shenzhen, Shenzhen, Guangdong, China
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3
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Ciezarek AG, Mehta TK, Man A, Ford AGP, Kavembe GD, Kasozi N, Ngatunga BP, Shechonge AH, Tamatamah R, Nyingi DW, Cnaani A, Ndiwa TC, Di Palma F, Turner GF, Genner MJ, Haerty W. Ancient and Recent Hybridization in the Oreochromis Cichlid Fishes. Mol Biol Evol 2024; 41:msae116. [PMID: 38865496 PMCID: PMC11221657 DOI: 10.1093/molbev/msae116] [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: 09/21/2023] [Revised: 05/30/2024] [Accepted: 06/04/2024] [Indexed: 06/14/2024] Open
Abstract
Cichlid fishes of the genus Oreochromis (tilapia) are among the most important fish for inland capture fisheries and global aquaculture. Deliberate introductions of non-native species for fisheries improvement and accidental escapees from farms have resulted in admixture with indigenous species. Such hybridization may be detrimental to native biodiversity, potentially leading to genomic homogenization of populations and the loss of important genetic material associated with local adaptation. By contrast, introgression may fuel diversification when combined with ecological opportunity, by supplying novel genetic combinations. To date, the role of introgression in the evolutionary history of tilapia has not been explored. Here we studied both ancient and recent hybridization in tilapia, using whole genome resequencing of 575 individuals from 23 species. We focused on Tanzania, a natural hotspot of tilapia diversity, and a country where hybridization between exotic and native species in the natural environment has been previously reported. We reconstruct the first genome-scale phylogeny of the genus and reveal prevalent ancient gene flow across the Oreochromis phylogeny. This has likely resulted in the hybrid speciation of one species, O. chungruruensis. We identify multiple cases of recent hybridization between native and introduced species in the wild, linked to the use of non-native species in both capture fisheries improvement and aquaculture. This has potential implications for both conservation of wild populations and the development of the global tilapia aquaculture industry.
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Affiliation(s)
- Adam G Ciezarek
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
- Centre of Environment, Fisheries and Aquaculture Science (Cefas), Scientific Advice for Fisheries Management Team (SAFM), Lowestoft NR33 0H5, UK
| | - Tarang K Mehta
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Angela Man
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Antonia G P Ford
- School of Life and Health Sciences, Whitelands College, University of Roehampton, London SW15 4NA, UK
| | | | - Nasser Kasozi
- National Agricultural Research Organisation, Buginyanya Zonal Agricultural Research and Development Institute, Mbale, Uganda
| | | | | | | | | | - Avner Cnaani
- Institute of Animal Science, Agricultural Research Organization, Rishon LeZion 7528809, Israel
| | - Titus C Ndiwa
- Department of Clinical Studies, University of Nairobi, Nairobi, Kenya
| | - Federica Di Palma
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TU, UK
| | - George F Turner
- School of Natural Sciences, Bangor University, Bangor LL57 2UW, UK
| | - Martin J Genner
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
| | - Wilfried Haerty
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
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Reyna-Blanco CS, Caduff M, Galimberti M, Leuenberger C, Wegmann D. Inference of Locus-Specific Population Mixtures from Linked Genome-Wide Allele Frequencies. Mol Biol Evol 2024; 41:msae137. [PMID: 38958167 PMCID: PMC11255385 DOI: 10.1093/molbev/msae137] [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: 11/06/2023] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/04/2024] Open
Abstract
Admixture between populations and species is common in nature. Since the influx of new genetic material might be either facilitated or hindered by selection, variation in mixture proportions along the genome is expected in organisms undergoing recombination. Various graph-based models have been developed to better understand these evolutionary dynamics of population splits and mixtures. However, current models assume a single mixture rate for the entire genome and do not explicitly account for linkage. Here, we introduce TreeSwirl, a novel method for inferring branch lengths and locus-specific mixture proportions by using genome-wide allele frequency data, assuming that the admixture graph is known or has been inferred. TreeSwirl builds upon TreeMix that uses Gaussian processes to estimate the presence of gene flow between diverged populations. However, in contrast to TreeMix, our model infers locus-specific mixture proportions employing a hidden Markov model that accounts for linkage. Through simulated data, we demonstrate that TreeSwirl can accurately estimate locus-specific mixture proportions and handle complex demographic scenarios. It also outperforms related D- and f-statistics in terms of accuracy and sensitivity to detect introgressed loci.
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Affiliation(s)
- Carlos S Reyna-Blanco
- Department of Biology, University of Fribourg, Fribourg 1700, Switzerland
- Swiss Institute of Bioinformatics, Fribourg 1700, Switzerland
| | - Madleina Caduff
- Department of Biology, University of Fribourg, Fribourg 1700, Switzerland
- Swiss Institute of Bioinformatics, Fribourg 1700, Switzerland
| | - Marco Galimberti
- Department of Biology, University of Fribourg, Fribourg 1700, Switzerland
- Swiss Institute of Bioinformatics, Fribourg 1700, Switzerland
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- Veterans Affairs Connecticut Healthcare System, West Haven, CT, USA
| | | | - Daniel Wegmann
- Department of Biology, University of Fribourg, Fribourg 1700, Switzerland
- Swiss Institute of Bioinformatics, Fribourg 1700, Switzerland
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5
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Bacon CD, Hill A. Hybridization in palms (Arecaceae). Ecol Evol 2024; 14:e70014. [PMID: 39011137 PMCID: PMC11246834 DOI: 10.1002/ece3.70014] [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: 09/13/2023] [Revised: 07/01/2024] [Accepted: 07/01/2024] [Indexed: 07/17/2024] Open
Abstract
Hybridization has significant evolutionary consequences across the Tree of Life. The process of hybridization has played a major role in plant evolution and has contributed to species richness and trait variation. Since morphological traits are partially a product of their environment, there may be a link between hybridization and ecology. Plant hybrid species richness is noted to be higher in harsh environments, and we explore this hypothesis with a keystone tropical plant lineage, palms (Arecaceae). Leveraging a recent literature review of naturally occurring palm hybrids, we developed a method to calculate hybrid frequency, and then tested if there is phylogenetic signal of hybrids using a phylogeny of all palms. Further, we used phylogenetic comparative methods to examine the interaction between hybrid frequency and presence in dry environments, on islands, and the species richness of genera. Phylogenetic generalized least squares models had stronger support than models of random association, indicating phylogenetic signal for the presence of hybrids in dry and island environments. However, all p-values were >.05 and therefore the correlation was poor between hybridization and the trait frequencies examined. Presence in particular environments are not strongly correlated to hybrid frequency, but phylogenetic signal suggests a role in its distribution in different habitats. Hybridization in palms is not evenly distributed across subfamilies, tribes, subtribes yet plays an important role in palm diversity, nonetheless. Increasing our understanding hybridization in this economically and culturally important plant family is essential, particularly since rates are projected to increase with climate change, reconfiguring the dynamics and distribution of biodiversity.
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Affiliation(s)
- Christine D. Bacon
- Department of Biological and Environmental SciencesUniversity of GothenburgGothenburgSweden
- Gothenburg Global Biodiversity CentreGothenburgSweden
| | - Adrian Hill
- Department of Biological and Environmental SciencesUniversity of GothenburgGothenburgSweden
- Gothenburg Global Biodiversity CentreGothenburgSweden
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Shi YJ, Mi JX, Huang JL, Tian FF, He F, Zhong Y, Yang HB, Wang F, Xiao Y, Yang LK, Zhang F, Chen LH, Wan XQ. A new species of Populus and the extensive hybrid speciation arising from it on the Qinghai-Tibet Plateau. Mol Phylogenet Evol 2024; 196:108072. [PMID: 38615706 DOI: 10.1016/j.ympev.2024.108072] [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: 10/10/2023] [Revised: 03/25/2024] [Accepted: 04/11/2024] [Indexed: 04/16/2024]
Abstract
While the diversity of species formation is broadly acknowledged, significant debate exists regarding the universal nature of hybrid species formation. Through an 18-year comprehensive study of all Populus species on the Qinghai-Tibet Plateau, 23 previously recorded species and 8 new species were identified. Based on morphological characteristics, these can be classified into three groups: species in section Leucoides, species with large leaves, and species with small leaves in section Tacamahaca. By conducting whole-genome re-sequencing of 150 genotypes from these 31 species, 2.28 million single nucleotide polymorphisms (SNPs) were identified. Phylogenetic analysis utilizing these SNPs not only revealed a highly intricate evolutionary network within the large-leaf species of section Tacamahaca but also confirmed that a new species, P. curviserrata, naturally hybridized with P. cathayana, P. szechuanica, and P. ciliata, resulting in 11 hybrid species. These findings indicate the widespread occurrence of hybrid species formation within this genus, with hybridization serving as a key evolutionary mechanism for Populus on the plateau. A novel hypothesis, "Hybrid Species Exterminating Their Ancestral Species (HSEAS)," is introduced to explain the mechanisms of hybrid species formation at three different scales: the entire plateau, the southeastern mountain region, and individual river valleys.
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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
| | - Jia-Xuan Mi
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Jin-Liang Huang
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Fei-Fei Tian
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Fang He
- 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, 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, China
| | - Fang Wang
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Yu Xiao
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Lin-Kai Yang
- 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, 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, China.
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Yañez A, Kinosian SP, Ponce MM, Gutierrez DG, Schwartsburd PB, Sundue M, Wolf PG. Striking genetic homogeneity in the widespread South American bracken. AMERICAN JOURNAL OF BOTANY 2024; 111:e16374. [PMID: 39001581 DOI: 10.1002/ajb2.16374] [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: 12/14/2023] [Revised: 05/01/2024] [Accepted: 05/06/2024] [Indexed: 07/24/2024]
Abstract
PREMISE Bracken (Pteridium, Dennstaedtiaceae) is a cosmopolitan genus of aggressive disturbance colonizers that are toxic to agricultural livestock. The taxonomy of Pteridium has been treated in multiple schemes, ranging from one to six species worldwide, with numerous subspecies and varieties. Recent work has focused on the worldwide distribution and systematics of the bracken fern, but South America has been poorly represented. We present the first continent-wide sampling and analysis of Pteridium esculentum, a Southern Hemisphere diploid species. METHODS Within South America, P. esculentum has several morphotypes, distinguished into subspecies by variation in indument and lamina architecture. We used double digest restriction site-associated DNA sequencing (ddRADSeq) to assess the phylogenetic relationships of P. esculentum subspecies. RESULTS We found a striking genetic homogeneity in the species, being able to support only two morphotypes from molecular data: P. e. arachnoideum and P. e. campestre. We had high confidence for shallow and deep phylogenetic relationships, but less support for relationships among crown groups. CONCLUSIONS We describe an east-west geographic pattern that would explain the relationships between populations; and, in contrast to previous studies, we detected differences with P. esculentum from Australia. These results will lay the foundations for studying variations in this species' behavior as a weed, as well as its impact on the production of agricultural livestock in South America.
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Affiliation(s)
- Agustina Yañez
- División Plantas Vasculares, Museo Argentino de Ciencias Naturales (MACN-CONICET), Av. Ángel Gallardo 740, Ciudad de Buenos Aires, C1405DJR, Argentina
| | - Sylvia P Kinosian
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, 85721, Arizona, USA
| | - M Mónica Ponce
- Instituto de Botánica Darwinion (IBODA-CONICET), Labardén 200, Casilla de Correo 22, San Isidro, B1642HYD, Buenos Aires, Argentina
| | - Diego G Gutierrez
- División Plantas Vasculares, Museo Argentino de Ciencias Naturales (MACN-CONICET), Av. Ángel Gallardo 740, Ciudad de Buenos Aires, C1405DJR, Argentina
| | - Pedro B Schwartsburd
- Laboratory of Systematics and Evolution of Plants, Department of Plant Biology, Federal University of Viçosa, Av. Peter Henry Rolfs s.n., Viçosa, 36570-900, MG, Brazil
| | - Michael Sundue
- Royal Botanic Garden Edinburgh, 20a Inverleith Row, Edinburgh, EH3 5LR, Scotland, UK
- The Pringle Herbarium, Department of Plant Biology, University of Vermont, Burlington, 111 Jeffords Hall, 63 Carrigan Drive, Vermont, 05405, USA
- Botanical Research, Institute of Texas, 1700 University Drive, Fort Worth, 76102, TX, USA
| | - Paul G Wolf
- Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, 35899, Alabama, USA
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Xia ZY, Chen X, Wang CC, Deng Q. Tracing the fine-scale demographic history and recent admixture in Hmong-Mien speakers. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2024; 184:e24945. [PMID: 38708925 DOI: 10.1002/ajpa.24945] [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: 06/24/2023] [Revised: 03/11/2024] [Accepted: 04/02/2024] [Indexed: 05/07/2024]
Abstract
The linguistic, historical, and subsistent uniqueness of Hmong-Mien (HM) speakers offers a wonderful opportunity to investigate how these factors impact the genetic structure. The genetic differentiation among HM speakers and their population history are not well characterized. Here, we generate genome-wide data from 65 Yao ethnicity samples and analyze them with published data, particularly by leveraging haplotype-based methods. We determined that the fine-scale genetic substructure of HM speakers corresponds better with linguistic classification than with geography. Particularly, parallels between serial founder events and language differentiations can be observed in West Hmongic speakers. Multiple lines of evidence indicate that ~500-year-old GaoHuaHua individuals are most closely related to West Hmongic-speaking Bunu. The strong genetic bottleneck of some HM-speaking groups, especially Bunu, could potentially be associated with their long-term practice of swidden agriculture to some degree. The inferred admixture dates for most of the HM speakers overlap with the reign of the Ming dynasty (1368-1644 CE). Besides a common genetic origin for HM speakers, their genetic ancestry is shared primarily with neighboring Han Chinese and Tai-Kadai speakers in south China. In conclusion, our analyses reveal that recent isolation and admixture events have contributed to the genetic population history of present-day HM speakers.
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Affiliation(s)
- Zi-Yang Xia
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- Department of Computational Biology, Cornell University, Ithaca, New York, USA
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Xingcai Chen
- Department of Human Anatomy, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, Nanning, China
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
- Department of Anthropology and Ethnology, Institute of Anthropology, Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Qiongying Deng
- Department of Human Anatomy, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, Nanning, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- Key Laboratory of Human Development and Disease Research, Guangxi Medical University, Education Department of Guangxi Zhuang Autonomous Region, Nanning, China
- Key Laboratory of Longevity and Aging-related Diseases of Chinese Ministry of Education, Guangxi Medical University, Nanning, Guangxi, China
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Setsuko S, Sugai K, Tamaki I, Hayama K, Kato H. Ecotype variation in the endemic tree Callicarpa subpubescens on small oceanic islands: genetic, phenotypic, and environmental insights. Heredity (Edinb) 2024; 132:309-319. [PMID: 38714843 PMCID: PMC11166659 DOI: 10.1038/s41437-024-00684-3] [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: 06/20/2023] [Revised: 04/11/2024] [Accepted: 04/14/2024] [Indexed: 06/13/2024] Open
Abstract
Callicarpa subpubescens, endemic to the Ogasawara Islands, is suggested to have multiple ecotypes in the Hahajima Islands, specifically in the central part of the Ogasawara Islands. In this study, associations between genetic groups and spatial distribution, habitat, leaf morphology, size structure, and flowering time of each genetic group were investigated on Hahajima and the satellite Imoutojima Islands. Genetic groups were identified using EST-SSR markers, revealing four ecotypes named based on morphological features: Dwarf (D), Glabrescent (G), Tall (T), and Middle (M), with M being a result of the hybridization of G and T. Ecotype D, adapted to dry environments, is characterized by small tree size, dense thick leaves with abundant hairs, and is distributed in dry scrub. Ecotype G, adapted to understory of mesic forests, lacks leaf hairs. Ecotype T, adapted to the canopy of mesic forests, has hairy leaves and is tall in tree height. Ecotype M, adapted to the canopy of mesic scrub or edges of mesic forests, has hairy leaves but with a shorter tree height than ecotype T. Flowering peaks differed among all ecotype pairs except G and M, but the flowering times more or less overlapped among all ecotypes, suggesting that pre-mating isolation among ecotypes is not perfect. Post-mating isolation is considered absent, as there were no differences in the results, germination, and survival rates of one-year seedlings among inter- and intra-ecotype crossings. The existence of such ecotypes provides valuable insights into the ongoing speciation processes adapting to the oceanic island environments.
