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Aubier TG, Kopp M, Linn IJ, Puebla O, Rafajlović M, Servedio MR. Negative Coupling: The Coincidence of Premating Isolating Barriers Can Reduce Reproductive Isolation. Cold Spring Harb Perspect Biol 2024; 16:a041435. [PMID: 38503505 PMCID: PMC11444250 DOI: 10.1101/cshperspect.a041435] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Speciation can be mediated by a variety of reproductive barriers, and the interaction among different barriers has often been shown to enhance overall reproductive isolation, a process referred to as "coupling." Here, we analyze a population genetics model to study the establishment of linkage disequilibrium (LD) among loci involved in multiple premating barriers, an aspect that has received little theoretical attention to date. We consider a simple genetic framework underlying two distinct premating barriers, each encoded by a preference locus and its associated mating trait locus. We show that their interaction can lead to a decrease in overall reproductive isolation relative to a situation with a single barrier, a process we call "negative coupling." More specifically, in our model, negative coupling results either from sexual selection that reduces divergence at all loci, or from reduced LD that occurs because the presence of many females with "mismatched" preferences causes the mating success of recombinant males to become high. Interestingly, the latter effect may even cause LD among preference loci to become negative when recombination rates among loci are low. We conclude that coincident reproductive barriers may not necessarily reinforce each other, and that the underlying loci may not necessarily develop a positive association.
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Affiliation(s)
- Thomas G Aubier
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 - Paul Sabatier (UT3), Toulouse, France
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Michael Kopp
- Aix Marseille Université, CNRS, Centrale Marseille, I2M, UMR 7373, 13331 Marseille Cedex 3, France
| | - Isaac J Linn
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Oscar Puebla
- Leibniz Centre for Tropical Marine Research, 28359 Bremen, Germany
- Institute for Chemistry and Biology of the Marine Environment (ICBM), 26111 Oldenburg, Germany
| | - Marina Rafajlović
- Department of Marine Sciences, University of Gothenburg, 405 30 Gothenburg, Sweden
- Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, 453 96 Strömstad, Sweden
| | - Maria R Servedio
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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Dunn PO, Sly ND, Freeman-Gallant CR, Henschen AE, Bossu CM, Ruegg KC, Minias P, Whittingham LA. Sexually selected differences in warbler plumage are related to a putative inversion on the Z chromosome. Mol Ecol 2024:e17525. [PMID: 39268700 DOI: 10.1111/mec.17525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 08/16/2024] [Indexed: 09/17/2024]
Abstract
Large structural variants in the genome, such as inversions, may play an important role in producing population structure and local adaptation to the environment through suppression of recombination. However, relatively few studies have linked inversions to phenotypic traits that are sexually selected and may play a role in reproductive isolation. Here, we found that geographic differences in the sexually selected plumage of a warbler, the common yellowthroat (Geothlypis trichas), are largely due to differences in the Z (sex) chromosome (males are ZZ), which contains at least one putative inversion spanning 40% (31/77 Mb) of its length. The inversions on the Z chromosome vary dramatically east and west of the Appalachian Mountains, which provides evidence of cryptic population structure within the range of the most widespread eastern subspecies (G. t. trichas). In an eastern (New York) and western (Wisconsin) population of this subspecies, female prefer different male ornaments; larger black facial masks are preferred in Wisconsin and larger yellow breasts are preferred in New York. The putative inversion also contains genes related to vision, which could influence mating preferences. Thus, structural variants on the Z chromosome are associated with geographic differences in male ornaments and female choice, which may provide a mechanism for maintaining different patterns of sexual selection in spite of gene flow between populations of the same subspecies.
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Affiliation(s)
- Peter O Dunn
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Nicholas D Sly
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | | | - Amberleigh E Henschen
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Christen M Bossu
- Department of Biology, Colorado State University, Ft. Collins, Colorado, USA
| | - Kristen C Ruegg
- Department of Biology, Colorado State University, Ft. Collins, Colorado, USA
| | - Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
| | - Linda A Whittingham
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
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3
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Groh C, Siriwardena GM, McMahon BJ. Diversity in Irish and British avifauna assemblages: What can variation in diversity profiles reveal about the forces that drive assemblage composition and structure? Ecol Evol 2024; 14:e70143. [PMID: 39139914 PMCID: PMC11319734 DOI: 10.1002/ece3.70143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 07/17/2024] [Accepted: 07/22/2024] [Indexed: 08/15/2024] Open
Abstract
Ireland and Britain are two islands located at Europe's westernmost edge, both of which act as the final breeding outposts for many bird species within their European ranges. Despite their similar geographic locations and geological histories, Ireland and Britain host different breeding avifauna assemblages. Diversity profiles, which can serve as more robust alternatives to classic diversity indices, were employed in this study to explore disparities in the two islands' breeding avifauna assemblages. Variations in assemblages were explored, along with their potential drivers, through analyses at three levels: island-scale breeding bird assemblage compositions, island-scale diversity profiles considering 49 common breeding species, and habitat-specific diversity profiles considering assemblages in east/central Irish farmland and East Anglian farmland. Analysis of the two islands' breeding avifauna assemblages revealed that the Irish assemblage is a complete subset of the British assemblage. Analyses of Irish and British assemblages at both an island scale and a habitat scale revealed patterns linking land use to trends within the two islands' avifauna assemblages. Irish assemblages contained greater proportions of insectivorous farmland species by abundance, while British assemblages contained greater proportions of seed-eating farmland species; both trends appeared to be related to structural differences in agricultural land use on the two islands. The British and East Anglian assemblages exhibited higher diversity across all analyses, which appeared to be driven by the assemblages' higher relative abundances of species that were most genetically distinct. This study highlights the ability of diversity profiles to impart more information than classic diversity indices by incorporating species similarity data.
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Affiliation(s)
- Camille Groh
- UCD School of Agriculture and Food ScienceUniversity College DublinDublinIreland
| | | | - Barry J. McMahon
- UCD School of Agriculture and Food ScienceUniversity College DublinDublinIreland
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4
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Gyllenhaal EF, Brady SS, DeCicco LH, Naikatini A, Hime PM, Manthey JD, Kelly J, Moyle RG, Andersen MJ. Waves of Colonization and Gene Flow in a Great Speciator. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.18.603796. [PMID: 39091784 PMCID: PMC11291091 DOI: 10.1101/2024.07.18.603796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Secondary contact between previously allopatric lineages offers a test of reproductive isolating mechanisms that may have accrued in isolation. Such instances of contact can produce stable hybrid zones-where reproductive isolation can further develop via reinforcement or phenotypic displacement-or result in the lineages merging. Ongoing secondary contact is most visible in continental systems, where steady input from parental taxa can occur readily. In oceanic island systems, however, secondary contact between closely related species of birds is relatively rare. When observed on sufficiently small islands, relative to population size, secondary contact likely represents a recent phenomenon. Here, we examine the dynamics of a group of birds whose apparent widespread hybridization influenced Ernst Mayr's foundational work on allopatric speciation: the whistlers of Fiji (Aves: Pachycephala). We demonstrate two clear instances of secondary contact within the Fijian archipelago, one resulting in a hybrid zone on a larger island, and the other resulting in a wholly admixed population on a smaller, adjacent island. We leveraged low genome-wide divergence in the hybrid zone to pinpoint a single genomic region associated with observed phenotypic differences. We use genomic data to present a new hypothesis that emphasizes rapid plumage evolution and post-divergence gene flow.
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Affiliation(s)
- Ethan F. Gyllenhaal
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Serina S. Brady
- Carnegie Museum of Natural History, Pittsburgh, Pennsylvania, USA
| | - Lucas H. DeCicco
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, USA
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | | | - Paul M. Hime
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, USA
- Present Address: McDonnell Genome Institute and Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Joseph D. Manthey
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - John Kelly
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - Robert G. Moyle
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, USA
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - Michael J. Andersen
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA
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5
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Blom MP, Peona V, Prost S, Christidis L, Benz BW, Jønsson KA, Suh A, Irestedt M. Hybridization in birds-of-paradise: Widespread ancestral gene flow despite strong sexual selection in a lek-mating system. iScience 2024; 27:110300. [PMID: 39055907 PMCID: PMC11269930 DOI: 10.1016/j.isci.2024.110300] [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: 02/16/2024] [Revised: 05/08/2024] [Accepted: 06/14/2024] [Indexed: 07/28/2024] Open
Abstract
Sexual selection can directly contribute to reproductive isolation and is an important mechanism that can lead to speciation. Lek-mating is one of the most extreme forms of sexual selection, but surprisingly does not seem to preclude occasional hybridization in nature. However, hybridization among lekking species may still be trivial if selection against offspring with intermediate phenotypes prohibits introgression. Here we investigate this further by sequencing the genomes of nearly all bird-of-paradise (Paradisaeidae) species and 10 museum specimens of putative hybrid origin. We find that intergeneric hybridization indeed still takes place despite extreme differentiation in form, plumage, and behavior. In parallel, the genomes of contemporary species contain widespread signatures of past introgression, demonstrating that hybridization has repeatedly resulted in shared genetic variation despite strong sexual isolation. Our study raises important questions about extrinsic factors that modulate hybridization probability and the evolutionary consequences of introgressive hybridization between lekking species.
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Affiliation(s)
- Mozes P.K. Blom
- Department for Evolutionary Diversity Dynamics, Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Research, 10115 Berlin, Germany
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 114 18 Stockholm, Sweden
| | - Valentina Peona
- Department of Organismal Biology – Systematic Biology, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, 752 36 Uppsala, Sweden
| | - Stefan Prost
- Ecology and Genetics Research Unit, University of Oulu, 90014 Oulu, Finland
| | - Les Christidis
- Faculty of Science and Engineering, Southern Cross University, Coffs Harbour, NSW 2450, Australia
| | - Brett W. Benz
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48108, USA
| | - Knud A. Jønsson
- Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 114 18 Stockholm, Sweden
| | - Alexander Suh
- Department of Organismal Biology – Systematic Biology, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, 752 36 Uppsala, Sweden
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 114 18 Stockholm, Sweden
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6
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Mackintosh C, Scott MF, Reuter M, Pomiankowski A. Locally adaptive inversions in structured populations. Genetics 2024; 227:iyae073. [PMID: 38709495 DOI: 10.1093/genetics/iyae073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 04/05/2024] [Accepted: 04/16/2024] [Indexed: 05/07/2024] Open
Abstract
Inversions have been proposed to facilitate local adaptation, by linking together locally coadapted alleles at different loci. Prior work addressing this question theoretically has considered the spread of inversions in "continent-island" scenarios in which there is a unidirectional flow of maladapted migrants into the island population. In this setting, inversions capturing locally adaptive haplotypes are most likely to invade when selection is weak, because stronger local selection (i) more effectively purges maladaptive alleles and (ii) generates linkage disequilibrium between adaptive alleles, thus lessening the advantage of inversions. We show this finding only holds under limited conditions by studying the establishment of inversions in a more general two-deme model, which explicitly considers the dynamics of allele frequencies in both populations linked by bidirectional migration. In this model, the level of symmetry between demes can be varied from complete asymmetry (continent-island) to complete symmetry. For symmetric selection and migration, strong selection increases the allele frequency divergence between demes thereby increasing the frequency of maladaptive alleles in migrants, favoring inversions-the opposite of the pattern seen in the asymmetric continent-island scenario. We also account for the likelihood that a new inversion captures an adaptive haplotype in the first instance. When considering the combined process of capture and invasion in "continent island" and symmetric scenarios, relatively strong selection increases inversion establishment probability. Migration must also be low enough that the inversion is likely to capture an adaptive allele combination, but not so low as to eliminate the inversion's advantage. Overall, our analysis suggests that inversions are likely to harbor larger effect alleles that experience relatively strong selection.
