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Santostasi NL, Bauduin S, Grente O, Gimenez O, Ciucci P. Simulating the efficacy of wolf-dog hybridization management with individual-based modeling. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2024:e14312. [PMID: 38894638 DOI: 10.1111/cobi.14312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 06/21/2024]
Abstract
Introgressive hybridization between wolves and dogs is a conservation concern due to its potentially deleterious long-term evolutionary consequences. European legislation requires that wolf-dog hybridization be mitigated through effective management. We developed an individual-based model (IBM) to simulate the life cycle of gray wolves that incorporates aspects of wolf sociality that affect hybridization rates (e.g., the dissolution of packs after the death of one/both breeders) with the goal of informing decision-making on management of wolf-dog hybridization. We applied our model by projecting hybridization dynamics in a local wolf population under different mate choice and immigration scenarios and contrasted results of removal of admixed individuals with their sterilization and release. In several scenarios, lack of management led to complete admixture, whereas reactive management interventions effectively reduced admixture in wolf populations. Management effectiveness, however, strongly depended on mate choice and number and admixture level of individuals immigrating into the wolf population. The inclusion of anthropogenic mortality affecting parental and admixed individuals (e.g., poaching) increased the probability of pack dissolution and thus increased the probability of interbreeding with dogs or admixed individuals and boosted hybridization and introgression rates in all simulation scenarios. Recognizing the necessity of additional model refinements (appropriate parameterization, thorough sensitivity analyses, and robust model validation) to generate management recommendations applicable in real-world scenarios, we maintain confidence in our model's potential as a valuable conservation tool that can be applied to diverse situations and species facing similar threats.
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Affiliation(s)
- Nina Luisa Santostasi
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Roma, Italy
- CEFE, CNRS, Univ. Montpellier, EPHE, IRD, Montpellier, France
- National Biodiversity Future Center, Palermo, Italy
| | - Sarah Bauduin
- Direction de la Recherche et Appui Scientifique, Service Conservation et Gestion des Espèces à Enjeux, Office Français de la Biodiversité, Juvignac, France
| | - Oksana Grente
- CEFE, CNRS, Univ. Montpellier, EPHE, IRD, Montpellier, France
| | - Olivier Gimenez
- CEFE, CNRS, Univ. Montpellier, EPHE, IRD, Montpellier, France
| | - Paolo Ciucci
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Roma, Italy
- National Biodiversity Future Center, Palermo, Italy
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2
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Marković M, Vidaković V, Popović Z. A Geometric Morphometrics Approach to the Study of Natural Variations and Hybrid Detection in Populations of Alnus incana (L.) Moench and Alnus rohlenae Vít, Douda and Mandák. PLANTS (BASEL, SWITZERLAND) 2024; 13:993. [PMID: 38611522 PMCID: PMC11013130 DOI: 10.3390/plants13070993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/25/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024]
Abstract
Landmark-based geometric morphometrics (GM) was used to examine, for the first time, spontaneous hybridization between Alnus incana (L.) Moench and Alnus rohlenae Vít, Douda and Mandák, and to assess inter- and intrapopulation variability in leaf shape, leaf size and venation in natural populations in Serbia (Western Balkans). Two geographically distant (30 km) and two close (1.2 km) populations were selected to examine hybridization. The variability in leaf shapes was assessed by canonical variate analysis and linear discriminant analysis performed on the symmetric component of variation. Covariation between the symmetric component of shape variation and the number of pairs of secondary leaf veins was investigated with partial least squares analysis. Static allometry was examined for the first time in the genus Alnus Mill. A higher proportion of A. incana leaves was classified as A. rohlenae in geographically close populations, which is in accordance with the hypothesis about spontaneous hybridization. No single leaf of A. rohlenae was classified as A. incana, indicating that putative hybrids can only be found in grey alder populations. This study demonstrates that GM is a powerful tool for species delimitation and hybrid detection in the genus Alnus and it can be used for preliminary screening in hybrid zones.
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3
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Diz AP, Skibinski DOF. Patterns of admixture and introgression in a mosaic Mytilus galloprovincialis and Mytilus edulis hybrid zone in SW England. Mol Ecol 2024; 33:e17233. [PMID: 38063472 DOI: 10.1111/mec.17233] [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] [Revised: 11/21/2023] [Accepted: 11/24/2023] [Indexed: 01/25/2024]
Abstract
The study of hybrid zones offers important insights into speciation. Earlier studies on hybrid populations of the marine mussel species Mytilus edulis and Mytilus galloprovincialis in SW England provided evidence of admixture but were constrained by the limited number of molecular markers available. We use 57 ancestry-informative SNPs, most of which have been mapped genetically, to provide evidence of distinctive differences between admixed populations in SW England and asymmetrical introgression from M. edulis to M. galloprovincialis. We combine the genetic study with analysis of phenotypic traits of potential ecological and adaptive significance. We demonstrate that hybrid individuals have brown mantle edges unlike the white or purple in the parental species, suggesting allelic or non-allelic genomic interactions. We report differences in gonad development stage between the species consistent with a prezygotic barrier between the species. By incorporating results from publications dating back to 1980, we confirm the long-term stability of the hybrid zone despite higher viability of M. galloprovincialis. This stability coincides with a dramatic change in temperature of UK coastal waters and suggests that these hybrid populations might be resisting the effects of global warming. However, a single SNP locus associated with the Notch transmembrane signalling protein shows a markedly different pattern of variation to the others and might be associated with adaptation of M. galloprovincialis to colder northern temperatures.
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Affiliation(s)
- Angel P Diz
- Centro de Investigación Mariña, Universidade de Vigo (CIM-UVIGO), Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain
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4
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Nieto Feliner G, Criado Ruiz D, Álvarez I, Villa-Machío I. The puzzle of plant hybridisation: a high propensity to hybridise but few hybrid zones reported. Heredity (Edinb) 2023; 131:307-315. [PMID: 37884616 PMCID: PMC10673867 DOI: 10.1038/s41437-023-00654-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 10/28/2023] Open
Abstract
An interesting conundrum was recently revealed by R. Abbott when he found that the number of hybrid zones reported in the literature for plants is very low, given the propensity of plants to hybridise. In another literature survey on hybrid zones performed over the period 1970-2022, we found that the number of hybrid zones reported for vertebrates was 2.3 times greater than that reported for vascular plants, even though there are about six times more vascular plant species than vertebrates. Looking at the number of papers reporting hybrid zones, there are 4.9 times more on vertebrates than on vascular plants. These figures support the relevance of this conundrum. In this paper we aim to shed light on this question by providing a structured discussion of the causes that may underlie this conundrum. We propose six non-mutually exclusive factors, namely lack or deficit of spatial structure, lack or deficit of genetic structure, effects of hybridisation between non-closely related species, lability of plant hybrid zones over time, botanists' perception of hybridisation, and deficit of population genetic data. There does not appear to be a single factor that explains our puzzle, which applies to all cases of plants where hybridisation is detected but no hybrid zone is reported. It is argued that some plant features suggest that the puzzle is not, at least entirely, due to insufficient knowledge of the specific cases, a hypothesis that should be addressed with a wider range of empirical data across different taxonomic groups.
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Affiliation(s)
| | - David Criado Ruiz
- Real Jardín Botánico (RJB), CSIC, Plaza de Murillo 2, 28014, Madrid, Spain
| | - Inés Álvarez
- Real Jardín Botánico (RJB), CSIC, Plaza de Murillo 2, 28014, Madrid, Spain
| | - Irene Villa-Machío
- Real Jardín Botánico (RJB), CSIC, Plaza de Murillo 2, 28014, Madrid, Spain
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5
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Simon L, Soares LS, Freitas LB. Disentangling the causes of high polymorphism sharing in sympatric Petunia species from subtropical highland grasslands: insights from nuclear diversity. Genet Mol Biol 2023; 46:e20230159. [PMID: 37931074 PMCID: PMC10619130 DOI: 10.1590/1678-4685-gmb-2023-0159] [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: 06/09/2023] [Accepted: 09/26/2023] [Indexed: 11/08/2023] Open
Abstract
Genetic polymorphism sharing between closely related and sympatric plant species could result from common ancestry, ancient or recent hybridization. Here we analyzed four Petunia species from the subtropical highland grasslands in southern South America based on nuclear diversity to disentangle the causes of high polymorphism sharing between them. We genotyped microsatellite loci, employed population genetic methods to estimate variability, species limits, and ancient and recent gene flow, and assigned individuals to genetic and taxonomic groups. Finally, we modeled evolutionary processes to determine the impact of Quaternary climate changes on species phylogenetic relationships. Our results indicated that genetic diversity was strongly influenced by expansion and habitat fragmentation during the Quaternary cycles. The extensive polymorphism sharing is mainly due to species' common ancestry, and we did not discard ancient hybridization. Nowadays, niche differentiation is the primary driver for maintaining genetic and morphological limits between the four analysed Petunia species and there is no recent gene flow between them.
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Affiliation(s)
- Luize Simon
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Porto Alegre, RS, Brazil
| | - Luana S Soares
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Porto Alegre, RS, Brazil
| | - Loreta B Freitas
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Porto Alegre, RS, Brazil
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6
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Carscadden KA, Batstone RT, Hauser FE. Origins and evolution of biological novelty. Biol Rev Camb Philos Soc 2023; 98:1472-1491. [PMID: 37056155 DOI: 10.1111/brv.12963] [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: 01/28/2022] [Revised: 03/30/2023] [Accepted: 04/03/2023] [Indexed: 04/15/2023]
Abstract
Understanding the origins and impacts of novel traits has been a perennial interest in many realms of ecology and evolutionary biology. Here, we build on previous evolutionary and philosophical treatments of this subject to encompass novelties across biological scales and eco-evolutionary perspectives. By defining novelties as new features at one biological scale that have emergent effects at other biological scales, we incorporate many forms of novelty that have previously been treated in isolation (such as novelty from genetic mutations, new developmental pathways, new morphological features, and new species). Our perspective is based on the fundamental idea that the emergence of a novelty, at any biological scale, depends on its environmental and genetic context. Through this lens, we outline a broad array of generative mechanisms underlying novelty and highlight how genomic tools are transforming our understanding of the origins of novelty. Lastly, we present several case studies to illustrate how novelties across biological scales and systems can be understood based on common mechanisms of change and their environmental and genetic contexts. Specifically, we highlight how gene duplication contributes to the evolution of new complex structures in visual systems; how genetic exchange in symbiosis alters functions of both host and symbiont, resulting in a novel organism; and how hybridisation between species can generate new species with new niches.