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Affiliation(s)
- Suzuki Setsuko
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan.
| | - Kyoko Sugai
- Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, 1060 Nishikawatsu-cho, Matsue, Shimane, 690-8504, Japan
| | - Ichiro Tamaki
- Gifu Field Science Center, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Kayo Hayama
- Ogasawara Environmental Planning Laboratory, Motochi, Ogasawara, Tokyo, 100-2211, Japan
| | - Hidetoshi Kato
- Makino Herbarium, Tokyo Metropolitan University, 1-1 Minami-Ohsawa, Hachioji, Tokyo, 192-0397, Japan
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10
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Bell KL, Noreuil A, Molloy EK, Fritz ML. Genetic and behavioral differences between above and below ground Culex pipiens bioforms. Heredity (Edinb) 2024; 132:221-231. [PMID: 38424351 PMCID: PMC11074123 DOI: 10.1038/s41437-024-00675-4] [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: 08/24/2022] [Revised: 01/26/2024] [Accepted: 02/05/2024] [Indexed: 03/02/2024] Open
Abstract
Efficiency of mosquito-borne disease transmission is dependent upon both the preference and fidelity of mosquitoes as they seek the blood of vertebrate hosts. While mosquitoes select their blood hosts through multi-modal integration of sensory cues, host-seeking is primarily an odor-guided behavior. Differences in mosquito responses to hosts and their odors have been demonstrated to have a genetic component, but the underlying genomic architecture of these responses has yet to be fully resolved. Here, we provide the first characterization of the genomic architecture of host preference in the polymorphic mosquito species, Culex pipiens. The species exists as two morphologically identical bioforms, each with distinct avian and mammalian host preferences. Cx. pipiens females with empirically measured host responses were prepared into reduced representation DNA libraries and sequenced to identify genomic regions associated with host preference. Multiple genomic regions associated with host preference were identified on all 3 Culex chromosomes, and these genomic regions contained clusters of chemosensory genes, as expected based on work in Anopheles gambiae complex mosquitoes and in Aedes aegypti. One odorant receptor and one odorant binding protein gene showed one-to-one orthologous relationships to differentially expressed genes in A. gambiae complex members with divergent host preferences. Overall, our work identifies a distinct set of odorant receptors and odorant binding proteins that may enable Cx. pipiens females to distinguish between their vertebrate blood host species, and opens avenues for future functional studies that could measure the unique contributions of each gene to host preference phenotypes.
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Affiliation(s)
- Katherine L Bell
- Department of Biology, University of Nevada, Reno, NV, 89557, USA.
| | - Anna Noreuil
- Department of Entomology, University of Maryland, College Park, MD, 20742, USA
| | - Erin K Molloy
- Department of Computer Science, University of Maryland, College Park, MD, 20742, USA
| | - Megan L Fritz
- Department of Entomology, University of Maryland, College Park, MD, 20742, USA.
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11
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Imwattana K, Aguero B, Nieto-Lugilde M, Duffy A, Jaramillo-Chico J, Hassel K, Afonina O, Lamkowski P, Jonathan Shaw A. Parallel patterns of genetic diversity and structure in circumboreal species of the Sphagnum capillifolium complex. AMERICAN JOURNAL OF BOTANY 2024; 111:e16348. [PMID: 38764292 DOI: 10.1002/ajb2.16348] [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: 08/30/2023] [Revised: 03/20/2024] [Accepted: 03/20/2024] [Indexed: 05/21/2024]
Abstract
PREMISE Shared geographical patterns of population genetic variation among related species is a powerful means to identify the historical events that drive diversification. The Sphagnum capillifolium complex is a group of closely related peat mosses within the Sphagnum subgenus Acutifolia and contains several circumboreal species whose ranges encompass both glaciated and unglaciated regions across the northern hemisphere. In this paper, we (1) inferred the phylogeny of subg. Acutifolia and (2) investigated patterns of population structure and genetic diversity among five circumboreal species within the S. capillifolium complex. METHODS We generated RAD sequencing data from most species of the subg. Acutifolia and samples from across the distribution ranges of circumboreal species within the S. capillifolium complex. RESULTS We resolved at least 14 phylogenetic clusters within the S. capillifolium complex. Five circumboreal species show some common patterns: One population system comprises plants in eastern North America and Europe, and another comprises plants in the Pacific Northwest or around the Beringian and Arctic regions. Alaska appears to be a hotspot for genetic admixture, genetic diversity, and sometimes endemic subclades. CONCLUSIONS Our results support the hypothesis that populations of five circumboreal species within the S. capillifolium complex survived in multiple refugia during the last glacial maximum. Long-distance dispersal out of refugia, population bottlenecks, and possible adaptations to conditions unique to each refugium could have contributed to current geographic patterns. These results indicate the important role of historical events in shaping the complex population structure of plants with broad distribution ranges.
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Affiliation(s)
- Karn Imwattana
- Department of Biology & L. E. Anderson Bryophyte Herbarium, Duke University, Durham, NC, USA
- Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Blanka Aguero
- Department of Biology & L. E. Anderson Bryophyte Herbarium, Duke University, Durham, NC, USA
| | - Marta Nieto-Lugilde
- Department of Biology & L. E. Anderson Bryophyte Herbarium, Duke University, Durham, NC, USA
| | - Aaron Duffy
- Department of Biology & L. E. Anderson Bryophyte Herbarium, Duke University, Durham, NC, USA
| | - Juan Jaramillo-Chico
- Department of Biology & L. E. Anderson Bryophyte Herbarium, Duke University, Durham, NC, USA
| | - Kristian Hassel
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Olga Afonina
- Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Russia
| | - Paul Lamkowski
- Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
- University of Applied Science Neubrandenburg
| | - A Jonathan Shaw
- Department of Biology & L. E. Anderson Bryophyte Herbarium, Duke University, Durham, NC, USA
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12
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Lee VK, Reynolds WT, Wallace J, Beluk N, Badaly D, Lo CW, Ceschin R, Panigrahy A. Quantitative Magnetic Resonance Cerebral Spinal Fluid Flow Properties and Executive Function Cognitive Outcomes in Congenital Heart Disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.19.24306104. [PMID: 38699300 PMCID: PMC11065010 DOI: 10.1101/2024.04.19.24306104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Cerebrospinal fluid (CSF) circulation has recently been shown to be important in nutrient distribution, waste removal, and neurogenesis. Increased CSF volumes are frequently observed in congenital heart disease (CHD) and are associated with neurodevelopmental deficits. This suggests prolonged perturbation to the CSF system and possible interference to its homeostatic function, which may contribute to the neurodevelopmental deficits in CHD. CSF flow has yet to be studied in CHD patients, but the pulsatile flow of CSF throughout the brain is driven mainly by cardiopulmonary circulation. Given the underlying heart defects in CHD, the cardiopulmonary circulatory mechanisms in CHD might be impaired with resultant perturbation on the CSF circulation. In this study, we determine whether CSF flow, using MRI measurements of static and dynamic pulsatile flow, is abnormal in youths with CHD compared to healthy controls in relation to executive cognitive function. CSF flow measurements were obtained on a total of 58 child and young adult participants (CHD=20, healthy controls = 38). The CSF flow was measured across the lumen of the Aqueduct of Sylvius using cardiac-gated phase-contrast MRI at 3.0T. Static pulsatility was characterized as anterograde and retrograde peak velocities, mean velocity, velocity variance measurements, and dynamic pulsatility calculated as each participant's CSF flow deviation from the study cohort's consensus flow measured with root mean squared deviation (RMSD) were obtained. The participants had neurocognitive assessments for executive function with focus on inhibition, cognitive flexibility, and working memory domains. The CHD group demonstrated greater dynamic pulsatility (higher overall flow RMSD over the entire CSF flow cycle) compared to controls (p=0.0353), with no difference detected in static pulsatility measures. However, lower static CSF flow pulsatility (anterograde peak velocity: p=0.0323) and lower dynamic CSF flow pulsatility (RMSD: p=0.0181) predicted poor inhibitory executive function outcome. Taken together, while the whole CHD group exhibited higher dynamic CSF flow pulsatility compared to controls, the subset of CHD subjects with relatively reduced static and dynamic CSF flow pulsatility had the worst executive functioning, specifically the inhibition domain. These findings suggest that altered CSF flow pulsatility may be central to not only brain compensatory mechanisms but can also drive cognitive impairment in CHD. Further studies are needed to investigate possible mechanistic etiologies of aberrant CSF pulsatility (i.e. primary cardiac hemodynamic disturbances, intrinsic brain vascular stiffness, altered visco-elastic properties of tissue, or glial-lymphatic disturbances), which can result in acquired small vessel brain injury (including microbleeds and white matter hyperintensities).
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13
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Liu X, Koyama S, Tomizuka K, Takata S, Ishikawa Y, Ito S, Kosugi S, Suzuki K, Hikino K, Koido M, Koike Y, Horikoshi M, Gakuhari T, Ikegawa S, Matsuda K, Momozawa Y, Ito K, Kamatani Y, Terao C. Decoding triancestral origins, archaic introgression, and natural selection in the Japanese population by whole-genome sequencing. SCIENCE ADVANCES 2024; 10:eadi8419. [PMID: 38630824 PMCID: PMC11023554 DOI: 10.1126/sciadv.adi8419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 03/07/2024] [Indexed: 04/19/2024]
Abstract
We generated Japanese Encyclopedia of Whole-Genome/Exome Sequencing Library (JEWEL), a high-depth whole-genome sequencing dataset comprising 3256 individuals from across Japan. Analysis of JEWEL revealed genetic characteristics of the Japanese population that were not discernible using microarray data. First, rare variant-based analysis revealed an unprecedented fine-scale genetic structure. Together with population genetics analysis, the present-day Japanese can be decomposed into three ancestral components. Second, we identified unreported loss-of-function (LoF) variants and observed that for specific genes, LoF variants appeared to be restricted to a more limited set of transcripts than would be expected by chance, with PTPRD as a notable example. Third, we identified 44 archaic segments linked to complex traits, including a Denisovan-derived segment at NKX6-1 associated with type 2 diabetes. Most of these segments are specific to East Asians. Fourth, we identified candidate genetic loci under recent natural selection. Overall, our work provided insights into genetic characteristics of the Japanese population.
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Affiliation(s)
- Xiaoxi Liu
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
| | - Satoshi Koyama
- Laboratory for Cardiovascular Genomics and Informatics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Kohei Tomizuka
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Sadaaki Takata
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yuki Ishikawa
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shuji Ito
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Laboratory for Bone and Joint Diseases, RIKEN Center for Medical Sciences, Tokyo, Japan
- Department of Orthopedic Surgery, Faculty of Medicine, Shimane University, Izumo, Japan
| | - Shunichi Kosugi
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kunihiko Suzuki
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Keiko Hikino
- Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Masaru Koido
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Yoshinao Koike
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Laboratory for Bone and Joint Diseases, RIKEN Center for Medical Sciences, Tokyo, Japan
- Department of Orthopedic Surgery, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Momoko Horikoshi
- Laboratory for Genomics of Diabetes and Metabolism, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Takashi Gakuhari
- Institute for the Study of Ancient Civilizations and Cultural Resources, College of Human and Social Sciences, Kanazawa University, Kanazawa, Japan
| | - Shiro Ikegawa
- Laboratory for Bone and Joint Diseases, RIKEN Center for Medical Sciences, Tokyo, Japan
| | - Kochi Matsuda
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kaoru Ito
- Laboratory for Cardiovascular Genomics and Informatics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- The Department of Applied Genetics, The School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
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14
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Tomlin CM, Rajaraman S, Sebesta JT, Scheen AC, Bendiksby M, Low YW, Salojärvi J, Michael TP, Albert VA, Lindqvist C. Allopolyploid origin and diversification of the Hawaiian endemic mints. Nat Commun 2024; 15:3109. [PMID: 38600100 PMCID: PMC11006916 DOI: 10.1038/s41467-024-47247-y] [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: 07/13/2023] [Accepted: 03/26/2024] [Indexed: 04/12/2024] Open
Abstract
Island systems provide important contexts for studying processes underlying lineage migration, species diversification, and organismal extinction. The Hawaiian endemic mints (Lamiaceae family) are the second largest plant radiation on the isolated Hawaiian Islands. We generated a chromosome-scale reference genome for one Hawaiian species, Stenogyne calaminthoides, and resequenced 45 relatives, representing 34 species, to uncover the continental origins of this group and their subsequent diversification. We further resequenced 109 individuals of two Stenogyne species, and their purported hybrids, found high on the Mauna Kea volcano on the island of Hawai'i. The three distinct Hawaiian genera, Haplostachys, Phyllostegia, and Stenogyne, are nested inside a fourth genus, Stachys. We uncovered four independent polyploidy events within Stachys, including one allopolyploidy event underlying the Hawaiian mints and their direct western North American ancestors. While the Hawaiian taxa may have principally diversified by parapatry and drift in small and fragmented populations, localized admixture may have played an important role early in lineage diversification. Our genomic analyses provide a view into how organisms may have radiated on isolated island chains, settings that provided one of the principal natural laboratories for Darwin's thinking about the evolutionary process.
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Affiliation(s)
- Crystal M Tomlin
- Department of Biological Sciences, University at Buffalo, New York, USA
| | - Sitaram Rajaraman
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | | | | | - Mika Bendiksby
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Yee Wen Low
- Singapore Botanic Gardens, National Parks Board, Singapore, Singapore
| | - Jarkko Salojärvi
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Todd P Michael
- The Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California, USA
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, New York, USA.
