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Feng X, Merilä J, Löytynoja A. Secondary Contact, Introgressive Hybridization, and Genome Stabilization in Sticklebacks. Mol Biol Evol 2024; 41:msae031. [PMID: 38366566 PMCID: PMC10903534 DOI: 10.1093/molbev/msae031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/20/2023] [Accepted: 02/09/2024] [Indexed: 02/18/2024] Open
Abstract
Advances in genomic studies have revealed that hybridization in nature is pervasive and raised questions about the dynamics of different genetic and evolutionary factors following the initial hybridization event. While recent research has proposed that the genomic outcomes of hybridization might be predictable to some extent, many uncertainties remain. With comprehensive whole-genome sequence data, we investigated the genetic introgression between 2 divergent lineages of 9-spined sticklebacks (Pungitius pungitius) in the Baltic Sea. We found that the intensity and direction of selection on the introgressed variation has varied across different genomic elements: while functionally important regions displayed reduced rates of introgression, promoter regions showed enrichment. Despite the general trend of negative selection, we identified specific genomic regions that were enriched for introgressed variants, and within these regions, we detected footprints of selection, indicating adaptive introgression. Geographically, we found the selection against the functional changes to be strongest in the vicinity of the secondary contact zone and weaken as a function of distance from the initial contact. Altogether, the results suggest that the stabilization of introgressed variation in the genomes is a complex, multistage process involving both negative and positive selection. In spite of the predominance of negative selection against introgressed variants, we also found evidence for adaptive introgression variants likely associated with adaptation to Baltic Sea environmental conditions.
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Affiliation(s)
- Xueyun Feng
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki 00014, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Juha Merilä
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki 00014, Finland
- Area of Ecology and Biodiversity, The School of Biological Sciences, Kadoorie Biological Sciences Building, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Ari Löytynoja
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
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2
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Rio J, Quilodrán CS, Currat M. Spatially explicit paleogenomic simulations support cohabitation with limited admixture between Bronze Age Central European populations. Commun Biol 2021; 4:1163. [PMID: 34621003 PMCID: PMC8497574 DOI: 10.1038/s42003-021-02670-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 09/13/2021] [Indexed: 02/08/2023] Open
Abstract
The Bronze Age is a complex period of social, cultural and economic changes. Recent paleogenomic studies have documented a large and rapid genetic change in early Bronze Age populations from Central Europe. However, the detailed demographic and genetic processes involved in this change are still debated. Here we have used spatially explicit simulations of genomic components to better characterize the demographic and migratory conditions that may have led to this change. We investigated various scenarios representing the expansion of pastoralists from the Pontic steppe, potentially linked to the Yamnaya cultural complex, and their interactions with local populations in Central Europe, considering various eco-evolutionary factors, such as population admixture, competition and long-distance dispersal. Our results do not support direct competition but rather the cohabitation of pastoralists and farmers in Central Europe, with limited gene flow between populations. They also suggest occasional long-distance migrations accompanying the expansion of pastoralists and a demographic decline in both populations following their initial contact. These results link recent archaeological and paleogenomic observations and move further the debate of genomic changes during the early Bronze Age.
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Affiliation(s)
- Jérémy Rio
- Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland
| | - Claudio S Quilodrán
- Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Mathias Currat
- Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.
- Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva, Switzerland.
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3
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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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Quilodrán CS, Tsoupas A, Currat M. The Spatial Signature of Introgression After a Biological Invasion With Hybridization. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.569620] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The accumulation of genome-wide molecular data has emphasized the important role of hybridization in the evolution of many organisms, which may carry introgressed genomic segments resulting from past admixture events with other taxa. Despite a number of examples of hybridization occurring during biological invasions, the resulting spatial patterns of genomic introgression remain poorly understood. Preliminary simulation studies have suggested a heterogeneous spatial level of introgression for invasive taxa after range expansion. We investigated in detail the robustness of this pattern and its persistence over time for both invasive and local organisms. Using spatially explicit simulations, we explored the spatial distribution of introgression across the area of colonization of an invasive taxon hybridizing with a local taxon. The general pattern for neutral loci supported by our results is an increasing introgression of local genes into the invasive taxon with the increase in the distance from the source of the invasion and a decreasing introgression of invasive genes into the local taxon. However, we also show there is some variation in this general trend depending on the scenario investigated. Spatial heterogeneity of introgression within a given taxon is thus an expected neutral pattern in structured populations after a biological invasion with a low to moderate amount of hybridization. We further show that this pattern is consistent with published empirical observations. Using additional simulations, we argue that the spatial pattern of Neanderthal introgression in modern humans, which has been documented to be higher in Asia than in Europe, can be explained by a model of hybridization with Neanderthals in Eurasia during the range expansion of modern humans from Africa. Our results support the view that weak hybridization during range expansion may explain spatially heterogeneous introgression patterns without the need to invoke selection.