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Affiliation(s)
- Kelly A Carscadden
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, 1900 Pleasant St, Boulder, CO, 80309, USA
| | - Rebecca T Batstone
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, 61801, USA
| | - Frances E Hauser
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario, M1C 1A4, Canada
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7
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Fiorini CF, de Camargo Smidt E, Lacey Knowles L, Leite Borba E. Hybridization boosters diversification in a Neotropical Bulbophyllum (Orchidaceae) group. Mol Phylogenet Evol 2023:107858. [PMID: 37329930 DOI: 10.1016/j.ympev.2023.107858] [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: 02/15/2023] [Revised: 06/06/2023] [Accepted: 06/10/2023] [Indexed: 06/19/2023]
Abstract
Genetic data shows that cryptic hybrids are more common than previously thought and that hybridization and introgression are widespread processes. Regardless, studies on hybridization are scarce for the highly speciose Bulbophyllum. The genus presents more than 2,200 species and many examples of recent radiations, in which hybridization is expected to be frequent. Currently, only four natural Bulbophyllum hybrids are recognized, all of them recently described based on morphological evidence. Here we test whether genomic evidence supports the hybrid status of two Neotropical Bulbophyllum species, while also evaluating the impact of this phenomenon on the genomes of the putative parental species. We also assess if there is evidence of hybridization among B. involutum and B. exaltatum, sister species that diverged recently. We leverage the power of next-generation sequence data, associated with model-based analysis for three systems putatively constituted by two parental species and one hybrid. All taxa belong to the Neotropical B. sect. Didactyle clade. We found evidence of hybridization in all studied systems. Despite the occurrence of hybridization, there are no signs of backcrossing. Because of the high propensity of hybridization across many taxa, the common occurrence of hybridization during the evolutionary history of B. sect. Didactyle means it is time to account for and examine its evolutionary role in these orchids.
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Affiliation(s)
- Cecilia F Fiorini
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil; Departamento de Botânica, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil.
| | - Eric de Camargo Smidt
- Departamento de Botânica, Universidade Federal do Paraná, Curitiba, Paraná, 81531-990, Brazil.
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48109-1085, USA.
| | - Eduardo Leite Borba
- Departamento de Botânica, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil.
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8
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Yu J, Niu Y, You Y, Cox CJ, Barrett RL, Trias-Blasi A, Guo J, Wen J, Lu L, Chen Z. Integrated phylogenomic analyses unveil reticulate evolution in Parthenocissus (Vitaceae), highlighting speciation dynamics in the Himalayan-Hengduan Mountains. THE NEW PHYTOLOGIST 2023; 238:888-903. [PMID: 36305244 DOI: 10.1111/nph.18580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
Hybridization caused by frequent environmental changes can lead both to species diversification (speciation) and to speciation reversal (despeciation), but the latter has rarely been demonstrated. Parthenocissus, a genus with its trifoliolate lineage in the Himalayan-Hengduan Mountains (HHM) region showing perplexing phylogenetic relationships, provides an opportunity for investigating speciation dynamics based on integrated evidence. We investigated phylogenetic discordance and reticulate evolution in Parthenocissus based on rigorous analyses of plastome and transcriptome data. We focused on reticulations in the trifoliolate lineage in the HHM region using a population-level genome resequencing dataset, incorporating evidence from morphology, distribution, and elevation. Comprehensive analyses confirmed multiple introgressions within Parthenocissus in a robust temporal-spatial framework. Around the HHM region, at least three hybridization hot spots were identified, one of which showed evidence of ongoing speciation reversal. We present a solid case study using an integrative methodological approach to investigate reticulate evolutionary history and its underlying mechanisms in plants. It demonstrates an example of speciation reversal through frequent hybridizations in the HHM region, which provides new perspectives on speciation dynamics in mountainous areas with strong topographic and environmental heterogeneity.
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Affiliation(s)
- Jinren Yu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanting Niu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- China National Botanical Garden, Beijing, 100093, China
| | - Yichen You
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cymon J Cox
- Centro de Ciências do Mar, Universidade do Algarve, Gambelas, Faro, 8005-319, Portugal
| | - Russell L Barrett
- National Herbarium of New South Wales, Australian Botanic Garden, Locked Bag 6002, Mount Annan, 2567, NSW, Australia
| | | | - Jing Guo
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC-166, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Limin Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zhiduan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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9
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Grabenstein KC, Otter KA, Burg TM, Taylor SA. Hybridization between closely related songbirds is related to human habitat disturbance. GLOBAL CHANGE BIOLOGY 2023; 29:955-968. [PMID: 36305309 DOI: 10.1111/gcb.16476] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 09/14/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
Human habitat disturbances can promote hybridization between closely related, but typically reproductively isolated, species. We explored whether human habitat disturbances are related to hybridization between two closely related songbirds, black-capped and mountain chickadees, using both genomic and citizen science data sets. First, we genotyped 409 individuals from across both species' ranges using reduced-representation genome sequencing and compared measures of genetic admixture to a composite measure of human landscape disturbance. Then, using eBird observations, we compared human landscape disturbance values for sites where phenotypically diagnosed hybrids were observed to locations where either parental species was observed to determine whether hybrid chickadees are reported in more disturbed areas. We found that hybridization between black-capped and mountain chickadees positively correlates with human habitat disturbances. From genomic data, we found that (1) hybrid index (HI) significantly increased with habitat disturbance, (2) more hybrids were sampled in disturbed habitats, (3) mean HIs were higher in disturbed habitats versus wild habitats, and (4) hybrids were detected in habitats with significantly higher disturbance values than parentals. Using eBird data, we found that both hybrid and black-capped chickadees were significantly more disturbance-associated than mountain chickadees. Surprisingly, we found that nearly every black-capped chickadee we sampled contained some proportion of hybrid ancestry, while we detected very few mountain chickadee backcrosses. Our results highlight that hybridization between black-capped and mountain chickadees is widespread, but initial hybridization is rare (few F1s were detected). We conclude that human habitat disturbances can erode pre-zygotic reproductive barriers between chickadees and that post-zygotic isolation is incomplete. Understanding what becomes of recently hybridizing species following large-scale habitat disturbances is a new, but pressing, consideration for successfully preserving genetic biodiversity in a rapidly changing world.
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Affiliation(s)
- Kathryn C Grabenstein
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, USA
| | - Ken A Otter
- Natural Resources and Environmental Studies, University of Northern British Columbia, Prince George, British Columbia, Canada
| | - Theresa M Burg
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Scott A Taylor
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, USA
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10
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Feng X, Merilä J, Löytynoja A. Complex population history affects admixture analyses in nine-spined sticklebacks. Mol Ecol 2022; 31:5386-5401. [PMID: 35962788 PMCID: PMC9828525 DOI: 10.1111/mec.16651] [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] [Received: 01/25/2022] [Revised: 08/02/2022] [Accepted: 08/08/2022] [Indexed: 01/12/2023]
Abstract
Introgressive hybridization is an important process in evolution but challenging to identify, undermining the efforts to understand its role and significance. On the contrary, many analytical methods assume direct descent from a single common ancestor, and admixture among populations can violate their assumptions and lead to seriously biased results. A detailed analysis of 888 whole-genome sequences of nine-spined sticklebacks (Pungitius pungitius) revealed a complex pattern of population ancestry involving multiple waves of gene flow and introgression across northern Europe. The two recognized lineages were found to have drastically different histories, and their secondary contact zone was wider than anticipated, displaying a smooth gradient of foreign ancestry with some curious deviations from the expected pattern. Interestingly, the freshwater isolates provided peeks into the past and helped to understand the intermediate states of evolutionary processes. Our analyses and findings paint a detailed picture of the complex colonization history of northern Europe and provide backdrop against which introgression and its role in evolution can be investigated. However, they also expose the challenges in analyses of admixed populations and demonstrate how hidden admixture and colonization history misleads the estimation of admixture proportions and population split times.
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Affiliation(s)
- Xueyun Feng
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
| | - Juha Merilä
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland,Area of Ecology and Biodiversity, Kadoorie Science BuildingThe University of Hong KongHong Kong, SARChina
| | - Ari Löytynoja
- Institute of Biotechnology, University of HelsinkiHelsinkiFinland
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11
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Migdałek G, Żelawski M. Measuring population-level plant gene flow with topological data analysis. ECOL INFORM 2022. [DOI: 10.1016/j.ecoinf.2022.101740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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12
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Beaudry FEG, Rifkin JL, Peake AL, Kim D, Jarvis-Cross M, Barrett SCH, Wright SI. Effects of the neo-X chromosome on genomic signatures of hybridization in Rumex hastatulus. Mol Ecol 2022; 31:3708-3721. [PMID: 35569016 DOI: 10.1111/mec.16496] [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: 02/14/2022] [Revised: 04/23/2022] [Accepted: 05/05/2022] [Indexed: 11/30/2022]
Abstract
Natural hybrid zones provide opportunities for studies of the evolution of reproductive isolation in wild populations. Although recent investigations have found that the formation of neo-sex chromosomes is associated with reproductive isolation, the mechanisms remain unclear in most cases. Here, we assess the contemporary structure of gene flow in the contact zone between largely allopatric cytotypes of the dioecious plant Rumex hastatulus, a species with evidence of sex chromosome turn-over. Males to the west of the Mississippi river, USA, have an X and a single Y chromosome, whereas populations to the east of the river have undergone a chromosomal rearrangement giving rise to a larger X and two Y chromosomes. Using reduced-representation sequencing, we provide evidence that hybrids form readily and survive multiple backcross generations in the field, demonstrating the potential for ongoing gene flow between the cytotypes. Cline analysis of each chromosome separately captured no signals of difference in cline shape between chromosomes. However, principal component regression revealed a significant increase in the contribution of individual SNPs to inter-cytotype differentiation on the neo-X chromosome, but no correlation with recombination rate. Cline analysis revealed that the only SNPs with significantly steeper clines than the genome average were located on the neo-X. Our data are consistent with a role for neo-sex chromosomes in reproductive isolation between R. hastatulus cytotypes. Our investigation highlights the importance of studying plant hybrid zones for understanding the evolution of sex chromosomes.
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Affiliation(s)
- Felix E G Beaudry
- The University of Toronto, Department of Ecology and Evolutionary Biology, Toronto, ON, Canada
| | - Joanna L Rifkin
- The University of Toronto, Department of Ecology and Evolutionary Biology, Toronto, ON, Canada
| | - Amanda L Peake
- The University of Toronto, Department of Ecology and Evolutionary Biology, Toronto, ON, Canada
| | - Deanna Kim
- The University of Toronto, Department of Ecology and Evolutionary Biology, Toronto, ON, Canada
| | - Madeline Jarvis-Cross
- The University of Toronto, Department of Ecology and Evolutionary Biology, Toronto, ON, Canada
| | - Spencer C H Barrett
- The University of Toronto, Department of Ecology and Evolutionary Biology, Toronto, ON, Canada
| | - Stephen I Wright
- The University of Toronto, Department of Ecology and Evolutionary Biology, Toronto, ON, Canada
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13
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Genomic patterns and the evolutionary origin of an invasive fungal pathogen (Hymenoscyphus fraxineus) in Europe. Basic Appl Ecol 2022. [DOI: 10.1016/j.baae.2021.12.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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14
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Clark MI, Bradburd GS, Akopyan M, Vega A, Rosenblum EB, Robertson JM. Genetic isolation by distance underlies colour pattern divergence in red-eyed treefrogs (Agalychnis callidryas). Mol Ecol 2022; 31:1666-1681. [PMID: 35034406 PMCID: PMC8923152 DOI: 10.1111/mec.16350] [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: 05/22/2021] [Revised: 10/21/2021] [Accepted: 01/04/2022] [Indexed: 10/19/2022]
Abstract
Investigating the spatial distribution of genetic and phenotypic variation can provide insights into the evolutionary processes that shape diversity in natural systems. We characterized patterns of genetic and phenotypic diversity to learn about drivers of colour-pattern diversification in red-eyed treefrogs (Agalychnis callidryas) in Costa Rica. Along the Pacific coast, red-eyed treefrogs have conspicuous leg colour patterning that transitions from orange in the north to purple in the south. We measured phenotypic variation of frogs, with increased sampling at sites where the orange-to-purple transition occurs. At the transition zone, we discovered the co-occurrence of multiple colour-pattern morphs. To explore possible causes of this variation, we generated a single nucleotide polymorphism data set to analyse population genetic structure, measure genetic diversity and infer the processes that mediate genotype-phenotype dynamics. We investigated how patterns of genetic relatedness correspond to individual measures of colour pattern along the coast, including testing for the role of hybridization in geographic regions where orange and purple phenotypic groups co-occur. We found no evidence that colour-pattern polymorphism in the transition zone arose through recent hybridization. Instead, a strong pattern of genetic isolation by distance indicates that colour-pattern variation was either retained through other processes such as ancestral colour polymorphisms or ancient secondary contact, or else it was generated by novel mutations. We found that phenotype changes along the Pacific coast more than would be expected based on genetic divergence and geographic distance alone. Combined, our results suggest the possibility of selective pressures acting on colour pattern at a small geographic scale.
