1
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Wong ELY, Filatov DA. The role of recombination landscape in species hybridisation and speciation. FRONTIERS IN PLANT SCIENCE 2023; 14:1223148. [PMID: 37484464 PMCID: PMC10361763 DOI: 10.3389/fpls.2023.1223148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 06/13/2023] [Indexed: 07/25/2023]
Abstract
It is now well recognised that closely related species can hybridize and exchange genetic material, which may promote or oppose adaptation and speciation. In some cases, interspecific hybridisation is very common, making it surprising that species identity is preserved despite active gene exchange. The genomes of most eukaryotic species are highly heterogeneous with regard to gene density, abundance of repetitive DNA, chromatin compactisation etc, which can make certain genomic regions more prone or more resistant to introgression of genetic material from other species. Heterogeneity in local recombination rate underpins many of the observed patterns across the genome (e.g. actively recombining regions are typically gene rich and depleted for repetitive DNA) and it can strongly affect the permeability of genomic regions to interspecific introgression. The larger the region lacking recombination, the higher the chance for the presence of species incompatibility gene(s) in that region, making the entire non- or rarely recombining block impermeable to interspecific introgression. Large plant genomes tend to have highly heterogeneous recombination landscape, with recombination frequently occurring at the ends of the chromosomes and central regions lacking recombination. In this paper we review the relationship between recombination and introgression in plants and argue that large rarely recombining regions likely play a major role in preserving species identity in actively hybridising plant species.
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Affiliation(s)
- Edgar L. Y. Wong
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
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2
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Bendall EE, Bagley RK, Sousa VC, Linnen CR. Faster-haplodiploid evolution under divergence-with-gene-flow: simulations and empirical data from pine-feeding hymenopterans. Mol Ecol 2022; 31:2348-2366. [PMID: 35231148 DOI: 10.1111/mec.16410] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/10/2022] [Accepted: 02/21/2022] [Indexed: 11/28/2022]
Abstract
Although haplodiploidy is widespread in nature, the evolutionary consequences of this mode of reproduction are not well characterized. Here, we examine how genome-wide hemizygosity and a lack of recombination in haploid males affects genomic differentiation in populations that diverge via natural selection while experiencing gene flow. First, we simulated diploid and haplodiploid "genomes" (500-kb loci) evolving under an isolation-with-migration model with mutation, drift, selection, migration, and recombination; and examined differentiation at neutral sites both tightly and loosely linked to a divergently selected site. So long as there is divergent selection and migration, sex-limited hemizygosity and recombination cause elevated differentiation (i.e., produce a "faster-haplodiploid effect") in haplodiploid populations relative to otherwise equivalent diploid populations, for both recessive and codominant mutations. Second, we used genome-wide SNP data to model divergence history and describe patterns of genomic differentiation between sympatric populations of Neodiprion lecontei and N. pinetum, a pair of pine sawfly species (order: Hymenoptera; family: Diprionidae) that are specialized on different pine hosts. These analyses support a history of continuous gene exchange throughout divergence and reveal a pattern of heterogeneous genomic differentiation that is consistent with divergent selection on many unlinked loci. Third, using simulations of haplodiploid and diploid populations evolving according to the estimated divergence history of N. lecontei and N. pinetum, we found that divergent selection would lead to higher differentiation in haplodiploids. Based on these results, we hypothesize that haplodiploids undergo divergence-with-gene-flow and sympatric speciation more readily than diploids.
