1
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Regan T, Hori TS, Bean TP. A chromosome-scale Mytilus edulis genome assembly for aquaculture, marine ecology, and evolution. G3 (BETHESDA, MD.) 2024; 14:jkae138. [PMID: 38935082 PMCID: PMC11304980 DOI: 10.1093/g3journal/jkae138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/12/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024]
Abstract
The smooth-shelled blue mussel, Mytilus edulis is part of the Mytilus species complex, encompassing at least three putative species: M. edulis, Mytilus galloprovincialis, and Mytilus trossulus. These three species occur on both sides of the Atlantic and hybridize in nature, and both M. edulis and M. galloprovincialis are important aquaculture species. They are also invasive species in many parts of the world. Here, we present a chromosome-level assembly of M. edulis. We used a combination of PacBio sequencing and Dovetail's Omni-C technology to generate an assembly with 14 long scaffolds containing 94% of the predicted length of the M. edulis genome (1.6 out of 1.7 Gb). Assembly statistics were as follows: total length = 1.65 Gb, N50 = 116 Mb, L50 = 7, and L90 = 13. BUSCO analysis showed 92.55% eukaryote BUSCOs identified. AB-Initio annotation using RNA-seq from mantle, gills, muscle, and foot predicted 47,128 genes. These gene models were combined with IsoSeq validation resulting in 45,379 full CDS protein sequences and 129,708 isoforms. Using GBS and shotgun sequencing, we also sequenced several eastern Canadian populations of Mytilus to characterize single-nucleotide as well as structural variance. This high-quality genome for M. edulis provides a platform to develop tools that can be used in breeding, molecular ecology and evolution to address questions of both commercial and environmental perspectives.
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Affiliation(s)
- Tim Regan
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Tiago S Hori
- Atlantic Aqua Farms Ltd., Charlottetown, Prince Edward Island, PE C1A 4A2, Canada
| | - Tim P Bean
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK
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2
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Maier PA, Vandergast AG, Bohonak AJ. Yosemite toad (Anaxyrus canorus) transcriptome reveals interplay between speciation genes and adaptive introgression. Mol Ecol 2024; 33:e17317. [PMID: 38488670 DOI: 10.1111/mec.17317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 02/15/2024] [Accepted: 02/23/2024] [Indexed: 04/09/2024]
Abstract
Genomes are heterogeneous during the early stages of speciation, with small 'islands' of DNA appearing to reflect strong adaptive differences, surrounded by vast seas of relative homogeneity. As species diverge, secondary contact zones between them can act as an interface and selectively filter through advantageous alleles of hybrid origin. Such introgression is another important adaptive process, one that allows beneficial mosaics of recombinant DNA ('rivers') to flow from one species into another. Although genomic islands of divergence appear to be associated with reproductive isolation, and genomic rivers form by adaptive introgression, it is unknown whether islands and rivers tend to be the same or different loci. We examined three replicate secondary contact zones for the Yosemite toad (Anaxyrus canorus) using two genomic data sets and a morphometric data set to answer the questions: (1) How predictably different are islands and rivers, both in terms of genomic location and gene function? (2) Are the adaptive genetic trait loci underlying tadpole growth and development reliably islands, rivers or neither? We found that island and river loci have significant overlap within a contact zone, suggesting that some loci are first islands, and later are predictably converted into rivers. However, gene ontology enrichment analysis showed strong overlap in gene function unique to all island loci, suggesting predictability in overall gene pathways for islands. Genome-wide association study outliers for tadpole development included LPIN3, a lipid metabolism gene potentially involved in climate change adaptation, that is island-like for all three contact zones, but also appears to be introgressing (as a river) across one zone. Taken together, our results suggest that adaptive divergence and introgression may be more complementary forces than currently appreciated.
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Affiliation(s)
- Paul A Maier
- Department of Biology, San Diego State University, San Diego, California, USA
- Family TreeDNA, Gene by Gene, Houston, Texas, USA
| | - Amy G Vandergast
- Western Ecological Research Center, San Diego Field Station, U.S. Geological Survey, San Diego, California, USA
| | - Andrew J Bohonak
- Department of Biology, San Diego State University, San Diego, California, USA
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3
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Willis AB, Ermolaeva E, Zyck A, Rognstad R, Davis S, Hilbish TJ. Integration of natural selection across the life cycle stabilizes a marine mussel hybrid zone. Ecol Evol 2024; 14:e11086. [PMID: 38469047 PMCID: PMC10925496 DOI: 10.1002/ece3.11086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/12/2024] [Accepted: 02/16/2024] [Indexed: 03/13/2024] Open
Abstract
Hybridization among related species is now recognized as common but it remains unclear how hybrid zones persist for prolonged periods. Here, we test the hypothesis that selection in different components of the life cycle may stabilize a hybrid zone. A hybrid zone occurs in southwest England between the marine mussels Mytilus edulis and M. galloprovincialis. Previous studies have found strong directional selection against alleles from M. edulis occurs among hybrids in the adult stage. Traditional hybrid zone models argue that alleles that are selected within the hybrid zone are replaced by migration from neighboring parental population into the hybrid zone. In this system, however, migration occurs out of this hybrid zone into neighboring parental populations. This hybrid zone should therefore be unstable and dissipate, yet this zone has persisted for more than 30 years. We tested and rejected the hypothesis that differences in fecundity may select for M. edulis alleles within this hybrid zone and thus counter the selection observed against these alleles among adults. We also tested the hypothesis that selection during the larval stage may counter selection against M. edulis alleles in the adult stage. We found that selection favors M. edulis alleles during the veliger stage of larval development. The direction and strength of selection during the larval stage are sufficient to counter strong selection during the adult portion of the life cycle. This hybrid zone is stabilized by opposing forms of directional selection operating in different portions of the life cycle.
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Affiliation(s)
- Allison B. Willis
- Department of Biological SciencesUniversity of South CarolinaColumbiaSouth CarolinaUSA
| | - Evgeniya Ermolaeva
- Department of Biological SciencesUniversity of South CarolinaColumbiaSouth CarolinaUSA
| | - Amaelia Zyck
- Department of Biological SciencesUniversity of South CarolinaColumbiaSouth CarolinaUSA
| | - Rhiannon Rognstad
- Department of Biological SciencesUniversity of South CarolinaColumbiaSouth CarolinaUSA
| | - Shannon Davis
- Department of Biological SciencesUniversity of South CarolinaColumbiaSouth CarolinaUSA
| | - Thomas J. Hilbish
- Department of Biological SciencesUniversity of South CarolinaColumbiaSouth CarolinaUSA
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4
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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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5
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Bruni G, Chiocchio A, Nascetti G, Cimmaruta R. Different patterns of introgression in a three species hybrid zone among European cave salamanders. Ecol Evol 2023; 13:e10437. [PMID: 37636870 PMCID: PMC10447881 DOI: 10.1002/ece3.10437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/29/2023] Open
Abstract
Hybrid zones occur where genetically distinct populations meet, mate and produce offspring with mixed ancestry. In Plethodontid salamanders, introgressive hybridization is a common phenomenon, where hybrids backcross with parental populations leading to the spread of new alleles into the parental genomes. Whereas many hybrid zones have been reported in American Plethodontid salamanders, only a single hybrid zone has been documented in European plethodontids so far, which is located at the Apuan Alps in the Italian Peninsula. Here, we describe a previously unreported hybrid zone in the Northern Apennines involving all the three Plethodontid salamander species inhabiting the Italian Peninsula. We found 21 new Speleomantes sites of occurrence, from a hitherto unexplored area located at the boundaries between three Speleomantes species ranges. Using mitochondrial (Cytb and ND2 genes) and nuclear markers (two diagnostic SNPs at the NCX1 gene), we revealed a three-way contact zone where all the three mainland species hybridize: S. strinatii, S. ambrosii and S. italicus. We observed a strong mitonuclear discordance, with mitochondrial markers showing a conspicuous geographic pattern, while diagnostic nuclear SNPs coexisted in both the same populations and individuals, providing evidence of hybridization in many possible combinations. The introgression is asymmetric, with S. italicus mitogenome usually associated with S. a. ambrosii and, to a lesser extent, to S. strinatii nuclear alleles. This finding confirms that Plethodontid are a group of choice to investigate hybridization mechanisms and suggests that behavioural, genetic and ecological components may concur in determining the direction and extent of introgression.
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Affiliation(s)
| | - Andrea Chiocchio
- Department of Ecological and Biological SciencesTuscia UniversityViterboItaly
| | - Giuseppe Nascetti
- Department of Ecological and Biological SciencesTuscia UniversityViterboItaly
| | - Roberta Cimmaruta
- Department of Ecological and Biological SciencesTuscia UniversityViterboItaly
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6
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Lapègue S, Reisser C, Harrang E, Heurtebise S, Bierne N. Genetic parallelism between European flat oyster populations at the edge of their natural range. Evol Appl 2023; 16:393-407. [PMID: 36793680 PMCID: PMC9923475 DOI: 10.1111/eva.13449] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 07/07/2022] [Accepted: 07/11/2022] [Indexed: 11/28/2022] Open
Abstract
Although all marine ecosystems have experienced global-scale losses, oyster reefs have shown the greatest. Therefore, substantial efforts have been dedicated to restoration of such ecosystems during the last two decades. In Europe, several pilot projects for the restoration of the native European flat oyster, Ostrea edulis, recently begun and recommendations to preserve genetic diversity and to conduct monitoring protocols have been made. In particular, an initial step is to test for genetic differentiation against homogeneity among the oyster populations potentially involved in such programs. Therefore, we conducted a new sampling of wild populations at the European scale and a new genetic analysis with 203 markers to (1) confirm and study in more detail the pattern of genetic differentiation between Atlantic and Mediterranean populations, (2) identify potential translocations that could be due to aquaculture practices and (3) investigate the populations at the fringe of the geographical range, since they seemed related despite their geographic distance. Such information should be useful to enlighten the choice of the animals to be translocated or reproduced in hatcheries for further restocking. After the confirmation of the general geographical pattern of genetic structure and the identification of one potential case of aquaculture transfer at a large scale, we were able to detect genomic islands of differentiation mainly in the form of two groups of linked markers, which could indicate the presence of polymorphic chromosomal rearrangements. Furthermore, we observed a tendency for these two islands and the most differentiated loci to show a parallel pattern of differentiation, grouping the North Sea populations with the Eastern Mediterranean and Black Sea populations, against geography. We discussed the hypothesis that this genetic parallelism could be the sign of a shared evolutionary history of the two groups of populations despite them being at the border of the distribution nowadays.
