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Kang Y, Wang Z, An K, Hou Q, Zhang Z, Su J. Introgression drives adaptation to the plateau environment in a subterranean rodent. BMC Biol 2024; 22:187. [PMID: 39218870 PMCID: PMC11368017 DOI: 10.1186/s12915-024-01986-y] [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: 01/27/2024] [Accepted: 08/18/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND Introgression has repeatedly been shown to play an important role in the adaptation of species to extreme environments, yet how introgression enables rodents with specialized subterranean lifestyle to acclimatize to high altitudes is still unclear. Myospalacinae is a group of subterranean rodents, among which the high-altitude plateau zokors (Eospalax baileyi) and the low-altitude Gansu zokors (E. cansus) are sympatrically distributed in the grassland ecosystems of the Qinghai-Tibet Plateau (QTP). Together, they provide a model for the study of the role of introgression in the adaptation of low-altitude subterranean rodents to high altitudes. RESULTS Applying low-coverage whole-genome resequencing and population genetics analyses, we identified evidence of adaptive introgression from plateau zokors into Gansu zokors, which likely facilitated the adaptation of the latter to the high-altitude environment of the QTP. We identified positively selected genes with functions related to energy metabolism, cardiovascular system development, calcium ion transport, and response to hypoxia which likely made critical contributions to adaptation to the plateau environment in both plateau zokors and high-altitude populations of Gansu zokors. CONCLUSIONS Introgression of genes associated with hypoxia adaptation from plateau zokors may have played a role in the adaptation of Gansu zokors to the plateau environment. Our study provides new insights into the understanding of adaptive evolution of species on the QTP and the importance of introgression in the adaptation of species to high-altitude environments.
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Affiliation(s)
- Yukun Kang
- College of Grassland Science, Key Laboratory of Grassland Ecosystem (Ministry of Education), Gansu Agricultural University, Lanzhou, 730070, China
- Gansu Agricultural University-Massey University Research Centre for Grassland Biodiversity, Gansu Agricultural University, Lanzhou, 730070, China
| | - Zhicheng Wang
- College of Grassland Science, Key Laboratory of Grassland Ecosystem (Ministry of Education), Gansu Agricultural University, Lanzhou, 730070, China
- Gansu Agricultural University-Massey University Research Centre for Grassland Biodiversity, Gansu Agricultural University, Lanzhou, 730070, China
| | - Kang An
- College of Grassland Science, Key Laboratory of Grassland Ecosystem (Ministry of Education), Gansu Agricultural University, Lanzhou, 730070, China
- Gansu Agricultural University-Massey University Research Centre for Grassland Biodiversity, Gansu Agricultural University, Lanzhou, 730070, China
| | - Qiqi Hou
- College of Grassland Science, Key Laboratory of Grassland Ecosystem (Ministry of Education), Gansu Agricultural University, Lanzhou, 730070, China
- Gansu Agricultural University-Massey University Research Centre for Grassland Biodiversity, Gansu Agricultural University, Lanzhou, 730070, China
| | - Zhiming Zhang
- College of Grassland Science, Key Laboratory of Grassland Ecosystem (Ministry of Education), Gansu Agricultural University, Lanzhou, 730070, China
- Gansu Agricultural University-Massey University Research Centre for Grassland Biodiversity, Gansu Agricultural University, Lanzhou, 730070, China
| | - Junhu Su
- College of Grassland Science, Key Laboratory of Grassland Ecosystem (Ministry of Education), Gansu Agricultural University, Lanzhou, 730070, China.
- Gansu Agricultural University-Massey University Research Centre for Grassland Biodiversity, Gansu Agricultural University, Lanzhou, 730070, China.
- Gansu Qilianshan Grassland Ecosystem Observation and Research Station, Wuwei, 733200, China.
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2
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Augustijnen H, Lucek K. Beyond gene flow: (non)-parallelism of secondary contact in a pair of highly differentiated sibling species. Mol Ecol 2024; 33:e17488. [PMID: 39119885 DOI: 10.1111/mec.17488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 07/01/2024] [Accepted: 07/10/2024] [Indexed: 08/10/2024]
Abstract
Replicated secondary contact zones can provide insights into the barriers to gene flow that are important during speciation and can reveal to which degree secondary contact may result in similar evolutionary outcomes. Here, we studied two secondary contact zones between highly differentiated Alpine butterflies of the genus Erebia using whole-genome resequencing data. We assessed the genomic relationships between populations and species and found hybridization to be rare, with no to little current or historical introgression in either contact zone. There are large similarities between contact zones, consistent with an allopatric origin of interspecific differentiation, with no indications for ongoing reinforcing selection. Consistent with expected reduced effective population size, we further find that scaffolds related to the Z-chromosome show increased differentiation compared to the already high levels across the entire genome, which could also hint towards a contribution of the Z chromosome to species divergence in this system. Finally, we detected the presence of the endosymbiont Wolbachia, which can cause reproductive isolation between its hosts, in all E. cassioides, while it appears to be fully or largely absent in contact zone populations of E. tyndarus. We discuss how this rare pattern may have arisen and how it may have affected the dynamics of speciation upon secondary contact.
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Affiliation(s)
- Hannah Augustijnen
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Kay Lucek
- Biodiversity Genomics Laboratory, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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3
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Horníková M, Lanier HC, Marková S, Escalante MA, Searle JB, Kotlík P. Genetic admixture drives climate adaptation in the bank vole. Commun Biol 2024; 7:863. [PMID: 39009753 PMCID: PMC11251159 DOI: 10.1038/s42003-024-06549-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 07/03/2024] [Indexed: 07/17/2024] Open
Abstract
Genetic admixture introduces new variants at relatively high frequencies, potentially aiding rapid responses to environmental changes. Here, we evaluate its role in adaptive variation related to climatic conditions in bank voles (Clethrionomys glareolus) in Britain, using whole-genome data. Our results reveal loci showing excess ancestry from one of the two postglacial colonist populations inconsistent with overall admixture patterns. Notably, loci associated with climate adaptation exhibit disproportionate amounts of excess ancestry, highlighting the impact of admixture between colonist populations on local adaptation. The results suggest strong and localized selection on climate-adaptive loci, as indicated by steep clines and/or shifted cline centres, during population replacement. A subset, including a haemoglobin gene, is associated with oxidative stress responses, underscoring a role of oxidative stress in local adaptation. Our study highlights the important contribution of admixture during secondary contact between populations from distinct climatic refugia enriching adaptive diversity. Understanding these dynamics is crucial for predicting future adaptive capacity to anthropogenic climate change.
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Affiliation(s)
- Michaela Horníková
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Hayley C Lanier
- Department of Biology, Program in Ecology & Evolutionary Biology, University of Oklahoma, Norman, OK, USA
- Sam Noble Museum, University of Oklahoma, Norman, OK, USA
| | - Silvia Marková
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Marco A Escalante
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Petr Kotlík
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic.
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4
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Wray A, Petrou E, Nichols KM, Pacunski R, LeClair L, Andrews KS, Kardos M, Hauser L. Contrasting effect of hybridization on genetic differentiation in three rockfish species with similar life history. Evol Appl 2024; 17:e13749. [PMID: 39035131 PMCID: PMC11259572 DOI: 10.1111/eva.13749] [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: 02/13/2023] [Revised: 06/21/2024] [Accepted: 06/25/2024] [Indexed: 07/23/2024] Open
Abstract
Hybridization can provide evolutionary benefits (e.g., population resilience to climate change) through the introduction of adaptive alleles and increase of genetic diversity. Nevertheless, management strategies may be designed based only on the parental species within a hybrid zone, without considering the hybrids. This can lead to ineffective spatial management of species, which can directly harm population diversity and negatively impact food webs. Three species of rockfish (Brown Rockfish (Sebastes caurinus), Copper Rockfish (S. auriculatus), and Quillback Rockfish (S. maliger)) are known to hybridize within Puget Sound, Washington, but genetic data from these species are used to infer population structure in the entire genus, including in species that do not hybridize. The goal of this project was to estimate the hybridization rates within the region and determine the effect of hybridization on geographic patterns of genetic structure. We sequenced 290 Brown, Copper, and Quillback rockfish using restriction-site associated DNA sequencing (RADseq) from four regions within and outside Puget Sound, Washington. We show that (i) hybridization within Puget Sound was asymmetrical, not recent, widespread among individuals, and relatively low level within the genome, (ii) hybridization affected population structure in Copper and Brown rockfish, but not in Quillback Rockfish and (iii) after taking hybridization into account we found limited directional dispersal in Brown and Copper rockfish, and evidence for two isolated populations in Quillback Rockfish. Our results suggest that rockfish population structure is species-specific, dependent on the extent of hybridization, and cannot be inferred from one species to another despite similar life history.
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Affiliation(s)
- Anita Wray
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWashingtonUSA
| | - Eleni Petrou
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWashingtonUSA
- Present address:
United States Geological Survey, Alaska Science CenterAnchorageAlaskaUSA
| | - Krista M. Nichols
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAASeattleWashingtonUSA
| | - Robert Pacunski
- Washington Department of Fish and WildlifeOlympiaWashingtonUSA
| | - Larry LeClair
- Washington Department of Fish and WildlifeOlympiaWashingtonUSA
| | - Kelly S. Andrews
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAASeattleWashingtonUSA
| | - Marty Kardos
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAASeattleWashingtonUSA
| | - Lorenz Hauser
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWashingtonUSA
- Zoology DepartmentNelson Mandela UniversityGqeberhaSouth Africa
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5
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Bolte CE, Phannareth T, Zavala-Paez M, Sutara BN, Can MF, Fitzpatrick MC, Holliday JA, Keller SR, Hamilton JA. Genomic insights into hybrid zone formation: The role of climate, landscape, and demography in the emergence of a novel hybrid lineage. Mol Ecol 2024; 33:e17430. [PMID: 38867593 DOI: 10.1111/mec.17430] [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: 02/21/2024] [Revised: 05/24/2024] [Accepted: 05/30/2024] [Indexed: 06/14/2024]
Abstract
Population demographic changes, alongside landscape, geographic and climate heterogeneity, can influence the timing, stability and extent of introgression where species hybridise. Thus, quantifying interactions across diverged lineages, and the relative contributions of interspecific genetic exchange and selection to divergence at the genome-wide level is needed to better understand the drivers of hybrid zone formation and maintenance. We used seven latitudinally arrayed transects to quantify the contributions of climate, geography and landscape features to broad patterns of genetic structure across the hybrid zone of Populus trichocarpa and P. balsamifera and evaluated the demographic context of hybridisation over time. We found genetic structure differed among the seven transects. While ancestry was structured by climate, landscape features influenced gene flow dynamics. Demographic models indicated a secondary contact event may have influenced contemporary hybrid zone formation with the origin of a putative hybrid lineage that inhabits regions with higher aridity than either of the ancestral groups. Phylogenetic relationships based on chloroplast genomes support the origin of this hybrid lineage inferred from demographic models based on the nuclear data. Our results point towards the importance of climate and landscape patterns in structuring the contact zones between P. trichocarpa and P. balsamifera and emphasise the value whole genome sequencing can have to advancing our understanding of how neutral processes influence divergence across space and time.
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Affiliation(s)
- Constance E Bolte
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Tommy Phannareth
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, Virginia, USA
| | - Michelle Zavala-Paez
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Brianna N Sutara
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | | | - Matthew C Fitzpatrick
- Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, Maryland, USA
| | - Jason A Holliday
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, Virginia, USA
| | - Stephen R Keller
- Department of Plant Biology, University of Vermont, Burlington, Vermont, USA
| | - Jill A Hamilton
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, Pennsylvania, USA
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6
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Münger X, Robin M, Dalén L, Grossen C. Facilitated introgression from domestic goat into Alpine ibex at immune loci. Mol Ecol 2024; 33:e17429. [PMID: 38847234 DOI: 10.1111/mec.17429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 04/29/2024] [Accepted: 05/08/2024] [Indexed: 07/09/2024]
Abstract
Hybridization can result in the transfer of adaptive genetic material from one species to another, known as adaptive introgression. Bottlenecked (and hence genetically depleted) species are expected to be particularly receptive to adaptive introgression, since introgression can introduce new or previously lost adaptive genetic variation. The Alpine ibex (Capra ibex), which recently recovered from near extinction, is known to hybridize with the domestic goat (Capra aegagrus hircus), and signals of introgression previously found at the major histocompatibility complex were suggested to potentially be adaptive. Here, we combine two ancient whole genomes of Alpine ibex with 29 modern Alpine ibex genomes and 31 genomes representing six related Capra species to investigate the genome-wide patterns of introgression and confirm the potential relevance of immune loci. We identified low rates of admixture in modern Alpine ibex through various F statistics and screening for putative introgressed tracts. Further results based on demographic modelling were consistent with introgression to have occurred during the last 300 years, coinciding with the known species bottleneck, and that in each generation, 1-2 out of 100 Alpine ibex had a domestic goat parent. The putatively introgressed haplotypes were enriched at immune-related genes, where the adaptive value of alternative alleles may give individuals with otherwise depleted genetic diversity a selective advantage. While interbreeding with domestic species is a prevalent issue in species conservation, in this specific case, it resulted in putative adaptive introgression. Our findings highlight the complex interplay between hybridization, adaptive evolution, and the potential risks and benefits associated with anthropogenic influences on wild species.