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15
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Du P, Zhu K, Qiao H, Zhang J, Meng H, Huang Z, Yu Y, Xie S, Allen E, Xiong J, Zhang B, Chang X, Ren X, Xu Y, Zhou Q, Han S, Jin L, Wei P, Wang CC, Wen S. Ancient genome of the Chinese Emperor Wu of Northern Zhou. Curr Biol 2024; 34:1587-1595.e5. [PMID: 38552628 DOI: 10.1016/j.cub.2024.02.059] [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: 02/03/2023] [Revised: 12/23/2023] [Accepted: 02/23/2024] [Indexed: 04/11/2024]
Abstract
Emperor Wu (, Wudi) of the Xianbei-led Northern Zhou dynasty, named Yuwen Yong (, 543-578 CE), was a highly influential emperor who reformed the system of regional troops, pacified the Turks, and unified the northern part of the country. His genetic profile and physical characteristics, including his appearance and potential diseases, have garnered significant interest from the academic community and the public. In this study, we have successfully generated a 0.343×-coverage genome of Wudi with 1,011,419 single-nucleotide polymorphisms (SNPs) on the 1240k panel. By analyzing pigmentation-relevant SNPs and conducting cranial CT-based facial reconstruction, we have determined that Wudi possessed a typical East or Northeast Asian appearance. Furthermore, pathogenic SNPs suggest Wudi faced an increased susceptibility to certain diseases, such as stroke. Wudi shared the closest genetic relationship with ancient Khitan and Heishui Mohe samples and modern Daur and Mongolian populations but also showed additional affinity with Yellow River (YR) farmers. We estimated that Wudi derived 61% of his ancestry from ancient Northeast Asians (ANAs) and nearly one-third from YR farmer-related groups. This can likely be attributed to continuous intermarriage between Xianbei royal families, and local Han aristocrats.1,2 Furthermore, our study has revealed genetic diversities among available ancient Xianbei individuals from different regions, suggesting that the formation of the Xianbei was a dynamic process influenced by admixture with surrounding populations.
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Affiliation(s)
- Panxin Du
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China; State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China; Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Kongyang Zhu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Hui Qiao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China; Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | | | - Hailiang Meng
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Zixiao Huang
- Department of History, Fudan University, Shanghai 200433, China
| | - Yao Yu
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China
| | - Shouhua Xie
- Department of History, Fudan University, Shanghai 200433, China
| | - Edward Allen
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China
| | - Jianxue Xiong
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China
| | - Baoshuai Zhang
- USTC Archaeometry Laboratory, University of Science and Technology of China, Hefei 230026, China
| | - Xin Chang
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China
| | - Xiaoying Ren
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China
| | - Yiran Xu
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China
| | - Qi Zhou
- Shanghai Federation of Social Science Associations, Shanghai 200020, China
| | - Sheng Han
- Department of History, Fudan University, Shanghai 200433, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China.
| | - Pianpian Wei
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China.
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China; Department of Anthropology and Ethnology, Institute of Anthropology, Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361005, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China; Institute of Artificial Intelligence, Xiamen University, Xiamen 361005, China.
| | - Shaoqing Wen
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China; Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China; MOE Laboratory for National Development and Intelligent Governance, Fudan University, Shanghai 200433, China; Center for the Belt and Road Archaeology and Ancient Civilizations, Shanghai 200433, China.
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16
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Agranat-Tamir L, Mooney JA, Rosenberg NA. Counting the genetic ancestors from source populations in members of an admixed population. Genetics 2024; 226:iyae011. [PMID: 38289724 PMCID: PMC10990421 DOI: 10.1093/genetics/iyae011] [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: 06/09/2023] [Revised: 11/02/2023] [Accepted: 01/12/2024] [Indexed: 02/01/2024] Open
Abstract
In a genetically admixed population, admixed individuals possess genealogical and genetic ancestry from multiple source groups. Under a mechanistic model of admixture, we study the number of distinct ancestors from the source populations that the admixture represents. Combining a mechanistic admixture model with a recombination model that describes the probability that a genealogical ancestor is a genetic ancestor, for a member of a genetically admixed population, we count genetic ancestors from the source populations-those genealogical ancestors from the source populations who contribute to the genome of the modern admixed individual. We compare patterns in the numbers of genealogical and genetic ancestors across the generations. To illustrate the enumeration of genetic ancestors from source populations in an admixed group, we apply the model to the African-American population, extending recent results on the numbers of African and European genealogical ancestors that contribute to the pedigree of an African-American chosen at random, so that we also evaluate the numbers of African and European genetic ancestors who contribute to random African-American genomes. The model suggests that the autosomal genome of a random African-American born in the interval 1960-1965 contains genetic contributions from a mean of 162 African (standard deviation 47, interquartile range 127-192) and 32 European ancestors (standard deviation 14, interquartile range 21-43). The enumeration of genetic ancestors can potentially be performed in other diploid species in which admixture and recombination models can be specified.
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Affiliation(s)
| | - Jazlyn A Mooney
- Department of Quantitative & Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Noah A Rosenberg
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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17
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Kess T, Lehnert SJ, Bentzen P, Duffy S, Messmer A, Dempson JB, Newport J, Whidden C, Robertson MJ, Chaput G, Breau C, April J, Gillis C, Kent M, Nugent CM, Bradbury IR. Variable parallelism in the genomic basis of age at maturity across spatial scales in Atlantic Salmon. Ecol Evol 2024; 14:e11068. [PMID: 38584771 PMCID: PMC10995719 DOI: 10.1002/ece3.11068] [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: 01/06/2024] [Accepted: 01/31/2024] [Indexed: 04/09/2024] Open
Abstract
Complex traits often exhibit complex underlying genetic architectures resulting from a combination of evolution from standing variation, hard and soft sweeps, and alleles of varying effect size. Increasingly, studies implicate both large-effect loci and polygenic patterns underpinning adaptation, but the extent that common genetic architectures are utilized during repeated adaptation is not well understood. Sea age or age at maturation represents a significant life history trait in Atlantic Salmon (Salmo salar), the genetic basis of which has been studied extensively in European Atlantic populations, with repeated identification of large-effect loci. However, the genetic basis of sea age within North American Atlantic Salmon populations remains unclear, as does the potential for a parallel trans-Atlantic genomic basis to sea age. Here, we used a large single-nucleotide polymorphism (SNP) array and low-coverage whole-genome resequencing to explore the genomic basis of sea age variation in North American Atlantic Salmon. We found significant associations at the gene and SNP level with a large-effect locus (vgll3) previously identified in European populations, indicating genetic parallelism, but found that this pattern varied based on both sex and geographic region. We also identified nonrepeated sets of highly predictive loci associated with sea age among populations and sexes within North America, indicating polygenicity and low rates of genomic parallelism. Despite low genome-wide parallelism, we uncovered a set of conserved molecular pathways associated with sea age that were consistently enriched among comparisons, including calcium signaling, MapK signaling, focal adhesion, and phosphatidylinositol signaling. Together, our results indicate parallelism of the molecular basis of sea age in North American Atlantic Salmon across large-effect genes and molecular pathways despite population-specific patterns of polygenicity. These findings reveal roles for both contingency and repeated adaptation at the molecular level in the evolution of life history variation.
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Affiliation(s)
- Tony Kess
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - Sarah J. Lehnert
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - Paul Bentzen
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
| | - Steven Duffy
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - Amber Messmer
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - J. Brian Dempson
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - Jason Newport
- Marine Environmental Research Infrastructure for Data Integration and Application NetworkHalifaxNova ScotiaCanada
| | | | - Martha J. Robertson
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - Gerald Chaput
- Fisheries and Oceans CanadaGulf Fisheries CentreMonctonNew BrunswickCanada
| | - Cindy Breau
- Fisheries and Oceans CanadaGulf Fisheries CentreMonctonNew BrunswickCanada
| | - Julien April
- Ministère des Forêts de la Faune et des ParcsQuebecQuebecCanada
| | - Carole‐Anne Gillis
- Gespe'gewa'gi, Mi'gma'qi, ListugujGespe'gewa'gi Institute of Natural UnderstandingQuebecQuebecCanada
| | - Matthew Kent
- Centre for Integrative GeneticsNorwegian University of Life SciencesÅsNorway
| | - Cameron M. Nugent
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - Ian R. Bradbury
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
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18
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Bedoya AM. Botany and geogenomics: Constraining geological hypotheses in the neotropics with large-scale genetic data derived from plants. AMERICAN JOURNAL OF BOTANY 2024; 111:e16306. [PMID: 38557829 DOI: 10.1002/ajb2.16306] [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: 01/20/2024] [Accepted: 01/24/2024] [Indexed: 04/04/2024]
Abstract
Decades of empirical research have revealed how the geological history of our planet shaped plant evolution by establishing well-known patterns (e.g., how mountain uplift resulted in high rates of diversification and replicate radiations in montane plant taxa). This follows a traditional approach where botanical data are interpreted in light of geological events. In this synthesis, I instead describe how by integrating natural history, phylogenetics, and population genetics, botanical research can be applied alongside geology and paleontology to inform our understanding of past geological and climatic processes. This conceptual shift aligns with the goals of the emerging field of geogenomics. In the neotropics, plant geogenomics is a powerful tool for the reciprocal exploration of two long standing questions in biology and geology: how the dynamic landscape of the region came to be and how it shaped the evolution of the richest flora. Current challenges that are specific to analytical approaches for plant geogenomics are discussed. I describe the scale at which various geological questions can be addressed from biological data and what makes some groups of plants excellent model systems for geogenomics research. Although plant geogenomics is discussed with reference to the neotropics, the recommendations given here for approaches to plant geogenomics can and should be expanded to exploring long-standing questions on how the earth evolved with the use of plant DNA.
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Affiliation(s)
- Ana M Bedoya
- Department of Biological Sciences, Louisiana State University, Baton Rouge, 70803, LA, USA
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19
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Sgarlata GM, Rasolondraibe E, Salmona J, Le Pors B, Ralantoharijaona T, Rakotonanahary A, Jan F, Manzi S, Iribar A, Zaonarivelo JR, Volasoa Andriaholinirina N, Rasoloharijaona S, Chikhi L. The genomic diversity of the Eliurus genus in northern Madagascar with a putative new species. Mol Phylogenet Evol 2024; 193:107997. [PMID: 38128795 DOI: 10.1016/j.ympev.2023.107997] [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: 02/10/2023] [Revised: 12/06/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
Madagascar exhibits extraordinarily high level of species richness and endemism, while being severely threatened by habitat loss and fragmentation (HL&F). In front of these threats to biodiversity, conservation effort can be directed, for instance, in the documentation of species that are still unknown to science, or in investigating how species respond to HL&F. The tufted-tail rats genus (Eliurus spp.) is the most speciose genus of endemic rodents in Madagascar, with 13 described species, which occupy two major habitat types: dry or humid forests. The large species diversity and association to specific habitat types make the Eliurus genus a suitable model for investigating species adaptation to new environments, as well as response to HL&F (dry vs humid). In the present study, we investigated Eliurus spp. genomic diversity across northern Madagascar, a region covered by both dry and humid fragmented forests. From the mitochondrial DNA (mtDNA) and nuclear genomic (RAD-seq) data of 124 Eliurus individuals sampled in poorly studied forests of northern Madagascar, we identified an undescribed Eliurus taxon (Eliurus sp. nova). We tested the hypothesis of a new Eliurus species using several approaches: i) DNA barcoding; ii) phylogenetic inferences; iii) species delimitation tests based on the Multi-Species Coalescent (MSC) model, iv) genealogical divergence index (gdi); v) an ad-hoc test of isolation-by-distance within versus between sister-taxa, vi) comparisons of %GC content patterns and vii) morphological analyses. All analyses support the recognition of the undescribed lineage as a putative distinct species. In addition, we show that Eliurus myoxinus, a species known from the dry forests of western Madagascar, is, surprisingly, found mostly in humid forests in northern Madagascar. In conclusion, we discuss the implications of such findings in the context of Eliurus species evolution and diversification, and use the distribution of northern Eliurus species as a proxy for reconstructing past changes in forest cover and vegetation type in northern Madagascar.
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Affiliation(s)
| | - Emmanuel Rasolondraibe
- Département de Biologie Animale et Ecologie, Faculté des Sciences, Université de Mahajanga, Mahajanga, Madagascar.
| | - Jordi Salmona
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal; Centre de Recherche sur la Biodiversité et l'Environnement (CRBE),Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 -Paul Sabatier (UT3), Toulouse, France.
| | - Barbara Le Pors
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal
| | - Tantely Ralantoharijaona
- Département de Biologie Animale et Ecologie, Faculté des Sciences, Université de Mahajanga, Mahajanga, Madagascar
| | - Ando Rakotonanahary
- Département de Biologie Animale et Ecologie, Faculté des Sciences, Université de Mahajanga, Mahajanga, Madagascar.
| | - Fabien Jan
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal
| | - Sophie Manzi
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE),Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 -Paul Sabatier (UT3), Toulouse, France.
| | - Amaia Iribar
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE),Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 -Paul Sabatier (UT3), Toulouse, France.
| | - John Rigobert Zaonarivelo
- Département des Sciences de la Nature et de l'Environnement, Université d'Antsiranana, 201 Antsiranana, Madagascar.
| | | | - Solofonirina Rasoloharijaona
- Département de Biologie Animale et Ecologie, Faculté des Sciences, Université de Mahajanga, Mahajanga, Madagascar
| | - Lounès Chikhi
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal; Centre de Recherche sur la Biodiversité et l'Environnement (CRBE),Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 -Paul Sabatier (UT3), Toulouse, France.
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20
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Trujillo D, Mastrangelo T, Estevez de Jensen C, Verle Rodrigues JC, Lawrie R, Massey SE. Accurate identification of Helicoverpa armigera-Helicoverpa zea hybrids using genome admixture analysis: implications for genomic surveillance. FRONTIERS IN INSECT SCIENCE 2024; 4:1339143. [PMID: 38469344 PMCID: PMC10926370 DOI: 10.3389/finsc.2024.1339143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/08/2024] [Indexed: 03/13/2024]
Abstract
Helicoverpa armigera, the cotton bollworm moth, is one of the world's most important crop pests, and is spreading throughout the New World from its original range in the Old World. In Brazil, invasive H. armigera has been reported to hybridize with local populations of Helicoverpa zea. The correct identification of H. armigera-H. zea hybrids is important in understanding the origin, spread and future outlook for New World regions that are affected by outbreaks, given that hybridization can potentially facilitate H. zea pesticide resistance and host plant range via introgression of H. armigera genes. Here, we present a genome admixture analysis of high quality genome sequences generated from two H. armigera-H. zea F1 hybrids generated in two different labs. Our admixture pipeline predicts 48.8% and 48.9% H. armigera for the two F1 hybrids, confirming its accuracy. Genome sequences from five H. zea and one H. armigera that were generated as part of the study show no evidence of hybridization. Interestingly, we show that four H. zea genomes generated from a previous study are predicted to possess a proportion of H. armigera genetic material. Using unsupervised clustering to identify non-hybridized H. armigera and H. zea genomes, 8511 ancestry informative markers (AIMs) were identified. Their relative frequencies are consistent with a minor H. armigera component in the four genomes, however its origin remains to be established. We show that the size and quality of genomic reference datasets are critical for accurate hybridization prediction. Consequently, we discuss potential pitfalls in genome admixture analysis of H. armigera-H. zea hybrids, and suggest measures that will improve such analyses.
