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Spurgin LG, Bosse M, Adriaensen F, Albayrak T, Barboutis C, Belda E, Bushuev A, Cecere JG, Charmantier A, Cichon M, Dingemanse NJ, Doligez B, Eeva T, Erikstad KE, Fedorov V, Griggio M, Heylen D, Hille S, Hinde CA, Ivankina E, Kempenaers B, Kerimov A, Krist M, Kvist L, Laine VN, Mänd R, Matthysen E, Nager R, Nikolov BP, Norte AC, Orell M, Ouyang J, Petrova-Dinkova G, Richner H, Rubolini D, Slagsvold T, Tilgar V, Török J, Tschirren B, Vágási CI, Yuta T, Groenen MAM, Visser ME, van Oers K, Sheldon BC, Slate J. The great tit HapMap project: A continental-scale analysis of genomic variation in a songbird. Mol Ecol Resour 2024; 24:e13969. [PMID: 38747336 DOI: 10.1111/1755-0998.13969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 04/10/2024] [Accepted: 04/29/2024] [Indexed: 06/04/2024]
Abstract
A major aim of evolutionary biology is to understand why patterns of genomic diversity vary within taxa and space. Large-scale genomic studies of widespread species are useful for studying how environment and demography shape patterns of genomic divergence. Here, we describe one of the most geographically comprehensive surveys of genomic variation in a wild vertebrate to date; the great tit (Parus major) HapMap project. We screened ca 500,000 SNP markers across 647 individuals from 29 populations, spanning ~30 degrees of latitude and 40 degrees of longitude - almost the entire geographical range of the European subspecies. Genome-wide variation was consistent with a recent colonisation across Europe from a South-East European refugium, with bottlenecks and reduced genetic diversity in island populations. Differentiation across the genome was highly heterogeneous, with clear 'islands of differentiation', even among populations with very low levels of genome-wide differentiation. Low local recombination rates were a strong predictor of high local genomic differentiation (FST), especially in island and peripheral mainland populations, suggesting that the interplay between genetic drift and recombination causes highly heterogeneous differentiation landscapes. We also detected genomic outlier regions that were confined to one or more peripheral great tit populations, probably as a result of recent directional selection at the species' range edges. Haplotype-based measures of selection were related to recombination rate, albeit less strongly, and highlighted population-specific sweeps that likely resulted from positive selection. Our study highlights how comprehensive screens of genomic variation in wild organisms can provide unique insights into spatio-temporal evolutionary dynamics.
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Affiliation(s)
- Lewis G Spurgin
- School of Biological Sciences, Norwich Research Park, University of East Anglia, Norwich, UK
- Department of Biology, Edward Grey Institute, University of Oxford, Oxford, UK
| | - Mirte Bosse
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
- Department of Ecological Science, Animal Ecology Group, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Frank Adriaensen
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Tamer Albayrak
- Department of Biology, Science and art Faculty, Mehmet Akif Ersoy University, Istiklal Yerleskesi, Burdur, Turkey
- Biology Education, Buca Faculty of Education, Mathematics and Science Education, Dokuz Eylül University, İzmir, Turkey
| | | | - Eduardo Belda
- Institut d'Investigació per a la Gestió Integrada de Zones Costaneres, Campus de Gandia, Universitat Politècnica de València, València, Spain
| | - Andrey Bushuev
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Jacopo G Cecere
- Area Avifauna Migratrice, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano Emilia, Italy
| | | | - Mariusz Cichon
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Niels J Dingemanse
- Behavioural Ecology, Faculty of Biology, LMU München, Planegg-Martinsried, Germany
| | - Blandine Doligez
- UMR CNRS 5558-LBBE, Biométrie et Biologie Évolutive, Villeurbanne, France
- Department of Ecology and Evolution, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Tapio Eeva
- Department of Biology, University of Turku, Turku, Finland
| | - Kjell Einar Erikstad
- Norwegian Institute for Nature Research, FRAM-High North Research Centre for Climate and the Environment, Tromsø, Norway
| | | | - Matteo Griggio
- Department of Biology, University of Padova, Padova, Italy
| | - Dieter Heylen
- Department of Biology, Edward Grey Institute, University of Oxford, Oxford, UK
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium
| | - Sabine Hille
- Institute of Wildlife Biology and Game Management, University of Natural Resources and Life Science, Vienna, Austria
| | - Camilla A Hinde
- Behavioural Ecology Group, Department of Life Sciences, Anglia Ruskin University, Cambridgeshire, UK
| | - Elena Ivankina
- Faculty of Biology, Zvenigorod Biological Station, Lomonosov Moscow State University, Moscow, Russia
| | - Bart Kempenaers
- Department of Ornithology, Max Planck Institute for Biological Intelligence, Seewiesen, Germany
| | - Anvar Kerimov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Milos Krist
- Department of Zoology, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Laura Kvist
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Veronika N Laine
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Raivo Mänd
- Department of Zoology, University of Tartu, Tartu, Estonia
| | - Erik Matthysen
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Ruedi Nager
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Boris P Nikolov
- Bulgarian Ornithological Centre, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Ana Claudia Norte
- MARE - Marine and Environmental Sciences Centre, Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal
| | - Markku Orell
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | | | - Gergana Petrova-Dinkova
- Bulgarian Ornithological Centre, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Heinz Richner
- Evolutionary Ecology Lab, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Diego Rubolini
- Dipartimento di Scienze e Politiche Ambientali, Università Degli Studi di Milano, Milan, Italy
| | - Tore Slagsvold
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Vallo Tilgar
- Department of Zoology, University of Tartu, Tartu, Estonia
| | - János Török
- Behavioural Ecology Group, Department of Systematic Zoology and Ecology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Barbara Tschirren
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | - Csongor I Vágási
- Evolutionary Ecology Group, Hungarian Department of Biology and Ecology, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Teru Yuta
- Yamashina Institute for Ornithology, Abiko, Japan
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
| | - Marcel E Visser
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, the Netherlands
| | - Kees van Oers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Ben C Sheldon
- Department of Biology, Edward Grey Institute, University of Oxford, Oxford, UK
| | - Jon Slate
- School of Biosciences, University of Sheffield, Sheffield, UK
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2
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Shpak M, Lawrence KN, Pool JE. The Precision and Power of Population Branch Statistics in Identifying the Genomic Signatures of Local Adaptation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.594139. [PMID: 38798330 PMCID: PMC11118325 DOI: 10.1101/2024.05.14.594139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Population branch statistics, which estimate the branch lengths of focal populations with respect to two outgroups, have been used as an alternative to FST-based genome-wide scans for identifying loci associated with local selective sweeps. In addition to the original population branch statistic (PBS), there are subsequently proposed branch rescalings: normalized population branch statistic (PBSn1), which adjusts focal branch length with respect to outgroup branch lengths at the same locus, and population branch excess (PBE), which also incorporates median branch lengths at other loci. PBSn1 and PBE have been proposed to be less sensitive to allele frequency divergence generated by background selection or geographically ubiquitous positive selection rather than local selective sweeps. However, the accuracy and statistical power of branch statistics have not been systematically assessed. To do so, we simulate genomes in representative large and small populations with varying proportions of sites evolving under genetic drift or background selection (approximated using variable Ne), local selective sweeps, and geographically parallel selective sweeps. We then assess the probability that local selective sweep loci are correctly identified as outliers by FST and by each of the branch statistics. We find that branch statistics consistently outperform FST at identifying local sweeps. When background selection and/or parallel sweeps are introduced, PBSn1 and especially PBE correctly identify local sweeps among their top outliers at a higher frequency than PBS. These results validate the greater specificity of rescaled branch statistics such as PBE to detect population-specific positive selection, supporting their use in genomic studies focused on local adaptation.
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Affiliation(s)
- Max Shpak
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, WI, USA
| | - Kadee N. Lawrence
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, WI, USA
| | - John E. Pool
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, WI, USA
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Errbii M, Ernst UR, Lajmi A, Privman E, Gadau J, Schrader L. Evolutionary genomics of socially polymorphic populations of Pogonomyrmex californicus. BMC Biol 2024; 22:109. [PMID: 38735942 PMCID: PMC11089791 DOI: 10.1186/s12915-024-01907-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 04/30/2024] [Indexed: 05/14/2024] Open
Abstract
BACKGROUND Social insects vary considerably in their social organization both between and within species. In the California harvester ant, Pogonomyrmex californicus (Buckley 1867), colonies are commonly founded and headed by a single queen (haplometrosis, primary monogyny). However, in some populations in California (USA), unrelated queens cooperate not only during founding (pleometrosis) but also throughout the life of the colony (primary polygyny). The genetic architecture and evolutionary dynamics of this complex social niche polymorphism (haplometrosis vs pleometrosis) have remained unknown. RESULTS We provide a first analysis of its genomic basis and evolutionary history using population genomics comparing individuals from a haplometrotic population to those from a pleometrotic population. We discovered a recently evolved (< 200 k years), 8-Mb non-recombining region segregating with the observed social niche polymorphism. This region shares several characteristics with supergenes underlying social polymorphisms in other socially polymorphic ant species. However, we also find remarkable differences from previously described social supergenes. Particularly, four additional genomic regions not in linkage with the supergene show signatures of a selective sweep in the pleometrotic population. Within these regions, we find for example genes crucial for epigenetic regulation via histone modification (chameau) and DNA methylation (Dnmt1). CONCLUSIONS Altogether, our results suggest that social morph in this species is a polygenic trait involving a potential young supergene. Further studies targeting haplo- and pleometrotic individuals from a single population are however required to conclusively resolve whether these genetic differences underlie the alternative social phenotypes or have emerged through genetic drift.
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Affiliation(s)
- Mohammed Errbii
- Molecular Evolution and Sociobiology Group, Institute for Evolution and Biodiversity, University of Münster, Hüfferstr. 1, Münster, DE-48149, Germany
| | - Ulrich R Ernst
- Molecular Evolution and Sociobiology Group, Institute for Evolution and Biodiversity, University of Münster, Hüfferstr. 1, Münster, DE-48149, Germany
- Present Address: Apicultural State Institute, University of Hohenheim, Erna-Hruschka-Weg 6, Stuttgart, DE-70599, Germany
- Center for Biodiversity and Integrative Taxonomy (KomBioTa), University of Hohenheim, Stuttgart, DE-70599, Germany
| | - Aparna Lajmi
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa, Israel
| | - Eyal Privman
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa, Israel
| | - Jürgen Gadau
- Molecular Evolution and Sociobiology Group, Institute for Evolution and Biodiversity, University of Münster, Hüfferstr. 1, Münster, DE-48149, Germany.
| | - Lukas Schrader
- Molecular Evolution and Sociobiology Group, Institute for Evolution and Biodiversity, University of Münster, Hüfferstr. 1, Münster, DE-48149, Germany.