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Affiliation(s)
- Xenia Münger
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Mathieu Robin
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Love Dalén
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Christine Grossen
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- WSL Swiss Federal Research Institute, Birmensdorf, Switzerland
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7
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Zhang F, Long R, Ma Z, Xiao H, Xu X, Liu Z, Wei C, Wang Y, Peng Y, Yang X, Shi X, Cao S, Li M, Xu M, He F, Jiang X, Zhang T, Wang Z, Li X, Yu LX, Kang J, Zhang Z, Zhou Y, Yang Q. Evolutionary genomics of climatic adaptation and resilience to climate change in alfalfa. MOLECULAR PLANT 2024; 17:867-883. [PMID: 38678365 DOI: 10.1016/j.molp.2024.04.013] [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: 12/11/2023] [Revised: 04/09/2024] [Accepted: 04/24/2024] [Indexed: 04/29/2024]
Abstract
Given the escalating impact of climate change on agriculture and food security, gaining insights into the evolutionary dynamics of climatic adaptation and uncovering climate-adapted variation can empower the breeding of climate-resilient crops to face future climate change. Alfalfa (Medicago sativa subsp. sativa), the queen of forages, shows remarkable adaptability across diverse global environments, making it an excellent model for investigating species responses to climate change. In this study, we performed population genomic analyses using genome resequencing data from 702 accessions of 24 Medicago species to unravel alfalfa's climatic adaptation and genetic susceptibility to future climate change. We found that interspecific genetic exchange has contributed to the gene pool of alfalfa, particularly enriching defense and stress-response genes. Intersubspecific introgression between M. sativa subsp. falcata (subsp. falcata) and alfalfa not only aids alfalfa's climatic adaptation but also introduces genetic burden. A total of 1671 genes were associated with climatic adaptation, and 5.7% of them were introgressions from subsp. falcata. By integrating climate-associated variants and climate data, we identified populations that are vulnerable to future climate change, particularly in higher latitudes of the Northern Hemisphere. These findings serve as a clarion call for targeted conservation initiatives and breeding efforts. We also identified pre-adaptive populations that demonstrate heightened resilience to climate fluctuations, illuminating a pathway for future breeding strategies. Collectively, this study enhances our understanding about the local adaptation mechanisms of alfalfa and facilitates the breeding of climate-resilient alfalfa cultivars, contributing to effective agricultural strategies for facing future climate change.
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Affiliation(s)
- Fan Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Ruicai Long
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhiyao Ma
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Hua Xiao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Xiaodong Xu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Zhongjie Liu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Chunxue Wei
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Yiwen 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 518000, China
| | - Yanling Peng
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Xuanwen Yang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Xiaoya Shi
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Shuo Cao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Mingna Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ming Xu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fei He
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xueqian Jiang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tiejun Zhang
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China
| | - Zhen Wang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Xianran Li
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163, USA
| | - Long-Xi Yu
- U.S. Department of Agriculture-Agricultural Research Service, Plant Germplasm Introduction and Testing Research, Prosser, WA 99350, USA
| | - Junmei Kang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhiwu Zhang
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163, USA
| | - Yongfeng Zhou
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China; National Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Qingchuan Yang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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8
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Maier PA, Vandergast AG, Bohonak AJ. Yosemite toad (Anaxyrus canorus) transcriptome reveals interplay between speciation genes and adaptive introgression. Mol Ecol 2024; 33:e17317. [PMID: 38488670 DOI: 10.1111/mec.17317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 02/15/2024] [Accepted: 02/23/2024] [Indexed: 04/09/2024]
Abstract
Genomes are heterogeneous during the early stages of speciation, with small 'islands' of DNA appearing to reflect strong adaptive differences, surrounded by vast seas of relative homogeneity. As species diverge, secondary contact zones between them can act as an interface and selectively filter through advantageous alleles of hybrid origin. Such introgression is another important adaptive process, one that allows beneficial mosaics of recombinant DNA ('rivers') to flow from one species into another. Although genomic islands of divergence appear to be associated with reproductive isolation, and genomic rivers form by adaptive introgression, it is unknown whether islands and rivers tend to be the same or different loci. We examined three replicate secondary contact zones for the Yosemite toad (Anaxyrus canorus) using two genomic data sets and a morphometric data set to answer the questions: (1) How predictably different are islands and rivers, both in terms of genomic location and gene function? (2) Are the adaptive genetic trait loci underlying tadpole growth and development reliably islands, rivers or neither? We found that island and river loci have significant overlap within a contact zone, suggesting that some loci are first islands, and later are predictably converted into rivers. However, gene ontology enrichment analysis showed strong overlap in gene function unique to all island loci, suggesting predictability in overall gene pathways for islands. Genome-wide association study outliers for tadpole development included LPIN3, a lipid metabolism gene potentially involved in climate change adaptation, that is island-like for all three contact zones, but also appears to be introgressing (as a river) across one zone. Taken together, our results suggest that adaptive divergence and introgression may be more complementary forces than currently appreciated.
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Affiliation(s)
- Paul A Maier
- Department of Biology, San Diego State University, San Diego, California, USA
- Family TreeDNA, Gene by Gene, Houston, Texas, USA
| | - Amy G Vandergast
- Western Ecological Research Center, San Diego Field Station, U.S. Geological Survey, San Diego, California, USA
| | - Andrew J Bohonak
- Department of Biology, San Diego State University, San Diego, California, USA
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9
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Touchette L, Godbout J, Lamothe M, Porth I, Isabel N. A cryptic syngameon within Betula shrubs revealed: Implications for conservation in changing subarctic environments. Evol Appl 2024; 17:e13689. [PMID: 38633131 PMCID: PMC11022622 DOI: 10.1111/eva.13689] [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: 08/08/2023] [Revised: 02/06/2024] [Accepted: 03/20/2024] [Indexed: 04/19/2024] Open
Abstract
Arctic and subarctic ecosystems are rapidly transforming due to global warming, emphasizing the need to understand the genetic diversity and adaptive strategies of northern plant species for effective conservation. This study focuses on Betula glandulosa, a native North American tundra shrub known as dwarf birch, which demonstrates an apparent capacity to adapt to changing climate conditions. To address the taxonomic challenges associated with shrub birches and logistical complexities of sampling in the northernmost areas where species' ranges overlap, we adopted a multicriteria approach. Incorporating molecular data, ploidy level assessment and leaf morphology, we aimed to distinguish B. glandulosa individuals from other shrub birch species sampled. Our results revealed three distinct species and their hybrids within the 537 collected samples, suggesting the existence of a shrub birch syngameon, a reproductive network of interconnected species. Additionally, we identified two discrete genetic clusters within the core species, B. glandulosa, that likely correspond to two different glacial lineages. A comparison between the nuclear and chloroplast SNP data emphasizes a long history of gene exchange between different birch species and genetic clusters. Furthermore, our results highlight the significance of incorporating interfertile congeneric species in conservation strategies and underscores the need for a holistic approach to conservation in the context of climate change, considering the complex dynamics of species interactions. While further research will be needed to describe this shrub birches syngameon and its constituents, this study is a first step in recognizing its existence and disseminating awareness among ecologists and conservation practitioners. This biological phenomenon, which offers evolutionary flexibility and resilience beyond what its constituent species can achieve individually, may have significant ecological implications.
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Affiliation(s)
- Lyne Touchette
- Department of Wood and Forest SciencesUniversité LavalQuebecQuebecCanada
- Natural Resources Canada, Canadian Forest ServiceLaurentian Forestry CentreQuebecQuebecCanada
- Centre for Forest ResearchUniversité LavalQuebecQuebecCanada
| | - Julie Godbout
- Ministère des Ressources naturelles et des Forêts, Direction de la recherche forestièreQuébecQuébecCanada
| | - Manuel Lamothe
- Natural Resources Canada, Canadian Forest ServiceLaurentian Forestry CentreQuebecQuebecCanada
| | - Ilga Porth
- Department of Wood and Forest SciencesUniversité LavalQuebecQuebecCanada
- Centre for Forest ResearchUniversité LavalQuebecQuebecCanada
| | - Nathalie Isabel
- Natural Resources Canada, Canadian Forest ServiceLaurentian Forestry CentreQuebecQuebecCanada
- Centre for Forest ResearchUniversité LavalQuebecQuebecCanada
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10
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Iverson ENK. Conservation Mitonuclear Replacement: Facilitated mitochondrial adaptation for a changing world. Evol Appl 2024; 17:e13642. [PMID: 38468713 PMCID: PMC10925831 DOI: 10.1111/eva.13642] [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: 10/23/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 03/13/2024] Open
Abstract
Most species will not be able to migrate fast enough to cope with climate change, nor evolve quickly enough with current levels of genetic variation. Exacerbating the problem are anthropogenic influences on adaptive potential, including the prevention of gene flow through habitat fragmentation and the erosion of genetic diversity in small, bottlenecked populations. Facilitated adaptation, or assisted evolution, offers a way to augment adaptive genetic variation via artificial selection, induced hybridization, or genetic engineering. One key source of genetic variation, particularly for climatic adaptation, are the core metabolic genes encoded by the mitochondrial genome. These genes influence environmental tolerance to heat, drought, and hypoxia, but must interact intimately and co-evolve with a suite of important nuclear genes. These coadapted mitonuclear genes form some of the important reproductive barriers between species. Mitochondrial genomes can and do introgress between species in an adaptive manner, and they may co-introgress with nuclear genes important for maintaining mitonuclear compatibility. Managers should consider the relevance of mitonuclear genetic variability in conservation decision-making, including as a tool for facilitating adaptation. I propose a novel technique dubbed Conservation Mitonuclear Replacement (CmNR), which entails replacing the core metabolic machinery of a threatened species-the mitochondrial genome and key nuclear loci-with those from a closely related species or a divergent population, which may be better-adapted to climatic changes or carry a lower genetic load. The most feasible route to CmNR is to combine CRISPR-based nuclear genetic editing with mitochondrial replacement and assisted reproductive technologies. This method preserves much of an organism's phenotype and could allow populations to persist in the wild when no other suitable conservation options exist. The technique could be particularly important on mountaintops, where rising temperatures threaten an alarming number of species with almost certain extinction in the next century.
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Affiliation(s)
- Erik N. K. Iverson
- Department of Integrative BiologyThe University of Texas at AustinAustinTexasUSA
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11
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Kulmuni J, Wiley B, Otto SP. On the fast track: hybrids adapt more rapidly than parental populations in a novel environment. Evol Lett 2024; 8:128-136. [PMID: 38370548 PMCID: PMC10871894 DOI: 10.1093/evlett/qrad002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 12/22/2022] [Accepted: 01/26/2023] [Indexed: 02/20/2024] Open
Abstract
Rates of hybridization are predicted to increase due to climate change and human activity that cause redistribution of species and bring previously isolated populations into contact. At the same time climate change leads to rapid changes in the environment, requiring populations to adapt rapidly in order to survive. A few empirical cases suggest hybridization can facilitate adaptation despite its potential for incompatibilities and deleterious fitness consequences. Here we use simulations and Fisher's Geometric model to evaluate the conditions and time frame of adaptation via hybridization in both diploids and haplodiploids. We find that hybrids adapt faster to new environments compared to parental populations in nearly all simulated scenarios, generating a fitness advantage that can offset intrinsic incompatibilities and last for tens of generations, regardless of whether the population was diploid or haplodiploid. Our results highlight the creative role of hybridization and suggest that hybridization may help contemporary populations adapt to the changing climate. However, adaptation by hybrids may well happen at the cost of reduced biodiversity, if previously isolated lineages collapse into one.
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Affiliation(s)
- Jonna Kulmuni
- Organismal & Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
- Tvärminne Zoological Station, University of Helsinki, Hanko, Finland
- Institute for Biodiversity and Ecosystem Dynamics, Department of Evolutionary and Population Biology, University of Amsterdam, Amsterdam, The Netherlands
| | - Bryn Wiley
- Department of Zoology and Biodiversity Research Center, University of British Columbia, Vancouver, Canada
| | - Sarah P Otto
- Department of Zoology and Biodiversity Research Center, University of British Columbia, Vancouver, Canada
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12
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Radušienė J, Karpavičienė B, Vilkickytė G, Marksa M, Raudonė L. Comparative Analysis of Root Phenolic Profiles and Antioxidant Activity of Five Native and Invasive Solidago L. Species. PLANTS (BASEL, SWITZERLAND) 2024; 13:132. [PMID: 38202440 PMCID: PMC10780316 DOI: 10.3390/plants13010132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 12/30/2023] [Accepted: 12/31/2023] [Indexed: 01/12/2024]
Abstract
The high environmental importance of invasive goldenrod has prompted research to find potential benefits that can be derived from these species. This study aimed to identify differences in root phenolic profiles among five Solidago species, thus providing valuable information on their potential applications and the botanical origin of the raw material. The roots of native S. virgaurea L., two alien species S. gigantea Aiton and S. canadensis L. and their hybrids S. ×niederederi Khek and S. ×snarskisii Gudž. & Žaln. were sampled from mixed-species stands in Lithuania. A complex of twelve phenolic acids and their derivatives was identified and quantified in methanol-water root extracts using the HPLC-PDA and LC/MS systems. The radical-scavenging capacities of the extracts were assessed by ABTS. The chemical content of the roots of S. virgaurea, S. gigantea and S. ×niederederi were statistically similar, while the roots of S. canadensis and S. ×snarskisii contained lower amounts of compounds than the other species. The PCA score-plot models of the phenolic profiles only partially confirmed the identification of S. ×niederederi and S. ×snarskisii as crosses between native and alien species. The findings from the phenolic profiles and the observed radical-scavenging activity of root extracts of Solidago species provide valuable insights into their potential applications in various fields.
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Affiliation(s)
- Jolita Radušienė
- Laboratory of Economic Botany, Nature Research Centre, Akademijos Str. 2, 08412 Vilnius, Lithuania;
| | - Birutė Karpavičienė
- Laboratory of Economic Botany, Nature Research Centre, Akademijos Str. 2, 08412 Vilnius, Lithuania;
| | - Gabrielė Vilkickytė
- Laboratory of Biopharmaceutical Research, Institute of Pharmaceutical Technologies, Lithuanian University of Health Sciences, Sukileliu Av. 13, 50162 Kaunas, Lithuania; (G.V.); (L.R.)