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Affiliation(s)
- Emily E Bendall
- Department of Biology, University of Kentucky, Lexington, Kentucky, 40506, USA.,Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Robin K Bagley
- Department of Biology, University of Kentucky, Lexington, Kentucky, 40506, USA.,Department of Evolution, Ecology, and Organismal Biology, The Ohio State University at Lima, Lima, OH, 45804, USA
| | - Vitor C Sousa
- CE3C - Centre for Ecology, Evolution and Environmental Changes, Department of Animal Biology, Faculdade de Ciências da Universidade de Lisboa, University of Lisbon, Campo Grande 1749-016, Lisboa, Portugal
| | - Catherine R Linnen
- Department of Biology, University of Kentucky, Lexington, Kentucky, 40506, USA
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3
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Filatov DA, Bendif EM, Archontikis OA, Hagino K, Rickaby REM. The mode of speciation during a recent radiation in open-ocean phytoplankton. Curr Biol 2021; 31:5439-5449.e5. [PMID: 34687611 DOI: 10.1016/j.cub.2021.09.073] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/03/2021] [Accepted: 09/24/2021] [Indexed: 12/30/2022]
Abstract
Despite the enormous ecological importance of marine phytoplankton, surprisingly little is known about how new phytoplankton species originate and evolve in the open ocean, in the absence of apparent geographic barriers that typically act as isolation mechanisms in speciation. To investigate the mechanism of open-ocean speciation, we combined fossil and climatic records from the late Quaternary with genome-wide evolutionary genetic analyses of speciation in the ubiquitous and abundant pelagic coccolithophore genus Gephyrocapsa (including G. huxleyi, formerly known as Emiliania huxleyi). Based on the analysis of 43 sequenced genomes, we report that the best-fitting scenario for all speciation events analyzed included an extended period of complete isolation followed by recent (Holocene) secondary contact, supporting the role of geographic or oceanographic barriers in population divergence and speciation. Consistent with this, fossil data reveal considerable diachroneity of species first occurrence. The timing of all speciation events coincided with glacial phases of glacial-interglacial cycles, suggesting that stronger isolation between the ocean basins and increased segregation of ecological niches during glaciations are important drivers of speciation in marine phytoplankton. The similarity across multiple speciation events implies the generality of this inferred speciation scenario for marine phytoplankton.
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Affiliation(s)
- Dmitry A Filatov
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
| | - El Mahdi Bendif
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK; Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
| | - Odysseas A Archontikis
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
| | - Kyoko Hagino
- Centre for Advanced Marine Core Research, Kochi University, Nankoku, Kochi 783-8502, Japan
| | - Rosalind E M Rickaby
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
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4
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White NJ, Butlin RK. Multidimensional divergent selection, local adaptation, and speciation. Evolution 2021; 75:2167-2178. [PMID: 34263939 DOI: 10.1111/evo.14312] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 06/29/2021] [Accepted: 07/05/2021] [Indexed: 12/24/2022]
Abstract
Divergent selection applied to one or more traits drives local adaptation and may lead to ecological speciation. Divergent selection on many traits might be termed "multidimensional" divergent selection. There is a commonly held view that multidimensional divergent selection is likely to promote local adaptation and speciation to a greater extent than unidimensional divergent selection. We disentangle the core concepts underlying dimensionality as a property of the environment, phenotypes, and genome. In particular, we identify a need to separate the overall strength of selection and the number of loci affected from dimensionality per se, and to distinguish divergence dimensionality from dimensionality of stabilizing selection. We then critically scrutinize this commonly held view that multidimensional selection promotes speciation, re-examining the evidence base from theory, experiments, and nature. We conclude that the evidence base is currently weak and generally suffers from confounding of possible causal effects. Finally, we propose several mechanisms by which multidimensional divergent selection and related processes might influence divergence, both as a driver and as a barrier.
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Affiliation(s)
- Nathan J White
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Roger K Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom.,Department of Marine Sciences, University of Gothenburg, Gothenburg, SE-40530, Sweden
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5
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Rafajlović M, Rambla J, Feder JL, Navarro A, Faria R. Inversions and genomic differentiation after secondary contact: When drift contributes to maintenance, not loss, of differentiation. Evolution 2021; 75:1288-1303. [PMID: 33844299 DOI: 10.1111/evo.14223] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 02/15/2021] [Accepted: 03/08/2021] [Indexed: 11/26/2022]
Abstract
Due to their effects on reducing recombination, chromosomal inversions may play an important role in speciation by establishing and/or maintaining linked blocks of genes causing reproductive isolation (RI) between populations. This view fits empirical data indicating that inversions typically harbor loci involved in RI. However, previous computer simulations of infinite populations with two to four loci involved in RI implied that, even with gene flux as low as 10-8 per gamete, per generation between alternative arrangements, inversions may not have large, qualitative advantages over collinear regions in maintaining population differentiation after secondary contact. Here, we report that finite population sizes can help counteract the homogenizing consequences of gene flux, especially when several fitness-related loci reside within the inversion. In these cases, the persistence time of differentiation after secondary contact can be similar to when gene flux is absent and notably longer than the persistence time without inversions. Thus, despite gene flux, population differentiation may be maintained for up to 100,000 generations, during which time new incompatibilities and/or local adaptations might accumulate and facilitate progress toward speciation. How often these conditions are met in nature remains to be determined.