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Affiliation(s)
- Sylvie Lapègue
- MARBEC, Univ Montpellier, CNRS Ifremer, IRD Montpellier France
| | - Céline Reisser
- MARBEC, Univ Montpellier, CNRS Ifremer, IRD Montpellier France
| | | | | | - Nicolas Bierne
- ISEM, Univ Montpellier, CNRS, EPHE, IRD Montpellier France
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7
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Sussarellu R, Chouvelon T, Aminot Y, Couteau J, Loppion G, Dégremont L, Lamy JB, Akcha F, Rouxel J, Berthelin C, Briaudeau T, Izagirre U, Mauffret A, Grouhel A, Burgeot T. Differences in chemical contaminants bioaccumulation and ecotoxicology biomarkers in Mytilus edulis and Mytilus galloprovincialis and their hybrids. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 292:118328. [PMID: 34653587 DOI: 10.1016/j.envpol.2021.118328] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 10/06/2021] [Accepted: 10/07/2021] [Indexed: 06/13/2023]
Abstract
The Mytilus mussels are spread all over the world and many related species coexist in several areas and can produce hybrid offspring. Mussels have been used for decades in national and international programs to monitor chemical contamination in the environment. Differences in bioaccumulation and biotransformation abilities between species and their hybrids should be evaluated to assess the comparability of the results obtained within the international biomonitoring programs. The objective of this study was to characterize bioaccumulation abilities and biomarker responses in Mytilus edulis, Mytilus galloprovincialis and their hybrids via an in situ transplantation experimentation on their progenies. Four mussel groups (M. edulis, M. galloprovincialis and two hybrids batches) issued from genetically characterized parents were transplanted for one year in Charente Maritime (France) to ensure their exposure to identical sources of contamination. The bioaccumulation of several families of contaminants (trace metals, polycyclic aromatic hydrocarbons, polybrominated diphenyl ethers, polychlorinated biphenyls), the response of several biomarkers (DNA strand breaks level, lysosomal membrane stability, metallothionein content, acetylcholine esterase activity) and some physiological parameters (growth, mortality, gonadal development), were analyzed. Differences were observed between species, however they were contaminant-specific. Variations in contaminants levels were observed between progenies, with higher levels of Cu, PBDE, PCB in M. edulis, and higher levels of Cd, Hg, Zn in M galloprovincialis. This study demonstrated that variations in contaminant bioaccumulation and different biomarker responses exist between Mytilus species in the field. Data on species or the presence of hybrid individuals (or introgression) is an important additional parameter to add to biomonitoring programs databases.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Tifanie Briaudeau
- Dept. of Zoology and Animal Cell Biology, Research Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU), Plentzia, Basque Country, Spain
| | - Urtzi Izagirre
- Dept. of Zoology and Animal Cell Biology, Research Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU), Plentzia, Basque Country, Spain
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8
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Nickel J, Schell T, Holtzem T, Thielsch A, Dennis SR, Schlick-Steiner BC, Steiner FM, Möst M, Pfenninger M, Schwenk K, Cordellier M. Hybridization Dynamics and Extensive Introgression in the Daphnia longispina Species Complex: New Insights from a High-Quality Daphnia galeata Reference Genome. Genome Biol Evol 2021; 13:6448229. [PMID: 34865004 PMCID: PMC8695838 DOI: 10.1093/gbe/evab267] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2021] [Indexed: 01/02/2023] Open
Abstract
Hybridization and introgression are recognized as an important source of variation that influence adaptive processes; both phenomena are frequent in the genus Daphnia, a keystone zooplankton taxon in freshwater ecosystems that comprises several species complexes. To investigate genome-wide consequences of introgression between species, we provide here the first high-quality genome assembly for a member of the Daphnia longispina species complex, Daphnia galeata. We further resequenced 49 whole genomes of three species of the complex and their interspecific hybrids both from genotypes sampled in the water column and from single resting eggs extracted from sediment cores. Populations from habitats with diverse ecological conditions offered an opportunity to study the dynamics of hybridization linked to ecological changes and revealed a high prevalence of hybrids. Using phylogenetic and population genomic approaches, we provide first insights into the intra- and interspecific genome-wide variability in this species complex and identify regions of high divergence. Finally, we assess the length of ancestry tracts in hybrids to characterize introgression patterns across the genome. Our analyses uncover a complex history of hybridization and introgression reflecting multiple generations of hybridization and backcrossing in the Daphnia longispina species complex. Overall, this study and the new resources presented here pave the way for a better understanding of ancient and contemporary gene flow in the species complex and facilitate future studies on resting egg banks accumulating in lake sediment.
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Affiliation(s)
- Jana Nickel
- Institute of Zoology, Universität Hamburg, Germany
| | - Tilman Schell
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Tania Holtzem
- Department of Ecology, University of Innsbruck, Austria
| | - Anne Thielsch
- Molecular Ecology, Institute for Environmental Sciences, University Koblenz-Landau, Landau in der Pfalz, Germany
| | - Stuart R Dennis
- Department of Aquatic Ecology, EAWAG, Dübendorf, Switzerland
| | | | | | - Markus Möst
- Department of Ecology, University of Innsbruck, Austria
| | - Markus Pfenninger
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany.,Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany.,IoME, Gutenberg University, Mainz, Germany
| | - Klaus Schwenk
- Molecular Ecology, Institute for Environmental Sciences, University Koblenz-Landau, Landau in der Pfalz, Germany
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9
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Arntzen JW, Jehle R, Wielstra B. Genetic and morphological data demonstrate hybridization and backcrossing in a pair of salamanders at the far end of the speciation continuum. Evol Appl 2021; 14:2784-2793. [PMID: 34950229 PMCID: PMC8674889 DOI: 10.1111/eva.13312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 09/05/2021] [Accepted: 10/01/2021] [Indexed: 12/23/2022] Open
Abstract
Deeply diverged yet hybridizing species provide a system to investigate the final stages of the speciation process. We study a hybridizing pair of salamander species-the morphologically and genetically drastically different newts Triturus cristatus and T. marmoratus-with a panel of 32 nuclear and mitochondrial genetic markers. Morphologically identified hybrids are mostly of the F1 generation and mothered by T. cristatus. The sex ratio of the F1 hybrid class is reciprocally skewed, with a preponderance of females in T. cristatus-mothered hybrids and males in T. marmoratus-mothered hybrids. This amounts to the Haldane effect operating in one direction of the cross. Deeper generation hybrids are occasionally produced, possibly including F1 hybrid × backcross hybrid offspring. Interspecific gene flow is low, yet skewed toward T. cristatus. This asymmetry may be caused by hybrid zone movement, with the superseding species being predisposed to introgression. The persisting gene flow between deeply differentiated species supports the notion that full genetic isolation may be selected against. Conversely, published morphological data suggest that introgressive hybridization is detrimental, with digital malformations occurring more frequently in the area of sympatry. Finally, to assist field identification, both within the area of natural range overlap and concerning anthropogenic introductions elsewhere, we document the phenotypical variation of two generations of hybrids compared with both parental species. We suggest that fluctuating range boundaries, ecological segregation, cytonuclear incompatibilities and hybrid breakdown through Bateson-Dobzhansky-Muller incompatibilities all contribute to species integrity, despite incomplete isolation during secondary contact.
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Affiliation(s)
- Jan W. Arntzen
- Naturalis Biodiversity CenterLeidenThe Netherlands
- Institute of BiologyLeiden UniversityLeidenThe Netherlands
| | - Robert Jehle
- School of Science, Engineering and EnvironmentUniversity of SalfordSalfordUK
| | - Ben Wielstra
- Naturalis Biodiversity CenterLeidenThe Netherlands
- Institute of BiologyLeiden UniversityLeidenThe Netherlands
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10
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Svedberg J, Shchur V, Reinman S, Nielsen R, Corbett-Detig R. Inferring Adaptive Introgression Using Hidden Markov Models. Mol Biol Evol 2021; 38:2152-2165. [PMID: 33502512 PMCID: PMC8097282 DOI: 10.1093/molbev/msab014] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Adaptive introgression-the flow of adaptive genetic variation between species or populations-has attracted significant interest in recent years and it has been implicated in a number of cases of adaptation, from pesticide resistance and immunity, to local adaptation. Despite this, methods for identification of adaptive introgression from population genomic data are lacking. Here, we present Ancestry_HMM-S, a hidden Markov model-based method for identifying genes undergoing adaptive introgression and quantifying the strength of selection acting on them. Through extensive validation, we show that this method performs well on moderately sized data sets for realistic population and selection parameters. We apply Ancestry_HMM-S to a data set of an admixed Drosophila melanogaster population from South Africa and we identify 17 loci which show signatures of adaptive introgression, four of which have previously been shown to confer resistance to insecticides. Ancestry_HMM-S provides a powerful method for inferring adaptive introgression in data sets that are typically collected when studying admixed populations. This method will enable powerful insights into the genetic consequences of admixture across diverse populations. Ancestry_HMM-S can be downloaded from https://github.com/jesvedberg/Ancestry_HMM-S/.
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Affiliation(s)
- Jesper Svedberg
- Department of Biomolecular Engineering, Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA
| | - Vladimir Shchur
- National Research University Higher School of Economics, Moscow, Russian Federation
| | - Solomon Reinman
- Department of Biomolecular Engineering, Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA
| | - Rasmus Nielsen
- National Research University Higher School of Economics, Moscow, Russian Federation
- Department of Integrative Biology and Department of Statistics, UC Berkeley, Berkeley, CA, USA
- Center for GeoGenetics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA
- National Research University Higher School of Economics, Moscow, Russian Federation
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11
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Benestan LM, Rougemont Q, Senay C, Normandeau E, Parent E, Rideout R, Bernatchez L, Lambert Y, Audet C, Parent GJ. Population genomics and history of speciation reveal fishery management gaps in two related redfish species ( Sebastes mentella and Sebastes fasciatus). Evol Appl 2021; 14:588-606. [PMID: 33664797 PMCID: PMC7896722 DOI: 10.1111/eva.13143] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 08/27/2020] [Accepted: 09/01/2020] [Indexed: 12/18/2022] Open
Abstract
Understanding the processes shaping population structure and reproductive isolation of marine organisms can improve their management and conservation. Using genomic markers combined with estimation of individual ancestries, assignment tests, spatial ecology, and demographic modeling, we (i) characterized the contemporary population structure, (ii) assessed the influence of space, fishing depth, and sampling years on contemporary distribution, and (iii) reconstructed the speciation history of two cryptic redfish species, Sebastes mentella and S. fasciatus. We genotyped 860 individuals in the Northwest Atlantic Ocean using 24,603 filtered single nucleotide polymorphisms (SNPs). Our results confirmed the clear genetic distinctiveness of the two species and identified three ecotypes within S. mentella and five populations in S. fasciatus. Multivariate analyses highlighted the influence of spatial distribution and depth on the overall genomic variation, while demographic modeling revealed that secondary contact models best explained inter- and intragenomic divergence. These species, ecotypes, and populations can be considered as a rare and wide continuum of genomic divergence in the marine environment. This acquired knowledge pertaining to the evolutionary processes driving population divergence and reproductive isolation will help optimizing the assessment of demographic units and possibly to refine fishery management units.