- Department of Analytical and Toxicological Chemistry, Lithuanian University of Health Sciences, Sukileliu Av. 13, 50162 Kaunas, Lithuania;
| | - Mindaugas Marksa
- Department of Analytical and Toxicological Chemistry, Lithuanian University of Health Sciences, Sukileliu Av. 13, 50162 Kaunas, Lithuania;
| | - Lina Raudonė
- Laboratory of Biopharmaceutical Research, Institute of Pharmaceutical Technologies, Lithuanian University of Health Sciences, Sukileliu Av. 13, 50162 Kaunas, Lithuania; (G.V.); (L.R.)
- Department of Pharmacognosy, Lithuanian University of Health Sciences, Sukileliu Av. 13, 50162 Kaunas, Lithuania
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13
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Ålund M, Cenzer M, Bierne N, Boughman JW, Cerca J, Comerford MS, Culicchi A, Langerhans B, McFarlane SE, Möst MH, North H, Qvarnström A, Ravinet M, Svanbäck R, Taylor SA. Anthropogenic Change and the Process of Speciation. Cold Spring Harb Perspect Biol 2023; 15:a041455. [PMID: 37788888 PMCID: PMC10691492 DOI: 10.1101/cshperspect.a041455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Anthropogenic impacts on the environment alter speciation processes by affecting both geographical contexts and selection patterns on a worldwide scale. Here we review evidence of these effects. We find that human activities often generate spatial isolation between populations and thereby promote genetic divergence but also frequently cause sudden secondary contact and hybridization between diverging lineages. Human-caused environmental changes produce new ecological niches, altering selection in diverse ways that can drive diversification; but changes also often remove niches and cause extirpations. Human impacts that alter selection regimes are widespread and strong in magnitude, ranging from local changes in biotic and abiotic conditions to direct harvesting to global climate change. Altered selection, and evolutionary responses to it, impacts early-stage divergence of lineages, but does not necessarily lead toward speciation and persistence of separate species. Altogether, humans both promote and hinder speciation, although new species would form very slowly relative to anthropogenic hybridization, which can be nearly instantaneous. Speculating about the future of speciation, we highlight two key conclusions: (1) Humans will have a large influence on extinction and "despeciation" dynamics in the short term and on early-stage lineage divergence, and thus potentially speciation in the longer term, and (2) long-term monitoring combined with easily dated anthropogenic changes will improve our understanding of the processes of speciation. We can use this knowledge to preserve and restore ecosystems in ways that promote (re-)diversification, increasing future opportunities of speciation and enhancing biodiversity.
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Affiliation(s)
- Murielle Ålund
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala 75236, Sweden
| | - Meredith Cenzer
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
| | - Nicolas Bierne
- ISEM, Université de Montpellier, CNRS, IRD, Montpellier 34095, France
| | - Janette W Boughman
- Department of Integrative Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - José Cerca
- CEES - Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo 0316, Norway
| | | | - Alessandro Culicchi
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala 75236, Sweden
| | - Brian Langerhans
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - S Eryn McFarlane
- Department of Botany, University of Wyoming, Laramie, Wyoming 82071, USA
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada
| | - Markus H Möst
- Research Department for Limnology, University of Innsbruck, Innsbruck 6020, Austria
| | - Henry North
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
| | - Anna Qvarnström
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala 75236, Sweden
| | - Mark Ravinet
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Richard Svanbäck
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala 75236, Sweden
| | - Scott A Taylor
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado 80309, USA
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14
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Gao C, Wang K, Hu X, Lei Y, Xu C, Tian Y, Sun G, Tian Y, Kang X, Li W. Conservation priority and run of homozygosity pattern assessment of global chicken genetic resources. Poult Sci 2023; 102:103030. [PMID: 37716234 PMCID: PMC10511814 DOI: 10.1016/j.psj.2023.103030] [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: 05/19/2023] [Revised: 07/30/2023] [Accepted: 08/11/2023] [Indexed: 09/18/2023] Open
Abstract
The conservation of genetic resources is becoming increasingly important for the sustainable development of the poultry industry. In the present study, we systematically analyzed the population structure, conservation priority, runs of homozygosity (ROH) of chicken breeds globally, and proposed rational conservation strategies. We used a 600K Affymetrix Axiom HD genotyping SNP array dataset of 2,429 chickens from 134 populations. The chickens were divided into 5 groups based on their country of origin and sampling location: Asian chickens (AS-LOC), African chickens (AF), European local chickens (EU-LOC), Asian breeds sampled in Germany (AS-DE), and European breeds sampled in Germany (EU-DE). The results indicated that the population structure was consistent with the actual geographical distribution of the populations. AS-LOC had the highest positive contribution to the total gene (HT, 1.00%,) and allelic diversity (AT, 0.0014%), the lowest inbreeding degree and the fastest linkage disequilibrium (LD) decay rate; the lowest contribution are derived by European ex situ chicken breeds (EU-DE:HT = -0.072%, AT = -0.0014%), which showed the highest inbreeding and slowest LD decay. Breeds farmed in ex situ (AS-DE, EU-DE) conditions exhibited reduced genetic diversity and increased inbreeding due to small population size. Given limited funds, it is a better choice for government to conserve the breeds with the highest contribution to genetic diversity in each group. Therefore, we evaluated the contribution of each breed to genetic and allelic diversity in 5 groups. Among each group, KUR(AF), BANG(AS-LOC), ALxx(EU-LOC), BHwsch(AS-DE), and ARw(EU-DE) had the highest contribution to gene diversity in the order of the above grouping. Similarly, according to the allelic diversity standard (in the same order), ZIMxx, PIxx, ALxx, SHsch, and ARsch had the highest contribution. After analyzing ROH, we found a total of 144,708 fragments and 27 islands. The gene and genome regions identified by the ROH islands and QTLs indicate that chicken breeds have potential for adaptation to different production systems. Based on these findings, it is recommended to prioritize the conservation of breeds with the highest genetic diversity in each group, while paying more attention to the conservation of Asian and African breeds. Furthermore, providing a valuable reference for the conservation and utilization of chicken.
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Affiliation(s)
- Chaoqun Gao
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, Henan, China; The Shennong Laboratory, Zhengzhou 450046, Henan, China
| | - Kejun Wang
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, Henan, China; The Shennong Laboratory, Zhengzhou 450046, Henan, China
| | - Xiaoyu Hu
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, Henan, China; The Shennong Laboratory, Zhengzhou 450046, Henan, China
| | - Yanru Lei
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, Henan, China; The Shennong Laboratory, Zhengzhou 450046, Henan, China
| | - Chunhong Xu
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, Henan, China; The Shennong Laboratory, Zhengzhou 450046, Henan, China
| | - Yixiang Tian
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang 453003, Henan, China
| | - Guirong Sun
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, Henan, China; The Shennong Laboratory, Zhengzhou 450046, Henan, China
| | - Yadong Tian
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, Henan, China; The Shennong Laboratory, Zhengzhou 450046, Henan, China
| | - Xiangtao Kang
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, Henan, China; The Shennong Laboratory, Zhengzhou 450046, Henan, China
| | - Wenting Li
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, Henan, China; The Shennong Laboratory, Zhengzhou 450046, Henan, China.
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15
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Gawrońska B, Marszałek M, Kosiński P, Podsiedlik M, Bednorz L, Zeyland J. No wonder, it is a hybrid. Natural hybridization between Jacobaea vulgaris and J. erucifolia revealed by molecular marker systems and its potential ecological impact. Ecol Evol 2023; 13:e10467. [PMID: 37664498 PMCID: PMC10468328 DOI: 10.1002/ece3.10467] [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: 03/07/2023] [Revised: 08/09/2023] [Accepted: 08/18/2023] [Indexed: 09/05/2023] Open
Abstract
Progressive changes in the environment are related to modifications of the habitat. Introducing exotic species, and interbreeding between species can lead to processes that in the case of rare species or small populations threatens their integrity. Given the declining trends of many populations due to increased hybridization, early recognition of hybrids becomes important in conservation management. Natural hybridization is prevalent in Jacobaea. There are many naturally occurring interspecific hybrids in this genus, including those between Jacobaea vulgaris and its relatives. Although Jacobaea erucifolia and J. vulgaris often co-occur and are considered closely related, apart from the few reports of German botanists on the existence of such hybrids, there is no information on research confirming hybridization between them. Morphologically intermediate individuals, found in the sympatric distributions of J. vulgaris and J. erucifolia, were hypothesized to be their hybrids. Two molecular marker systems (nuclear and chloroplast DNA markers) were employed to test this hypothesis and characterize putative hybrids. Nuclear and chloroplast DNA sequencing results and taxon-specific amplified fragment length polymorphism (AFLP) fragment distribution analysis confirmed the hybrid nature of all 25 putative hybrids. The AFLP patterns of most hybrids demonstrated a closer relationship to J. erucifolia, suggesting frequent backcrossing. Moreover, they showed that several individuals previously described as pure were probably also of hybrid origin, backcrosses to J. erucifolia and J. vulgaris. This study provides the first molecular confirmation that natural hybrids between J. vulgaris and J. erucifolia occur in Poland. Hybridization appeared to be bidirectional but asymmetrical with J. vulgaris as the usual maternal parent.
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Affiliation(s)
- Barbara Gawrońska
- Department of Biochemistry and Biotechnology, Faculty of Agronomy, Horticulture and BioengineeringPoznań University of Life SciencesPoznańPoland
| | - Małgorzata Marszałek
- Department of Biochemistry and Biotechnology, Faculty of Agronomy, Horticulture and BioengineeringPoznań University of Life SciencesPoznańPoland
| | - Piotr Kosiński
- Department of Botany, Faculty of Agronomy, Horticulture and BioengineeringPoznań University of Life SciencesPoznańPoland
- Institute of DendrologyPolish Academy of SciencesKórnikPoland
| | - Marek Podsiedlik
- Natural History Collections, Faculty of BiologyAdam Mickiewicz University in PoznańPoznańPoland
| | - Leszek Bednorz
- Department of Botany, Faculty of Agronomy, Horticulture and BioengineeringPoznań University of Life SciencesPoznańPoland
| | - Joanna Zeyland
- Department of Biochemistry and Biotechnology, Faculty of Agronomy, Horticulture and BioengineeringPoznań University of Life SciencesPoznańPoland
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16
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Powell DM. Losing the forest for the tree? On the wisdom of subpopulation management. Zoo Biol 2023; 42:591-604. [PMID: 37218348 DOI: 10.1002/zoo.21776] [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: 07/19/2022] [Revised: 03/24/2023] [Accepted: 04/26/2023] [Indexed: 05/24/2023]
Abstract
Animal habitats are changing around the world in many ways, presenting challenges to the survival of species. Zoo animal populations are also challenged by small population sizes and limited genetic diversity. Some ex situ populations are managed as subpopulations based on presumed subspecies or geographic locality and related concerns over genetic purity or taxonomic integrity. However, these decisions can accelerate the loss of genetic diversity and increase the likelihood of population extinction. Here I challenge the wisdom of subpopulation management, pointing out significant concerns in the literature with delineation of species, subspecies, and evolutionarily significant units. I also review literature demonstrating the value of gene flow for preserving adaptive potential, the often-misunderstood role of hybridization in evolution, and the likely overstated concerns about outbreeding depression, and preservation of local adaptations. I argue that the most effective way to manage animal populations for the long term be they in human care, in the wild, or if a captive population is being managed for reintroduction, is to manage for maximum genetic diversity rather than managing subpopulations focusing on taxonomic integrity, genetic purity, or geographic locale because selection in the future, rather than the past, will determine what genotypes and phenotypes are the most fit. Several case studies are presented to challenge the wisdom of subpopulation management and stimulate thinking about the preservation of genomes rather than species, subspecies, or lineages because those units evolved in habitats that are likely very different from those habitats today and in the future.
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Affiliation(s)
- David M Powell
- Department of Reproductive & Behavioral Sciences, Saint Louis Zoo, Saint Louis, Missouri, USA
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17
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Cairns KM, Crowther MS, Parker HG, Ostrander EA, Letnic M. Genome-wide variant analyses reveal new patterns of admixture and population structure in Australian dingoes. Mol Ecol 2023; 32:4133-4150. [PMID: 37246949 PMCID: PMC10524503 DOI: 10.1111/mec.16998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 04/29/2023] [Accepted: 05/05/2023] [Indexed: 05/30/2023]
Abstract
Admixture between species is a cause for concern in wildlife management. Canids are particularly vulnerable to interspecific hybridisation, and genetic admixture has shaped their evolutionary history. Microsatellite DNA testing, relying on a small number of genetic markers and geographically restricted reference populations, has identified extensive domestic dog admixture in Australian dingoes and driven conservation management policy. But there exists a concern that geographic variation in dingo genotypes could confound ancestry analyses that use a small number of genetic markers. Here, we apply genome-wide single-nucleotide polymorphism (SNP) genotyping to a set of 402 wild and captive dingoes collected from across Australia and then carry out comparisons to domestic dogs. We then perform ancestry modelling and biogeographic analyses to characterise population structure in dingoes and investigate the extent of admixture between dingoes and dogs in different regions of the continent. We show that there are at least five distinct dingo populations across Australia. We observed limited evidence of dog admixture in wild dingoes. Our work challenges previous reports regarding the occurrence and extent of dog admixture in dingoes, as our ancestry analyses show that previous assessments severely overestimate the degree of domestic dog admixture in dingo populations, particularly in south-eastern Australia. These findings strongly support the use of genome-wide SNP genotyping as a refined method for wildlife managers and policymakers to assess and inform dingo management policy and legislation moving forwards.