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Affiliation(s)
- Marina Rafajlović
- Department of Marine Sciences, University of Gothenburg, Gothenburg, SE-40530, Sweden.,Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, SE-40530, Sweden
| | - Jordi Rambla
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Experimental and Health Sciences, Universitat Pompeu Fabra. PRBB, Barcelona, 08003, Spain.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, 08003, Spain
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, 46556
| | - Arcadi Navarro
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Experimental and Health Sciences, Universitat Pompeu Fabra. PRBB, Barcelona, 08003, Spain.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, 08003, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra, Barcelona, 08003, Spain.,BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation, Barcelona, 08005, Spain
| | - Rui Faria
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Experimental and Health Sciences, Universitat Pompeu Fabra. PRBB, Barcelona, 08003, Spain.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom.,CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO, Laboratório Associado, Universidade do Porto, Vairão, 4480-661, Portugal
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El Ayari T, Trigui El Menif N, Hamer B, Cahill AE, Bierne N. The hidden side of a major marine biogeographic boundary: a wide mosaic hybrid zone at the Atlantic-Mediterranean divide reveals the complex interaction between natural and genetic barriers in mussels. Heredity (Edinb) 2019; 122:770-784. [PMID: 30675016 DOI: 10.1038/s41437-018-0174-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 11/25/2018] [Accepted: 11/30/2018] [Indexed: 01/26/2023] Open
Abstract
The Almeria-Oran Front (AOF) is a recognised hotspot of genetic differentiation in the sea, with genetic discontinuities reported in more than 50 species. The AOF is a barrier to dispersal and an ecological boundary; both can determine the position of these genetic breaks. However, the maintenance of genetic differentiation is likely reinforced by genetic barriers. A general drawback of previous studies is an insufficient density of sampling sites at the transition zone, with a conspicuous lack of samples from the southern coastline. We analysed the fine-scale genetic structure in the mussel Mytilus galloprovincialis using a few ancestry-informative loci previously identified from genome scans. We discovered a 600-km-wide mosaic hybrid zone eastward of the AOF along the Algerian coasts. This mosaic zone provides a new twist to our understanding of the Atlantic-Mediterranean transition because it demonstrates that the two lineages can live in sympatry with ample opportunities to interbreed in a large area, but they hardly do so. This implies that some form of reproductive isolation must exist to maintain the two genetic backgrounds locally cohesive. The mosaic zone ends with an abrupt genetic shift at a barrier to dispersal in the Gulf of Bejaia, Eastern Algeria. Simulations of endogenous or exogenous selection in models that account for the geography and hydrodynamic features of the region support the hypothesis that sister hybrid zones could have been differentially trapped at two alternative barriers to dispersal and/or environmental boundaries, at Almeria in the north and Bejaia in the south. A preponderantly unidirectional north-south gene flow next to the AOF can also maintain a patch of intrinsically maintained genetic background in the south and the mosaic structure, even in the absence of local adaptation. Our results concur with the coupling hypothesis that suggests that natural barriers can explain the position of genetic breaks, while their maintenance depends on genetic barriers.
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Affiliation(s)
- Tahani El Ayari
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France.,Faculty of Sciences of Bizerta, Laboratory of Environment Bio-monitoring, University of Carthage, 7021, Zarzouna, Bizerta, Tunisia
| | - Najoua Trigui El Menif
- Faculty of Sciences of Bizerta, Laboratory of Environment Bio-monitoring, University of Carthage, 7021, Zarzouna, Bizerta, Tunisia
| | - Bojan Hamer
- Ruđer Bošković Institute, Center for Marine and Environmental Research, Grad Zagreb, Croatia
| | | | - Nicolas Bierne
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France.