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Affiliation(s)
- Meaghan I. Clark
- Department of Biology, California State University Northridge, Northridge, California, USA,Department of integrative Biology, Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, Michigan, USA,W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, Michigan, USA
| | - Gideon S. Bradburd
- Department of integrative Biology, Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, Michigan, USA
| | - Maria Akopyan
- Department of Biology, California State University Northridge, Northridge, California, USA,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | | | - Erica Bree Rosenblum
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, USA,Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, California, USA
| | - Jeanne M. Robertson
- Department of Biology, California State University Northridge, Northridge, California, USA,Department of Herpetology, Natural History Museum of Los Angeles County, Los Angeles, California, USA
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15
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Muniz AC, Pimenta RJG, Cruz MV, Rodrigues JG, Buzatti RSDO, Heuertz M, Lemos‐Filho JP, Lovato MB. Hybrid zone of a tree in a Cerrado/Atlantic Forest ecotone as a hotspot of genetic diversity and conservation. Ecol Evol 2022; 12:e8540. [PMID: 35127043 PMCID: PMC8803295 DOI: 10.1002/ece3.8540] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 12/17/2021] [Indexed: 01/10/2023] Open
Abstract
The Cerrado, the largest Neotropical savanna, and the Brazilian Atlantic Forest form large ecotonal areas where savanna and forest habitats occupy adjacent patches with closely related species occurring side by side, providing opportunities for hybridization. Here, we investigated the evolutionary divergence between the savanna and forest ecotypes of the widely distributed tree Plathymenia reticulata (n = 233 individuals). Genetic structure analysis of P. reticulata was congruent with the recognition of two ecotypes, whose divergence captured the largest proportion of genetic variance in the data (F CT = 0.222 and F ST = 0.307). The ecotonal areas between the Cerrado and the Atlantic Forest constitute a hybrid zone in which a diversity of hybrid classes was observed, most of them corresponding to second-generation hybrids (F2) or backcrosses. Gene flow occurred mainly toward the forest ecotype. The genetic structure was congruent with isolation by environment, and environmental correlates of divergence were identified. The observed pattern of high genetic divergence between ecotypes may reflect an incipient speciation process in P. reticulata. The low genetic diversity of the P. reticulata forest ecotype indicate that it is threatened in areas with high habitat loss on Atlantic Forest. In addition, the high divergence from the savanna ecotype suggests it should be treated as a different unit of management. The high genetic diversity found in the ecotonal hybrid zone supports the view of ecotones as important areas for the origin and conservation of biodiversity in the Neotropics.
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Affiliation(s)
- André Carneiro Muniz
- Departamento de Genética, Ecologia e EvoluçãoUniversidade Federal de Minas GeraisBelo HorizonteBrazil
| | | | - Mariana Vargas Cruz
- Departamento de Genética, Ecologia e EvoluçãoUniversidade Federal de Minas GeraisBelo HorizonteBrazil
| | | | | | | | - José P. Lemos‐Filho
- Departamento de BotânicaUniversidade Federal de Minas GeraisBelo HorizonteBrazil
| | - Maria Bernadete Lovato
- Departamento de Genética, Ecologia e EvoluçãoUniversidade Federal de Minas GeraisBelo HorizonteBrazil
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16
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Dziech A. Identification of Wolf-Dog Hybrids in Europe – An Overview of Genetic Studies. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.760160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Significant development of genetic tools during the last decades provided opportunities for more detailed analyses and deeper understanding of species hybridization. New genetic markers allowed for reliable identification of admixed individuals deriving from recent hybridization events (a few generations) and those originating from crossings up to 19 generations back. Implementation of microsatellites (STRs) together with Bayesian clustering provided abundant knowledge regarding presence of admixed individuals in numerous populations and helped understand the problematic nature of studying hybridization (i.a., defining a reliable thresholds for recognizing individuals as admixed or obtaining well-grounded results representing actual proportion of hybrids in a population). Nevertheless, their utilization is limited to recent crossbreeding events. Single Nucleotide Polymorphisms (SNPs) proved to be more sensible tools for admixture analyses furnishing more reliable knowledge, especially for older generation backcrosses. Small sets of Ancestry Informative Markers (AIMs) of both types of markers were effective enough to implement in monitoring programs, however, SNPs seem to be more appropriate because of their ability to identify admixed individuals up to 3rd generations. The main aim of this review is to summarize abundant knowledge regarding identification of wolf-dog hybrids in Europe and discuss the most relevant problems relating to the issue, together with advantages and disadvantages of implemented markers and approaches.
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17
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Zalmat AS, Sotola VA, Nice CC, Martin NH. Genetic structure in Louisiana Iris species reveals patterns of recent and historical admixture. AMERICAN JOURNAL OF BOTANY 2021; 108:2257-2268. [PMID: 34618352 DOI: 10.1002/ajb2.1758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 08/10/2021] [Accepted: 08/18/2021] [Indexed: 06/13/2023]
Abstract
PREMISE When divergent lineages come into secondary contact, reproductive isolation may be incomplete, thus providing an opportunity to investigate how speciation is manifested in the genome. The Louisiana Irises (Iris, series Hexagonae) comprise a group of three or more ecologically and reproductively divergent lineages that can produce hybrids where they come into contact. We estimated standing genetic variation to understand the current distribution of population structure in the Louisiana Irises. METHODS We used genotyping-by-sequencing techniques to sample the genomes of Louisiana Iris species across their ranges. We sampled 20 populations (n = 632 individuals) across 11,249 loci and used Entropy and PCA models to assess population genetic data. RESULTS We discovered evidence for interspecific gene flow in parts of the range. Our analysis revealed patterns of population structure at odds with widely accepted nominal taxonomy. We discovered undescribed hybrid populations, designated as belonging to the I. brevicaulis lineage. Iris nelsonii shared significant ancestry with only one of the purported parent species, I. fulva, evidence inconsistent with a hybrid origin. CONCLUSIONS This study provides several key findings important to the investigation of standing genetic variation in the Louisiana Iris species complex. Compared to the other nominal species, I. brevicaulis contains a large amount of genetic diversity. In addition, we discovered a previously unknown hybrid zone between I. brevicaulis and I. hexagona along the Texas coast. Finally, our results do not support the long-standing hypothesis that I. nelsonii has mixed ancestry from three parental taxa.
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Affiliation(s)
- Alexander S Zalmat
- Department of Biology, Texas State University, San Marcos, Texas, 78666-0202, USA
| | - V Alex Sotola
- Department of Genetics, University of Georgia, Athens, Georgia, 30602-7223, USA
| | - Chris C Nice
- Department of Biology, Texas State University, San Marcos, Texas, 78666-0202, USA
| | - Noland H Martin
- Department of Biology, Texas State University, San Marcos, Texas, 78666-0202, USA
- Director of the Population and Conservation Biology Program, Department of Biology, Texas State University, San Marcos, Texas, 78666-0202, USA
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18
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Del-Rio G, Rego MA, Whitney BM, Schunck F, Silveira LF, Faircloth BC, Brumfield RT. Displaced clines in an avian hybrid zone (Thamnophilidae: Rhegmatorhina) within an Amazonian interfluve. Evolution 2021; 76:455-475. [PMID: 34626500 DOI: 10.1111/evo.14377] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 08/25/2021] [Accepted: 09/01/2021] [Indexed: 12/24/2022]
Abstract
Secondary contact between species often results in the formation of a hybrid zone, with the eventual fates of the hybridizing species dependent on evolutionary and ecological forces. We examine this process in the Amazon Basin by conducting the first genomic and phenotypic characterization of the hybrid zone formed after secondary contact between two obligate army-ant-followers: the White-breasted Antbird (Rhegmatorhina hoffmannsi) and the Harlequin Antbird (Rhegmatorhina berlepschi). We found a major geographic displacement (∼120 km) between the mitochondrial and nuclear clines, and we explore potential hypotheses for the displacement, including sampling error, genetic drift, and asymmetric cytonuclear incompatibilities. We cannot exclude roles for sampling error and genetic drift in contributing to the discordance; however, the data suggest expansion and unidirectional introgression of hoffmannsi into the distribution of berlepschi.
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Affiliation(s)
- Glaucia Del-Rio
- Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, 70803.,Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803
| | - Marco A Rego
- Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, 70803.,Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803
| | - Bret M Whitney
- Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, 70803.,Museu de Zoologia, Universidade de São Paulo, São Paulo, SP, 04263-000, Brazil
| | - Fabio Schunck
- Museu de Zoologia, Universidade de São Paulo, São Paulo, SP, 04263-000, Brazil
| | - Luís F Silveira
- Museu de Zoologia, Universidade de São Paulo, São Paulo, SP, 04263-000, Brazil
| | - Brant C Faircloth
- Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, 70803.,Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803
| | - Robb T Brumfield
- Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, 70803.,Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803
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19
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Barrios-Leal DY, Menezes RST, Ribeiro JV, Bizzo L, Melo de Sene F, Neves-da-Rocha J, Manfrin MH. A holocenic and dynamic hybrid zone between two cactophilic Drosophila species in a coastal lowland plain of the Brazilian Atlantic Forest. J Evol Biol 2021; 34:1737-1751. [PMID: 34538008 DOI: 10.1111/jeb.13934] [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: 02/04/2021] [Revised: 08/31/2021] [Accepted: 09/06/2021] [Indexed: 11/30/2022]
Abstract
Hybridization and introgression are processes that contribute to shaping biological diversity. The factors promoting the formation of these processes are multiples but poorly explored in a biogeographical and ecological context. In the southeast coastal plain of the Brazilian Atlantic Forest, a hybrid zone was described between two closely related cactophilic species, Drosophila antonietae and D. serido. Here, we revisited and analysed specimens from this hybrid zone to evaluate its temporal and spatial dynamic. We examined allopatric and sympatric populations of the flies using independent sources of data such as mitochondrial and nuclear sequences, microsatellite loci, morphometrics of wings and male genitalia, and climatic niche models. We also verified the emergence of the flies from necrotic tissues of collected cacti to verify the role of host association for the population dynamics. Our results support the existence of a hybrid zone due to secondary contact and limited to the localities where the two species are currently in contact. Furthermore, we detected asymmetric bidirectional introgression and the maintenance of the species integrity, ecological association and morphological characters, suggesting selection and limited introgression. Considering our paleomodels, probably this hybrid zone is recent and the contact occurred during the Holocene to the present day, favoured by range expansion of their populations due to expansion of open and dry areas in eastern South America during palaeoclimatic and geomorphological events.
