151
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Naciri Y, Linder HP. The genetics of evolutionary radiations. Biol Rev Camb Philos Soc 2020; 95:1055-1072. [PMID: 32233014 DOI: 10.1111/brv.12598] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 03/12/2020] [Accepted: 03/17/2020] [Indexed: 02/06/2023]
Abstract
With the realization that much of the biological diversity on Earth has been generated by discrete evolutionary radiations, there has been a rapid increase in research into the biotic (key innovations) and abiotic (key environments) circumstances in which such radiations took place. Here we focus on the potential importance of population genetic structure and trait genetic architecture in explaining radiations. We propose a verbal model describing the stages of an evolutionary radiation: first invading a suitable adaptive zone and expanding both spatially and ecologically through this zone; secondly, diverging genetically into numerous distinct populations; and, finally, speciating. There are numerous examples of the first stage; the difficulty, however, is explaining how genetic diversification can take place from the establishment of a, presumably, genetically depauperate population in a new adaptive zone. We explore the potential roles of epigenetics and transposable elements (TEs), of neutral process such as genetic drift in combination with trait genetic architecture, of gene flow limitation through isolation by distance (IBD), isolation by ecology and isolation by colonization, the possible role of intra-specific competition, and that of admixture and hybridization in increasing the genetic diversity of the founding populations. We show that many of the predictions of this model are corroborated. Most radiations occur in complex adaptive zones, which facilitate the establishment of many small populations exposed to genetic drift and divergent selection. We also show that many radiations (especially those resulting from long-distance dispersal) were established by polyploid lineages, and that many radiating lineages have small genome sizes. However, there are several other predictions which are not (yet) possible to test: that epigenetics has played a role in radiations, that radiations occur more frequently in clades with small gene flow distances, or that the ancestors of radiations had large fundamental niches. At least some of these may be testable in the future as more genome and epigenome data become available. The implication of this model is that many radiations may be hard polytomies because the genetic divergence leading to speciation happens within a very short time, and that the divergence history may be further obscured by hybridization. Furthermore, it suggests that only lineages with the appropriate genetic architecture will be able to radiate, and that such a radiation will happen in a meta-population environment. Understanding the genetic architecture of a lineage may be an essential part of accounting for why some lineages radiate, and some do not.
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Affiliation(s)
- Yamama Naciri
- Plant Systematics and Biodiversity Laboratory, Department of Botany and Plant biology of the University of Geneva, 1 Chemin de l'Impératrice, CH-1292, Chambésy, Geneva, Switzerland
| | - H Peter Linder
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, Switzerland
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152
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Bourgeois YXC, Bertrand JAM, Delahaie B, Holota H, Thébaud C, Milá B. Differential divergence in autosomes and sex chromosomes is associated with intra-island diversification at a very small spatial scale in a songbird lineage. Mol Ecol 2020; 29:1137-1153. [PMID: 32107807 DOI: 10.1111/mec.15396] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 02/12/2020] [Accepted: 02/20/2020] [Indexed: 12/16/2022]
Abstract
Recently diverged taxa showing marked phenotypic and ecological diversity provide optimal systems to understand the genetic processes underlying speciation. We used genome-wide markers to investigate the diversification of the Reunion grey white-eye (Zosterops borbonicus) on the small volcanic island of Reunion (Mascarene archipelago), where this species complex exhibits four geographical forms that are parapatrically distributed across the island and differ strikingly in plumage colour. One form restricted to the highlands is separated by a steep ecological gradient from three distinct lowland forms which meet at narrow hybrid zones that are not associated with environmental variables. Analyses of genomic variation based on single nucleotide polymorphism data from genotyping-by-sequencing and pooled RAD-seq approaches show that signatures of selection associated with elevation can be found at multiple regions across the genome, whereas most loci associated with the lowland forms are located on the Z sex chromosome. We identified TYRP1, a Z-linked colour gene, as a likely candidate locus underlying colour variation among lowland forms. Tests of demographic models revealed that highland and lowland forms diverged in the presence of gene flow, and divergence has progressed as gene flow was restricted by selection at loci across the genome. This system holds promise for investigating how adaptation and reproductive isolation shape the genomic landscape of divergence at multiple stages of the speciation process.