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Affiliation(s)
- Carl Mackintosh
- Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK
- CoMPLEX, University College London, Gower Street, London WC1E 6BT, UK
- CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff 29680, France
- Sorbonne Universités, UPMC Université Paris VI, Roscoff 29680, France
| | - Michael F Scott
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Max Reuter
- Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Andrew Pomiankowski
- Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK
- CoMPLEX, University College London, Gower Street, London WC1E 6BT, UK
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7
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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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8
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Cornman RS. A genomic hotspot of diversifying selection and structural change in the hoary bat ( Lasiurus cinereus). PeerJ 2024; 12:e17482. [PMID: 38832043 PMCID: PMC11146322 DOI: 10.7717/peerj.17482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 05/07/2024] [Indexed: 06/05/2024] Open
Abstract
Background Previous work found that numerous genes positively selected within the hoary bat (Lasiurus cinereus) lineage are physically clustered in regions of conserved synteny. Here I further validate and expand on those finding utilizing an updated L. cinereus genome assembly and additional bat species as well as other tetrapod outgroups. Methods A chromosome-level assembly was generated by chromatin-contact mapping and made available by DNAZoo (www.dnazoo.org). The genomic organization of orthologous genes was extracted from annotation data for multiple additional bat species as well as other tetrapod clades for which chromosome-level assemblies were available from the National Center for Biotechnology Information (NCBI). Tests of branch-specific positive selection were performed for L. cinereus using PAML as well as with the HyPhy package for comparison. Results Twelve genes exhibiting significant diversifying selection in the L. cinereus lineage were clustered within a 12-Mb genomic window; one of these (Trpc4) also exhibited diversifying selection in bats generally. Ten of the 12 genes are landmarks of two distinct blocks of ancient synteny that are not linked in other tetrapod clades. Bats are further distinguished by frequent structural rearrangements within these synteny blocks, which are rarely observed in other Tetrapoda. Patterns of gene order and orientation among bat taxa are incompatible with phylogeny as presently understood, implying parallel evolution or subsequent reversals. Inferences of positive selection were found to be robust to alternative phylogenetic topologies as well as a strong shift in background nucleotide composition in some taxa. Discussion This study confirms and further localizes a genomic hotspot of protein-coding divergence in the hoary bat, one that also exhibits an increased tempo of structural change in bats compared with other mammals. Most genes in the two synteny blocks have elevated expression in brain tissue in humans and model organisms, and genetic studies implicate the selected genes in cranial and neurological development, among other functions.
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Affiliation(s)
- Robert S. Cornman
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, United States
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9
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Müller IA, Thörn F, Rajan S, Ericson PGP, Dumbacher JP, Maiah G, Blom MPK, Jønsson KA, Irestedt M. Species-specific dynamics may cause deviations from general biogeographical predictions - evidence from a population genomics study of a New Guinean endemic passerine bird family (Melampittidae). PLoS One 2024; 19:e0293715. [PMID: 38781204 PMCID: PMC11115331 DOI: 10.1371/journal.pone.0293715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 03/26/2024] [Indexed: 05/25/2024] Open
Abstract
The family Melampittidae is endemic to New Guinea and consists of two monotypic genera: Melampitta lugubris (Lesser Melampitta) and Megalampitta gigantea (Greater Melampitta). Both Melampitta species have scattered and disconnected distributions across New Guinea in the central mountain range and in some of the outlying ranges. While M. lugubris is common and found in most montane regions of the island, M. gigantaea is elusive and known from only six localities in isolated pockets on New Guinea with very specific habitats of limestone and sinkholes. In this project, we apply museomics to determine the population structure and demographic history of these two species. We re-sequenced the genomes of all seven known M. gigantaea samples housed in museum collections as well as 24 M. lugubris samples from across its distribution. By comparing population structure between the two species, we investigate to what extent habitat dependence, such as in M. gigantaea, may affect population connectivity. Phylogenetic and population genomic analyses, as well as acoustic variation revealed that M. gigantaea consists of a single population in contrast to M. lugubris that shows much stronger population structure across the island. We suggest a recent collapse of M. gigantaea into its fragmented habitats as an explanation to its unexpected low diversity and lack of population structure. The deep genetic divergences between the M. lugubris populations on the Vogelkop region, in the western central range and the eastern central range, respectively, suggests that these three populations should be elevated to full species level. This work sheds new light on the mechanisms that have shaped the intriguing distribution of the two species within this family and is a prime example of the importance of museum collections for genomic studies of poorly known and rare species.
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Affiliation(s)
- Ingo A. Müller
- Department of Zoology, Division of Systematics and Evolution, Stockholm University, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Leibniz Institut für Evolutions- und Biodiversitätsforschung, Museum für Naturkunde, Berlin, Germany
| | - Filip Thörn
- Department of Zoology, Division of Systematics and Evolution, Stockholm University, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Leibniz Institut für Evolutions- und Biodiversitätsforschung, Museum für Naturkunde, Berlin, Germany
| | - Samyuktha Rajan
- Department of Zoology, Division of Ethology, Stockholm University, Stockholm, Sweden
| | - Per G. P. Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - John P. Dumbacher
- Department of Ornithology and Mammalogy, California Academy of Sciences, San Francisco, CA, United States of America
| | - Gibson Maiah
- New Guinea Binatang Research Center, Madang, Papua New Guinea
| | - Mozes P. K. Blom
- Leibniz Institut für Evolutions- und Biodiversitätsforschung, Museum für Naturkunde, Berlin, Germany
| | - Knud A. Jønsson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
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10
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Burban E, Tenaillon MI, Glémin S. RIDGE, a tool tailored to detect gene flow barriers across species pairs. Mol Ecol Resour 2024; 24:e13944. [PMID: 38419376 DOI: 10.1111/1755-0998.13944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/19/2024] [Accepted: 02/05/2024] [Indexed: 03/02/2024]
Abstract
Characterizing the processes underlying reproductive isolation between diverging lineages is central to understanding speciation. Here, we present RIDGE-Reproductive Isolation Detection using Genomic polymorphisms-a tool tailored for quantifying gene flow barrier proportion and identifying the relevant genomic regions. RIDGE relies on an Approximate Bayesian Computation with a model-averaging approach to accommodate diverse scenarios of lineage divergence. It captures heterogeneity in effective migration rate along the genome while accounting for variation in linked selection and recombination. The barrier detection test relies on numerous summary statistics to compute a Bayes factor, offering a robust statistical framework that facilitates cross-species comparisons. Simulations revealed RIDGE's efficiency in capturing signals of ongoing migration. Model averaging proved particularly valuable in scenarios of high model uncertainty where no migration or migration homogeneity can be wrongly assumed, typically for recent divergence times <0.1 2Ne generations. Applying RIDGE to four published crow data sets, we first validated our tool by identifying a well-known large genomic region associated with mate choice patterns. Second, while we identified a significant overlap of outlier loci using RIDGE and traditional genomic scans, our results suggest that a substantial portion of previously identified outliers are likely false positives. Outlier detection relies on allele differentiation, relative measures of divergence and the count of shared polymorphisms and fixed differences. Our analyses also highlight the value of incorporating multiple summary statistics including our newly developed outlier ones that can be useful in challenging detection conditions.
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Affiliation(s)
- Ewen Burban
- University of Rennes, CNRS, ECOBIO-UMR 6553, Rennes, France
| | - Maud I Tenaillon
- University Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette, France
| | - Sylvain Glémin
- University of Rennes, CNRS, ECOBIO-UMR 6553, Rennes, France
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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11
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Sebastianelli M, Lukhele SM, Secomandi S, de Souza SG, Haase B, Moysi M, Nikiforou C, Hutfluss A, Mountcastle J, Balacco J, Pelan S, Chow W, Fedrigo O, Downs CT, Monadjem A, Dingemanse NJ, Jarvis ED, Brelsford A, vonHoldt BM, Kirschel ANG. A genomic basis of vocal rhythm in birds. Nat Commun 2024; 15:3095. [PMID: 38653976 DOI: 10.1038/s41467-024-47305-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 03/22/2024] [Indexed: 04/25/2024] Open
Abstract
Vocal rhythm plays a fundamental role in sexual selection and species recognition in birds, but little is known of its genetic basis due to the confounding effect of vocal learning in model systems. Uncovering its genetic basis could facilitate identifying genes potentially important in speciation. Here we investigate the genomic underpinnings of rhythm in vocal non-learning Pogoniulus tinkerbirds using 135 individual whole genomes distributed across a southern African hybrid zone. We find rhythm speed is associated with two genes that are also known to affect human speech, Neurexin-1 and Coenzyme Q8A. Models leveraging ancestry reveal these candidate loci also impact rhythmic stability, a trait linked with motor performance which is an indicator of quality. Character displacement in rhythmic stability suggests possible reinforcement against hybridization, supported by evidence of asymmetric assortative mating in the species producing faster, more stable rhythms. Because rhythm is omnipresent in animal communication, candidate genes identified here may shape vocal rhythm across birds and other vertebrates.
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Affiliation(s)
- Matteo Sebastianelli
- Department of Biological Sciences, University of Cyprus, PO Box 20537, Nicosia, 1678, Cyprus.
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 751 23, Uppsala, Sweden.
| | - Sifiso M Lukhele
- Department of Biological Sciences, University of Cyprus, PO Box 20537, Nicosia, 1678, Cyprus
| | - Simona Secomandi
- Department of Biological Sciences, University of Cyprus, PO Box 20537, Nicosia, 1678, Cyprus
| | - Stacey G de Souza
- Department of Biological Sciences, University of Cyprus, PO Box 20537, Nicosia, 1678, Cyprus
| | - Bettina Haase
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
| | - Michaella Moysi
- Department of Biological Sciences, University of Cyprus, PO Box 20537, Nicosia, 1678, Cyprus
| | - Christos Nikiforou
- Department of Biological Sciences, University of Cyprus, PO Box 20537, Nicosia, 1678, Cyprus
| | - Alexander Hutfluss
- Behavioural Ecology, Faculty of Biology, LMU Munich (LMU), 82152, Planegg-Martinsried, Germany
| | | | - Jennifer Balacco
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
| | | | | | - Olivier Fedrigo
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
| | - Colleen T Downs
- Centre for Functional Biodiversity, School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, 3209, South Africa
| | - Ara Monadjem
- Department of Biological Sciences, University of Eswatini, Kwaluseni, Eswatini
- Mammal Research Institute, Department of Zoology & Entomology, University of Pretoria, Private Bag 20, Hatfield, 0028, Pretoria, South Africa
| | - Niels J Dingemanse
- Behavioural Ecology, Faculty of Biology, LMU Munich (LMU), 82152, Planegg-Martinsried, Germany
| | - Erich D Jarvis
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Alan Brelsford
- Department of Evolution, Ecology and Organismal Biology, University of California Riverside, Riverside, CA, 92521, USA
| | - Bridgett M vonHoldt
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Alexander N G Kirschel
- Department of Biological Sciences, University of Cyprus, PO Box 20537, Nicosia, 1678, Cyprus.
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12
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Maier PA, Vandergast AG, Bohonak AJ. Yosemite toad (Anaxyrus canorus) transcriptome reveals interplay between speciation genes and adaptive introgression. Mol Ecol 2024; 33:e17317. [PMID: 38488670 DOI: 10.1111/mec.17317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 02/15/2024] [Accepted: 02/23/2024] [Indexed: 04/09/2024]
Abstract
Genomes are heterogeneous during the early stages of speciation, with small 'islands' of DNA appearing to reflect strong adaptive differences, surrounded by vast seas of relative homogeneity. As species diverge, secondary contact zones between them can act as an interface and selectively filter through advantageous alleles of hybrid origin. Such introgression is another important adaptive process, one that allows beneficial mosaics of recombinant DNA ('rivers') to flow from one species into another. Although genomic islands of divergence appear to be associated with reproductive isolation, and genomic rivers form by adaptive introgression, it is unknown whether islands and rivers tend to be the same or different loci. We examined three replicate secondary contact zones for the Yosemite toad (Anaxyrus canorus) using two genomic data sets and a morphometric data set to answer the questions: (1) How predictably different are islands and rivers, both in terms of genomic location and gene function? (2) Are the adaptive genetic trait loci underlying tadpole growth and development reliably islands, rivers or neither? We found that island and river loci have significant overlap within a contact zone, suggesting that some loci are first islands, and later are predictably converted into rivers. However, gene ontology enrichment analysis showed strong overlap in gene function unique to all island loci, suggesting predictability in overall gene pathways for islands. Genome-wide association study outliers for tadpole development included LPIN3, a lipid metabolism gene potentially involved in climate change adaptation, that is island-like for all three contact zones, but also appears to be introgressing (as a river) across one zone. Taken together, our results suggest that adaptive divergence and introgression may be more complementary forces than currently appreciated.
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Affiliation(s)
- Paul A Maier
- Department of Biology, San Diego State University, San Diego, California, USA
- Family TreeDNA, Gene by Gene, Houston, Texas, USA
| | - Amy G Vandergast
- Western Ecological Research Center, San Diego Field Station, U.S. Geological Survey, San Diego, California, USA
| | - Andrew J Bohonak
- Department of Biology, San Diego State University, San Diego, California, USA
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13
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Wang L, Xue Z, Tian Y, Zeng W, Zhang T, Lu H. A single-cell transcriptome atlas of Lueyang black-bone chicken skin. Poult Sci 2024; 103:103513. [PMID: 38350389 PMCID: PMC10875617 DOI: 10.1016/j.psj.2024.103513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/15/2024] Open
Abstract
As the largest organ of the body, the skin participates in various physiological activities, such as barrier function, sensory function, and temperature regulation, thereby maintaining the balance between the body and the natural environment. To date, compositional and transcriptional profiles in chicken skin cells have not been reported. Here, we report detailed transcriptome analyses of cell populations present in the skin of a black-feather chicken and a white-feather chicken using single-cell RNA sequencing (scRNA-seq). By analyzing cluster-specific gene expression profiles, we identified 12 cell clusters, and their corresponding cell types were also characterized. Subsequently, we characterized the subpopulations of keratinocytes, myocytes, mesenchymal cells, fibroblasts, and melanocytes. It is worth noting that we have identified a subpopulation of keratinocytes involved in pigment granule capture and a subpopulation of melanocytes involved in pigment granule deposition, both of which have a higher cell abundance in black-feather chicken compared to white-feather chicken. Meanwhile, we also compared the cellular heterogeneity features of Lueyang black-bone chicken skin with different feather colors. In addition, we also screened out 12 genes those could be potential markers of melanocytes. Finally, we validated the specific expression of SGK1, WNT5A, CTSC, TYR, and LAPTM5 in black-feather chicken, which may be the key candidate genes determining the feather color differentiation of Lueyang black-bone chicken. In summary, this study first revealed the transcriptome characteristics of chicken skin cells via scRNA-seq technology. These datasets provide valuable information for the study of avian skin characteristics and have important implications for future poultry breeding.