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Affiliation(s)
- Dora Yovana Barrios-Leal
- Pós-Graduação, Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Rodolpho S T Menezes
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
| | - João Victor Ribeiro
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
| | - Luiz Bizzo
- UNIVALI - Universidade do Vale do Itajaí, Itajaí, Santa Catarina, Brazil.,Centro Universitário - Católica de Santa Catarina, Jaraguá do Sul, Santa Catarina, Brazil
| | - Fabio Melo de Sene
- Pós-Graduação, Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil.,Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
| | - João Neves-da-Rocha
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
| | - Maura Helena Manfrin
- Pós-Graduação, Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil.,Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
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20
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Jahner JP, Parchman TL, Matocq MD. Multigenerational backcrossing and introgression between two woodrat species at an abrupt ecological transition. Mol Ecol 2021; 30:4245-4258. [PMID: 34219316 DOI: 10.1111/mec.16056] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/28/2021] [Indexed: 12/27/2022]
Abstract
When organisms experience secondary contact after allopatric divergence, genomic regions can introgress differentially depending on their relationships with adaptation, reproductive isolation, recombination, and drift. Analyses of genome-wide patterns of divergence and introgression could provide insight into the outcomes of hybridization and the potential relationship between allopatric divergence and reproductive isolation. Here, we generate population genetic data (26,262 SNPs; 353 individuals) using a reduced-representation sequencing approach to quantify patterns of ancestry, differentiation, and introgression between a pair of ecologically distinct mammals-the desert woodrat (N. lepida) and Bryant's woodrat (N. bryanti)-that hybridize at a sharp ecotone in southern California. Individual ancestry estimates confirmed that hybrids were rare in this bimodal hybrid zone, and entirely consisted of a few F1 individuals and a broad range of multigenerational backcrosses. Genomic cline analyses indicated more than half of loci had elevated introgression from one genomic background into the other. However, introgression was not associated with relative or absolute measures of divergence, and loci with extreme values for both were not typically found near detoxification enzymes previously implicated in dietary specialization for woodrats. The decoupling of differentiation and introgression suggests that processes other than adaptation, such as drift, may underlie the extreme clines at this contact zone.
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Affiliation(s)
- Joshua P Jahner
- Department of Biology, University of Nevada, Reno, Nevada, USA.,Department of Botany, University of Wyoming, Laramie, Wyoming, USA
| | - Thomas L Parchman
- Department of Biology, University of Nevada, Reno, Nevada, USA.,Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, Nevada, USA
| | - Marjorie D Matocq
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, Nevada, USA.,Department of Natural Resources and Environmental Science, University of Nevada, Reno, Nevada, USA
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21
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Russell T, Cullingham C, Ball M, Pybus M, Coltman D. Extent and direction of introgressive hybridization of mule and white-tailed deer in western Canada. Evol Appl 2021; 14:1914-1925. [PMID: 34295372 PMCID: PMC8288014 DOI: 10.1111/eva.13250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 05/02/2021] [Indexed: 01/05/2023] Open
Abstract
Hybridization of mule deer (Odocoileus hemionus) and white-tailed deer (O. virginianus) appears to be a semi-regular occurrence in western North America. Previous studies confirmed the presence of hybrids in a variety of sympatric habitats, but their developing molecular resources limited identification to the earliest, most admixed generations. For this reason, estimates of hybrid production in wild populations often rely on anecdotal reports. As well, white-tailed deer populations' continued encroachment into historically mule deer-occupied habitats due to changes in land use, habitat homogenization, and a warming climate may increase opportunities for interspecific encounters. We sought to quantify the prevalence and extent of hybrid deer in the prairies of western Canada using a SNP assay with enhanced discriminating power. By updating the available molecular resources, we sought to identify and characterize previously cryptic introgression. We also investigated the influence of various parameters on hybridity by way of logistic regression. We observed overall hybridization rates of ~1.0%, slightly lower than that reported by previous studies, and found white-tailed-like hybrids to be more common than their mule deer-like counterparts. Here, we build upon past studies of hybridization in North American deer by increasing hybrid detection power, expanding sample sizes, demonstrating a new molecular resource applicable to future research and observing asymmetrical directionality of introgression.
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Affiliation(s)
- Ty Russell
- Department of Biological SciencesUniversity of AlbertaEdmontonCanada
- Present address:
LGL Limited Environmental Research AssociatesSidneyCanada
| | | | - Mark Ball
- Alberta Fish and WildlifeEdmontonCanada
| | | | - David Coltman
- Department of Biological SciencesUniversity of AlbertaEdmontonCanada
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22
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Pflugbeil G, Affenzeller M, Tribsch A, Comes HP. Primary hybrid zone formation in Tephroseris helenitis (Asteraceae), following postglacial range expansion along the central Northern Alps. Mol Ecol 2021; 30:1704-1720. [PMID: 33548078 PMCID: PMC8048512 DOI: 10.1111/mec.15832] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 11/26/2022]
Abstract
Distinguishing between secondary versus primary hybrid zone formation remains a challenging task as, for instance, the time window in which these historical (vicariant) versus contemporary (environmental-selective) processes are distinguishable may be relatively narrow. Here, we examine the origin and structure of a transition zone between two subspecies of Tephroseris helenitis along the central Northern Alps, using molecular (AFLP) and morphological (achene type) data in combination with ecological niche models (ENMs) to hindcast ranges at the Last Glacial Maximum (LGM) and mid-Holocene. Samples were collected over a c. 350 km long transect, largely covered by ice during the LGM. Genetically nonadmixed individuals of subspp. helenitis versus salisburgensis dominated the westernmost versus eastern transect areas, with admixed individuals occurring in between. Clines for achene morphology and outlier loci potentially under climate-driven selection were steep, largely noncoincidental, and displaced to the east of the cline centre for neutral AFLPs. During the LGM, ssp. helenitis should have been able to persist in a refugium southwest of the transect, while suitable habitat for ssp. salisburgensis was apparently absent at this time. Together with patterns of genetic and clinal variation, our ENM data are suggestive of a primary hybrid zone that originated after the species' postglacial, eastward expansion. The observed clinal changes may thus reflect random/nonadaptive processes during expansion and selection on particular loci, and possibly achene type, in response to a long-term, west-to-east climate gradient in the direction of more stressful (e.g., wetter/cooler) conditions. Overall, this study adds to the vast hybrid zone literature a rare example of a hybrid zone caused by primary differentiation within a plant species, underlaid by historical range expansion.
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Affiliation(s)
- Georg Pflugbeil
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | | | - Andreas Tribsch
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Hans Peter Comes
- Department of Biosciences, University of Salzburg, Salzburg, Austria
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23
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Semenov GA, Linck E, Enbody ED, Harris RB, Khaydarov DR, Alström P, Andersson L, Taylor SA. Asymmetric introgression reveals the genetic architecture of a plumage trait. Nat Commun 2021; 12:1019. [PMID: 33589637 PMCID: PMC7884433 DOI: 10.1038/s41467-021-21340-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 01/20/2021] [Indexed: 01/04/2023] Open
Abstract
Genome-wide variation in introgression rates across hybrid zones offers a powerful opportunity for studying population differentiation. One poorly understood pattern of introgression is the geographic displacement of a trait implicated in lineage divergence from genome-wide population boundaries. While difficult to interpret, this pattern can facilitate the dissection of trait genetic architecture because traits become uncoupled from their ancestral genomic background. We studied an example of trait displacement generated by the introgression of head plumage coloration from personata to alba subspecies of the white wagtail. A previous study of their hybrid zone in Siberia revealed that the geographic transition in this sexual signal that mediates assortative mating was offset from other traits and genetic markers. Here we show that head plumage is associated with two small genetic regions. Despite having a simple genetic architecture, head plumage inheritance is consistent with partial dominance and epistasis, which could contribute to its asymmetric introgression. Hybrid zones are windows into the evolutionary process. Semenov et al. find that the head plumage differences between white wagtail subspecies have a simple genetic basis involving two small genetic regions, in which partially dominant and epistatic interactions help to explain how this sexual signal has become decoupled from other plumage traits.
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Affiliation(s)
- Georgy A Semenov
- Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA.
| | - Ethan Linck
- UNM Biology, University of New Mexico, Albuquerque, NM, Mexico
| | - Erik D Enbody
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | | | | | - Per Alström
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.,Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Scott A Taylor
- Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
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24
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Shastry V, Adams PE, Lindtke D, Mandeville EG, Parchman TL, Gompert Z, Buerkle CA. Model-based genotype and ancestry estimation for potential hybrids with mixed-ploidy. Mol Ecol Resour 2021; 21:1434-1451. [PMID: 33482035 DOI: 10.1111/1755-0998.13330] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 12/11/2020] [Accepted: 01/11/2021] [Indexed: 11/29/2022]
Abstract
Non-random mating among individuals can lead to spatial clustering of genetically similar individuals and population stratification. This deviation from panmixia is commonly observed in natural populations. Consequently, individuals can have parentage in single populations or involving hybridization between differentiated populations. Accounting for this mixture and structure is important when mapping the genetics of traits and learning about the formative evolutionary processes that shape genetic variation among individuals and populations. Stratified genetic relatedness among individuals is commonly quantified using estimates of ancestry that are derived from a statistical model. Development of these models for polyploid and mixed-ploidy individuals and populations has lagged behind those for diploids. Here, we extend and test a hierarchical Bayesian model, called entropy, which can use low-depth sequence data to estimate genotype and ancestry parameters in autopolyploid and mixed-ploidy individuals (including sex chromosomes and autosomes within individuals). Our analysis of simulated data illustrated the trade-off between sequencing depth and genome coverage and found lower error associated with low-depth sequencing across a larger fraction of the genome than with high-depth sequencing across a smaller fraction of the genome. The model has high accuracy and sensitivity as verified with simulated data and through analysis of admixture among populations of diploid and tetraploid Arabidopsis arenosa.
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Affiliation(s)
| | - Paula E Adams
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA
| | - Dorothea Lindtke
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | | | | | | | - C Alex Buerkle
- Department of Botany, University of Wyoming, Laramie, WY, USA
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25
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Ha YH, Oh SH, Lee SR. Genetic Admixture in the Population of Wild Apple ( Malus Sieversii) from the Tien Shan Mountains, Kazakhstan. Genes (Basel) 2021; 12:104. [PMID: 33467767 PMCID: PMC7829876 DOI: 10.3390/genes12010104] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/01/2021] [Accepted: 01/12/2021] [Indexed: 01/14/2023] Open
Abstract
There is growing attention given to gene flow between crops and the wild relatives as global landscapes have been rapidly converted into agricultural farm fields over the past century. Crop-to-wild introgression may advance the extinction risks of rare plants through demographic swamping and/or genetic swamping. Malus sieversii, the progenitor of the apple, is exclusively distributed along the Tien Shan mountains. Habitat fragmentation and hybridization between M. sieversii and the cultivated apples have been proposed to be the causal mechanism of the accelerated extinction risk. We examined the genetic diversity pattern of eleven wild and domesticated apple populations and assessed the gene flow between M. sieversii and the cultivated apples in Kazakhstan using thirteen nuclear microsatellite loci. On average, apple populations harbored fairly high within-population diversity, whereas population divergences were very low suggesting likely influence of human-mediated dispersal. Assignment results showed a split pattern between the cultivated and wild apples and frequent admixture among the apple populations. Coupled with the inflated contemporary migration rates, the admixture pattern might be the signature of increased human intervention within the recent past. Our study highlighted the prevalent crop to wild gene flow of apples occurring in Kazakhstan, proposing an accelerated risk of genetic swamping.