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Affiliation(s)
- Kylie M. Cairns
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Mathew S. Crowther
- School of Life and Environmental Sciences, University of Sydney, New South Wales 2006, Australia
| | - Heidi G. Parker
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Elaine A. Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Mike Letnic
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
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18
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Staude IR, Ebersbach J. Neophytes may promote hybridization and adaptations to a changing planet. Ecol Evol 2023; 13:e10405. [PMID: 37593753 PMCID: PMC10427993 DOI: 10.1002/ece3.10405] [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: 03/21/2023] [Revised: 07/14/2023] [Accepted: 07/24/2023] [Indexed: 08/19/2023] Open
Abstract
Human activities erode geographic barriers, facilitating hybridization among previously isolated taxa. However, limited empirical research exists on the consequences of introduced species (neophytes) for hybridization and subsequent evolutionary outcomes. To address this knowledge gap, we employed a macroecological approach. First, we examined the spatial and phylogenetic overlap between neophytes and hybrids by integrating the Plants of the World Online database with the Global Naturalized Alien Flora database. Second, leveraging the largest dated plant phylogeny available, we compared diversification rates between genera containing hybrids and neophytes versus those without. Third, focusing on the extensively studied hybrid flora of Britain, we studied the spatial distributions of hybrids in relation to neophyte and native parents, assessing potential adaptations to anthropogenic disturbances and impacts on native species. Overall, our findings highlight positive ties between contemporary biodiversity redistribution and hybridization. Spatially (across countries) and phylogenetically (across genera), neophyte incidence was positively associated with hybrid incidence. Genera comprising both hybrids and neophytes displayed significantly higher diversification rates. Neophyte hybrids primarily occupied areas with a higher human footprint, with limited evidence of hybrids threatening native species throughout their range in more natural habitats. These results challenge the notion that species naturalizations and hybridizations exclusively yield negative outcomes for biodiversity. While it is conceivable that anthropogenic hybridization may facilitate recombination of genetic variation and contribute to conserving genetic diversity in disturbed environments, further research is needed to fully understand these processes.
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Affiliation(s)
- Ingmar R. Staude
- Institute of BiologyLeipzig UniversityLeipzigGermany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
| | - Jana Ebersbach
- Institute of BiologyLeipzig UniversityLeipzigGermany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
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19
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Mitić ZS, Nikolić JS, Dimitrijević IS, Jevtović SČ, Nikolić BM, Zlatković BK, Stojanović GS. Cuticular Wax Variability of Abies alba, A.×borisii-regis and A. cephalonica from the Balkans: Chemophenetic and Ecological Aspects. Chem Biodivers 2023; 20:e202300553. [PMID: 37329266 DOI: 10.1002/cbdv.202300553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/10/2023] [Accepted: 06/16/2023] [Indexed: 06/19/2023]
Abstract
This is the first study on cuticular wax variability of Abies alba, A.×borisii-regis and A. cephalonica, using 18 native populations from the assumed hybrid zone in the Balkan Peninsula. Presence of 13 n-alkanes with chain-lengths ranging from C21 to C33 , one primary alcohol, two diterpenes, one triterpene and one sterol was determined in hexane extracts of 269 needle samples. The multivariate statistical analyses at the population level entirely failed in supporting circumscription of Balkan Abies taxa and therefore, in identifying hybrid populations. However, performed at the species level, these analyses revealed a certain tendency of differentiation between A. alba and A. cephalonica, while individuals of A.×borisii-regis were largely overlapped by the clouds of both parent species. Finally, the correlation analysis suggested that the observed variation of wax compounds was probably genetically conditioned and that it does not represent an adaptive response to various environmental factors.
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Affiliation(s)
- Zorica S Mitić
- Department of Biology and Ecology, Faculty of Sciences and Mathematics, University of Niš, Višegradska 33, 18000, Niš, Serbia
| | - Jelena S Nikolić
- Department of Biology and Ecology, Faculty of Sciences and Mathematics, University of Niš, Višegradska 33, 18000, Niš, Serbia
| | - Ivana S Dimitrijević
- Department of Chemistry, Faculty of Sciences and Mathematics, University of Niš, Višegradska 33, 18000, Niš, Serbia
| | - Snežana Č Jevtović
- Department of Chemistry, Faculty of Sciences and Mathematics, University of Niš, Višegradska 33, 18000, Niš, Serbia
| | | | - Bojan K Zlatković
- Department of Biology and Ecology, Faculty of Sciences and Mathematics, University of Niš, Višegradska 33, 18000, Niš, Serbia
| | - Gordana S Stojanović
- Department of Chemistry, Faculty of Sciences and Mathematics, University of Niš, Višegradska 33, 18000, Niš, Serbia
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20
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Zalewska-Gałosz J, Kwiatkowska M, Prančl J, Skubała K, Lučanová M, Gebler D, Szoszkiewicz K. Origin, genetic structure and evolutionary potential of the natural hybrid Ranunculus circinatus × R. fluitans. Sci Rep 2023; 13:9030. [PMID: 37270656 DOI: 10.1038/s41598-023-36253-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 05/31/2023] [Indexed: 06/05/2023] Open
Abstract
Understanding the genetic variability of hybrids provides information on their current and future evolutionary role. In this paper, we focus on the interspecific hybrid Ranunculus circinatus × R. fluitans that forms spontaneously within the group Ranuculus L. sect. Batrachium DC. (Ranunculaceae Juss.). Genome-wide DNA fingerprinting using amplified fragment length polymorphisms (AFLP) was employed to determine the genetic variation among 36 riverine populations of the hybrid and their parental species. The results demonstrate a strong genetic structure of R. circinatus × R. fluitans within Poland (Central Europe), which is attributed to independent hybridization events, sterility of hybrid individuals, vegetative propagation, and isolation through geographical distance within populations. The hybrid R. circinatus × R. fluitans is a sterile triploid, but, as we have shown in this study, it may participate in subsequent hybridization events, resulting in a ploidy change that can lead to spontaneous fertility recovery. The ability to produce unreduced female gametes of the hybrid R. circinatus × R. fluitans and the parental species R. fluitans is an important evolutionary mechanism in Ranunculus sect. Batrachium that could give rise to new taxa.
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Affiliation(s)
- J Zalewska-Gałosz
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387, Kraków, Poland.
| | - M Kwiatkowska
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387, Kraków, Poland
| | - J Prančl
- Institute of Botany, Czech Academy of Sciences, Zámek 1, 252 43, Průhonice, Czech Republic
| | - K Skubała
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387, Kraków, Poland
| | - M Lučanová
- Institute of Botany, Czech Academy of Sciences, Zámek 1, 252 43, Průhonice, Czech Republic
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - D Gebler
- Department of Ecology and Environmental Protection, Poznan University of Life Sciences, Wojska Polskiego 28, 60-637, Poznań, Poland
| | - K Szoszkiewicz
- Department of Ecology and Environmental Protection, Poznan University of Life Sciences, Wojska Polskiego 28, 60-637, Poznań, Poland
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21
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Wei S, Zhang Q, Tang S, Liao W. Genetic and ecophysiological evidence that hybridization facilitated lineage diversification in yellow Camellia (Theaceae) species: a case study of natural hybridization between C. micrantha and C. flavida. BMC PLANT BIOLOGY 2023; 23:154. [PMID: 36944951 PMCID: PMC10031943 DOI: 10.1186/s12870-023-04164-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 03/11/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Hybridization is generally considered an important creative evolutionary force, yet this evolutionary process is still poorly characterized in karst plants. In this study, we focus on natural hybridization in yellow Camellia species, a group of habitat specialists confined to karst/non-karst habitats in southwestern China. RESULTS Based on population genome data obtain from double digest restriction-site associated DNA (ddRAD) sequencing, we found evidence for natural hybridization and introgression between C. micrantha and C. flavida, and specifically confirmed their hybrid population, C. "ptilosperma". Ecophysiological results suggested that extreme hydraulic traits were fixed in C. "ptilosperma", these being consistent with its distinct ecological niche, which lies outside its parental ranges. CONCLUSION The identified hybridization event is expected to have played a role in generating novel variation during, in which the hybrid population displays different phenological characteristics and novel ecophysiological traits associated with the colonization of a new niche in limestone karst.
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Affiliation(s)
- Sujuan Wei
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guangxi Normal University, Guilin, 541004, China
| | - Qiwei Zhang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guangxi Normal University, Guilin, 541004, China
| | - Shaoqing Tang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guangxi Normal University, Guilin, 541004, China.
| | - Wenbo Liao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
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22
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Torres E, García-Fernández A, Iñigo D, Lara-Romero C, Morente-López J, Prieto-Benítez S, Rubio Teso ML, Iriondo JM. Facilitated Adaptation as A Conservation Tool in the Present Climate Change Context: A Methodological Guide. PLANTS (BASEL, SWITZERLAND) 2023; 12:1258. [PMID: 36986946 PMCID: PMC10053585 DOI: 10.3390/plants12061258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/04/2023] [Accepted: 03/07/2023] [Indexed: 06/18/2023]
Abstract
Climate change poses a novel threat to biodiversity that urgently requires the development of adequate conservation strategies. Living organisms respond to environmental change by migrating to locations where their ecological niche is preserved or by adapting to the new environment. While the first response has been used to develop, discuss and implement the strategy of assisted migration, facilitated adaptation is only beginning to be considered as a potential approach. Here, we present a review of the conceptual framework for facilitated adaptation, integrating advances and methodologies from different disciplines. Briefly, facilitated adaptation involves a population reinforcement that introduces beneficial alleles to enable the evolutionary adaptation of a focal population to pressing environmental conditions. To this purpose, we propose two methodological approaches. The first one (called pre-existing adaptation approach) is based on using pre-adapted genotypes existing in the focal population, in other populations, or even in closely related species. The second approach (called de novo adaptation approach) aims to generate new pre-adapted genotypes from the diversity present in the species through artificial selection. For each approach, we present a stage-by-stage procedure, with some techniques that can be used for its implementation. The associated risks and difficulties of each approach are also discussed.
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Affiliation(s)
- Elena Torres
- Departamento de Biotecnología-Biología Vegetal, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Alfredo García-Fernández
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
| | - Diana Iñigo
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
| | - Carlos Lara-Romero
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
| | - Javier Morente-López
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
- Grupo de Investigación de Ecología y Evolución en Islas, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), 38206 Tenerife, Spain
| | - Samuel Prieto-Benítez
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
- Ecotoxicology of Air Pollution, Environmental Department, CIEMAT, 28040 Madrid, Spain
| | - María Luisa Rubio Teso
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
| | - José M. Iriondo
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
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23
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Hansen MM. Prepping for climate change by introgressive hybridization. Trends Genet 2023:S0168-9525(23)00083-5. [PMID: 37005189 DOI: 10.1016/j.tig.2023.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 03/23/2023] [Indexed: 04/03/2023]
Abstract
Species and populations may adapt to climate change by microevolutionary processes. However, standing genetic variation can be insufficient for this to occur. An interesting new study of a system of rainbowfish species shows that intraspecific hybridization enriches gene pools with adaptive variation that may allow persistence in a changing climate.
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24
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Tian Z, Cheng J, Xu J, Feng D, Zhong J, Yuan X, Zhang Z, Zhang Y, Mao Z, Qiang S. Cytogeography of Naturalized Solidago canadensis Populations in Europe. PLANTS (BASEL, SWITZERLAND) 2023; 12:1113. [PMID: 36903973 PMCID: PMC10005290 DOI: 10.3390/plants12051113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/25/2023] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
Autopolyploidization has driven the successful invasion of Solidago canadensis in East Asia. However, it was believed that only diploid S. canadensis invaded Europe, whereas polyploids never did. Here, molecular identification, ploidy level, and morphological traits of ten S. canadensis populations collected in Europe were compared with previously identified S. canadensis populations from other continents and S. altissima populations. Furthermore, the ploidy-driven geographical differentiation pattern of S. canadensis in different continents was investigated. All ten European populations were identified as S. canadensis with five diploid and five hexaploid populations. Significant differences in morphological traits existed among diploids and polyploids (tetraploids and hexaploids), rather than between polyploids from different introduced ranges and between S. altissima and polyploidy S. canadensis. The invasive hexaploids and diploids had few differences in latitudinal distributions in Europe, which was similar to the native range but different from a distinct climate-niche differentiation in Asia. This may be attributed to the bigger difference in climate between Asia and Europe and North America. The morphological and molecular evidences proved the invasion of polyploid S. canadensis in Europe and suggest that S. altissima may be merged into a complex of S. canadensis species. Our study may be concluded that geographical and ecological niche differentiation of an invasive plant driven by ploidy depends on the degree of difference in the environmental factors between the introduced and native range, which provides new insight into the invasive mechanism.
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25
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DeVos TB, Bock DG, Kolbe JJ. Rapid introgression of non-native alleles following hybridization between a native Anolis lizard species and a cryptic invader across an urban landscape. Mol Ecol 2023; 32:2930-2944. [PMID: 36811388 DOI: 10.1111/mec.16897] [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: 03/08/2022] [Revised: 02/14/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023]
Abstract
Invasive species can impact native populations through competition, predation, habitat alteration, and disease transmission, but also genetically through hybridization. Potential outcomes of hybridization span the continuum from extinction to hybrid speciation and can be further complicated by anthropogenic habitat disturbance. Hybridization between the native green anole lizard (Anolis carolinensis) and a morphologically similar invader (A. porcatus) in south Florida provides an ideal opportunity to study interspecific admixture across a heterogeneous landscape. We used reduced-representation sequencing to describe introgression in this hybrid system and to test for a relationship between urbanization and non-native ancestry. Our findings indicate that hybridization between green anole lineages was probably a limited, historic event, producing a hybrid population characterized by a diverse continuum of ancestry proportions. Genomic cline analyses revealed rapid introgression and disproportionate representation of non-native alleles at many loci and no evidence for reproductive isolation between parental species. Three loci were associated with urban habitat characteristics; urbanization and non-native ancestry were positively correlated, although this relationship did not remain significant when accounting for spatial nonindependence. Ultimately, our study demonstrates the persistence of non-native genetic material even in the absence of ongoing immigration, indicating that selection favouring non-native alleles can override the demographic limitation of low propagule pressure. We also note that not all outcomes of admixture between native and non-native species should be considered intrinsically negative. Hybridization with ecologically robust invaders can lead to adaptive introgression, which may facilitate the long-term survival of native populations otherwise unable to adapt to anthropogenically mediated global change.