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Affiliation(s)
- Laura M. Benestan
- CEFEUniv Montpellier, CNRS, EPHE‐PSL UniversityIRD, Univ Paul Valéry Montpellier 3MontpellierFrance
| | - Quentin Rougemont
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Caroline Senay
- Fisheries and Oceans CanadaMaurice‐Lamontagne InstituteMont‐JoliQCCanada
| | - Eric Normandeau
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Eric Parent
- Fisheries and Oceans CanadaMaurice‐Lamontagne InstituteMont‐JoliQCCanada
| | - Rick Rideout
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreN.L.St. John’sCanada
| | - Louis Bernatchez
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Yvan Lambert
- Fisheries and Oceans CanadaMaurice‐Lamontagne InstituteMont‐JoliQCCanada
| | - Céline Audet
- Institut des sciences de la mer de RimouskiUniversité du Québec à RimouskiRimouskiQCCanada
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12
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Leroy T, Rougemont Q. Introduction to Population Genomics Methods. Methods Mol Biol 2021; 2222:287-324. [PMID: 33301100 DOI: 10.1007/978-1-0716-0997-2_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
High-throughput sequencing technologies have provided an unprecedented opportunity to study the different evolutionary forces that have shaped present-day patterns of genetic diversity, with important implications for many directions in plant biology research. To manage such massive quantities of sequencing data, biologists, however, need new additional skills in informatics and statistics. In this chapter, our objective is to introduce population genomics methods to beginners following a learning-by-doing strategy in order to help the reader to analyze the sequencing data by themselves. Conducted analyses cover several main areas of evolutionary biology, such as an initial description of the evolutionary history of a given species or the identification of genes targeted by natural or artificial selection. In addition to the practical advices, we performed re-analyses of two cases studies with different kind of data: a domesticated cereal (African rice) and a non-domesticated tree species (sessile oak). All the code needed to replicate this work is publicly available on github ( https://github.com/ThibaultLeroyFr/Intro2PopGenomics/ ).
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Affiliation(s)
- Thibault Leroy
- Montpellier Institute of Evolutionary Sciences (ISEM), Université de Montpellier, Montpellier, France. .,Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria.
| | - Quentin Rougemont
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec, QC, Canada
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13
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Simon A, Fraïsse C, El Ayari T, Liautard-Haag C, Strelkov P, Welch JJ, Bierne N. How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels. J Evol Biol 2020; 34:208-223. [PMID: 33045123 DOI: 10.1111/jeb.13709] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 08/20/2020] [Accepted: 09/16/2020] [Indexed: 12/19/2022]
Abstract
The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study 'replicated' instances of secondary contact between closely related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry-informative panel of such SNPs. We then compared their frequencies in newly sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi-stable variants (Dobzhansky-Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact.
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Affiliation(s)
- Alexis Simon
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Christelle Fraïsse
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France.,Institute of Science and Technology Austria, Klosterneuburg, Austria, Austria
| | - Tahani El Ayari
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | | | - Petr Strelkov
- St. Petersburg State University, St. Petersburg, Russia.,Laboratory of Monitoring and Conservation of Natural Arctic Ecosystems, Murmansk Arctic State University, Murmansk, Russia
| | - John J Welch
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Nicolas Bierne
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
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14
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Duranton M, Allal F, Valière S, Bouchez O, Bonhomme F, Gagnaire PA. The contribution of ancient admixture to reproductive isolation between European sea bass lineages. Evol Lett 2020; 4:226-242. [PMID: 32547783 PMCID: PMC7293100 DOI: 10.1002/evl3.169] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 01/02/2020] [Accepted: 03/05/2020] [Indexed: 12/20/2022] Open
Abstract
Understanding how new species arise through the progressive establishment of reproductive isolation (RI) barriers between diverging populations is a major goal in Evolutionary Biology. An important result of speciation genomics studies is that genomic regions involved in RI frequently harbor anciently diverged haplotypes that predate the reconstructed history of species divergence. The possible origins of these old alleles remain much debated, as they relate to contrasting mechanisms of speciation that are not yet fully understood. In the European sea bass (Dicentrarchus labrax), the genomic regions involved in RI between Atlantic and Mediterranean lineages are enriched for anciently diverged alleles of unknown origin. Here, we used haplotype-resolved whole-genome sequences to test whether divergent haplotypes could have originated from a closely related species, the spotted sea bass (Dicentrarchus punctatus). We found that an ancient admixture event between D. labrax and D. punctatus is responsible for the presence of shared derived alleles that segregate at low frequencies in both lineages of D. labrax. An exception to this was found within regions involved in RI between the two D. labrax lineages. In those regions, archaic tracts originating from D. punctatus locally reached high frequencies or even fixation in Atlantic genomes but were almost absent in the Mediterranean. We showed that the ancient admixture event most likely occurred between D. punctatus and the D. labrax Atlantic lineage, while Atlantic and Mediterranean D. labrax lineages were experiencing allopatric isolation. Our results suggest that local adaptive introgression and/or the resolution of genomic conflicts provoked by ancient admixture have probably contributed to the establishment of RI between the two D. labrax lineages.
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Affiliation(s)
- Maud Duranton
- ISEM Univ Montpellier, CNRS, EPHE, IRD Montpellier France
| | - François Allal
- MARBEC Université de Montpellier, Ifremer-CNRS-IRD-UM Palavas-les-Flots 34250 France
| | - Sophie Valière
- INRA, US 1426, GeT-PlaGe Genotoul Castanet-Tolosan 31326 France
| | - Olivier Bouchez
- INRA, US 1426, GeT-PlaGe Genotoul Castanet-Tolosan 31326 France
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15
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Popovic I, Matias AMA, Bierne N, Riginos C. Twin introductions by independent invader mussel lineages are both associated with recent admixture with a native congener in Australia. Evol Appl 2020; 13:515-532. [PMID: 32431733 PMCID: PMC7045716 DOI: 10.1111/eva.12857] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 06/27/2019] [Accepted: 07/24/2019] [Indexed: 01/04/2023] Open
Abstract
Introduced species can impose profound impacts on the evolution of receiving communities with which they interact. If native and introduced taxa remain reproductively semi-isolated, human-mediated secondary contact may promote genetic exchange across newly created hybrid zones, potentially impacting native genetic diversity and invasive species spread. Here, we investigate the contributions of recent divergence histories and ongoing (post-introduction) gene flow between the invasive marine mussel, Mytilus galloprovincialis, and a morphologically indistinguishable and taxonomically contentious native Australian taxon, Mytilus planulatus. Using transcriptome-wide markers, we demonstrate that two contemporary M. galloprovincialis introductions into south-eastern Australia originate from genetically divergent lineages from its native range in the Mediterranean Sea and Atlantic Europe, where both introductions have led to repeated instances of admixture between introduced and endemic populations. Through increased genome-wide resolution of species relationships, combined with demographic modelling, we validate that mussels sampled in Tasmania are representative of the endemic Australian taxon (M. planulatus), but share strong genetic affinities to M. galloprovincialis. Demographic inferences indicate late-Pleistocene divergence times and historical gene flow between the Tasmanian endemic lineage and northern M. galloprovincialis, suggesting that native and introduced taxa have experienced a period of historical isolation of at least 100,000 years. Our results demonstrate that many genomic loci and sufficient sampling of closely related lineages in both sympatric (e.g. Australian populations) and allopatric (e.g. northern hemisphere Mytilus taxa) ranges are necessary to accurately (a) interpret patterns of intraspecific differentiation and to (b) distinguish contemporary invasive introgression from signatures left by recent divergence histories in high dispersal marine species. More broadly, our study fills a significant gap in systematic knowledge of native Australian biodiversity and sheds light on the intrinsic challenges for invasive species research when native and introduced species boundaries are not well defined.
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Affiliation(s)
- Iva Popovic
- School of Biological SciencesUniversity of QueenslandSt LuciaQldAustralia
| | | | - Nicolas Bierne
- Institut des Sciences de l’EvolutionUMR 5554CNRS‐IRD‐EPHE‐UMUniversité de MontpellierMontpellierFrance
| | - Cynthia Riginos
- School of Biological SciencesUniversity of QueenslandSt LuciaQldAustralia
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16
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Coolen JWP, Boon AR, Crooijmans R, van Pelt H, Kleissen F, Gerla D, Beermann J, Birchenough SNR, Becking LE, Luttikhuizen PC. Marine stepping-stones: Connectivity of Mytilus edulis populations between offshore energy installations. Mol Ecol 2020; 29:686-703. [PMID: 31989703 PMCID: PMC7065051 DOI: 10.1111/mec.15364] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 12/10/2019] [Accepted: 01/20/2020] [Indexed: 12/21/2022]
Abstract
Recent papers have suggested that epifaunal organisms use artificial structures as stepping-stones to spread to areas that are too distant to reach in a single generation. With thousands of artificial structures present in the North Sea, we test the hypothesis that these structures are connected by water currents and act as an interconnected reef. Population genetic structure of the blue mussel, Mytilus edulis, was expected to follow a pattern predicted by a particle tracking model (PTM). Correlation between population genetic differentiation, based on microsatellite markers, and particle exchange was tested. Specimens of M. edulis were found at each location, although the PTM indicated that locations >85 km offshore were isolated from coastal subpopulations. The fixation coefficient FST correlated with the number of arrivals in the PTM. However, the number of effective migrants per generation as inferred from coalescent simulations did not show a strong correlation with the arriving particles. Isolation by distance analysis showed no increase in isolation with increasing distance and we did not find clear structure among the populations. The marine stepping-stone effect is obviously important for the distribution of M. edulis in the North Sea and it may influence ecologically comparable species in a similar way. In the absence of artificial shallow hard substrates, M. edulis would be unlikely to survive in offshore North Sea waters.