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Affiliation(s)
- Ling Wang
- School of Biological Science and Engineering, Shaanxi University of Technology, 723001 Hanzhong, China
- Qinba State Key Laboratory of Biological Resources and Ecological Environment, 723001 Hanzhong, China
- Engineering Research Center of Quality Improvement and Safety Control of Qinba Special Meat Products, Universities of Shaanxi Province, 723001 Hanzhong, China
- QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C., Shaanxi University of Technology, 723001 Hanzhong, China
| | - Zhen Xue
- School of Biological Science and Engineering, Shaanxi University of Technology, 723001 Hanzhong, China
| | - Yingmin Tian
- School of Mathematics and Computer Science, Shaanxi University of Technology, 723001 Hanzhong, China
| | - Wenxian Zeng
- School of Biological Science and Engineering, Shaanxi University of Technology, 723001 Hanzhong, China
- Qinba State Key Laboratory of Biological Resources and Ecological Environment, 723001 Hanzhong, China
- Engineering Research Center of Quality Improvement and Safety Control of Qinba Special Meat Products, Universities of Shaanxi Province, 723001 Hanzhong, China
| | - Tao Zhang
- School of Biological Science and Engineering, Shaanxi University of Technology, 723001 Hanzhong, China
- Qinba State Key Laboratory of Biological Resources and Ecological Environment, 723001 Hanzhong, China
- Engineering Research Center of Quality Improvement and Safety Control of Qinba Special Meat Products, Universities of Shaanxi Province, 723001 Hanzhong, China
- QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C., Shaanxi University of Technology, 723001 Hanzhong, China
| | - Hongzhao Lu
- School of Biological Science and Engineering, Shaanxi University of Technology, 723001 Hanzhong, China
- Qinba State Key Laboratory of Biological Resources and Ecological Environment, 723001 Hanzhong, China
- Engineering Research Center of Quality Improvement and Safety Control of Qinba Special Meat Products, Universities of Shaanxi Province, 723001 Hanzhong, China
- QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C., Shaanxi University of Technology, 723001 Hanzhong, China
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14
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Nosil P, Gompert Z, Funk DJ. Divergent dynamics of sexual and habitat isolation at the transition between stick insect populations and species. Nat Commun 2024; 15:2273. [PMID: 38480699 PMCID: PMC10937975 DOI: 10.1038/s41467-024-46294-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 02/22/2024] [Indexed: 03/17/2024] Open
Abstract
Speciation is often viewed as a continuum along which populations diverge until they become reproductively-isolated species. However, such divergence may be heterogeneous, proceeding in fits and bursts, rather than being uniform and gradual. We show in Timema stick insects that one component of reproductive isolation evolves non-uniformly across this continuum, whereas another does not. Specifically, we use thousands of host-preference and mating trials to study habitat and sexual isolation among 42 pairs of taxa spanning a range of genomic differentiation and divergence time. We find that habitat isolation is uncoupled from genomic differentiation within species, but accumulates linearly with it between species. In contrast, sexual isolation accumulates linearly across the speciation continuum, and thus exhibits similar dynamics to morphological traits not implicated in reproductive isolation. The results show different evolutionary dynamics for different components of reproductive isolation and highlight a special relevance for species status in the process of speciation.
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Affiliation(s)
- Patrik Nosil
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | | | - Daniel J Funk
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
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15
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Merrill RM, Arenas-Castro H, Feller AF, Harenčár J, Rossi M, Streisfeld MA, Kay KM. Genetics and the Evolution of Prezygotic Isolation. Cold Spring Harb Perspect Biol 2024; 16:a041439. [PMID: 37848246 PMCID: PMC10835618 DOI: 10.1101/cshperspect.a041439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Abstract
The significance of prezygotic isolation for speciation has been recognized at least since the Modern Synthesis. However, fundamental questions remain. For example, how are genetic associations between traits that contribute to prezygotic isolation maintained? What is the source of genetic variation underlying the evolution of these traits? And how do prezygotic barriers affect patterns of gene flow? We address these questions by reviewing genetic features shared across plants and animals that influence prezygotic isolation. Emerging technologies increasingly enable the identification and functional characterization of the genes involved, allowing us to test established theoretical expectations. Embedding these genes in their developmental context will allow further predictions about what constrains the evolution of prezygotic isolation. Ongoing improvements in statistical and computational tools will reveal how pre- and postzygotic isolation may differ in how they influence gene flow across the genome. Finally, we highlight opportunities for progress by combining theory with appropriate data.
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Affiliation(s)
- Richard M Merrill
- Faculty of Biology, Division of Evolutionary Biology, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - Henry Arenas-Castro
- School of Biological Sciences, University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Anna F Feller
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
- Arnold Arboretum of Harvard University, Boston, Massachusetts 02131, USA
| | - Julia Harenčár
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, California 95060, USA
| | - Matteo Rossi
- Faculty of Biology, Division of Evolutionary Biology, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - Matthew A Streisfeld
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403-5289, USA
| | - Kathleen M Kay
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, California 95060, USA
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16
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Zhou W, Zhang N, Huang K, Lin H, Tu J, Zheng C, Que P, Chiang CY, Martinez J, Naerhulan H, Székely T, Zhang Z, Liu Y. Divergent Selection in Low Recombination Regions Shapes the Genomic Islands in Two Incipient Shorebird Species. Mol Biol Evol 2024; 41:msae006. [PMID: 38225175 PMCID: PMC10835341 DOI: 10.1093/molbev/msae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 01/02/2024] [Accepted: 01/08/2024] [Indexed: 01/17/2024] Open
Abstract
Speciation in the face of gene flow is usually associated with a heterogeneous genomic landscape of divergence in nascent species pairs. However, multiple factors, such as divergent selection and local recombination rate variation, can influence the formation of these genomic islands. Examination of the genomic landscapes of species pairs that are still in the early stages of speciation provides an insight into this conundrum. In this study, population genomic analyses were undertaken using a wide range of sampling and whole-genome resequencing data from 96 unrelated individuals of Kentish plover (Charadrius alexandrinus) and white-faced plover (Charadrius dealbatus). We suggest that the two species exhibit varying levels of population admixture along the Chinese coast and on the Taiwan Island. Genome-wide analyses for introgression indicate that ancient introgression had occurred in Taiwan population, and gene flow is still ongoing in mainland coastal populations. Furthermore, we identified a few genomic regions with significant levels of interspecific differentiation and local recombination suppression, which contain several genes potentially associated with disease resistance, coloration, and regulation of plumage molting and thus may be relevant to the phenotypic and ecological divergence of the two nascent species. Overall, our findings suggest that divergent selection in low recombination regions may be a main force in shaping the genomic islands in two incipient shorebird species.
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Affiliation(s)
- Wenjun Zhou
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Nan Zhang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
| | - Kaichi Huang
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, Bc, Canada
| | - Hongzhou Lin
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
| | - Jie Tu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
| | - Chenqing Zheng
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
| | - Pinjia Que
- Ministry of Education Key Laboratory for Biodiversity Sciences and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan Academy of Giant Panda, Chengdu, China
| | - Chung-Yu Chiang
- Department of Environmental Science, Tunghai University, Taichung, Taiwan, China
| | | | - Halimubieke Naerhulan
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Tamás Székely
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
- Ministry of Education Key Laboratory for Biodiversity Sciences and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Zhengwang Zhang
- Ministry of Education Key Laboratory for Biodiversity Sciences and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yang Liu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
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17
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Cumer T, Machado AP, San-Jose LM, Ducrest AL, Simon C, Roulin A, Goudet J. The genomic architecture of continuous plumage colour variation in the European barn owl ( Tyto alba). Proc Biol Sci 2024; 291:20231995. [PMID: 38196365 PMCID: PMC10777144 DOI: 10.1098/rspb.2023.1995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/30/2023] [Indexed: 01/11/2024] Open
Abstract
The maintenance of colour variation in wild populations has long fascinated evolutionary biologists, although most studies have focused on discrete traits exhibiting rather simple inheritance patterns and genetic architectures. However, the study of continuous colour traits and their potentially oligo- or polygenic genetic bases remains rare in wild populations. We studied the genetics of the continuously varying white-to-rufous plumage coloration of the European barn owl (Tyto alba) using a genome-wide association approach on the whole-genome data of 75 individuals. We confirmed a mutation at the melanocortin-1-receptor gene (MC1R) is involved in the coloration and identified two new regions, located in super-scaffolds 9 and 42. The combination of the three regions explains most of the colour variation (80.37%, 95% credible interval 58.45-100%). One discovered region, located in the sex chromosome, differs between the most extreme colorations in owls sharing a specific MC1R genotype. This region may play a role in the colour sex dimorphism of this species, possibly in interaction with the autosomal MC1R. We thus provide insights into the genetic architecture of continuous colour variation, pointing to an oligogenic basis with potential epistatic effects among loci that should aid future studies understanding how continuous colour variation is maintained in nature.
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Affiliation(s)
- Tristan Cumer
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, Lausanne CH-1015, Switzerland
| | - Ana Paula Machado
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, Lausanne CH-1015, Switzerland
| | - Luis M. San-Jose
- Laboratoire Évolution and Diversité Biologique, UMR 5174, CNRS, Université Toulouse III Paul Sabatier, Toulouse, France
| | - Anne-Lyse Ducrest
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, Lausanne CH-1015, Switzerland
| | - Céline Simon
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, Lausanne CH-1015, Switzerland
| | - Alexandre Roulin
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, Lausanne CH-1015, Switzerland
| | - Jérôme Goudet
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, Lausanne CH-1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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18
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Mirchandani CD, Shultz AJ, Thomas GWC, Smith SJ, Baylis M, Arnold B, Corbett-Detig R, Enbody E, Sackton TB. A Fast, Reproducible, High-throughput Variant Calling Workflow for Population Genomics. Mol Biol Evol 2024; 41:msad270. [PMID: 38069903 PMCID: PMC10764099 DOI: 10.1093/molbev/msad270] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/27/2023] [Accepted: 11/22/2023] [Indexed: 01/05/2024] Open
Abstract
The increasing availability of genomic resequencing data sets and high-quality reference genomes across the tree of life present exciting opportunities for comparative population genomic studies. However, substantial challenges prevent the simple reuse of data across different studies and species, arising from variability in variant calling pipelines, data quality, and the need for computationally intensive reanalysis. Here, we present snpArcher, a flexible and highly efficient workflow designed for the analysis of genomic resequencing data in nonmodel organisms. snpArcher provides a standardized variant calling pipeline and includes modules for variant quality control, data visualization, variant filtering, and other downstream analyses. Implemented in Snakemake, snpArcher is user-friendly, reproducible, and designed to be compatible with high-performance computing clusters and cloud environments. To demonstrate the flexibility of this pipeline, we applied snpArcher to 26 public resequencing data sets from nonmammalian vertebrates. These variant data sets are hosted publicly to enable future comparative population genomic analyses. With its extensibility and the availability of public data sets, snpArcher will contribute to a broader understanding of genetic variation across species by facilitating the rapid use and reuse of large genomic data sets.