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Affiliation(s)
- Tyler B DeVos
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Dan G Bock
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | - Jason J Kolbe
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA
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26
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Pfeilsticker TR, Jones RC, Steane DA, Vaillancourt RE, Potts BM. Molecular insights into the dynamics of species invasion by hybridisation in Tasmanian eucalypts. Mol Ecol 2023; 32:2913-2929. [PMID: 36807951 DOI: 10.1111/mec.16892] [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: 08/29/2022] [Revised: 11/26/2022] [Accepted: 01/26/2023] [Indexed: 02/22/2023]
Abstract
In plants where seed dispersal is limited compared with pollen dispersal, hybridisation may enhance gene exchange and species dispersal. We provide genetic evidence of hybridisation contributing to the expansion of the rare Eucalyptus risdonii into the range of the widespread Eucalyptus amygdalina. These closely related tree species are morphologically distinct, and observations suggest that natural hybrids occur along their distribution boundaries and as isolated trees or in small patches within the range of E. amygdalina. Hybrid phenotypes occur outside the range of normal dispersal for E. risdonii seed, yet in some hybrid patches small individuals resembling E. risdonii occur and are hypothesised to be a result of backcrossing. Using 3362 genome-wide SNPs assessed from 97 individuals of E. risdonii and E. amygdalina and 171 hybrid trees, we show that (i) isolated hybrids match the genotypes expected of F1 /F2 hybrids, (ii) there is a continuum in the genetic composition among the isolated hybrid patches from patches dominated by F1 /F2 -like genotypes to those dominated by E. risdonii-backcross genotypes, and (iii) the E. risdonii-like phenotypes in the isolated hybrid patches are most-closely related to proximal larger hybrids. These results suggest that the E. risdonii phenotype has been resurrected in isolated hybrid patches established from pollen dispersal, providing the first steps in its invasion of suitable habitat by long-distance pollen dispersal and complete introgressive displacement of E. amygdalina. Such expansion accords with the population demographics, common garden performance data, and climate modelling which favours E. risdonii and highlights a role of interspecific hybridisation in climate change adaptation and species expansion.
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Affiliation(s)
- Thais R Pfeilsticker
- School of Natural Sciences and ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania, Australia
| | - Rebecca C Jones
- School of Natural Sciences and ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania, Australia
| | - Dorothy A Steane
- School of Natural Sciences and ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania, Australia
| | - René E Vaillancourt
- School of Natural Sciences and ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania, Australia
| | - Brad M Potts
- School of Natural Sciences and ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania, Australia
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27
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Satler JD, Herre EA, Heath TA, Machado CA, Gómez Zúñiga A, Jandér KC, Eaton DAR, Nason JD. Pollinator and host sharing lead to hybridization and introgression in Panamanian free-standing figs, but not in their pollinator wasps. Ecol Evol 2023; 13:e9673. [PMID: 36699574 PMCID: PMC9848820 DOI: 10.1002/ece3.9673] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 11/20/2022] [Accepted: 12/02/2022] [Indexed: 01/20/2023] Open
Abstract
Obligate pollination mutualisms, in which plant and pollinator lineages depend on each other for reproduction, often exhibit high levels of species specificity. However, cases in which two or more pollinator species share a single host species (host sharing), or two or more host species share a single pollinator species (pollinator sharing), are known to occur in current ecological time. Further, evidence for host switching in evolutionary time is increasingly being recognized in these systems. The degree to which departures from strict specificity differentially affect the potential for hybridization and introgression in the associated host or pollinator is unclear. We addressed this question using genome-wide sequence data from five sympatric Panamanian free-standing fig species (Ficus subgenus Pharmacosycea, section Pharmacosycea) and their six associated fig-pollinator wasp species (Tetrapus). Two of the five fig species, F. glabrata and F. maxima, were found to regularly share pollinators. In these species, ongoing hybridization was demonstrated by the detection of several first-generation (F1) hybrid individuals, and historical introgression was indicated by phylogenetic network analysis. By contrast, although two of the pollinator species regularly share hosts, all six species were genetically distinct and deeply divergent, with no evidence for either hybridization or introgression. This pattern is consistent with results from other obligate pollination mutualisms, suggesting that, in contrast to their host plants, pollinators appear to be reproductively isolated, even when different species of pollinators mate in shared hosts.
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Affiliation(s)
- Jordan D. Satler
- Department of Ecology, Evolution, and Organismal BiologyIowa State UniversityAmesIowaUSA
| | | | - Tracy A. Heath
- Department of Ecology, Evolution, and Organismal BiologyIowa State UniversityAmesIowaUSA
| | | | | | - K. Charlotte Jandér
- Department of Ecology and Genetics, Plant Ecology and EvolutionUppsala UniversityUppsalaSweden
| | - Deren A. R. Eaton
- Department of Ecology, Evolution and Environmental BiologyColumbia UniversityNew YorkNew YorkUSA
| | - John D. Nason
- Department of Ecology, Evolution, and Organismal BiologyIowa State UniversityAmesIowaUSA
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28
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Thompson LM, Thurman LL, Cook CN, Beever EA, Sgrò CM, Battles A, Botero CA, Gross JE, Hall KR, Hendry AP, Hoffmann AA, Hoving C, LeDee OE, Mengelt C, Nicotra AB, Niver RA, Pérez‐Jvostov F, Quiñones RM, Schuurman GW, Schwartz MK, Szymanski J, Whiteley A. Connecting research and practice to enhance the evolutionary potential of species under climate change. CONSERVATION SCIENCE AND PRACTICE 2023. [DOI: 10.1111/csp2.12855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Laura M. Thompson
- U.S. Geological Survey (USGS), National Climate Adaptation Science Center and the University of Tennessee Knoxville Tennessee USA
| | | | - Carly N. Cook
- School of Biological Sciences Monash University Melbourne Australia
| | - Erik A. Beever
- USGS, Northern Rocky Mountain Science Center and Montana State University Bozeman Montana USA
| | - Carla M. Sgrò
- School of Biological Sciences Monash University Melbourne Australia
| | | | | | - John E. Gross
- National Park Service (NPS) Climate Change Response Program Fort Collins Colorado USA
| | | | | | | | | | - Olivia E. LeDee
- USGS, Midwest Climate Adaptation Science Center Saint Paul Minnesota USA
| | | | | | - Robyn A. Niver
- U.S. Fish and Wildlife Service (USFWS), Branch of Listing and Policy Support Bailey's Crossroads Virginia USA
| | | | - Rebecca M. Quiñones
- Massachusetts Division of Fisheries and Wildlife Westborough Massachusetts USA
| | - Gregor W. Schuurman
- National Park Service (NPS) Climate Change Response Program Fort Collins Colorado USA
| | - Michael K. Schwartz
- U.S. Forest Service, National Genomics Center for Wildlife and Fish Conservation Missoula Montana USA
| | - Jennifer Szymanski
- USFWS, Branch of SSA Science Support, Division of Endangered Species Onalaska Wisconsin USA
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29
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Suh YH, Ligon RA, Rohwer VG. Revisiting the Baltimore-Bullock's Oriole hybrid zone reveals changing plumage colour in Bullock's Orioles. ROYAL SOCIETY OPEN SCIENCE 2022; 9:221211. [PMID: 36533198 PMCID: PMC9748506 DOI: 10.1098/rsos.221211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 11/18/2022] [Indexed: 06/17/2023]
Abstract
Hybrid zones are dynamic areas where populations of two or more interbreeding species may change through an influx of novel genetic material resulting from hybridization or selection on standing genetic variation. Documenting changes in populations through time, however, is challenging because repeated samples are often missing or because long-term storage can affect trait morphologies, especially colour traits that may fade through time. We document a change in carotenoid-based orange breast feathers of Bullock's Orioles (Icterus bullockii) from the Great Plains hybrid zone, USA. Contemporary Bullock's Orioles are more orange than historic individuals from the same location sampled approximately 60 years ago. Spectrophotometry revealed that contemporary Bullock's Orioles resemble orange colour profiles of Baltimore Orioles (I. galbula), the species with which they hybridize. Fading or changes in diet hypotheses do not appear to explain the shift in colour we report for Bullock's Orioles. We propose that these changes in colour are facilitated through introgression with Baltimore Orioles, and favoured by females that choose brighter, more orange males. Our study highlights the long memory of natural history collections and how they offer new insights to the dynamic roll of hybrid zones in trait evolution between interacting species.
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Affiliation(s)
- Young Ha Suh
- Department of Ecology and Evolutionary Biology, Cornell University Museum of Vertebrates, Ithaca, NY 14853, USA
- Cornell Lab of Ornithology, Ithaca, NY 14850, USA
| | | | - Vanya G. Rohwer
- Department of Ecology and Evolutionary Biology, Cornell University Museum of Vertebrates, Ithaca, NY 14853, USA
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30
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Barnes TM, Karlin M, vonHoldt BM, Adams JR, Waits LP, Hinton JW, Henderson J, Brzeski KE. Genetic diversity and family groups detected in a coyote population with red wolf ancestry on Galveston Island, Texas. BMC Ecol Evol 2022; 22:134. [PMID: 36376792 PMCID: PMC9664737 DOI: 10.1186/s12862-022-02084-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 10/20/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Hybridization can be a conservation concern if genomic introgression leads to the loss of an endangered species' unique genome, or when hybrid offspring are sterile or less fit than their parental species. Yet hybridization can also be an adaptive management tool if rare populations are inbred and have reduced genetic variation, and there is the opportunity to enhance genetic variation through hybridization. The red wolf (Canis rufus) is a critically endangered wolf endemic to the eastern United States, where all extant red wolves are descended from 14 founders which has led to elevated levels of inbreeding over time. Red wolves were considered extirpated from the wild by 1980, but before they disappeared, they interbred with encroaching coyotes creating a genetically admixed population of canids along coastal Texas and Louisiana. In 2018, a genetic study identified individuals on Galveston Island, Texas with significant amounts of red wolf ancestry. We collected 203 fecal samples from Galveston for a more in-depth analysis of this population to identify the amount of red wolf ancestry present and potential mechanisms that support retention of red wolf ancestry on the landscape. RESULTS We identified 24 individual coyotes from Galveston Island and 8 from mainland Texas with greater than 10% red wolf ancestry. Two of those individuals from mainland Texas had greater than 50% red wolf ancestry estimates. Additionally, this population had 5 private alleles that were absent in the North American reference canid populations used in this study, which included 107 southeastern coyotes, 19 captive red wolves, and 38 gray wolves, possibly representing lost red wolf genetic variation. We also identified several individuals on Galveston Island and the mainland of Texas that retained a unique red wolf mitochondrial haplotype present in the red wolf founding population. On Galveston Island, we identified a minimum of four family groups and found coyotes on the island to be highly related, but not genetically depauperate. We did not find clear associations between red wolf ancestry estimates and landscape features, such as open green space or developed areas. CONCLUSION Our results confirm the presence of substantial red wolf ancestry persisting on Galveston Island and adjacent mainland Texas. This population has the potential to benefit future red wolf conservation efforts through novel reproductive techniques and possibly through de-introgression strategies, with the goals of recovering extinct red wolf genetic variation and reducing inbreeding within the species.
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Affiliation(s)
- Tanner M Barnes
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, USA
| | - Melissa Karlin
- Department of Physics and Environmental Science, St. Mary's University, San Antonio, TX, USA
| | - Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Jennifer R Adams
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, USA
| | - Lisette P Waits
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, USA
| | | | | | - Kristin E Brzeski
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, USA.
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31
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Gaertner K, Michell C, Tapanainen R, Goffart S, Saari S, Soininmäki M, Dufour E, Pohjoismäki JLO. Molecular phenotyping uncovers differences in basic housekeeping functions among closely related species of hares (
Lepus
spp., Lagomorpha: Leporidae). Mol Ecol 2022. [PMID: 36320183 DOI: 10.1111/mec.16755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 09/16/2022] [Accepted: 10/06/2022] [Indexed: 11/15/2022]
Abstract
Speciation is a fundamental evolutionary process, which results in genetic differentiation of populations and manifests as discrete morphological, physiological and behavioural differences. Each species has travelled its own evolutionary trajectory, influenced by random drift and driven by various types of natural selection, making the association of genetic differences between the species with the phenotypic differences extremely complex to dissect. In the present study, we have used an in vitro model to analyse in depth the genetic and gene regulation differences between fibroblasts of two closely related mammals, the arctic/subarctic mountain hare (Lepus timidus Linnaeus) and the temperate steppe-climate adapted brown hare (Lepus europaeus Pallas). We discovered the existence of a species-specific expression pattern of 1623 genes, manifesting in differences in cell growth, cell cycle control, respiration, and metabolism. Interspecific differences in the housekeeping functions of fibroblast cells suggest that speciation acts on fundamental cellular processes, even in these two interfertile species. Our results help to understand the molecular constituents of a species difference on a cellular level, which could contribute to the maintenance of the species boundary.