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Ma LJ, Cao LJ, Chen JC, Tang MQ, Song W, Yang FY, Shen XJ, Ren YJ, Yang Q, Li H, Hoffmann AA, Wei SJ. Rapid and Repeated Climate Adaptation Involving Chromosome Inversions following Invasion of an Insect. Mol Biol Evol 2024; 41:msae044. [PMID: 38401527 PMCID: PMC10924284 DOI: 10.1093/molbev/msae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/23/2024] [Accepted: 02/20/2024] [Indexed: 02/26/2024] Open
Abstract
Following invasion, insects can become adapted to conditions experienced in their invasive range, but there are few studies on the speed of adaptation and its genomic basis. Here, we examine a small insect pest, Thrips palmi, following its contemporary range expansion across a sharp climate gradient from the subtropics to temperate areas. We first found a geographically associated population genetic structure and inferred a stepping-stone dispersal pattern in this pest from the open fields of southern China to greenhouse environments of northern regions, with limited gene flow after colonization. In common garden experiments, both the field and greenhouse groups exhibited clinal patterns in thermal tolerance as measured by critical thermal maximum (CTmax) closely linked with latitude and temperature variables. A selection experiment reinforced the evolutionary potential of CTmax with an estimated h2 of 6.8% for the trait. We identified 3 inversions in the genome that were closely associated with CTmax, accounting for 49.9%, 19.6%, and 8.6% of the variance in CTmax among populations. Other genomic variations in CTmax outside the inversion region were specific to certain populations but functionally conserved. These findings highlight rapid adaptation to CTmax in both open field and greenhouse populations and reiterate the importance of inversions behaving as large-effect alleles in climate adaptation.
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Affiliation(s)
- Li-Jun Ma
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Li-Jun Cao
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Jin-Cui Chen
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Meng-Qing Tang
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Wei Song
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Fang-Yuan Yang
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Xiu-Jing Shen
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Ya-Jing Ren
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Qiong Yang
- Bio21 Institute, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Hu Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Ary Anthony Hoffmann
- Bio21 Institute, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Shu-Jun Wei
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
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Booker TR, Yeaman S, Whiting JR, Whitlock MC. The WZA: A window-based method for characterizing genotype-environment associations. Mol Ecol Resour 2024; 24:e13768. [PMID: 36785926 DOI: 10.1111/1755-0998.13768] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 01/17/2023] [Accepted: 01/23/2023] [Indexed: 02/15/2023]
Abstract
Genotype-environment association (GEA) studies have the potential to identify the genetic basis of local adaptation in natural populations. Specifically, GEA approaches look for a correlation between allele frequencies and putatively selective features of the environment. Genetic markers with extreme evidence of correlation with the environment are presumed to be tagging the location of alleles that contribute to local adaptation. In this study, we propose a new method for GEA studies called the Weighted-Z Analysis (WZA) that combines information from closely linked sites into analysis windows in a way that was inspired by methods for calculating FST . Performing GEA methods in analysis windows has the advantage that it takes advantage of the increased linkage disequilibrium expected surrounding sites subject to local adaptation. We analyse simulations modelling local adaptation to heterogeneous environments to compare the WZA with existing methods. In the majority of cases we tested, the WZA either outperformed single-SNP (single nucleotide polymorphism)-based approaches or performed similarly. In particular, the WZA outperformed individual SNP approaches when a small number of individuals or demes were sampled. Particularly troubling, we found that some GEA methods exhibit very high false positive rates. We applied the WZA to previously published data from lodgepole pine and identified candidate loci that were identified in the original study alongside numerous loci that were not found in the original study.
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Affiliation(s)
- Tom R Booker
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - James R Whiting
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Michael C Whitlock
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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6
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Haltiner L, Spaak P, Dennis SR, Feulner PGD. Population genetic insights into establishment, adaptation, and dispersal of the invasive quagga mussel across perialpine lakes. Evol Appl 2024; 17:e13620. [PMID: 38283608 PMCID: PMC10809192 DOI: 10.1111/eva.13620] [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: 04/25/2023] [Revised: 10/13/2023] [Accepted: 11/10/2023] [Indexed: 01/30/2024] Open
Abstract
Human activities have facilitated the invasion of freshwater ecosystems by various organisms. Especially, invasive bivalves such as the quagga mussels, Dreissena bugensis, have the potential to alter ecosystem function as they heavily affect the food web. Quagga mussels occur in high abundance, have a high filtration rate, quickly spread within and between waterbodies via pelagic larvae, and colonize various substrates. They have invaded various waterbodies across the Northern Hemisphere. In Central Europe, they have invaded multiple large and deep perialpine lakes with first recordings in Lake Geneva in 2015 and 2016 in Lake Constance. In the deep perialpine lakes, quagga mussels quickly colonized the littoral zone but are also abundant deeper (>80 m), where they are often thinner and brighter shelled. We analysed 675 quagga mussels using ddRAD sequencing to gain in-depth insights into the genetic population structure of quagga mussels across Central European lakes and across various sites and depth habitats in Lake Constance. We revealed substantial genetic differentiation amongst quagga mussel populations from three unconnected lakes, and all populations showed high genetic diversity and effective population size. In Lake Constance, we detected no genetic differentiation amongst quagga mussels sampled across different sites and depth habitats. We also did not identify any convincing candidate loci evidential for adaptation along a depth gradient and a transplant experiment showed no indications of local adaptation to living in the deep based on investigating growth and survival. Hence, the shallow-water and the deep-water morphotypes seem to be a result of phenotypic plasticity rather than local adaptation to depth. In conclusion, our ddRAD approach revealed insight into the establishment of genetically distinct quagga mussel populations in three perialpine lakes and suggests that phenotypic plasticity and life history traits (broadcast spawner with high fecundity and dispersing pelagic larvae) facilitate the fast spread and colonization of various depth habitats by the quagga mussel.
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Affiliation(s)
- Linda Haltiner
- Aquatic EcologySwiss Federal Institute of Aquatic Science and Technology (Eawag)DübendorfSwitzerland
- Environmental Systems SciencesETH ZürichZürichSwitzerland
| | - Piet Spaak
- Aquatic EcologySwiss Federal Institute of Aquatic Science and Technology (Eawag)DübendorfSwitzerland
- Environmental Systems SciencesETH ZürichZürichSwitzerland
| | - Stuart R. Dennis
- Aquatic EcologySwiss Federal Institute of Aquatic Science and Technology (Eawag)DübendorfSwitzerland
- Present address:
Department IT servicesSwiss Federal Institute of Aquatic Science and Technology (Eawag)DübendorfSwitzerland
| | - Philine G. D. Feulner
- Fish Ecology and Evolution, Center for Ecology, Evolution and BiogeochemistrySwiss Federal Institute of Aquatic Science and Technology (Eawag)KastanienbaumSwitzerland
- Aquatic Ecology, Institute of Ecology and EvolutionUniversity of BernBernSwitzerland
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7
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Soudi S, Jahani M, Todesco M, Owens GL, Bercovich N, Rieseberg LH, Yeaman S. Repeatability of adaptation in sunflowers reveals that genomic regions harbouring inversions also drive adaptation in species lacking an inversion. eLife 2023; 12:RP88604. [PMID: 38095362 PMCID: PMC10721221 DOI: 10.7554/elife.88604] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023] Open
Abstract
Local adaptation commonly involves alleles of large effect, which experience fitness advantages when in positive linkage disequilibrium (LD). Because segregating inversions suppress recombination and facilitate the maintenance of LD between locally adapted loci, they are also commonly found to be associated with adaptive divergence. However, it is unclear what fraction of an adaptive response can be attributed to inversions and alleles of large effect, and whether the loci within an inversion could still drive adaptation in the absence of its recombination-suppressing effect. Here, we use genome-wide association studies to explore patterns of local adaptation in three species of sunflower: Helianthus annuus, Helianthus argophyllus, and Helianthus petiolaris, which each harbour a large number of species-specific inversions. We find evidence of significant genome-wide repeatability in signatures of association to phenotypes and environments, which are particularly enriched within regions of the genome harbouring an inversion in one species. This shows that while inversions may facilitate local adaptation, at least some of the loci can still harbour mutations that make substantial contributions without the benefit of recombination suppression in species lacking a segregating inversion. While a large number of genomic regions show evidence of repeated adaptation, most of the strongest signatures of association still tend to be species-specific, indicating substantial genotypic redundancy for local adaptation in these species.
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Affiliation(s)
- Shaghayegh Soudi
- Department of Biological Sciences, University of CalgaryCalgaryCanada
| | - Mojtaba Jahani
- Department of Biological Sciences, University of CalgaryCalgaryCanada
- Department of Botany, University of British ColumbiaVancouverCanada
| | - Marco Todesco
- Department of Botany, University of British ColumbiaVancouverCanada
- Michael Smith Laboratories, University of British ColumbiaVancouverCanada
- Irving K. Barber Faculty of Science, University of British Columbia OkanaganKelownaCanada
| | | | | | | | - Sam Yeaman
- Department of Biological Sciences, University of CalgaryCalgaryCanada
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8
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Amin MR, Hasan M, Arnab SP, DeGiorgio M. Tensor Decomposition-based Feature Extraction and Classification to Detect Natural Selection from Genomic Data. Mol Biol Evol 2023; 40:msad216. [PMID: 37772983 PMCID: PMC10581699 DOI: 10.1093/molbev/msad216] [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: 03/02/2023] [Revised: 08/10/2023] [Accepted: 09/14/2023] [Indexed: 09/30/2023] Open
Abstract
Inferences of adaptive events are important for learning about traits, such as human digestion of lactose after infancy and the rapid spread of viral variants. Early efforts toward identifying footprints of natural selection from genomic data involved development of summary statistic and likelihood methods. However, such techniques are grounded in simple patterns or theoretical models that limit the complexity of settings they can explore. Due to the renaissance in artificial intelligence, machine learning methods have taken center stage in recent efforts to detect natural selection, with strategies such as convolutional neural networks applied to images of haplotypes. Yet, limitations of such techniques include estimation of large numbers of model parameters under nonconvex settings and feature identification without regard to location within an image. An alternative approach is to use tensor decomposition to extract features from multidimensional data although preserving the latent structure of the data, and to feed these features to machine learning models. Here, we adopt this framework and present a novel approach termed T-REx, which extracts features from images of haplotypes across sampled individuals using tensor decomposition, and then makes predictions from these features using classical machine learning methods. As a proof of concept, we explore the performance of T-REx on simulated neutral and selective sweep scenarios and find that it has high power and accuracy to discriminate sweeps from neutrality, robustness to common technical hurdles, and easy visualization of feature importance. Therefore, T-REx is a powerful addition to the toolkit for detecting adaptive processes from genomic data.