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Affiliation(s)
- Young-Ho Ha
- Division of Forest Diversity, Korea National Arboretum, Pocheon 11186, Korea; (Y.-H.H.); (S.-H.O.)
- Department of Life Sciences, Gachon University, Seongnam 13120, Korea
| | - Seung-Hwan Oh
- Division of Forest Diversity, Korea National Arboretum, Pocheon 11186, Korea; (Y.-H.H.); (S.-H.O.)
| | - Soo-Rang Lee
- Department of Biology Education, College of Natural Sciences, 309 Pilmun-Daero, Dong-Gu, Gwangju 61452, Korea
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26
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Allan V, Vetriventhan M, Senthil R, Geetha S, Deshpande S, Rathore A, Kumar V, Singh P, Reddymalla S, Azevedo VCR. Genome-Wide DArTSeq Genotyping and Phenotypic Based Assessment of Within and Among Accessions Diversity and Effective Sample Size in the Diverse Sorghum, Pearl Millet, and Pigeonpea Landraces. FRONTIERS IN PLANT SCIENCE 2020; 11:587426. [PMID: 33381130 PMCID: PMC7768014 DOI: 10.3389/fpls.2020.587426] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 11/05/2020] [Indexed: 05/30/2023]
Abstract
Germplasm should be conserved in such a way that the genetic integrity of a given accession is maintained. In most genebanks, landraces constitute a major portion of collections, wherein the extent of genetic diversity within and among landraces of crops vary depending on the extent of outcrossing and selection intensity infused by farmers. In this study, we assessed the level of diversity within and among 108 diverse landraces and wild accessions using both phenotypic and genotypic characterization. This included 36 accessions in each of sorghum, pearl millet, and pigeonpea, conserved at ICRISAT genebank. We genotyped about 15 to 25 individuals within each accession, totaling 1,980 individuals using the DArTSeq approach. This resulted in 45,249, 19,052, and 8,211 high-quality single nucleotide polymorphisms (SNPs) in pearl millet, sorghum, and pigeonpea, respectively. Sorghum had the lowest average phenotypic (0.090) and genotypic (0.135) within accession distances, while pearl millet had the highest average phenotypic (0.227) and genotypic (0.245) distances. Pigeonpea had an average of 0.203 phenotypic and 0.168 genotypic within accession distances. Analysis of molecular variance also confirms the lowest variability within accessions of sorghum (26.3%) and the highest of 80.2% in pearl millet, while an intermediate in pigeonpea (57.0%). The effective sample size required to capture maximum variability and to retain rare alleles while regeneration ranged from 47 to 101 for sorghum, 155 to 203 for pearl millet, and 77 to 89 for pigeonpea accessions. This study will support genebank curators, in understanding the dynamics of population within and among accessions, in devising appropriate germplasm conservation strategies, and aid in their utilization for crop improvement.
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Affiliation(s)
- Victor Allan
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University (TNAU), Coimbatore, India
| | - Mani Vetriventhan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Ramachandran Senthil
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - S. Geetha
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University (TNAU), Coimbatore, India
| | - Santosh Deshpande
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Vinod Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Prabhat Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Surender Reddymalla
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Vânia C. R. Azevedo
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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Barreto SB, Knowles LL, Affonso PRADM, Batalha-Filho H. Riverscape properties contribute to the origin and structure of a hybrid zone in a Neotropical freshwater fish. J Evol Biol 2020; 33:1530-1542. [PMID: 32862491 DOI: 10.1111/jeb.13689] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 11/28/2022]
Abstract
Understanding the structure of hybrid zones provides valuable insights about species boundaries and speciation, such as the evolution of barriers to gene flow and the strength of selection. In river networks, studying evolutionary processes in hybrid zones can be especially challenging, given the influence of past and current river properties along with biological species-specific traits. Here, we suggest that a natural hybrid zone between two divergent lineages of the sexually dimorphic Neotropical fish Nematocharax venustus was probably established by secondary contact as a result of a river capture event between the Contas and Pardo river basins. This putative river capture is supported by hydrogeological evidence of elbows of capture, wind gaps and geological faults. The morphological (colour pattern) and genetic (mtDNA and RADseq) variation reveal a clinal transition between parental lineages along the main river, with predominance of F2 hybrids at the centre of the hybrid zone, absence of early generation backcrosses and different levels of hybridization in the tributaries. We highlight that different sources of information are crucial for understanding how the riverscape spatial history influences the connectivity between and within river systems and, consequently, the dynamics of gene flow between freshwater lineages/species.
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Affiliation(s)
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
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28
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Mimura M, Suga M. Ambiguous species boundaries: Hybridization and morphological variation in two closely related Rubus species along altitudinal gradients. Ecol Evol 2020; 10:7476-7486. [PMID: 32760542 PMCID: PMC7391560 DOI: 10.1002/ece3.6473] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 05/11/2020] [Accepted: 05/13/2020] [Indexed: 11/23/2022] Open
Abstract
Although hybridization frequently occurs among plant species, hybrid zones of divergent lineages formed at species boundaries are less common and may not be apparent in later generations of hybrids with more parental-like phenotypes, as a consequence of backcrossing. To determine the effects of dispersal and selection on species boundaries, we compared clines in leaf traits and molecular hybrid index along two hybrid zones on Yakushima Island, Japan, in which a temperate (Rubus palmatus) and subtropical (Rubus grayanus) species of wild raspberry are found. Leaf sinus depth in the two hybrid zones had narrower clines at 600 m a.s.l. than the molecular hybrid index and common garden tests confirmed that some leaf traits, including leaf sinus depth that is a major trait used in species identification, are genetically divergent between these closely related species. The sharp transition in leaf phenotypic traits compared to molecular markers indicated divergent selection pressure on the hybrid zone structure. We suggest that species boundaries based on neutral molecular data may differ from those based on observed morphological traits.
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Affiliation(s)
- Makiko Mimura
- Department of BiologyGraduate School of Natural Science and TechnologyOkayama UniversityOkayamaJapan
| | - Mihoko Suga
- Graduate School of AgricultureTamagawa UniversityTokyoJapan
- Present address:
Sacred Heart SchoolTokyoJapan
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29
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Muniz AC, Lemos-Filho JP, Souza HA, Marinho RC, Buzatti RS, Heuertz M, Lovato MB. The protected tree Dimorphandra wilsonii (Fabaceae) is a population of inter-specific hybrids: recommendations for conservation in the Brazilian Cerrado/Atlantic Forest ecotone. ANNALS OF BOTANY 2020; 126:191-203. [PMID: 32277237 PMCID: PMC7304468 DOI: 10.1093/aob/mcaa066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 04/09/2020] [Indexed: 06/01/2023]
Abstract
BACKGROUNDS AND AIMS Dimorphandra wilsonii Rizzini, a critically endangered and protected tree, has a restricted distribution in the ecotone between the Cerrado and the Atlantic Forest in south-eastern Brazil. In this area, it co-occurs with D. mollis Benth., a common tree from the Cerrado, and D. exaltata Schott., a rare tree from the Atlantic Forest. Previous studies of D. wilsonii indicated heterozygosity excess at the individual level. Field observation of some intermediate phenotypes between D. wilsonii and both congeners suggests hybridization of D. wilsonii with D. mollis and/or D. exaltata. Here, we tested the hypothesis that D. wilsonii may have originated from hybridization between D. exaltata and D. mollis. We also performed cytogenetic analysis to examine if the heterozygosity excess could be explained by polyploidy in D. wilsonii. METHODS We evaluated the genetic diversity and population structure of D. wilsonii using 11 nuclear simple sequence repeats (SSRs) genotyped in 152 individuals sampled across the taxon's range. We performed comparative genetic analyses using overlapping SSR markers between D. wilsonii and previously published SSR data in D. mollis and D. exaltata to subsequently perform a series of allelic comparisons, multivariate and Bayesian analysis. KEY RESULTS Our results suggest that D. wilsonii individuals are most likely to correspond to F1 hybrids between D. exaltata and D. mollis. Cytogenetic analysis indicated that D. wilsonii is diploid with the same chromosome number as D. mollis (2n = 2x = 28). CONCLUSIONS Our study raises questions about the taxonomic status and the evolutionary future of D. wilsonii. We suggest that the conservation and management strategy for D. wilsonii should be revised and that it should take into account both parental Dimorphandra species in the ecotone, with special emphasis on the threatened D. exaltata. Finally, this study highlights the value of genetic information for the design of conservation strategies.
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Affiliation(s)
- André Carneiro Muniz
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, CP, Belo Horizonte, Brazil
| | - José Pires Lemos-Filho
- Departamento de Botânica, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Helena Augusta Souza
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, CP, Belo Horizonte, Brazil
| | | | - Renata Santiago Buzatti
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, CP, Belo Horizonte, Brazil
| | | | - Maria Bernadete Lovato
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, CP, Belo Horizonte, Brazil
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30
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Schnitzler CK, Turchetto C, Teixeira MC, Freitas LB. What could be the fate of secondary contact zones between closely related plant species? Genet Mol Biol 2020; 43:e20190271. [PMID: 32556035 PMCID: PMC7299303 DOI: 10.1590/1678-4685-gmb-2019-0271] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 03/24/2020] [Indexed: 11/26/2022] Open
Abstract
Interspecific hybridization has been fundamental in plant evolution.
Nevertheless, the fate of hybrid zones throughout the generations remains poorly
addressed. We analyzed a pair of recently diverged, interfertile, and sympatric
Petunia species to ask what fate the interspecific hybrid
population has met over time. We analyzed the genetic diversity in two
generations from two contact sites and evaluated the effect of introgression. To
do this, we collected all adult plants from the contact zones, including
canonicals and intermediary colored individuals, and compared them with purebred
representatives of both species based on seven highly informative microsatellite
loci. We compared the genetic diversity observed in the contact zones with what
is seen in isolated populations of each species, considering two generations of
these annual species. Our results have confirmed the genetic differentiation
between the species and the hybrid origin of the majority of the intermediary
colored individuals. We also observed a differentiation related to genetic
variability and inbreeding levels among the populations. Over time, there were
no significant differences per site related to genetic diversity or phenotype
composition. We found two stable populations kept by high inbreeding and
backcross rates that influence the genetic diversity of their parental species
through introgression.