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Affiliation(s)
- Dario Trujillo
- Department of Agro-Environmental Sciences, University of Puerto Rico - Mayaguez, Mayaguez, Puerto Rico
| | - Thiago Mastrangelo
- Universidade de São Paulo, Centro de Energia Nuclear na Agricultura, Piracicaba, SP, Brazil
| | | | | | - Roger Lawrie
- Center for Excellence in Quarantine and Invasive Species (CEQUIS), Estacion Experimental Agricola, San Juan, Puerto Rico
| | - Steven E. Massey
- Department of Biology, University of Puerto Rico - Rio Piedras, San Juan, Puerto Rico
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21
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Haeussermann I, Hasselmann M. Complex European invasion history of Anoplophora glabripennis (Motschulsky): new insights in its population genomic differentiation using genotype-by-sequencing. Sci Rep 2024; 14:4263. [PMID: 38383537 PMCID: PMC10881967 DOI: 10.1038/s41598-024-54567-y] [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: 09/15/2023] [Accepted: 02/14/2024] [Indexed: 02/23/2024] Open
Abstract
Anthropogenic activities like trade facilitate increasing rates of biological invasions. Asian long-horned beetle (ALB), which is naturally distributed in eastern Asia (China, Korean peninsula), was introduced via wood packing materials (WPM) used in trade to North America (1996) and Europe (2001). We used 7810 single nucleotide polymorphisms (SNPs) derived by a genotype-by-sequencing (GBS) approach to decipher the introduction patterns into Europe. This is applied for the first time on European ALB outbreaks from Germany, Switzerland, and Italy, both from still active and already eradicated infestations. The genome-wide SNPs detected signs of small and highly structured populations within Europe, showing clear founder effects. The very high population differentiation is presumably derived from multiple independent introductions to Europe, which are spatially restricted in mating. By admixture and phylogenetic analyses, some cases of secondary dispersal were observed. Furthermore, some populations suggest admixture, which might have been originated by either multiple introductions from different sources into the new sites or recurrent introductions from an admixed source population. Our results confirmed a complex invasion history of the ALB into Europe and the usability of GBS obtained SNPs in invasion science even without source populations.
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Affiliation(s)
- Iris Haeussermann
- Institute of Animal Science, Department of Livestock Population Genomics, Centre for Biodiversity and Integrative Taxonomy (KomBioTa), University of Hohenheim, Stuttgart, Germany.
| | - Martin Hasselmann
- Institute of Animal Science, Department of Livestock Population Genomics, Centre for Biodiversity and Integrative Taxonomy (KomBioTa), University of Hohenheim, Stuttgart, Germany
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22
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Schmidt TL, Thia JA, Hoffmann AA. How Can Genomics Help or Hinder Wildlife Conservation? Annu Rev Anim Biosci 2024; 12:45-68. [PMID: 37788416 DOI: 10.1146/annurev-animal-021022-051810] [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] [Indexed: 10/05/2023]
Abstract
Genomic data are becoming increasingly affordable and easy to collect, and new tools for their analysis are appearing rapidly. Conservation biologists are interested in using this information to assist in management and planning but are typically limited financially and by the lack of genomic resources available for non-model taxa. It is therefore important to be aware of the pitfalls as well as the benefits of applying genomic approaches. Here, we highlight recent methods aimed at standardizing population assessments of genetic variation, inbreeding, and forms of genetic load and methods that help identify past and ongoing patterns of genetic interchange between populations, including those subjected to recent disturbance. We emphasize challenges in applying some of these methods and the need for adequate bioinformatic support. We also consider the promises and challenges of applying genomic approaches to understand adaptive changes in natural populations to predict their future adaptive capacity.
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Affiliation(s)
- Thomas L Schmidt
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia;
| | - Joshua A Thia
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia;
| | - Ary A Hoffmann
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia;
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23
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Leaché AD, Davis HR, Feldman CR, Fujita MK, Singhal S. Repeated patterns of reptile diversification in Western North America supported by the Northern Alligator Lizard (Elgaria coerulea). J Hered 2024; 115:57-71. [PMID: 37982433 PMCID: PMC10838131 DOI: 10.1093/jhered/esad073] [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: 07/07/2023] [Accepted: 11/09/2023] [Indexed: 11/21/2023] Open
Abstract
Understanding the processes that shape genetic diversity by either promoting or preventing population divergence can help identify geographic areas that either facilitate or limit gene flow. Furthermore, broadly distributed species allow us to understand how biogeographic and ecogeographic transitions affect gene flow. We investigated these processes using genomic data in the Northern Alligator Lizard (Elgaria coerulea), which is widely distributed in Western North America across diverse ecoregions (California Floristic Province and Pacific Northwest) and mountain ranges (Sierra Nevada, Coastal Ranges, and Cascades). We collected single-nucleotide polymorphism data from 120 samples of E. coerulea. Biogeographic analyses of squamate reptiles with similar distributions have identified several shared diversification patterns that provide testable predictions for E. coerulea, including deep genetic divisions in the Sierra Nevada, demographic stability of southern populations, and recent post-Pleistocene expansion into the Pacific Northwest. We use genomic data to test these predictions by estimating the structure, connectivity, and phylogenetic history of populations. At least 10 distinct populations are supported, with mixed-ancestry individuals situated at most population boundaries. A species tree analysis provides strong support for the early divergence of populations in the Sierra Nevada Mountains and recent diversification into the Pacific Northwest. Admixture and migration analyses detect gene flow among populations in the Lower Cascades and Northern California, and a spatial analysis of gene flow identified significant barriers to gene flow across both the Sierra Nevada and Coast Ranges. The distribution of genetic diversity in E. coerulea is uneven, patchy, and interconnected at population boundaries. The biogeographic patterns seen in E. coerulea are consistent with predictions from co-distributed species.
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Affiliation(s)
- Adam D Leaché
- Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, United States
| | - Hayden R Davis
- Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, United States
| | - Chris R Feldman
- Department of Biology and Program in Ecology, Evolution and Conservation Biology, University of Nevada, Reno, NV, United States
| | - Matthew K Fujita
- Department of Biology, The University of Texas at Arlington, Arlington, TX, United States
| | - Sonal Singhal
- Department of Biology, California State University - Dominguez Hills, Carson, CA, United States
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24
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Delapieve MLS, Rocha LA, Reis RE. Phylogenomics of the narrowly endemic Eurycheilichthys (Siluriformes: Loricariidae): Sympatric species with non-sister relationships suggest mainly allopatric speciation. Mol Phylogenet Evol 2024; 190:107970. [PMID: 37995894 DOI: 10.1016/j.ympev.2023.107970] [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: 07/17/2023] [Revised: 11/09/2023] [Accepted: 11/20/2023] [Indexed: 11/25/2023]
Abstract
Armored catfishes of the genus Eurycheilichthys are endemic to Southern Brazil and Misiones (Argentina) comprising nine species of small size, with a high degree of sympatry and species diversity distributed in two river basins. Here we use new genome-wide data to infer a species phylogeny and test species boundaries for this poorly known group. We estimate 1) the phylogenetic relationships of the species of Eurycheilichthys based on 29,350 loci in 65 individuals of nine species plus outgroups, and 2) the population structure and differentiation based on 43,712 loci and 62 individuals to estimate how geography may have acted on speciation and formation of the sympatric species groups. Analyses support the monophyly of the genus and suggest two species-inclusive clades (East and West) with high support and very recently diverged species. Western clade contains E. limulus (from upper Jacuí River basin) that is sister to Western species of the Taquari-Antas basin plus E. paucidens. The Eastern clade contains E. pantherinus (from Uruguay River basin) sister to the Eastern species of the Taquari-Antas basin E. coryphaenus, plus the central-distributed species E. planus and E. vacariensis, and the more widely-distributed species E. luisae. Eurycheilichthys luisae is not monophyletic and may contain one or more cryptic species or hybrid individuals. A stronger diversity on structure of lineages on the Taquari-Antas, when compared to upper Uruguay and Jacuí River basins, and the fact that most of the sympatrically distributed taxa have non-sister relationships suggest a scenario of mainly allopatric speciation and may indicate a more dynamic landscape with headwater capture events among these tributaries.
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Affiliation(s)
- Maria Laura S Delapieve
- Laboratory of Vertebrate Systematics, Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Av. Ipiranga 6681, 90619-900 Porto Alegre, RS, Brazil.
| | - Luiz A Rocha
- Section of Ichthyology, California Academy of Sciences, 55 Music Concourse Drive, Golden Gate Park, San Francisco, CA 94118, USA
| | - Roberto E Reis
- Laboratory of Vertebrate Systematics, Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Av. Ipiranga 6681, 90619-900 Porto Alegre, RS, Brazil
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25
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D'Atanasio E, Risi F, Ravasini F, Montinaro F, Hajiesmaeil M, Bonucci B, Pistacchia L, Amoako-Sakyi D, Bonito M, Onidi S, Colombo G, Semino O, Destro Bisol G, Anagnostou P, Metspalu M, Tambets K, Trombetta B, Cruciani F. The genomic echoes of the last Green Sahara on the Fulani and Sahelian people. Curr Biol 2023; 33:5495-5504.e4. [PMID: 37995693 DOI: 10.1016/j.cub.2023.10.075] [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: 05/04/2023] [Revised: 09/28/2023] [Accepted: 10/31/2023] [Indexed: 11/25/2023]
Abstract
The population history of the Sahara/Sahelian belt is understudied, despite previous work highlighting complex dynamics.1,2,3,4,5,6,7 The Sahelian Fulani, i.e., the largest nomadic pastoral population in the world,8 represent an interesting case because they show a non-negligible proportion of an Eurasian genetic component, usually explained by recent admixture with northern Africans.1,2,5,6,7,9,10,11,12 Nevertheless, their origins are largely unknown, although several hypotheses have been proposed, including a possible link to ancient peoples settled in the Sahara during its last humid phase (Green Sahara, 12,000-5,000 years before present [BP]).13,14,15 To shed light about the Fulani ancient genetic roots, we produced 23 high-coverage (30×) whole genomes from Fulani individuals from 8 Sahelian countries, plus 17 samples from other African groups and 3 from Europeans as controls, for a total of 43 new whole genomes. These data have been compared with 814 published modern whole genomes2,16,17,18 and with relevant published ancient sequences (> 1,800 samples).19 These analyses showed some evidence that the non-sub-Saharan genetic ancestry component of the Fulani might have also been shaped by older events,1,5,6 possibly tracing the Fulani origins to unsampled ancient Green Saharan population(s). The joint analysis of modern and ancient samples allowed us to shed light on the genetic ancestry composition of such ancient Saharans, suggesting a similarity with Late Neolithic Moroccans and possibly pointing to a link with the spread of cattle herding. We also identified two different Fulani clusters whose admixture pattern may be informative about the historical Fulani movements and their later involvement in the western African empires.
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Affiliation(s)
- Eugenia D'Atanasio
- Institute of Molecular Biology and Pathology, National Research Council, 00185 Rome, Italy.
| | - Flavia Risi
- Department of Biology and Biotechnology, Sapienza University of Rome, 00185 Rome, Italy
| | - Francesco Ravasini
- Department of Biology and Biotechnology, Sapienza University of Rome, 00185 Rome, Italy
| | - Francesco Montinaro
- Department of Biology, University of Bari, 70121 Bari, Italy; Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Mogge Hajiesmaeil
- Department of Biology and Biotechnology, Sapienza University of Rome, 00185 Rome, Italy
| | | | - Letizia Pistacchia
- Institute of Molecular Biology and Pathology, National Research Council, 00185 Rome, Italy; Department of Biology and Biotechnology, Sapienza University of Rome, 00185 Rome, Italy
| | - Daniel Amoako-Sakyi
- Department of Microbiology and Immunology, University of Cape Coast, Cape Coast, Ghana
| | - Maria Bonito
- Department of Biology and Biotechnology, Sapienza University of Rome, 00185 Rome, Italy
| | - Sara Onidi
- Department of Biology and Biotechnology, Sapienza University of Rome, 00185 Rome, Italy
| | - Giulia Colombo
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | - Ornella Semino
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | - Giovanni Destro Bisol
- Department of Enviromental Biology, Sapienza University of Rome, 00185 Rome, Italy; Istituto Italiano di Antropologia, 00185 Rome, Italy
| | - Paolo Anagnostou
- Department of Enviromental Biology, Sapienza University of Rome, 00185 Rome, Italy
| | - Mait Metspalu
- Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | | | - Beniamino Trombetta
- Department of Biology and Biotechnology, Sapienza University of Rome, 00185 Rome, Italy
| | - Fulvio Cruciani
- Institute of Molecular Biology and Pathology, National Research Council, 00185 Rome, Italy; Department of Biology and Biotechnology, Sapienza University of Rome, 00185 Rome, Italy.
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26
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Xiao H, Liu Z, Wang N, Gaut BS, Zhou Y. Reply to Blanco-Pastor: Introgression and heterozygosity complicated grapevine domestication. Proc Natl Acad Sci U S A 2023; 120:e2314162120. [PMID: 38011557 DOI: 10.1073/pnas.2314162120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023] Open
Affiliation(s)
- 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 518120, 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 518120, China
| | - Nan Wang
- 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 518120, China
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 95616
| | - 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 518120, 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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27
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Alexander Pyron R. Unsupervised machine learning for species delimitation, integrative taxonomy, and biodiversity conservation. Mol Phylogenet Evol 2023; 189:107939. [PMID: 37804960 DOI: 10.1016/j.ympev.2023.107939] [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: 06/12/2023] [Revised: 09/25/2023] [Accepted: 10/04/2023] [Indexed: 10/09/2023]
Abstract
Integrative taxonomy, combining data from multiple axes of biologically relevant variation, is a major goal of systematics. Ideally, such taxonomies will derive from similarly integrative species-delimitation analyses. Yet, most current methods rely solely or primarily on molecular data, with other layers often incorporated only in a post hoc qualitative or comparative manner. A major limitation is the difficulty of devising quantitative parametric models linking different datasets in a unified ecological and evolutionary framework. Machine Learning (ML) methods offer flexibility in this arena by easily learning high-dimensional associations between observations (e.g., individual specimens) across a wide array of input features (e.g., genetics, geography, environment, and phenotype) to delimit statistically meaningful clusters. Here, I implement an unsupervised method using Self-Organizing (or "Kohonen") Maps (SOMs) for such purposes. Recent extensions called "SuperSOMs" can integrate multiple layers, each of which exerts independent influence on a two-dimensional output grid via empirically estimated weights. The grid cells are then delimited into K distinct units that can be interpreted as species or other entities. I show empirical examples in salamanders (Desmognathus) and snakes (Storeria) with layers representing alleles, space, climate, and traits. Simulations reveal that the SuperSOM approach can detect K = 1, tends not to over-split, reflects contributions from all layers, and limits large layers (e.g., genetic matrices) from overwhelming other datasets, desirable properties addressing major concerns from previous studies. Finally, I suggest that these and similar methods could integrate conservation-relevant layers such as population trends and human encroachment to delimit management units from an explicitly quantitative framework grounded in the ecology and evolution of species limits and boundaries.
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Affiliation(s)
- R Alexander Pyron
- Department of Biological Sciences, The George Washington University, Washington, DC 20052 USA.