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Affiliation(s)
- Md Ruhul Amin
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Mahmudul Hasan
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Sandipan Paul Arnab
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Michael DeGiorgio
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
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9
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Everitt T, Wallberg A, Christmas MJ, Olsson A, Hoffmann W, Neumann P, Webster MT. The Genomic Basis of Adaptation to High Elevations in Africanized Honey Bees. Genome Biol Evol 2023; 15:evad157. [PMID: 37625795 PMCID: PMC10484329 DOI: 10.1093/gbe/evad157] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 08/11/2023] [Accepted: 08/18/2023] [Indexed: 08/27/2023] Open
Abstract
A range of different genetic architectures underpin local adaptation in nature. Honey bees (Apis mellifera) in the Eastern African Mountains harbor high frequencies of two chromosomal inversions that likely govern adaptation to this high-elevation habitat. In the Americas, honey bees are hybrids of European and African ancestries and adaptation to latitudinal variation in climate correlates with the proportion of these ancestries across the genome. It is unknown which, if either, of these forms of genetic variation governs adaptation in honey bees living at high elevations in the Americas. Here, we performed whole-genome sequencing of 29 honey bees from both high- and low-elevation populations in Colombia. Analysis of genetic ancestry indicated that both populations were predominantly of African ancestry, but the East African inversions were not detected. However, individuals in the higher elevation population had significantly higher proportions of European ancestry, likely reflecting local adaptation. Several genomic regions exhibited particularly high differentiation between highland and lowland bees, containing candidate loci for local adaptation. Genes that were highly differentiated between highland and lowland populations were enriched for functions related to reproduction and sperm competition. Furthermore, variation in levels of European ancestry across the genome was correlated between populations of honey bees in the highland population and populations at higher latitudes in South America. The results are consistent with the hypothesis that adaptation to both latitude and elevation in these hybrid honey bees are mediated by variation in ancestry at many loci across the genome.
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Affiliation(s)
- Turid Everitt
- Department Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Andreas Wallberg
- Department Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Matthew J Christmas
- Department Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anna Olsson
- Department Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Wolfgang Hoffmann
- Grupo de Biocalorimetría, Universidad de Pamplona, Pamplona, Colombia
| | - Peter Neumann
- Institute of Bee Health, Vetsuisse Faculty, University of Bern and Agroscope, Bern, Switzerland
| | - Matthew T Webster
- Department Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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10
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Rougemont Q, Xuereb A, Dallaire X, Moore JS, Normandeau E, Perreault-Payette A, Bougas B, Rondeau EB, Withler RE, Van Doornik DM, Crane PA, Naish KA, Garza JC, Beacham TD, Koop BF, Bernatchez L. Long-distance migration is a major factor driving local adaptation at continental scale in Coho salmon. Mol Ecol 2023; 32:542-559. [PMID: 35000273 DOI: 10.1111/mec.16339] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 11/19/2021] [Accepted: 12/23/2021] [Indexed: 01/25/2023]
Abstract
Inferring the genomic basis of local adaptation is a long-standing goal of evolutionary biology. Beyond its fundamental evolutionary implications, such knowledge can guide conservation decisions for populations of conservation and management concern. Here, we investigated the genomic basis of local adaptation in the Coho salmon (Oncorhynchus kisutch) across its entire North American range. We hypothesized that extensive spatial variation in environmental conditions and the species' homing behaviour may promote the establishment of local adaptation. We genotyped 7829 individuals representing 217 sampling locations at more than 100,000 high-quality RADseq loci to investigate how recombination might affect the detection of loci putatively under selection and took advantage of the precise description of the demographic history of the species from our previous work to draw accurate population genomic inferences about local adaptation. The results indicated that genetic differentiation scans and genetic-environment association analyses were both significantly affected by variation in recombination rate as low recombination regions displayed an increased number of outliers. By taking these confounding factors into consideration, we revealed that migration distance was the primary selective factor driving local adaptation and partial parallel divergence among distant populations. Moreover, we identified several candidate single nucleotide polymorphisms associated with long-distance migration and altitude including a gene known to be involved in adaptation to altitude in other species. The evolutionary implications of our findings are discussed along with conservation applications.
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Affiliation(s)
- Quentin Rougemont
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada.,CEFE, Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175, CNRS, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier, Montpellier, France
| | - Amanda Xuereb
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Xavier Dallaire
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Jean-Sébastien Moore
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Eric Normandeau
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Alysse Perreault-Payette
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Bérénice Bougas
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Eric B Rondeau
- Department of Fisheries and Ocean, Pacific Biological Station, Nanaimo, British Columbia, Canada.,Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Ruth E Withler
- Department of Fisheries and Ocean, Pacific Biological Station, Nanaimo, British Columbia, Canada
| | - Donald M Van Doornik
- National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northwest Fisheries Science Center, Manchester Research Station, Port Orchard, Washington, USA
| | - Penelope A Crane
- Conservation Genetics Laboratory, U.S. Fish and Wildlife Service, Anchorage, Alaska, USA
| | - Kerry A Naish
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, USA
| | - John Carlos Garza
- Department of Ocean Sciences and Institute of Marine Sciences, University of California Santa Cruz, Santa Cruz, California, USA
| | - Terry D Beacham
- Department of Fisheries and Ocean, Pacific Biological Station, Nanaimo, British Columbia, Canada
| | - Ben F Koop
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
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11
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Koch EL, Ravinet M, Westram AM, Johannesson K, Butlin RK. Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution. Evolution 2022; 76:2332-2346. [PMID: 35994296 PMCID: PMC9826283 DOI: 10.1111/evo.14602] [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: 02/02/2022] [Revised: 06/24/2022] [Accepted: 07/23/2022] [Indexed: 01/22/2023]
Abstract
Chromosomal inversions have been shown to play a major role in a local adaptation by suppressing recombination between alternative arrangements and maintaining beneficial allele combinations. However, so far, their importance relative to the remaining genome remains largely unknown. Understanding the genetic architecture of adaptation requires better estimates of how loci of different effect sizes contribute to phenotypic variation. Here, we used three Swedish islands where the marine snail Littorina saxatilis has repeatedly evolved into two distinct ecotypes along a habitat transition. We estimated the contribution of inversion polymorphisms to phenotypic divergence while controlling for polygenic effects in the remaining genome using a quantitative genetics framework. We confirmed the importance of inversions but showed that contributions of loci outside inversions are of similar magnitude, with variable proportions dependent on the trait and the population. Some inversions showed consistent effects across all sites, whereas others exhibited site-specific effects, indicating that the genomic basis for replicated phenotypic divergence is only partly shared. The contributions of sexual dimorphism as well as environmental factors to phenotypic variation were significant but minor compared to inversions and polygenic background. Overall, this integrated approach provides insight into the multiple mechanisms contributing to parallel phenotypic divergence.
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Affiliation(s)
- Eva L. Koch
- School of BiosciencesUniversity of SheffieldSheffieldUK,Department of ZoologyUniversity of CambridgeCambridgeUK
| | - Mark Ravinet
- School of Life SciencesUniversity of NottinghamNottinghamUK
| | - Anja M. Westram
- Institute of Science and Technology Austria (ISTA)KlosterneuburgAustria,Faculty of Biosciences and AquacultureNord UniversityBodøNorway
| | - Kerstin Johannesson
- Marine Science, Tjärnö Marine LaboratoryUniversity of GothenburgGothenburgSweden
| | - Roger K. Butlin
- School of BiosciencesUniversity of SheffieldSheffieldUK,Marine Science, Tjärnö Marine LaboratoryUniversity of GothenburgGothenburgSweden
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12
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Li Y, Lake L, Chauhan YS, Taylor J, Sadras VO. Genetic basis and adaptive implications of temperature-dependent and temperature-independent effects of drought on chickpea reproductive phenology. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4981-4995. [PMID: 35526198 DOI: 10.1093/jxb/erac195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 05/05/2022] [Indexed: 06/14/2023]
Abstract
Water deficit often hastens flowering of pulses partially because droughted plants are hotter. Separating temperature-independent and temperature-dependent effects of drought is important to understand, model, and manipulate phenology. We define a new trait, drought effect on phenology (DEP), as the difference in flowering time between irrigated and rainfed crops, and use FST genome scanning to probe for genomic regions under selection for this trait in chickpea (Cicer arietinum). Owing to the negligible variation in daylength in our dataset, variation in phenology with sowing date was attributed to temperature and water; hence, genomic regions overlapping for early- and late-sown crops would associate with temperature-independent effects and non-overlapping genomic regions would associate with temperature-dependent effects. Thermal-time to flowering was shortened with increasing water stress, as quantified with carbon isotope composition. Genomic regions on chromosomes 4-8 were under selection for DEP. An overlapping region for early and late sowing on chromosome 8 revealed a temperature-independent effect with four candidate genes: BAM1, BAM2, HSL2, and ANT. The non-overlapping regions included six candidate genes: EMF1, EMF2, BRC1/TCP18, BZR1, NPGR1, and ERF1. Modelling showed that DEP reduces the likelihood of drought and heat stress at the expense of increased likelihood of cold stress. Accounting for DEP would improve genetic and phenotypic models of phenology.
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Affiliation(s)
- Yongle Li
- School of Agriculture, Food and Wine, The University of Adelaide, Australia
| | - Lachlan Lake
- School of Agriculture, Food and Wine, The University of Adelaide, Australia
- South Australian Research and Development Institute, Australia
| | | | - Julian Taylor
- School of Agriculture, Food and Wine, The University of Adelaide, Australia
| | - Victor O Sadras
- School of Agriculture, Food and Wine, The University of Adelaide, Australia
- South Australian Research and Development Institute, Australia
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13
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Whiting JR, Paris JR, van der Zee MJ, Fraser BA. AF‐vapeR
: A multivariate genome scan for detecting parallel evolution using allele frequency change vectors. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- James R. Whiting
- Department of Biosciences University of Exeter Exeter UK
- Department of Biological Sciences University of Calgary Calgary Alberta Canada
| | - Josephine R. Paris
- Department of Biosciences University of Exeter Exeter UK
- Department of Health, Life and Environmental Sciences University of L'Aquila L'Aquila Italy
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14
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Schaal SM, Haller BC, Lotterhos KE. Inversion invasions: when the genetic basis of local adaptation is concentrated within inversions in the face of gene flow. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210200. [PMID: 35694752 PMCID: PMC9189506 DOI: 10.1098/rstb.2021.0200] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Across many species where inversions have been implicated in local adaptation, genomes often evolve to contain multiple, large inversions that arise early in divergence. Why this occurs has yet to be resolved. To address this gap, we built forward-time simulations in which inversions have flexible characteristics and can invade a metapopulation undergoing spatially divergent selection for a highly polygenic trait. In our simulations, inversions typically arose early in divergence, captured standing genetic variation upon mutation, and then accumulated many small-effect loci over time. Under special conditions, inversions could also arise late in adaptation and capture locally adapted alleles. Polygenic inversions behaved similarly to a single supergene of large effect and were detectable by genome scans. Our results show that characteristics of adaptive inversions found in empirical studies (e.g. multiple large, old inversions that are FST outliers, sometimes overlapping with other inversions) are consistent with a highly polygenic architecture, and inversions do not need to contain any large-effect genes to play an important role in local adaptation. By combining a population and quantitative genetic framework, our results give a deeper understanding of the specific conditions needed for inversions to be involved in adaptation when the genetic architecture is polygenic. This article is part of the theme issue 'Genomic architecture of supergenes: causes and evolutionary consequences'.