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Affiliation(s)
- Carolina K Schnitzler
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Evolução Molecular, Porto Alegre, RS, Brazil
| | - Caroline Turchetto
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Evolução Molecular, Porto Alegre, RS, Brazil
| | - Marcelo C Teixeira
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Evolução Molecular, Porto Alegre, RS, Brazil
| | - Loreta B Freitas
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Evolução Molecular, Porto Alegre, RS, Brazil
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31
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Nagamitsu T, Uchiyama K, Izuno A, Shimizu H, Nakanishi A. Environment-dependent introgression from Quercus dentata to a coastal ecotype of Quercus mongolica var. crispula in northern Japan. THE NEW PHYTOLOGIST 2020; 226:1018-1028. [PMID: 31424559 PMCID: PMC7216917 DOI: 10.1111/nph.16131] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 08/09/2019] [Indexed: 05/25/2023]
Abstract
Introgression from one species in a specific environment to another may facilitate colonization of the environment by the recipient species. However, such environment-dependent introgression has been clarified in limited plant taxa. In northern Japan, there are two interfertile oak species: Quercus dentata (Qd) in coastal areas and Q. mongolica var. crispula (Qc) in inland areas. However, at higher latitudes where Qd is rare, a coastal Qc ecotype with Qd-like traits is distributed in the coastal areas. We distinguished inland Qc, coastal Qc, and coastal Qd populations based on genome-wide genotypes and multitrait phenotypes and verified introgression from coastal Qd to coastal Qc using reduced library sequencing. Genotypes and phenotypes differed among the populations, and coastal Qc was intermediate between inland Qc and coastal Qd. The ABBA-BABA test showed introgression from coastal Qd to coastal Qc. In coastal Qc, we found various stages of introgression after the first generation of backcross but detected no genomic regions where introgression was enhanced. Overall, we show evidence for introgression from a coastal species to an ecotype of an inland species, which has colonized the coastal environment. It remains unclear whether introgressed alleles are selected in the coastal environment.
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Affiliation(s)
- Teruyoshi Nagamitsu
- Hokkaido Research Center, Forestry and Forest Products Research InstituteForest Research and Management OrganizationSapporo062‐8516Japan
| | - Kentaro Uchiyama
- Department of Forest Molecular Genetics and BiotechnologyForestry and Forest Products Research InstituteForest Research and Management OrganizationTsukuba305‐8687Japan
| | - Ayako Izuno
- Department of Forest Molecular Genetics and BiotechnologyForestry and Forest Products Research InstituteForest Research and Management OrganizationTsukuba305‐8687Japan
| | - Hajime Shimizu
- Greenery Research and Information CenterForestry Research InstituteHokkaido Research OrganizationBibai079‐0198Japan
| | - Atsushi Nakanishi
- Hokkaido Research Center, Forestry and Forest Products Research InstituteForest Research and Management OrganizationSapporo062‐8516Japan
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32
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Patton AH, Margres MJ, Epstein B, Eastman J, Harmon LJ, Storfer A. Hybridizing salamanders experience accelerated diversification. Sci Rep 2020; 10:6566. [PMID: 32300150 PMCID: PMC7162952 DOI: 10.1038/s41598-020-63378-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 03/23/2020] [Indexed: 11/09/2022] Open
Abstract
Whether hybridization generates or erodes species diversity has long been debated, but to date most studies have been conducted at small taxonomic scales. Salamanders (order Caudata) represent a taxonomic order in which hybridization plays a prevalent ecological and evolutionary role. We employed a recently developed model of trait-dependent diversification to test the hypothesis that hybridization impacts the diversification dynamics of species that are currently hybridizing. We find strong evidence supporting this hypothesis, showing that hybridizing salamander lineages have significantly greater net-diversification rates than non-hybridizing lineages. This pattern is driven by concurrently increased speciation rates and decreased extinction rates in hybridizing lineages. Our results support the hypothesis that hybridization can act as a generative force in macroevolutionary diversification.
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Affiliation(s)
- Austin H Patton
- Washington State University, School of Biological Sciences, Pullman, WA, 99164, USA.
| | - Mark J Margres
- Washington State University, School of Biological Sciences, Pullman, WA, 99164, USA.,Harvard University, Department of Organismic and Evolutionary Biology, Cambridge, MA, 02138, USA
| | - Brendan Epstein
- Washington State University, School of Biological Sciences, Pullman, WA, 99164, USA.,University of Minnesota, College of Biological Sciences, Saint Paul, MN, 55108, USA
| | | | - Luke J Harmon
- University of Idaho, Department of Biological Sciences and IBEST, Moscow, ID, 83844, USA
| | - Andrew Storfer
- Washington State University, School of Biological Sciences, Pullman, WA, 99164, USA
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Taillebois L, Sabatino S, Manicki A, Daverat F, Nachón DJ, Lepais O. Variable outcomes of hybridization between declining Alosa alosa and Alosa fallax. Evol Appl 2020; 13:636-651. [PMID: 32211057 PMCID: PMC7086104 DOI: 10.1111/eva.12889] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 09/20/2019] [Accepted: 09/24/2019] [Indexed: 12/19/2022] Open
Abstract
Hybridization dynamics between co-occurring species in environments where human-mediated changes take place are important to quantify for furthering our understanding of human impacts on species evolution and for informing management. The allis shad Alosa alosa (Linnaeus, 1758) and twaite shad Alosa fallax (Lacépède, 1803), two clupeids sister species, have been severely impacted by human activities across Europe. The shrinkage of A. alosa distribution range along with the decline of the remaining populations' abundance threatens its persistence. The main objective was to evaluate the extent of hybridization and introgression between those interacting species. We developed a set of 77 species-specific SNP loci that allowed a better resolution than morphological traits as they enabled the detection of hybrids up to the third generation. Variable rates of contemporary hybridization and introgression patterns were detected in 12 studied sites across the French Atlantic coast. Mitochondrial markers revealed a cyto-nuclear discordance almost invariably involving A. alosa individuals with an A. fallax mitochondrial DNA and provided evidence of historical asymmetric introgression. Overall, contemporary and historical introgression revealed by nuclear and mitochondrial markers strongly suggests that a transfer of genes occurs from A. fallax toward A. alosa genome since at least four generations. Moreover, the outcomes of introgression greatly depend on the catchments where local processes are thought to occur. Undoubtedly, interspecific interaction and gene flow should not be overlooked when considering the management of those species.
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Affiliation(s)
- Laura Taillebois
- ECOBIOPINRAUniversité de Pau et Pays de l’AdourSaint‐Pée‐sur‐NivelleFrance
| | | | - Aurélie Manicki
- ECOBIOPINRAUniversité de Pau et Pays de l’AdourSaint‐Pée‐sur‐NivelleFrance
| | | | - David José Nachón
- EABXIRSTEACestas CedexFrance
- Estación de Hidrobioloxía ‘Encoro do Con’Universidade de Santiago de CompostelaVilagarcía de ArousaSpain
| | - Olivier Lepais
- ECOBIOPINRAUniversité de Pau et Pays de l’AdourSaint‐Pée‐sur‐NivelleFrance
- BIOGECOINRA, Univ. BordeauxCestasFrance
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Wehenkel C, Mariscal-Lucero SDR, González-Elizondo MS, Aguirre-Galindo VA, Fladung M, López-Sánchez CA. Tall Pinus luzmariae trees with genes from P. herrerae. PeerJ 2020; 8:e8648. [PMID: 32149029 PMCID: PMC7049253 DOI: 10.7717/peerj.8648] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 01/27/2020] [Indexed: 11/20/2022] Open
Abstract
CONTEXT Pinus herrerae and P. luzmariae are endemic to western Mexico, where they cover an area of more than 1 million hectares. Pinus herrerae is also cultivated in field trials in South Africa and South America, because of its considerable economic importance as a source of timber and resin. Seed quality, afforestation success and desirable traits may all be influenced by the presence of hybrid trees in seed stands. AIMS We aimed to determine the degree of hybridization between P. herrerae and P. luzmariae in seed stands of each species located in the Sierra Madre Occidental, Durango, Mexico. METHODS AFLP molecular markers from samples of 171 trees across five populations were analyzed with STRUCTURE and NewHybrids software to determine the degree of introgressive hybridization. The accuracy of STRUCTURE and NewHybrids in detecting hybrids was quantified using the software Hybridlab 1.0. Morphological analysis of 131 samples from two populations of P. herrerae and two populations of P. luzmariae was also conducted by Random Forest classification. The data were compared by Principal Coordinate Analysis (PCoA) in GenAlex 6.501. RESULTS Hybridization between Pinus herrerae and P. luzmariae was observed in all seed stands under study and resulted in enhancement of desirable silvicultural traits in the latter species. In P. luzmariae, only about 16% molecularly detected hybrids correspond to those identified on a morphological basis. However, the morphology of P. herrerae is not consistent with the molecularly identified hybrids from one population and is only consistent with 3.3 of those from the other population. CONCLUSIONS This is the first report of hybrid vigour (heterosis) in Mexican pines. Information about hybridization and introgression is essential for developing effective future breeding programs, successful establishment of plantations and management of natural forest stands. Understanding how natural hybridization may influence the evolution and adaptation of pines to climate change is a cornerstone to sustainable forest management including adaptive silviculture.
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Affiliation(s)
- Christian Wehenkel
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Durango, Mexico
| | - Samantha del Rocío Mariscal-Lucero
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Durango, Mexico
- Instituto Tecnológico del Valle del Guadiana, Tecnológico Nacional de México, Durango, Mexico
| | | | - Víctor A. Aguirre-Galindo
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Durango, Mexico
| | | | - Carlos A. López-Sánchez
- Department of Organisms and Systems Biology, University of Oviedo, Polytechnic School of Mieres, Asturias, Spain
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35
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Caniglia R, Galaverni M, Velli E, Mattucci F, Canu A, Apollonio M, Mucci N, Scandura M, Fabbri E. A standardized approach to empirically define reliable assignment thresholds and appropriate management categories in deeply introgressed populations. Sci Rep 2020; 10:2862. [PMID: 32071323 PMCID: PMC7028925 DOI: 10.1038/s41598-020-59521-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 01/28/2020] [Indexed: 11/09/2022] Open
Abstract
Anthropogenic hybridization is recognized as a major threat to the long-term survival of natural populations. While identifying F1 hybrids might be simple, the detection of older admixed individuals is far from trivial and it is still debated whether they should be targets of management. Examples of anthropogenic hybridization have been described between wolves and domestic dogs, with numerous cases detected in the Italian wolf population. After selecting appropriate wild and domestic reference populations, we used empirical and simulated 39-autosomal microsatellite genotypes, Bayesian assignment and performance analyses to develop a workflow to detect different levels of wolf x dog admixture. Membership proportions to the wild cluster (qiw) and performance indexes identified two q-thresholds which allowed to efficiently classify the analysed genotypes into three assignment classes: pure (with no or negligible domestic ancestry), older admixed (with a marginal domestic ancestry) and recent admixed (with a clearly detectable domestic ancestry) animals. Based on their potential to spread domestic variants, such classes were used to define three corresponding management categories: operational pure, introgressed and operational hybrid individuals. Our multiple-criteria approach can help wildlife managers and decision makers in more efficiently targeting the available resources for the long-term conservation of species threatened by anthropogenic hybridization.
