1
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Lucek K, Giménez MD, Joron M, Rafajlović M, Searle JB, Walden N, Westram AM, Faria R. The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution. Cold Spring Harb Perspect Biol 2023; 15:a041447. [PMID: 37604585 PMCID: PMC10626258 DOI: 10.1101/cshperspect.a041447] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
Chromosomal rearrangements (CRs) have been known since almost the beginning of genetics. While an important role for CRs in speciation has been suggested, evidence primarily stems from theoretical and empirical studies focusing on the microevolutionary level (i.e., on taxon pairs where speciation is often incomplete). Although the role of CRs in eukaryotic speciation at a macroevolutionary level has been supported by associations between species diversity and rates of evolution of CRs across phylogenies, these findings are limited to a restricted range of CRs and taxa. Now that more broadly applicable and precise CR detection approaches have become available, we address the challenges in filling some of the conceptual and empirical gaps between micro- and macroevolutionary studies on the role of CRs in speciation. We synthesize what is known about the macroevolutionary impact of CRs and suggest new research avenues to overcome the pitfalls of previous studies to gain a more comprehensive understanding of the evolutionary significance of CRs in speciation across the tree of life.
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Affiliation(s)
- Kay Lucek
- Biodiversity Genomics Laboratory, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Mabel D Giménez
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Genética Humana de Misiones (IGeHM), Parque de la Salud de la Provincia de Misiones "Dr. Ramón Madariaga," N3300KAZ Posadas, Misiones, Argentina
- Facultad de Ciencias Exactas Químicas y Naturales, Universidad Nacional de Misiones, N3300LQH Posadas, Misiones, Argentina
| | - Mathieu Joron
- Centre d'Ecologie Fonctionnelle et Evolutive, Université de Montpellier, CNRS, EPHE, IRD, 34293 Montpellier, France
| | - Marina Rafajlović
- Department of Marine Sciences, University of Gothenburg, 405 30 Gothenburg, Sweden
- Centre for Marine Evolutionary Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853, USA
| | - Nora Walden
- Centre for Organismal Studies, University of Heidelberg, 69117 Heidelberg, Germany
| | - Anja Marie Westram
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria
- Faculty of Biosciences and Aquaculture, Nord University, 8026 Bodø, Norway
| | - Rui Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado;
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
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2
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Moraes AP, Engel TBJ, Forni-Martins ER, de Barros F, Felix LP, Cabral JS. Are chromosome number and genome size associated with habit and environmental niche variables? Insights from the Neotropical orchids. ANNALS OF BOTANY 2022; 130:11-25. [PMID: 35143612 PMCID: PMC9295925 DOI: 10.1093/aob/mcac021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/09/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND AND AIMS The entangled relationship of chromosome number and genome size with species distribution has been the subject of study for almost a century, but remains an open question due to previous ecological and phylogenetic knowledge constraints. To better address this subject, we used the clade Maxillariinae, a widely distributed and karyotypically known orchid group, as a model system to infer such relationships in a robust methodological framework. METHODS Based on the literature and new data, we gathered the chromosome number and genome size for 93 and 64 species, respectively. We built a phylogenetic hypothesis and assessed the best macroevolutionary model for both genomic traits. Additionally, we collected together ecological data (preferences for bioclimatic variables, elevation and habit) used as explanatory variables in multivariate phylogenetic models explaining genomic traits. Finally, the impact of polyploidy was estimated by running the analyses with and without polyploids in the sample. KEY RESULTS The association between genomic and ecological data varied depending on whether polyploids were considered or not. Without polyploids, chromosome number failed to present consistent associations with ecological variables. With polyploids, there was a tendency to waive epiphytism and colonize new habitats outside humid forests. The genome size showed association with ecological variables: without polyploids, genome increase was associated with flexible habits, with higher elevation and with drier summers; with polyploids, genome size increase was associated with colonizing drier environments. CONCLUSIONS The chromosome number and genome size variations, essential but neglected traits in the ecological niche, are shaped in the Maxillariinae by both neutral and adaptive evolution. Both genomic traits are partially correlated to bioclimatic variables and elevation, even when controlling for phylogenetic constraints. While polyploidy was associated with shifts in the environmental niche, the genome size emerges as a central trait in orchid evolution by the association between small genome size and epiphytism, a key innovation to Neotropical orchid diversification.
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Affiliation(s)
| | - Thaissa Brogliato Junqueira Engel
- Universidade de Campinas – UNICAMP, Instituto de Biologia, Departamento de Biologia Vegetal, Programa de Pós Graduação em Biologia Vegetal, Campinas, 13083-970, São Paulo, Brazil
| | - Eliana R Forni-Martins
- Universidade de Campinas – UNICAMP, Instituto de Biologia, Departamento de Biologia Vegetal, Programa de Pós Graduação em Biologia Vegetal, Campinas, 13083-970, São Paulo, Brazil
| | - Fábio de Barros
- Instituto de Botânica, Núcleo de Pesquisa Orquidário do Estado, São Paulo, 04045-972, São Paulo, Brazil
| | - Leonardo P Felix
- Universidade Federal da Paraíba – UFPB, Campus II, Departamento de Ciências Biológicas, Areia, 58397-000, Paraíba, Brazil
| | - Juliano Sarmento Cabral
- University of Würzburg, Ecosystem Modeling, Center for Computational and Theoretical Biology (CCTB), Klara-Oppenheimer-Weg 32, D-97074, Würzburg, Germany
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3
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Shakya SB, Wang-Claypool CY, Cicero C, Bowie RCK, Mason NA. Neo-sex chromosome evolution and phenotypic differentiation across an elevational gradient in horned larks (Eremophila Alpestris). Mol Ecol 2022; 31:1783-1799. [PMID: 35048444 DOI: 10.1111/mec.16357] [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: 08/02/2021] [Revised: 12/16/2021] [Accepted: 01/07/2022] [Indexed: 11/29/2022]
Abstract
Genetic structure and phenotypic variation among populations is affected by both geographic distance and environmental variation across species' distributions. Understanding the relative contributions of isolation by distance (IBD) and isolation by environment (IBE) is important for elucidating population dynamics across habitats and ecological gradients. In this study, we compared phenotypic and genetic variation among Horned Lark (Eremophila alpestris) populations from 10 sites encompassing an elevational gradient from low-elevation desert scrub in Death Valley (285 a.s.l.) to high-elevation meadows in the White Mountains of the Sierra Nevada of California (greater than 3000 m a.s.l.). Using a ddRAD dataset of 28,474 SNPs aligned to a high-quality reference genome, we compared genetic structure with elevational, environmental, and spatial distance to quantify how different aspects of the landscape drive genomic and phenotypic differentiation in Horned Larks. We found larger-bodied birds were associated with sites that had less seasonality and higher annual precipitation, and longer spurs occurred in soils with more clay and silt content, less sand, and finer fragments. Larks have large neo-sex chromosomes, and we found that associations with elevation and environmental variation were much stronger among neo-sex chromosomes compared to autosomes. Furthermore, we found that putative chromosomal translocations, fusions, and inversions were associated with elevation and may underlie local adaptation across an elevational gradient in Horned Larks. Our results suggest that genetic variation in Horned Larks is affected more by IBD than IBE, but specific phenotypes and genomic regions-particually on neo-sex chromosomes-bear stronger associations with the environment.