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Affiliation(s)
- Cade D Mirchandani
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Allison J Shultz
- Ornithology Department, Natural History Museum of Los Angeles County, Los Angeles, CA 90007, USA
| | | | - Sara J Smith
- Informatics Group, Harvard University, Cambridge, MA, USA
- Biology, Mount Royal University, Calgary, AB T3E 6K6, Canada
| | - Mara Baylis
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Brian Arnold
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Center for Statistics and Machine Learning, Princeton University, Princeton, NJ, USA
| | - Russ Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Erik Enbody
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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19
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Trapote E, Moreno-González V, Canestrari D, Rutz C, Baglione V. Fitness benefits of alternated chick provisioning in cooperatively breeding carrion crows. J Anim Ecol 2024; 93:95-108. [PMID: 38078562 DOI: 10.1111/1365-2656.14033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 10/23/2023] [Indexed: 01/11/2024]
Abstract
In most bird species, parents raise offspring cooperatively. In some cases, this cooperation extends to helpers-at-the-nest who assist the breeders with a range of tasks. While cooperative food provisioning might merely arise incidentally, as a result of the efforts of carers that act independently from each other, recent studies suggest that birds may coordinate by taking turns in visiting the nest. However, evidence that such coordination emerges because individuals actively respond to each other's behaviour is controversial, and the potential benefits of carers' alternation remain unknown. We addressed this knowledge gap by analysing a multiyear dataset for cooperatively breeding carrion crows Corvus corone, comprising 8693 nest visits across 50 groups. Our results reveal that turn-taking does occur in this species and that all group members, regardless of their sex and social role (breeder/helper), tend to alternate at the nest with other carers rather than to make repeat visits. Importantly, we found that the body mass of nestlings increased significantly with the degree of carers' alternation, possibly because well-coordinated groups provided food at more regular intervals. Using earlier monitoring data, the observed increase in body mass is predicted to substantially boost postfledging survival rates. Our analyses demonstrate that alternation in nestling provisioning has measurable fitness benefits in this study system. This raises the possibility that cooperatively breeding carrion crows, as well as other bird species with similarly coordinated brood provisioning, exhibit specialized behavioural strategies that enable effective alternation.
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Affiliation(s)
- Eva Trapote
- Departamento de Biodiversidad y Gestión Ambiental, Universidad de León, León, Spain
| | | | - Daniela Canestrari
- Departamento de Biodiversidad y Gestión Ambiental, Universidad de León, León, Spain
| | - Christian Rutz
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, UK
| | - Vittorio Baglione
- Departamento de Biodiversidad y Gestión Ambiental, Universidad de León, León, Spain
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20
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Recuerda M, Palacios M, Frías O, Hobson K, Nabholz B, Blanco G, Milá B. Adaptive phenotypic and genomic divergence in the common chaffinch (Fringilla coelebs) following niche expansion within a small oceanic island. J Evol Biol 2023; 36:1226-1241. [PMID: 37485603 DOI: 10.1111/jeb.14200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 06/06/2023] [Accepted: 06/09/2023] [Indexed: 07/25/2023]
Abstract
According to models of ecological speciation, adaptation to adjacent, contrasting habitat types can lead to population divergence given strong enough environment-driven selection to counteract the homogenizing effect of gene flow. We tested this hypothesis in the common chaffinch (Fringilla coelebs) on the small island of La Palma, Canary Islands, where it occupies two markedly different habitats. Isotopic (δ13 C, δ15 N) analysis of feathers indicated that birds in the two habitats differed in ecosystem and/or diet, and analysis of phenotypic traits revealed significant differences in morphology and plumage colouration that are consistent with ecomorphological and ecogeographical predictions respectively. A genome-wide survey of single-nucleotide polymorphism revealed marked neutral structure that was consistent with geography and isolation by distance, suggesting low dispersal. In contrast, loci putatively under selection identified through genome-wide association and genotype-environment association analyses, revealed amarked adaptive divergence between birds in both habitats. Loci associated with phenotypic and environmental differences among habitats were distributed across the genome, as expected for polygenic traits involved in local adaptation. Our results suggest a strong role for habitat-driven local adaptation in population divergence in the chaffinches of La Palma, a process that appears to be facilitated by a strong reduction in effective dispersal distances despite the birds' high dispersal capacity.
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Affiliation(s)
- María Recuerda
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Mercè Palacios
- Department of Biodiversity, Ecology and Evolution, Universidad Complutense de Madrid, Madrid, Spain
| | - Oscar Frías
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Keith Hobson
- Biology Department, Western University, London, Ontario, Canada
| | - Benoit Nabholz
- Institut des Sciences de l'Évolution de Montpellier (ISEM), CNRS, EPHE, IRD, Université de Montpellier, Montpellier, France
- Institut Universitaire de France (IUF), Paris, France
| | - Guillermo Blanco
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Borja Milá
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
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21
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Wang XF, Zhang YX, Niu YQ, Sha Y, Wang ZH, Zhang ZB, Yang J, Liu B, Li LF. Post-hybridization introgression and natural selection promoted genomic divergence of Aegilops speltoides and the four S*-genome diploid species. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1500-1513. [PMID: 37313760 DOI: 10.1111/tpj.16334] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 06/15/2023]
Abstract
Understanding how different driving forces have promoted biological divergence and speciation is one of the central issues in evolutionary biology. The Triticum/Aegilops species complex contains 13 diploid species belonging to the A-, B- and D-lineages and offers an ideal system to address the evolutionary dynamics of lineage fusion and splitting. Here, we sequenced the whole genomes of one S-genome species (Aegilops speltoides) of the B-lineage and four S*-genome diploid species (Aegilops bicornis, Aegilops longissima, Aegilops sharonensis and Aegilops searsii) of the D-lineage at the population level. We performed detailed comparisons of the five species and with the other four representative A-, B- and D-lineage species. Our estimates identified frequent genetic introgressions from A- and B-lineages to the D-lineage species. A remarkable observation is the contrasting distributions of putative introgressed loci by the A- and B-lineages along all the seven chromosomes to the extant D-lineage species. These genetic introgressions resulted in high levels of genetic divergence at centromeric regions between Ae. speltoides (B-lineage) and the other four S*-genome diploid species (D-lineage), while natural selection is a potential contributor to divergence among the four S*-genome species at telomeric regions. Our study provides a genome-wide view on how genetic introgression and natural selection acted together yet chromosome-regionally divided to promote genomic divergence among the five S- and S*-genome diploid species, which provides new and nuanced insights into the evolutionary history of the Triticum/Aegilops species complex.
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Affiliation(s)
- Xin-Feng Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yu-Xin Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yu-Qian Niu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yan Sha
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zhen-Hui Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun, 130118, China
| | - Zhi-Bin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ji Yang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Lin-Feng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
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22
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Catalán A, Merondun J, Knief U, Wolf JBW. Chromatin accessibility, not 5mC methylation covaries with partial dosage compensation in crows. PLoS Genet 2023; 19:e1010901. [PMID: 37747941 PMCID: PMC10575545 DOI: 10.1371/journal.pgen.1010901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 10/13/2023] [Accepted: 08/07/2023] [Indexed: 09/27/2023] Open
Abstract
The evolution of genetic sex determination is often accompanied by degradation of the sex-limited chromosome. Male heterogametic systems have evolved convergent, epigenetic mechanisms restoring the resulting imbalance in gene dosage between diploid autosomes (AA) and the hemizygous sex chromosome (X). Female heterogametic systems (AAf Zf, AAm ZZm) tend to only show partial dosage compensation (0.5 < Zf:AAf < 1) and dosage balance (0.5
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Affiliation(s)
- Ana Catalán
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
- Division of Evolutionary Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Justin Merondun
- Division of Evolutionary Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Ulrich Knief
- Division of Evolutionary Biology, LMU Munich, Planegg-Martinsried, Germany
- Evolutionary Biology & Ecology,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Jochen B. W. Wolf
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
- Division of Evolutionary Biology, LMU Munich, Planegg-Martinsried, Germany
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23
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Crawford NG, McGreevy TJ, Mullen SP, Schneider CJ. The genetic basis of conspicuous coloration in the Guadeloupean anole: Evolution by sexual and ecological selection. Ecol Evol 2023; 13:e10266. [PMID: 37435022 PMCID: PMC10330958 DOI: 10.1002/ece3.10266] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 07/13/2023] Open
Abstract
Understanding how natural selection acts on the genome and contributes to the process of speciation is a primary aim of the study of evolution. Here we used natural variation in two subspecies of the Guadeloupean anole (Anolis marmoratus ssp.), from the island of Guadeloupe in the Lesser Antilles, to explore the genomic basis of adaptation and speciation in Anolis lizards. These subspecies inhabit distinct ecological environments and display marked differences in adult male color and pattern. We sequenced the complete genomes of 20 anoles, 10 from each subspecies, at 1.4× coverage. We used genome-wide scans of population differentiation, allele frequency spectrum, and linkage disequilibrium to characterize the genomic architecture within and between the subspecies. While most of the genome was undifferentiated, we observed five large divergent regions. Within these regions we identified blocks, 5 kb pairs in length, enriched for fixed single nucleotide polymorphisms. These blocks encompass 97 genes, two of which are candidate pigmentation genes. One is melanophilin (mlph), which helps transport melanosomes within melanocytes. The other is a cluster of differentiation 36 (cd36), which regulates carotenoid pigment sequestration. We used high-pressure liquid chromatography to confirm that carotenoid pigments are significantly more abundant in the conspicuous orange-pigmented skin of male A. m. marmoratus suggesting that cd36 may be regulating pigment deposition in this tissue. We identified for the first time a carotenoid gene that is a potential target of divergent sexual selection and may be contributing to the early stages of speciation in Anolis lizards.
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Affiliation(s)
| | - Thomas J. McGreevy
- Department of BiologyBoston UniversityBostonMassachusettsUSA
- Department of Natural Resources ScienceUniversity of Rhode IslandKingstonRhode IslandUSA
| | - Sean P. Mullen
- Department of BiologyBoston UniversityBostonMassachusettsUSA
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24
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Wood AW, Szpiech ZA, Lovette IJ, Smith BT, Toews DPL. Genomes of the extinct Bachman's warbler show high divergence and no evidence of admixture with other extant Vermivora warblers. Curr Biol 2023:S0960-9822(23)00690-5. [PMID: 37329885 DOI: 10.1016/j.cub.2023.05.058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 04/25/2023] [Accepted: 05/25/2023] [Indexed: 06/19/2023]
Abstract
Bachman's warbler1 (Vermivora bachmanii)-last sighted in 1988-is one of the only North American passerines to recently go extinct.2,3,4 Given extensive ongoing hybridization of its two extant congeners-the blue-winged warbler (V. cyanoptera) and golden-winged warbler (V. chrysoptera)5,6,7,8-and shared patterns of plumage variation between Bachman's warbler and hybrids between those extant species, it has been suggested that Bachman's warbler might have also had a component of hybrid ancestry. Here, we use historic DNA (hDNA) and whole genomes of Bachman's warblers collected at the turn of the 20th century to address this. We combine these data with the two extant Vermivora species to examine patterns of population differentiation, inbreeding, and gene flow. In contrast to the admixture hypothesis, the genomic evidence is consistent with V. bachmanii having been a highly divergent, reproductively isolated species, with no evidence of introgression. We show that these three species have similar levels of runs of homozygosity (ROH), consistent with effects of a small long-term effective population size or population bottlenecks, with one V. bachmanii outlier showing numerous long ROH and a FROH greater than 5%. We also found-using population branch statistic estimates-previously undocumented evidence of lineage-specific evolution in V. chrysoptera near a pigmentation gene candidate, CORIN, which is a known modifier of ASIP, which is in turn involved in melanic throat and mask coloration in this family of birds. Together, these genomic results also highlight how natural history collections are such invaluable repositories of information about extant and extinct species.
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Affiliation(s)
- Andrew W Wood
- Department of Biology, Pennsylvania State University, 619 Mueller Laboratory, University Park, State College, PA 16802, USA
| | - Zachary A Szpiech
- Department of Biology, Pennsylvania State University, 619 Mueller Laboratory, University Park, State College, PA 16802, USA; Institute for Computational and Data Sciences, Pennsylvania State University, University Park, State College, PA 16802, USA
| | - Irby J Lovette
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, 159 Sapsucker Woods Road, Ithaca, NY 14850, USA
| | - Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - David P L Toews
- Department of Biology, Pennsylvania State University, 619 Mueller Laboratory, University Park, State College, PA 16802, USA.