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Affiliation(s)
- Yann X C Bourgeois
- School of Biological Sciences, University of Portsmouth, Portsmouth, UK.,Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université Paul Sabatier, Toulouse, France
| | - Joris A M Bertrand
- Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université Paul Sabatier, Toulouse, France.,Laboratoire Génome & Développement des Plantes, UMR 5096, Université de Perpignan Via Domitia, Perpignan, France
| | - Boris Delahaie
- Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université Paul Sabatier, Toulouse, France.,Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Hélène Holota
- Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université Paul Sabatier, Toulouse, France
| | - Christophe Thébaud
- Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université Paul Sabatier, Toulouse, France
| | - Borja Milá
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
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153
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Ottenburghs J. Digest: Exploring genomic islands of differentiation on the Z chromosome of hummingbirds .. Evolution 2020; 74:793-794. [PMID: 32196651 DOI: 10.1111/evo.13964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 03/18/2020] [Indexed: 11/29/2022]
Abstract
What evolutionary processes shaped the genomic landscape of differentiation in Selasphorus hummingbirds? Battey shows that the islands of differentiation on the Z chromosome are most likely the outcome of linked selection. Furthermore, these islands might contain barrier loci that contribute to reproductive isolation between these hybridizing hummingbirds.
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Affiliation(s)
- Jente Ottenburghs
- Department of Ecology and Genetics, Uppsala University, Uppsala, 75236, Sweden
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154
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Wang J, Street NR, Park EJ, Liu J, Ingvarsson PK. Evidence for widespread selection in shaping the genomic landscape during speciation of Populus. Mol Ecol 2020; 29:1120-1136. [PMID: 32068935 DOI: 10.1111/mec.15388] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 02/13/2020] [Accepted: 02/14/2020] [Indexed: 12/13/2022]
Abstract
Increasing our understanding of how evolutionary processes drive the genomic landscape of variation is fundamental to a better understanding of the genomic consequences of speciation. However, genome-wide patterns of within- and between- species variation have not been fully investigated in most forest tree species despite their global ecological and economic importance. Here, we use whole-genome resequencing data from four Populus species spanning the speciation continuum to reconstruct their demographic histories and investigate patterns of diversity and divergence within and between species. Using Populus trichocarpa as an outgroup species, we further infer the genealogical relationships and estimate the extent of ancient introgression among the three aspen species (Populus tremula, Populus davidiana and Populus tremuloides) throughout the genome. Our results show substantial variation in these patterns along the genomes with this variation being strongly predicted by local recombination rates and the density of functional elements. This implies that the interaction between recurrent selection and intrinsic genomic features has dramatically sculpted the genomic landscape over long periods of time. In addition, our findings provide evidence that, apart from background selection, recent positive selection and long-term balancing selection have also been crucial components in shaping patterns of genome-wide variation during the speciation process.
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Affiliation(s)
- Jing Wang
- Key Laboratory for Bio-Resources and Eco-Environment, College of Life Science, Sichuan University, Chengdu, China
| | - Nathaniel R Street
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Eung-Jun Park
- Department of Bioresources, National Institute of Forest Science, Suwon, Korea
| | - Jianquan Liu
- Key Laboratory for Bio-Resources and Eco-Environment, College of Life Science, Sichuan University, Chengdu, China
| | - Pär K Ingvarsson
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
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155
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Abstract
Sex differences in overall recombination rates are well known, but little theoretical or empirical attention has been given to how and why sexes differ in their recombination landscapes: the patterns of recombination along chromosomes. In the first scientific review of this phenomenon, we find that recombination is biased toward telomeres in males and more uniformly distributed in females in most vertebrates and many other eukaryotes. Notable exceptions to this pattern exist, however. Fine-scale recombination patterns also frequently differ between males and females. The molecular mechanisms responsible for sex differences remain unclear, but chromatin landscapes play a role. Why these sex differences evolve also is unclear. Hypotheses suggest that they may result from sexually antagonistic selection acting on coding genes and their regulatory elements, meiotic drive in females, selection during the haploid phase of the life cycle, selection against aneuploidy, or mechanistic constraints. No single hypothesis, however, can adequately explain the evolution of sex differences in all cases. Sex-specific recombination landscapes have important consequences for population differentiation and sex chromosome evolution.