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7
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Meier JI, Marques DA, Wagner CE, Excoffier L, Seehausen O. Genomics of Parallel Ecological Speciation in Lake Victoria Cichlids. Mol Biol Evol 2018; 35:1489-1506. [DOI: 10.1093/molbev/msy051] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Joana Isabel Meier
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Computational and Molecular Population Genetics (CMPG), Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - David Alexander Marques
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Computational and Molecular Population Genetics (CMPG), Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Catherine Elise Wagner
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Laurent Excoffier
- Computational and Molecular Population Genetics (CMPG), Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ole Seehausen
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
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8
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Gante HF, Matschiner M, Malmstrøm M, Jakobsen KS, Jentoft S, Salzburger W. Genomics of speciation and introgression in Princess cichlid fishes from Lake Tanganyika. Mol Ecol 2016; 25:6143-6161. [DOI: 10.1111/mec.13767] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 05/30/2016] [Accepted: 07/11/2016] [Indexed: 01/02/2023]
Affiliation(s)
- Hugo F. Gante
- Zoological Institute University of Basel Vesalgasse 1 4051 Basel Switzerland
| | - Michael Matschiner
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
| | - Martin Malmstrøm
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
| | - Kjetill S. Jakobsen
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
| | - Sissel Jentoft
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
- Department of Natural Sciences University of Agder 4604 Kristiansand Norway
| | - Walter Salzburger
- Zoological Institute University of Basel Vesalgasse 1 4051 Basel Switzerland
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
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9
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Filatov DA, Osborne OG, Papadopulos AST. Demographic history of speciation in a Senecio altitudinal hybrid zone on Mt. Etna. Mol Ecol 2016; 25:2467-81. [PMID: 26994342 DOI: 10.1111/mec.13618] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 02/29/2016] [Accepted: 02/29/2016] [Indexed: 01/16/2023]
Abstract
Hybrid zones typically form as a result of species coming into secondary contact, but can also be established in situ as an ecotonal hybrid zone, a situation which has been reported far less frequently. An altitudinal hybrid zone on Mount Etna between two ragwort species (the low elevation Senecio chrysanthemifolius and high elevation S. aethnensis) could potentially represent either of these possibilities. However, a scenario of secondary contact vs. speciation with gene flow has not been explicitly tested. Here, we test these alternatives and demonstrate that the data do not support secondary contact. Furthermore, we report that the previous analyses of speciation history of these species were based on admixed populations, which has led to inflated estimates of ongoing, interspecific gene flow. Our new analyses, based on 'pure' S. aethnensis and S. chrysanthemifolius populations, reveal gene exchange of less than one effective migrant per generation, a level low enough to allow the species to accumulate neutral, genomewide differences. Overall, our results are consistent with a scenario of speciation with gene flow and a divergence time which coincides with the rise of Mt. Etna to altitudes above 2000 m (~150 KY). Further work to quantify the role of adaptation to contrasting environments of high and low altitudes will be needed to support the scenario of recent ecological speciation in this system.
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Affiliation(s)
- Dmitry A Filatov
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Owen G Osborne
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Alexander S T Papadopulos
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.,Royal Botanic Gardens, Kew, Richmond, TW9 3AB, UK
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10
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Arias CF, Van Belleghem S, McMillan WO. Genomics at the evolving species boundary. CURRENT OPINION IN INSECT SCIENCE 2016; 13:7-15. [PMID: 27436548 DOI: 10.1016/j.cois.2015.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 10/07/2015] [Indexed: 06/06/2023]
Abstract
Molecular studies on hybridization date back to Dobzhansky who compared chromosomal banding patterns to determine if interspecific gene flow occurred in nature [1]. Now, the advent of high-throughput sequencing provides increasingly fine insights into genomic differentiation between incipient taxa that are changing our view of adaptation and speciation and the links between the two. Empirical data from hybridizing taxa demonstrate highly heterogeneous patterns of genomic differentiation. Although underlining reasons for this heterogeneity are complex, studies of hybridizing taxa offers some of the best insights into the regions of the genome under divergent selection and the role these regions play in species boundaries. The challenge moving forward is to develop a better theoretical framework that fully leverages these powerful natural experiments.
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Affiliation(s)
- Carlos F Arias
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Panamá, Panama; Biology Program, Faculty of Natural Science and Mathematics, Universidad del Rosario, Carrera 24 # 63c-69, Bogotá 111221, Colombia
| | - Steven Van Belleghem
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Panamá, Panama; Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom; Department of Biology, Center for Applied Tropical Ecology and Conservation, University of Puerto Rico, Rio Piedras, Puerto Rico
| | - W Owen McMillan
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Panamá, Panama.