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28
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Tao L, Yuan H, Zhu K, Liu X, Guo J, Min R, He H, Cao D, Yang X, Zhou Z, Wang R, Zhao D, Ma H, Chen J, Zhao J, Li Y, He Y, Suo D, Zhang R, Li S, Li L, Yang F, Li H, Zhang L, Jin L, Wang CC. Ancient genomes reveal millet farming-related demic diffusion from the Yellow River into southwest China. Curr Biol 2023; 33:4995-5002.e7. [PMID: 37852263 DOI: 10.1016/j.cub.2023.09.055] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/12/2023] [Accepted: 09/22/2023] [Indexed: 10/20/2023]
Abstract
The study of southwest China is vital for understanding the dispersal and development of farming because of the coexistence of millet and rice in this region since the Neolithic period.1,2 However, the process of the Neolithic transition in southwest China is largely unknown, mainly due to the lack of ancient DNA from the Neolithic period. Here, we report genome-wide data from 11 human samples from the Gaoshan and Haimenkou sites with mixed farming of millet and rice dating to between 4,500 and 3,000 years before present in southwest China. The two ancient groups derived approximately 90% of their ancestry from the Neolithic Yellow River farmers, suggesting a demic diffusion of millet farming to southwest China. We inferred their remaining ancestry to be derived from a Hòabìnhian-related hunter-gatherer lineage. We did not detect rice farmer-related ancestry in the two ancient groups, which indicates that they likely adopted rice farming without genetic assimilation. We, however, observed rice farmer-related ancestry in the formation of some present-day Tibeto-Burman populations. Our results suggested the occurrence of both demic and cultural diffusion in the development of Neolithic mixed farming in some parts of southwest China.
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Affiliation(s)
- Le Tao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Haibing Yuan
- Center for Archaeological Science, Sichuan University, Chengdu 610064, China.
| | - Kongyang Zhu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Xiangyu Liu
- Chengdu Municipal Institute of Cultural Relics and Archaeology, Chengdu 610008, China
| | - Jianxin Guo
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361005, China.
| | - Rui Min
- Yunnan Institute of Cultural Relics and Archaeology, Kunming 650118, China
| | - Haifeng He
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Doudou Cao
- Department of Archaeology, University of Cambridge, Cambridge CB2 3DZ, UK
| | - Xiaomin Yang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361005, China
| | - Zhiqing Zhou
- Chengdu Municipal Institute of Cultural Relics and Archaeology, Chengdu 610008, China
| | - Rui Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Deyun Zhao
- Center for Archaeological Science, Sichuan University, Chengdu 610064, China; School of Archaeology and Museology, Sichuan University, Chengdu 610064, China; National Demonstration Center for Experimental Archaeology Education, Sichuan University, Chengdu 610064, China
| | - Hao Ma
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Jian Chen
- Chengdu Municipal Institute of Cultural Relics and Archaeology, Chengdu 610008, China
| | - Jing Zhao
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361005, China
| | - Yingfu Li
- Center for Archaeological Science, Sichuan University, Chengdu 610064, China; School of Archaeology and Museology, Sichuan University, Chengdu 610064, China; National Demonstration Center for Experimental Archaeology Education, Sichuan University, Chengdu 610064, China
| | - Yuanhong He
- Center for Archaeological Science, Sichuan University, Chengdu 610064, China; School of Archaeology and Museology, Sichuan University, Chengdu 610064, China; National Demonstration Center for Experimental Archaeology Education, Sichuan University, Chengdu 610064, China
| | - Dehao Suo
- Center for Archaeological Science, Sichuan University, Chengdu 610064, China; School of Archaeology and Museology, Sichuan University, Chengdu 610064, China; National Demonstration Center for Experimental Archaeology Education, Sichuan University, Chengdu 610064, China
| | - Ruojing Zhang
- Center for Archaeological Science, Sichuan University, Chengdu 610064, China; School of Archaeology and Museology, Sichuan University, Chengdu 610064, China; National Demonstration Center for Experimental Archaeology Education, Sichuan University, Chengdu 610064, China
| | - Shuai Li
- Center for Archaeological Science, Sichuan University, Chengdu 610064, China; School of Archaeology and Museology, Sichuan University, Chengdu 610064, China; National Demonstration Center for Experimental Archaeology Education, Sichuan University, Chengdu 610064, China
| | - Lan Li
- Center for Archaeological Science, Sichuan University, Chengdu 610064, China; School of Archaeology and Museology, Sichuan University, Chengdu 610064, China; National Demonstration Center for Experimental Archaeology Education, Sichuan University, Chengdu 610064, China
| | - Feng Yang
- Center for Archaeological Science, Sichuan University, Chengdu 610064, China; School of Archaeology and Museology, Sichuan University, Chengdu 610064, China; National Demonstration Center for Experimental Archaeology Education, Sichuan University, Chengdu 610064, China
| | - Haichao Li
- Center for Archaeological Science, Sichuan University, Chengdu 610064, China; School of Archaeology and Museology, Sichuan University, Chengdu 610064, China; National Demonstration Center for Experimental Archaeology Education, Sichuan University, Chengdu 610064, China
| | - Liang Zhang
- Center for Archaeological Science, Sichuan University, Chengdu 610064, China; School of Archaeology and Museology, Sichuan University, Chengdu 610064, China; National Demonstration Center for Experimental Archaeology Education, Sichuan University, Chengdu 610064, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200433, China; Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China; Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361005, China; Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, Fujian, China; Institute of Artificial Intelligence, Xiamen University, Xiamen 361005, Fujian, China.
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29
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Myers BM, Burns KJ, Clark CJ, Brelsford A. Sampling affects population genetic inference: A case study of the Allen's (Selasphorus sasin) and rufous hummingbird (Selasphorus rufus). J Hered 2023; 114:625-636. [PMID: 37455658 DOI: 10.1093/jhered/esad044] [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: 11/05/2022] [Accepted: 07/12/2023] [Indexed: 07/18/2023] Open
Abstract
Gene flow can affect evolutionary inference when species are undersampled. Here, we evaluate the effects of gene flow and geographic sampling on demographic inference of 2 hummingbirds that hybridize, Allen's hummingbird (Selasphorus sasin) and rufous hummingbird (Selasphorus rufus). Using whole-genome data and extensive geographic sampling, we find widespread connectivity, with introgression far beyond the Allen's × rufous hybrid zone, although the Z chromosome resists introgression beyond the hybrid zone. We test alternative hypotheses of speciation history of Allen's, rufous, and Calliope (S. calliope) hummingbird and find that rufous hummingbird is the sister taxon to Allen's hummingbird, and Calliope hummingbird is the outgroup. A model treating the 2 subspecies of Allen's hummingbird as a single panmictic population fit observed genetic data better than models treating the subspecies as distinct populations, in contrast to morphological and behavioral differences and analyses of spatial population structure. With additional sampling, our study builds upon recent studies that came to conflicting conclusions regarding the evolutionary histories of these 2 species. Our results stress the importance of thorough geographic sampling when assessing demographic history in the presence of gene flow.
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Affiliation(s)
- Brian M Myers
- Department of Biological Sciences, San Diego State University, San Diego, CA, United States
| | - Kevin J Burns
- Department of Biological Sciences, San Diego State University, San Diego, CA, United States
| | - Christopher J Clark
- Department of Evolution, Ecology, and Organismal Biology, Speith Hall, University of California, Riverside, CA, United States
| | - Alan Brelsford
- Department of Evolution, Ecology, and Organismal Biology, Speith Hall, University of California, Riverside, CA, United States
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30
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Jamieson A, Carmagnini A, Howard-McCombe J, Doherty S, Hirons A, Dimopoulos E, Lin AT, Allen R, Anderson-Whymark H, Barnett R, Batey C, Beglane F, Bowden W, Bratten J, De Cupere B, Drew E, Foley NM, Fowler T, Fox A, Geigl EM, Gotfredsen AB, Grange T, Griffiths D, Groß D, Haruda A, Hjermind J, Knapp Z, Lebrasseur O, Librado P, Lyons LA, Mainland I, McDonnell C, Muñoz-Fuentes V, Nowak C, O'Connor T, Peters J, Russo IRM, Ryan H, Sheridan A, Sinding MHS, Skoglund P, Swali P, Symmons R, Thomas G, Trolle Jensen TZ, Kitchener AC, Senn H, Lawson D, Driscoll C, Murphy WJ, Beaumont M, Ottoni C, Sykes N, Larson G, Frantz L. Limited historical admixture between European wildcats and domestic cats. Curr Biol 2023; 33:4751-4760.e14. [PMID: 37935117 DOI: 10.1016/j.cub.2023.08.031] [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: 03/09/2023] [Revised: 06/07/2023] [Accepted: 08/09/2023] [Indexed: 11/09/2023]
Abstract
Domestic cats were derived from the Near Eastern wildcat (Felis lybica), after which they dispersed with people into Europe. As they did so, it is possible that they interbred with the indigenous population of European wildcats (Felis silvestris). Gene flow between incoming domestic animals and closely related indigenous wild species has been previously demonstrated in other taxa, including pigs, sheep, goats, bees, chickens, and cattle. In the case of cats, a lack of nuclear, genome-wide data, particularly from Near Eastern wildcats, has made it difficult to either detect or quantify this possibility. To address these issues, we generated 75 ancient mitochondrial genomes, 14 ancient nuclear genomes, and 31 modern nuclear genomes from European and Near Eastern wildcats. Our results demonstrate that despite cohabitating for at least 2,000 years on the European mainland and in Britain, most modern domestic cats possessed less than 10% of their ancestry from European wildcats, and ancient European wildcats possessed little to no ancestry from domestic cats. The antiquity and strength of this reproductive isolation between introduced domestic cats and local wildcats was likely the result of behavioral and ecological differences. Intriguingly, this long-lasting reproductive isolation is currently being eroded in parts of the species' distribution as a result of anthropogenic activities.
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Affiliation(s)
- Alexandra Jamieson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, OX1 3TG Oxford, UK; Palaeogenomics Group, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universität, 80539 Munich, Germany
| | - Alberto Carmagnini
- Palaeogenomics Group, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universität, 80539 Munich, Germany; School of Biological and Chemical Sciences, Queen Mary University of London, E1 4NS London, UK
| | - Jo Howard-McCombe
- School of Biological Sciences, University of Bristol, BS8 1TQ Bristol, UK; RZSS WildGenes Laboratory, Royal Zoological Society of Scotland, EH12 6TS Edinburgh, UK
| | - Sean Doherty
- Department of Archaeology, University of Exeter, EX4 4QE Exeter, UK
| | - Alexandra Hirons
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, OX1 3TG Oxford, UK
| | - Evangelos Dimopoulos
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, OX1 3TG Oxford, UK; Department of Veterinary Medicine, University of Cambridge, CB3 0ES Cambridge, UK
| | - Audrey T Lin
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Richard Allen
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, OX1 3TG Oxford, UK
| | - Hugo Anderson-Whymark
- Department of Scottish History and Archaeology, National Museums Scotland, EH1 1JF Edinburgh, UK
| | - Ross Barnett
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Colleen Batey
- Institute for Northern Studies, University of the Highlands and Islands, KW15 1FL Kirkwall, UK; Department of Archaeology, University of Durham, DH1 3LE Durham, UK
| | - Fiona Beglane
- CERIS, School of Science, Atlantic Technological University, F91 YW50 Sligo, Ireland
| | - Will Bowden
- Department of Classics and Archaeology, University of Nottingham, NG7 2RD Nottingham, UK
| | - John Bratten
- Department of Anthropology, University of West Florida, Pensacola, FL 32514, USA
| | - Bea De Cupere
- Royal Belgian Institute of Natural Sciences, 1000 Brussels, Belgium
| | - Ellie Drew
- York Archaeological Trust, YO1 7BX York, UK
| | - Nicole M Foley
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Tom Fowler
- Department of Classics and Archaeology, University of Nottingham, NG7 2RD Nottingham, UK
| | - Allison Fox
- Manx National Heritage, Manx Museum, IM1 3LY Douglas, Isle of Man
| | - Eva-Maria Geigl
- Université Paris-Cité, CNRS, Institut Jacques Monod, 75013 Paris, France
| | | | - Thierry Grange
- Université Paris-Cité, CNRS, Institut Jacques Monod, 75013 Paris, France
| | - David Griffiths
- Department for Continuing Education, University of Oxford, OX1 2JA Oxford, UK
| | - Daniel Groß
- Museum Lolland-Falster, 4800 Nykøbing Falster, Denmark
| | - Ashleigh Haruda
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, OX1 3TG Oxford, UK
| | | | - Zoe Knapp
- Department of Archaeology, University of Reading, RG6 6AB Reading, UK
| | - Ophélie Lebrasseur
- Centre for Anthropobiology and Genomics of Toulouse, CNRS UMR 5288, Universite de Toulouse, Universite Paul Sabatier, 31000 Toulouse, France; The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, OX1 3TG Oxford, UK
| | - Pablo Librado
- Centre for Anthropobiology and Genomics of Toulouse, CNRS UMR 5288, Universite de Toulouse, Universite Paul Sabatier, 31000 Toulouse, France
| | - Leslie A Lyons
- Department of Veterinary Medicine & Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Ingrid Mainland
- UHI Archaeology Institute, University of the Highlands and Islands, Orkney, Scotland
| | | | - Violeta Muñoz-Fuentes
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SD Cambridge, UK
| | - Carsten Nowak
- Centre for Wildlife Genetics & LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberg Research Institute, 60325 Frankfurt, Germany
| | - Terry O'Connor
- BioArCh, Department of Archaeology, University of York, YO10 5DD York, UK
| | - Joris Peters
- SNSB, State Collection of Palaeoanatomy Munich, 85586 Poing, Germany; Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universität, 80539 Munich, Germany
| | | | - Hannah Ryan
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, OX1 3TG Oxford, UK
| | - Alison Sheridan
- Department of Scottish History and Archaeology, National Museums Scotland, EH1 1JF Edinburgh, UK
| | | | | | - Pooja Swali
- The Francis Crick Institute, NW1 1AT London, UK
| | | | - Gabor Thomas
- Department of Archaeology, University of Reading, RG6 6AB Reading, UK
| | - Theis Zetner Trolle Jensen
- Section for Molecular Ecology and Evolution, GLOBE Institute, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, EH1 1JF Edinburgh, UK; School of Geosciences, University of Edinburgh, EH8 9XP Edinburgh, UK
| | - Helen Senn
- RZSS WildGenes Laboratory, Royal Zoological Society of Scotland, EH12 6TS Edinburgh, UK
| | - Daniel Lawson
- School of Mathematics, University of Bristol, BS8 1UG Bristol, UK
| | | | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Mark Beaumont
- School of Biological Sciences, University of Bristol, BS8 1TQ Bristol, UK
| | - Claudio Ottoni
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, 00133 Roma, Italy
| | - Naomi Sykes
- Department of Archaeology, University of Exeter, EX4 4QE Exeter, UK
| | - Greger Larson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, OX1 3TG Oxford, UK.
| | - Laurent Frantz
- Palaeogenomics Group, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universität, 80539 Munich, Germany; School of Biological and Chemical Sciences, Queen Mary University of London, E1 4NS London, UK.