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Affiliation(s)
- Sara M Schaal
- Department of Marine and Environmental Sciences, Northeastern University, Nahant, MA, USA
| | - Benjamin C Haller
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Katie E Lotterhos
- Department of Marine and Environmental Sciences, Northeastern University, Nahant, MA, USA
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15
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Tigano A, Khan R, Omer AD, Weisz D, Dudchenko O, Multani AS, Pathak S, Behringer RR, Aiden EL, Fisher H, MacManes MD. Chromosome size affects sequence divergence between species through the interplay of recombination and selection. Evolution 2022; 76:782-798. [PMID: 35271737 PMCID: PMC9314927 DOI: 10.1111/evo.14467] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 12/12/2021] [Indexed: 01/21/2023]
Abstract
The structure of the genome shapes the distribution of genetic diversity and sequence divergence. To investigate how the relationship between chromosome size and recombination rate affects sequence divergence between species, we combined empirical analyses and evolutionary simulations. We estimated pairwise sequence divergence among 15 species from three different mammalian clades-Peromyscus rodents, Mus mice, and great apes-from chromosome-level genome assemblies. We found a strong significant negative correlation between chromosome size and sequence divergence in all species comparisons within the Peromyscus and great apes clades but not the Mus clade, suggesting that the dramatic chromosomal rearrangements among Mus species may have masked the ancestral genomic landscape of divergence in many comparisons. Our evolutionary simulations showed that the main factor determining differences in divergence among chromosomes of different sizes is the interplay of recombination rate and selection, with greater variation in larger populations than in smaller ones. In ancestral populations, shorter chromosomes harbor greater nucleotide diversity. As ancestral populations diverge, diversity present at the onset of the split contributes to greater sequence divergence in shorter chromosomes among daughter species. The combination of empirical data and evolutionary simulations revealed that chromosomal rearrangements, demography, and divergence times may also affect the relationship between chromosome size and divergence, thus deepening our understanding of the role of genome structure in the evolution of species divergence.
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Affiliation(s)
- Anna Tigano
- Molecular, Cellular, and Biomedical Sciences DepartmentUniversity of New HampshireDurhamNH03824USA,Hubbard Center for Genome StudiesUniversity of New HampshireDurhamNH03824USA,Current address: Department of BiologyUniversity of British Columbia – Okanagan CampusKelownaBCV1 V 1V7Canada
| | - Ruqayya Khan
- The Center for Genome ArchitectureDepartment of Molecular and Human GeneticsBaylor College of MedicineHoustonTX77030USA
| | - Arina D. Omer
- The Center for Genome ArchitectureDepartment of Molecular and Human GeneticsBaylor College of MedicineHoustonTX77030USA
| | - David Weisz
- The Center for Genome ArchitectureDepartment of Molecular and Human GeneticsBaylor College of MedicineHoustonTX77030USA
| | - Olga Dudchenko
- The Center for Genome ArchitectureDepartment of Molecular and Human GeneticsBaylor College of MedicineHoustonTX77030USA,Department of Computer ScienceDepartment of Computational and Applied MathematicsRice UniversityHoustonTX77030USA
| | - Asha S. Multani
- Department of GeneticsM.D. Anderson Cancer CenterUniversity of TexasHoustonTX77030USA
| | - Sen Pathak
- Department of GeneticsM.D. Anderson Cancer CenterUniversity of TexasHoustonTX77030USA
| | - Richard R. Behringer
- Department of GeneticsM.D. Anderson Cancer CenterUniversity of TexasHoustonTX77030USA
| | - Erez L. Aiden
- The Center for Genome ArchitectureDepartment of Molecular and Human GeneticsBaylor College of MedicineHoustonTX77030USA,Department of Computer ScienceDepartment of Computational and Applied MathematicsRice UniversityHoustonTX77030USA,Center for Theoretical and Biological PhysicsRice UniversityHoustonTX77030USA,Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China,School of Agriculture and EnvironmentUniversity of Western AustraliaPerthWA6009Australia
| | - Heidi Fisher
- Department of BiologyUniversity of MarylandCollege ParkMD20742USA
| | - Matthew D. MacManes
- Molecular, Cellular, and Biomedical Sciences DepartmentUniversity of New HampshireDurhamNH03824USA,Hubbard Center for Genome StudiesUniversity of New HampshireDurhamNH03824USA
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16
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Salloum PM, Santure AW, Lavery SD, de Villemereuil P. Finding the adaptive needles in a population-structured haystack: a case study in a New Zealand mollusc. J Anim Ecol 2022; 91:1209-1221. [PMID: 35318661 PMCID: PMC9311215 DOI: 10.1111/1365-2656.13692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 03/09/2022] [Indexed: 11/30/2022]
Abstract
Genetic adaptation to future environmental conditions is crucial to help species persist as the climate changes. Genome scans are powerful tools to understand adaptive landscapes, enabling us to correlate genetic diversity with environmental gradients while disentangling neutral from adaptive variation. However, low gene flow can lead to both local adaptation and highly structured populations, and is a major confounding factor for genome scans, resulting in an inflated number of candidate loci. Here, we compared candidate locus detection in a marine mollusc (Onithochiton neglectus), taking advantage of a natural geographical contrast in the levels of genetic structure between its populations. O. neglectus is endemic to New Zealand and distributed throughout an environmental gradient from the subtropical north to the subantarctic south. Due to a brooding developmental mode, populations tend to be locally isolated. However, adult hitchhiking on rafting kelp increases connectivity among southern populations. We applied two genome scans for outliers (Bayescan and PCAdapt) and two genotype–environment association (GEA) tests (BayeScEnv and RDA). To limit issues with false positives, we combined results using the geometric mean of q‐values and performed association tests with random environmental variables. This novel approach is a compromise between stringent and relaxed approaches widely used before, and allowed us to classify candidate loci as low confidence or high confidence. Genome scans for outliers detected a large number of significant outliers in strong and moderately structured populations. No high‐confidence GEA loci were detected in the context of strong population structure. However, 86 high‐confidence loci were associated predominantly with latitudinally varying abiotic factors in the less structured southern populations. This suggests that the degree of connectivity driven by kelp rafting over the southern scale may be insufficient to counteract local adaptation in this species. Our study supports the expectation that genome scans may be prone to errors in highly structured populations. Nonetheless, it also empirically demonstrates that careful statistical controls enable the identification of candidate loci that invite more detailed investigations. Ultimately, genome scans are valuable tools to help guide further research aiming to determine the potential of non‐model species to adapt to future environments.
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Affiliation(s)
- P M Salloum
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - A W Santure
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - S D Lavery
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Institute of Marine Science, Leigh Marine Laboratory, University of Auckland, Warkworth, New Zealand
| | - P de Villemereuil
- Institut de Systématique, Évolution, Biodiversité (ISYEB), École Pratique des Hautes Études
- PSL, MNHN, CNRS, SU, UA, Paris, France
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17
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Versoza CJ, Rivera JA, Rosenblum EB, Vital-García C, Hews DK, Pfeifer SP. The recombination landscapes of spiny lizards (genus Sceloporus). G3 GENES|GENOMES|GENETICS 2022; 12:6433156. [PMID: 34878100 PMCID: PMC9210290 DOI: 10.1093/g3journal/jkab402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 11/14/2021] [Indexed: 11/16/2022]
Abstract
Despite playing a critical role in evolutionary processes and outcomes, relatively little is known about rates of recombination in the vast majority of species, including squamate reptiles—the second largest order of extant vertebrates, many species of which serve as important model organisms in evolutionary and ecological studies. This paucity of data has resulted in limited resolution on questions related to the causes and consequences of rate variation between species and populations, the determinants of within-genome rate variation, as well as the general tempo of recombination rate evolution on this branch of the tree of life. In order to address these questions, it is thus necessary to begin broadening our phylogenetic sampling. We here provide the first fine-scale recombination maps for two species of spiny lizards, Sceloporus jarrovii and Sceloporus megalepidurus, which diverged at least 12 Mya. As might be expected from similarities in karyotype, population-scaled recombination landscapes are largely conserved on the broad-scale. At the same time, considerable variation exists at the fine-scale, highlighting the importance of incorporating species-specific recombination maps in future population genomic studies.
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Affiliation(s)
- Cyril J Versoza
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85281, USA
| | - Julio A Rivera
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Erica Bree Rosenblum
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Cuauhcihuatl Vital-García
- Departamento de Ciencias Veterinarias, Programa de Maestría en Ciencia Animal, Universidad Autónoma de Ciudad Juárez México, Chihuahua 32315, Mexico
| | - Diana K Hews
- Department of Biology, Indiana State University, Terre Haute, IN 47809, USA
| | - Susanne P Pfeifer
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85281, USA
- Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85281, USA
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18
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Dukić M, Bomblies K. Male and female recombination landscapes of diploid Arabidopsis arenosa. Genetics 2022; 220:6499271. [PMID: 35100396 PMCID: PMC8893250 DOI: 10.1093/genetics/iyab236] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/17/2021] [Indexed: 12/13/2022] Open
Abstract
Abstract
The number and placement of meiotic crossover events during meiosis have important implications for the fidelity of chromosome segregation as well as patterns of inheritance. Despite the functional importance of recombination, recombination landscapes vary widely among and within species, and this can have a strong impact on evolutionary processes. A good knowledge of recombination landscapes is important for model systems in evolutionary and ecological genetics, since it can improve interpretation of genomic patterns of differentiation and genome evolution, and provides an important starting point for understanding the causes and consequences of recombination rate variation. Arabidopsis arenosa is a powerful evolutionary genetic model for studying the molecular basis of adaptation and recombination rate evolution. Here, we generate genetic maps for 2 diploid A. arenosa individuals from distinct genetic lineages where we have prior knowledge that meiotic genes show evidence of selection. We complement the genetic maps with cytological approaches to map and quantify recombination rates, and test the idea that these populations might have distinct patterns of recombination. We explore how recombination differs at the level of populations, individuals, sexes and genomic regions. We show that the positioning of crossovers along a chromosome correlates with their number, presumably a consequence of crossover interference, and discuss how this effect can cause differences in recombination landscape among sexes or species. We identify several instances of female segregation distortion. We found that averaged genome-wide recombination rate is lower and sex differences subtler in A. arenosa than in Arabidopsis thaliana.