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Affiliation(s)
- Romolo Caniglia
- Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell' Emilia, Bologna, Italy.
| | | | - Edoardo Velli
- Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell' Emilia, Bologna, Italy
| | - Federica Mattucci
- Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell' Emilia, Bologna, Italy
| | - Antonio Canu
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Marco Apollonio
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Nadia Mucci
- Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell' Emilia, Bologna, Italy
| | - Massimo Scandura
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Elena Fabbri
- Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell' Emilia, Bologna, Italy
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36
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Zhang Z, Bendixsen DP, Janzen T, Nolte AW, Greig D, Stelkens R. Recombining Your Way Out of Trouble: The Genetic Architecture of Hybrid Fitness under Environmental Stress. Mol Biol Evol 2020; 37:167-182. [PMID: 31518427 PMCID: PMC6984367 DOI: 10.1093/molbev/msz211] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Hybridization between species can either promote or impede adaptation. But we know very little about the genetic basis of hybrid fitness, especially in nondomesticated organisms, and when populations are facing environmental stress. We made genetically variable F2 hybrid populations from two divergent Saccharomyces yeast species. We exposed populations to ten toxins and sequenced the most resilient hybrids on low coverage using ddRADseq to investigate four aspects of their genomes: 1) hybridity, 2) interspecific heterozygosity, 3) epistasis (positive or negative associations between nonhomologous chromosomes), and 4) ploidy. We used linear mixed-effect models and simulations to measure to which extent hybrid genome composition was contingent on the environment. Genomes grown in different environments varied in every aspect of hybridness measured, revealing strong genotype–environment interactions. We also found selection against heterozygosity or directional selection for one of the parental alleles, with larger fitness of genomes carrying more homozygous allelic combinations in an otherwise hybrid genomic background. In addition, individual chromosomes and chromosomal interactions showed significant species biases and pervasive aneuploidies. Against our expectations, we observed multiple beneficial, opposite-species chromosome associations, confirmed by epistasis- and selection-free computer simulations, which is surprising given the large divergence of parental genomes (∼15%). Together, these results suggest that successful, stress-resilient hybrid genomes can be assembled from the best features of both parents without paying high costs of negative epistasis. This illustrates the importance of measuring genetic trait architecture in an environmental context when determining the evolutionary potential of genetically diverse hybrid populations.
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Affiliation(s)
- Zebin Zhang
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Devin P Bendixsen
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Thijs Janzen
- Max Planck Institute for Evolutionary Biology, Plön, Germany.,Institute of Biology and Environmental Sciences, University of Oldenburg, Oldenburg, Germany
| | - Arne W Nolte
- Max Planck Institute for Evolutionary Biology, Plön, Germany.,Institute of Biology and Environmental Sciences, University of Oldenburg, Oldenburg, Germany
| | - Duncan Greig
- Max Planck Institute for Evolutionary Biology, Plön, Germany.,Centre for Life's Origins and Evolution (CLOE), Department of Genetics, Evolution, and Environment, University College London, London, United Kingdom
| | - Rike Stelkens
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden.,Max Planck Institute for Evolutionary Biology, Plön, Germany
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McFarlane SE, Hunter DC, Senn HV, Smith SL, Holland R, Huisman J, Pemberton JM. Increased genetic marker density reveals high levels of admixture between red deer and introduced Japanese sika in Kintyre, Scotland. Evol Appl 2020; 13:432-441. [PMID: 31993087 PMCID: PMC6976951 DOI: 10.1111/eva.12880] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 09/01/2019] [Accepted: 10/10/2019] [Indexed: 12/14/2022] Open
Abstract
Hybridization is a natural process at species range boundaries, but increasing numbers of species are hybridizing due to direct or indirect human activities. In such cases of anthropogenic hybridization, subsequent introgression can threaten the survival of native species. To date, many such systems have been studied with too few genetic markers to assess the level of threat resulting from advanced backcrossing. Here, we use 44,999 single nucleotide polymorphisms (SNPs) and the ADMIXTURE program to study two areas of Scotland where a panel of 22 diagnostic microsatellites previously identified introgression between native red deer (Cervus elaphus) and introduced Japanese sika (Cervus nippon). In Kintyre, we reclassify 26% of deer from the pure species categories to the hybrid category whereas in the NW Highlands we only reclassify 2%. As expected, the reclassified individuals are mostly advanced backcrosses. We also investigate the ability of marker panels selected on different posterior allele frequency criteria to find hybrids assigned by the full marker set and show that in our data, ancestry informative markers (i.e. those that are highly differentiated between the species, but not fixed) are better than diagnostic markers (those markers that are fixed between the species) because they are more evenly distributed in the genome. Diagnostic loci are concentrated on the X chromosome to the detriment of autosomal coverage.
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Affiliation(s)
- S. Eryn McFarlane
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
- Department of BiologyLund UniversityLundSweden
| | - Darren C. Hunter
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | - Helen V. Senn
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
- WildGenes LaboratoryRoyal Zoological Society of ScotlandEdinburghUK
| | - Stephanie L. Smith
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
- The Royal (Dick) School of Veterinary StudiesUniversity of EdinburghEaster Bush CampusMidlothian, EdinburghUK
| | - Rebecca Holland
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
| | - Jisca Huisman
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
| | - Josephine M. Pemberton
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
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Scordato ESC, Smith CCR, Semenov GA, Liu Y, Wilkins MR, Liang W, Rubtsov A, Sundev G, Koyama K, Turbek SP, Wunder MB, Stricker CA, Safran RJ. Migratory divides coincide with reproductive barriers across replicated avian hybrid zones above the Tibetan Plateau. Ecol Lett 2019; 23:231-241. [DOI: 10.1111/ele.13420] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/25/2019] [Accepted: 10/15/2019] [Indexed: 01/02/2023]
Affiliation(s)
- Elizabeth S. C. Scordato
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
- Department of Biological Sciences California State Polytechnic University Pomona CA USA
| | - Chris C. R. Smith
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
| | - Georgy A. Semenov
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
- Institute of Ecology and Systematics of Animals Novosibirsk Russia
| | - Yu Liu
- Queen Mary University of London London England
- Beijing Normal University Beijing China
| | - Matthew R. Wilkins
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
- Vanderbilt University Center for Science Outreach Nashville TN37212 USA
| | - Wei Liang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands College of Life Sciences Hainan Normal University Haikou571158 China
| | | | - Gomboobaatar Sundev
- National University of Mongolia P. O. Box 537 Ulaanbaatar210646 Mongolia
- Mongolian Ornithological Society P. O. Box 537 Ulaanbaatar210646 Mongolia
| | - Kazuo Koyama
- Japan Bird Research Association Tokyo Japan183‐0034
| | - Sheela P. Turbek
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
| | - Michael B. Wunder
- Department of Integrative Biology University of Colorado Denver Denver CO USA
| | | | - Rebecca J. Safran
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
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Sequeira F, Bessa-Silva A, Tarroso P, Sousa-Neves T, Vallinoto M, Gonçalves H, Martínez-Solano I. Discordant patterns of introgression across a narrow hybrid zone between two cryptic lineages of an Iberian endemic newt. J Evol Biol 2019; 33:202-216. [PMID: 31677317 DOI: 10.1111/jeb.13562] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 10/15/2019] [Accepted: 10/25/2019] [Indexed: 11/30/2022]
Abstract
The study of natural hybrid zones can illuminate aspects of lineage divergence and speciation in morphologically cryptic taxa. We studied a hybrid zone between two highly divergent but morphologically similar lineages (south-western and south-eastern) of the Iberian endemic Bosca's newt (Lissotriton boscai) in SW Iberia with a multilocus dataset (microsatellites, nuclear and mitochondrial genes). STRUCTURE and NEWHYBRIDS analyses retrieved few admixed individuals, which classified as backcrosses involving parental individuals of the south-western lineage. Our results show asymmetric introgression of mtDNA beyond the contact from this lineage into the south-eastern lineage. Analysis of nongeographic introgression patterns revealed asymmetries in the direction of introgression, but except for mtDNA, we did not find evidence for nonconcordant introgression patterns across nuclear loci. Analysis of a 150-km transect across the hybrid zone showed broadly coincident cline widths (ca. 3.2-27.9 km), and concordant cline centres across all markers, except for mtDNA that is displaced ca. 60 km northward. Results from ecological niche modelling show that the hybrid zone is in a climatically homogenous area with suitable habitat for the species, suggesting that contact between the two lineages is unlikely to occur further south as their distributions are currently separated by an extensive area of unfavourable habitat. Taken together, our findings suggest the genetic structure of this hybrid zone results from the interplay of historical (biogeographic) and population-level processes. The narrowness and coincidence of genetic clines can be explained by weak selection against hybrids and reflect a degree of reproductive isolation that is consistent with cryptic speciation.