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Affiliation(s)
- Joop W. P. Coolen
- Wageningen Marine ResearchDen HelderThe Netherlands
- Aquatic Ecology and Water Quality Management GroupWageningen UniversityWageningenThe Netherlands
| | - Arjen R. Boon
- Deltares, Marine and Coastal SystemsDelftThe Netherlands
| | - Richard Crooijmans
- Animal Breeding and Genomics CentreWageningen UniversityWageningenThe Netherlands
| | | | - Frank Kleissen
- Deltares, Marine and Coastal SystemsDelftThe Netherlands
| | - Daan Gerla
- Wageningen Marine ResearchDen HelderThe Netherlands
| | - Jan Beermann
- Department of Functional EcologyAlfred Wegener Institute Helmholtz Centre for Polar and Marine ResearchBremerhavenGermany
- Helmholtz Institute for Functional Marine BiodiversityOldenburgGermany
| | | | - Leontine E. Becking
- Wageningen Marine ResearchDen HelderThe Netherlands
- Marine Animal Ecology GroupWageningen UniversityWageningenThe Netherlands
| | - Pieternella C. Luttikhuizen
- Department of Coastal SystemsNIOZ Royal Netherlands Institute for Sea ResearchUtrecht UniversityDen BurgThe Netherlands
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17
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Moest M, Van Belleghem SM, James JE, Salazar C, Martin SH, Barker SL, Moreira GRP, Mérot C, Joron M, Nadeau NJ, Steiner FM, Jiggins CD. Selective sweeps on novel and introgressed variation shape mimicry loci in a butterfly adaptive radiation. PLoS Biol 2020; 18:e3000597. [PMID: 32027643 PMCID: PMC7029882 DOI: 10.1371/journal.pbio.3000597] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 02/19/2020] [Accepted: 01/15/2020] [Indexed: 11/21/2022] Open
Abstract
Natural selection leaves distinct signatures in the genome that can reveal the targets and history of adaptive evolution. By analysing high-coverage genome sequence data from 4 major colour pattern loci sampled from nearly 600 individuals in 53 populations, we show pervasive selection on wing patterns in the Heliconius adaptive radiation. The strongest signatures correspond to loci with the greatest phenotypic effects, consistent with visual selection by predators, and are found in colour patterns with geographically restricted distributions. These recent sweeps are similar between co-mimics and indicate colour pattern turn-over events despite strong stabilising selection. Using simulations, we compare sweep signatures expected under classic hard sweeps with those resulting from adaptive introgression, an important aspect of mimicry evolution in Heliconius butterflies. Simulated recipient populations show a distinct 'volcano' pattern with peaks of increased genetic diversity around the selected target, characteristic of sweeps of introgressed variation and consistent with diversity patterns found in some populations. Our genomic data reveal a surprisingly dynamic history of colour pattern selection and co-evolution in this adaptive radiation.
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Affiliation(s)
- Markus Moest
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
- Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Steven M. Van Belleghem
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
- Department of Biology, University of Puerto Rico, Rio Piedras, Puerto Rico
| | - Jennifer E. James
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, United States of America
| | - Camilo Salazar
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del Rosario, Bogota D.C., Colombia
| | - Simon H. Martin
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Sarah L. Barker
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Gilson R. P. Moreira
- Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Claire Mérot
- IBIS, Department of Biology, Université Laval, Québec, Canada
| | - Mathieu Joron
- Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 CNRS—Université de Montpellier—Université Paul Valéry Montpellier—EPHE, Montpellier, France
| | - Nicola J. Nadeau
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | | | - Chris D. Jiggins
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
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18
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Quilodrán CS, Ruegg K, Sendell‐Price AT, Anderson EC, Coulson T, Clegg SM. The multiple population genetic and demographic routes to islands of genomic divergence. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13324] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Kristen Ruegg
- Department of Zoology University of Oxford Oxford UK
- Center for Tropical Research Institute of the Environment and Sustainability University of California, Los Angeles Los Angeles CA USA
- Department of Biology Colorado State University Fort Collins CO USA
| | | | - Eric C. Anderson
- Fisheries Ecology Division Southwest Fisheries Science Center National Marine Fisheries ServiceNOAA Santa Cruz CA USA
| | - Tim Coulson
- Department of Zoology University of Oxford Oxford UK
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19
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Marques DA, Lucek K, Sousa VC, Excoffier L, Seehausen O. Admixture between old lineages facilitated contemporary ecological speciation in Lake Constance stickleback. Nat Commun 2019; 10:4240. [PMID: 31534121 PMCID: PMC6751218 DOI: 10.1038/s41467-019-12182-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 08/27/2019] [Indexed: 01/25/2023] Open
Abstract
Ecological speciation can sometimes rapidly generate reproductively isolated populations coexisting in sympatry, but the origin of genetic variation permitting this is rarely known. We previously explored the genomics of very recent ecological speciation into lake and stream ecotypes in stickleback from Lake Constance. Here, we reconstruct the origin of alleles underlying ecological speciation by combining demographic modelling on genome-wide single nucleotide polymorphisms, phenotypic data and mitochondrial sequence data in the wider European biogeographical context. We find that parallel differentiation between lake and stream ecotypes across replicate lake-stream ecotones resulted from recent secondary contact and admixture between old East and West European lineages. Unexpectedly, West European alleles that introgressed across the hybrid zone at the western end of the lake, were recruited to genomic islands of differentiation between ecotypes at the eastern end of the lake. Our results highlight an overlooked outcome of secondary contact: ecological speciation facilitated by admixture variation. Ecological speciation can proceed rapidly, but the origin of genetic variation facilitating it has remained elusive. Here, the authors show that secondary contact and introgression between deeply diverged lineages of stickleback fish facilitated rapid ecological speciation into lake and stream ecotypes in Lake Constance.
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Affiliation(s)
- David A Marques
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.,Department of Fish Ecology and Evolution, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland.,Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland
| | - Kay Lucek
- Department of Environmental Sciences, University of Basel, Schönbeinstrasse 6, CH-4056, Basel, Switzerland
| | - Vitor C Sousa
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.,Centre for Ecology, Evolution and Environmental Changes, University of Lisbon, Campo Grande 016, 1749-016, Lisbon, Portugal
| | - Laurent Excoffier
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.,Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Ole Seehausen
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland. .,Department of Fish Ecology and Evolution, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland.
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20
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Riquet F, Liautard-Haag C, Woodall L, Bouza C, Louisy P, Hamer B, Otero-Ferrer F, Aublanc P, Béduneau V, Briard O, El Ayari T, Hochscheid S, Belkhir K, Arnaud-Haond S, Gagnaire PA, Bierne N. Parallel pattern of differentiation at a genomic island shared between clinal and mosaic hybrid zones in a complex of cryptic seahorse lineages. Evolution 2019; 73:817-835. [PMID: 30854632 DOI: 10.1111/evo.13696] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 01/19/2019] [Accepted: 01/24/2019] [Indexed: 01/02/2023]
Abstract
Diverging semi-isolated lineages either meet in narrow clinal hybrid zones, or have a mosaic distribution associated with environmental variation. Intrinsic reproductive isolation is often emphasized in the former and local adaptation in the latter, although both reduce gene flow between groups. Rarely are these two patterns of spatial distribution reported in the same study system. Here, we report that the long-snouted seahorse Hippocampus guttulatus is subdivided into discrete panmictic entities by both types of hybrid zones. Along the European Atlantic coasts, a northern and a southern lineage meet in the southwest of France where they coexist in sympatry-i.e., in the same geographical zone-with little hybridization. In the Mediterranean Sea, two lineages have a mosaic distribution, associated with lagoon-like and marine habitats. A fifth lineage was identified in the Black Sea. Genetic homogeneity over large spatial scales contrasts with isolation maintained in sympatry or close parapatry at a fine scale. A high variation in locus-specific introgression rates provides additional evidence that partial reproductive isolation must be maintaining the divergence. We find that fixed differences between lagoon and marine populations in the Mediterranean Sea belong to the most differentiated SNPs between the two Atlantic lineages, against the genome-wide pattern of structure that mostly follow geography. These parallel outlier SNPs cluster on a single chromosome-wide island of differentiation. Since Atlantic lineages do not map to lagoon-sea habitat variation, genetic parallelism at the genomic island suggests a shared genetic barrier contributes to reproductive isolation in contrasting contexts-i.e., spatial versus ecological. We discuss how a genomic hotspot of parallel differentiation could have evolved and become associated both with space and with a patchy environment in a single study system.
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Affiliation(s)
- Florentine Riquet
- Institut des Sciences de l'Evolution de Montpellier, Université Montpellier, Montpellier, France.,CNRS Institut des Sciences de l'Evolution, UMR5554 UM-CNRS-IRD-EPHE, Sète, France
| | - Cathy Liautard-Haag
- Institut des Sciences de l'Evolution de Montpellier, Université Montpellier, Montpellier, France.,CNRS Institut des Sciences de l'Evolution, UMR5554 UM-CNRS-IRD-EPHE, Sète, France
| | - Lucy Woodall
- Department of Zoology, University of Oxford, Wytham, OX2 8QJ, United Kingdom.,Natural History Museum, London, SW7 5BD, United Kingdom
| | - Carmen Bouza
- Department of Genetics, Faculty of Veterinary Science, Universidade de Santiago de Compostela, Lugo, Spain
| | - Patrick Louisy
- ECOMERS Laboratory, University of Nice Sophia Antipolis, Faculty of Sciences, Parc Valrose, Nice, France.,Association Peau-Bleue, 46 rue des Escais, Agde, France
| | - Bojan Hamer
- Center for Marine Research, Ruder Boskovic Institute, Giordano Paliaga 5, 52210, Rovinj, Croatia
| | - Francisco Otero-Ferrer
- Grupo en Biodiversidad y Conservación, IU-ECOAQUA, Universidad de Las Palmas de Gran Canaria, Crta. Taliarte s/n, 35214, Telde, Spain
| | - Philippe Aublanc
- Institut océanographique Paul Ricard, Ile des Embiez, Six-Fours-les-Plages, France
| | - Vickie Béduneau
- Océarium du Croisic, Avenue de Saint Goustan, Le Croisic, France
| | - Olivier Briard
- Aquarium de Biarritz, Biarritz Océan, Plateau de l'Atalaye, Biarritz, France
| | - Tahani El Ayari
- Institut des Sciences de l'Evolution de Montpellier, Université Montpellier, Montpellier, France.,CNRS Institut des Sciences de l'Evolution, UMR5554 UM-CNRS-IRD-EPHE, Sète, France
| | - Sandra Hochscheid
- Stazione Zoologica Anton Dohrn, Department Research Infrastructures for Marine Biological Resources, Aquarium Unit, Napoli, Italy
| | - Khalid Belkhir
- Institut des Sciences de l'Evolution de Montpellier, Université Montpellier, Montpellier, France.,CNRS Institut des Sciences de l'Evolution, UMR5554 UM-CNRS-IRD-EPHE, Sète, France
| | - Sophie Arnaud-Haond
- Institut des Sciences de l'Evolution de Montpellier, Université Montpellier, Montpellier, France.,Ifremer-MARine Biodiversity, Exploitation and Conservation, UMR 9190 IRD-IFREMER-UM-CNRS, Sète, France
| | - Pierre-Alexandre Gagnaire
- Institut des Sciences de l'Evolution de Montpellier, Université Montpellier, Montpellier, France.,CNRS Institut des Sciences de l'Evolution, UMR5554 UM-CNRS-IRD-EPHE, Sète, France
| | - Nicolas Bierne
- Institut des Sciences de l'Evolution de Montpellier, Université Montpellier, Montpellier, France.,CNRS Institut des Sciences de l'Evolution, UMR5554 UM-CNRS-IRD-EPHE, Sète, France
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21
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Fraïsse C, Roux C, Gagnaire PA, Romiguier J, Faivre N, Welch JJ, Bierne N. The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: the effects of sequencing techniques and sampling strategies. PeerJ 2018; 6:e5198. [PMID: 30083438 PMCID: PMC6071616 DOI: 10.7717/peerj.5198] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 06/19/2018] [Indexed: 01/25/2023] Open
Abstract
Genome-scale diversity data are increasingly available in a variety of biological systems, and can be used to reconstruct the past evolutionary history of species divergence. However, extracting the full demographic information from these data is not trivial, and requires inferential methods that account for the diversity of coalescent histories throughout the genome. Here, we evaluate the potential and limitations of one such approach. We reexamine a well-known system of mussel sister species, using the joint site frequency spectrum (jSFS) of synonymous mutations computed either from exome capture or RNA-seq, in an Approximate Bayesian Computation (ABC) framework. We first assess the best sampling strategy (number of: individuals, loci, and bins in the jSFS), and show that model selection is robust to variation in the number of individuals and loci. In contrast, different binning choices when summarizing the jSFS, strongly affect the results: including classes of low and high frequency shared polymorphisms can more effectively reveal recent migration events. We then take advantage of the flexibility of ABC to compare more realistic models of speciation, including variation in migration rates through time (i.e., periodic connectivity) and across genes (i.e., genome-wide heterogeneity in migration rates). We show that these models were consistently selected as the most probable, suggesting that mussels have experienced a complex history of gene flow during divergence and that the species boundary is semi-permeable. Our work provides a comprehensive evaluation of ABC demographic inference in mussels based on the coding jSFS, and supplies guidelines for employing different sequencing techniques and sampling strategies. We emphasize, perhaps surprisingly, that inferences are less limited by the volume of data, than by the way in which they are analyzed.