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Affiliation(s)
- Marinela Dukić
- Department of Biology, Plant Evolutionary Genetics, Institute of Plant Molecular Biology, ETH Zürich, Zürich 8092, Switzerland
| | - Kirsten Bomblies
- Department of Biology, Plant Evolutionary Genetics, Institute of Plant Molecular Biology, ETH Zürich, Zürich 8092, Switzerland
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19
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Termignoni-Garcia F, Kirchman JJ, Clark J, Edwards SV. Comparative Population Genomics of Cryptic Speciation and Adaptive Divergence in Bicknell's and Gray-Cheeked Thrushes (Aves: Catharus bicknelli and Catharus minimus). Genome Biol Evol 2022; 14:evab255. [PMID: 34999784 PMCID: PMC8743040 DOI: 10.1093/gbe/evab255] [Citation(s) in RCA: 7] [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] [Accepted: 11/10/2021] [Indexed: 02/07/2023] Open
Abstract
Cryptic speciation may occur when reproductive isolation is recent or the accumulation of morphological differences between sister lineages is slowed by stabilizing selection preventing phenotypic differentiation. In North America, Bicknell's Thrush (Catharus bicknelli) and its sister species, the Gray-cheeked Thrush (Catharus minimus), are parapatrically breeding migratory songbirds, distinguishable in nature only by subtle differences in song and coloration, and were recognized as distinct species only in the 1990s. Previous molecular studies have estimated that the species diverged approximately 120,000-420,000 YBP and found very low levels of introgression despite their similarity and sympatry in the spring (prebreeding) migration. To further clarify the history, genetic divergence, genomic structure, and adaptive processes in C. bicknelli and C. minimus, we sequenced and assembled high-coverage reference genomes of both species and resequenced genomes from population samples of C. bicknelli, C. minimus, and two individuals of the Swainson's Thrush (Catharus ustulatus). The genome of C. bicknelli exhibits markedly higher abundances of transposable elements compared with other Catharus and chicken. Demographic and admixture analyses confirm moderate genome-wide differentiation (Fst ≈ 0.10) and limited gene flow between C. bicknelli and C. minimus, but suggest a more recent divergence than estimates based on mtDNA. We find evidence of rapid evolution of the Z-chromosome and elevated divergence consistent with natural selection on genomic regions near genes involved with neuronal processes in C. bicknelli. These genomes are a useful resource for future investigations of speciation, migration, and adaptation in Catharus thrushes.
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Affiliation(s)
- Flavia Termignoni-Garcia
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, USA
| | | | - Johnathan Clark
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, USA
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, USA
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20
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Rieseberg L, Warschefsky E, O'Boyle B, Taberlet P, Ortiz-Barrientos D, Kane NC, Sibbett B. Editorial 2022. Mol Ecol 2021; 31:1-30. [PMID: 34957606 DOI: 10.1111/mec.16328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 12/10/2021] [Indexed: 11/30/2022]
Affiliation(s)
- Loren Rieseberg
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Univ. Grenoble Alpes, Grenoble Cedex 9, France
| | - Daniel Ortiz-Barrientos
- School of Biological Sciences, The University of Queenland, St. Lucia, Queensland, Australia
| | - Nolan C Kane
- University of Colorado at Boulder, Boulder, Colorado, USA
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21
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Koot E, Wu C, Ruza I, Hilario E, Storey R, Wells R, Chagné D, Wellenreuther M. Genome-wide analysis reveals the genetic stock structure of hoki ( Macruronus novaezelandiae). Evol Appl 2021; 14:2848-2863. [PMID: 34950233 PMCID: PMC8674887 DOI: 10.1111/eva.13317] [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: 08/16/2021] [Revised: 10/14/2021] [Accepted: 10/18/2021] [Indexed: 12/23/2022] Open
Abstract
The assessment of the genetic structuring of biodiversity is crucial for management and conservation. This is particularly critical for widely distributed and highly mobile deep-water teleosts, such as hoki (Macruronus novaezelandiae). This species is significant to Māori people and supports the largest commercial fishery in New Zealand, but uncertainty about its stock structure presents a challenge for management. Here, we apply a comprehensive genomic analysis to shed light on the demographic structure of this species by (1) assembling the genome, (2) generating a catalogue of genome-wide SNPs to infer the stock structure and (3) identifying regions of the genome under selection. The final genome assembly used short and long reads and is near complete, representing 93.8% of BUSCO genes, and consisting of 566 contigs totalling 501 Mb. Whole-genome re-sequencing of 510 hoki sampled from 14 locations around New Zealand and Australia, at a read depth greater than 10×, produced 227,490 filtered SNPs. Analyses of these SNPs were able to resolve the stock structure of hoki into two genetically and geographically distinct clusters, one including the Australian and the other one all New Zealand locations, indicating genetic exchange between these regions is limited. Location differences within New Zealand samples were much more subtle (global F ST = 0.0006), and while small and significant differences could be detected, they did not conclusively identify additional substructures. Ten putative adaptive SNPs were detected within the New Zealand samples, but these also did not geographically partition the dataset further. Contemporary and historical N e estimation suggest the current New Zealand population of hoki is large yet declining. Overall, our study provides the first genomic resources for hoki and provides detailed insights into the fine-scale population genetic structure to inform the management of this species.
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Affiliation(s)
- Emily Koot
- The New Zealand Institute for Plant and Food Research LtdPalmerston NorthNew Zealand
| | - Chen Wu
- The New Zealand Institute for Plant and Food Research LtdAucklandNew Zealand
| | - Igor Ruza
- The New Zealand Institute for Plant and Food Research LtdNelsonNew Zealand
| | - Elena Hilario
- The New Zealand Institute for Plant and Food Research LtdAucklandNew Zealand
| | - Roy Storey
- The New Zealand Institute for Plant and Food Research LtdTe PukeNew Zealand
| | | | - David Chagné
- The New Zealand Institute for Plant and Food Research LtdPalmerston NorthNew Zealand
| | - Maren Wellenreuther
- The New Zealand Institute for Plant and Food Research LtdNelsonNew Zealand
- School of Biological SciencesThe University of AucklandAucklandNew Zealand
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22
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Burbrink FT, Bernstein JM, Kuhn A, Gehara M, Ruane S. Ecological Divergence and the History of Gene Flow in the Nearctic Milksnakes (Lampropeltis triangulum Complex). Syst Biol 2021; 71:839-858. [PMID: 35043210 DOI: 10.1093/sysbio/syab093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/11/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
Many phylogeographic studies on species with large ranges have found genetic-geographic structure associated with changes in habitat and physical barriers preventing or reducing gene flow. These interactions with geographic space, contemporary and historical climate, and biogeographic barriers have complex effects on contemporary population genetic structure and processes of speciation. While allopatric speciation at biogeographic barriers is considered the primary mechanism for generating species, more recently it has been shown that parapatric modes of divergence may be equally or even more common. With genomic data and better modeling capabilities, we can more clearly define causes of speciation in relation to biogeography and migration between lineages, the location of hybrid zones with respect to the ecology of parental lineages, and differential introgression of genes between taxa. Here, we examine the origins of three Nearctic milksnakes (Lampropeltis elapsoides, Lampropeltis triangulum and Lampropeltis gentilis) using genome-scale data to better understand species diversification. Results from artificial neural networks show that a mix of a strong biogeographic barrier, environmental changes, and physical space has affected genetic structure in these taxa. These results underscore conspicuous environmental changes that occur as the sister taxa L. triangulum and L. gentilis diverged near the Great Plains into the forested regions of the Eastern Nearctic. This area has been recognized as a region for turnover for many vertebrate species, but as we show here the contemporary boundary does not isolate these sister species. These two species likely formed in the mid-Pleistocene and have remained partially reproductively isolated over much of this time, showing differential introgression of loci. We also demonstrate that when L. triangulum and L. gentilis are each in contact with the much older L. elapsoides, some limited gene flow has occurred. Given the strong agreement between nuclear and mtDNA genomes, along with estimates of ecological niche, we suggest that all three lineages should continue to be recognized as unique species. Furthermore, this work emphasizes the importance of considering complex modes of divergence and differential allelic introgression over a complex landscape when testing mechanisms of speciation. [Cline; delimitation; Eastern Nearctic; Great Plains; hybrids; introgression; speciation.].
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Affiliation(s)
- Frank T Burbrink
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Justin M Bernstein
- Department of Biological Sciences, Rutgers University Newark, 195 University Ave, Newark, NJ 07102, USA
| | - Arianna Kuhn
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Marcelo Gehara
- Department of Earth and Environmental Sciences, Rutgers University Newark, 195 University Ave, Newark, NJ 07102, USA
| | - Sara Ruane
- Department of Earth and Environmental Sciences, Rutgers University Newark, 195 University Ave, Newark, NJ 07102, USA.,Amphibian and Reptile Collection, Negaunee Integrative Research Center, Field Museum of Natural History, 1400 S Lake Shore Dr, Chicago, IL 60605, USA
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23
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Turbek SP, Semenov GA, Enbody ED, Campagna L, Taylor SA. Variable Signatures of Selection Despite Conserved Recombination Landscapes Early in Speciation. J Hered 2021; 112:485-496. [PMID: 34499149 DOI: 10.1093/jhered/esab054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/08/2021] [Indexed: 11/14/2022] Open
Abstract
Recently diverged taxa often exhibit heterogeneous landscapes of genomic differentiation, characterized by regions of elevated differentiation on an otherwise homogeneous background. While divergence peaks are generally interpreted as regions responsible for reproductive isolation, they can also arise due to background selection, selective sweeps unrelated to speciation, and variation in recombination and mutation rates. To investigate the association between patterns of recombination and landscapes of genomic differentiation during the early stages of speciation, we generated fine-scale recombination maps for six southern capuchino seedeaters (Sporophila) and two subspecies of White Wagtail (Motacilla alba), two recent avian radiations in which divergent selection on pigmentation genes has likely generated peaks of differentiation. We compared these recombination maps to those of Collared (Ficedula albicollis) and Pied Flycatchers (Ficedula hypoleuca), non-sister taxa characterized by moderate genomic divergence and a heterogenous landscape of genomic differentiation shaped in part by background selection. Although recombination landscapes were conserved within all three systems, we documented a weaker negative correlation between recombination rate and genomic differentiation in the recent radiations. All divergence peaks between capuchinos, wagtails, and flycatchers were located in regions with lower-than-average recombination rates, and most divergence peaks in capuchinos and flycatchers fell in regions of exceptionally reduced recombination. Thus, co-adapted allelic combinations in these regions may have been protected early in divergence, facilitating rapid diversification. Despite largely conserved recombination landscapes, divergence peaks are specific to each focal comparison in capuchinos, suggesting that regions of elevated differentiation have not been generated by variation in recombination rate alone.
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Affiliation(s)
- Sheela P Turbek
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Georgy A Semenov
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Erik D Enbody
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Leonardo Campagna
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Ithaca, NY, USA.,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Scott A Taylor
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
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24
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James ME, Wilkinson MJ, Bernal DM, Liu H, North HL, Engelstädter J, Ortiz-Barrientos D. Phenotypic and genotypic parallel evolution in parapatric ecotypes of Senecio. Evolution 2021; 75:3115-3131. [PMID: 34687472 PMCID: PMC9299460 DOI: 10.1111/evo.14387] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 12/11/2022]
Abstract
The independent and repeated adaptation of populations to similar environments often results in the evolution of similar forms. This phenomenon creates a strong correlation between phenotype and environment and is referred to as parallel evolution. However, we are still largely unaware of the dynamics of parallel evolution, as well as the interplay between phenotype and genotype within natural systems. Here, we examined phenotypic and genotypic parallel evolution in multiple parapatric Dune‐Headland coastal ecotypes of an Australian wildflower, Senecio lautus. We observed a clear trait‐environment association in the system, with all replicate populations having evolved along the same phenotypic evolutionary trajectory. Similar phenotypes have arisen via mutational changes occurring in different genes, although many share the same biological functions. Our results shed light on how replicated adaptation manifests at the phenotypic and genotypic levels within populations, and highlight S. lautus as one of the most striking cases of phenotypic parallel evolution in nature.