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Affiliation(s)
- Kateryna Gaertner
- Mitochondrial Bioenergetics and Metabolism, Faculty of Medicine and Health Technology FI‐33014 Tampere University Tampere Finland
| | - Craig Michell
- Department of Environmental and Biological Sciences FI‐80101 University of Eastern Finland Kuopio Finland
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia
| | - Riikka Tapanainen
- Department of Environmental and Biological Sciences FI‐80101 University of Eastern Finland Kuopio Finland
| | - Steffi Goffart
- Department of Environmental and Biological Sciences FI‐80101 University of Eastern Finland Kuopio Finland
| | - Sina Saari
- Mitochondrial Bioenergetics and Metabolism, Faculty of Medicine and Health Technology FI‐33014 Tampere University Tampere Finland
| | - Manu Soininmäki
- Department of Environmental and Biological Sciences FI‐80101 University of Eastern Finland Kuopio Finland
| | - Eric Dufour
- Mitochondrial Bioenergetics and Metabolism, Faculty of Medicine and Health Technology FI‐33014 Tampere University Tampere Finland
| | - Jaakko L. O. Pohjoismäki
- Department of Environmental and Biological Sciences FI‐80101 University of Eastern Finland Kuopio Finland
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vonHoldt BM, Brzeski KE, Aardema ML, Schell CJ, Rutledge LY, Fain SR, Shutt AC, Linderholm A, Murphy WJ. Persistence and expansion of cryptic endangered red wolf genomic ancestry along the American Gulf coast. Mol Ecol 2022; 31:5440-5454. [PMID: 34585803 DOI: 10.1111/mec.16200] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 09/03/2021] [Accepted: 09/22/2021] [Indexed: 12/24/2022]
Abstract
Admixture and introgression play a critical role in adaptation and genetic rescue that has only recently gained a deeper appreciation. Here, we explored the geographical and genomic landscape of cryptic ancestry of the endangered red wolf that persists within the genome of a ubiquitous sister taxon, the coyote, all while the red wolf has been extinct in the wild since the early 1980s. We assessed admixture across 120,621 single nucleotiode polymorphism (SNP) loci genotyped in 293 canid genomes. We found support for increased red wolf ancestry along a west-to-east gradient across the southern United States associated with historical admixture in the past 100 years. Southwestern Louisiana and southeastern Texas, the geographical zone where the last red wolves were known prior to extinction in the wild, contained the highest and oldest levels of red wolf ancestry. Further, given the paucity of inferences based on chromosome types, we compared patterns of ancestry on the X chromosome and autosomes. We additionally aimed to explore the relationship between admixture timing and recombination rate variation to investigate gene flow events. We found that X-linked regions of low recombination rates were depleted of introgression, relative to the autosomes, consistent with the large X effect and enrichment with loci involved in maintaining reproductive isolation. Recombination rate was positively correlated with red wolf ancestry across coyote genomes, consistent with theoretical predictions. The geographical and genomic extent of cryptic red wolf ancestry can provide novel genomic resources for recovery plans targeting the conservation of the endangered red wolf.
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Affiliation(s)
- Bridgett M vonHoldt
- Ecology & Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Kristin E Brzeski
- College of Forest Resources and Environment Science, Michigan Technological University, Houghton, Michigan, USA
| | - Matthew L Aardema
- Department of Biology, Montclair State University, Montclair, New Jersey, USA.,Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
| | - Christopher J Schell
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, USA
| | - Linda Y Rutledge
- Biology Department, Trent University, Peterborough, Ontario, Canada
| | - Steven R Fain
- USFWS, Clark R. Bavin National Forensics Laboratory, Ashland, Oregon, USA
| | | | - Anna Linderholm
- Department of Anthropology, Texas A&M University, College Station, Texas, USA
| | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, USA
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Wang X, Li G, Jiang Y, Tang J, Fan Y, Ren J. Genomic insights into the conservation and population genetics of two Chinese native goat breeds. J Anim Sci 2022; 100:skac274. [PMID: 35998083 PMCID: PMC9585554 DOI: 10.1093/jas/skac274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 08/20/2022] [Indexed: 11/14/2022] Open
Abstract
Chinese goats are an important group of goats worldwide. However, there are few studies on the conservation priority, genetic relationship, and potential gene flow between Chinese and global goat breeds. Here, we genotyped 239 goats from conservation populations of the Chinese Guangfeng and Ganxi breeds using the GoatSNP50 BeadChip. The conservation priority, population structure, selection signatures and introgression of these goats were analyzed in the context of 36 global goat breeds. First, we showed that Guangfeng and Ganxi goats had the largest effective population sizes across the global breeds 13 generations ago. Nevertheless, Ganxi goats have recently experienced a high degree of inbreeding, resulting in their conservation priority based on total gene and allelic diversities being lower than that of most other Chinese breeds (including Guangfeng goats). Population structure and admixture analyses showed that an average of 18% of Guangfeng genomic components were introgressed from Boer goats approximately 18-yr ago. Next, we reconstructed the subfamily structure of the core populations of Guangfeng and Ganxi goats, and proposed reasonable conservation strategies for inbreeding management. Moreover, a list of candidate genes under selection for fertility, immunity, growth, and meat quality were detected in Guangfeng and Ganxi goats. Finally, we identified some genes related to body development and reproduction, which were introgressed from Boer goats and may be beneficial for improving performance and productivity of Guangfeng goats. In conclusion, this study not only provides new insights into the conservation and utilization of Guangfeng and Ganxi goats but also enriches our understanding of artificial introgression from exotic goats into Chinese local goats.
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Affiliation(s)
- Xiaopeng Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Guixin Li
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Yongchuang Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Jianhong Tang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Laboratory Animal Engineering Research Center of Ganzhou, Gannan Medical University, Ganzhou 341000, China
| | - Yin Fan
- Department of Animal Science, Jiangxi Biotech Vocational College, Nanchang 330200, China
| | - Jun Ren
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
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Grummer JA, Booker TR, Matthey-Doret R, Nietlisbach P, Thomaz AT, Whitlock MC. The immediate costs and long-term benefits of assisted gene flow in large populations. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2022; 36:e13911. [PMID: 35390208 DOI: 10.1111/cobi.13911] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 12/11/2021] [Accepted: 12/24/2021] [Indexed: 06/14/2023]
Abstract
With the genetic health of many plant and animal populations deteriorating due to climate change outpacing adaptation, interventions, such as assisted gene flow (AGF), may provide genetic variation necessary for populations to adapt to climate change. We ran genetic simulations to mimic different AGF scenarios in large populations and measured their outcomes on population-level fitness to determine circumstances in which it is worthwhile to perform AGF. In the absence of inbreeding depression, AGF was beneficial within a few generations only when introduced genotypes had much higher fitness than local individuals and traits affecting fitness were controlled by a few genes of large effect. AGF was harmful over short periods (e.g., first ∼10-20 generations) if there was strong outbreeding depression or introduced deleterious genetic variation. When the adaptive trait was controlled by many loci of small effect, the benefits of AGF took over 10 generations to realize-potentially too long for most climate-related management scenarios. The genomic integrity of the recipient population typically remained intact following AGF; the amount of genetic material from the donor population usually constituted no more of the recipient population's genome than the fraction of the population introduced. Significant genomic turnover (e.g., >50% replacement) only occurred when the selective advantage of the adaptive trait and translocation fraction were extremely high. Our results will be useful when adaptive management is used to maintain the genetic health and productivity of large populations under climate change.
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Affiliation(s)
- Jared A Grummer
- Biodiversity Research Centre and Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Tom R Booker
- Biodiversity Research Centre and Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Remi Matthey-Doret
- Biodiversity Research Centre and Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Pirmin Nietlisbach
- Biodiversity Research Centre and Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- School of Biological Sciences, Illinois State University, Normal, Illinois, USA
| | - Andréa T Thomaz
- Biodiversity Research Centre and Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Michael C Whitlock
- Biodiversity Research Centre and Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
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Vedder D, Lens L, Martin CA, Pellikka P, Adhikari H, Heiskanen J, Engler JO, Sarmento Cabral J. Hybridization may aid evolutionary rescue of an endangered East African passerine. Evol Appl 2022; 15:1177-1188. [PMID: 35899253 PMCID: PMC9309464 DOI: 10.1111/eva.13440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/26/2022] [Accepted: 06/08/2022] [Indexed: 11/29/2022] Open
Abstract
Introgressive hybridization is a process that enables gene flow across species barriers through the backcrossing of hybrids into a parent population. This may make genetic material, potentially including relevant environmental adaptations, rapidly available in a gene pool. Consequently, it has been postulated to be an important mechanism for enabling evolutionary rescue, that is the recovery of threatened populations through rapid evolutionary adaptation to novel environments. However, predicting the likelihood of such evolutionary rescue for individual species remains challenging. Here, we use the example of Zosterops silvanus, an endangered East African highland bird species suffering from severe habitat loss and fragmentation, to investigate whether hybridization with its congener Zosterops flavilateralis might enable evolutionary rescue of its Taita Hills population. To do so, we employ an empirically parameterized individual-based model to simulate the species' behaviour, physiology and genetics. We test the population's response to different assumptions of mating behaviour and multiple scenarios of habitat change. We show that as long as hybridization does take place, evolutionary rescue of Z. silvanus is likely. Intermediate hybridization rates enable the greatest long-term population growth, due to trade-offs between adaptive and maladaptive introgressed alleles. Habitat change did not have a strong effect on population growth rates, as Z. silvanus is a strong disperser and landscape configuration is therefore not the limiting factor for hybridization. Our results show that targeted gene flow may be a promising avenue to help accelerate the adaptation of endangered species to novel environments, and demonstrate how to combine empirical research and mechanistic modelling to deliver species-specific predictions for conservation planning.
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Affiliation(s)
- Daniel Vedder
- Ecosystem Modelling Group, Center for Computational and Theoretical BiologyUniversity of WürzburgWürzburgGermany
- Department of Ecosystem ServicesHelmholtz Centre for Environmental Research – UFZLeipzigGermany
- Institute of BiodiversityFriedrich Schiller University JenaJenaGermany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
| | - Luc Lens
- Terrestrial Ecology Unit, Biology DepartmentGhent UniversityGhentBelgium
| | - Claudia A. Martin
- Terrestrial Ecology Unit, Biology DepartmentGhent UniversityGhentBelgium
| | - Petri Pellikka
- Department of Geosciences and GeographyUniversity of HelsinkiHelsinkiFinland
- State Key Laboratory for Information Engineering in Surveying, Mapping and Remote SensingWuhan UniversityWuhanChina
| | - Hari Adhikari
- Department of Geosciences and GeographyUniversity of HelsinkiHelsinkiFinland
| | - Janne Heiskanen
- Department of Geosciences and GeographyUniversity of HelsinkiHelsinkiFinland
| | - Jan O. Engler
- Terrestrial Ecology Unit, Biology DepartmentGhent UniversityGhentBelgium
- Landscape Research, Department of GeographyGhent UniversityGhentBelgium
- Computational Landscape EcologyTechnische Universität DresdenDresdenGermany
| | - Juliano Sarmento Cabral
- Ecosystem Modelling Group, Center for Computational and Theoretical BiologyUniversity of WürzburgWürzburgGermany
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vonHoldt BM, Hinton JW, Shutt AC, Murphy SM, Karlin ML, Adams JR, Waits LP, Brzeski KE. Reviving ghost alleles: Genetically admixed coyotes along the American Gulf Coast are critical for saving the endangered red wolf. SCIENCE ADVANCES 2022; 8:eabn7731. [PMID: 35767623 PMCID: PMC9242586 DOI: 10.1126/sciadv.abn7731] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
The last known red wolves were captured in southwestern Louisiana and eastern Texas in 1980 to establish a captive breeding population. Before their extirpation, gene flow with coyotes resulted in the persistence of endangered red wolf genetic variation in local coyote populations. We assessed genomic ancestry and morphology of coyotes in southwestern Louisiana. We detected that 38 to 62% of the coyote genomes contained red wolf ancestry acquired in the past 30 years and have an admixture profile similar to that of the canids captured before the extirpation of red wolves. We further documented a positive correlation between ancestry and weight. Our findings highlight the importance of hybrids and admixed genomes as a reservoir of endangered species ancestry for innovative conservation efforts. Together, this work presents an unprecedented system that conservation can leverage to enrich the recovery program of an endangered species.
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Affiliation(s)
- Bridgett M. vonHoldt
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | | | | | - Sean M. Murphy
- Forestry and Natural Resources, University of Kentucky, Lexington, KY, USA
| | - Melissa L. Karlin
- Department of Physics and Environmental Science, St. Mary’s University, San Antonio, TX, USA
| | - Jennifer R. Adams
- Laboratory for Ecological, Evolutionary and Conservation Genetics, Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, USA
| | - Lisette P. Waits
- Laboratory for Ecological, Evolutionary and Conservation Genetics, Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, USA
| | - Kristin E. Brzeski
- College of Forest Resources and Environment Science, Michigan Technological University, Houghton, MI, USA
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García G, Gutiérrez V, Ríos N. Living in Temporary Ponds Loading Giant Genomes: The Neotropical Annual Killifish Genus Austrolebias as New Outstanding Evolutionary Model. Front Genet 2022; 13:903683. [PMID: 35795213 PMCID: PMC9251178 DOI: 10.3389/fgene.2022.903683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/05/2022] [Indexed: 12/02/2022] Open
Abstract
The term Annual killifish describes a short-lived and amazing group of vertebrates inhabiting temporary ponds exposed to an extremely variable environment during its short lifespan in South America and Africa, leading to the death of the entire adult population during the dry season. Austrolebias is a specious genus of the family Rivulidae, with ∼58 currently recognized species, extensively distributed in the temperate Neotropical region. Herein, we reviewed different aspects of the evolutionary biology with emphasis on the genome dynamic linked to the burst speciation process in this genus. Austrolebias constitutes an excellent model to study the genomic evolutionary processes underlying speciation events, since all the species of this genus analyzed so far share an unusually large genome size, with an average DNA content of 5.95 ± 0.45 picograms per diploid cell (mean C-value of about 2.98 pg). The drastic nuclear DNA–increasing would be associated with a considerable proportion of transposable elements (TEs) found in the Austrolebias genomes. The genomic proportion of the moderately repetitive DNA in the A. charrua genome represents approximately twice (45%) the amount of the repetitive components of the highly related sympatric and syntopic rivulinae taxon Cynopoecilus melanotaenia (25%), as well as from other rivulids and actinopterygian fish. These events could explain the great genome instability, the high genetic diversity, chromosome variability, as well as the morphological diversity in species of Austrolebias. Thus, species of this genus represent new model systems linking different evolutionary processes: drastic genome increase, massive TEs genomic representation, high chromosome instability, occurrence of natural hybridization between sister species, and burst speciation events.