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31
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Yüncü E, Işıldak U, Williams MP, Huber CD, Flegontova O, Vyazov LA, Changmai P, Flegontov P. False discovery rates of qpAdm-based screens for genetic admixture. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.25.538339. [PMID: 37904998 PMCID: PMC10614728 DOI: 10.1101/2023.04.25.538339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Although a broad range of methods exists for reconstructing population history from genome-wide single nucleotide polymorphism data, just a few methods gained popularity in archaeogenetics: principal component analysis (PCA); ADMIXTURE, an algorithm that models individuals as mixtures of multiple ancestral sources represented by actual or inferred populations; formal tests for admixture such as f3-statistics and D/f4-statistics; and qpAdm, a tool for fitting two-component and more complex admixture models to groups or individuals. Despite their popularity in archaeogenetics, which is explained by modest computational requirements and ability to analyze data of various types and qualities, protocols relying on qpAdm that screen numerous alternative models of varying complexity and find "fitting" models (often considering both estimated admixture proportions and p-values as a composite criterion of model fit) remain untested on complex simulated population histories in the form of admixture graphs of random topology. We analyzed genotype data extracted from such simulations and tested various types of high-throughput qpAdm protocols ("rotating" and "non-rotating", with or without temporal stratification of target groups and proxy ancestry sources, and with or without a "model competition" step). We caution that high-throughput qpAdm protocols may be inappropriate for exploratory analyses in poorly studied regions/periods since their false discovery rates varied between 12% and 68% depending on the details of the protocol and on the amount and quality of simulated data (i.e., >12% of fitting two-way admixture models imply gene flows that were not simulated). We demonstrate that for reducing false discovery rates of qpAdm protocols to nearly 0% it is advisable to use large SNP sets with low missing data rates, the rotating qpAdm protocol with a strictly enforced rule that target groups do not pre-date their proxy sources, and an unsupervised ADMIXTURE analysis as a way to verify feasible qpAdm models. Our study has a number of limitations: for instance, these recommendations depend on the assumption that the underlying genetic history is a complex admixture graph and not a stepping-stone model.
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Affiliation(s)
- Eren Yüncü
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Ulaş Işıldak
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Matthew P. Williams
- Department of Biology, Eberly College of Science, Pennsylvania State University, PA, USA
| | - Christian D. Huber
- Department of Biology, Eberly College of Science, Pennsylvania State University, PA, USA
| | - Olga Flegontova
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia
| | - Leonid A. Vyazov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Piya Changmai
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Pavel Flegontov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
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32
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van Waaij J, Li S, Garcia-Erill G, Albrechtsen A, Wiuf C. Evaluation of population structure inferred by principal component analysis or the admixture model. Genetics 2023; 225:iyad157. [PMID: 37611212 DOI: 10.1093/genetics/iyad157] [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: 06/06/2023] [Revised: 06/06/2023] [Accepted: 08/16/2023] [Indexed: 08/25/2023] Open
Abstract
Principal component analysis (PCA) is commonly used in genetics to infer and visualize population structure and admixture between populations. PCA is often interpreted in a way similar to inferred admixture proportions, where it is assumed that individuals belong to one of several possible populations or are admixed between these populations. We propose a new method to assess the statistical fit of PCA (interpreted as a model spanned by the top principal components) and to show that violations of the PCA assumptions affect the fit. Our method uses the chosen top principal components to predict the genotypes. By assessing the covariance (and the correlation) of the residuals (the differences between observed and predicted genotypes), we are able to detect violation of the model assumptions. Based on simulations and genome-wide human data, we show that our assessment of fit can be used to guide the interpretation of the data and to pinpoint individuals that are not well represented by the chosen principal components. Our method works equally on other similar models, such as the admixture model, where the mean of the data is represented by linear matrix decomposition.
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Affiliation(s)
- Jan van Waaij
- Department of Mathematical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Song Li
- Department of Mathematical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Genís Garcia-Erill
- Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Anders Albrechtsen
- Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Carsten Wiuf
- Department of Mathematical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
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33
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Garcia-Erill G, Hanghøj K, Heller R, Wiuf C, Albrechtsen A. Estimating admixture pedigrees of recent hybrids without a contiguous reference genome. Mol Ecol Resour 2023; 23:1604-1619. [PMID: 37400991 DOI: 10.1111/1755-0998.13830] [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: 01/16/2023] [Revised: 05/30/2023] [Accepted: 06/15/2023] [Indexed: 07/05/2023]
Abstract
The genome of recently admixed individuals or hybrids has characteristic genetic patterns that can be used to learn about their recent admixture history. One of these are patterns of interancestry heterozygosity, which can be inferred from SNP data from either called genotypes or genotype likelihoods, without the need for information on genomic location. This makes them applicable to a wide range of data that are often used in evolutionary and conservation genomic studies, such as low-depth sequencing mapped to scaffolds and reduced representation sequencing. Here we implement maximum likelihood estimation of interancestry heterozygosity patterns using two complementary models. We furthermore develop apoh (Admixture Pedigrees of Hybrids), a software that uses estimates of paired ancestry proportions to detect recently admixed individuals or hybrids, and to suggest possible admixture pedigrees. It furthermore calculates several hybrid indices that make it easier to identify and rank possible admixture pedigrees that could give rise to the estimated patterns. We implemented apoh both as a command line tool and as a Graphical User Interface that allows the user to automatically and interactively explore, rank and visualize compatible recent admixture pedigrees, and calculate the different summary indices. We validate the performance of the method using admixed family trios from the 1000 Genomes Project. In addition, we show its applicability on identifying recent hybrids from RAD-seq data of Grant's gazelle (Nanger granti and Nanger petersii) and whole genome low-depth data of waterbuck (Kobus ellipsiprymnus) which shows complex admixture of up to four populations.
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Affiliation(s)
| | - Kristian Hanghøj
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Heller
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Carsten Wiuf
- Department of Mathematical Sciences, University of Copenhagen, Copenhagen, Denmark
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34
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Bhowmik N, Seaborn T, Ringwall KA, Dahlen CR, Swanson KC, Hulsman Hanna LL. Genetic Distinctness and Diversity of American Aberdeen Cattle Compared to Common Beef Breeds in the United States. Genes (Basel) 2023; 14:1842. [PMID: 37895190 PMCID: PMC10606367 DOI: 10.3390/genes14101842] [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: 08/11/2023] [Revised: 09/10/2023] [Accepted: 09/19/2023] [Indexed: 10/29/2023] Open
Abstract
American Aberdeen (AD) cattle in the USA descend from an Aberdeen Angus herd originally brought to the Trangie Agricultural Research Centre, New South Wales, AUS. Although put under specific selection pressure for yearling growth rate, AD remain genomically uncharacterized. The objective was to characterize the genetic diversity and structure of purebred and crossbred AD cattle relative to seven common USA beef breeds using available whole-genome SNP data. A total of 1140 animals consisting of 404 purebred (n = 8 types) and 736 admixed individuals (n = 10 types) was used. Genetic diversity metrics, an analysis of molecular variance, and a discriminant analysis of principal components were employed. When linkage disequilibrium was not accounted for, markers influenced basic diversity parameter estimates, especially for AD cattle. Even so, intrapopulation and interpopulation estimates separate AD cattle from other purebred types (e.g., Latter's pairwise FST ranged from 0.1129 to 0.2209), where AD cattle were less heterozygous and had lower allelic richness than other purebred types. The admixed AD-influenced cattle were intermediate to other admixed types for similar parameters. The diversity metrics separation and differences support strong artificial selection pressures during and after AD breed development, shaping the evolution of the breed and making them genomically distinct from similar breeds.
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Affiliation(s)
- Nayan Bhowmik
- Department of Animal Sciences, North Dakota State University, Fargo, ND 58108, USA
| | - Travis Seaborn
- School of Natural Resource Sciences, North Dakota State University, Fargo, ND 58108, USA
| | - Kris A. Ringwall
- Dickinson Research Extension Center, North Dakota State University, Dickinson, ND 58601, USA
| | - Carl R. Dahlen
- Department of Animal Sciences, North Dakota State University, Fargo, ND 58108, USA
| | - Kendall C. Swanson
- Department of Animal Sciences, North Dakota State University, Fargo, ND 58108, USA
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35
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Pedrazzini C, Strasser H, Zemp N, Holderegger R, Widmer F, Enkerli J. Spatial and temporal patterns in the population genomics of the European cockchafer Melolontha melolontha in the Alpine region. Evol Appl 2023; 16:1586-1597. [PMID: 37752964 PMCID: PMC10519412 DOI: 10.1111/eva.13588] [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: 03/24/2023] [Revised: 08/04/2023] [Accepted: 08/12/2023] [Indexed: 09/28/2023] Open
Abstract
The European cockchafer Melolontha melolontha is an agricultural pest in many European countries. Populations have a synchronized 3 or 4 years life cycle, leading to temporally isolated populations. Despite the economic importance and availability of comprehensive historical as well as current records on cockchafer occurrence, population genomic analyses of M. melolontha are missing. For example, the effects of geographic separation caused by the mountainous terrain of the Alps and of temporal isolation on the genomic structure of M. melolontha still remain unknown. To address this gap, we genotyped 475 M. melolontha adults collected during 3 years from 35 sites in a central Alpine region. Subsequent population structure analyses discriminated two main genetic clusters, i.e., the South Tyrol cluster including collections located southeast of the Alpine mountain range, and a northwestern alpine cluster with all the other collections, reflecting distinct evolutionary history and geographic barriers. The "passo di Resia" linking South and North Tyrol represented a regional contact zone of the two genetic clusters, highlighting genomic differentiation between the collections from the northern and southern regions. Although the collections from northwestern Italy were assigned to the northwestern alpine genetic cluster, they displayed evidence of admixture with the South Tyrolean genetic cluster, suggesting shared ancestry. A linear mixed model confirmed that both geographic distance and, to a lower extent, also temporal isolation had a significant effect on the genetic distance among M. melolontha populations. These effects may be attributed to limited dispersal capacity and reproductive isolation resulting from synchronized and non-synchronized swarming flights, respectively. This study contributes to the understanding of the phylogeography of an organism that is recognized as an agricultural problem and provides significant information on the population genomics of insect species with prolonged temporally shifted and locally synchronized life cycles.
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Affiliation(s)
- Chiara Pedrazzini
- Molecular Ecology, AgroscopeZürichSwitzerland
- Institute of Environmental Systems ScienceETHZürichSwitzerland
| | - Hermann Strasser
- Institute of MicrobiologyLeopold‐Franzens University InnsbruckInnsbruckAustria
| | - Niklaus Zemp
- Genetic Diversity Centre (GDC)ETHZürichSwitzerland
| | - Rolf Holderegger
- Institute of Environmental Systems ScienceETHZürichSwitzerland
- Swiss Federal Research Institute WSLBirmensdorfSwitzerland
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36
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Moorjani P, Hellenthal G. Methods for Assessing Population Relationships and History Using Genomic Data. Annu Rev Genomics Hum Genet 2023; 24:305-332. [PMID: 37220313 PMCID: PMC11040641 DOI: 10.1146/annurev-genom-111422-025117] [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] [Indexed: 05/25/2023]
Abstract
Genetic data contain a record of our evolutionary history. The availability of large-scale datasets of human populations from various geographic areas and timescales, coupled with advances in the computational methods to analyze these data, has transformed our ability to use genetic data to learn about our evolutionary past. Here, we review some of the widely used statistical methods to explore and characterize population relationships and history using genomic data. We describe the intuition behind commonly used approaches, their interpretation, and important limitations. For illustration, we apply some of these techniques to genome-wide autosomal data from 929 individuals representing 53 worldwide populations that are part of the Human Genome Diversity Project. Finally, we discuss the new frontiers in genomic methods to learn about population history. In sum, this review highlights the power (and limitations) of DNA to infer features of human evolutionary history, complementing the knowledge gleaned from other disciplines, such as archaeology, anthropology, and linguistics.
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Affiliation(s)
- Priya Moorjani
- Department of Molecular and Cell Biology and Center for Computational Biology, University of California, Berkeley, California, USA;
| | - Garrett Hellenthal
- UCL Genetics Institute and Research Department of Genetics, Evolution, and Environment, University College London, London, United Kingdom;
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37
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Tan T, Atkinson EG. Strategies for the Genomic Analysis of Admixed Populations. Annu Rev Biomed Data Sci 2023; 6:105-127. [PMID: 37127050 PMCID: PMC10871708 DOI: 10.1146/annurev-biodatasci-020722-014310] [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] [Indexed: 05/03/2023]
Abstract
Admixed populations constitute a large portion of global human genetic diversity, yet they are often left out of genomics analyses. This exclusion is problematic, as it leads to disparities in the understanding of the genetic structure and history of diverse cohorts and the performance of genomic medicine across populations. Admixed populations have particular statistical challenges, as they inherit genomic segments from multiple source populations-the primary reason they have historically been excluded from genetic studies. In recent years, however, an increasing number of statistical methods and software tools have been developed to account for and leverage admixture in the context of genomics analyses. Here, we provide a survey of such computational strategies for the informed consideration of admixture to allow for the well-calibrated inclusion of mixed ancestry populations in large-scale genomics studies, and we detail persisting gaps in existing tools.
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Affiliation(s)
- Taotao Tan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA;
| | - Elizabeth G Atkinson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA;
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38
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Beck JJ, Ahmed T, Finnicum CT, Zwinderman K, Ehli EA, Boomsma DI, Hottenga JJ. Genetic Ancestry Estimates within Dutch Family Units and Across Genotyping Arrays: Insights from Empirical Analysis Using Two Estimation Methods. Genes (Basel) 2023; 14:1497. [PMID: 37510400 PMCID: PMC10379078 DOI: 10.3390/genes14071497] [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: 06/13/2023] [Revised: 07/12/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Accurate inference of genetic ancestry is crucial for population-based association studies, accounting for population heterogeneity and structure. This study analyzes genome-wide SNP data from the Netherlands Twin Register to compare genetic ancestry estimates. The focus is on the comparison of ancestry estimates between family members and individuals genotyped on multiple arrays (Affymetrix 6.0, Affymetrix Axiom, and Illumina GSA). Two conventional methods, principal component analysis and ADMIXTURE, were implemented to estimate ancestry, each serving its specific purpose, rather than for direct comparison. The results reveal that as the degree of genetic relatedness decreases, the Euclidean distances of genetic ancestry estimates between family members significantly increase (empirical p < 0.001), regardless of the estimation method and genotyping array. Ancestry estimates among individuals genotyped on multiple arrays also show statistically significant differences (empirical p < 0.001). Additionally, this study investigates the relationship between the ancestry estimates of non-identical twin offspring with ancestrally diverse parents and those with ancestrally similar parents. The results indicate a statistically significant weak correlation between the variation in ancestry estimates among offspring and differences in ancestry estimates among parents (Spearman's rho: 0.07, p = 0.005). This study highlights the utility of current methods in inferring genetic ancestry, emphasizing the importance of reference population composition in determining ancestry estimates.