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Affiliation(s)
- Maddie E James
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD, 4072, Australia.,Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Melanie J Wilkinson
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD, 4072, Australia.,Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Diana M Bernal
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD, 4072, Australia.,Current Address: Biousos Neotropicales S.A.S, Bogotá, Colombia
| | - Huanle Liu
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD, 4072, Australia.,Current Address: Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, 08003, Spain
| | - Henry L North
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD, 4072, Australia.,Current Address: Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, United Kingdom
| | - Jan Engelstädter
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Daniel Ortiz-Barrientos
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD, 4072, Australia.,Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, QLD, 4072, Australia
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25
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Di C, Murga Moreno J, Salazar-Tortosa DF, Lauterbur ME, Enard D. Decreased recent adaptation at human mendelian disease genes as a possible consequence of interference between advantageous and deleterious variants. eLife 2021; 10:69026. [PMID: 34636724 PMCID: PMC8526059 DOI: 10.7554/elife.69026] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 10/02/2021] [Indexed: 11/27/2022] Open
Abstract
Advances in genome sequencing have improved our understanding of the genetic basis of human diseases, and thousands of human genes have been associated with different diseases. Recent genomic adaptation at disease genes has not been well characterized. Here, we compare the rate of strong recent adaptation in the form of selective sweeps between mendelian, non-infectious disease genes and non-disease genes across distinct human populations from the 1000 Genomes Project. We find that mendelian disease genes have experienced far less selective sweeps compared to non-disease genes especially in Africa. Investigating further the possible causes of the sweep deficit at disease genes, we find that this deficit is very strong at disease genes with both low recombination rates and with high numbers of associated disease variants, but is almost non-existent at disease genes with higher recombination rates or lower numbers of associated disease variants. Because segregating recessive deleterious variants have the ability to interfere with adaptive ones, these observations strongly suggest that adaptation has been slowed down by the presence of interfering recessive deleterious variants at disease genes. These results suggest that disease genes suffer from a transient inability to adapt as fast as the rest of the genome.
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Affiliation(s)
- Chenlu Di
- University of Arizona Department of Ecology and Evolutionary Biology, Tucson, United States
| | - Jesus Murga Moreno
- Institut de Biotecnologia i de Biomedicina and Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - M Elise Lauterbur
- University of Arizona Department of Ecology and Evolutionary Biology, Tucson, United States
| | - David Enard
- University of Arizona Department of Ecology and Evolutionary Biology, Tucson, United States
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26
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The evolutionary genomics of species' responses to climate change. Nat Ecol Evol 2021; 5:1350-1360. [PMID: 34373621 DOI: 10.1038/s41559-021-01526-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 07/05/2021] [Indexed: 02/06/2023]
Abstract
Climate change is a threat to biodiversity. One way that this threat manifests is through pronounced shifts in the geographical range of species over time. To predict these shifts, researchers have primarily used species distribution models. However, these models are based on assumptions of niche conservatism and do not consider evolutionary processes, potentially limiting their accuracy and value. To incorporate evolution into the prediction of species' responses to climate change, researchers have turned to landscape genomic data and examined information about local genetic adaptation using climate models. Although this is an important advancement, this approach currently does not include other evolutionary processes-such as gene flow, population dispersal and genomic load-that are critical for predicting the fate of species across the landscape. Here, we briefly review the current practices for the use of species distribution models and for incorporating local adaptation. We next discuss the rationale and theory for considering additional processes, reviewing how they can be incorporated into studies of species' responses to climate change. We summarize with a conceptual framework of how manifold layers of information can be combined to predict the potential response of specific populations to climate change. We illustrate all of the topics using an exemplar dataset and provide the source code as potential tutorials. This Perspective is intended to be a step towards a more comprehensive integration of population genomics with climate change science.
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27
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Burbrink FT, Ruane S. Contemporary Philosophy and Methods for Studying Speciation and Delimiting Species. ICHTHYOLOGY & HERPETOLOGY 2021. [DOI: 10.1643/h2020073] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Frank T. Burbrink
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, New York 10024; . Send reprint requests to this address
| | - Sara Ruane
- Earth and Environmental Sciences: Ecology and Evolution, Rutgers University–Newark, 195 University Avenue, Newark, New Jersey 07102
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28
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Mérot C, Berdan EL, Cayuela H, Djambazian H, Ferchaud AL, Laporte M, Normandeau E, Ragoussis J, Wellenreuther M, Bernatchez L. Locally Adaptive Inversions Modulate Genetic Variation at Different Geographic Scales in a Seaweed Fly. Mol Biol Evol 2021; 38:3953-3971. [PMID: 33963409 PMCID: PMC8382925 DOI: 10.1093/molbev/msab143] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Across a species range, multiple sources of environmental heterogeneity, at both small and large scales, create complex landscapes of selection, which may challenge adaptation, particularly when gene flow is high. One key to multidimensional adaptation may reside in the heterogeneity of recombination along the genome. Structural variants, like chromosomal inversions, reduce recombination, increasing linkage disequilibrium among loci at a potentially massive scale. In this study, we examined how chromosomal inversions shape genetic variation across a species range and ask how their contribution to adaptation in the face of gene flow varies across geographic scales. We sampled the seaweed fly Coelopa frigida along a bioclimatic gradient stretching across 10° of latitude, a salinity gradient, and a range of heterogeneous, patchy habitats. We generated a chromosome-level genome assembly to analyze 1,446 low-coverage whole genomes collected along those gradients. We found several large nonrecombining genomic regions, including putative inversions. In contrast to the collinear regions, inversions and low-recombining regions differentiated populations more strongly, either along an ecogeographic cline or at a fine-grained scale. These genomic regions were associated with environmental factors and adaptive phenotypes, albeit with contrasting patterns. Altogether, our results highlight the importance of recombination in shaping adaptation to environmental heterogeneity at local and large scales.
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Affiliation(s)
- Claire Mérot
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - Emma L Berdan
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Hugo Cayuela
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | | | - Anne-Laure Ferchaud
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - Martin Laporte
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - Eric Normandeau
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | | | - Maren Wellenreuther
- Seafood Research Unit, Plant & Food Research, Port Nelson, Nelson, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
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29
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Comeault AA, Kautt AF, Matute DR. Genomic signatures of admixture and selection are shared among populations of Zaprionus indianus across the western hemisphere. Mol Ecol 2021; 30:6193-6210. [PMID: 34233050 PMCID: PMC9290797 DOI: 10.1111/mec.16066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 06/27/2021] [Accepted: 07/01/2021] [Indexed: 11/28/2022]
Abstract
Introduced species have become an increasingly common component of biological communities around the world. A central goal in invasion biology is therefore to identify the demographic and evolutionary factors that underlie successful introductions. Here we use whole genome sequences, collected from populations in the native and introduced range of the African fig fly, Zaprionus indianus, to quantify genetic relationships among them, identify potential sources of the introductions, and test for selection at different spatial scales. We find that geographically widespread populations in the western hemisphere are genetically more similar to each other than to lineages sampled across Africa, and that these populations share a mixture of alleles derived from differentiated African lineages. Using patterns of allele‐sharing and demographic modelling we show that Z. indinaus have undergone a single expansion across the western hemisphere with admixture between African lineages predating this expansion. We also find support for selection that is shared across populations in the western hemisphere, and in some cases, with a subset of African populations. This suggests either that parallel selection has acted across a large part of Z. indianus's introduced range; or, more parsimoniously, that Z. indianus has experienced selection early on during (or prior‐to) its expansion into the western hemisphere. We suggest that the range expansion of Z. indianus has been facilitated by admixture and selection, and that management of this invasion could focus on minimizing future admixture by controlling the movement of individuals within this region rather than between the western and eastern hemisphere.
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Affiliation(s)
- Aaron A Comeault
- Molecular Ecology and Evolution Group, School of Natural Sciences, Bangor University, Bangor, UK
| | - Andreas F Kautt
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Daniel R Matute
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
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30
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North HL, McGaughran A, Jiggins CD. Insights into invasive species from whole-genome resequencing. Mol Ecol 2021; 30:6289-6308. [PMID: 34041794 DOI: 10.1111/mec.15999] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/12/2021] [Accepted: 04/30/2021] [Indexed: 12/12/2022]
Abstract
Studies of invasive species can simultaneously inform management strategies and quantify rapid evolution in the wild. The role of genomics in invasion science is increasingly recognised, and the growing availability of reference genomes for invasive species is paving the way for whole-genome resequencing studies in a wide range of systems. Here, we survey the literature to assess the application of whole-genome resequencing data in invasion biology. For some applications, such as the reconstruction of invasion routes in time and space, sequencing the whole genome of many individuals can increase the accuracy of existing methods. In other cases, population genomic approaches such as haplotype analysis can permit entirely new questions to be addressed and new technologies applied. To date whole-genome resequencing has only been used in a handful of invasive systems, but these studies have confirmed the importance of processes such as balancing selection and hybridization in allowing invasive species to reuse existing adaptations and rapidly overcome the challenges of a foreign ecosystem. The use of genomic data does not constitute a paradigm shift per se, but by leveraging new theory, tools, and technologies, population genomics can provide unprecedented insight into basic and applied aspects of invasion science.
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Affiliation(s)
- Henry L North
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Angela McGaughran
- Te Aka Mātuatua/School of Science, University of Waikato, Hamilton, New Zealand
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge, UK
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31
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Schweizer G, Haider MB, Barroso GV, Rössel N, Münch K, Kahmann R, Dutheil JY. Population Genomics of the Maize Pathogen Ustilago maydis: Demographic History and Role of Virulence Clusters in Adaptation. Genome Biol Evol 2021; 13:evab073. [PMID: 33837781 PMCID: PMC8120014 DOI: 10.1093/gbe/evab073] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2021] [Indexed: 11/14/2022] Open
Abstract
The tight interaction between pathogens and their hosts results in reciprocal selective forces that impact the genetic diversity of the interacting species. The footprints of this selection differ between pathosystems because of distinct life-history traits, demographic histories, or genome architectures. Here, we studied the genome-wide patterns of genetic diversity of 22 isolates of the causative agent of the corn smut disease, Ustilago maydis, originating from five locations in Mexico, the presumed center of origin of this species. In this species, many genes encoding secreted effector proteins reside in so-called virulence clusters in the genome, an arrangement that is so far not found in other filamentous plant pathogens. Using a combination of population genomic statistical analyses, we assessed the geographical, historical, and genome-wide variation of genetic diversity in this fungal pathogen. We report evidence of two partially admixed subpopulations that are only loosely associated with geographic origin. Using the multiple sequentially Markov coalescent model, we inferred the demographic history of the two pathogen subpopulations over the last 0.5 Myr. We show that both populations experienced a recent strong bottleneck starting around 10,000 years ago, coinciding with the assumed time of maize domestication. Although the genome average genetic diversity is low compared with other fungal pathogens, we estimated that the rate of nonsynonymous adaptive substitutions is three times higher in genes located within virulence clusters compared with nonclustered genes, including nonclustered effector genes. These results highlight the role that these singular genomic regions play in the evolution of this pathogen.