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Affiliation(s)
- Jason M. Sardell
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712
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156
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Brand P, Hinojosa-Díaz IA, Ayala R, Daigle M, Yurrita Obiols CL, Eltz T, Ramírez SR. The evolution of sexual signaling is linked to odorant receptor tuning in perfume-collecting orchid bees. Nat Commun 2020; 11:244. [PMID: 31932598 PMCID: PMC6957680 DOI: 10.1038/s41467-019-14162-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 12/18/2019] [Indexed: 12/16/2022] Open
Abstract
Sexual signaling is an important reproductive barrier known to evolve early during the formation of new species, but the genetic mechanisms that facilitate the divergence of sexual signals remain elusive. Here we isolate a gene linked to the rapid evolution of a signaling trait in a pair of nascent neotropical orchid bee lineages, Euglossa dilemma and E. viridissima. Male orchid bees acquire chemical compounds from their environment to concoct species-specific perfumes to later expose during courtship. We find that the two lineages acquire chemically distinct perfumes and are reproductively isolated despite low levels of genome-wide differentiation. Remarkably, variation in perfume chemistry coincides with rapid divergence in few odorant receptor (OR) genes. Using functional assays, we demonstrate that the derived variant of Or41 in E. dilemma is specific towards its species-specific major perfume compound, whereas the ancestral variant in E. viridissima is broadly tuned to multiple odorants. Our results show that OR evolution likely played a role in the divergence of sexual communication in natural populations.
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Affiliation(s)
- Philipp Brand
- Department of Evolution and Ecology, Center for Population Biology, University of California, 1 Shields Avenue, 95616, Davis, California, USA.
- Laboratory of Neurophysiology and Behavior, The Rockefeller University, 1230 York Avenue, 10065, New York, New York, USA.
| | - Ismael A Hinojosa-Díaz
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito s/n Ciudad Universitaria Delegación Coyoacán, Apartado Postal 70-153, Ciudad de México, 04510, Mexico
| | - Ricardo Ayala
- Estación de Biología Chamela, Instituto de Biología, Universidad Nacional Autónoma de México, Apartado Postal 21, San Patricio, Jalisco, 48980, Mexico
| | - Michael Daigle
- Department of Evolution and Ecology, Center for Population Biology, University of California, 1 Shields Avenue, 95616, Davis, California, USA
| | - Carmen L Yurrita Obiols
- Centro de Estudios Conservacionistas, Universidad de San Carlos de Guatemala, Avenida La Reforma, 0-63, Guatemala, 01000, Guatemala
| | - Thomas Eltz
- Department of Animal Ecology, Evolution and Biodiversity, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Santiago R Ramírez
- Department of Evolution and Ecology, Center for Population Biology, University of California, 1 Shields Avenue, 95616, Davis, California, USA.
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157
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Lumley LM, Pouliot E, Laroche J, Boyle B, Brunet BMT, Levesque RC, Sperling FAH, Cusson M. Continent-wide population genomic structure and phylogeography of North America's most destructive conifer defoliator, the spruce budworm ( Choristoneura fumiferana). Ecol Evol 2020; 10:914-927. [PMID: 32015854 PMCID: PMC6988549 DOI: 10.1002/ece3.5950] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/28/2019] [Accepted: 12/02/2019] [Indexed: 02/01/2023] Open
Abstract
The spruce budworm, Choristoneura fumiferana, is presumed to be panmictic across vast regions of North America. We examined the extent of panmixia by genotyping 3,650 single nucleotide polymorphism (SNP) loci in 1975 individuals from 128 collections across the continent. We found three spatially structured subpopulations: Western (Alaska, Yukon), Central (southeastern Yukon to the Manitoba-Ontario border), and Eastern (Manitoba-Ontario border to the Atlantic). Additionally, the most diagnostic genetic differentiation between the Central and Eastern subpopulations was chromosomally restricted to a single block of SNPs that may constitute an island of differentiation within the species. Geographic differentiation in the spruce budworm parallels that of its principal larval host, white spruce (Picea glauca), providing evidence that spruce budworm and spruce trees survived in the Beringian refugium through the Last Glacial Maximum and that at least two isolated spruce budworm populations diverged with spruce/fir south of the ice sheets. Gene flow in the spruce budworm may also be affected by mountains in western North America, habitat isolation in West Virginia, regional adaptations, factors related to dispersal, and proximity of other species in the spruce budworm species complex. The central and eastern geographic regions contain individuals that assign to Eastern and Central subpopulations, respectively, indicating that these barriers are not complete. Our discovery of previously undetected geographic and genomic structure in the spruce budworm suggests that further population modelling of this ecologically important insect should consider regional differentiation, potentially co-adapted blocks of genes, and gene flow between subpopulations.