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Affiliation(s)
- Jeffrey J Beck
- Avera Institute for Human Genetics, Avera McKennan Hospital and University Health Center, Sioux Falls, SD 57105, USA
| | - Talitha Ahmed
- Department of Biological Psychology, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
| | - Casey T Finnicum
- Avera Institute for Human Genetics, Avera McKennan Hospital and University Health Center, Sioux Falls, SD 57105, USA
| | - Koos Zwinderman
- Department of Clinical Epidemiology, Biostatistics, and Bioinformatics, Academic Medical Center Amsterdam, 1105 AZ Amsterdam, The Netherlands
- Amsterdam Public Health (APH) Research Institute, 1081 BT Amsterdam, The Netherlands
| | - Erik A Ehli
- Avera Institute for Human Genetics, Avera McKennan Hospital and University Health Center, Sioux Falls, SD 57105, USA
| | - Dorret I Boomsma
- Avera Institute for Human Genetics, Avera McKennan Hospital and University Health Center, Sioux Falls, SD 57105, USA
- Department of Biological Psychology, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
- Amsterdam Public Health (APH) Research Institute, 1081 BT Amsterdam, The Netherlands
| | - Jouke Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
- Amsterdam Public Health (APH) Research Institute, 1081 BT Amsterdam, The Netherlands
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39
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Louis M, Korlević P, Nykänen M, Archer F, Berrow S, Brownlow A, Lorenzen ED, O'Brien J, Post K, Racimo F, Rogan E, Rosel PE, Sinding MHS, van der Es H, Wales N, Fontaine MC, Gaggiotti OE, Foote AD. Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters. Nat Commun 2023; 14:4020. [PMID: 37463880 DOI: 10.1038/s41467-023-39532-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 06/16/2023] [Indexed: 07/20/2023] Open
Abstract
Parallel evolution provides strong evidence of adaptation by natural selection due to local environmental variation. Yet, the chronology, and mode of the process of parallel evolution remains debated. Here, we harness the temporal resolution of paleogenomics to address these long-standing questions, by comparing genomes originating from the mid-Holocene (8610-5626 years before present, BP) to contemporary pairs of coastal-pelagic ecotypes of bottlenose dolphin. We find that the affinity of ancient samples to coastal populations increases as the age of the samples decreases. We assess the youngest genome (5626 years BP) at sites previously inferred to be under parallel selection to coastal habitats and find it contained coastal-associated genotypes. Thus, coastal-associated variants rose to detectable frequencies close to the emergence of coastal habitat. Admixture graph analyses reveal a reticulate evolutionary history between pelagic and coastal populations, sharing standing genetic variation that facilitated rapid adaptation to newly emerged coastal habitats.
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Affiliation(s)
- Marie Louis
- Centre for Biological Diversity, Sir Harold Mitchell Building and Dyers Brae, University of St Andrews, St Andrews, KY16 9TH, Scotland, UK.
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark.
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, The Netherlands.
- Greenland Institute of Natural Resources, Kivioq 2, Nuuk, 3900, Greenland.
| | - Petra Korlević
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Milaja Nykänen
- Department of Environmental and Biological Sciences, PO Box 111, FI-80101, Joensuu, Finland
- School of Biological, Earth and Environmental Sciences, University College Cork, North Mall, Cork, Ireland
| | - Frederick Archer
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, NOAA, 8901 La Jolla Shores Drive, La Jolla, CA, 92037, USA
| | - Simon Berrow
- Irish Whale and Dolphin Group, Kilrush, Co Clare, Ireland
- Marine and Freshwater Research Centre, Department of Natural Sciences, School of Science and Computing, Atlantic Technological University, Dublin Road, H91 T8NW, Galway, Ireland
| | - Andrew Brownlow
- Scottish Marine Animal Stranding Scheme, Institute of Biodiversity, Animal Health & Comparative Medicine College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Eline D Lorenzen
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark
| | - Joanne O'Brien
- Irish Whale and Dolphin Group, Kilrush, Co Clare, Ireland
- Marine and Freshwater Research Centre, Department of Natural Sciences, School of Science and Computing, Atlantic Technological University, Dublin Road, H91 T8NW, Galway, Ireland
| | - Klaas Post
- Natural History Museum Rotterdam, Westzeedijk 345, 3015 AA, Rotterdam, Netherlands
| | - Fernando Racimo
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark
| | - Emer Rogan
- School of Biological, Earth and Environmental Sciences, University College Cork, North Mall, Cork, Ireland
| | - Patricia E Rosel
- Marine Mammal and Turtle Division, Southeast Fisheries Science Center, NOAA, 646 Cajundome Boulevard, Lafayette, LA, 70506, USA
| | - Mikkel-Holger S Sinding
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Henry van der Es
- Natural History Museum Rotterdam, Westzeedijk 345, 3015 AA, Rotterdam, Netherlands
| | - Nathan Wales
- University of York, BioArCh, Environment Building, Wentworth Way, Heslington, York, YO10 5DD, UK
| | - Michael C Fontaine
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, The Netherlands
- MIVEGEC (Université de Montpellier, CNRS 5290, IRD 229) Institut de Recherche pour le Développement (IRD), F-34394, Montpellier, France
| | - Oscar E Gaggiotti
- Centre for Biological Diversity, Sir Harold Mitchell Building and Dyers Brae, University of St Andrews, St Andrews, KY16 9TH, Scotland, UK
| | - Andrew D Foote
- Department of Natural History, Norwegian University of Science and Technology (NTNU), NO-7491, Trondheim, Norway.
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0316, Oslo, Norway.
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40
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Slovák M, Melichárková A, Štubňová EG, Kučera J, Mandáková T, Smyčka J, Lavergne S, Passalacqua NG, Vďačný P, Paun O. Pervasive Introgression During Rapid Diversification of the European Mountain Genus Soldanella (L.) (Primulaceae). Syst Biol 2023; 72:491-504. [PMID: 36331548 PMCID: PMC10276626 DOI: 10.1093/sysbio/syac071] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 10/26/2022] [Accepted: 10/31/2022] [Indexed: 03/19/2024] Open
Abstract
Hybridization is a key mechanism involved in lineage diversification and speciation, especially in ecosystems that experienced repeated environmental oscillations. Recently radiated plant groups, which have evolved in mountain ecosystems impacted by historical climate change provide an excellent model system for studying the impact of gene flow on speciation. We combined organellar (whole-plastome) and nuclear genomic data (RAD-seq) with a cytogenetic approach (rDNA FISH) to investigate the effects of hybridization and introgression on evolution and speciation in the genus Soldanella (snowbells, Primulaceae). Pervasive introgression has already occurred among ancestral lineages of snowbells and has persisted throughout the entire evolutionary history of the genus, regardless of the ecology, cytotype, or distribution range size of the affected species. The highest extent of introgression has been detected in the Carpathian species, which is also reflected in their extensive karyotype variation. Introgression occurred even between species with dysploid and euploid cytotypes, which were considered to be reproductively isolated. The magnitude of introgression detected in snowbells is unprecedented in other mountain genera of the European Alpine System investigated hitherto. Our study stresses the prominent evolutionary role of hybridization in facilitating speciation and diversification on the one hand, but also enriching previously isolated genetic pools. [chloroplast capture; diversification; dysploidy; European Alpine system; introgression; nuclear-cytoplasmic discordance; ribosomal DNA.].
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Affiliation(s)
- Marek Slovák
- Department of Evolution and Systematics, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Institute of Botany, Bratislava, Slovakia
- Department of Botany, Charles University, Prague, Czech Republic
| | - Andrea Melichárková
- Department of Evolution and Systematics, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Institute of Botany, Bratislava, Slovakia
| | - Eliška Gbúrová Štubňová
- Department of Evolution and Systematics, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Institute of Botany, Bratislava, Slovakia
- Slovak National Museum, Natural History Museum, Bratislava, Slovakia
| | - Jaromír Kučera
- Department of Evolution and Systematics, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Institute of Botany, Bratislava, Slovakia
| | - Terezie Mandáková
- Central European Institute of Technology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, CZ-625 00 Brno, Czech Republic
| | - Jan Smyčka
- Department of Botany, Charles University, Prague, Czech Republic
- Center for Theoretical Study, Charles University and the Academy of Sciences of the Czech Republic, Jilská 1, 110 00 Praha, Czech Republic
- Université Grenoble Alpes, University of Savoie Mont Blanc, CNRS, Grenoble, France
| | - Sébastien Lavergne
- Université Grenoble Alpes, University of Savoie Mont Blanc, CNRS, Grenoble, France
| | | | - Peter Vďačný
- Department of Zoology, Comenius University in Bratislava, Bratislava, Slovakia
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
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41
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Ortiz V, Chang HX, Sang H, Jacobs J, Malvick DK, Baird R, Mathew FM, Estévez de Jensen C, Wise KA, Mosquera GM, Chilvers MI. Population genomic analysis reveals geographic structure and climatic diversification for Macrophomina phaseolina isolated from soybean and dry bean across the United States, Puerto Rico, and Colombia. Front Genet 2023; 14:1103969. [PMID: 37351341 PMCID: PMC10282554 DOI: 10.3389/fgene.2023.1103969] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 04/20/2023] [Indexed: 06/24/2023] Open
Abstract
Macrophomina phaseolina causes charcoal rot, which can significantly reduce yield and seed quality of soybean and dry bean resulting from primarily environmental stressors. Although charcoal rot has been recognized as a warm climate-driven disease of increasing concern under global climate change, knowledge regarding population genetics and climatic variables contributing to the genetic diversity of M. phaseolina is limited. This study conducted genome sequencing for 95 M. phaseolina isolates from soybean and dry bean across the continental United States, Puerto Rico, and Colombia. Inference on the population structure using 76,981 single nucleotide polymorphisms (SNPs) revealed that the isolates exhibited a discrete genetic clustering at the continental level and a continuous genetic differentiation regionally. A majority of isolates from the United States (96%) grouped in a clade with a predominantly clonal genetic structure, while 88% of Puerto Rican and Colombian isolates from dry bean were assigned to a separate clade with higher genetic diversity. A redundancy analysis (RDA) was used to estimate the contributions of climate and spatial structure to genomic variation (11,421 unlinked SNPs). Climate significantly contributed to genomic variation at a continental level with temperature seasonality explaining the most variation while precipitation of warmest quarter explaining the most when spatial structure was accounted for. The loci significantly associated with multivariate climate were found closely to the genes related to fungal stress responses, including transmembrane transport, glycoside hydrolase activity and a heat-shock protein, which may mediate climatic adaptation for M. phaseolina. On the contrary, limited genome-wide differentiation among populations by hosts was observed. These findings highlight the importance of population genetics and identify candidate genes of M. phaseolina that can be used to elucidate the molecular mechanisms that underly climatic adaptation to the changing climate.
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Affiliation(s)
- Viviana Ortiz
- Department of Plant, Soil and Microbial Sciences, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, United States
- Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, MI, United States
| | - Hao-Xun Chang
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
| | - Hyunkyu Sang
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, Republic of Korea
| | - Janette Jacobs
- Department of Plant, Soil and Microbial Sciences, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, United States
| | - Dean K. Malvick
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Richard Baird
- BCH-EPP Department, Mississippi State University, Mississippi State, MS, United States
| | - Febina M. Mathew
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
| | | | - Kiersten A. Wise
- Department of Plant Pathology, College of Agriculture, Food and Environment, University of Kentucky, Princeton, KY, United States
| | - Gloria M. Mosquera
- Plant Pathology, Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), The Americas Hub, Palmira, Colombia
| | - Martin I. Chilvers
- Department of Plant, Soil and Microbial Sciences, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, United States
- Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, MI, United States
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42
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Abalde S, Crocetta F, Tenorio MJ, D'Aniello S, Fassio G, Rodríguez-Flores PC, Uribe JE, M L Afonso C, Oliverio M, Zardoya R. Hidden species diversity and mito-nuclear discordance within the Mediterranean cone snail, Lautoconus ventricosus. Mol Phylogenet Evol 2023:107838. [PMID: 37286063 DOI: 10.1016/j.ympev.2023.107838] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 05/15/2023] [Accepted: 05/31/2023] [Indexed: 06/09/2023]
Abstract
The Mediterranean cone snail, Lautoconus ventricosus, is currently considered a single species inhabiting the whole Mediterranean basin and the adjacent Atlantic coasts. Yet, no population genetic study has assessed its taxonomic status. Here, we collected 245 individuals from 75 localities throughout the Mediterranean Sea and used cox1 barcodes, complete mitochondrial genomes, and genome skims to test whether L. ventricosus represents a complex of cryptic species. The maximum likelihood phylogeny based on complete mitochondrial genomes recovered six main clades (hereby named blue, brown, green, orange, red, and violet) with sufficient sequence divergence to be considered putative species. On the other hand, phylogenomic analyses based on 437 nuclear genes only recovered four out of the six clades: blue and orange clades were thoroughly mixed and the brown one was not recovered. This mito-nuclear discordance revealed instances of incomplete lineage sorting and introgression, and may have caused important differences in the dating of main cladogenetic events. Species delimitation tests proposed the existence of at least three species: green, violet, and red+blue+orange (i.e., cyan). Green plus cyan (with sympatric distributions) and violet, had West and East Mediterranean distributions, respectively, mostly separated by the Siculo-Tunisian biogeographical barrier. Morphometric analyses of the shell using species hypotheses as factor and shell length as covariate showed that the discrimination power of the studied parameters was only 70.2%, reinforcing the cryptic nature of the uncovered species, and the importance of integrative taxonomic approaches considering morphology, ecology, biogeography, and mitochondrial and nuclear population genetic variation.
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Affiliation(s)
- Samuel Abalde
- Department of Zoology, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden; Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain.
| | - Fabio Crocetta
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy
| | - Manuel J Tenorio
- Departamento CMIM y Q. Inorgánica-INBIO, Facultad de Ciencias, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
| | - Salvatore D'Aniello
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy
| | - Giulia Fassio
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Zoology-Viale dell'Università 32, 00185 Rome, Italy
| | - Paula C Rodríguez-Flores
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain; Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge MA 02138, USA
| | - Juan E Uribe
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - Carlos M L Afonso
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, 8005 - 139 Faro, Portugal
| | - Marco Oliverio
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Zoology-Viale dell'Università 32, 00185 Rome, Italy
| | - Rafael Zardoya
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain
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43
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Wu H, Wang Z, Zhang Y, Frantz L, Roos C, Irwin DM, Zhang C, Liu X, Wu D, Huang S, Gu T, Liu J, Yu L. Hybrid origin of a primate, the gray snub-nosed monkey. Science 2023; 380:eabl4997. [PMID: 37262139 DOI: 10.1126/science.abl4997] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 07/06/2022] [Indexed: 06/03/2023]
Abstract
Hybridization is widely recognized as promoting both species and phenotypic diversity. However, its role in mammalian evolution is rarely examined. We report historical hybridization among a group of snub-nosed monkeys (Rhinopithecus) that resulted in the origin of a hybrid species. The geographically isolated gray snub-nosed monkey Rhinopithecus brelichi shows a stable mixed genomic ancestry derived from the golden snub-nosed monkey (Rhinopithecus roxellana) and the ancestor of black-white (Rhinopithecus bieti) and black snub-nosed monkeys (Rhinopithecus strykeri). We further identified key genes derived from the parental lineages, respectively, that may have contributed to the mosaic coat coloration of R. brelichi, which likely promoted premating reproductive isolation of the hybrid from parental lineages. Our study highlights the underappreciated role of hybridization in generating species and phenotypic diversity in mammals.