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25
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Marshall AF, Balloux F, Hemmings N, Brekke P. Systematic review of avian hatching failure and implications for conservation. Biol Rev Camb Philos Soc 2023; 98:807-832. [PMID: 36635252 DOI: 10.1111/brv.12931] [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: 01/25/2022] [Revised: 12/21/2022] [Accepted: 12/30/2022] [Indexed: 01/14/2023]
Abstract
Avian hatching failure is a widespread phenomenon, affecting around 10% of all eggs that are laid and not lost to predation, damage, or desertion. Our understanding of hatching failure is limited in terms of both its underpinning mechanisms and its occurrence across different populations. It is widely acknowledged that rates of hatching failure are higher in threatened species and in populations maintained in captivity compared to wild, non-threatened species, but these differences have rarely been quantified and any broader patterns remain unexplored. To examine the associations between threat status, management interventions, and hatching failure across populations we conducted a phylogenetically controlled multilevel meta-analysis across 231 studies and 241 species of birds. Our data set included both threatened (Critically Endangered, Endangered, and Vulnerable) and non-threatened (Near Threatened and Least Concern) species across wild and captive populations, as well as 'wild managed' ('free-living') populations. We found the mean overall rate of hatching failure across all populations to be 16.79%, with the hatching failure rate of wild, non-threatened species being 12.40%. We found that populations of threatened species experienced significantly higher mean hatching failure than populations of non-threatened species. Different levels of management were also associated with different rates of hatching failure, with wild populations experiencing the lowest rate of hatching failure, followed by wild managed populations, and populations in captivity experiencing the highest rate. Similarly, populations that were subject to the specific management interventions of artificial incubation, supplementary feeding, and artificial nest provision displayed significantly higher rates of hatching failure than populations without these interventions. The driver of this correlation between hatching failure and management remains unclear, but could be an indirect result of threatened species being more likely to have lower hatching success and also being more likely to be subject to management, indicating that conservation efforts are fittingly being focused towards the species potentially most at risk from extinction. This is the most comprehensive comparative analysis of avian hatching failure that has been conducted to date, and the first to quantify explicitly how threat status and management are associated with the rate of hatching failure in a population. We discuss the implications of our results, focusing on their potential applications to conservation. Although we identified several factors clearly associated with variation in hatching failure, a significant amount of heterogeneity was not explained by our meta-analytical model, indicating that other factors influencing hatching failure were not included here. We discuss what these factors might be and suggest avenues for further research. Finally, we discuss the inconsistency in how hatching failure is defined and reported within the literature, and propose a standardised definition to be used in future studies which will enable better comparison across populations and ensure that the most accurate information is used to support management decisions.
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Affiliation(s)
- Ashleigh F Marshall
- Institute of Zoology, Zoological Society of London, Outer Circle, Regent's Park, London, NW1 4RY, UK
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - François Balloux
- UCL Genetics Institute, University College London, London, WC1E 6BT, UK
| | - Nicola Hemmings
- Department of Animal & Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Patricia Brekke
- Institute of Zoology, Zoological Society of London, Outer Circle, Regent's Park, London, NW1 4RY, UK
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26
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Frantz SI, Small CM, Cresko WA, Singh ND. Ovarian transcriptional response to Wolbachia infection in D. melanogaster in the context of between-genotype variation in gene expression. G3 (BETHESDA, MD.) 2023; 13:jkad047. [PMID: 36857313 PMCID: PMC10151400 DOI: 10.1093/g3journal/jkad047] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 08/22/2022] [Accepted: 01/07/2023] [Indexed: 03/02/2023]
Abstract
Wolbachia is a maternally transmitted endosymbiotic bacteria that infects a wide variety of arthropod and nematode hosts. The effects of Wolbachia on host biology are far-reaching and include changes in host gene expression. However, previous work on the host transcriptional response has generally been investigated in the context of a single host genotype. Thus, the relative effect of Wolbachia infection versus vs. host genotype on gene expression is unknown. Here, we explicitly test the relative roles of Wolbachia infection and host genotype on host gene expression by comparing the ovarian transcriptomes of 4 strains of Drosophila melanogaster (D. melanogaster) infected and uninfected with Wolbachia. Our data suggest that infection explains a small amount of transcriptional variation, particularly in comparison to variation in gene expression among strains. However, infection specifically affects genes related to cell cycle, translation, and metabolism. We also find enrichment of cell division and recombination processes among genes with infection-associated differential expression. Broadly, the transcriptomic changes identified in this study provide novel understanding of the relative magnitude of the effect of Wolbachia infection on gene expression in the context of host genetic variation and also point to genes that are consistently differentially expressed in response to infection among multiple genotypes.
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Affiliation(s)
- Sophia I Frantz
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403USA
| | - Clayton M Small
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403USA
- Presidential Initiative in Data Science, University of Oregon, Eugene, OR, 97403USA
| | - William A Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403USA
- Presidential Initiative in Data Science, University of Oregon, Eugene, OR, 97403USA
| | - Nadia D Singh
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403USA
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27
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Xue Z, Wang L, Tian Y, Yang Y, Li P, Yang G, Lu H, Wang S, Zeng W, Zhang T. A genome-wide scan to identify signatures of selection in Lueyang black -bone chicken. Poult Sci 2023; 102:102721. [PMID: 37186968 DOI: 10.1016/j.psj.2023.102721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/05/2023] [Accepted: 04/10/2023] [Indexed: 05/17/2023] Open
Abstract
Lueyang black-bone chicken is a domestic breed in China. The genetic mechanism of the formation of important economic traits of this breed has not been studied systematically. Therefore, in this study, whole genome resequencing was used to systematically analyze and evaluate the genetic diversity of the black-feather and white-feather populations, and to screen and identify key genes related to phenotypes. The results of principal component analysis and population structure analysis showed that Lueyang black-feathered chickens and white-feathered chickens could be divided into 2 subgroups, and the genetic diversity of black-feathered chicken was richer than that of white-feathered chickens. Linkage disequilibrium analysis also showed that the selection intensity of black-feathered chickens was lower than for white-feathered chickens, which was mainly due to the small population size of white-feathered chickens and a certain degree of inbreeding. Fixation index (FST) analysis revealed that the candidate genes related to feather color traits were G-gamma, FA, FERM, Kelch, TGFb, Arf, FERM, and melanin synthesis-related gene tyrosinase (TYR). Based on Kyoto Encyclopedia of Genes and Genomes enrichment analysis, Jak-STAT, mTOR, and TGF-β signaling pathways were mainly related to melanogenesis and plume color. The findings of this study supported important information for the evaluation and protection of chicken genetic resources and help to analyze the unique genetic phenotypes such as melanin deposition and feather color of Lueyang black-bone chicken. Additionally, it could provide basic research data for the improvement and breeding of Lueyang black-bone chicken with characteristic traits.
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Affiliation(s)
- Zhen Xue
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, Shaanxi, China
| | - Ling Wang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, Shaanxi, China; Engineering Research Center of quality improvement and safety control of Qinba special meat products, Universities of Shaanxi Province, Hanzhong 723001, Shaanxi, China; QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C., Shaanxi University of Technology, Hanzhong 723001 Shaanxi, China; Shaanxi Union Research Center of University and Enterprise for Zhenba Bacon, Hanzhong 723001, Shaanxi, China
| | - Yingmin Tian
- School of Mathematics and Computer Science, Shaanxi University of Technology, Hanzhong 723001, Shaanxi, China
| | - Yufei Yang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, Shaanxi, China
| | - Pan Li
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, Shaanxi, China
| | - Ge Yang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, Shaanxi, China
| | - Hongzhao Lu
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, Shaanxi, China; Engineering Research Center of quality improvement and safety control of Qinba special meat products, Universities of Shaanxi Province, Hanzhong 723001, Shaanxi, China; Shaanxi Union Research Center of University and Enterprise for Zhenba Bacon, Hanzhong 723001, Shaanxi, China
| | - Shanshan Wang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, Shaanxi, China; Engineering Research Center of quality improvement and safety control of Qinba special meat products, Universities of Shaanxi Province, Hanzhong 723001, Shaanxi, China; QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C., Shaanxi University of Technology, Hanzhong 723001 Shaanxi, China; Shaanxi Union Research Center of University and Enterprise for Zhenba Bacon, Hanzhong 723001, Shaanxi, China
| | - Wenxian Zeng
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, Shaanxi, China; Engineering Research Center of quality improvement and safety control of Qinba special meat products, Universities of Shaanxi Province, Hanzhong 723001, Shaanxi, China; Qinba State Key Laboratory of Biological Resources and Ecological Environment, Hanzhong 723001, Shaanxi, China
| | - Tao Zhang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, Shaanxi, China; Engineering Research Center of quality improvement and safety control of Qinba special meat products, Universities of Shaanxi Province, Hanzhong 723001, Shaanxi, China; QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C., Shaanxi University of Technology, Hanzhong 723001 Shaanxi, China; Shaanxi Union Research Center of University and Enterprise for Zhenba Bacon, Hanzhong 723001, Shaanxi, China; Qinba State Key Laboratory of Biological Resources and Ecological Environment, Hanzhong 723001, Shaanxi, China.
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28
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Cohen IR, Marron A. Evolution is driven by natural autoencoding: reframing species, interaction codes, cooperation and sexual reproduction. Proc Biol Sci 2023; 290:20222409. [PMID: 36855872 PMCID: PMC9975652 DOI: 10.1098/rspb.2022.2409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
Abstract
The continuity of life and its evolution, we proposed, emerge from an interactive group process manifested in networks of interaction. We term this process survival of the fitted. Here, we reason that survival of the fitted results from a natural computational process we term natural autoencoding. Natural autoencoding works by retaining repeating biological interactions while non-repeatable interactions disappear. (i) We define a species by its species interaction code, which consists of a compact description of the repeating interactions of species organisms with their external and internal environments. Species interaction codes are descriptions recorded in the biological infrastructure that enables repeating interactions. Encoding and decoding are interwoven. (ii) Evolution proceeds by natural autoencoding of sustained changes in species interaction codes. DNA is only one element in natural autoencoding. (iii) Natural autoencoding accounts for the paradox of genome randomization in sexual reproduction-recombined genomes are analogous to the diversified inputs required for artificial autoencoding. The increase in entropy generated by genome randomization compensates for the decrease in entropy generated by organized life. (iv) Natural autoencoding and artificial autoencoding algorithms manifest defined similarities and differences. Recognition of the importance of fittedness could well serve the future of a humanly livable biosphere.
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Affiliation(s)
- Irun R. Cohen
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Assaf Marron
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
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29
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Aubier TG, Bürger R, Servedio MR. The effectiveness of pseudomagic traits in promoting premating isolation. Proc Biol Sci 2023; 290:20222108. [PMID: 36883275 PMCID: PMC9993058 DOI: 10.1098/rspb.2022.2108] [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: 10/20/2022] [Accepted: 02/10/2023] [Indexed: 03/09/2023] Open
Abstract
Upon the secondary contact of populations, speciation with gene flow is greatly facilitated when the same pleiotropic loci are both subject to divergent ecological selection and induce non-random mating, leading to loci with this fortuitous combination of functions being referred to as 'magic trait' loci. We use a population genetics model to examine whether 'pseudomagic trait' complexes, composed of physically linked loci fulfilling these two functions, are as efficient in promoting premating isolation as magic traits. We specifically measure the evolution of choosiness, which controls the strength of assortative mating. We show that, surprisingly, pseudomagic trait complexes, and to a lesser extent also physically unlinked loci, can lead to the evolution of considerably stronger assortative mating preferences than do magic traits, provided polymorphism at the involved loci is maintained. This is because assortative mating preferences are generally favoured when there is a risk of producing maladapted recombinants, as occurs with non-magic trait complexes but not with magic traits (since pleiotropy precludes recombination). Contrary to current belief, magic traits may not be the most effective genetic architecture for promoting strong premating isolation. Therefore, distinguishing between magic traits and pseudomagic trait complexes is important when inferring their role in premating isolation. This calls for further fine-scale genomic research on speciation genes.
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Affiliation(s)
- Thomas G. Aubier
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier Toulouse III, UMR 5174, CNRS/IRD, 31077 Toulouse, France
| | - Reinhard Bürger
- Department of Mathematics, University of Vienna, 1090 Vienna, Austria
| | - Maria R. Servedio
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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30
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Xie W, Guo Z, Wang J, He Z, Li Y, Feng X, Zhong C, Shi S. Evolution of woody plants to the land-sea interface - The atypical genomic features of mangroves with atypical phenotypic adaptation. Mol Ecol 2023; 32:1351-1365. [PMID: 35771769 DOI: 10.1111/mec.16587] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 11/30/2022]
Abstract
How plants adapt and diverge in extreme environments is a key question of plant evolution and ecology. Mangrove invasion of intertidal environments is facilitated by adaptive phenotypes such as aerial roots, salt-secreting leaf, and viviparity, and genomic mechanisms including whole genome duplication and transposable element number reduction. However, a number of mangroves lack these typical phenotypes. The question we ask is whether these phenotypically atypical mangroves also have distinct genomic features? The sibling mangrove species Lumnitzera littorea and Lumnitzera racemosa provide a model to study this question. We sequenced and assembled their genomes to chromosome level, together with a closely related species Combretum micranthum. While most mangroves have small genomes, the genomes of both Lumnitzera species are large (1443 and 1317 Mb) and carry a high proportion of repeat sequences (~75%). Moreover, Lumnitzera species have not undergone post-gamma whole-genome duplications. Their genome size increased mainly due to the expansion of repeat sequences in their ancestors. However, Lumnitzera genomes have reduced transposable elements by constraining the proliferation of new LTR-RTs. Meanwhile, the two species have more gene families contracted than expanded, and some gene families with reversed size change may underlie their differentiation in root morphology and local distribution. We identified 86 chromosomal inversions, five of which are measured between 6.5 and 12.8 megabases. A number of genes located in these inversions function in pigment biosynthesis, a process likely involved in flower colour differentiation between the Lumnitzera species. We conclude that the mangroves with atypical phenotypes also have atypical genomic evolution.