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Affiliation(s)
- Christelle Fraïsse
- Institut des Sciences de l’Evolution UMR5554, University Montpellier, CNRS, IRD, EPHE, Montpellier, France
- Department of Genetics, University of Cambridge, Cambridge, UK
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Camille Roux
- Université de Lille, Unité Evo-Eco-Paléo (EEP), UMR 8198, Villeneuve d’Ascq, France
| | - Pierre-Alexandre Gagnaire
- Institut des Sciences de l’Evolution UMR5554, University Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Jonathan Romiguier
- Institut des Sciences de l’Evolution UMR5554, University Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Nicolas Faivre
- Institut des Sciences de l’Evolution UMR5554, University Montpellier, CNRS, IRD, EPHE, Montpellier, France
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - John J. Welch
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Nicolas Bierne
- Institut des Sciences de l’Evolution UMR5554, University Montpellier, CNRS, IRD, EPHE, Montpellier, France
- Department of Genetics, University of Cambridge, Cambridge, UK
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22
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Female-biased dispersal and non-random gene flow of MC1R variants do not result in a migration load in barn owls. Heredity (Edinb) 2018; 122:305-314. [PMID: 30006569 DOI: 10.1038/s41437-018-0115-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 06/18/2018] [Accepted: 06/19/2018] [Indexed: 11/08/2022] Open
Abstract
Non-random gene flow is a widely neglected force in evolution and ecology. This genotype-dependent dispersal is difficult to assess, yet can impact the genetic variation of natural populations and their fitness. In this work, we demonstrate a high immigration rate of barn owls (Tyto alba) inside a Swiss population surveyed during 15 years. Using ten microsatellite loci as an indirect method to characterize dispersal, two-third of the genetic tests failed to detect a female-biased dispersal, and Monte Carlo simulations confirmed a low statistical power to detect sex-biased dispersal in case of high dispersal rate of both sexes. The capture-recapture data revealed a female-biased dispersal associated with an excess of heterozygote for the melanocortin-1 receptor gene (MC1R), which is responsible for their ventral rufous coloration. Thus, female homozygotes for the MC1RWHITE allele might be negatively selected during dispersal. Despite the higher immigration of females that are heterozygote at MC1R, non-random gene flow should not lead to a migration load regarding this gene because we did not detect an effect of MC1R on survival and reproductive success in our local population. The present study highlights the usefulness of using multiple methods to correctly decrypt dispersal and gene flow. Moreover, despite theoretical expectations, we show that non-random dispersal of particular genotypes does not necessarily lead to migration load in recipient populations.
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23
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Schmickl R, Marburger S, Bray S, Yant L. Hybrids and horizontal transfer: introgression allows adaptive allele discovery. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5453-5470. [PMID: 29096001 DOI: 10.1093/jxb/erx297] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Evolution has devised countless remarkable solutions to diverse challenges. Understanding the mechanistic basis of these solutions provides insights into how biological systems can be subtly tweaked without maladaptive consequences. The knowledge gained from illuminating these mechanisms is equally important to our understanding of fundamental evolutionary mechanisms as it is to our hopes of developing truly rational plant breeding and synthetic biology. In particular, modern population genomic approaches are proving very powerful in the detection of candidate alleles for mediating consequential adaptations that can be tested functionally. Especially striking are signals gained from contexts involving genetic transfers between populations, closely related species, or indeed between kingdoms. Here we discuss two major classes of these scenarios, adaptive introgression and horizontal gene flow, illustrating discoveries made across kingdoms.
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Affiliation(s)
- Roswitha Schmickl
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, 252 43 Průhonice, Czech Republic
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague, Czech Republic
| | - Sarah Marburger
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Sian Bray
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Levi Yant
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
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Martin SH, Jiggins CD. Interpreting the genomic landscape of introgression. Curr Opin Genet Dev 2017; 47:69-74. [PMID: 28923541 DOI: 10.1016/j.gde.2017.08.007] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 08/28/2017] [Accepted: 08/31/2017] [Indexed: 11/17/2022]
Abstract
Introgression, the transfer of genetic material between species through hybridisation, occurs in many taxa and has important consequences. Genomic studies allow us to characterise the landscape of introgression across the genome, shedding light on both its adaptive benefits and the incompatibilities that help to maintain species barriers. Studies taking a genome-wide view suggest that adaptive introgression may be common, but that introgressed variation between many species is selected against throughout much of the genome. Confounding factors can complicate interpretations from these data, and computational simulations have proved vital to illustrate expected patterns under different scenarios. Future developments will move beyond correlative evidence to explicit models that account for how selection and genetic drift influence introgressed variation.
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Affiliation(s)
- Simon H Martin
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom.
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
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25
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Turissini DA, Matute DR. Fine scale mapping of genomic introgressions within the Drosophila yakuba clade. PLoS Genet 2017; 13:e1006971. [PMID: 28873409 PMCID: PMC5600410 DOI: 10.1371/journal.pgen.1006971] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 09/15/2017] [Accepted: 08/09/2017] [Indexed: 12/15/2022] Open
Abstract
The process of speciation involves populations diverging over time until they are genetically and reproductively isolated. Hybridization between nascent species was long thought to directly oppose speciation. However, the amount of interspecific genetic exchange (introgression) mediated by hybridization remains largely unknown, although recent progress in genome sequencing has made measuring introgression more tractable. A natural place to look for individuals with admixed ancestry (indicative of introgression) is in regions where species co-occur. In west Africa, D. santomea and D. yakuba hybridize on the island of São Tomé, while D. yakuba and D. teissieri hybridize on the nearby island of Bioko. In this report, we quantify the genomic extent of introgression between the three species of the Drosophila yakuba clade (D. yakuba, D. santomea), D. teissieri). We sequenced the genomes of 86 individuals from all three species. We also developed and applied a new statistical framework, using a hidden Markov approach, to identify introgression. We found that introgression has occurred between both species pairs but most introgressed segments are small (on the order of a few kilobases). After ruling out the retention of ancestral polymorphism as an explanation for these similar regions, we find that the sizes of introgressed haplotypes indicate that genetic exchange is not recent (>1,000 generations ago). We additionally show that in both cases, introgression was rarer on X chromosomes than on autosomes which is consistent with sex chromosomes playing a large role in reproductive isolation. Even though the two species pairs have stable contemporary hybrid zones, providing the opportunity for ongoing gene flow, our results indicate that genetic exchange between these species is currently rare.
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Affiliation(s)
- David A. Turissini
- Biology Department, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Daniel R. Matute
- Biology Department, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
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26
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Bauchet G, Grenier S, Samson N, Bonnet J, Grivet L, Causse M. Use of modern tomato breeding germplasm for deciphering the genetic control of agronomical traits by Genome Wide Association study. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:875-889. [PMID: 28188333 DOI: 10.1007/s00122-017-2857-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 01/16/2017] [Indexed: 05/20/2023]
Abstract
A panel of 300 tomato accessions including breeding materials was built and characterized with >11,000 SNP. A population structure in six subgroups was identified. Strong heterogeneity in linkage disequilibrium and recombination landscape among groups and chromosomes was shown. GWAS identified several associations for fruit weight, earliness and plant growth. Genome-wide association studies (GWAS) have become a method of choice in quantitative trait dissection. First limited to highly polymorphic and outcrossing species, it is now applied in horticultural crops, notably in tomato. Until now GWAS in tomato has been performed on panels of heirloom and wild accessions. Using modern breeding materials would be of direct interest for breeding purpose. To implement GWAS on a large panel of 300 tomato accessions including 168 breeding lines, this study assessed the genetic diversity and linkage disequilibrium decay and revealed the population structure and performed GWA experiment. Genetic diversity and population structure analyses were based on molecular markers (>11,000 SNP) covering the whole genome. Six genetic subgroups were revealed and associated to traits of agronomical interest, such as fruit weight and disease resistance. Estimates of linkage disequilibrium highlighted the heterogeneity of its decay among genetic subgroups. Haplotype definition allowed a fine characterization of the groups and their recombination landscape revealing the patterns of admixture along the genome. Selection footprints showed results in congruence with introgressions. Taken together, all these elements refined our knowledge of the genetic material included in this panel and allowed the identification of several associations for fruit weight, plant growth and earliness, deciphering the genetic architecture of these complex traits and identifying several new loci useful for tomato breeding.