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Affiliation(s)
| | | | - Néstor Ríos
- Sección Genética Evolutiva, Facultad de Ciencias, UdelaR, Montevideo, Uruguay
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38
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Cao K, Peng Z, Zhao X, Li Y, Liu K, Arus P, Fang W, Chen C, Wang X, Wu J, Fei Z, Wang L. Chromosome-level genome assemblies of four wild peach species provide insights into genome evolution and genetic basis of stress resistance. BMC Biol 2022; 20:139. [PMID: 35698132 PMCID: PMC9195245 DOI: 10.1186/s12915-022-01342-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 05/30/2022] [Indexed: 12/25/2022] Open
Abstract
Background Peach (Prunus persica) is an economically important stone fruit crop in Rosaceae and widely cultivated in temperate and subtropical regions, emerging as an excellent material to study the interaction between plant and environment. During its genus, there are four wild species of peach, all living in harsh environments. For example, one of the wild species, P. mira, originates from the Qinghai-Tibet Plateau (QTP) and exhibits strong cold/ultraviolet ray environmental adaptations. Although remarkable progresses in the gene discovery of fruit quality-related traits in peach using previous assembled genome were obtained, genomic basis of the response of these wild species to different geographical environments remains unclear. Results To uncover key genes regulating adaptability in different species and analyze the role of genetic variations in resistance formation, we performed de novo genome assembling of four wild relatives of peach (P. persica), P. mira, P. davidiana, P. kansuensis, and P. ferganensis and resequenced 175 peach varieties. The phylogenetic tree showed that the divergence time of P. mira and other wild relatives of peach was 11.5 million years ago, which was consistent with the drastic crustal movement of QTP. Abundant genetic variations were identified in four wild species when compared to P. persica, and the results showed that plant-pathogen interaction pathways were enriched in genes containing small insertions and deletions and copy number variations in all four wild relatives of peach. Then, the data were used to identify new genes and variations regulating resistance. For example, presence/absence variations which result from a hybridization event that occurred between P. mira and P. dulcis enhanced the resistance of their putative hybrid, P. davidiana. Using bulked segregant analysis, we located the nematode resistance locus of P. kansuensis in chromosome 2. Within the mapping region, a deletion in the promoter of one NBS-LRR gene was found to involve the resistance by regulating gene expression. Furthermore, combined with RNA-seq and selective sweeps analysis, we proposed that a deletion in the promoter of one CBF gene was essential for high-altitude adaptation of P. mira through increasing its resistance to low temperature. Conclusions In general, the reference genomes assembled in the study facilitate our understanding of resistance mechanism of perennial fruit crops, and provide valuable resources for future breeding and improvement. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01342-y.
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Affiliation(s)
- Ke Cao
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China.
| | - Zhen Peng
- Novogene Bioinformatics Institute, Beijing, People's Republic of China
| | - Xing Zhao
- Novogene Bioinformatics Institute, Beijing, People's Republic of China
| | - Yong Li
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Kuozhan Liu
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Pere Arus
- IRTA, Centre de Recerca en Agrigenòmica, CSIC-IRTA-UAB-UB, Campus UAB - Edifici CRAG, Cerdanyola del Vallès (Bellaterra), Barcelona, Spain
| | - Weichao Fang
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Changwen Chen
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Xinwei Wang
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Jinlong Wu
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, 14853, USA
| | - Lirong Wang
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China. .,National Horticulture Germplasm Resources Center, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China.
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Wu Z, Wang Z, Xie D, Zhang J, Cai P, Li X, Xu X, Li T, Zhao J. Extensive Sympatry and Frequent Hybridization of Ecologically Divergent Aquatic Plants on the Qinghai-Tibetan Plateau. FRONTIERS IN PLANT SCIENCE 2022; 13:851151. [PMID: 35646042 PMCID: PMC9135455 DOI: 10.3389/fpls.2022.851151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 04/13/2022] [Indexed: 06/15/2023]
Abstract
Hybridization has fascinated biologists in recent centuries for its evolutionary importance, especially in plants. Hybrid zones are commonly located in regions across environmental gradients due to more opportunities to contact and ecological heterogeneity. For aquatic taxa, intrazonal character makes broad overlapping regions in intermediate environments between related species. However, we have limited information on the hybridization pattern of aquatic taxa in alpines, especially submerged macrophytes. In this study, we aimed to test the hypotheses that niche overlap and hybridization might be extensive in related aquatic plants across an altitudinal gradient. We evaluated the niche overlap in three related species pairs on the Qinghai-Tibetan Plateau and assessed the spatial pattern of hybrid populations. Obvious niche overlap and common hybridization were revealed in all three pairs of related aquatic plants. The plateau edge and river basins were broad areas for the sympatry of divergent taxa, where a large proportion of hybrid populations occurred. Hybrids are also discretely distributed in diverse habitats on the plateau. Differences in the extent of niche overlap, genetic incompatibility and phylogeographic history might lead to variation differences in hybridization patterns among the three species pairs. Our results suggested that plateau areas are a hotspot for ecologically divergent aquatic species to contact and mate and implied that hybridization may be important for the freshwater biodiversity of highlands.
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Affiliation(s)
- Zhigang Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Zhong Wang
- Department of Ecology, College of Life Science, Wuhan University, Wuhan, China
| | - Dong Xie
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- National Wetland Ecosystem Field Station of Taihu Lake, National Forestry Administration, Suzhou, China
| | - Juan Zhang
- Department of Ecology, College of Life Science, Wuhan University, Wuhan, China
| | - Pengsen Cai
- Department of Ecology, College of Life Science, Wuhan University, Wuhan, China
| | - Xing Li
- Department of Ecology, College of Life Science, Wuhan University, Wuhan, China
| | - Xinwei Xu
- Department of Ecology, College of Life Science, Wuhan University, Wuhan, China
| | - Tao Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jindong Zhao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- State Key Laboratory of Protein and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing, China
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40
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Weyna A, Bourouina L, Galtier N, Romiguier J. Detection of F1 hybrids from single-genome data reveals frequent hybridization in Hymenoptera and particularly ants. Mol Biol Evol 2022; 39:6562163. [PMID: 35363317 PMCID: PMC9021736 DOI: 10.1093/molbev/msac071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Hybridization occupies a central role in many fundamental evolutionary processes, such as speciation or adaptation. Yet, despite its pivotal importance in evolution, little is known about the actual prevalence and distribution of current hybridization across the tree of life. Here we develop and implement a new statistical method enabling the detection of F1 hybrids from single-individual genome sequencing data. Using simulations and sequencing data from known hybrid systems, we first demonstrate the specificity of the method, and identify its statistical limits. Next, we showcase the method by applying it to available sequencing data from more than 1,500 species of Arthropods, including Hymenoptera, Hemiptera, Coleoptera, Diptera, and Archnida. Among these taxa, we find Hymenoptera, and especially ants, to display the highest number of candidate F1 hybrids, suggesting higher rates of recent hybridization between previously isolated gene pools in these groups. The prevalence of F1 hybrids was heterogeneously distributed across ants, with taxa including many candidates tending to harbor specific ecological and life-history traits. This work shows how large-scale genomic comparative studies of recent hybridization can be implemented, uncovering the determinants of first-generation hybridization across whole taxa.
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Affiliation(s)
- Arthur Weyna
- Institut des Sciences de l'Evolution (UMR 5554), University of Montpellier, CNRS
| | - Lucille Bourouina
- Institut des Sciences de l'Evolution (UMR 5554), University of Montpellier, CNRS
| | - Nicolas Galtier
- Institut des Sciences de l'Evolution (UMR 5554), University of Montpellier, CNRS
| | - Jonathan Romiguier
- Institut des Sciences de l'Evolution (UMR 5554), University of Montpellier, CNRS
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VanWallendael A, Lowry DB, Hamilton JA. One hundred years into the study of ecotypes, new advances are being made through large-scale field experiments in perennial plant systems. CURRENT OPINION IN PLANT BIOLOGY 2022; 66:102152. [PMID: 35065527 DOI: 10.1016/j.pbi.2021.102152] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/31/2021] [Accepted: 11/03/2021] [Indexed: 06/14/2023]
Abstract
A hundred years after Turesson first clearly described how locally adaptive variation is distributed within species, plant biologists are making major breakthroughs in our understanding of mechanisms underlying adaptation from local populations to the scale of continents. Although the genetics of local adaptation has typically been studied in smaller reciprocal transplant experiments, it is now being evaluated with whole genomes in large-scale networks of common garden experiments with perennial switchgrass and poplar trees. These studies support the hypothesis that a complex combination of loci, both with and without adaptive trade-offs, underlies local adaptation and that hybridization and adaptive introgression play a key role in the evolution of these species. Future studies incorporating high-throughput phenotyping, gene expression, and modeling will be used to predict responses of these species to climate change.
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Affiliation(s)
- Acer VanWallendael
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA; Department of Energy Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA; Program in Ecology, Evolution, and Behaviour, Michigan State University, East Lansing, MI, 48824, USA; Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA
| | - David B Lowry
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA; Department of Energy Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA; Program in Ecology, Evolution, and Behaviour, Michigan State University, East Lansing, MI, 48824, USA; Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA.
| | - Jill A Hamilton
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA, 16801, USA
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42
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Buck R, Flores-Rentería L. The Syngameon Enigma. PLANTS (BASEL, SWITZERLAND) 2022; 11:895. [PMID: 35406874 PMCID: PMC9002738 DOI: 10.3390/plants11070895] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/21/2022] [Accepted: 03/25/2022] [Indexed: 05/17/2023]
Abstract
Despite their evolutionary relevance, multispecies networks or syngameons are rarely reported in the literature. Discovering how syngameons form and how they are maintained can give insight into processes such as adaptive radiations, island colonizations, and the creation of new hybrid lineages. Understanding these complex hybridization networks is even more pressing with anthropogenic climate change, as syngameons may have unique synergistic properties that will allow participating species to persist. The formation of a syngameon is not insurmountable, as several ways for a syngameon to form have been proposed, depending mostly on the magnitude and frequency of gene flow events, as well as the relatedness of its participants. Episodic hybridization with small amounts of introgression may keep syngameons stable and protect their participants from any detrimental effects of gene flow. As genomic sequencing becomes cheaper and more species are included in studies, the number of known syngameons is expected to increase. Syngameons must be considered in conservation efforts as the extinction of one participating species may have detrimental effects on the survival of all other species in the network.
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Affiliation(s)
- Ryan Buck
- Department of Biology, San Diego State University, San Diego, CA 92182, USA;
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43
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Islam SS, Xue X, Caballero-Solares A, Bradbury IR, Rise ML, Fleming IA. Distinct early life stage gene expression effects of hybridization among European and North American farmed and wild Atlantic salmon populations. Mol Ecol 2022; 31:2712-2729. [PMID: 35243721 DOI: 10.1111/mec.16418] [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: 09/20/2021] [Revised: 01/29/2022] [Accepted: 02/21/2022] [Indexed: 11/27/2022]
Abstract
Due to multi-generation domestication selection, farmed and wild Atlantic salmon diverge genetically, which raises concerns about potential genetic interactions among escaped farmed and wild populations and disruption of local adaptation through introgression. When farmed strains of distant geographic origin are used, it is unknown whether the genetic consequences posed by escaped farmed fish will be greater than if more locally derived strains are used. Quantifying gene transcript expression differences among divergent farmed, wild and F1 hybrids under controlled conditions is one of the ways to explore the consequences of hybridization. We compared the transcriptomes of fry at the end of yolk sac absorption of a European (EO) farmed ("StofnFiskur", Norwegian strain), a North American (NA) farmed (Saint John River, NB strain), a Newfoundland (NF) wild population with EO ancestry, and related F1 hybrids using 44K microarrays. Our findings indicate that the wild population showed greater transcriptome differences from the EO farmed strain than that of the NA farmed strain. We also found the largest differences in global gene expression between the two farmed strains. We detected the fewest differentially expressed transcripts between F1 hybrids and domesticated/wild maternal strains. We also found that the differentially expressed genes between cross types over-represented GO terms associated with metabolism, development, growth, immune response, and redox homeostasis processes. These findings suggest that the interbreeding of escaped EO/NA farmed and NF wild population would alter gene transcription, and the consequences of hybridization would be greater from escaped EO farmed than NA farmed salmon, resulting in potential effects on the wild populations.