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Affiliation(s)
- Wei Xie
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Zixiao Guo
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Jiayan Wang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Ziwen He
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Yulong Li
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, Guangdong, China.,School of Ecology, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Xiao Feng
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Cairong Zhong
- Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou, Hainan, China
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, Guangdong, China
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31
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Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. On the origin and structure of haplotype blocks. Mol Ecol 2023; 32:1441-1457. [PMID: 36433653 PMCID: PMC10946714 DOI: 10.1111/mec.16793] [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: 01/13/2022] [Revised: 11/16/2022] [Accepted: 11/18/2022] [Indexed: 11/27/2022]
Abstract
The term "haplotype block" is commonly used in the developing field of haplotype-based inference methods. We argue that the term should be defined based on the structure of the Ancestral Recombination Graph (ARG), which contains complete information on the ancestry of a sample. We use simulated examples to demonstrate key features of the relationship between haplotype blocks and ancestral structure, emphasizing the stochasticity of the processes that generate them. Even the simplest cases of neutrality or of a "hard" selective sweep produce a rich structure, often missed by commonly used statistics. We highlight a number of novel methods for inferring haplotype structure, based on the full ARG, or on a sequence of trees, and illustrate how they can be used to define haplotype blocks using an empirical data set. While the advent of new, computationally efficient methods makes it possible to apply these concepts broadly, they (and additional new methods) could benefit from adding features to explore haplotype blocks, as we define them. Understanding and applying the concept of the haplotype block will be essential to fully exploit long and linked-read sequencing technologies.
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Affiliation(s)
- Daria Shipilina
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, Uppsala, Sweden
- Institute of Science and Technology Austria, Klosterneuburg, Austria
- Swedish Collegium for Advanced Study, Uppsala, Sweden
| | - Arka Pal
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Sean Stankowski
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | | | - Nicholas H Barton
- Institute of Science and Technology Austria, Klosterneuburg, Austria
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32
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Peona V, Kutschera VE, Blom MPK, Irestedt M, Suh A. Satellite DNA evolution in Corvoidea inferred from short and long reads. Mol Ecol 2023; 32:1288-1305. [PMID: 35488497 DOI: 10.1111/mec.16484] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 04/11/2022] [Accepted: 04/17/2022] [Indexed: 11/29/2022]
Abstract
Satellite DNA (satDNA) is a fast-evolving portion of eukaryotic genomes. The homogeneous and repetitive nature of such satDNA causes problems during the assembly of genomes, and therefore it is still difficult to study it in detail in nonmodel organisms as well as across broad evolutionary timescales. Here, we combined the use of short- and long-read data to explore the diversity and evolution of satDNA between individuals of the same species and between genera of birds spanning ~40 millions of years of bird evolution using birds-of-paradise (Paradisaeidae) and crow (Corvus) species. These avian species highlighted the presence of a GC-rich Corvoidea satellitome composed of 61 satellite families and provided a set of candidate satDNA monomers for being centromeric on the basis of length, abundance, homogeneity and transcription. Surprisingly, we found that the satDNA of crow species rapidly diverged between closely related species while the satDNA appeared more similar between birds-of-paradise species belonging to different genera.
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Affiliation(s)
- Valentina Peona
- Department of Organismal Biology - Systematic Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Verena E Kutschera
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Mozes P K Blom
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Museum für Naturkunde, Leibniz Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Alexander Suh
- Department of Organismal Biology - Systematic Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,School of Biological Sciences-Organisms and the Environment, University of East Anglia, Norwich, UK
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33
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Kessler C, Wootton E, Shafer ABA. Speciation without gene-flow in hybridizing deer. Mol Ecol 2023; 32:1117-1132. [PMID: 36516402 DOI: 10.1111/mec.16824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 12/01/2022] [Accepted: 12/05/2022] [Indexed: 12/15/2022]
Abstract
Under the ecological speciation model, divergent selection acts on ecological differences between populations, gradually creating barriers to gene flow and ultimately leading to reproductive isolation. Hybridisation is part of this continuum and can both promote and inhibit the speciation process. Here, we used white-tailed (Odocoileus virginianus) and mule deer (O. hemionus) to investigate patterns of speciation in hybridizing sister species. We quantified genome-wide historical introgression and performed genome scans to look for signatures of four different selection scenarios. Despite ample modern evidence of hybridisation, we found negligible patterns of ancestral introgression and no signatures of divergence with gene flow, rather localized patterns of allopatric and balancing selection were detected across the genome. Genes under balancing selection were related to immunity, MHC and sensory perception of smell, the latter of which is consistent with deer biology. The deficiency of historical gene-flow suggests that white-tailed and mule deer were spatially separated during the glaciation cycles of the Pleistocene and genome wide differentiation accrued via genetic drift. Dobzhansky-Muller incompatibilities and selection against hybrids are hypothesised to be acting, and diversity correlations to recombination rates suggests these sister species are far along the speciation continuum.
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Affiliation(s)
- Camille Kessler
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
| | - Eric Wootton
- Biochemistry & Molecular Biology, Trent University, Peterborough, Ontario, Canada
| | - Aaron B A Shafer
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
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34
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Johnson O, Ribas CC, Aleixo A, Naka LN, Harvey MG, Brumfield RT. Amazonian birds in more dynamic habitats have less population genetic structure and higher gene flow. Mol Ecol 2023; 32:2186-2205. [PMID: 36798996 DOI: 10.1111/mec.16886] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/18/2023]
Abstract
Understanding the factors that govern variation in genetic structure across species is key to the study of speciation and population genetics. Genetic structure has been linked to several aspects of life history, such as foraging strategy, habitat association, migration distance, and dispersal ability, all of which might influence dispersal and gene flow. Comparative studies of population genetic data from species with differing life histories provide opportunities to tease apart the role of dispersal in shaping gene flow and population genetic structure. Here, we examine population genetic data from sets of bird species specialized on a series of Amazonian habitat types hypothesized to filter for species with dramatically different dispersal abilities: stable upland forest, dynamic floodplain forest, and highly dynamic riverine islands. Using genome-wide markers, we show that habitat type has a significant effect on population genetic structure, with species in upland forest, floodplain forest, and riverine islands exhibiting progressively lower levels of structure. Although morphological traits used as proxies for individual-level dispersal ability did not explain this pattern, population genetic measures of gene flow are elevated in species from more dynamic riverine habitats. Our results suggest that the habitat in which a species occurs drives the degree of population genetic structuring via its impact on long-term fluctuations in levels of gene flow, with species in highly dynamic habitats having particularly elevated gene flow. These differences in genetic variation across taxa specialized in distinct habitats may lead to disparate responses to environmental change or habitat-specific diversification dynamics over evolutionary time scales.
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Affiliation(s)
- Oscar Johnson
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Camila C Ribas
- Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Amazonas, Brazil
| | - Alexandre Aleixo
- Museu Paraense Emílio Goeldi (MPEG), Belém, Pará, Brazil.,Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland.,Instituto Tecnológico Vale, Belém, Brazil
| | - Luciano N Naka
- Laboratório de Ecologia & Evolução de Aves, Departamento de Zoologia, Universidade Federal de Pernambuco, Recife, Brazil
| | - Michael G Harvey
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, USA
| | - Robb T Brumfield
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, USA
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35
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Lu CW, Huang ST, Cheng SJ, Lin CT, Hsu YC, Yao CT, Dong F, Hung CM, Kuo HC. Genomic architecture underlying morphological and physiological adaptation to high elevation in a songbird. Mol Ecol 2023; 32:2234-2251. [PMID: 36748940 DOI: 10.1111/mec.16875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/17/2023] [Accepted: 02/03/2023] [Indexed: 02/08/2023]
Abstract
Organisms often acquire physiological and morphological modifications to conquer ecological challenges when colonizing new environments which lead to their adaptive evolution. However, deciphering the genomic mechanism of ecological adaptation is difficult because ecological environments are often too complex for straightforward interpretation. Thus, we examined the adaptation of a widespread songbird-the rufous-capped babbler (Cyanoderma ruficeps)-to a relatively simple system: distinct environments across elevational gradients on the mountainous island of Taiwan. We focused on the genomic sequences of 43 birds from five populations to show that the Taiwan group split from its sister group in mainland China around 1-2 million years ago (Ma) and colonized the montane habitats of Taiwan at least twice around 0.03-0.22 Ma. The montane and lowland Taiwan populations diverged with gene flow between them, suggesting strong selection associated with different elevations. We found that the montane babblers had smaller beaks than the lowland ones, consistent with Allen's rule, and identified candidate genes-COL9A1 and SOX11-underlying the beak size changes. We also found that altitudinally divergent mutations were mostly located in noncoding regions and tended to accumulate in chromosomal inversions and autosomes. The altitudinally divergent mutations might regulate genes related to haematopoietic, metabolic, immune, auditory and vision functions, as well as cerebrum morphology and plumage development. The results reveal the genomic bases of morphological and physiological adaptation in this species to the low temperature, hypoxia and high UV light environment at high elevation. These findings improve our understanding of how ecological adaptation drives population divergence from the perspective of genomic architecture.
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Affiliation(s)
- Chia-Wei Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Shih-Ting Huang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Shun-Jen Cheng
- Department of Natural Resources and Environmental Studies, National Dong Hwa University, Hualien, Taiwan
| | - Chen-Tau Lin
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Yu-Cheng Hsu
- Department of Natural Resources and Environmental Studies, National Dong Hwa University, Hualien, Taiwan
| | - Cheng-Te Yao
- Division of Zoology, Endemic Species Research Institute, Nantou, Taiwan
| | - Feng Dong
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Chih-Ming Hung
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Hao-Chih Kuo
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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36
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Alaei Kakhki N, Schweizer M, Lutgen D, Bowie RCK, Shirihai H, Suh A, Schielzeth H, Burri R. A Phylogenomic Assessment of Processes Underpinning Convergent Evolution in Open-Habitat Chats. Mol Biol Evol 2023; 40:6964684. [PMID: 36578177 PMCID: PMC10161543 DOI: 10.1093/molbev/msac278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 11/01/2022] [Accepted: 12/16/2022] [Indexed: 12/30/2022] Open
Abstract
Insights into the processes underpinning convergent evolution advance our understanding of the contributions of ancestral, introgressed, and novel genetic variation to phenotypic evolution. Phylogenomic analyses characterizing genome-wide gene tree heterogeneity can provide first clues about the extent of ILS and of introgression and thereby into the potential of these processes or (in their absence) the need to invoke novel mutations to underpin convergent evolution. Here, we were interested in understanding the processes involved in convergent evolution in open-habitat chats (wheatears of the genus Oenanthe and their relatives). To this end, based on whole-genome resequencing data from 50 taxa of 44 species, we established the species tree, characterized gene tree heterogeneity, and investigated the footprints of ILS and introgression within the latter. The species tree corroborates the pattern of abundant convergent evolution, especially in wheatears. The high levels of gene tree heterogeneity in wheatears are explained by ILS alone only for 30% of internal branches. For multiple branches with high gene tree heterogeneity, D-statistics and phylogenetic networks identified footprints of introgression. Finally, long branches without extensive ILS between clades sporting similar phenotypes provide suggestive evidence for the role of novel mutations in the evolution of these phenotypes. Together, our results suggest that convergent evolution in open-habitat chats involved diverse processes and highlight that phenotypic diversification is often complex and best depicted as a network of interacting lineages.