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Affiliation(s)
- Subir B Shakya
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Cynthia Y Wang-Claypool
- Museum of Vertebrate Zoology, University of California, Berkeley, California, USA.,Department of Integrative Biology, University of California, Berkeley, California, USA
| | - Carla Cicero
- Museum of Vertebrate Zoology, University of California, Berkeley, California, USA
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology, University of California, Berkeley, California, USA.,Department of Integrative Biology, University of California, Berkeley, California, USA
| | - Nicholas A Mason
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA.,Museum of Vertebrate Zoology, University of California, Berkeley, California, USA
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4
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Poignet M, Johnson Pokorná M, Altmanová M, Majtánová Z, Dedukh D, Albrecht T, Reif J, Osiejuk TS, Reifová R. Comparison of Karyotypes in Two Hybridizing Passerine Species: Conserved Chromosomal Structure but Divergence in Centromeric Repeats. Front Genet 2021; 12:768987. [PMID: 34938317 PMCID: PMC8687609 DOI: 10.3389/fgene.2021.768987] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/10/2021] [Indexed: 11/23/2022] Open
Abstract
Changes in chromosomal structure involving chromosomal rearrangements or copy number variation of specific sequences can play an important role in speciation. Here, we explored the chromosomal structure of two hybridizing passerine species; the common nightingale (Luscinia megarhynchos) and the thrush nightingale (Luscinia luscinia), using conventional cytogenetic approaches, immunostaining of meiotic chromosomes, fluorescence in situ hybridization as well as comparative genomic hybridization (CGH). We found that the two nightingale species show conserved karyotypes with the same diploid chromosome number of 2n = 84. In addition to standard chromosomes, both species possessed a small germline restricted chromosome of similar size as a microchromosome. Just a few subtle changes in chromosome morphology were observed between the species, suggesting that only a limited number of chromosomal rearrangements occurred after the species divergence. The interspecific CGH experiment suggested that the two nightingale species might have diverged in centromeric repetitive sequences in most macro- and microchromosomes. In addition, some chromosomes showed changes in copy number of centromeric repeats between the species. The observation of very similar karyotypes in the two nightingale species is consistent with a generally slow rate of karyotype evolution in birds. The divergence of centromeric sequences between the two species could theoretically cause meiotic drive or reduced fertility in interspecific hybrids. Nevertheless, further studies are needed to evaluate the potential role of chromosomal structural variations in nightingale speciation.
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Affiliation(s)
- Manon Poignet
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Martina Johnson Pokorná
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Marie Altmanová
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Zuzana Majtánová
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Dmitry Dedukh
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Tomáš Albrecht
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Jiří Reif
- Institute for Environmental Studies, Faculty of Science, Charles University, Prague, Czech Republic
- Department of Zoology and Laboratory of Ornithology, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Tomasz S. Osiejuk
- Department of Behavioural Ecology, Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Radka Reifová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
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5
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Lopez KA, McDiarmid CS, Griffith SC, Lovette IJ, Hooper DM. Evaluating evidence of mitonuclear incompatibilities with the sex chromosomes in an avian hybrid zone. Evolution 2021; 75:1395-1414. [PMID: 33908624 DOI: 10.1111/evo.14243] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 02/15/2021] [Accepted: 04/11/2021] [Indexed: 12/13/2022]
Abstract
The exploration of hybrid zones and the intergenomic conflicts exposed through hybridization provide windows into the processes of divergence and speciation. Sex chromosomes and mitonuclear incompatibilities have strong associations with the genetics of hybrid dysfunction. In ZW sex-determining systems, maternal co-inheritance of the mitochondrial and W chromosomes immediately exposes incompatibilities between these maternal contributions of one species and the Z chromosome of another. We analyze mitochondrial and Z chromosome admixture in the long-tailed finch (Poephila acuticauda) of Australia, where hybridizing subspecies differ prominently in Z chromosome genotype and in bill color, yet the respective centers of geographic admixture for these two traits are offset by 350 km. We report two well-defined mitochondrial clades that diverged ∼0.5 million years ago. Mitochondrial contact is geographically co-located within a hybrid zone of Z chromosome admixture and is displaced from bill color admixture by nearly 400 km. Consistent with Haldane's rule expectations, hybrid zone females are significantly less likely than males to carry an admixed Z chromosome or have mismatched Z-mitochondrial genotypes. Furthermore, there are significantly fewer than expected mitonuclear mismatches in hybrid zone females and paternal backcross males. Results suggest a potential for mitonuclear/sex chromosome incompatibilities in the emergence of reproductive isolation in this system.
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Affiliation(s)
- Kelsie A Lopez
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, USA
| | - Callum S McDiarmid
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Simon C Griffith
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Irby J Lovette
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, USA
| | - Daniel M Hooper
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, USA.,Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
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6
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Junker J, Rick JA, McIntyre PB, Kimirei I, Sweke EA, Mosille JB, Wehrli B, Dinkel C, Mwaiko S, Seehausen O, Wagner CE. Structural genomic variation leads to genetic differentiation in Lake Tanganyika's sardines. Mol Ecol 2020; 29:3277-3298. [PMID: 32687665 DOI: 10.1111/mec.15559] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 06/27/2020] [Accepted: 06/29/2020] [Indexed: 01/03/2023]
Abstract
Identifying patterns in genetic structure and the genetic basis of ecological adaptation is a core goal of evolutionary biology and can inform the management and conservation of species that are vulnerable to population declines exacerbated by climate change. We used reduced-representation genomic sequencing methods to gain a better understanding of genetic structure among and within populations of Lake Tanganyika's two sardine species, Limnothrissa miodon and Stolothrissa tanganicae. Samples of these ecologically and economically important species were collected across the length of Lake Tanganyika, as well as from nearby Lake Kivu, where L. miodon was introduced in 1959. Our results reveal differentiation within both S. tanganicae and L. miodon that is not explained by geography. Instead, this genetic differentiation is due to the presence of large sex-specific regions in the genomes of both species, but involving different polymorphic sites in each species. Our results therefore indicate rapidly evolving XY sex determination in the two species. Additionally, we found evidence of a large chromosomal rearrangement in L. miodon, creating two homokaryotypes and one heterokaryotype. We found all karyotypes throughout Lake Tanganyika, but the frequencies vary along a north-south gradient and differ substantially in the introduced Lake Kivu population. We do not find evidence for significant isolation by distance, even over the hundreds of kilometres covered by our sampling, but we do find shallow population structure.
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Affiliation(s)
- Julian Junker
- EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland.,Division of Aquatic Ecology, Institute of Ecology & Evolution, University of Bern, Bern, Switzerland
| | - Jessica A Rick
- Department of Botany and Program in Ecology, University of Wyoming, Laramie, WY, USA
| | - Peter B McIntyre
- Department of Natural Resources, Cornell University, Ithaca, NY, USA
| | - Ismael Kimirei
- Tanzania Fisheries Research Institute (TAFIRI), Dar es Salaam, Tanzania
| | - Emmanuel A Sweke
- Tanzania Fisheries Research Institute (TAFIRI), Dar es Salaam, Tanzania.,Deep Sea Fishing Authority (DSFA), Zanzibar, Tanzania
| | - Julieth B Mosille
- Tanzania Fisheries Research Institute (TAFIRI), Dar es Salaam, Tanzania
| | - Bernhard Wehrli
- EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland.,Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Zürich, Switzerland
| | - Christian Dinkel
- EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Salome Mwaiko
- EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland.,Division of Aquatic Ecology, Institute of Ecology & Evolution, University of Bern, Bern, Switzerland
| | - Ole Seehausen
- EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland.,Division of Aquatic Ecology, Institute of Ecology & Evolution, University of Bern, Bern, Switzerland
| | - Catherine E Wagner
- Department of Botany and Program in Ecology, University of Wyoming, Laramie, WY, USA
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7
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Peñalba JV, Deng Y, Fang Q, Joseph L, Moritz C, Cockburn A. Genome of an iconic Australian bird: High-quality assembly and linkage map of the superb fairy-wren (Malurus cyaneus). Mol Ecol Resour 2020; 20:560-578. [PMID: 31821695 DOI: 10.1111/1755-0998.13124] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/09/2019] [Accepted: 12/02/2019] [Indexed: 12/13/2022]
Abstract
The superb fairy-wren, Malurus cyaneus, is one of the most iconic Australian passerine species. This species belongs to an endemic Australasian clade, Meliphagides, which diversified early in the evolution of the oscine passerines. Today, the oscine passerines comprise almost half of all avian species diversity. Despite the rapid increase of available bird genome assemblies, this part of the avian tree has not yet been represented by a high-quality reference. To rectify that, we present the first high-quality genome assembly of a Meliphagides representative: the superb fairy-wren. We combined Illumina shotgun and mate-pair sequences, PacBio long-reads, and a genetic linkage map from an intensively sampled pedigree of a wild population to generate this genome assembly. Of the final assembled 1.07-Gb genome, 975 Mb (90.4%) was anchored onto 25 pseudochromosomes resulting in a final superscaffold N50 of 68.11 Mb. This high-quality bird genome assembly is one of only a handful which is also accompanied by a genetic map and recombination landscape. In comparison to other pedigree-based bird genetic maps, we find that the fairy-wren genetic map more closely resembles those of Taeniopygia guttata and Parus major maps, unlike the Ficedula albicollis map which more closely resembles that of Gallus gallus. Lastly, we also provide a predictive gene and repeat annotation of the genome assembly. This new high-quality, annotated genome assembly will be an invaluable resource not only regarding the superb fairy-wren species and relatives but also broadly across the avian tree by providing a novel reference point for comparative genomic analyses.