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Affiliation(s)
- Shahinur S Islam
- Department of Ocean Sciences, Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, A1C 5S7, Canada
| | - Xi Xue
- Department of Ocean Sciences, Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, A1C 5S7, Canada
| | - Albert Caballero-Solares
- Department of Ocean Sciences, Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, A1C 5S7, Canada
| | - Ian R Bradbury
- Department of Ocean Sciences, Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, A1C 5S7, Canada.,Salmonids Section, Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, 80 East White Hills Road, St. John's, NL, A1C 5X, Canada
| | - Matthew L Rise
- Department of Ocean Sciences, Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, A1C 5S7, Canada
| | - Ian A Fleming
- Department of Ocean Sciences, Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, A1C 5S7, Canada
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44
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Wambugu PW, Henry R. Supporting in situ conservation of the genetic diversity of crop wild relatives using genomic technologies. Mol Ecol 2022; 31:2207-2222. [PMID: 35170117 PMCID: PMC9303585 DOI: 10.1111/mec.16402] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/08/2022] [Accepted: 02/11/2022] [Indexed: 11/27/2022]
Abstract
The last decade has witnessed huge technological advances in genomics, particularly in DNA sequencing. Here, we review the actual and potential application of genomics in supporting in situ conservation of crop wild relatives (CWRs). In addition to helping in prioritization of protection of CWR taxa and in situ conservation sites, genome analysis is allowing the identification of novel alleles that need to be prioritized for conservation. Genomics is enabling the identification of potential sources of important adaptive traits that can guide the establishment or enrichment of in situ genetic reserves. Genomic tools also have the potential for developing a robust framework for monitoring and reporting genome‐based indicators of genetic diversity changes associated with factors such as land use or climate change. These tools have been demonstrated to have an important role in managing the conservation of populations, supporting sustainable access and utilization of CWR diversity, enhancing accelerated domestication of new crops and forensic genomics thus preventing misappropriation of genetic resources. Despite this great potential, many policy makers and conservation managers have failed to recognize and appreciate the need to accelerate the application of genomics to support the conservation and management of biodiversity in CWRs to underpin global food security. Funding and inadequate genomic expertise among conservation practitioners also remain major hindrances to the widespread application of genomics in conservation.
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Affiliation(s)
- Peterson W Wambugu
- Kenya Agricultural and Livestock Research Organization, Genetic Resources Research Institute, P.O. Box 30148, 00100, Nairobi, Kenya
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, 4072, Australia.,ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland, Brisbane, QLD, 4072, Australia
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45
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Kearns AM, Campana MG, Slikas B, Berry L, Saitoh T, Cibois A, Fleischer RC. Conservation genomics and systematics of a near-extinct island radiation. Mol Ecol 2022; 31:1995-2012. [PMID: 35119154 DOI: 10.1111/mec.16382] [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: 10/14/2021] [Revised: 01/16/2022] [Accepted: 01/24/2022] [Indexed: 11/27/2022]
Abstract
Conservation benefits from incorporating genomics to explore the impacts of population declines, inbreeding, loss of genetic variation and hybridization. Here we use the near-extinct Mariana Islands reedwarbler radiation to showcase how ancient DNA approaches can allow insights into the population dynamics of extinct species and threatened populations for which historical museum specimens or material with low DNA yield (e.g., scats, feathers) are the only sources for DNA. Despite their having paraphyletic mtDNA, nuclear SNPs support the distinctiveness of critically endangered Acrocephalus hiwae and the other three species in the radiation that went extinct between the 1960s and 1990s. Two extinct species, A. yamashinae and A. luscinius, were deeply divergent from each other and from a third less differentiated lineage containing A. hiwae and extinct A. nijoi. Both mtDNA and SNPs suggest that the two isolated populations of A. hiwae from Saipan and Alamagan Islands are sufficiently distinct to warrant subspecies recognition and separate conservation management. We detected no significant differences in genetic diversity or inbreeding between Saipan and Alamagan, nor strong signatures of geographic structuring within either island. However, the implications of possible signatures of inbreeding in both Saipan and Alamagan, and long-term population declines in A. hiwae that predate modern anthropogenic threats require further study with denser population sampling. Our study highlights the value conservation genomics studies of island radiations have as windows onto the possible future for the world's biota as climate change and habitat destruction increasingly fragments their ranges and contributes to rapid declines in population abundances.
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Affiliation(s)
- Anna M Kearns
- Center for Conservation Genomics, Smithsonian's National Zoological Park and Conservation Biology Institute, Washington, DC, 20008, USA
| | - Michael G Campana
- Center for Conservation Genomics, Smithsonian's National Zoological Park and Conservation Biology Institute, Washington, DC, 20008, USA
| | - Beth Slikas
- Center for Conservation Genomics, Smithsonian's National Zoological Park and Conservation Biology Institute, Washington, DC, 20008, USA.,Center for Evolution & Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Lainie Berry
- Department of Lands and Natural Resources, Commonwealth of the Northern Mariana Islands, Saipan, MP, 96950, USA.,Hawaii Department of Land and Natural Resources-Division of Forestry and Wildlife, Honolulu, HI, 96813, USA
| | - Takema Saitoh
- Yamashina Institute for Ornithology, 115 Konoyama, Abiko, Chiba, 270-1145, Japan
| | - Alice Cibois
- Natural History Museum of Geneva, CP, 6434, 1211, Geneva, Switzerland
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian's National Zoological Park and Conservation Biology Institute, Washington, DC, 20008, USA
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46
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Combe FJ, Jaster L, Ricketts A, Haukos D, Hope AG. Population genomics of free-ranging Great Plains white-tailed and mule deer reflects a long history of interspecific hybridization. Evol Appl 2022; 15:111-131. [PMID: 35126651 PMCID: PMC8792484 DOI: 10.1111/eva.13330] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/21/2021] [Accepted: 11/22/2021] [Indexed: 12/11/2022] Open
Abstract
Hybridization is a natural process at species-range boundaries that may variably promote the speciation process or break down species barriers but minimally will influence management outcomes of distinct populations. White-tailed deer (Odocoileus virginianus) and mule deer (Odocoileus hemionus) have broad and overlapping distributions in North America and a recognized capacity for interspecific hybridization. In response to contemporary environmental change to any of one or multiple still-unknown factors, mule deer range is contracting westward accompanied by a westward expansion of white-tailed deer, leading to increasing interactions, opportunities for gene flow, and associated conservation implications. To quantify genetic diversity, phylogenomic structure, and dynamics of hybridization in sympatric populations of white-tailed and mule deer, we used mitochondrial cytochrome b data coupled with SNP loci discovered with double-digest restriction site-associated DNA sequencing. We recovered 25,018 SNPs across 92 deer samples from both species, collected from two regions of western Kansas. Eight individuals with unambiguous external morphology representing both species were of hybrid origin (8.7%), and represented the product of multi-generational backcrossing. Mitochondrial data showed both ancient and recent directional discordance with morphological species assignments, reflecting a legacy of mule deer males mating with white-tailed deer females. Mule deer had lower genetic diversity than white-tailed deer, and both mitochondrial and nuclear data suggest contemporary mule deer effective population decline. Landscape genetic analyses show relative isolation between the two study regions for white-tailed deer, but greater connectivity among mule deer, with predominant movement from north to south. Collectively, our results suggest a long history of gene flow between these species in the Great Plains and hint at evolutionary processes that purge incompatible functional genomic elements as a result of hybridization. Surviving hybrids evidently may be reproductive, but with unknown consequences for the future integrity of these species, population trajectories, or relative susceptibility to emerging pathogens.
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Affiliation(s)
- Fraser J. Combe
- Division of BiologyKansas State UniversityManhattanKansasUSA
| | - Levi Jaster
- Kansas Department of Wildlife and ParksTopekaKansasUSA
| | - Andrew Ricketts
- Department of Horticulture and Natural Sciences, Wildlife and Outdoor Enterprise ManagementKansas State UniversityManhattanKansasUSA
| | - David Haukos
- Division of BiologyU.S. Geological SurveyKansas Cooperative Fish and Wildlife Research UnitKansas State UniversityManhattanKansasUSA
| | - Andrew G. Hope
- Division of BiologyKansas State UniversityManhattanKansasUSA
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47
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Adavoudi R, Pilot M. Consequences of Hybridization in Mammals: A Systematic Review. Genes (Basel) 2021; 13:50. [PMID: 35052393 PMCID: PMC8774782 DOI: 10.3390/genes13010050] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/14/2021] [Accepted: 12/20/2021] [Indexed: 12/18/2022] Open
Abstract
Hybridization, defined as breeding between two distinct taxonomic units, can have an important effect on the evolutionary patterns in cross-breeding taxa. Although interspecific hybridization has frequently been considered as a maladaptive process, which threatens species genetic integrity and survival via genetic swamping and outbreeding depression, in some cases hybridization can introduce novel adaptive variation and increase fitness. Most studies to date focused on documenting hybridization events and analyzing their causes, while relatively little is known about the consequences of hybridization and its impact on the parental species. To address this knowledge gap, we conducted a systematic review of studies on hybridization in mammals published in 2010-2021, and identified 115 relevant studies. Of 13 categories of hybridization consequences described in these studies, the most common negative consequence (21% of studies) was genetic swamping and the most common positive consequence (8%) was the gain of novel adaptive variation. The total frequency of negative consequences (49%) was higher than positive (13%) and neutral (38%) consequences. These frequencies are biased by the detection possibilities of microsatellite loci, the most common genetic markers used in the papers assessed. As negative outcomes are typically easier to demonstrate than positive ones (e.g., extinction vs hybrid speciation), they may be over-represented in publications. Transition towards genomic studies involving both neutral and adaptive variation will provide a better insight into the real impacts of hybridization.
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Affiliation(s)
| | - Małgorzata Pilot
- Museum and Institute of Zoology, Polish Academy of Sciences, ul. Nadwiślańska 108, 80-680 Gdańsk, Poland;
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48
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Baltazar‐Soares M, Brans KI, Eizaguirre C. Human‐induced evolution: Signatures, processes and mechanisms underneath anthropogenic footprints on natural systems. Evol Appl 2021. [PMCID: PMC8549613 DOI: 10.1111/eva.13305] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The impact of human activities on the global environment has increased to such an extent that the current geological era has been coined the Anthropocene. Studies dedicated to understanding the evolutionary consequences of human‐induced selection on all levels of diversity (species, populations, traits, genes) provide direct knowledge about the mechanisms underlying species' responses and their evolutionary potential. A better understanding of the effects of human‐induced selection is needed to leverage evolved mechanisms to develop appropriate conservation programmes to guarantee the maintenance of healthy systems. In this special issue, we focus on different types of human‐mediated selection pressures, from the direct harvesting of individuals (e.g. hunting, fishing), to the more pervasive effects of climate change. Contributions highlight the diversity of human‐induced selection pressures ranging from fisheries, trophy‐hunting, poaching and domestication to climate change, and pollution. With those, we question whether there are parallel evolutionary solutions across fisheries systems, whether hunting pressures alter population dynamics and population structure, and whether climate change is an evolutionary dead‐end. The contributions reflect the direction of travel of the field and the solutions to mitigate the impact of human activities.
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Affiliation(s)
| | - Kristien I. Brans
- Department of Biology Laboratory of Aquatic Ecology, Evolution and Conservation KU Leuven Leuven Belgium
| | - Christophe Eizaguirre
- School of Biological and Chemical Sciences Queen Mary University of London London UK
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49
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Jofre GI, Rosenthal GG. A narrow window for geographic cline analysis using genomic data: Effects of age, drift, and migration on error rates. Mol Ecol Resour 2021; 21:2278-2287. [PMID: 33979028 DOI: 10.1111/1755-0998.13428] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 05/04/2021] [Accepted: 05/07/2021] [Indexed: 01/11/2023]
Abstract
The use of genomic and phenotypic data to scan for outliers is a mainstay for studies of hybridization and speciation. Geographic cline analysis of natural hybrid zones is widely used to identify putative signatures of selection by detecting deviations from baseline patterns of introgression. As with other outlier-based approaches, demographic histories can make neutral regions appear to be under selection and vice versa. In this study, we use a forward-time individual-based simulation approach to evaluate the robustness of geographic cline analysis under different evolutionary scenarios. We modelled multiple stepping-stone hybrid zones with distinct age, deme sizes, and migration rates, and evolving under different types of selection. We found that drift distorts cline shapes and increases false positive rates for signatures of selection. This effect increases with hybrid zone age, particularly if migration between demes is low. Drift can also distort the signature of deleterious effects of hybridization, with genetic incompatibilities and particularly underdominance prone to spurious typing as adaptive introgression. Our results suggest that geographic clines are most useful for outlier analysis in young hybrid zones with large populations of hybrid individuals. Current approaches may overestimate adaptive introgression and underestimate selection against maladaptive genotypes.
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Affiliation(s)
- Gaston I Jofre
- Department of Biology, Texas A&M University, TAMU, College Station, TX, USA.,Centro de Investigaciones Cientıficas de las Huastecas "Aguazarca", Calnali Hidalgo, Mexico.,Department of Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Gil G Rosenthal
- Department of Biology, Texas A&M University, TAMU, College Station, TX, USA.,Centro de Investigaciones Cientıficas de las Huastecas "Aguazarca", Calnali Hidalgo, Mexico
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50
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Demographic modeling informs functional connectivity and management interventions in Graham’s beardtongue. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01392-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
AbstractFunctional connectivity (i.e., the movement of individuals across a landscape) is essential for the maintenance of genetic variation and persistence of rare species. However, illuminating the processes influencing functional connectivity and ultimately translating this knowledge into management practice remains a fundamental challenge. Here, we combine various population structure analyses with pairwise, population-specific demographic modeling to investigate historical functional connectivity in Graham’s beardtongue (Penstemon grahamii), a rare plant narrowly distributed across a dryland region of the western US. While principal component and population structure analyses indicated an isolation-by-distance pattern of differentiation across the species’ range, spatial inferences of effective migration exposed an abrupt shift in population ancestry near the range center. To understand these seemingly conflicting patterns, we tested various models of historical gene flow and found evidence for recent admixture (~ 3400 generations ago) between populations near the range center. This historical perspective reconciles population structure patterns and suggests management efforts should focus on maintaining connectivity between these previously isolated lineages to promote the ongoing transfer of genetic variation. Beyond providing species-specific knowledge to inform management options, our study highlights how understanding demographic history may be critical to guide conservation efforts when interpreting population genetic patterns and inferring functional connectivity.
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