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Affiliation(s)
- Niloofar Alaei Kakhki
- Department of Population Ecology, Institute of Ecology and Evolution, Friedrich-Schiller-University Jena, Jena, Germany
| | - Manuel Schweizer
- Natural History Museum Bern, Bern, Switzerland.,Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Dave Lutgen
- Department of Population Ecology, Institute of Ecology and Evolution, Friedrich-Schiller-University Jena, Jena, Germany.,Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Swiss Ornithological Institute, Sempach, Switzerland
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA.,Department of Integrative Biology, University of California, Berkeley, CA, USA
| | | | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom.,Department of Organismal Biology - Systematic Biology (EBC), Science for Life Laboratory, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Holger Schielzeth
- Department of Population Ecology, Institute of Ecology and Evolution, Friedrich-Schiller-University Jena, Jena, Germany.,German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany
| | - Reto Burri
- Department of Population Ecology, Institute of Ecology and Evolution, Friedrich-Schiller-University Jena, Jena, Germany.,Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Swiss Ornithological Institute, Sempach, Switzerland
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37
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Wang X, He Z, Guo Z, Yang M, Xu S, Chen Q, Shao S, Li S, Zhong C, Duke NC, Shi S. Extensive gene flow in secondary sympatry after allopatric speciation. Natl Sci Rev 2022; 9:nwac280. [PMID: 36694801 PMCID: PMC9869077 DOI: 10.1093/nsr/nwac280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 12/04/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022] Open
Abstract
In the conventional view, species are separate gene pools delineated by reproductive isolation (RI). In an alternative view, species may also be delineated by a small set of 'speciation genes' without full RI, a view that has gained broad acceptance. A recent survey, however, suggested that the extensive literature on 'speciation with gene flow' is mostly (if not all) about exchanges in the early stages of speciation. There is no definitive evidence that the observed gene flow actually happened after speciation is completed. Here, we wish to know whether 'good species' (defined by the 'secondary sympatry' test) do continue to exchange genes and, importantly, under what conditions such exchanges can be observed. De novo whole-genome assembly and re-sequencing of individuals across the range of two closely related mangrove species (Rhizophora mucronata and R. stylosa) reveal the genomes to be well delineated in allopatry. They became sympatric in northeastern Australia but remain distinct species. Nevertheless, their genomes harbor ∼4000-10 000 introgression blocks averaging only about 3-4 Kb. These fine-grained introgressions indicate continual gene flow long after speciation as non-introgressable 'genomic islets,' ∼1.4 Kb in size, often harbor diverging genes of flower or gamete development. The fine-grained introgression in secondary sympatry may help settle the debate about sympatric vs. micro-allopatric speciation. In conclusion, true 'good species' may often continue to exchange genes but the opportunity for detection is highly constrained.
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Affiliation(s)
| | | | | | - Ming Yang
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA98195, USA
| | - Shaohua Xu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou510275, China
| | - Qipian Chen
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou510275, China
| | - Shao Shao
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou510275, China
| | - Sen Li
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou510275, China
| | - Cairong Zhong
- Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou571100, China
| | - Norman C Duke
- Centre for Tropical Water and Aquatic Ecosystem Research, James Cook University, Townsville, QLD 4811, Australia
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38
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Tigano A, Russello MA. The genomic basis of reproductive and migratory behaviour in a polymorphic salmonid. Mol Ecol 2022; 31:6588-6604. [PMID: 36208020 DOI: 10.1111/mec.16724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/21/2022] [Accepted: 09/29/2022] [Indexed: 01/13/2023]
Abstract
Recent ecotypic differentiation provides unique opportunities to investigate the genomic basis and architecture of local adaptation, while offering insights into how species form and persist. Sockeye salmon (Oncorhynchus nerka) exhibit migratory and resident ("kokanee") ecotypes, which are further distinguished into shore-spawning and stream-spawning reproductive ecotypes. Here, we analysed 36 sockeye (stream-spawning) and kokanee (stream- and shore-spawning) genomes from a system where they co-occur and have recent common ancestry (Okanagan Lake/River in British Columbia, Canada) to investigate the genomic basis of reproductive and migratory behaviour. Examination of the genomic landscape of differentiation, differences in allele frequencies and genotype-phenotype associations revealed three main blocks of sequence differentiation on chromosomes 7, 12 and 20, associated with migratory behaviour, spawning location and spawning timing. Structural variants identified in these same areas suggest they could contribute to ecotypic differentiation directly as causal variants or via maintenance of their genomic architecture through recombination suppression mechanisms. Genes in these regions were related to spatial memory and swimming endurance (SYNGAP, TPM3), as well as eye and brain development (including SIX6), potentially associated with differences in migratory behaviour and visual habitats across spawning locations, respectively. Additional genes (GREB1L, ROCK1) identified here have been associated with timing of migration in other salmonids and could explain variation in timing of O. nerka spawning. Together, these results based on the joint analysis of sequence and structural variation represent a significant advance in our understanding of the genomic landscape of ecotypic differentiation at different stages in the speciation continuum.
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Affiliation(s)
- Anna Tigano
- Department of Biology, The University of British Columbia, Kelowna, British Columbia, Canada
| | - Michael A Russello
- Department of Biology, The University of British Columbia, Kelowna, British Columbia, Canada
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39
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Affiliation(s)
- Chung-I Wu
- Chung-I Wu School of Life Sciences, Sun Yat-Sen University, China
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40
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Campagna L, Mo Z, Siepel A, Uy JAC. Selective sweeps on different pigmentation genes mediate convergent evolution of island melanism in two incipient bird species. PLoS Genet 2022; 18:e1010474. [PMID: 36318577 PMCID: PMC9624418 DOI: 10.1371/journal.pgen.1010474] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 10/12/2022] [Indexed: 11/19/2022] Open
Abstract
Insular organisms often evolve predictable phenotypes, like flightlessness, extreme body sizes, or increased melanin deposition. The evolutionary forces and molecular targets mediating these patterns remain mostly unknown. Here we study the Chestnut-bellied Monarch (Monarcha castaneiventris) from the Solomon Islands, a complex of closely related subspecies in the early stages of speciation. On the large island of Makira M. c. megarhynchus has a chestnut belly, whereas on the small satellite islands of Ugi, and Santa Ana and Santa Catalina (SA/SC) M. c. ugiensis is entirely iridescent blue-black (i.e., melanic). Melanism has likely evolved twice, as the Ugi and SA/SC populations were established independently. To investigate the genetic basis of melanism on each island we generated whole genome sequence data from all three populations. Non-synonymous mutations at the MC1R pigmentation gene are associated with melanism on SA/SC, while ASIP, an antagonistic ligand of MC1R, is associated with melanism on Ugi. Both genes show evidence of selective sweeps in traditional summary statistics and statistics derived from the ancestral recombination graph (ARG). Using the ARG in combination with machine learning, we inferred selection strength, timing of onset and allele frequency trajectories. MC1R shows evidence of a recent, strong, soft selective sweep. The region including ASIP shows more complex signatures; however, we find evidence for sweeps in mutations near ASIP, which are comparatively older than those on MC1R and have been under relatively strong selection. Overall, our study shows convergent melanism results from selective sweeps at independent molecular targets, evolving in taxa where coloration likely mediates reproductive isolation with the neighboring chestnut-bellied subspecies. Chestnut-bellied Monarchs (Monarcha castaneiventris ugiensis) from two archipelagos in the Solomon Islands have evolved entirely black plumage from a chestnut ancestor (Monarcha castaneiventris megarhynchus), a phenomenon known as island melanism. We obtain and analyze whole genome sequences using traditional summary statistics and new methods that combine inference of the ancestral recombination graph with machine learning. We find multiple lines of evidence for independent selective sweeps on the MC1R and ASIP genes, a receptor/ligand pair which regulates the production of melanin. Melanism on each archipelago is mediated by mutations in one of these two genes. Mutations in and around MC1R underwent a recent soft sweep experiencing strong selection on the islands of Santa Ana and Santa Catalina, whereas selection was also strong but comparatively older for ASIP on the island of Ugi. We show how melanism originated under positive selection on independent molecular targets, evolving convergently in taxa where coloration mediates reproductive isolation.
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Affiliation(s)
- Leonardo Campagna
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Ithaca, New York, United States of America
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, United States of America
- * E-mail: (LC); (JACU)
| | - Ziyi Mo
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - J. Albert C. Uy
- Department of Biology, University of Rochester, Rochester, New York, United States of America
- * E-mail: (LC); (JACU)
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41
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Early stages of sympatric homoploid hybrid speciation in crater lake cichlid fishes. Nat Commun 2022; 13:5893. [PMID: 36202802 PMCID: PMC9537415 DOI: 10.1038/s41467-022-33319-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/13/2022] [Indexed: 11/27/2022] Open
Abstract
Homoploid hybrid speciation (i.e., hybrid speciation without a change in ploidy) has traditionally been considered to be rare in animals. Only few accepted empirical examples of homoploid hybrid speciation in nature exist, and in only one previous case (insects) was it convincingly shown that this process occurred in complete sympatry. Here, we report an instance of sympatric homoploid hybrid speciation in Midas cichlid fishes in Crater Lake Xiloá, Nicaragua. The hybrid lineage, albeit at an early stage of speciation, has genomically and phenotypically diverged from both of its two parental species. Together with a distinct stable isotope signature this suggests that this hybrid lineages occupies a different trophic niche compared to the other sympatric Midas cichlid species in Crater Lake Xiloá. Here, the authors present a rare example of sympatric homoploid hybrid speciation, without ploidy changes, in the Midas cichlid fishes from Nicaragua. Midas cichlid hybrids occupy a different ecological niche, likely facilitated by body shape adaptations.
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42
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Nikolakis ZL, Adams RH, Wade KJ, Lund AJ, Carlton EJ, Castoe TA, Pollock DD. Prospects for genomic surveillance for selection in schistosome parasites. FRONTIERS IN EPIDEMIOLOGY 2022; 2:932021. [PMID: 38455290 PMCID: PMC10910990 DOI: 10.3389/fepid.2022.932021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 09/12/2022] [Indexed: 03/09/2024]
Abstract
Schistosomiasis is a neglected tropical disease caused by multiple parasitic Schistosoma species, and which impacts over 200 million people globally, mainly in low- and middle-income countries. Genomic surveillance to detect evidence for natural selection in schistosome populations represents an emerging and promising approach to identify and interpret schistosome responses to ongoing control efforts or other environmental factors. Here we review how genomic variation is used to detect selection, how these approaches have been applied to schistosomes, and how future studies to detect selection may be improved. We discuss the theory of genomic analyses to detect selection, identify experimental designs for such analyses, and review studies that have applied these approaches to schistosomes. We then consider the biological characteristics of schistosomes that are expected to respond to selection, particularly those that may be impacted by control programs. Examples include drug resistance, host specificity, and life history traits, and we review our current understanding of specific genes that underlie them in schistosomes. We also discuss how inherent features of schistosome reproduction and demography pose substantial challenges for effective identification of these traits and their genomic bases. We conclude by discussing how genomic surveillance for selection should be designed to improve understanding of schistosome biology, and how the parasite changes in response to selection.
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Affiliation(s)
- Zachary L. Nikolakis
- Department of Biology, University of Texas at Arlington, Arlington, TX, United States
| | - Richard H. Adams
- Department of Biological and Environmental Sciences, Georgia College and State University, Milledgeville, GA, United States
| | - Kristen J. Wade
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, United States
| | - Andrea J. Lund
- Department of Environmental and Occupational Health, Colorado School of Public Health, University of Colorado, Anschutz, Aurora, CO, United States
| | - Elizabeth J. Carlton
- Department of Environmental and Occupational Health, Colorado School of Public Health, University of Colorado, Anschutz, Aurora, CO, United States
| | - Todd A. Castoe
- Department of Biology, University of Texas at Arlington, Arlington, TX, United States
| | - David D. Pollock
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, United States
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43
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Ng EYX, Li S, Zhang D, Garg KM, Song G, Martinez J, Hung LM, Tu VT, Fuchs J, Dong L, Olsson U, Huang Y, Alström P, Rheindt FE, Lei F. Genome‐wide
SNPs
confirm plumage polymorphism and hybridisation within a
Cyornis
flycatcher species complex. ZOOL SCR 2022. [DOI: 10.1111/zsc.12568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Elize Y. X. Ng
- Department of Biological Sciences National University of Singapore Singapore Singapore
- Discipline of Biological Science, School of Natural Sciences University of Tasmania Hobart Tasmania Australia
| | - Siqi Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
- College of Life Sciences Shaanxi Normal University Xi'an China
| | - Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Kritika M. Garg
- Department of Biological Sciences National University of Singapore Singapore Singapore
- Centre for Interdisciplinary Archaeological Research Ashoka University Sonipat India
- Department of Biology Ashoka University Sonipat India
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
| | | | - Le Manh Hung
- Institute of Ecology and Biological Resources, Graduate University of Science and Technology Vietnam Academy of Science and Technology Hanoi Vietnam
| | - Vuong Tan Tu
- Institute of Ecology and Biological Resources, Graduate University of Science and Technology Vietnam Academy of Science and Technology Hanoi Vietnam
| | - Jérôme Fuchs
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle CNRS, 22 S U, EPHE, UA CP51 Paris France
| | - Lu Dong
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences Beijing Normal University Beijing China
| | - Urban Olsson
- Systematics and Biodiversity, Department of Biology and Environmental Sciences University of Gothenburg Gothenburg Sweden
- Gothenburg Global Biodiversity Center Göteborg Sweden
| | - Yuan Huang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Per Alström
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre Uppsala University Uppsala Sweden
| | - Frank E. Rheindt
- Department of Biological Sciences National University of Singapore Singapore Singapore
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
- Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China
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44
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Mallet J, Mullen SP. Reproductive isolation is a heuristic, not a measure: a commentary on Westram et al., 2022. J Evol Biol 2022; 35:1175-1182. [PMID: 36063161 DOI: 10.1111/jeb.14052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 12/17/2022]
Abstract
Reproductive isolation is the heuristic basis of the biological species concept, but what is it? Westram et al. (this issue) propose that it is a measurable quantity, "barrier strength," that prevents gene flow among populations. However, their attempt to make the concept of reproductive isolation more scientific is unlikely to satisfy the diverse opinions of all evolutionary biologists. There are many different opinions about the nature of species, even under the biological species concept. Complete reproductive isolation, where gene flow is effectively zero, is regarded by some biologists as an important end point of speciation. Others, including Westram et al., argue for a more nuanced approach, and they also suggest that reproductive isolation may differ in different parts of the genome due to variation in genetic linkage to divergently selected loci. In contrast to both these approaches, we favour as a key criterion of speciation the stable coexistence of divergent populations in sympatry. Obviously, such populations must be reproductively isolated in some sense, but neither the fraction of the genome that is exchanged, nor measures of overall barrier strength acting on neutral variation will yield very precise predictions as to species status. Although an overall measure of reproductive isolation is virtually unattainable for these reasons, its early generation components, such as assortative mating, divergent selection, or hybrid inviability and sterility are readily measurable and remain informative. For example, we can make the prediction that to remain divergent in sympatry, almost all sexual species will require strong assortative mating, as well as some sort of ecological or intrinsic selection against hybrids and introgressed variants.