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Quilodrán CS, Montoya-Burgos JI, Currat M. Harmonizing hybridization dissonance in conservation. Commun Biol 2020; 3:391. [PMID: 32694629 PMCID: PMC7374702 DOI: 10.1038/s42003-020-1116-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 06/25/2020] [Indexed: 12/24/2022] Open
Abstract
A dramatic increase in the hybridization between historically allopatric species has been induced by human activities. However, the notion of hybridization seems to lack consistency in two respects. On the one hand, it is inconsistent with the biological species concept, which does not allow for interbreeding between species, and on the other hand, it is considered either as an evolutionary process leading to the emergence of new biodiversity or as a cause of biodiversity loss, with conservation implications. In the first case, we argue that conservation biology should avoid the discussion around the species concept and delimit priorities of conservation units based on the impact on biodiversity if taxa are lost. In the second case, we show that this is not a paradox but an intrinsic property of hybridization, which should be considered in conservation programmes. We propose a novel view of conservation guidelines, in which human-induced hybridization may also be a tool to enhance the likelihood of adaptation to changing environmental conditions or to increase the genetic diversity of taxa affected by inbreeding depression. The conservation guidelines presented here represent a guide for the development of programmes aimed at protecting biodiversity as a dynamic evolutionary system.
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Affiliation(s)
- Claudio S Quilodrán
- Department of Zoology, University of Oxford, Oxford, United Kingdom.
- Laboratory of Anthropology, Genetics and Peopling History, Anthropology Unit, Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.
| | - Juan I Montoya-Burgos
- Laboratory of Vertebrate Evolution, Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (IGE3), Geneva, Switzerland
| | - Mathias Currat
- Laboratory of Anthropology, Genetics and Peopling History, Anthropology Unit, Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (IGE3), Geneva, Switzerland
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Tonzo V, Papadopoulou A, Ortego J. Genomic footprints of an old affair: Single nucleotide polymorphism data reveal historical hybridization and the subsequent evolution of reproductive barriers in two recently diverged grasshoppers with partly overlapping distributions. Mol Ecol 2020; 29:2254-2268. [DOI: 10.1111/mec.15475] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 05/10/2020] [Accepted: 05/11/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Vanina Tonzo
- Department of Integrative Ecology Estación Biológica de Doñana (EBD‐CSIC) Seville Spain
| | - Anna Papadopoulou
- Department of Biological Sciences University of Cyprus Nicosia Cyprus
| | - Joaquín Ortego
- Department of Integrative Ecology Estación Biológica de Doñana (EBD‐CSIC) Seville Spain
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Abstract
Range expansions lead to distinctive patterns of genetic variation in populations, even in the absence of selection. These patterns and their genetic consequences have been well studied for populations advancing through successive short-ranged migration events. However, most populations harbor some degree of long-range dispersal, experiencing rare yet consequential migration events over arbitrarily long distances. Although dispersal is known to strongly affect spatial genetic structure during range expansions, the resulting patterns and their impact on neutral diversity remain poorly understood. Here, we systematically study the consequences of long-range dispersal on patterns of neutral variation during range expansion in a class of dispersal models which spans the extremes of local (effectively short-ranged) and global (effectively well-mixed) migration. We find that sufficiently long-ranged dispersal leaves behind a mosaic of monoallelic patches, whose number and size are highly sensitive to the distribution of dispersal distances. We develop a coarse-grained model which connects statistical features of these spatial patterns to the evolution of neutral diversity during the range expansion. We show that growth mechanisms that appear qualitatively similar can engender vastly different outcomes for diversity: Depending on the tail of the dispersal distance distribution, diversity can be either preserved (i.e., many variants survive) or lost (i.e., one variant dominates) at long times. Our results highlight the impact of spatial and migratory structure on genetic variation during processes as varied as range expansions, species invasions, epidemics, and the spread of beneficial mutations in established populations.
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Elleouet JS, Aitken SN. Long-distance pollen dispersal during recent colonization favors a rapid but partial recovery of genetic diversity in Picea sitchensis. THE NEW PHYTOLOGIST 2019; 222:1088-1100. [PMID: 30485444 DOI: 10.1111/nph.15615] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 11/22/2018] [Indexed: 06/09/2023]
Abstract
Tree species in the northern hemisphere are currently subject to rapid anthropogenic climate change and are shifting their ranges in response. This prompts questions about the mechanisms allowing tree populations to respond quickly to selection pressures when establishing into new areas. Focusing on the northern expanding range edge of Picea sitchensis, a widespread conifer of western North America, we ask how genetic structure and diversity develop during colonization, and assess the role of demographic history in shaping the evolutionary trajectory of an establishing population. We combined 500 yr of tree-ring and genotyping-by-sequencing data in 639 trees at the expansion front on the Kodiak Archipelago. We show that alleles accumulated rapidly during an increase in recruitment rate in the early 1700s. A shift from foreign to local pollen flow subsequently homogenized genetic structure at the expansion front. Taking advantage of the exceptional longevity of conifers, we highlight the major role of long-distance pollen dispersal in the rapid but incomplete recovery of genetic diversity during the initial stages of colonization. We also warn that slow initial population growth as well as long-lasting dominance of local gene flow by early founders could increase evolutionary load under a rapidly changing climate.