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Affiliation(s)
- Joshua V Peñalba
- Division of Evolutionary Biology, Ludwig Maximilian University of Munich, Munich, Germany
| | | | - Qi Fang
- BGI-Shenzhen, Shenzhen, China
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO National Research Collections, Australia, Canberra, ACT, Australia
| | - Craig Moritz
- Centre for Biodiversity Analysis, Acton, ACT, Australia.,Division of Ecology and Evolution, Australian National University, Acton, ACT, Australia
| | - Andrew Cockburn
- Division of Ecology and Evolution, Australian National University, Acton, ACT, Australia
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8
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Kinsella CM, Ruiz-Ruano FJ, Dion-Côté AM, Charles AJ, Gossmann TI, Cabrero J, Kappei D, Hemmings N, Simons MJP, Camacho JPM, Forstmeier W, Suh A. Programmed DNA elimination of germline development genes in songbirds. Nat Commun 2019; 10:5468. [PMID: 31784533 PMCID: PMC6884545 DOI: 10.1038/s41467-019-13427-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 11/08/2019] [Indexed: 02/08/2023] Open
Abstract
In some eukaryotes, germline and somatic genomes differ dramatically in their composition. Here we characterise a major germline–soma dissimilarity caused by a germline-restricted chromosome (GRC) in songbirds. We show that the zebra finch GRC contains >115 genes paralogous to single-copy genes on 18 autosomes and the Z chromosome, and is enriched in genes involved in female gonad development. Many genes are likely functional, evidenced by expression in testes and ovaries at the RNA and protein level. Using comparative genomics, we show that genes have been added to the GRC over millions of years of evolution, with embryonic development genes bicc1 and trim71 dating to the ancestor of songbirds and dozens of other genes added very recently. The somatic elimination of this evolutionarily dynamic chromosome in songbirds implies a unique mechanism to minimise genetic conflict between germline and soma, relevant to antagonistic pleiotropy, an evolutionary process underlying ageing and sexual traits. Songbirds have extensive germline–soma genome differences due to developmental elimination of a germline-specific chromosome (GRC). Here, the authors show that the GRC contains dozens of expressed developmental genes, some of which have been on the GRC since the ancestor of all songbirds.
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Affiliation(s)
- Cormac M Kinsella
- Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, SE-752 36, Uppsala, Sweden.,Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands
| | - Francisco J Ruiz-Ruano
- Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, SE-752 36, Uppsala, Sweden. .,Department of Genetics, University of Granada, E-18071, Granada, Spain. .,Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, SE-752 36, Uppsala, Sweden.
| | - Anne-Marie Dion-Côté
- Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, SE-752 36, Uppsala, Sweden.,Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, 14853, USA.,Département de Biologie, Université de Moncton, Moncton, NB, E1A 3E9, Canada
| | - Alexander J Charles
- Department of Animal and Plant Sciences, University of Sheffield, S10 2TN, Sheffield, UK
| | - Toni I Gossmann
- Department of Animal and Plant Sciences, University of Sheffield, S10 2TN, Sheffield, UK.,Department of Animal Behaviour, Bielefeld University, D-33501, Bielefeld, Germany
| | - Josefa Cabrero
- Department of Genetics, University of Granada, E-18071, Granada, Spain
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 117596, Singapore, Singapore
| | - Nicola Hemmings
- Department of Animal and Plant Sciences, University of Sheffield, S10 2TN, Sheffield, UK
| | - Mirre J P Simons
- Department of Animal and Plant Sciences, University of Sheffield, S10 2TN, Sheffield, UK
| | | | | | - Alexander Suh
- Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, SE-752 36, Uppsala, Sweden. .,Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, SE-752 36, Uppsala, Sweden.
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9
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Wang H, Sawai A, Toji N, Sugioka R, Shibata Y, Suzuki Y, Ji Y, Hayase S, Akama S, Sese J, Wada K. Transcriptional regulatory divergence underpinning species-specific learned vocalization in songbirds. PLoS Biol 2019; 17:e3000476. [PMID: 31721761 PMCID: PMC6853299 DOI: 10.1371/journal.pbio.3000476] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 09/18/2019] [Indexed: 11/19/2022] Open
Abstract
Learning of most motor skills is constrained in a species-specific manner. However, the proximate mechanisms underlying species-specific learned behaviors remain poorly understood. Songbirds acquire species-specific songs through learning, which is hypothesized to depend on species-specific patterns of gene expression in functionally specialized brain regions for vocal learning and production, called song nuclei. Here, we leveraged two closely related songbird species, zebra finch, owl finch, and their interspecific first-generation (F1) hybrids, to relate transcriptional regulatory divergence between species with the production of species-specific songs. We quantified genome-wide gene expression in both species and compared this with allele-specific expression in F1 hybrids to identify genes whose expression in song nuclei is regulated by species divergence in either cis- or trans-regulation. We found that divergence in transcriptional regulation altered the expression of approximately 10% of total transcribed genes and was linked to differential gene expression between the two species. Furthermore, trans-regulatory changes were more prevalent than cis-regulatory and were associated with synaptic formation and transmission in song nucleus RA, the avian analog of the mammalian laryngeal motor cortex. We identified brain-derived neurotrophic factor (BDNF) as an upstream mediator of trans-regulated genes in RA, with a significant correlation between individual variation in BDNF expression level and species-specific song phenotypes in F1 hybrids. This was supported by the fact that the pharmacological overactivation of BDNF receptors altered the expression of its trans-regulated genes in the RA, thus disrupting the learned song structures of adult zebra finch songs at the acoustic and sequence levels. These results demonstrate functional neurogenetic associations between divergence in region-specific transcriptional regulation and species-specific learned behaviors.
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Affiliation(s)
- Hongdi Wang
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Azusa Sawai
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Noriyuki Toji
- Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Rintaro Sugioka
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Yukino Shibata
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Yuika Suzuki
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Yu Ji
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Shin Hayase
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Satoru Akama
- National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Jun Sese
- National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Humanome Lab Inc., Tokyo, Japan
| | - Kazuhiro Wada
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
- Faculty of Science, Hokkaido University, Sapporo, Japan
- Department of Biological Sciences, Hokkaido University, Sapporo, Japan
- * E-mail:
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10
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Connallon T, Olito C, Dutoit L, Papoli H, Ruzicka F, Yong L. Local adaptation and the evolution of inversions on sex chromosomes and autosomes. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0423. [PMID: 30150221 DOI: 10.1098/rstb.2017.0423] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2018] [Indexed: 11/12/2022] Open
Abstract
Spatially varying selection with gene flow can favour the evolution of inversions that bind locally adapted alleles together, facilitate local adaptation and ultimately drive genomic divergence between species. Several studies have shown that the rates of spread and establishment of new inversions capturing locally adaptive alleles depend on a suite of evolutionary factors, including the strength of selection for local adaptation, rates of gene flow and recombination, and the deleterious mutation load carried by inversions. Because the balance of these factors is expected to differ between X (or Z) chromosomes and autosomes, opportunities for inversion evolution are likely to systematically differ between these genomic regions, though such scenarios have not been formally modelled. Here, we consider the evolutionary dynamics of X-linked and autosomal inversions in populations evolving at a balance between migration and local selection. We identify three factors that lead to asymmetric rates of X-linked and autosome inversion establishment: (1) sex-biased migration, (2) dominance of locally adapted alleles and (3) chromosome-specific deleterious mutation loads. This theory predicts an elevated rate of fixation, and depressed opportunities for polymorphism, for X-linked inversions. Our survey of data on the genomic distribution of polymorphic and fixed inversions supports both theoretical predictions.This article is part of the theme issue 'Linking local adaptation with the evolution of sex differences'.