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Affiliation(s)
- Guillaume Bauchet
- Syngenta Seeds, 12 Chemin de l'Hobit, 31790, Saint Sauveur, France
- INRA, UR1052, Centre de Recherche PACA, GAFL, 67 Allée des Chênes, Domaine Saint Maurice, CS60094, 84143, Montfavet Cedex, France
- Boyce Thompson Institute, Cornell University, 533 Tower Rd, Ithaca, NY, 14853, USA
| | - Stéphane Grenier
- Syngenta Seeds, 12 Chemin de l'Hobit, 31790, Saint Sauveur, France
| | - Nicolas Samson
- Syngenta Seeds, 12 Chemin de l'Hobit, 31790, Saint Sauveur, France
| | - Julien Bonnet
- Syngenta Seeds, 12 Chemin de l'Hobit, 31790, Saint Sauveur, France
| | - Laurent Grivet
- Syngenta Seeds, 12 Chemin de l'Hobit, 31790, Saint Sauveur, France
| | - Mathilde Causse
- INRA, UR1052, Centre de Recherche PACA, GAFL, 67 Allée des Chênes, Domaine Saint Maurice, CS60094, 84143, Montfavet Cedex, France.
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27
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Bertrand JAM, Borsa P, Chen WJ. Phylogeography of the sergeants Abudefduf sexfasciatus and A. vaigiensis reveals complex introgression patterns between two widespread and sympatric Indo-West Pacific reef fishes. Mol Ecol 2017; 26:2527-2542. [PMID: 28160340 DOI: 10.1111/mec.14044] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 01/19/2017] [Accepted: 01/25/2017] [Indexed: 01/02/2023]
Abstract
On evolutionary timescales, sea level oscillations lead to recurrent spatio-temporal variation in species distribution and population connectivity. In this situation, applying classical concepts of biogeography is challenging yet necessary to understand the mechanisms underlying biodiversity in highly diverse marine ecosystems such as coral reefs. We aimed at studying the outcomes of such complex biogeographic dynamics on reproductive isolation by sampling populations across a wide spatial range of a species-rich fish genus: the sergeants (Pomacentridae: Abudefduf). We generated a mutlilocus data set that included ten morpho-species from 32 Indo-West Pacific localities. We observed a pattern of mito-nuclear discordance in two common and widely distributed species: Abudefduf sexfasciatus and Abudefduf vaigiensis. The results showed three regional sublineages (Indian Ocean, Coral Triangle region, western Pacific) in A. sexfasciatus (0.6-1.5% divergence at cytb). The other species, A. vaigiensis, is polyphyletic and consists of three distinct genetic lineages (A, B and C) (9% divergence at cytb) whose geographic ranges overlap. Although A. vaigiensis A and A. sexfasciatus were found to be distinct based on nuclear information, A. vaigiensis A was found to be nested within A. sexfasciatus in the mitochondrial gene tree. A. sexfasciatus from the Coral Triangle region and A. vaigiensis A were not differentiated from each other at the mitochondrial locus. We then used coalescent-based simulation to characterize a spatially widespread but weak gene flow between the two species. We showed that these fishes are good candidates to investigate the evolutionary complexity of the discrepancies between phenotypic and genetic similarity in closely related species.
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Affiliation(s)
- Joris A M Bertrand
- Institute of Oceanography, National Taiwan University, N°1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
| | - Philippe Borsa
- Institut de recherche pour le développement, UMR 250 'Ecologie marine tropicale des océans Pacifique et Indien', 101 promenade Roger-Laroque Anse Vata, BP A5, 98848 Nouméa cedex, New Caledonia
| | - Wei-Jen Chen
- Institute of Oceanography, National Taiwan University, N°1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
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28
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Viard F, David P, Darling JA. Marine invasions enter the genomic era: three lessons from the past, and the way forward. Curr Zool 2016; 62:629-642. [PMID: 29491950 PMCID: PMC5804250 DOI: 10.1093/cz/zow053] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 04/15/2016] [Indexed: 01/22/2023] Open
Abstract
The expanding scale and increasing rate of marine biological invasions have been documented since the early 20th century. Besides their global ecological and economic impacts, non-indigenous species (NIS) also have attracted much attention as opportunities to explore important eco-evolutionary processes such as rapid adaptation, long-distance dispersal and range expansion, and secondary contacts between divergent evolutionary lineages. In this context, genetic tools have been extensively used in the past 20 years. Three important issues appear to have emerged from such studies. First, the study of NIS has revealed unexpected cryptic diversity in what had previously been assumed homogeneous entities. Second, there has been surprisingly little evidence of strong founder events accompanying marine introductions, a pattern possibly driven by large propagule loads. Third, the evolutionary processes leading to successful invasion have been difficult to ascertain due to faint genetic signals. Here we explore the potential of novel tools associated with high-throughput sequencing (HTS) to address these still pressing issues. Dramatic increase in the number of loci accessible via HTS has the potential to radically increase the power of analyses aimed at species delineation, exploring the population genomic consequences of range expansions, and examining evolutionary processes such as admixture, introgression, and adaptation. Nevertheless, the value of this new wealth of genomic data will ultimately depend on the ability to couple it with expanded "traditional" efforts, including exhaustive sampling of marine populations over large geographic scales, integrated taxonomic analyses, and population level exploration of quantitative trait differentiation through common-garden and other laboratory experiments.
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Affiliation(s)
- Frédérique Viard
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 7144, Lab. Adaptation Et Diversité En Milieu Marin, Team Div&Co, Station Biologique De Roscoff, Roscoff 29682, France
| | - Patrice David
- CEFE UMR 5175, CNRS-Université De Montpellier-UM III-EPHE, 1919 Route De Mende, Montpellier Cedex 34293, France
| | - John A. Darling
- National Exposure Research Laboratory, United States Environmental Protection Agency, Research Triangle Park, NC 27711, USA
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29
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Mathiesen SS, Thyrring J, Hemmer-Hansen J, Berge J, Sukhotin A, Leopold P, Bekaert M, Sejr MK, Nielsen EE. Genetic diversity and connectivity within Mytilus spp. in the subarctic and Arctic. Evol Appl 2016; 10:39-55. [PMID: 28035234 PMCID: PMC5192891 DOI: 10.1111/eva.12415] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 08/07/2016] [Indexed: 12/20/2022] Open
Abstract
Climate changes in the Arctic are predicted to alter distributions of marine species. However, such changes are difficult to quantify because information on present species distribution and the genetic variation within species is lacking or poorly examined. Blue mussels, Mytilus spp., are ecosystem engineers in the coastal zone globally. To improve knowledge of distribution and genetic structure of the Mytilus edulis complex in the Arctic, we analyzed 81 SNPs in 534 Mytilus spp. individuals sampled at 13 sites to provide baseline data for distribution and genetic variation of Mytilus mussels in the European Arctic. Mytilus edulis was the most abundant species found with a clear genetic split between populations in Greenland and the Eastern Atlantic. Surprisingly, analyses revealed the presence of Mytilus trossulus in high Arctic NW Greenland (77°N) and Mytilus galloprovincialis or their hybrids in SW Greenland, Svalbard, and the Pechora Sea. Furthermore, a high degree of hybridization and introgression between species was observed. Our study highlights the importance of distinguishing between congener species, which can display local adaptation and suggests that information on dispersal routes and barriers is essential for accurate predictions of regional susceptibility to range expansions or invasions of boreal species in the Arctic.
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Affiliation(s)
- Sofie Smedegaard Mathiesen
- Department of Bioscience Arctic Research Centre Aarhus University Aarhus C Denmark; Section for Marine Living Resources National Institute of Aquatic Resources Technical University of Denmark Silkeborg Denmark
| | - Jakob Thyrring
- Department of Bioscience Arctic Research Centre Aarhus University Aarhus C Denmark
| | - Jakob Hemmer-Hansen
- Section for Marine Living Resources National Institute of Aquatic Resources Technical University of Denmark Silkeborg Denmark
| | - Jørgen Berge
- Faculty of Biosciences, Fisheries and Economics UiT The Arctic University of Norway Tromsø Norway; The University Centre in Svalbard Longyearbyen Norway
| | - Alexey Sukhotin
- White Sea Biological Station Zoological Institute of Russian Academy of Sciences St. Petersburg Russia; Invertebrate Zoology Department St. Petersburg State University St. Petersburg Russia
| | - Peter Leopold
- Faculty of Biosciences, Fisheries and Economics UiT The Arctic University of Norway Tromsø Norway
| | | | - Mikael Kristian Sejr
- Department of Bioscience Arctic Research Centre Aarhus University Aarhus C Denmark
| | - Einar Eg Nielsen
- Section for Marine Living Resources National Institute of Aquatic Resources Technical University of Denmark Silkeborg Denmark
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30
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Bouchemousse S, Liautard-Haag C, Bierne N, Viard F. Distinguishing contemporary hybridization from past introgression with postgenomic ancestry-informative SNPs in strongly differentiated Ciona species. Mol Ecol 2016; 25:5527-5542. [PMID: 27662427 DOI: 10.1111/mec.13854] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/09/2016] [Accepted: 09/16/2016] [Indexed: 12/13/2022]
Abstract
Biological introductions bring into contact species that can still hybridize. The evolutionary outcomes of such secondary contacts may be diverse (e.g. adaptive introgression from or into the introduced species) but are not yet well examined in the wild. The recent secondary contact between the non-native sea squirt Ciona robusta (formerly known as C. intestinalis type A) and its native congener C. intestinalis (formerly known as C. intestinalis type B), in the Western English Channel, provides an excellent case study to examine. To examine contemporary hybridization between the two species, we developed a panel of 310 ancestry-informative SNPs from a population transcriptomic study. Hybridization rates were examined on 449 individuals sampled in eight sites from the sympatric range and five sites from allopatric ranges. The results clearly showed an almost complete absence of contemporary hybridization between the two species in syntopic localities, with only one-first-generation hybrid and no other genotype compatible with recent backcrosses. Despite the almost lack of contemporary hybridization, shared polymorphisms were observed in sympatric and allopatric populations of both species. Furthermore, one allopatric population from SE Pacific exhibited a higher rate of shared polymorphisms compared to all other C. robusta populations. Altogether, these results indicate that the observed level of shared polymorphism is more probably the outcome of ancient gene flow spread afterwards at a worldwide scale. They also emphasize efficient reproductive barriers preventing hybridization between introduced and native species, which suggests hybridization should not impede too much the expansion and the establishment of the non-native species in its introduction range.