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Affiliation(s)
- Hong Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Zefu Wang
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yuxing Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Laurent Frantz
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University of Munich, D-80539 Munich, Germany
- School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Chenglin Zhang
- Beijing Key Laboratory of Captive Wildlife Technologies in Beijing Zoo, Beijing, China
| | - Xuefeng Liu
- Beijing Key Laboratory of Captive Wildlife Technologies in Beijing Zoo, Beijing, China
| | - Dongdong Wu
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | | | - Tongtong Gu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Jianquan Liu
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
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44
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Arango-Isaza E, Capodiferro MR, Aninao MJ, Babiker H, Aeschbacher S, Achilli A, Posth C, Campbell R, Martínez FI, Heggarty P, Sadowsky S, Shimizu KK, Barbieri C. The genetic history of the Southern Andes from present-day Mapuche ancestry. Curr Biol 2023:S0960-9822(23)00607-3. [PMID: 37279753 DOI: 10.1016/j.cub.2023.05.013] [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: 11/03/2022] [Revised: 03/01/2023] [Accepted: 05/05/2023] [Indexed: 06/08/2023]
Abstract
The southernmost regions of South America harbor some of the earliest evidence of human presence in the Americas. However, connections with the rest of the continent and the contextualization of present-day indigenous ancestries remain poorly resolved. In this study, we analyze the genetic ancestry of one of the largest indigenous groups in South America: the Mapuche. We generate genome-wide data from 64 participants from three Mapuche populations in Southern Chile: Pehuenche, Lafkenche, and Huilliche. Broadly, we describe three main ancestry blocks with a common origin, which characterize the Southern Cone, the Central Andes, and Amazonia. Within the Southern Cone, ancestors of the Mapuche lineages differentiated from those of the Far South during the Middle Holocene and did not experience further migration waves from the north. We find that the deep genetic split between the Central and Southern Andes is followed by instances of gene flow, which may have accompanied the southward spread of cultural traits from the Central Andes, including crops and loanwords from Quechua into Mapudungun (the language of the Mapuche). Finally, we report close genetic relatedness between the three populations analyzed, with the Huilliche characterized additionally by intense recent exchanges with the Far South. Our findings add new perspectives on the genetic (pre)history of South America, from the first settlement through to the present-day indigenous presence. Follow-up fieldwork took these results back to the indigenous communities to contextualize the genetic narrative alongside indigenous knowledge and perspectives.
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Affiliation(s)
- Epifanía Arango-Isaza
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich 8057, Switzerland; Center for the Interdisciplinary Study of Language Evolution, University of Zurich, Zurich 8050, Switzerland.
| | - Marco Rosario Capodiferro
- Trinity College Dublin, Dublin 2, Ireland; Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia 27100, Italy
| | | | - Hiba Babiker
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Simon Aeschbacher
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich 8057, Switzerland
| | - Alessandro Achilli
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia 27100, Italy
| | - Cosimo Posth
- Institute for Archaeological Sciences, Archaeo, and Palaeogenetics, University of Tübingen, Tübingen 72074, Germany; Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen 72074, Germany
| | - Roberto Campbell
- Escuela de Antropología, Pontificia Universidad Católica de Chile, Santiago 6904411, Chile
| | - Felipe I Martínez
- Escuela de Antropología, Pontificia Universidad Católica de Chile, Santiago 6904411, Chile; Center for Intercultural and Indigenous Research, Santiago 7820436, Chile
| | - Paul Heggarty
- "Waves" ERC Group, Department of Human Behavior, Evolution and Culture, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Scott Sadowsky
- Department of Linguistics and Literature, Universidad de Cartagena, Cartagena 130001, Colombia
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich 8057, Switzerland; Center for the Interdisciplinary Study of Language Evolution, University of Zurich, Zurich 8050, Switzerland
| | - Chiara Barbieri
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich 8057, Switzerland; Center for the Interdisciplinary Study of Language Evolution, University of Zurich, Zurich 8050, Switzerland; Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany.
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45
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Stull GW, Pham KK, Soltis PS, Soltis DE. Deep reticulation: the long legacy of hybridization in vascular plant evolution. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:743-766. [PMID: 36775995 DOI: 10.1111/tpj.16142] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 02/02/2023] [Accepted: 02/07/2023] [Indexed: 05/27/2023]
Abstract
Hybridization has long been recognized as a fundamental evolutionary process in plants but, until recently, our understanding of its phylogenetic distribution and biological significance across deep evolutionary scales has been largely obscure. Over the past decade, genomic and phylogenomic datasets have revealed, perhaps not surprisingly, that hybridization, often associated with polyploidy, has been common throughout the evolutionary history of plants, particularly in various lineages of flowering plants. However, phylogenomic studies have also highlighted the challenges of disentangling signals of ancient hybridization from other sources of genomic conflict (in particular, incomplete lineage sorting). Here, we provide a critical review of ancient hybridization in vascular plants, outlining well-documented cases of ancient hybridization across plant phylogeny, as well as the challenges unique to documenting ancient versus recent hybridization. We provide a definition for ancient hybridization, which, to our knowledge, has not been explicitly attempted before. Further documenting the extent of deep reticulation in plants should remain an important research focus, especially because published examples likely represent the tip of the iceberg in terms of the total extent of ancient hybridization. However, future research should increasingly explore the macroevolutionary significance of this process, in terms of its impact on evolutionary trajectories (e.g. how does hybridization influence trait evolution or the generation of biodiversity over long time scales?), as well as how life history and ecological factors shape, or have shaped, the frequency of hybridization across geologic time and plant phylogeny. Finally, we consider the implications of ubiquitous ancient hybridization for how we conceptualize, analyze, and classify plant phylogeny. Networks, as opposed to bifurcating trees, represent more accurate representations of evolutionary history in many cases, although our ability to infer, visualize, and use networks for comparative analyses is highly limited. Developing improved methods for the generation, visualization, and use of networks represents a critical future direction for plant biology. Current classification systems also do not generally allow for the recognition of reticulate lineages, and our classifications themselves are largely based on evidence from the chloroplast genome. Updating plant classification to better reflect nuclear phylogenies, as well as considering whether and how to recognize hybridization in classification systems, will represent an important challenge for the plant systematics community.
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Affiliation(s)
- Gregory W Stull
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013, USA
| | - Kasey K Pham
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
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46
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Buswell VG, Ellis JS, Huml JV, Wragg D, Barnett MW, Brown A, Knight ME. When One's Not Enough: Colony Pool-Seq Outperforms Individual-Based Methods for Assessing Introgression in Apis mellifera mellifera. INSECTS 2023; 14:insects14050421. [PMID: 37233049 DOI: 10.3390/insects14050421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 05/27/2023]
Abstract
The human management of honey bees (Apis mellifera) has resulted in the widespread introduction of subspecies outside of their native ranges. One well known example of this is Apis mellifera mellifera, native to Northern Europe, which has now been significantly introgressed by the introduction of C lineage honey bees. Introgression has consequences for species in terms of future adaptive potential and long-term viability. However, estimating introgression in colony-living haplodiploid species is challenging. Previous studies have estimated introgression using individual workers, individual drones, multiple drones, and pooled workers. Here, we compare introgression estimates via three genetic approaches: SNP array, individual RAD-seq, and pooled colony RAD-seq. We also compare two statistical approaches: a maximum likelihood cluster program (ADMIXTURE) and an incomplete lineage sorting model (ABBA BABA). Overall, individual approaches resulted in lower introgression estimates than pooled colonies when using ADMIXTURE. However, the pooled colony ABBA BABA approach resulted in generally lower introgression estimates than all three ADMIXTURE estimates. These results highlight that sometimes one individual is not enough to assess colony-level introgression, and future studies that do use colony pools should not be solely dependent on clustering programs for introgression estimates.
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Affiliation(s)
- Victoria G Buswell
- School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
- Information and Computational Sciences, The James Hutton Institute, Dundee DD2 5DA, UK
| | - Jonathan S Ellis
- School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
| | - J Vanessa Huml
- School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
| | - David Wragg
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Roslin EH25 9RG, UK
- Beebytes Analytics CIC, Roslin Innovation Centre, Easter Bush Campus, Roslin EH25 9RG, UK
| | - Mark W Barnett
- Beebytes Analytics CIC, Roslin Innovation Centre, Easter Bush Campus, Roslin EH25 9RG, UK
| | - Andrew Brown
- B4, Newton Farm Metherell, Cornwall, Callington PL17 8DQ, UK
| | - Mairi E Knight
- School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
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47
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Cullingham C, Peery RM, Miller JM. A roadmap to robust discriminant analysis of principal components. Mol Ecol Resour 2023; 23:519-522. [PMID: 36282622 DOI: 10.1111/1755-0998.13724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/14/2022] [Accepted: 10/21/2022] [Indexed: 10/31/2022]
Abstract
Identification of population structure is a common goal for a variety of applications, including conservation, wildlife management, and medical genetics. The outcome of these analyses can have far reaching implications; therefore, it is important to ensure an understanding of the strengths and weaknesses of the methodologies used. Increasing in popularity, the discriminant analysis of principal components (DAPC) method incorporates combinations of genetic variables (alleles) into a model that differentiates individuals into genetic clusters. However, users may not have a full understanding of how to best parameterize the model. In this issue of Thia (Molecular Ecology Resources, 2022) looks under the hood of the DAPC. Using simulated data, he demonstrates the importance of careful parameter selection in developing a DAPC model, what the implications are for over-fitting the model, and finally, how best to evaluate the results of DAPC models. This work highlights the issues that can arise when over-parameterizing the DAPC model when gene flow is high among clusters and provides important guidelines to ensure researchers are making conclusions that are biologically relevant.
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Affiliation(s)
| | - Rhiannon M Peery
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Joshua M Miller
- Biological Sciences, MacEwan University, Edmonton, Alberta, Canada
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48
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Wilmot H, Druet T, Hulsegge I, Gengler N, Calus M. Estimation of inbreeding, between-breed genomic relatedness and definition of sub-populations in red-pied cattle breeds. Animal 2023; 17:100793. [PMID: 37087997 DOI: 10.1016/j.animal.2023.100793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 03/16/2023] [Accepted: 03/21/2023] [Indexed: 03/31/2023] Open
Abstract
Currently, enhancing the collaboration between related breeds is of main importance to increase the competitivity and the sustainability of local breeds. One type of collaboration is the development of an across-breed reference population that will allow a better management of local breeds. For this purpose, the genomic relatedness between the local target breed and possible breeds to be included in the reference population should be estimated. In Europe, there are several local red-pied cattle breeds that would benefit from this kind of collaboration. However, how different red-pied cattle breeds from the Benelux are related to each other and can collaborate is still unclear. The objectives of this study were therefore: (1) to estimate the level of inbreeding of the East Belgian Red and White (EBRW), the Red-Pied of the Ösling (RPO) and Dutch red-pied cattle breeds; (2) to determine the genomic relatedness of several red-pied cattle breeds, with a special focus on two endangered breeds: the EBRW and the RPO, and (3) based on the second objective, to detect animals from other breeds that were genomically close enough to be considered as advantageous in the creation of an across-breed reference population of EBRW or RPO. The estimated inbreeding levels based on runs of homozygosity were relatively low for almost all the studied breeds and especially for the EBRW and RPO. This would imply that inbreeding is currently not an issue in these two endangered breeds and that their sustainability is not threatened by their level of inbreeding. The results from the principal component analysis, the phylogenetic tree and the clustering all highlighted that the EBRW and RPO breeds were included in the genomic continuum of the studied red-pied cattle breeds and can be therefore considered as genomically close to Dutch red-pied cattle breeds, highlighting the possibility of a collaboration between these breeds. Especially, EBRW animals were closely related to Deep Red and Improved Red animals while, to a lesser extent, the RPO animals were closely related to the Meuse-Rhine-Yssel breed. Based on these results, we could use distance measures, based either on the principal component analysis or clustering, to detect animals from Dutch breeds that were genomically closest to the EBRW or RPO breeds. This will finally allow the building of an across-breed reference population for EBRW or RPO for further genomic evaluations, considering these genomically closest animals from other breeds.
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49
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Boria RA, Blois JL. Phylogeography within the Peromyscus maniculatus species group: Understanding past distribution of genetic diversity and areas of refugia in western North America. Mol Phylogenet Evol 2023; 180:107701. [PMID: 36623612 DOI: 10.1016/j.ympev.2023.107701] [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: 06/30/2022] [Revised: 12/09/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023]
Abstract
The effects of anthropogenic climate change on biodiversity have been recognized on every continent, ocean, and across different taxonomic groups. Here, we study the range dynamics and demography of a cosmopolitan species: the deer mouse, Peromyscus maniculatus. We generated a multilocus SNP dataset using the ddRADseq protocol for 218 individuals across the geographic range within three western North American lineages of this species group. We evaluated population structure using several methods and explored the correlation between geographic and genetic distances. We modeled the demographic history using a site frequency spectrum approach and used a machine learning algorithm to infer current and past (Last Glacial Maximum; LGM) environmental suitability. Lastly, we explored the origin of population expansion for the identified lineages. The genome-wide SNP dataset was able to identify-three regionally distinct groups- 1) P. m. gambelii (southern California); 2) P. keeni (Pacific Northwest); 3) P. m. sonoriensis (a broad population spanning the Pacific Northwest through central California and across the Rocky Mountains into the Great Plains). Demographic analysis indicated the splits between the three populations occurred within the last 500 thousand years, with one very recent (late Holocene) split. Ecological niche models for each of these lineages predicted suitable environment present throughout their known ranges for current conditions, and a severe reduction of northern habitat in the past. The deer mouse has responded to past climate changes by expanding its range during interglacial periods and contracting its range during glacial periods leading to strong population differentiation. But lower magnitude climate change or other processes within the Holocene interglacial period led to population differentiation as well, which is likely still ongoing today given the substantial anthropogenic climate change and other landscape transformations caused by humans during the Anthropocene. By understanding the historical processes that led to the contemporary geographic distribution of biodiversity, we can determine the relative importance of different factors that shape biodiversity, now and into the future.
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Affiliation(s)
- Robert A Boria
- School of Natural Sciences, University of California- Merced, Merced, CA 95343, USA; Present address: Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Jessica L Blois
- School of Natural Sciences, University of California- Merced, Merced, CA 95343, USA
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50
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Luqman H, Wegmann D, Fior S, Widmer A. Climate-induced range shifts drive adaptive response via spatio-temporal sieving of alleles. Nat Commun 2023; 14:1080. [PMID: 36841810 PMCID: PMC9968346 DOI: 10.1038/s41467-023-36631-9] [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: 06/17/2022] [Accepted: 02/09/2023] [Indexed: 02/27/2023] Open
Abstract
Quaternary climate fluctuations drove many species to shift their geographic ranges, in turn shaping their genetic structures. Recently, it has been argued that adaptation may have accompanied species range shifts via the "sieving" of genotypes during colonisation and establishment. However, this has not been directly demonstrated, and knowledge remains limited on how different evolutionary forces, which are typically investigated separately, interacted to jointly mediate species responses to past climatic change. Here, through whole-genome re-sequencing of over 1200 individuals of the carnation Dianthus sylvestris coupled with integrated population genomic and gene-environment models, we reconstruct the past neutral and adaptive landscape of this species as it was shaped by the Quaternary glacial cycles. We show that adaptive responses emerged concomitantly with the post-glacial range shifts and expansions of this species in the last 20 thousand years. This was due to the heterogenous sieving of adaptive alleles across space and time, as populations expanded out of restrictive glacial refugia into the broader and more heterogeneous range of habitats available in the present-day inter-glacial. Our findings reveal a tightly-linked interplay of migration and adaptation under past climate-induced range shifts, which we show is key to understanding the spatial patterns of adaptive variation we see in species today.
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Affiliation(s)
- Hirzi Luqman
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland. .,McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK.
| | - Daniel Wegmann
- Department of Biology, University of Fribourg, Fribourg, Switzerland.,Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Simone Fior
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland.
| | - Alex Widmer
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland.
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