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Affiliation(s)
- Tim Connallon
- School of Biological Sciences, and Centre for Geometric Biology, Monash University, Clayton, 3800 Victoria, Australia
| | - Colin Olito
- School of Biological Sciences, and Centre for Geometric Biology, Monash University, Clayton, 3800 Victoria, Australia.,Department of Biology, Section for Evolutionary Ecology, Lund University, 22362 Lund, Sweden
| | - Ludovic Dutoit
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden.,Department of Zoology, University of Otago, 9054 Dunedin, New Zealand
| | - Homa Papoli
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
| | - Filip Ruzicka
- Research Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Lengxob Yong
- Centre for Ecology and Conservation, University of Exeter, Penryn TR10 9FE, UK
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11
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Nadachowska-Brzyska K, Burri R, Ellegren H. Footprints of adaptive evolution revealed by whole Z chromosomes haplotypes in flycatchers. Mol Ecol 2019; 28:2290-2304. [PMID: 30653779 PMCID: PMC6852393 DOI: 10.1111/mec.15021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 09/13/2018] [Accepted: 09/14/2018] [Indexed: 01/19/2023]
Abstract
Detecting positive selection using genomic data is critical to understanding the role of adaptive evolution. Of particular interest in this context is sex chromosomes since they are thought to play a special role in local adaptation and speciation. We sought to circumvent the challenges associated with statistical phasing when using haplotype-based statistics in sweep scans by benefitting from that whole chromosome haplotypes of the sex chromosomes can be obtained by resequencing of individuals of the hemizygous sex. We analyzed whole Z chromosome haplotypes from 100 females from several populations of four black and white flycatcher species (in birds, females are ZW and males ZZ). Based on integrated haplotype score (iHS) and number of segregating sites by length (nSL) statistics, we found strong and frequent haplotype structure in several regions of the Z chromosome in each species. Most of these sweep signals were population-specific, with essentially no evidence for regions under selection shared among species. Some completed sweeps were revealed by the cross-population extended haplotype homozygosity (XP-EHH) statistic. Importantly, by using statistically phased Z chromosome data from resequencing of males, we failed to recover the signals of selection detected in analyses based on whole chromosome haplotypes from females; instead, what likely represent false signals of selection were frequently seen. This highlights the power issues in statistical phasing and cautions against conclusions from selection scans using such data. The detection of frequent selective sweeps on the avian Z chromosome supports a large role of sex chromosomes in adaptive evolution.
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Affiliation(s)
| | - Reto Burri
- Department of Evolutionary Biology, University of Uppsala, Uppsala, Sweden.,Department of Population Ecology, Friedrich Schiller University Jena, Jena, Germany
| | - Hans Ellegren
- Department of Evolutionary Biology, University of Uppsala, Uppsala, Sweden
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12
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Abstract
An unusual supernumerary chromosome has been reported for two related avian species, the zebra and Bengalese finches. This large, germline-restricted chromosome (GRC) is eliminated from somatic cells and spermatids and transmitted via oocytes only. Its origin, distribution among avian lineages, and function were mostly unknown so far. Using immunolocalization of key meiotic proteins, we found that GRCs of varying size and genetic content are present in all 16 songbird species investigated and absent from germline genomes of all eight examined bird species from other avian orders. Results of fluorescent in situ hybridization of microdissected GRC probes and their sequencing indicate that GRCs show little homology between songbird species and contain a variety of repetitive elements and unique sequences with paralogs in the somatic genome. Our data suggest that the GRC evolved in the common ancestor of all songbirds and underwent significant changes in the extant descendant lineages.
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13
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Boman J, Frankl-Vilches C, da Silva Dos Santos M, de Oliveira EHC, Gahr M, Suh A. The Genome of Blue-Capped Cordon-Bleu Uncovers Hidden Diversity of LTR Retrotransposons in Zebra Finch. Genes (Basel) 2019; 10:E301. [PMID: 31013951 PMCID: PMC6523648 DOI: 10.3390/genes10040301] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 04/05/2019] [Accepted: 04/05/2019] [Indexed: 02/02/2023] Open
Abstract
Avian genomes have perplexed researchers by being conservative in both size and rearrangements, while simultaneously holding the blueprints for a massive species radiation during the last 65 million years (My). Transposable elements (TEs) in bird genomes are relatively scarce but have been implicated as important hotspots for chromosomal inversions. In zebra finch (Taeniopygia guttata), long terminal repeat (LTR) retrotransposons have proliferated and are positively associated with chromosomal breakpoint regions. Here, we present the genome, karyotype and transposons of blue-capped cordon-bleu (Uraeginthus cyanocephalus), an African songbird that diverged from zebra finch at the root of estrildid finches 10 million years ago (Mya). This constitutes the third linked-read sequenced genome assembly and fourth in-depth curated TE library of any bird. Exploration of TE diversity on this brief evolutionary timescale constitutes a considerable increase in resolution for avian TE biology and allowed us to uncover 4.5 Mb more LTR retrotransposons in the zebra finch genome. In blue-capped cordon-bleu, we likewise observed a recent LTR accumulation indicating that this is a shared feature of Estrildidae. Curiously, we discovered 25 new endogenous retrovirus-like LTR retrotransposon families of which at least 21 are present in zebra finch but were previously undiscovered. This highlights the importance of studying close relatives of model organisms.
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Affiliation(s)
- Jesper Boman
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, SE-752 36 Uppsala, Sweden.
| | - Carolina Frankl-Vilches
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany.
| | - Michelly da Silva Dos Santos
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, Pará, and Faculdade de Ciências Naturais (ICEN), Universidade Federal do Pará, Belém 66075-110, Brazil.
| | - Edivaldo H C de Oliveira
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, Pará, and Faculdade de Ciências Naturais (ICEN), Universidade Federal do Pará, Belém 66075-110, Brazil.
| | - Manfred Gahr
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany.
| | - Alexander Suh
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, SE-752 36 Uppsala, Sweden.
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14
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Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds. Nat Ecol Evol 2019; 3:834-844. [DOI: 10.1038/s41559-019-0850-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 02/22/2019] [Indexed: 11/09/2022]
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15
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Sclavi B, Herrick J. Genome size variation and species diversity in salamanders. J Evol Biol 2019; 32:278-286. [DOI: 10.1111/jeb.13412] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 12/14/2018] [Accepted: 12/20/2018] [Indexed: 12/13/2022]
Affiliation(s)
| | - John Herrick
- Department of Physics; Simon Fraser University; Burnaby British Columbia Canada
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16
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Hooper DM, Griffith SC, Price TD. Sex chromosome inversions enforce reproductive isolation across an avian hybrid zone. Mol Ecol 2018; 28:1246-1262. [PMID: 30230092 DOI: 10.1111/mec.14874] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/23/2018] [Accepted: 08/27/2018] [Indexed: 12/11/2022]
Abstract
Across hybrid zones, the sex chromosomes are often more strongly differentiated than the autosomes. This is regularly attributed to the greater frequency of reproductive incompatibilities accumulating on sex chromosomes and their exposure in the heterogametic sex. Working within an avian hybrid zone, we explore the possibility that chromosome inversions differentially accumulate on the Z chromosome compared to the autosomes and thereby contribute to Z chromosome differentiation. We analyse the northern Australian hybrid zone between two subspecies of the long-tailed finch (Poephila acuticauda), first described based on differences in bill colour, using reduced-representation genomic sequencing for 293 individuals over a 1,530-km transect. Autosomal differentiation between subspecies is minimal. In contrast, 75% of the Z chromosome is highly differentiated and shows a steep genomic cline, which is displaced 350 km to the west of the cline in bill colour. Differentiation is associated with two or more putative chromosomal inversions, each predominating in one subspecies. If inversions reduce recombination between hybrid incompatibilities, they are selectively favoured and should therefore accumulate in hybrid zones. We argue that this predisposes inversions to differentially accumulate on the Z chromosome. One genomic region affecting bill colour is on the Z, but the main candidates are on chromosome 8. This and the displacement of the bill colour and Z chromosome cline centres suggest that bill colour has not strongly contributed to inversion accumulation. Based on cline width, however, the Z chromosome and bill colour both contribute to reproductive isolation established between this pair of subspecies.