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Affiliation(s)
- James Mallet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Sean P Mullen
- Department of Biology, Boston University, Boston, Massachusetts, USA
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45
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Ericson PGP, Irestedt M, Zuccon D, Larsson P, Tison JL, Emslie SD, Götherström A, Hume JP, Werdelin L, Qu Y. A 14,000-year-old genome sheds light on the evolution and extinction of a Pleistocene vulture. Commun Biol 2022; 5:857. [PMID: 35999361 PMCID: PMC9399080 DOI: 10.1038/s42003-022-03811-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/05/2022] [Indexed: 11/23/2022] Open
Abstract
The New World Vulture [Coragyps] occidentalis (L. Miller, 1909) is one of many species that were extinct by the end of the Pleistocene. To understand its evolutionary history we sequenced the genome of a 14,000 year old [Coragyps] occidentalis found associated with megaherbivores in the Peruvian Andes. occidentalis has been viewed as the ancestor, or possibly sister, to the extant Black Vulture Coragyps atratus, but genomic data shows occidentalis to be deeply nested within the South American clade of atratus. Coragyps atratus inhabits lowlands, but the fossil record indicates that occidentalis mostly occupied high elevations. Our results suggest that occidentalis evolved from a population of atratus in southwestern South America that colonized the High Andes 300 to 400 kya. The morphological and morphometric differences between occidentalis and atratus may thus be explained by ecological diversification following from the natural selection imposed by this new and extreme, high elevation environment. The sudden evolution of a population with significantly larger body size and different anatomical proportions than atratus thus constitutes an example of punctuated evolution. 14,000 year old DNA reveals the evolutionary dynamics and adaptations of South American vultures.
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Affiliation(s)
- Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, SE-10405, Stockholm, Sweden.
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, SE-10405, Stockholm, Sweden
| | - Dario Zuccon
- Institut de Systématique, Evolution, Biodiversité (ISYEB), UMR7205 CNRS MNHN UPMC EPHE Sorbonne Université, Muséum National d'Histoire Naturelle, 75005, Paris, France
| | - Petter Larsson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, SE-10405, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Jean-Luc Tison
- Department of Laboratory Medicine, Örebro University Hospital; Södra Grev Rosengatan, SE-70185, Örebro, Sweden
| | - Steven D Emslie
- Department of Biology and Marine Biology, University of North Carolina; Wilmington, 601S. College Road, Wilmington, NC, 28403, USA
| | - Anders Götherström
- Centre for Palaeogenetics, Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, SE-10691, Stockholm, Sweden
| | - Julian P Hume
- Bird Group, Department of Life Sciences, Natural History Museum, Akeman St, Tring, Herts, UK
| | - Lars Werdelin
- Department of Palaeobiology, Swedish Museum of Natural History, P.O. Box 50007, SE-10405, Stockholm, Sweden
| | - Yanhua Qu
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, SE-10405, Stockholm, Sweden. .,Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
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46
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Kersten Y, Friedrich-Müller B, Nieder A. A brain atlas of the carrion crow (Corvus corone). J Comp Neurol 2022; 530:3011-3038. [PMID: 35938778 DOI: 10.1002/cne.25392] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 06/30/2022] [Accepted: 07/04/2022] [Indexed: 11/06/2022]
Abstract
Corvidae, passerine songbirds such as jays, crows, and ravens known as corvids, have become model systems for the study of avian cognition. The superior cognitive capabilities of corvids mainly emerge from a disproportionally large telencephalon found in these species. However, a systematic mapping of the neuroanatomy of the corvid brain, and the telencephalon in particular, is lacking so far. Here, we present a brain atlas of the carrion crow, Corvus corone, with special emphasis on the telencephalic pallium. We applied four staining techniques to brain slices (Nissl, myelin, combination of Nissl and myelin, and tyrosine hydroxylase targeting catecholaminergic neurons). This allowed us to identify brain nuclei throughout the brain and delineate the known pallial subdivisions termed hyperpallium, entopallium, mesopallium, nidopallium, arcopallium, and hippocampal complex. The extent of these subdivisions and brain nuclei are described according to stereotaxic coordinates. In addition, 3D depictions of pallial regions were reconstructed from these slices. While the overall organization of the carrion crow's brain matches other songbird brains, the relative proportions and expansions of associative pallial areas differ considerably in agreement with enhanced cognitive skills found in corvids. The presented global organization of the crow brain in stereotaxic coordinates will help to guide future neurobiological studies in corvids.
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Affiliation(s)
- Ylva Kersten
- Animal Physiology Unit, Institute of Neurobiology, University of Tübingen, Tübingen, Germany
| | | | - Andreas Nieder
- Animal Physiology Unit, Institute of Neurobiology, University of Tübingen, Tübingen, Germany
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47
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Introgression at the emerging secondary contact zone of magpie Pica pica subspecies (Aves: Corvidae): integrating data on nuclear and mitochondrial markers, vocalizations, and field observations. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00568-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Abstract
Zones of secondary contact provide a good opportunity to investigate the origin and dynamics of reproductive isolation between related populations. We analyzed genetic and phenotypic patterns and gene flow between two subspecies of the Eurasian magpie Pica pica s.l. which recently came into contact after presumably long periods of isolation. We describe the distribution of subspecies in a young contact zone at Argun’ river basin in southern Siberia where populations occur in parapatry and an older hybrid population in eastern Mongolia. Based on genome-wide SNP data, we analyzed patterns and strength of gene flow between the subspecies. Our results indicate occasional hybridization with backcrossing and asymmetric introgression along a wide range in Transbaikalia and locally in eastern Mongolia. Males of P. p. jankowskii apparently exhibit higher dispersal ability towards the west compared to P. p. leucoptera (towards the east). The former occasionally migrates to eastern Mongolia and Transbaikalia where introgression of nuclear, but not mitochondrial DNA was evident. Bioacoustic investigations showed differences between the subspecies in speed and structure of vocalization. We discovered intermediate calls of hybrid magpies and bilingual birds alternating calls that are typical for the two taxa. Furthermore, we found dramatically decreased reproductive success in hybridogeneous populations. By complementing our results with established phylogeographic patterns of P. pica s.l. based on a mitochondrial marker sequence, and considering indications of sterility of hybrids in the contact zone, we propose to elevate the two corresponding subspecies to species level: P. pica for the western form and P. serica for the eastern form.
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48
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Gibert JM. [Small scale evolution]. Biol Aujourdhui 2022; 216:41-47. [PMID: 35876520 DOI: 10.1051/jbio/2022008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Indexed: 06/15/2023]
Abstract
Small-scale evolution or microevolution concerns evolution at the intra-specific level or between closely related species. At the intra-specific level, it allows the analysis of the evolutionary forces at work: mutation, genetic drift, migration and selection. Moreover, because of the short evolutionary time, it is easier to identify the genetic basis of observed phenotypic differences. Most studies focus on current populations but more and more analyses are performed on ancient DNA. This provides important information for tracing the history of populations and also allows the reconstruction of phenotypes of individuals that disappeared several thousand years ago. In this short review, I present studies showing how pre-zygotic or post-zygotic barriers involved in species formation are set up using the example of the geographical barrier due to the formation of the Isthmus of Panama and that of the heterochromatin divergence in Drosophilidae. I also describe the different approaches that have been used to identify the genetic basis of well known phenotypic variations: candidate gene approach (about melanism in felines), QTL mapping (variation in the number of lateral bone plates in sticklebacks), association study (pigmentation in the Asian ladybird). Finally, I illustrate the key impact of natural selection with the iconic example of the evolution of the beak of Galapagos finches, and the role of certain developmental genes in its morphological diversification.
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Affiliation(s)
- Jean-Michel Gibert
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire de Biologie du Développement, UMR 7622, 9 quai St-Bernard 75005 Paris, France
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49
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Ramos-Gonzalez D, Saenko SV, Davison A. Deep structure, long-distance migration and admixture in the colour polymorphic land snail Cepaea nemoralis. J Evol Biol 2022; 35:1110-1125. [PMID: 35830483 PMCID: PMC9541890 DOI: 10.1111/jeb.14060] [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: 03/11/2022] [Revised: 05/20/2022] [Accepted: 06/12/2022] [Indexed: 12/03/2022]
Abstract
Although snails of the genus Cepaea have historically been important in studying colour polymorphism, an ongoing issue is that there is a lack of knowledge of the underlying genetics of the polymorphism, as well as an absence of genomic data to put findings in context. We, therefore, used phylogenomic methods to begin to investigate the post‐glacial history of Cepaea nemoralis, with a long‐term aim to understand the roles that selection and drift have in determining both European‐wide and local patterns of colour polymorphism. By combining prior and new mitochondrial DNA data from over 1500 individuals with ddRAD genomic data from representative individuals across Europe, we show that patterns of differentiation are primarily due to multiple deeply diverged populations of snails. Minimally, there is a widespread Central European population and additional diverged groups in Northern Spain, the Pyrenees, as well as likely Italy and South Eastern Europe. The genomic analysis showed that the present‐day snails in Ireland and possibly some other locations are likely descendants of admixture between snails from the Pyrenees and the Central European group, an observation that is consistent with prior inferences from mitochondrial DNA alone. The interpretation is that C. nemoralis may have arrived in Ireland via long‐distance migration from the Pyrenean region, subsequently admixing with arrivals from elsewhere. This work, therefore, provides a baseline expectation for future studies on the genetics of the colour polymorphism, as well as providing a comparator for similar species.
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Affiliation(s)
| | - Suzanne V Saenko
- Evolutionary Ecology, Naturalis Biodiversity Center, Leiden, The Netherlands.,Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Angus Davison
- School of Life Sciences, University of Nottingham, Nottingham, UK
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50
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Friis G, Vizueta J, Ketterson ED, Milá B. A high-quality genome assembly and annotation of the dark-eyed junco Junco hyemalis, a recently diversified songbird. G3 (BETHESDA, MD.) 2022; 12:jkac083. [PMID: 35404451 PMCID: PMC9157146 DOI: 10.1093/g3journal/jkac083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/31/2022] [Indexed: 11/26/2022]
Abstract
The dark-eyed junco (Junco hyemalis) is one of the most common passerines of North America, and has served as a model organism in studies related to ecophysiology, behavior, and evolutionary biology for over a century. It is composed of at least 6 distinct, geographically structured forms of recent evolutionary origin, presenting remarkable variation in phenotypic traits, migratory behavior, and habitat. Here, we report a high-quality genome assembly and annotation of the dark-eyed junco generated using a combination of shotgun libraries and proximity ligation Chicago and Dovetail Hi-C libraries. The final assembly is ∼1.03 Gb in size, with 98.3% of the sequence located in 30 full or nearly full chromosome scaffolds, and with a N50/L50 of 71.3 Mb/5 scaffolds. We identified 19,026 functional genes combining gene prediction and similarity approaches, of which 15,967 were associated to GO terms. The genome assembly and the set of annotated genes yielded 95.4% and 96.2% completeness scores, respectively when compared with the BUSCO avian dataset. This new assembly for J. hyemalis provides a valuable resource for genome evolution analysis, and for identifying functional genes involved in adaptive processes and speciation.
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Affiliation(s)
- Guillermo Friis
- Department of Biodiversity and Evolutionary Biology, National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid 28006, Spain
| | - Joel Vizueta
- Centre for Social Evolution, University of Copenhaguen, Copenhaguen 1165, Denmark
| | - Ellen D Ketterson
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Borja Milá
- Department of Biodiversity and Evolutionary Biology, National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid 28006, Spain
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