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Affiliation(s)
- Gabriel Schweizer
- Department of Organismic Interactions, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
| | - Muhammad Bilal Haider
- Max-Planck-Institute for Evolutionary Biology, Research Group Molecular Systems Evolution, Plön, Germany
| | - Gustavo V Barroso
- Max-Planck-Institute for Evolutionary Biology, Research Group Molecular Systems Evolution, Plön, Germany
| | - Nicole Rössel
- Department of Organismic Interactions, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
| | - Karin Münch
- Department of Organismic Interactions, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
| | - Regine Kahmann
- Department of Organismic Interactions, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
| | - Julien Y Dutheil
- Department of Organismic Interactions, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
- Max-Planck-Institute for Evolutionary Biology, Research Group Molecular Systems Evolution, Plön, Germany
- Institute of Evolutionary Sciences of Montpellier, University of Montpellier 2, France
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32
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Grummer JA, Whitlock MC, Schulte PM, Taylor EB. Growth genes are implicated in the evolutionary divergence of sympatric piscivorous and insectivorous rainbow trout (Oncorhynchus mykiss). BMC Ecol Evol 2021; 21:63. [PMID: 33888062 PMCID: PMC8063319 DOI: 10.1186/s12862-021-01795-9] [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: 01/25/2021] [Accepted: 04/12/2021] [Indexed: 12/26/2022] Open
Abstract
Background Identifying ecologically significant phenotypic traits and the genomic mechanisms that underly them are crucial steps in understanding traits associated with population divergence. We used genome-wide data to identify genomic regions associated with key traits that distinguish two ecomorphs of rainbow trout (Oncorhynchus mykiss)—insectivores and piscivores—that coexist for the non-breeding portion of the year in Kootenay Lake, southeastern British Columbia. “Gerrards” are large-bodied, rapidly growing piscivores with high metabolic rates that spawn north of Kootenay Lake in the Lardeau River, in contrast to the insectivorous populations that are on average smaller in body size, with lower growth and metabolic rates, mainly forage on aquatic insects, and spawn in tributaries immediately surrounding Kootenay Lake. We used pool-seq data representing ~ 60% of the genome and 80 fish per population to assess the level of genomic divergence between ecomorphs and to identify and interrogate loci that may play functional or selective roles in their divergence. Results Genomic divergence was high between sympatric insectivores and piscivores (\documentclass[12pt]{minimal}
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\begin{document}$$F_{\text{ST}}$$\end{document}FST = 0.188), and in fact higher than between insectivorous populations from Kootenay Lake and the Blackwater River (\documentclass[12pt]{minimal}
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\begin{document}$$F_{\text{ST}}$$\end{document}FST = 0.159) that are > 500 km apart. A window-based \documentclass[12pt]{minimal}
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\begin{document}$$F_{\text{ST}}$$\end{document}FST analysis did not reveal “islands” of genomic differentiation; however, the window with highest \documentclass[12pt]{minimal}
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\begin{document}$$F_{\text{ST}}$$\end{document}FST estimate did include a gene associated with insulin secretion. Although we explored the use of the “Local score” approach to identify genomic outlier regions, this method was ultimately not used because simulations revealed a high false discovery rate (~ 20%). Gene ontology (GO) analysis identified several growth processes as enriched in genes occurring in the ~ 200 most divergent genomic windows, indicating many loci of small effect involved in growth and growth-related metabolic processes are associated with the divergence of these ecomorphs. Conclusion Our results reveal a high degree of genomic differentiation between piscivorous and insectivorous populations and indicate that the large body piscivorous phenotype is likely not due to one or a few loci of large effect. Rather, the piscivore phenotype may be controlled by several loci of small effect, thus highlighting the power of whole-genome resequencing in identifying genomic regions underlying population-level phenotypic divergences. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01795-9.
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Affiliation(s)
- Jared A Grummer
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, 6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada.
| | - Michael C Whitlock
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, 6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada
| | - Patricia M Schulte
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, 6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada
| | - Eric B Taylor
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, 6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada.,Beaty Biodiversity Museum, University of British Columbia, 6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada
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Bal TMP, Llanos-Garrido A, Chaturvedi A, Verdonck I, Hellemans B, Raeymaekers JAM. Adaptive Divergence under Gene Flow along an Environmental Gradient in Two Coexisting Stickleback Species. Genes (Basel) 2021; 12:435. [PMID: 33803820 PMCID: PMC8003309 DOI: 10.3390/genes12030435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 12/13/2022] Open
Abstract
There is a general and solid theoretical framework to explain how the interplay between natural selection and gene flow affects local adaptation. Yet, to what extent coexisting closely related species evolve collectively or show distinctive evolutionary responses remains a fundamental question. To address this, we studied the population genetic structure and morphological differentiation of sympatric three-spined and nine-spined stickleback. We conducted genotyping-by-sequencing and morphological trait characterisation using 24 individuals of each species from four lowland brackish water (LBW), four lowland freshwater (LFW) and three upland freshwater (UFW) sites in Belgium and the Netherlands. This combination of sites allowed us to contrast populations from isolated but environmentally similar locations (LFW vs. UFW), isolated but environmentally heterogeneous locations (LBW vs. UFW), and well-connected but environmentally heterogenous locations (LBW vs. LFW). Overall, both species showed comparable levels of genetic diversity and neutral genetic differentiation. However, for all three spatial scales, signatures of morphological and genomic adaptive divergence were substantially stronger among populations of the three-spined stickleback than among populations of the nine-spined stickleback. Furthermore, most outlier SNPs in the two species were associated with local freshwater sites. The few outlier SNPs that were associated with the split between brackish water and freshwater populations were located on one linkage group in three-spined stickleback and two linkage groups in nine-spined stickleback. We conclude that while both species show congruent evolutionary and genomic patterns of divergent selection, both species differ in the magnitude of their response to selection regardless of the geographical and environmental context.
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Affiliation(s)
- Thijs M. P. Bal
- Faculty of Biosciences and Aquaculture, Nord University, N-8049 Bodø, Norway;
| | | | - Anurag Chaturvedi
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland;
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, B-3000 Leuven, Belgium; (I.V.); (B.H.)
| | - Io Verdonck
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, B-3000 Leuven, Belgium; (I.V.); (B.H.)
| | - Bart Hellemans
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, B-3000 Leuven, Belgium; (I.V.); (B.H.)
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Pyhäjärvi T, Mattila TM. New model species for arctic-alpine plant molecular ecology. Mol Ecol Resour 2021; 21:637-640. [PMID: 33501729 DOI: 10.1111/1755-0998.13335] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 12/22/2022]
Abstract
Arctic and alpine, high latitude and high elevation environments are one of the most stressful environments for species to inhabit. This harshness manifests itself in lower species richness in comparison to more southern vegetation zones (Francis & Currie, 2003). Furthermore, the climatic oscillations-past and predicted-have the most dramatic effect on these ecosystems. For example, in regions of continental ice sheets-the northernmost part of Western Europe and North America-the Arctic species assemblages are no older than a few thousands of years, which is a relatively short period from an evolutionary perspective. Although similar environments may have existed further south during the Ice Age, allowing some preadaptation for the Arctic species, the current habitat is a unique combination of environmental factors such as the climate, soil, bedrock, and photoperiod. Hence, understanding the evolutionary forces shaping Arctic-alpine species will be important for predicting these vulnerable environments' population viability and adaptive potential in the future. In this issue of Molecular Ecology Resources, Nowak et al. (Molecular Ecology Resources) present extensive genome-wide resources for an Arctic-alpine plant Draba nivalis. This adds a valuable new member into the cabbage family models for evolutionary genetics and adaptation studies, to accompany e.g., Arabidopsis (Nature Genetics, 43, 476; Nature, 408, 796), Arabis (Nature Plants, 1, 14023) and Capsella (Nature Genetics, 45, 831). A whole new avenue will open up for molecular ecological studies not only for D. nivalis, but the whole large Draba genus with its diverse ecological and evolutionary characteristics.
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Affiliation(s)
- Tanja Pyhäjärvi
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Tiina M Mattila
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
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35
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Rieseberg L, Warschefsky E, O’Boyle B, Taberlet P, Ortiz‐Barrientos D, Kane NC, Sibbett B. Editorial 2021. Mol Ecol 2020. [DOI: 10.1111/mec.15759] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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36
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Booker TR, Yeaman S, Whitlock MC. Global adaptation complicates the interpretation of genome scans for local adaptation. Evol Lett 2020; 5:4-15. [PMID: 33552532 PMCID: PMC7857299 DOI: 10.1002/evl3.208] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/27/2020] [Accepted: 11/12/2020] [Indexed: 12/14/2022] Open
Abstract
Spatially varying selection promotes variance in allele frequencies, increasing genetic differentiation between the demes of a metapopulation. For that reason, outliers in the genome‐wide distribution of summary statistics measuring genetic differentiation, such as FST, are often interpreted as evidence for alleles that contribute to local adaptation. However, theoretical studies have shown that in spatially structured populations the spread of beneficial mutations with spatially uniform fitness effects can also induce transient genetic differentiation. In recent years, numerous empirical studies have suggested that such species‐wide, or global, adaptation makes a substantial contribution to molecular evolution. In this perspective, we discuss how commonly such global adaptation may influence the genome‐wide distribution of FST and generate genetic differentiation patterns, which could be mistaken for local adaptation. To illustrate this, we use forward‐in‐time population genetic simulations assuming parameters for the rate and strength of beneficial mutations consistent with estimates from natural populations. We demonstrate that the spread of globally beneficial mutations in parapatric populations may frequently generate FST outliers, which could be misinterpreted as evidence for local adaptation. The spread of beneficial mutations causes selective sweeps at flanking sites, so in some cases, the effects of global versus local adaptation may be distinguished by examining patterns of nucleotide diversity within and between populations in addition to FST. However, when local adaptation has been only recently established, it may be much more difficult to distinguish from global adaptation, due to less accumulation of linkage disequilibrium at flanking sites. Through our discussion, we conclude that a large fraction of FST outliers that are presumed to arise from local adaptation may instead be due to global adaptation.