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Affiliation(s)
- Daniel M Hooper
- Cornell Lab of Ornithology, Cornell University, Ithaca, New York.,Committe on Evolutionary Biology, University of Chicago, Chicago, Illinois
| | - Simon C Griffith
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Trevor D Price
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois
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17
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Toomey MB, Marques CI, Andrade P, Araújo PM, Sabatino S, Gazda MA, Afonso S, Lopes RJ, Corbo JC, Carneiro M. A non-coding region near Follistatin controls head colour polymorphism in the Gouldian finch. Proc Biol Sci 2018; 285:20181788. [PMID: 30282656 PMCID: PMC6191701 DOI: 10.1098/rspb.2018.1788] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 09/05/2018] [Indexed: 12/17/2022] Open
Abstract
Discrete colour morphs coexisting within a single population are common in nature. In a broad range of organisms, sympatric colour morphs often display major differences in other traits, including morphology, physiology or behaviour. Despite the repeated occurrence of this phenomenon, our understanding of the genetics that underlie multi-trait differences and the factors that promote the long-term maintenance of phenotypic variability within a freely interbreeding population are incomplete. Here, we investigated the genetic basis of red and black head colour in the Gouldian finch (Erythrura gouldiae), a classic polymorphic system in which naturally occurring colour morphs also display differences in aggressivity and reproductive success. We show that the candidate locus is a small (approx. 70 kb) non-coding region mapping to the Z chromosome near the Follistatin (FST) gene. Unlike recent findings in other systems where phenotypic morphs are explained by large inversions containing hundreds of genes (so-called supergenes), we did not identify any structural rearrangements between the two haplotypes using linked-read sequencing technology. Nucleotide divergence between the red and black alleles was high when compared to the remainder of the Z chromosome, consistent with their maintenance as balanced polymorphisms over several million years. Our results illustrate how pleiotropic phenotypes can arise from simple genetic variation, probably regulatory in nature.
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Affiliation(s)
- Matthew B Toomey
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Cristiana I Marques
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
| | - Pedro Andrade
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
| | - Pedro M Araújo
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
- Centro de Ciências do Mar e do Ambiente, Departamento de Ciências da Vida, Universidade de Coimbra, 3004-517 Coimbra, Portugal
| | - Stephen Sabatino
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Małgorzata A Gazda
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
| | - Sandra Afonso
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Ricardo J Lopes
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Joseph C Corbo
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Miguel Carneiro
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
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18
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Colquitt BM, Mets DG, Brainard MS. Draft genome assembly of the Bengalese finch, Lonchura striata domestica, a model for motor skill variability and learning. Gigascience 2018; 7:1-6. [PMID: 29618046 PMCID: PMC5861438 DOI: 10.1093/gigascience/giy008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 12/12/2017] [Accepted: 02/06/2018] [Indexed: 12/18/2022] Open
Abstract
Background Vocal learning in songbirds has emerged as a powerful model for sensorimotor learning. Neurobehavioral studies of Bengalese finch (Lonchura striata domestica) song, naturally more variable and plastic than songs of other finch species, have demonstrated the importance of behavioral variability for initial learning, maintenance, and plasticity of vocalizations. However, the molecular and genetic underpinnings of this variability and the learning it supports are poorly understood. Findings To establish a platform for the molecular analysis of behavioral variability and plasticity, we generated an initial draft assembly of the Bengalese finch genome from a single male animal to 151× coverage and an N50 of 3.0 MB. Furthermore, we developed an initial set of gene models using RNA-seq data from 8 samples that comprise liver, muscle, cerebellum, brainstem/midbrain, and forebrain tissue from juvenile and adult Bengalese finches of both sexes. Conclusions We provide a draft Bengalese finch genome and gene annotation to facilitate the study of the molecular-genetic influences on behavioral variability and the process of vocal learning. These data will directly support many avenues for the identification of genes involved in learning, including differential expression analysis, comparative genomic analysis (through comparison to existing avian genome assemblies), and derivation of genetic maps for linkage analysis. Bengalese finch gene models and sequences will be essential for subsequent manipulation (molecular or genetic) of genes and gene products, enabling novel mechanistic investigations into the role of variability in learned behavior.
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Affiliation(s)
- Bradley M Colquitt
- Department of Physiology, University of California-San Francisco, San Francisco, 94158 California
| | - David G Mets
- Department of Physiology, University of California-San Francisco, San Francisco, 94158 California
| | - Michael S Brainard
- Department of Physiology, University of California-San Francisco, San Francisco, 94158 California
- Howard Hughes Medical Institute, Chevy Chase, Maryland
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19
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20
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Samuk K. Inversions and the origin of behavioral differences in cod. Mol Ecol 2017; 25:2111-3. [PMID: 27213696 DOI: 10.1111/mec.13624] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 03/21/2016] [Indexed: 11/27/2022]
Abstract
How does adaptation manage to occur in the face of overwhelming gene flow? One popular idea is that the suppression of recombination, for example the fixation of a chromosomal inversion, can maintain linkage disequilibrium between groups of locally adapted alleles that would otherwise be degraded by gene flow. This idea has captured the imagination of many geneticists and evolutionary biologists, but we still have only a basic understanding of its general importance. In this issue of Molecular Ecology, Kirubakaran et al. () examine the role of recombination suppression in a particularly fascinating example of adaptation in the face of gene flow: the evolution of migratory differences between interbreeding populations of cod. Along the north coast of Norway, two types of cod breed in the near-shore waters: a 'stationary' form that lives near the coast year round, and a 'migratory' form that lives far offshore and only returns to the coast to breed. Using a combination of approaches, Kirubakaran et al. () deftly demonstrate that the migratory form has completely fixed two adjacent inversions containing a suite of genes closely connected to migratory behaviour and feeding differences. This work provides an excellent example of how recombination suppression can facilitate adaptive divergence, and helps us understand the geographic and temporal scales over which genomic structural variation evolves.
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Affiliation(s)
- Kieran Samuk
- Department of Zoology, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T1Z4, Canada
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21
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Trans-oceanic genomic divergence of Atlantic cod ecotypes is associated with large inversions. Heredity (Edinb) 2017; 119:418-428. [PMID: 28930288 PMCID: PMC5677996 DOI: 10.1038/hdy.2017.54] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Revised: 07/13/2017] [Accepted: 08/05/2017] [Indexed: 01/03/2023] Open
Abstract
Chromosomal rearrangements such as inversions can play a crucial role in maintaining polymorphism underlying complex traits and contribute to the process of speciation. In Atlantic cod (Gadus morhua), inversions of several megabases have been identified that dominate genomic differentiation between migratory and nonmigratory ecotypes in the Northeast Atlantic. Here, we show that the same genomic regions display elevated divergence and contribute to ecotype divergence in the Northwest Atlantic as well. The occurrence of these inversions on both sides of the Atlantic Ocean reveals a common evolutionary origin, predating the >100 000-year-old trans-Atlantic separation of Atlantic cod. The long-term persistence of these inversions indicates that they are maintained by selection, possibly facilitated by coevolution of genes underlying complex traits. Our data suggest that migratory behaviour is derived from more stationary, ancestral ecotypes. Overall, we identify several large genomic regions—each containing hundreds of genes—likely involved in the maintenance of genomic divergence in Atlantic cod on both sides of the Atlantic Ocean.
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22
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Mandrioli M, Zambonini G, Manicardi GC. Comparative Gene Mapping as a Tool to Understand the Evolution of Pest Crop Insect Chromosomes. Int J Mol Sci 2017; 18:ijms18091919. [PMID: 28880213 PMCID: PMC5618568 DOI: 10.3390/ijms18091919] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 08/31/2017] [Accepted: 09/05/2017] [Indexed: 11/22/2022] Open
Abstract
The extent of the conservation of synteny and gene order in aphids has been previously investigated only by comparing a small subset of linkage groups between the pea aphid Acyrthosiphon pisum and a few other aphid species. Here we compared the localization of eight A. pisum scaffolds (covering more than 5 Mb and 83 genes) in respect to the Drosophila melanogaster Muller elements identifying orthologous loci spanning all the four A. pisum chromosomes. Comparison of the genetic maps revealed a conserved synteny across different loci suggesting that the study of the fruit fly Muller elements could favour the identification of chromosomal markers useful for the study of chromosomal rearrangements in aphids. A. pisum is the first aphid species to have its genome sequenced and the finding that there are several chromosomal regions in synteny between Diptera and Hemiptera indicates that the genomic tools developed in A. pisum will be broadly useful not only for the study of other aphids but also for other insect species.
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Affiliation(s)
- Mauro Mandrioli
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena 41125, Italy.
| | - Giada Zambonini
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena 41125, Italy.
| | - Gian Carlo Manicardi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena 41125, Italy.