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Affiliation(s)
- Sarah Bouchemousse
- UPMC Univ Paris 6, UMR 7144, Equipe DIVCO, Sorbonne Universités, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France.,CNRS, UMR 7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | - Cathy Liautard-Haag
- Station Marine - OSU OREME, Université de Montpellier, 2 Rue des Chantiers, 34200, Sète, France.,CNRS-UM-IRD-EPHE, UMR 5554, Institut des Sciences de l'Evolution, Place Eugène Bataillon, 34095, Montpellier, France
| | - Nicolas Bierne
- Station Marine - OSU OREME, Université de Montpellier, 2 Rue des Chantiers, 34200, Sète, France.,CNRS-UM-IRD-EPHE, UMR 5554, Institut des Sciences de l'Evolution, Place Eugène Bataillon, 34095, Montpellier, France
| | - Frédérique Viard
- UPMC Univ Paris 6, UMR 7144, Equipe DIVCO, Sorbonne Universités, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France. .,CNRS, UMR 7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France.
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31
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Pacheco-Sierra G, Gompert Z, Domínguez-Laso J, Vázquez-Domínguez E. Genetic and morphological evidence of a geographically widespread hybrid zone between two crocodile species,Crocodylus acutusandCrocodylus moreletii. Mol Ecol 2016; 25:3484-98. [DOI: 10.1111/mec.13694] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 04/07/2016] [Accepted: 05/02/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Gualberto Pacheco-Sierra
- Departamento de Ecología de la Biodiversidad; Instituto de Ecología; Universidad Nacional Autónoma de México; Ap. Postal 70-275 Ciudad Universitaria México DF 04510 México
- Posgrado en Ciencias Biológicas; Universidad Nacional Autónoma de México; Coyoacán México DF 04510 México
| | - Zachariah Gompert
- Department of Biology and Ecology Center; Utah State University; Logan UT 84322 USA
| | | | - Ella Vázquez-Domínguez
- Departamento de Ecología de la Biodiversidad; Instituto de Ecología; Universidad Nacional Autónoma de México; Ap. Postal 70-275 Ciudad Universitaria México DF 04510 México
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32
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vonHoldt BM, Kays R, Pollinger JP, Wayne RK. Admixture mapping identifies introgressed genomic regions in North American canids. Mol Ecol 2016; 25:2443-53. [PMID: 27106273 DOI: 10.1111/mec.13667] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 04/12/2016] [Accepted: 04/15/2016] [Indexed: 12/21/2022]
Abstract
Hybrid zones typically contain novel gene combinations that can be tested by natural selection in a unique genetic context. Parental haplotypes that increase fitness can introgress beyond the hybrid zone, into the range of parental species. We used the Affymetrix canine SNP genotyping array to identify genomic regions tagged by multiple ancestry informative markers that are more frequent in an admixed population than expected. We surveyed a hybrid zone formed in the last 100 years as coyotes expanded their range into eastern North America. Concomitant with expansion, coyotes hybridized with wolves and some populations became more wolflike, such that coyotes in the northeast have the largest body size of any coyote population. Using a set of 3102 ancestry informative markers, we identified 60 differentially introgressed regions in 44 canines across this admixture zone. These regions are characterized by an excess of exogenous ancestry and, in northeastern coyotes, are enriched for genes affecting body size and skeletal proportions. Further, introgressed wolf-derived alleles have penetrated into Southern US coyote populations. Because no wolves currently exist in this area, these alleles are unlikely to have originated from recent hybridization. Instead, they probably originated from intraspecific gene flow or ancient admixture. We show that grey wolf and coyote admixture has far-reaching effects and, in addition to phenotypically transforming admixed populations, allows for the differential movement of alleles from different parental species to be tested in new genomic backgrounds.
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Affiliation(s)
- Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Roland Kays
- North Carolina Museum of Natural Science and NC State University, Raleigh, NC, 27612, USA
| | - John P Pollinger
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
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33
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Oyarzún PA, Toro JE, Cañete JI, Gardner JP. Bioinvasion threatens the genetic integrity of native diversity and a natural hybrid zone: smooth-shelled blue mussels (Mytilusspp.) in the Strait of Magellan. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12687] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Pablo A. Oyarzún
- Instituto de Ciencias Marinas y Limnológicas (ICML); Facultad de Ciencias Universidad Austral de Chile; Independencia 641 Valdivia Chile
- PhD program in Marine Biology; Universidad Austral de Chile; Valdivia (UACH) Chile
| | - Jorge E. Toro
- Instituto de Ciencias Marinas y Limnológicas (ICML); Facultad de Ciencias Universidad Austral de Chile; Independencia 641 Valdivia Chile
| | - Juan I. Cañete
- Facultad de Ciencias; Universidad de Magallanes; Punta Arenas Chile
| | - Jonathan P.A. Gardner
- Centre for Marine Environmental and Economic Research; Victoria University of Wellington; P O Box 600 Wellington 6140 New Zealand
- Key Laboratory of Freshwater Animal Breeding; Ministry of Agriculture; College of Fisheries; Huazhong Agricultural University; Wuhan 430070 China
- Freshwater Aquaculture Collaborative Innovation Centre of Hubei Province; Wuhan 430070 China
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34
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Saarman NP, Pogson GH. Introgression between invasive and native blue mussels (genusMytilus) in the central California hybrid zone. Mol Ecol 2015; 24:4723-38. [DOI: 10.1111/mec.13340] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 07/28/2015] [Accepted: 07/29/2015] [Indexed: 01/05/2023]
Affiliation(s)
- Norah P. Saarman
- Department of Ecology and Evolutionary Biology; Yale University; PO Box 208106 New Haven CT 06520-8106 USA
| | - Grant H. Pogson
- Department of Ecology and Evolutionary Biology; UC Santa Cruz; Santa Cruz CA 95064 USA
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35
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Beck EA, Thompson AC, Sharbrough J, Brud E, Llopart A. Gene flow between Drosophila yakuba and Drosophila santomea in subunit V of cytochrome c oxidase: A potential case of cytonuclear cointrogression. Evolution 2015; 69:1973-86. [PMID: 26155926 PMCID: PMC5042076 DOI: 10.1111/evo.12718] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Revised: 06/13/2015] [Accepted: 06/16/2015] [Indexed: 12/11/2022]
Abstract
Introgression is the effective exchange of genetic information between species through natural hybridization. Previous genetic analyses of the Drosophila yakuba—D. santomea hybrid zone showed that the mitochondrial genome of D. yakuba had introgressed into D. santomea and completely replaced its native form. Since mitochondrial proteins work intimately with nuclear‐encoded proteins in the oxidative phosphorylation (OXPHOS) pathway, we hypothesized that some nuclear genes in OXPHOS cointrogressed along with the mitochondrial genome. We analyzed nucleotide variation in the 12 nuclear genes that form cytochrome c oxidase (COX) in 33 Drosophila lines. COX is an OXPHOS enzyme composed of both nuclear‐ and mitochondrial‐encoded proteins and shows evidence of cytonuclear coadaptation in some species. Using maximum‐likelihood methods, we detected significant gene flow from D. yakuba to D. santomea for the entire COX complex. Interestingly, the signal of introgression is concentrated in the three nuclear genes composing subunit V, which shows population migration rates significantly greater than the background level of introgression in these species. The detection of introgression in three proteins that work together, interact directly with the mitochondrial‐encoded core, and are critical for early COX assembly suggests this could be a case of cytonuclear cointrogression.
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Affiliation(s)
- Emily A Beck
- Interdisciplinary Graduate Program in Genetics, The University of Iowa, Iowa City, Iowa, 52242
| | - Aaron C Thompson
- The Department of Biology, The University of Iowa, Iowa City, IA, 52242
| | - Joel Sharbrough
- The Department of Biology, The University of Iowa, Iowa City, IA, 52242
| | - Evgeny Brud
- The Department of Biology, The University of Iowa, Iowa City, IA, 52242
| | - Ana Llopart
- Interdisciplinary Graduate Program in Genetics, The University of Iowa, Iowa City, Iowa, 52242. .,The Department of Biology, The University of Iowa, Iowa City, IA, 52242.
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36
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Fraïsse C, Belkhir K, Welch JJ, Bierne N. Local interspecies introgression is the main cause of extreme levels of intraspecific differentiation in mussels. Mol Ecol 2015; 25:269-86. [DOI: 10.1111/mec.13299] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 06/19/2015] [Accepted: 06/19/2015] [Indexed: 12/15/2022]
Affiliation(s)
- Christelle Fraïsse
- Institut des Sciences de l'Evolution (UMR 5554); CNRS - Université Montpellier; Place Eugène Bataillon 34095 Montpellier France
- Station Marine; Université Montpellier; 2 rue des Chantiers 34200 Sète France
- Department of Genetics; University of Cambridge; Downing Street CB2 3EH Cambridge UK
| | - Khalid Belkhir
- Institut des Sciences de l'Evolution (UMR 5554); CNRS - Université Montpellier; Place Eugène Bataillon 34095 Montpellier France
| | - John J. Welch
- Department of Genetics; University of Cambridge; Downing Street CB2 3EH Cambridge UK
| | - Nicolas Bierne
- Institut des Sciences de l'Evolution (UMR 5554); CNRS - Université Montpellier; Place Eugène Bataillon 34095 Montpellier France
- Station Marine; Université Montpellier; 2 rue des Chantiers 34200 Sète France
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37
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Gagnaire PA, Broquet T, Aurelle D, Viard F, Souissi A, Bonhomme F, Arnaud-Haond S, Bierne N. Using neutral, selected, and hitchhiker loci to assess connectivity of marine populations in the genomic era. Evol Appl 2015; 8:769-86. [PMID: 26366195 PMCID: PMC4561567 DOI: 10.1111/eva.12288] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 06/05/2015] [Indexed: 12/14/2022] Open
Abstract
Estimating the rate of exchange of individuals among populations is a central concern to evolutionary ecology and its applications to conservation and management. For instance, the efficiency of protected areas in sustaining locally endangered populations and ecosystems depends on reserve network connectivity. The population genetics theory offers a powerful framework for estimating dispersal distances and migration rates from molecular data. In the marine realm, however, decades of molecular studies have met limited success in inferring genetic connectivity, due to the frequent lack of spatial genetic structure in species exhibiting high fecundity and dispersal capabilities. This is especially true within biogeographic regions bounded by well-known hotspots of genetic differentiation. Here, we provide an overview of the current methods for estimating genetic connectivity using molecular markers and propose several directions for improving existing approaches using large population genomic datasets. We highlight several issues that limit the effectiveness of methods based on neutral markers when there is virtually no genetic differentiation among samples. We then focus on alternative methods based on markers influenced by selection. Although some of these methodologies are still underexplored, our aim was to stimulate new research to test how broadly they are applicable to nonmodel marine species. We argue that the increased ability to apply the concepts of cline analyses will improve dispersal inferences across physical and ecological barriers that reduce connectivity locally. We finally present how neutral markers hitchhiking with selected loci can also provide information about connectivity patterns within apparently well-mixed biogeographic regions. We contend that one of the most promising applications of population genomics is the use of outlier loci to delineate relevant conservation units and related eco-geographic features across which connectivity can be measured.