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11
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Gante HF, Doadrio I, Alves MJ, Dowling TE. Semi-permeable species boundaries in Iberian barbels (Barbus and Luciobarbus, Cyprinidae). BMC Evol Biol 2015; 15:111. [PMID: 26066794 PMCID: PMC4465174 DOI: 10.1186/s12862-015-0392-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 05/28/2015] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND The evolution of species boundaries and the relative impact of selection and gene flow on genomic divergence are best studied in populations and species pairs exhibiting various levels of divergence along the speciation continuum. We studied species boundaries in Iberian barbels, Barbus and Luciobarbus, a system of populations and species spanning a wide degree of genetic relatedness, as well as geographic distribution and range overlap. We jointly analyze multiple types of molecular markers and morphological traits to gain a comprehensive perspective on the nature of species boundaries in these cyprinid fishes. RESULTS Intraspecific molecular and morphological differentiation is visible among many populations. Genomes of all sympatric species studied are porous to gene flow, even if they are not sister species. Compared to their allopatric counterparts, sympatric representatives of different species share alleles and show an increase in all measures of nucleotide polymorphism (S, Hd, K, π and θ). High molecular diversity is particularly striking in L. steindachneri from the Tejo and Guadiana rivers, which co-varies with other sympatric species. Interestingly, different nuclear markers introgress across species boundaries at various levels, with distinct impacts on population trees. As such, some loci exhibit limited introgression and population trees resemble the presumed species tree, while alleles at other loci introgress more freely and population trees reflect geographic affinities and interspecific gene flow. Additionally, extent of introgression decreases with increasing genetic divergence in hybridizing species pairs. CONCLUSIONS We show that reproductive isolation in Iberian Barbus and Luciobarbus is not complete and species boundaries are semi-permeable to (some) gene flow, as different species (including non-sister) are exchanging genes in areas of sympatry. Our results support a speciation-with-gene-flow scenario with heterogeneous barriers to gene flow across the genome, strengthening with genetic divergence. This is consistent with observations coming from other systems and supports the notion that speciation is not instantaneous but a gradual process, during which different species are still able to exchange some genes, while selection prevents gene flow at other loci. We also provide evidence for a hybrid origin of a barbel ecotype, L. steindachneri, suggesting that ecology plays a key role in species coexistence and hybridization in Iberian barbels. This ecotype with intermediate, yet variable, molecular, morphological, trophic and ecological characteristics is the local product of introgressive hybridization of L. comizo with up to three different species (with L. bocagei in the Tejo, with L. microcephalus and L. sclateri in the Guadiana). In spite of the homogenizing effects of ongoing gene flow, species can still be discriminated using a combination of morphological and molecular markers. Iberian barbels are thus an ideal system for the study of species boundaries, since they span a wide range of genetic divergences, with diverse ecologies and degrees of sympatry.
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Affiliation(s)
- Hugo F Gante
- School of Life Sciences, Arizona State University, 85287-4601, Tempe, AZ, USA.
- Museu Nacional de História Natural e da Ciência, Centre for Ecology, Evolution and Environmental Changes (Ce3C), Universidade de Lisboa, Rua da Escola Politécnica 58, 1250-102, Lisbon, Portugal.
- Current address: Zoological Institute, University of Basel, 4051, Basel, Switzerland.
| | - Ignacio Doadrio
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, c/José Gutiérrez Abascal 2, 28006, Madrid, Spain.
| | - Maria Judite Alves
- Museu Nacional de História Natural e da Ciência, Centre for Ecology, Evolution and Environmental Changes (Ce3C), Universidade de Lisboa, Rua da Escola Politécnica 58, 1250-102, Lisbon, Portugal.
| | - Thomas E Dowling
- School of Life Sciences, Arizona State University, 85287-4601, Tempe, AZ, USA.
- Current address: Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, 48202, Detroit, MI, USA.
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12
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Feder JL, Nosil P, Flaxman SM. Assessing when chromosomal rearrangements affect the dynamics of speciation: implications from computer simulations. Front Genet 2014; 5:295. [PMID: 25206365 PMCID: PMC4144205 DOI: 10.3389/fgene.2014.00295] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 08/08/2014] [Indexed: 12/03/2022] Open
Abstract
Many hypotheses have been put forth to explain the origin and spread of inversions, and their significance for speciation. Several recent genic models have proposed that inversions promote speciation with gene flow due to the adaptive significance of the genes contained within them and because of the effects inversions have on suppressing recombination. However, the consequences of inversions for the dynamics of genome wide divergence across the speciation continuum remain unclear, an issue we examine here. We review a framework for the genomics of speciation involving the congealing of the genome into alternate adaptive states representing species (“genome wide congealing”). We then place inversions in this context as examples of how genetic hitchhiking can potentially hasten genome wide congealing. Specifically, we use simulation models to (i) examine the conditions under which inversions may speed genome congealing and (ii) quantify predicted magnitudes of these effects. Effects of inversions on promoting speciation were most common and pronounced when inversions were initially fixed between populations before secondary contact and adaptation involved many genes with small fitness effects. Further work is required on the role of underdominance and epistasis between a few loci of major effect within inversions. The results highlight five important aspects of the roles of inversions in speciation: (i) the geographic context of the origins and spread of inversions, (ii) the conditions under which inversions can facilitate divergence, (iii) the magnitude of that facilitation, (iv) the extent to which the buildup of divergence is likely to be biased within vs. outside of inversions, and (v) the dynamics of the appearance and disappearance of exceptional divergence within inversions. We conclude by discussing the empirical challenges in showing that inversions play a central role in facilitating speciation with gene flow.