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23
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Chromosomal inversion differences correlate with range overlap in passerine birds. Nat Ecol Evol 2017; 1:1526-1534. [PMID: 29185507 DOI: 10.1038/s41559-017-0284-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 07/19/2017] [Indexed: 11/08/2022]
Abstract
Chromosomal inversions evolve frequently but the reasons for this remain unclear. We used cytological descriptions of 411 species of passerine birds to identify large pericentric inversion differences between species, based on the position of the centromere. Within 81 small clades comprising 284 of the species, we found 319 differences on the 9 largest autosomes combined, 56 on the Z chromosome, and 55 on the W chromosome. We also identified inversions present within 32 species. Using a new fossil-calibrated phylogeny, we examined the phylogenetic, demographic and genomic context in which these inversions have evolved. The number of inversion differences between closely related species is consistently predicted by whether the ranges of species overlap, even when time is controlled for as far as is possible. Fixation rates vary across the autosomes, but inversions are more likely to be fixed on the Z chromosome than the average autosome. Variable mutagenic input alone (estimated by chromosome size, map length, GC content or repeat density) cannot explain the differences between chromosomes in the number of inversions fixed. Together, these results support a model in which inversions increase because of their effects on recombination suppression in the face of hybridization. Other factors associated with hybridization may also contribute, including the possibility that inversions contain incompatibility alleles, making taxa less likely to collapse following secondary contact.
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24
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A sex-linked supergene controls sperm morphology and swimming speed in a songbird. Nat Ecol Evol 2017; 1:1168-1176. [DOI: 10.1038/s41559-017-0235-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 06/06/2017] [Indexed: 01/08/2023]
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25
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A sex-chromosome inversion causes strong overdominance for sperm traits that affect siring success. Nat Ecol Evol 2017; 1:1177-1184. [PMID: 29046576 DOI: 10.1038/s41559-017-0236-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 06/06/2017] [Indexed: 01/23/2023]
Abstract
Male reproductive success depends on the competitive ability of sperm to fertilize the ova, which should lead to strong selection on sperm characteristics. This raises the question of how heritable variation in sperm traits is maintained. Here we show that in zebra finches (Taeniopygia guttata) nearly half of the variance in sperm morphology is explained by an inversion on the Z chromosome with a 40% allele frequency in the wild. The sperm of males that are heterozygous for the inversion had the longest midpieces and the highest velocity. Furthermore, such males achieved the highest fertility and the highest siring success, both within-pair and extra-pair. Males homozygous for the derived allele show detrimental sperm characteristics and the lowest siring success. Our results suggest heterozygote advantage as the mechanism that maintains the inversion polymorphism and hence variance in sperm design and in fitness.
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26
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Vijay N, Weissensteiner M, Burri R, Kawakami T, Ellegren H, Wolf JBW. Genomewide patterns of variation in genetic diversity are shared among populations, species and higher-order taxa. Mol Ecol 2017; 26:4284-4295. [PMID: 28570015 DOI: 10.1111/mec.14195] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 05/10/2017] [Accepted: 05/17/2017] [Indexed: 12/15/2022]
Abstract
Genomewide screens of genetic variation within and between populations can reveal signatures of selection implicated in adaptation and speciation. Genomic regions with low genetic diversity and elevated differentiation reflective of locally reduced effective population sizes (Ne ) are candidates for barrier loci contributing to population divergence. Yet, such candidate genomic regions need not arise as a result of selection promoting adaptation or advancing reproductive isolation. Linked selection unrelated to lineage-specific adaptation or population divergence can generate comparable signatures. It is challenging to distinguish between these processes, particularly when diverging populations share ancestral genetic variation. In this study, we took a comparative approach using population assemblages from distant clades assessing genomic parallelism of variation in Ne . Utilizing population-level polymorphism data from 444 resequenced genomes of three avian clades spanning 50 million years of evolution, we tested whether population genetic summary statistics reflecting genomewide variation in Ne would covary among populations within clades, and importantly, also among clades where lineage sorting has been completed. All statistics including population-scaled recombination rate (ρ), nucleotide diversity (π) and measures of genetic differentiation between populations (FST , PBS, dxy ) were significantly correlated across all phylogenetic distances. Moreover, genomic regions with elevated levels of genetic differentiation were associated with inferred pericentromeric and subtelomeric regions. The phylogenetic stability of diversity landscapes and stable association with genomic features support a role of linked selection not necessarily associated with adaptation and speciation in shaping patterns of genomewide heterogeneity in genetic diversity.
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Affiliation(s)
- Nagarjun Vijay
- Department of Evolutionary Biology and SciLifeLab, Uppsala University, Uppsala, Sweden.,Lab of Molecular and Genomic Evolution, Department of Ecology and Evolutionary Biology, College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI, USA
| | - Matthias Weissensteiner
- Department of Evolutionary Biology and SciLifeLab, Uppsala University, Uppsala, Sweden.,Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Reto Burri
- Department of Evolutionary Biology and SciLifeLab, Uppsala University, Uppsala, Sweden.,Department of Population Ecology, Friedrich Schiller University Jena, Jena, Germany
| | - Takeshi Kawakami
- Department of Evolutionary Biology and SciLifeLab, Uppsala University, Uppsala, Sweden.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Hans Ellegren
- Department of Evolutionary Biology and SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Jochen B W Wolf
- Department of Evolutionary Biology and SciLifeLab, Uppsala University, Uppsala, Sweden.,Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
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27
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Weissensteiner MH, Pang AWC, Bunikis I, Höijer I, Vinnere-Petterson O, Suh A, Wolf JBW. Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications. Genome Res 2017; 27:697-708. [PMID: 28360231 PMCID: PMC5411765 DOI: 10.1101/gr.215095.116] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 03/10/2017] [Indexed: 12/27/2022]
Abstract
Accurate and contiguous genome assembly is key to a comprehensive understanding of the processes shaping genomic diversity and evolution. Yet, it is frequently constrained by constitutive heterochromatin, usually characterized by highly repetitive DNA. As a key feature of genome architecture associated with centromeric and subtelomeric regions, it locally influences meiotic recombination. In this study, we assess the impact of large tandem repeat arrays on the recombination rate landscape in an avian speciation model, the Eurasian crow. We assembled two high-quality genome references using single-molecule real-time sequencing (long-read assembly [LR]) and single-molecule optical maps (optical map assembly [OM]). A three-way comparison including the published short-read assembly (SR) constructed for the same individual allowed assessing assembly properties and pinpointing misassemblies. By combining information from all three assemblies, we characterized 36 previously unidentified large repetitive regions in the proximity of sequence assembly breakpoints, the majority of which contained complex arrays of a 14-kb satellite repeat or its 1.2-kb subunit. Using whole-genome population resequencing data, we estimated the population-scaled recombination rate (ρ) and found it to be significantly reduced in these regions. These findings are consistent with an effect of low recombination in regions adjacent to centromeric or subtelomeric heterochromatin and add to our understanding of the processes generating widespread heterogeneity in genetic diversity and differentiation along the genome. By combining three different technologies, our results highlight the importance of adding a layer of information on genome structure that is inaccessible to each approach independently.
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Affiliation(s)
- Matthias H Weissensteiner
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilian University of Munich, 82152 Planegg-Martinsried, Germany
| | | | - Ignas Bunikis
- SciLife Lab Uppsala, Uppsala University SE-751 85 Uppsala, Sweden
| | - Ida Höijer
- SciLife Lab Uppsala, Uppsala University SE-751 85 Uppsala, Sweden
| | | | - Alexander Suh
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Jochen B W Wolf
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilian University of Munich, 82152 Planegg-Martinsried, Germany
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28
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Kozak GM, Wadsworth CB, Kahne SC, Bogdanowicz SM, Harrison RG, Coates BS, Dopman EB. A combination of sexual and ecological divergence contributes to rearrangement spread during initial stages of speciation. Mol Ecol 2017. [DOI: 10.111/mwc.1403610.1111/mec.14036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Genevieve M. Kozak
- Department of Biology Tufts University 200 Boston Ave. Ste. 4700 Medford MA 02155 USA
| | - Crista B. Wadsworth
- Department of Biology Tufts University 200 Boston Ave. Ste. 4700 Medford MA 02155 USA
- Harvard TH Chan School of Public Health 677 Huntington Ave. Boston MA 02115 USA
| | - Shoshanna C. Kahne
- Department of Biology Tufts University 200 Boston Ave. Ste. 4700 Medford MA 02155 USA
| | - Steven M. Bogdanowicz
- Department of Ecology and Evolutionary Biology Cornell University 215 Tower Road Ithaca NY 14853 USA
| | - Richard G. Harrison
- Department of Ecology and Evolutionary Biology Cornell University 215 Tower Road Ithaca NY 14853 USA
| | - Brad S. Coates
- Corn Insects and Crop Genetics Research Unit USDA‐ARS Iowa State University 103 Genetics Laboratory Ames IA 50011 USA
| | - Erik B. Dopman
- Department of Biology Tufts University 200 Boston Ave. Ste. 4700 Medford MA 02155 USA
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29
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Höllinger I, Hermisson J. Bounds to parapatric speciation: A Dobzhansky-Muller incompatibility model involving autosomes, X chromosomes, and mitochondria. Evolution 2017; 71:1366-1380. [PMID: 28272742 DOI: 10.1111/evo.13223] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 02/22/2017] [Indexed: 12/16/2022]
Abstract
We investigate the conditions for the origin and maintenance of postzygotic isolation barriers, so called (Bateson-)Dobzhansky-Muller incompatibilities or DMIs, among populations that are connected by gene flow. Specifically, we compare the relative stability of pairwise DMIs among autosomes, X chromosomes, and mitochondrial genes. In an analytical approach based on a continent-island framework, we determine how the maximum permissible migration rates depend on the genomic architecture of the DMI, on sex bias in migration rates, and on sex-dependence of allelic and epistatic effects, such as dosage compensation. Our results show that X-linkage of DMIs can enlarge the migration bounds relative to autosomal DMIs or autosome-mitochondrial DMIs, in particular in the presence of dosage compensation. The effect is further strengthened with male-biased migration. This mechanism might contribute to a higher density of DMIs on the X chromosome (large X-effect) that has been observed in several species clades. Furthermore, our results agree with empirical findings of higher introgression rates of autosomal compared to X-linked loci.