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Affiliation(s)
- Tom R Booker
- Department of Forest and Conservation Sciences University of British Columbia Vancouver Canada.,Biodiversity Research Centre University of British Columbia Vancouver Canada
| | - Sam Yeaman
- Department of Biological Sciences University of Calgary Calgary Canada
| | - Michael C Whitlock
- Biodiversity Research Centre University of British Columbia Vancouver Canada.,Department of Zoology University of British Columbia Vancouver Canada
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Guzinski J, Ruggeri P, Ballenghien M, Mauger S, Jacquemin B, Jollivet C, Coudret J, Jaugeon L, Destombe C, Valero M. Seascape Genomics of the Sugar Kelp Saccharina latissima along the North Eastern Atlantic Latitudinal Gradient. Genes (Basel) 2020; 11:E1503. [PMID: 33322137 PMCID: PMC7763533 DOI: 10.3390/genes11121503] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 12/23/2022] Open
Abstract
Temperature is one of the most important range-limiting factors for many seaweeds. Driven by the recent climatic changes, rapid northward shifts of species' distribution ranges can potentially modify the phylogeographic signature of Last Glacial Maximum. We explored this question in detail in the cold-tolerant kelp species Saccharina latissima, using microsatellites and double digest restriction site-associated DNA sequencing ( ddRAD-seq) derived single nucleotide polymorphisms (SNPs) to analyze the genetic diversity and structure in 11 sites spanning the entire European Atlantic latitudinal range of this species. In addition, we checked for statistical correlation between genetic marker allele frequencies and three environmental proxies (sea surface temperature, salinity, and water turbidity). Our findings revealed that genetic diversity was significantly higher for the northernmost locality (Spitsbergen) compared to the southern ones (Northern Iberia), which we discuss in light of the current state of knowledge on phylogeography of S. latissima and the potential influence of the recent climatic changes on the population structure of this species. Seven SNPs and 12 microsatellite alleles were found to be significantly associated with at least one of the three environmental variables. We speculate on the putative adaptive functions of the genes associated with the outlier markers and the importance of these markers for successful conservation and aquaculture strategies for S. latissima in this age of rapid global change.
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Affiliation(s)
- Jaromir Guzinski
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone KT15 3NB, Surrey, UK
| | - Paolo Ruggeri
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
- Xelect ltd, Horizon House, Abbey Walk, St Andrews KY16 9LB, Scotland, UK
| | - Marion Ballenghien
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
- UMR 7144, Adaptation et Diversité en Milieu Marin, CNRS, Sorbonne Université, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France
| | - Stephane Mauger
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
| | - Bertrand Jacquemin
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
- CEVA, 83 Presqu’île de Pen Lan, 22610 Pleubian, France
| | - Chloe Jollivet
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
- Ecole polytechnique de Lausanne (EPFL), SV-IBI UPOATES, Route cantonale, CH-1015 Lausanne, Switzerland
| | - Jerome Coudret
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
| | - Lucie Jaugeon
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
| | - Christophe Destombe
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
| | - Myriam Valero
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
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Genomic islands of differentiation in a rapid avian radiation have been driven by recent selective sweeps. Proc Natl Acad Sci U S A 2020; 117:30554-30565. [PMID: 33199636 DOI: 10.1073/pnas.2015987117] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Numerous studies of emerging species have identified genomic "islands" of elevated differentiation against a background of relative homogeneity. The causes of these islands remain unclear, however, with some signs pointing toward "speciation genes" that locally restrict gene flow and others suggesting selective sweeps that have occurred within nascent species after speciation. Here, we examine this question through the lens of genome sequence data for five species of southern capuchino seedeaters, finch-like birds from South America that have undergone a species radiation during the last ∼50,000 generations. By applying newly developed statistical methods for ancestral recombination graph inference and machine-learning methods for the prediction of selective sweeps, we show that previously identified islands of differentiation in these birds appear to be generally associated with relatively recent, species-specific selective sweeps, most of which are predicted to be soft sweeps acting on standing genetic variation. Many of these sweeps coincide with genes associated with melanin-based variation in plumage, suggesting a prominent role for sexual selection. At the same time, a few loci also exhibit indications of possible selection against gene flow. These observations shed light on the complex manner in which natural selection shapes genome sequences during speciation.
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Stevison LS, McGaugh SE. It's time to stop sweeping recombination rate under the genome scan rug. Mol Ecol 2020; 29:4249-4253. [PMID: 33058346 DOI: 10.1111/mec.15690] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/04/2020] [Accepted: 09/29/2020] [Indexed: 01/03/2023]
Abstract
Different parts of the genome can vary widely in their evolutionary histories and sequence divergence from other species. Indeed, some of the most interesting biology (e.g., hybridization, horizontal gene transfer, variable mutation rates across the genome) is revealed by the discordant relationships between taxa across the genome. The goal for much of evolutionary genetics is centred on understanding the evolutionary processes by which such varied signatures arise and are maintained. Many evolutionary genetics studies seek to identify signatures of positive selection between two closely related ecotypes or taxa by delineating regions with particularly high divergence relative to a genome-wide average, often termed "divergence outliers." In a From the Cover article in this issue of Molecular Ecology, Booker et al. take a major step forward in showing that recombination rate differences are sufficient to create false positive divergence outliers, even under neutrality. They demonstrate that the variance of genome scan metrics is especially high in regions with low recombination rates, consistent with previous work. Furthermore, they show that both relative and absolute measures of divergence (FST and DXY , respectively) as well as other commonly used statistics in genome scans (e.g., πW , Tajima's D and H12) all have similar covariance between variance and local recombination rate. Finally, Booker et al. show that low recombination regions will tend to produce more outliers if genome-wide averages are used as cut-offs to define genomic outliers. Booker et al.'s results suggest that recombination rate variation, even under neutral conditions, can shape genome scans for selection, and this important variable can no longer be ignored.
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Affiliation(s)
- Laurie S Stevison
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Suzanne E McGaugh
- Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, USA
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40
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Ruzicka F, Dutoit L, Czuppon P, Jordan CY, Li X, Olito C, Runemark A, Svensson EI, Yazdi HP, Connallon T. The search for sexually antagonistic genes: Practical insights from studies of local adaptation and statistical genomics. Evol Lett 2020; 4:398-415. [PMID: 33014417 PMCID: PMC7523564 DOI: 10.1002/evl3.192] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/13/2020] [Accepted: 07/28/2020] [Indexed: 12/16/2022] Open
Abstract
Sexually antagonistic (SA) genetic variation-in which alleles favored in one sex are disfavored in the other-is predicted to be common and has been documented in several animal and plant populations, yet we currently know little about its pervasiveness among species or its population genetic basis. Recent applications of genomics in studies of SA genetic variation have highlighted considerable methodological challenges to the identification and characterization of SA genes, raising questions about the feasibility of genomic approaches for inferring SA selection. The related fields of local adaptation and statistical genomics have previously dealt with similar challenges, and lessons from these disciplines can therefore help overcome current difficulties in applying genomics to study SA genetic variation. Here, we integrate theoretical and analytical concepts from local adaptation and statistical genomics research-including F ST and F IS statistics, genome-wide association studies, pedigree analyses, reciprocal transplant studies, and evolve-and-resequence experiments-to evaluate methods for identifying SA genes and genome-wide signals of SA genetic variation. We begin by developing theoretical models for between-sex F ST and F IS, including explicit null distributions for each statistic, and using them to critically evaluate putative multilocus signals of sex-specific selection in previously published datasets. We then highlight new statistics that address some of the limitations of F ST and F IS, along with applications of more direct approaches for characterizing SA genetic variation, which incorporate explicit fitness measurements. We finish by presenting practical guidelines for the validation and evolutionary analysis of candidate SA genes and discussing promising empirical systems for future work.
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Affiliation(s)
- Filip Ruzicka
- School of Biological SciencesMonash UniversityClaytonVIC 3800Australia
| | - Ludovic Dutoit
- Department of ZoologyUniversity of OtagoDunedin9054New Zealand
| | - Peter Czuppon
- Institute of Ecology and Environmental Sciences, UPEC, CNRS, IRD, INRASorbonne UniversitéParis75252France
- Center for Interdisciplinary Research in Biology, CNRS, Collège de FrancePSL Research UniversityParis75231France
| | - Crispin Y. Jordan
- School of Biomedical SciencesUniversity of EdinburghEdinburghEH8 9XDUnited Kingdom
| | - Xiang‐Yi Li
- Institute of BiologyUniversity of NeuchâtelNeuchatelCH‐2000Switzerland
| | - Colin Olito
- Department of BiologyLund UniversityLundSE‐22362Sweden
| | - Anna Runemark
- Department of BiologyLund UniversityLundSE‐22362Sweden
| | | | | | - Tim Connallon
- School of Biological SciencesMonash UniversityClaytonVIC 3800Australia
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Perrier C, Rougemont Q, Charmantier A. Demographic history and genomics of local adaptation in blue tit populations. Evol Appl 2020; 13:1145-1165. [PMID: 32684952 PMCID: PMC7359843 DOI: 10.1111/eva.13035] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 05/11/2020] [Accepted: 05/18/2020] [Indexed: 12/24/2022] Open
Abstract
Understanding the genomic processes underlying local adaptation is a central aim of modern evolutionary biology. This task requires identifying footprints of local selection but also estimating spatio‐temporal variations in population demography and variations in recombination rate and in diversity along the genome. Here, we investigated these parameters in blue tit populations inhabiting deciduous versus evergreen forests, and insular versus mainland areas, in the context of a previously described strong phenotypic differentiation. Neighboring population pairs of deciduous and evergreen habitats were weakly genetically differentiated (FST = 0.003 on average), nevertheless with a statistically significant effect of habitat type on the overall genetic structure. This low differentiation was consistent with the strong and long‐lasting gene flow between populations inferred by demographic modeling. In turn, insular and mainland populations were moderately differentiated (FST = 0.08 on average), in line with the inference of moderate ancestral migration, followed by isolation since the end of the last glaciation. Effective population sizes were large, yet smaller on the island than on the mainland. Weak and nonparallel footprints of divergent selection between deciduous and evergreen populations were consistent with their high connectivity and the probable polygenic nature of local adaptation in these habitats. In turn, stronger footprints of divergent selection were identified between long isolated insular versus mainland birds and were more often found in regions of low recombination, as expected from theory. Lastly, we identified a genomic inversion on the mainland, spanning 2.8 Mb. These results provide insights into the demographic history and genetic architecture of local adaptation in blue tit populations at multiple geographic scales.
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Affiliation(s)
- Charles Perrier
- Centre d'Ecologie Fonctionnelle et Evolutive UMR 5175 CNRS Univ Montpellier CNRS EPHE IRD Univ Paul Valéry Montpellier 3 Montpellier France.,Centre de Biologie pour la Gestion des Populations UMR CBGP INRAE CIRAD IRD Montpellier SupAgro Univ Montpellier Montpellier France
| | - Quentin Rougemont
- Département de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec Québec Canada
| | - Anne Charmantier
- Centre d'Ecologie Fonctionnelle et Evolutive UMR 5175 CNRS Univ Montpellier CNRS EPHE IRD Univ Paul Valéry Montpellier 3 Montpellier France
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