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Affiliation(s)
- Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame Notre Dame, IN, USA
| | - Patrik Nosil
- Department of Animal and Plant Sciences, University of Sheffield Sheffield, UK
| | - Samuel M Flaxman
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, CO, USA
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13
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Harrison RG, Larson EL. Hybridization, Introgression, and the Nature of Species Boundaries. J Hered 2014; 105 Suppl 1:795-809. [DOI: 10.1093/jhered/esu033] [Citation(s) in RCA: 418] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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Feder JL, Nosil P, Wacholder AC, Egan SP, Berlocher SH, Flaxman SM. Genome-Wide Congealing and Rapid Transitions across the Speciation Continuum during Speciation with Gene Flow. J Hered 2014; 105 Suppl 1:810-20. [DOI: 10.1093/jhered/esu038] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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15
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Cruickshank TE, Hahn MW. Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow. Mol Ecol 2014; 23:3133-57. [DOI: 10.1111/mec.12796] [Citation(s) in RCA: 764] [Impact Index Per Article: 76.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 05/05/2014] [Accepted: 05/07/2014] [Indexed: 12/18/2022]
Affiliation(s)
| | - Matthew W. Hahn
- Department of Biology; Indiana University; Bloomington IN 47405 USA
- School of Informatics and Computing; Indiana University; Bloomington IN 47405 USA
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Comeault AA, Soria-Carrasco V, Gompert Z, Farkas TE, Buerkle CA, Parchman TL, Nosil P. Genome-Wide Association Mapping of Phenotypic Traits Subject to a Range of Intensities of Natural Selection in Timema cristinae. Am Nat 2014; 183:711-27. [DOI: 10.1086/675497] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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17
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Feder JL, Flaxman SM, Egan SP, Comeault AA, Nosil P. Geographic Mode of Speciation and Genomic Divergence. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2013. [DOI: 10.1146/annurev-ecolsys-110512-135825] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jeffrey L. Feder
- Department of Biological Sciences,
- Environmental Change Initiative, and
- Advanced Diagnostics and Therapeutics, University of Notre Dame, Notre Dame, Indiana 46556; ,
| | - Samuel M. Flaxman
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309;
| | - Scott P. Egan
- Department of Biological Sciences,
- Advanced Diagnostics and Therapeutics, University of Notre Dame, Notre Dame, Indiana 46556; ,
| | - Aaron A. Comeault
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S102TN, United Kingdom; ,
| | - Patrik Nosil
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S102TN, United Kingdom; ,
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Alshahid M, Wakil SM, Al-Najai M, Muiya NP, Elhawari S, Gueco D, Andres E, Hagos S, Mazhar N, Meyer BF, Dzimiri N. New susceptibility locus for obesity and dyslipidaemia on chromosome 3q22.3. Hum Genomics 2013; 7:15. [PMID: 23738802 PMCID: PMC3681549 DOI: 10.1186/1479-7364-7-15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 05/13/2013] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The muscle Ras (MRAS) gene resides on chromosome 3q22.3 and encodes a member of the membrane-associated Ras small GTPase proteins, which function as signal transducers in multiple processes including cell growth and differentiation. Its role in cardiovascular disease is not fully understood yet. In a preliminary study in heterozygous familial hypercholesterolaemia, we identified a locus linking the early onset of coronary artery disease (CAD) to chromosome 3q.22 and elected to sequence the MRAS gene using the MegaBACE DNA analysis system. In the present study, we investigated the association of seven single-nucleotide polymorphisms (SNPs) at this locus with CAD and its dyslipidaemia-related risk traits in 4,650 Saudi angiographed individuals using TaqMan assays by the Applied Biosystems real-time Prism 7900HT Sequence Detection System. RESULTS Among the studied SNPs, rs6782181 (p = 0.017) and rs9818870T (p = 0.009) were associated with CAD following adjustment for sex, age and other confounding risk factors. The rs6782181_GG also conferred risk for obesity (1,764 cases vs. 2,586 controls) [1.16(1.03-1.30); p = 0.017], hypercholesterolaemia (1,686 vs. 2,744) [1.23(1.02-1.47); p = 0.019], hypertriglyceridaemia (1,155 vs. 3,496) [1.29(1.01-1.45); p = 0.043] and low high-density lipoprotein-cholesterol (lHDL-chol) levels (1,935 vs. 2,401) [1.15(1.02-1.30); p = 0.023] after adjustment. Additionally, rs253662_(CT+TT) [1.16(1.01-1.32); p = 0.030] was associated with lHDL-chol levels. Interestingly, rs253662 (p = 0.014) and rs6782181 (p = 0.019) were protective against acquiring high low-density lipoprotein-cholesterol (hLDL-chol) levels (p = 0.014), while rs1720819 showed similar effects against CAD (p < 0.0001). More importantly, a 7-mer haplotype, ACCTGAC (χ2 = 7.66; p = 0.0056), constructed from the studied SNPs, its 6-mer derivative CCTGAC (χ2 = 6.90; p = 0.0086) and several other shorter derivatives conferred risk for obesity. hLDL-chol was weakly linked to CTAA (χ2 = 3.79; p = 0.052) and CCT (χ2 = 4.32; p = 0.038), while several other haplotypes were protective against both obesity and hLDL-chol level. CONCLUSION Our results demonstrate that the genomic locus for the MRAS gene confers risk for CAD, obesity and dyslipidaemia and point to the possible involvement of other genes or regulatory elements at this locus, rather than changes in the M-Ras protein function, in these events.
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Affiliation(s)
- Maie Alshahid
- King Faisal Heart Institute, MBC-16, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Salma M Wakil
- Genetics Department, MBC-03, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Mohammed Al-Najai
- Genetics Department, MBC-03, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Nzioka P Muiya
- Genetics Department, MBC-03, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Samar Elhawari
- Genetics Department, MBC-03, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Daisy Gueco
- Genetics Department, MBC-03, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Editha Andres
- Genetics Department, MBC-03, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Samia Hagos
- Genetics Department, MBC-03, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Nejat Mazhar
- Genetics Department, MBC-03, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Brian F Meyer
- King Faisal Heart Institute, MBC-16, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Nduna Dzimiri
- Genetics Department, MBC-03, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
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19
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Flaxman SM, Feder JL, Nosil P. Genetic hitchhiking and the dynamic buildup of genomic divergence during speciation with gene flow. Evolution 2013; 67:2577-91. [PMID: 24033168 DOI: 10.1111/evo.12055] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2012] [Accepted: 01/02/2013] [Indexed: 12/22/2022]
Abstract
A major issue in evolutionary biology is explaining patterns of differentiation observed in population genomic data, as divergence can be due to both direct selection on a locus and genetic hitchhiking. "Divergence hitchhiking" (DH) theory postulates that divergent selection on a locus reduces gene flow at physically linked sites, facilitating the formation of localized clusters of tightly linked, diverged loci. "Genome hitchhiking" (GH) theory emphasizes genome-wide effects of divergent selection. Past theoretical investigations of DH and GH focused on static snapshots of divergence. Here, we used simulations assessing a variety of strengths of selection, migration rates, population sizes, and mutation rates to investigate the relative importance of direct selection, GH, and DH in facilitating the dynamic buildup of genomic divergence as speciation proceeds through time. When divergently selected mutations were limiting, GH promoted divergence, but DH had little measurable effect. When populations were small and divergently selected mutations were common, DH enhanced the accumulation of weakly selected mutations, but this contributed little to reproductive isolation. In general, GH promoted reproductive isolation by reducing effective migration rates below that due to direct selection alone, and was important for genome-wide "congealing" or "coupling" of differentiation (F(ST)) across loci as speciation progressed.
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Affiliation(s)
- Samuel M Flaxman
- Department of Ecology and Evolutionary Biology, N211 Ramaley Hall, University of Colorado, Boulder, Colorado.
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