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Affiliation(s)
- Ilse Höllinger
- Mathematics and BioSciences Group, Faculty of Mathematics and Max F. Perutz Laboratories, University of Vienna, Vienna, Austria.,Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Joachim Hermisson
- Mathematics and BioSciences Group, Faculty of Mathematics and Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
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30
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Kozak GM, Wadsworth CB, Kahne SC, Bogdanowicz SM, Harrison RG, Coates BS, Dopman EB. A combination of sexual and ecological divergence contributes to rearrangement spread during initial stages of speciation. Mol Ecol 2017; 26:2331-2347. [PMID: 28141898 DOI: 10.1111/mec.14036] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Revised: 12/12/2016] [Accepted: 01/10/2017] [Indexed: 01/04/2023]
Abstract
Chromosomal rearrangements between sympatric species often contain multiple loci contributing to assortative mating, local adaptation and hybrid sterility. When and how these associations arise during the process of speciation remains a subject of debate. Here, we address the relative roles of local adaptation and assortative mating on the dynamics of rearrangement evolution by studying how a rearrangement covaries with sexual and ecological trait divergence within a species. Previously, a chromosomal rearrangement that suppresses recombination on the Z (sex) chromosome was identified in European corn borer moths (Ostrinia nubilalis). We further characterize this recombination suppressor and explore its association with variation in sex pheromone communication and seasonal ecological adaptation in pairs of populations that are divergent in one or both of these characteristics. Direct estimates of recombination suppression in pedigree mapping families indicated that more than 39% of the Z chromosome (encompassing up to ~10 megabases and ~300 genes) resides within a nonrecombining unit, including pheromone olfactory receptor genes and a major quantitative trait locus that contributes to ecotype differences (Pdd). Combining direct and indirect estimates of recombination suppression, we found that the rearrangement was occasionally present between sexually isolated strains (E vs. Z) and between divergent ecotypes (univoltine vs. bivoltine). However, it was only consistently present when populations differed in both sexual and ecological traits. Our results suggest that independent of the forces that drove the initial establishment of the rearrangement, a combination of sexual and ecological divergence is required for rearrangement spread during speciation.
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Affiliation(s)
- Genevieve M Kozak
- Department of Biology, Tufts University, 200 Boston Ave. Ste. 4700, Medford, MA, 02155, USA
| | - Crista B Wadsworth
- Department of Biology, Tufts University, 200 Boston Ave. Ste. 4700, Medford, MA, 02155, USA.,Harvard TH Chan School of Public Health, 677 Huntington Ave., Boston, MA, 02115, USA
| | - Shoshanna C Kahne
- Department of Biology, Tufts University, 200 Boston Ave. Ste. 4700, Medford, MA, 02155, USA
| | - Steven M Bogdanowicz
- Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Road, Ithaca, NY, 14853, USA
| | - Richard G Harrison
- Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Road, Ithaca, NY, 14853, USA
| | - Brad S Coates
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Iowa State University, 103 Genetics Laboratory, Ames, IA, 50011, USA
| | - Erik B Dopman
- Department of Biology, Tufts University, 200 Boston Ave. Ste. 4700, Medford, MA, 02155, USA
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31
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Potter S, Bragg JG, Blom MPK, Deakin JE, Kirkpatrick M, Eldridge MDB, Moritz C. Chromosomal Speciation in the Genomics Era: Disentangling Phylogenetic Evolution of Rock-wallabies. Front Genet 2017; 8:10. [PMID: 28265284 PMCID: PMC5301020 DOI: 10.3389/fgene.2017.00010] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 01/18/2017] [Indexed: 12/24/2022] Open
Abstract
The association of chromosome rearrangements (CRs) with speciation is well established, and there is a long history of theory and evidence relating to "chromosomal speciation." Genomic sequencing has the potential to provide new insights into how reorganization of genome structure promotes divergence, and in model systems has demonstrated reduced gene flow in rearranged segments. However, there are limits to what we can understand from a small number of model systems, which each only tell us about one episode of chromosomal speciation. Progressing from patterns of association between chromosome (and genic) change, to understanding processes of speciation requires both comparative studies across diverse systems and integration of genome-scale sequence comparisons with other lines of evidence. Here, we showcase a promising example of chromosomal speciation in a non-model organism, the endemic Australian marsupial genus Petrogale. We present initial phylogenetic results from exon-capture that resolve a history of divergence associated with extensive and repeated CRs. Yet it remains challenging to disentangle gene tree heterogeneity caused by recent divergence and gene flow in this and other such recent radiations. We outline a way forward for better integration of comparative genomic sequence data with evidence from molecular cytogenetics, and analyses of shifts in the recombination landscape and potential disruption of meiotic segregation and epigenetic programming. In all likelihood, CRs impact multiple cellular processes and these effects need to be considered together, along with effects of genic divergence. Understanding the effects of CRs together with genic divergence will require development of more integrative theory and inference methods. Together, new data and analysis tools will combine to shed light on long standing questions of how chromosome and genic divergence promote speciation.
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Affiliation(s)
- Sally Potter
- Research School of Biology, Australian National University, ActonACT, Australia
- Australian Museum Research Institute, Australian Museum, SydneyNSW, Australia
| | - Jason G. Bragg
- National Herbarium of New South Wales, The Royal Botanic Gardens and Domain Trust, SydneyNSW, Australia
| | - Mozes P. K. Blom
- Department of Bioinformatics and Genetics, Swedish Museum of Natural HistoryStockholm, Sweden
| | - Janine E. Deakin
- Institute for Applied Ecology, University of Canberra, BruceACT, Australia
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas, AustinTX, USA
| | - Mark D. B. Eldridge
- Australian Museum Research Institute, Australian Museum, SydneyNSW, Australia
| | - Craig Moritz
- Research School of Biology, Australian National University, ActonACT, Australia
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32
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Kapusta A, Suh A. Evolution of bird genomes-a transposon's-eye view. Ann N Y Acad Sci 2016; 1389:164-185. [DOI: 10.1111/nyas.13295] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 10/06/2016] [Accepted: 10/11/2016] [Indexed: 02/06/2023]
Affiliation(s)
- Aurélie Kapusta
- Department of Human Genetics; University of Utah School of Medicine; Salt Lake City Utah
| | - Alexander Suh
- Department of Evolutionary Biology (EBC); Uppsala University; Uppsala Sweden
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33
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Martinez PA, Jacobina UP, Fernandes RV, Brito C, Penone C, Amado TF, Fonseca CR, Bidau CJ. A comparative study on karyotypic diversification rate in mammals. Heredity (Edinb) 2016; 118:366-373. [PMID: 27804966 DOI: 10.1038/hdy.2016.110] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 09/19/2016] [Accepted: 09/27/2016] [Indexed: 01/23/2023] Open
Abstract
Chromosomal rearrangements have a relevant role in organismic evolution. However, little is known about the mechanisms that lead different phylogenetic clades to have different chromosomal rearrangement rates. Here, we investigate the causes behind the wide karyotypic diversity exhibited by mammals. In particular, we analyzed the role of metabolic, reproductive, biogeographic and genomic characteristics on the rates of macro- and microstructural karyotypic diversification (rKD) using comparative phylogenetic methods. We found evidence that reproductive characteristics such as larger litter size per year and longevity, by allowing a higher number of meioses in absolute time, favor a higher probability of chromosomal change. Furthermore, families with large geographic distributions but containing species with restricted geographic ranges showed a greater probability of fixation of macrostructural chromosomal changes in different geographic areas. Finally, rKD does not evolve by Brownian motion because the mutation rate depends on the concerted evolution of repetitive sequences. The decisive factors of rKD evolution will be natural selection, genetic drift and meiotic drive that will eventually allow or not the fixation of the rearrangements. Our results indicate that mammalian karyotypic diversity is influenced by historical and adaptive mechanisms where reproductive and genomic factors modulate the rate of chromosomal change.