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Affiliation(s)
- Joane S Elleouet
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC, Canada, V6T1Z4
| | - Sally N Aitken
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC, Canada, V6T1Z4
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Whole-Genome Analysis of Introgression Between the Spotted Owl and Barred Owl ( Strix occidentalis and Strix varia, Respectively; Aves: Strigidae) in Western North America. G3-GENES GENOMES GENETICS 2018; 8:3945-3952. [PMID: 30355766 PMCID: PMC6288836 DOI: 10.1534/g3.118.200754] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
As the barred owl (Strix varia; Aves: Strigiformes: Strigidae) expands throughout western North America, hybridization between barred and spotted owls (Strix varia and S. occidentalis, respectively), if abundant, may lead to genetic swamping of the endangered spotted owl. We analyzed low-coverage, whole-genome sequence data from fifty-one barred and spotted owls to investigate recent introgression between these two species. Although we obtained genomic confirmation that these species can and do hybridize and backcross, we found no evidence of widespread introgression. Plumage characteristics of western S. varia that suggested admixture with S. occidentalis appear unrelated to S. occidentalis ancestry and may instead reflect local selection.
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Kim BY, Huber CD, Lohmueller KE. Deleterious variation shapes the genomic landscape of introgression. PLoS Genet 2018; 14:e1007741. [PMID: 30346959 PMCID: PMC6233928 DOI: 10.1371/journal.pgen.1007741] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 11/13/2018] [Accepted: 10/05/2018] [Indexed: 11/19/2022] Open
Abstract
While it is appreciated that population size changes can impact patterns of deleterious variation in natural populations, less attention has been paid to how gene flow affects and is affected by the dynamics of deleterious variation. Here we use population genetic simulations to examine how gene flow impacts deleterious variation under a variety of demographic scenarios, mating systems, dominance coefficients, and recombination rates. Our results show that admixture between populations can temporarily reduce the genetic load of smaller populations and cause increases in the frequency of introgressed ancestry, especially if deleterious mutations are recessive. Additionally, when fitness effects of new mutations are recessive, between-population differences in the sites at which deleterious variants exist creates heterosis in hybrid individuals. Together, these factors lead to an increase in introgressed ancestry, particularly when recombination rates are low. Under certain scenarios, introgressed ancestry can increase from an initial frequency of 5% to 30–75% and fix at many loci, even in the absence of beneficial mutations. Further, deleterious variation and admixture can generate correlations between the frequency of introgressed ancestry and recombination rate or exon density, even in the absence of other types of selection. The direction of these correlations is determined by the specific demography and whether mutations are additive or recessive. Therefore, it is essential that null models of admixture include both demography and deleterious variation before invoking other mechanisms to explain unusual patterns of genetic variation. Individuals from distinct populations sometimes will produce fertile offspring and will exchange genetic material in a process called hybridization. Genomes of hybrid individuals often show non-random patterns of hybrid ancestry across the genome, where some regions have a high frequency of ancestry from the second population and other regions have less. Typically, this pattern has been attributed to adaptive introgression, where beneficial genetic variants are passed from one population to the other, or to genomic incompatibilities between these distinct species. However, other mechanisms could lead to these heterogeneous patterns of ancestry in hybrids. Here we use simulations to investigate whether deleterious mutations affect the patterns of introgressed ancestry across genomes. We show that when ancestry from a larger population is added to a smaller population, the ancestry from the larger population dramatically increases in frequency because it carries fewer deleterious mutations. This occurs even in the absence of beneficial mutations in either population. Additionally, we show that differences in sex chromosome evolution relative to autosomes, or differences in mating system, can affect patterns of introgression in similar ways. Our study argues that deleterious mutations should be included in population genetic models used to identify unusual regions of the genome that appear to be under selection in hybrids.
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Affiliation(s)
- Bernard Y. Kim
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, United States of America
| | - Christian D. Huber
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, United States of America
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, United States of America
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, California, United States of America
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
- * E-mail:
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Bonnet T, Leblois R, Rousset F, Crochet PA. A reassessment of explanations for discordant introgressions of mitochondrial and nuclear genomes. Evolution 2017; 71:2140-2158. [DOI: 10.1111/evo.13296] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/23/2017] [Accepted: 06/05/2017] [Indexed: 01/03/2023]
Affiliation(s)
- Timothée Bonnet
- Department of Evolutionary Biology and Environmental Studies (IEU); University of Zurich; Zurich Switzerland
- Research School of Biology; The Australian National University; Canberra Australia
| | - Raphaël Leblois
- Institut National de la Recherche Agronomique, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro); Campus International de Baillarguet; Montferrier-sur-Lez France
- Institut de Biologie Computationnelle; Université de Montpellier; 860 rue St Priest 34095 Montpellier Cedex 5 34095 Montpellier France
| | - François Rousset
- Institut de Biologie Computationnelle; Université de Montpellier; 860 rue St Priest 34095 Montpellier Cedex 5 34095 Montpellier France
- Institut des Sciences de l'Évolution (UM2-CNRS); Université Montpellier 2; Montpellier France
| | - Pierre-André Crochet
- CEFE UMR 5175; CNRS - Université de Montpellier - Université Paul-Valéry Montpellier - EPHE; 1919 route de Mende 34293 Montpellier cedex 5 France
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