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Affiliation(s)
- Pierre-Alexandre Gagnaire
- Université de Montpellier Montpellier, France ; CNRS - Institut des Sciences de l'Evolution, UMR 5554 UM-CNRS-IRD-EPHE, Station Méditerranéenne de l'Environnement Littoral Sète, France
| | - Thomas Broquet
- CNRS team Diversity and connectivity of coastal marine landscapes, Station Biologique de Roscoff Roscoff, France ; Sorbonne Universités, UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff Roscoff, France
| | - Didier Aurelle
- Aix Marseille Université, CNRS-IRD-Avignon Université, IMBE UMR 7263 Marseille, France
| | - Frédérique Viard
- CNRS team Diversity and connectivity of coastal marine landscapes, Station Biologique de Roscoff Roscoff, France ; Sorbonne Universités, UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff Roscoff, France
| | | | - François Bonhomme
- Université de Montpellier Montpellier, France ; CNRS - Institut des Sciences de l'Evolution, UMR 5554 UM-CNRS-IRD-EPHE, Station Méditerranéenne de l'Environnement Littoral Sète, France
| | - Sophie Arnaud-Haond
- Université de Montpellier Montpellier, France ; Ifremer, UMR "Ecosystèmes Marins Exploités" Sète, France
| | - Nicolas Bierne
- Université de Montpellier Montpellier, France ; CNRS - Institut des Sciences de l'Evolution, UMR 5554 UM-CNRS-IRD-EPHE, Station Méditerranéenne de l'Environnement Littoral Sète, France
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38
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Zhang Y, Mu H, Lau SCK, Zhang Z, Qiu JW. Sperm proteome of Mytilus galloprovincialis: Insights into the evolution of fertilization proteins in marine mussels. Proteomics 2015; 15:4175-9. [PMID: 26046548 DOI: 10.1002/pmic.201500066] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 04/15/2015] [Accepted: 06/02/2015] [Indexed: 12/19/2022]
Abstract
Cataloging the sperm proteome of an animal can improve our understanding of its sperm-egg interaction and speciation, but such data are available for only a few free-spawning invertebrates. This study aimed to identify the sperm proteome of Mytilus galloprovincialis, a free-spawning marine mussel. We integrated public transcriptome datasets by de novo assembly, and applied SDS-PAGE coupled LC-MS/MS analysis to profile the sperm proteome, resulting in the identification of 550 proteins. Comparing the homologous sperm protein coding genes between M. galloprovincialis and its closely related species M. edulis revealed that fertilization proteins have the highest mean nonsynonymous substitution rate (Ka/Ks = 0.62) among 11 functional groups, consistent with previous reports of positive selection of several fertilization proteins in Mytilus. Moreover, 78 sperm proteins in different functional groups have Ka/Ks values > 0.5, indicating the presence of many candidate sperm proteins for further analysis of rapid interspecific divergence. The MS data are available in ProteomeXchange with the identifier PXD001665.
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Affiliation(s)
- Yanjie Zhang
- Department of Biology, Hong Kong Baptist University, Hong Kong, P. R. China
| | - Huawei Mu
- Department of Biology, Hong Kong Baptist University, Hong Kong, P. R. China
| | - Stanley C K Lau
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, P. R. China
| | - Zhifeng Zhang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, P. R. China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, P. R. China
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39
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The genetic architecture of hybridisation between two lineages of greenshell mussels. Heredity (Edinb) 2014; 114:344-55. [PMID: 25424842 DOI: 10.1038/hdy.2014.108] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 10/12/2014] [Accepted: 10/17/2014] [Indexed: 11/08/2022] Open
Abstract
A multidisciplinary approach has identified sigmoidal genetic clines on the east and west coasts in central New Zealand where low-density ecological interactions occur between northern and southern lineages of the endemic greenshell mussel, Perna canaliculus. The sigmoidal clines indicate the existence of a mussel hybrid zone in a region of genetic discontinuities for many continuously distributed coastal taxa, in particular marine invertebrates. Examination of the genetic architecture of the hybrid zone revealed the differential contribution of individual microsatellite loci and/or alleles to defining the zone of interaction and no evidence of increased allelic richness or heterozygosity inside versus outside the hybrid zone. Genomics cline analysis identified one locus in particular (Pcan1-27) as being different from neutral expectations, thereby contributing to lineage differentiation. Estimates of contemporary gene flow revealed very high levels of within-lineage self-recruitment and a hybrid zone composed mostly (~85%) of northern immigrants. Broad scale interpretation of these results is consistent with a zone of genetic interaction that was generated between 0.3 and 1.3 million years before present at a time of pronounced global sea-level change. At that time, the continuous distribution of the greenshell mussel was split into northern and southern groups, which differentiated to become distinct lineages, and which have subsequently been reunited (secondary contact) resulting in the generation of the hybrid zone at ~42°S.
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40
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Robinson JD, Bunnefeld L, Hearn J, Stone GN, Hickerson MJ. ABC inference of multi-population divergence with admixture from unphased population genomic data. Mol Ecol 2014; 23:4458-71. [PMID: 25113024 PMCID: PMC4285295 DOI: 10.1111/mec.12881] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 08/04/2014] [Accepted: 08/06/2014] [Indexed: 01/13/2023]
Abstract
Rapidly developing sequencing technologies and declining costs have made it possible to collect genome-scale data from population-level samples in nonmodel systems. Inferential tools for historical demography given these data sets are, at present, underdeveloped. In particular, approximate Bayesian computation (ABC) has yet to be widely embraced by researchers generating these data. Here, we demonstrate the promise of ABC for analysis of the large data sets that are now attainable from nonmodel taxa through current genomic sequencing technologies. We develop and test an ABC framework for model selection and parameter estimation, given histories of three-population divergence with admixture. We then explore different sampling regimes to illustrate how sampling more loci, longer loci or more individuals affects the quality of model selection and parameter estimation in this ABC framework. Our results show that inferences improved substantially with increases in the number and/or length of sequenced loci, while less benefit was gained by sampling large numbers of individuals. Optimal sampling strategies given our inferential models included at least 2000 loci, each approximately 2 kb in length, sampled from five diploid individuals per population, although specific strategies are model and question dependent. We tested our ABC approach through simulation-based cross-validations and illustrate its application using previously analysed data from the oak gall wasp, Biorhiza pallida.
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Affiliation(s)
- John D Robinson
- Department of Biology, City College of New York, 160 Convent Ave., MR 526, New York, NY, 10031, USA
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41
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Roux C, Fraïsse C, Castric V, Vekemans X, Pogson GH, Bierne N. Can we continue to neglect genomic variation in introgression rates when inferring the history of speciation? A case study in a Mytilus hybrid zone. J Evol Biol 2014; 27:1662-75. [PMID: 24913446 DOI: 10.1111/jeb.12425] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 04/25/2014] [Accepted: 04/25/2014] [Indexed: 11/28/2022]
Abstract
The use of molecular data to reconstruct the history of divergence and gene flow between populations of closely related taxa represents a challenging problem. It has been proposed that the long-standing debate about the geography of speciation can be resolved by comparing the likelihoods of a model of isolation with migration and a model of secondary contact. However, data are commonly only fit to a model of isolation with migration and rarely tested against the secondary contact alternative. Furthermore, most demographic inference methods have neglected variation in introgression rates and assume that the gene flow parameter (Nm) is similar among loci. Here, we show that neglecting this source of variation can give misleading results. We analysed DNA sequences sampled from populations of the marine mussels, Mytilus edulis and M. galloprovincialis, across a well-studied mosaic hybrid zone in Europe and evaluated various scenarios of speciation, with or without variation in introgression rates, using an Approximate Bayesian Computation (ABC) approach. Models with heterogeneous gene flow across loci always outperformed models assuming equal migration rates irrespective of the history of gene flow being considered. By incorporating this heterogeneity, the best-supported scenario was a long period of allopatric isolation during the first three-quarters of the time since divergence followed by secondary contact and introgression during the last quarter. By contrast, constraining migration to be homogeneous failed to discriminate among any of the different models of gene flow tested. Our simulations thus provide statistical support for the secondary contact scenario in the European Mytilus hybrid zone that the standard coalescent approach failed to confirm. Our results demonstrate that genomic variation in introgression rates can have profound impacts on the biological conclusions drawn from inference methods and needs to be incorporated in future studies.
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Affiliation(s)
- C Roux
- Université Montpellier 2, Montpellier, France; CNRS-UMR5554 Institut des Sciences de l'Evolution, Station Méditerranéenne de l'Environnement Littoral, Sète, France; Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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42
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Gosset CC, Do Nascimento J, Augé MT, Bierne N. Evidence for adaptation from standing genetic variation on an antimicrobial peptide gene in the musselMytilus edulis. Mol Ecol 2014; 23:3000-12. [DOI: 10.1111/mec.12784] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 04/24/2014] [Accepted: 04/25/2014] [Indexed: 12/30/2022]
Affiliation(s)
- Célia C. Gosset
- Université Montpellier 2; Place Eugène Bataillon 34095 Montpellier France
- CNRS - Institut des Sciences de l'Evolution; UMR5554; Station Méditerranéenne de l'Environnement Littoral; Sète France
| | - Joana Do Nascimento
- Université Montpellier 2; Place Eugène Bataillon 34095 Montpellier France
- CNRS - Institut des Sciences de l'Evolution; UMR5554; Station Méditerranéenne de l'Environnement Littoral; Sète France
- Littoral Environnement et Sociétés; UMR7266; 2 rue Olympe de Gouges 17000 La Rochelle France
| | - Marie-Thérèse Augé
- Université Montpellier 2; Place Eugène Bataillon 34095 Montpellier France
- CNRS - Institut des Sciences de l'Evolution; UMR5554; Station Méditerranéenne de l'Environnement Littoral; Sète France
| | - Nicolas Bierne
- Université Montpellier 2; Place Eugène Bataillon 34095 Montpellier France
- CNRS - Institut des Sciences de l'Evolution; UMR5554; Station Méditerranéenne de l'Environnement Littoral; Sète France
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