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Affiliation(s)
- P A Martinez
- PIBi Lab-Laboratorio de Pesquisas Integrativas em Biodiversidade, Pós-Graduação em Ecologia e Conservação, Universidade Federal de Sergipe, São Cristovão, Brazil
| | | | - R V Fernandes
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - C Brito
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - C Penone
- Institute of Plant Science, University of Bern, Bern, Switzerland
| | - T F Amado
- BioMa-Biodiversity and Macroecology Lab, Department of Biology and Geology, Physics and Inorganic Chemistry, Rey Juan Carlos University, Mostoles, Spain
| | - C R Fonseca
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - C J Bidau
- Paraná y Los Claveles, Garupá, Argentina
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34
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Dagilis AJ, Kirkpatrick M. Prezygotic isolation, mating preferences, and the evolution of chromosomal inversions. Evolution 2016; 70:1465-72. [PMID: 27174252 DOI: 10.1111/evo.12954] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Revised: 04/26/2016] [Accepted: 05/02/2016] [Indexed: 12/12/2022]
Abstract
Chromosomal inversions are frequently implicated in isolating species. Models have shown how inversions can evolve in the context of postmating isolation. Inversions are also frequently associated with mating preferences, a topic that has not been studied theoretically. Here, we show how inversions can spread by capturing a mating preference locus and one or more loci involved with epistatic incompatibilities. Inversions can be established under broad conditions ranging from near panmixis to nearly complete speciation. These results provide a hypothesis to explain the growing number of examples of inversions associated with premating isolating mechanisms.
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Affiliation(s)
- Andrius J Dagilis
- Department of Integrative Biology, University of Texas, Austin, Texas, 78712.
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas, Austin, Texas, 78712
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35
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Tigano A, Friesen VL. Genomics of local adaptation with gene flow. Mol Ecol 2016; 25:2144-64. [DOI: 10.1111/mec.13606] [Citation(s) in RCA: 241] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 02/22/2016] [Accepted: 03/01/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Anna Tigano
- Department of Biology; Queen's University; Kingston ON K7L 3N6 Canada
| | - Vicki L. Friesen
- Department of Biology; Queen's University; Kingston ON K7L 3N6 Canada
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36
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Kim KW, Griffith SC, Burke T. Linkage mapping of a polymorphic plumage locus associated with intermorph incompatibility in the Gouldian finch (Erythrura gouldiae). Heredity (Edinb) 2016; 116:409-16. [PMID: 26786066 PMCID: PMC4806697 DOI: 10.1038/hdy.2015.114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 11/25/2015] [Accepted: 12/11/2015] [Indexed: 01/04/2023] Open
Abstract
Colour polymorphism is known to facilitate speciation but the genetic basis of animal pigmentation and how colour polymorphisms contribute to speciation is poorly understood. Restricted recombination may promote linkage disequilibrium between the colour locus and incompatibility genes. Genomic rearrangement and the position of relevant loci within a chromosome are important factors that influence the frequency of recombination. Therefore, it is important to know the position of the colour locus, gene order and recombination landscape of the chromosome to understand the mechanism that generates incompatibilities between morphs. Recent studies showed remarkable pre- and postzygotic incompatibilities between sympatric colour morphs of the Gouldian finch (Erythrura gouldiae), in which head feather colour is genetically determined by a single sex-linked locus, Red. We constructed a genetic map for the Z chromosome of the Gouldian finch (male-specific map distance=131 cM), using 618 captive-bred birds and 34 microsatellite markers, to investigate the extent of inter- and intraspecific genomic rearrangements and variation in recombination rate within the Z chromosome. We refined the location of the Red locus to a ~7.2-cM interval in a region with a moderate recombination rate but outside the least-recombining, putative centromeric region. There was no evidence of chromosome-wide genomic rearrangements between the chromosomes carrying the red or black alleles with the current marker resolution. This work will contribute to identifying the causal gene, which will in turn enable alternative explanations for the association between incompatibility and colouration, such as fine-scale linkage disequilibrium, genomic rearrangements and pleiotropy, to be tested.
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Affiliation(s)
- K-W Kim
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - S C Griffith
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - T Burke
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
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37
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Sved JA, Chen Y, Shearman D, Frommer M, Gilchrist AS, Sherwin WB. Extraordinary conservation of entire chromosomes in insects over long evolutionary periods. Evolution 2015; 70:229-34. [PMID: 26639450 DOI: 10.1111/evo.12831] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 11/11/2015] [Indexed: 01/16/2023]
Abstract
Comparison of the genomes of different Drosophila species has shown that six different chromosomes, the so-called ''Muller elements," constitute the building blocks for all Drosophila species. Here, we confirm previous results suggesting that this conservation of the Muller elements extends far beyond Drosophila, to at least tephritid fruit flies, thought to have diverged from drosophilids 60-70 mYr ago. Less than 10 percent of genes differ in chromosome location between the two insect groups. Within chromosomes, however, the order is highly scrambled, as expected from the comparison between Drosophila species. The data also support the notion that the sex chromosomes of tephritid flies originated from an ancestor of the dot chromosome 4 of Drosophila. Overall, therefore, no new chromosome has been created for perhaps a billion generations over the two evolutionary lines. This stability at the chromosome level, which appears to extend to all Diptera including mosquitoes, is in stark contrast to other groups such as mammals, birds, fish and plants, in which chromosome numbers and organization vary enormously among species that have diverged over much fewer generations.
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Affiliation(s)
- John A Sved
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Yizhou Chen
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW 2568, Australia
| | - Deborah Shearman
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Marianne Frommer
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - A Stuart Gilchrist
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - William B Sherwin
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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38
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Singhal S, Leffler EM, Sannareddy K, Turner I, Venn O, Hooper DM, Strand AI, Li Q, Raney B, Balakrishnan CN, Griffith SC, McVean G, Przeworski M. Stable recombination hotspots in birds. Science 2015; 350:928-32. [PMID: 26586757 PMCID: PMC4864528 DOI: 10.1126/science.aad0843] [Citation(s) in RCA: 177] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The DNA-binding protein PRDM9 has a critical role in specifying meiotic recombination hotspots in mice and apes, but it appears to be absent from other vertebrate species, including birds. To study the evolution and determinants of recombination in species lacking the gene that encodes PRDM9, we inferred fine-scale genetic maps from population resequencing data for two bird species: the zebra finch, Taeniopygia guttata, and the long-tailed finch, Poephila acuticauda. We found that both species have recombination hotspots, which are enriched near functional genomic elements. Unlike in mice and apes, most hotspots are shared between the two species, and their conservation seems to extend over tens of millions of years. These observations suggest that in the absence of PRDM9, recombination targets functional features that both enable access to the genome and constrain its evolution.
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Affiliation(s)
- Sonal Singhal
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA. Department of Systems Biology, Columbia University, New York, NY 10032, USA.
| | - Ellen M Leffler
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Keerthi Sannareddy
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Isaac Turner
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Oliver Venn
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Daniel M Hooper
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL 60637, USA
| | - Alva I Strand
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Qiye Li
- China National Genebank, BGI-Shenzhen, Shenzhen 518083, China
| | - Brian Raney
- Center for Biomolecular Science and Engineering, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Simon C Griffith
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Gil McVean
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Molly Przeworski
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA. Department of Systems Biology, Columbia University, New York, NY 10032, USA.
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