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Affiliation(s)
- Fernando Sequeira
- Laboratorio Associado, CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Vairão, Portugal
| | - Adam Bessa-Silva
- Laboratório de Evolução (LEVO), Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Pará, Brasil
| | - Pedro Tarroso
- Laboratorio Associado, CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Vairão, Portugal
| | - Tiago Sousa-Neves
- Laboratorio Associado, CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Vairão, Portugal.,Museu Paraense Emílio Goeldi, Coordenação de Zoologia, Pará, Brasil
| | - Marcelo Vallinoto
- Laboratorio Associado, CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Vairão, Portugal.,Laboratório de Evolução (LEVO), Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Pará, Brasil
| | - Helena Gonçalves
- Laboratorio Associado, CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Vairão, Portugal.,Museu de História Natural e da Ciência, Universidade do Porto, Porto, Portugal
| | - Iñigo Martínez-Solano
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC (MNCN-CSIC), Madrid, Spain
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40
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Corrêa AS, Cordeiro EM, Omoto C. Agricultural insect hybridization and implications for pest management. PEST MANAGEMENT SCIENCE 2019; 75:2857-2864. [PMID: 31124266 DOI: 10.1002/ps.5495] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 05/17/2019] [Accepted: 05/21/2019] [Indexed: 06/09/2023]
Abstract
Biological invasions, the expansion of agricultural frontiers, and climate change favor encounters of divergent lineages of animals and plants, increasing the likelihood of hybridization. However, hybridization of insect species and its consequences for agroecosystems have not received sufficient attention. Gene exchange between distinct and distant genetic pools can improve the survival and reproduction of insect pests, and threaten beneficial insects in disturbed agricultural environments. Hybridization may be the underlying explanation for the recurrent pest outbreaks and control failures in putative hybrid zones, as suspected for bollworm, corn borer, whiteflies, and stink bugs. Reliable predictions of the types of changes that can be expected in pest insect genomes and fitness, and of their impacts on the fate of species and populations remain elusive. Typical steps in pest management, such as insect identification, pest monitoring, and control are likely affected by gene flow and adaptive introgression mediated by hybridization, and we do not have ways to respond to or mitigate the problem. To address the adverse effects of farming intensification and global trade, we must ensure that current integrated pest management programs incorporate up-to-date monitoring and diagnostic tools. The rapid identification of hybrids, quantification of levels of introgression, and in-depth knowledge of what genes have been transferred may help to explain and predict insect population outbreaks and control failures in the future. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Alberto S Corrêa
- Department of Entomology and Acarology, University of São Paulo, Luiz de Queiroz College of Agriculture (USP/ESALQ), Piracicaba, Brazil
| | - Erick Mg Cordeiro
- Department of Entomology and Acarology, University of São Paulo, Luiz de Queiroz College of Agriculture (USP/ESALQ), Piracicaba, Brazil
| | - Celso Omoto
- Department of Entomology and Acarology, University of São Paulo, Luiz de Queiroz College of Agriculture (USP/ESALQ), Piracicaba, Brazil
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41
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Donfrancesco V, Ciucci P, Salvatori V, Benson D, Andersen LW, Bassi E, Blanco JC, Boitani L, Caniglia R, Canu A, Capitani C, Chapron G, Czarnomska SD, Fabbri E, Galaverni M, Galov A, Gimenez O, Godinho R, Greco C, Hindrikson M, Huber D, Hulva P, Jedrzejewski W, Kusak J, Linnell JDC, Llaneza L, López-Bao JV, Männil P, Marucco F, Mattioli L, Milanesi P, Milleret C, Mysłajek RW, Ordiz A, Palacios V, Pedersen HC, Pertoldi C, Pilot M, Randi E, Rodríguez A, Saarma U, Sand H, Scandura M, Stronen AV, Tsingarska E, Mukherjee N. Unravelling the Scientific Debate on How to Address Wolf-Dog Hybridization in Europe. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00175] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
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42
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Billerman SM, Cicero C, Bowie RCK, Carling MD. Phenotypic and genetic introgression across a moving woodpecker hybrid zone. Mol Ecol 2019; 28:1692-1708. [DOI: 10.1111/mec.15043] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 01/22/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Shawn M. Billerman
- Department of Zoology and Physiology University of Wyoming Laramie Wyoming
- Program in Ecology University of Wyoming Laramie Wyoming
| | - Carla Cicero
- Museum of Vertebrate Zoology University of California Berkeley California
| | - Rauri C. K. Bowie
- Museum of Vertebrate Zoology University of California Berkeley California
- Department of Integrative Biology University of California Berkeley California
| | - Matthew D. Carling
- Department of Zoology and Physiology University of Wyoming Laramie Wyoming
- Program in Ecology University of Wyoming Laramie Wyoming
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43
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Haselhorst MSH, Parchman TL, Buerkle CA. Genetic evidence for species cohesion, substructure and hybrids in spruce. Mol Ecol 2019; 28:2029-2045. [DOI: 10.1111/mec.15056] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 02/10/2019] [Accepted: 02/11/2019] [Indexed: 12/18/2022]
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44
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Seabra SG, Silva SE, Nunes VL, Sousa VC, Martins J, Marabuto E, Rodrigues ASB, Pina‐Martins F, Laurentino TG, Rebelo MT, Figueiredo E, Paulo OS. Genomic signatures of introgression between commercial and native bumblebees, Bombus terrestris, in western Iberian Peninsula-Implications for conservation and trade regulation. Evol Appl 2019; 12:679-691. [PMID: 30976302 PMCID: PMC6439495 DOI: 10.1111/eva.12732] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 10/24/2018] [Accepted: 10/27/2018] [Indexed: 01/02/2023] Open
Abstract
Human-mediated introductions of species may have profound impacts on native ecosystems. One potential impact with largely unforeseen consequences is the potential admixture of introduced with autochthonous species through hybridization. Throughout the world, bumblebees have been deliberately introduced for crop pollination with known negative impacts on native pollinators. Given the likely allochthonous origin of commercial bumblebees used in Portugal (subspecies Bombus terrestris terrestris and B. t. dalmatinus), our aim was to assess their putative introgression with the native Iberian subspecies B. terrestris lusitanicus. We analysed one mitochondrial gene, cytochrome c oxidase subunit I (COX1) and genomic data involving thousands of genome-wide restriction-site-associated DNA markers (RAD-seq). In the mitochondrial COX1 analyses, we detected one relatively common haplotype in commercial bumblebees, also present in wild samples collected nearby the greenhouses where the commercial hives are used. In the RAD-seq analysis, we found a clear genetic differentiation between native and commercial lineages. Furthermore, we detected candidate hybrids in the wild, as well as putatively escaped commercial bumblebees, some of which being potentially fertile males. Although we cannot assess directly the fitness effects of introgressed alleles, there is a risk of maladaptive allele introgression to the local bumblebee subspecies, which can negatively impact autochthon populations. One immediate recommendation to farmers is for the proper disposal of hive boxes, after their use in greenhouses, so as to minimize the risk of escapees contaminating native populations. On the other hand, the feasibility of using local subspecies B. t. lusitanicus, preferably with local production, should be evaluated.
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Affiliation(s)
- Sofia G. Seabra
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de CiênciasUniversidade de LisboaLisboaPortugal
| | - Sara E. Silva
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de CiênciasUniversidade de LisboaLisboaPortugal
| | - Vera L. Nunes
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de CiênciasUniversidade de LisboaLisboaPortugal
| | - Vitor C. Sousa
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de CiênciasUniversidade de LisboaLisboaPortugal
| | - Joana Martins
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de AgronomiaUniversidade de LisboaLisboaPortugal
- Present address:
SAPEC AgroLisboaPortugal
| | - Eduardo Marabuto
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de CiênciasUniversidade de LisboaLisboaPortugal
| | - Ana S. B. Rodrigues
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Natural History and Systematics (NHS) Research Group /MUHNAC ‐ Museu Nacional de História Natural e da CiênciaUniversidade de LisboaLisboaPortugal
| | - Francisco Pina‐Martins
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de CiênciasUniversidade de LisboaLisboaPortugal
| | | | - Maria Teresa Rebelo
- Centre for Environmental and Marine Studies (CESAM), Departamento de Biologia Animal, Faculdade de CiênciasUniversidade de LisboaLisboaPortugal
| | - Elisabete Figueiredo
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de AgronomiaUniversidade de LisboaLisboaPortugal
| | - Octávio S. Paulo
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de CiênciasUniversidade de LisboaLisboaPortugal
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45
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Abbott RJ. A mixing-isolation-mixing model of speciation can potentially explain hotspots of species diversity. Natl Sci Rev 2019; 6:290-291. [PMID: 34691866 PMCID: PMC8291541 DOI: 10.1093/nsr/nwy112] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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46
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Alex Sotola V, Ruppel DS, Bonner TH, Nice CC, Martin NH. Asymmetric introgression between fishes in the Red River basin of Texas is associated with variation in water quality. Ecol Evol 2019; 9:2083-2095. [PMID: 30847094 PMCID: PMC6392354 DOI: 10.1002/ece3.4901] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/05/2018] [Accepted: 12/13/2018] [Indexed: 01/01/2023] Open
Abstract
When ecologically divergent taxa encounter one another, hybrid zones can form when reproductive isolation is incomplete. The location of such hybrid zones can be influenced by environmental variables, and an ecological context can provide unique insights into the mechanisms by which species diverge and are maintained. Two ecologically differentiated species of small benthic fishes, the endemic and imperiled prairie chub, Macrhybopsis australis, and the shoal chub, Macrhybopsis hyostoma, are locally sympatric within the upper Red River Basin of Texas. We integrated population genomic data and environmental data to investigate species divergence and the maintenance of species boundaries in these two species. We found evidence of advanced-generation asymmetric hybridization and introgression, with shoal chub alleles introgressing more frequently into prairie chubs than the reciprocal. Using a Bayesian Genomic Cline framework, patterns of genomic introgression were revealed to be quite heterogeneous, yet shoal chub alleles were found to have likely selectively introgressed across species boundaries significantly more often than prairie chub alleles, potentially explaining some of the observed asymmetry in hybridization. These patterns were remarkably consistent across two sampled geographic regions of hybridization. Several environmental variables were found to significantly predict individual admixture, suggesting ecological isolation might maintain species boundaries.
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Affiliation(s)
| | | | | | - Chris C. Nice
- Biology DepartmentTexas State UniversitySan MarcosTexas
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47
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Bohling J, Small M, Von Bargen J, Louden A, DeHaan P. Comparing inferences derived from microsatellite and RADseq datasets: a case study involving threatened bull trout. CONSERV GENET 2019. [DOI: 10.1007/s10592-018-1134-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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48
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Pacheco-Sierra G, Vázquez-Domínguez E, Pérez-Alquicira J, Suárez-Atilano M, Domínguez-Laso J. Ancestral Hybridization Yields Evolutionary Distinct Hybrids Lineages and Species Boundaries in Crocodiles, Posing Unique Conservation Conundrums. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00138] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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49
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Chhatre VE, Evans LM, DiFazio SP, Keller SR. Adaptive introgression and maintenance of a trispecies hybrid complex in range‐edge populations of
Populus. Mol Ecol 2018; 27:4820-4838. [DOI: 10.1111/mec.14820] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 07/19/2018] [Accepted: 07/20/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Vikram E. Chhatre
- Department of Plant Biology University of Vermont Burlington Vermont
| | - Luke M. Evans
- Department of Ecology and Evolutionary Biology Institute of Behavioral Genetics University of Colorado Boulder Colorado
| | | | - Stephen R. Keller
- Department of Plant Biology University of Vermont Burlington Vermont
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50
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Leitwein M, Gagnaire PA, Desmarais E, Berrebi P, Guinand B. Genomic consequences of a recent three-way admixture in supplemented wild brown trout populations revealed by local ancestry tracts. Mol Ecol 2018; 27:3466-3483. [PMID: 30054960 DOI: 10.1111/mec.14816] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 07/11/2018] [Accepted: 07/19/2018] [Indexed: 12/20/2022]
Abstract
Understanding the evolutionary consequences of human-mediated introductions of domesticated strains into the wild and their subsequent admixture with natural populations is of major concern in conservation biology. However, the genomic impacts of stocking from distinct sources (locally derived vs. divergent) on the genetic integrity of wild populations remain poorly understood. We designed an approach based on estimating local ancestry along individual chromosomes to provide a detailed picture of genomic admixture in supplemented populations. We used this approach to document admixture consequences in the brown trout Salmo trutta, for which decades of stocking practices have profoundly impacted the genetic make-up of wild populations. In southern France, small local Mediterranean populations have been subject to successive introductions of domestic strains derived from the Atlantic and Mediterranean lineages. To address the impact of stocking, we evaluate the extent of admixture from both domestic strains within populations, using 75,684 mapped SNPs obtained from double-digested restriction site-associated DNA sequencing. Then, the chromosomal ancestry profiles of admixed individuals reveal a wider diversity of hybrid and introgressed genotypes than estimated using classical methods for inferring ancestry and hybrid pedigrees. In addition, the length distribution of introgressed tracts retained different timings of introgression between the two domestic strains. We finally reveal opposite consequences of admixture on the level of polymorphism of the recipient populations between domestic strains. Our study illustrates the potential of using the information contained in the genomic mosaic of ancestry tracts in combination with classical methods based on allele frequencies for analysing multiple-way admixture with population genomic data.
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Affiliation(s)
- Maeva Leitwein
- ISEM, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
| | | | - Erick Desmarais
- ISEM, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
| | - Patrick Berrebi
- ISEM, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
| | - Bruno Guinand
- ISEM, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France.,Département Biologie-Ecologie, Université de Montpellier, Montpellier Cedex 5, France
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