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Affiliation(s)
- Lisa M. Lumley
- Royal Alberta MuseumEdmontonABCanada
- Laurentian Forestry CentreNatural Resources CanadaQuebec CityQCCanada
- Université LavalQuebec CityQCCanada
| | - Esther Pouliot
- Laurentian Forestry CentreNatural Resources CanadaQuebec CityQCCanada
| | | | | | | | | | | | - Michel Cusson
- Laurentian Forestry CentreNatural Resources CanadaQuebec CityQCCanada
- Université LavalQuebec CityQCCanada
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158
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Beaudry FEG, Barrett SCH, Wright SI. Ancestral and neo-sex chromosomes contribute to population divergence in a dioecious plant. Evolution 2019; 74:256-269. [PMID: 31808547 DOI: 10.1111/evo.13892] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 10/16/2019] [Accepted: 11/11/2019] [Indexed: 12/18/2022]
Abstract
Empirical evidence from several animal groups suggests sex chromosomes disproportionately contribute to reproductive isolation. This effect may be enhanced when sex chromosomes are associated with turnover of sex determination systems resulting from structural rearrangements to the chromosomes. We investigated these predictions in the dioecious plant Rumex hastatulus, which is composed of populations of two different sex chromosome cytotypes caused by an X-autosome fusion. Using population genomic analyses, we investigated the demographic history of R. hastatulus and explored the contributions of ancestral and neo-sex chromosomes to population genetic divergence. Our study revealed that the cytotypes represent genetically divergent populations with evidence for historical but not contemporary gene flow between them. In agreement with classical predictions, we found that the ancestral X chromosome was disproportionately divergent compared with the rest of the genome. Excess differentiation was also observed on the Y chromosome, even when we used measures of differentiation that control for differences in effective population size. Our estimates of the timing of the origin of neo-sex chromosomes in R. hastatulus are coincident with cessation of gene flow, suggesting that the chromosomal fusion event that gave rise to the origin of the XYY cytotype may have also contributed to reproductive isolation.
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Affiliation(s)
- Felix E G Beaudry
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Spencer C H Barrett
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
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159
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Campillo LC, Barley AJ, Thomson RC. Model-Based Species Delimitation: Are Coalescent Species Reproductively Isolated? Syst Biol 2019; 69:708-721. [DOI: 10.1093/sysbio/syz072] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 09/06/2019] [Accepted: 10/22/2019] [Indexed: 12/31/2022] Open
Abstract
Abstract
A large and growing fraction of systematists define species as independently evolving lineages that may be recognized by analyzing the population genetic history of alleles sampled from individuals belonging to those species. This has motivated the development of increasingly sophisticated statistical models rooted in the multispecies coalescent process. Specifically, these models allow for simultaneous estimation of the number of species present in a sample of individuals and the phylogenetic history of those species using only DNA sequence data from independent loci. These methods hold extraordinary promise for increasing the efficiency of species discovery but require extensive validation to ensure that they are accurate and precise. Whether the species identified by these methods correspond to the species that would be recognized by alternative species recognition criteria (such as measurements of reproductive isolation) is currently an open question and a subject of vigorous debate. Here, we perform an empirical test of these methods by making use of a classic model system in the history of speciation research, flies of the genus Drosophila. Specifically, we use the uniquely comprehensive data on reproductive isolation that is available for this system, along with DNA sequence data, to ask whether Drosophila species inferred under the multispecies coalescent model correspond to those recognized by many decades of speciation research. We found that coalescent based and reproductive isolation-based methods of inferring species boundaries are concordant for 77% of the species pairs. We explore and discuss potential explanations for these discrepancies. We also found that the amount of prezygotic isolation between two species is a strong predictor of the posterior probability of species boundaries based on DNA sequence data, regardless of whether the species pairs are sympatrically or allopatrically distributed. [BPP; Drosophila speciation; genetic distance; multispecies coalescent.]
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Affiliation(s)
- Luke C Campillo
- School of Life Sciences, University of Hawai’i, Honolulu, HI 96822, USA
| | - Anthony J Barley
- School of Life Sciences, University of Hawai’i, Honolulu, HI 96822, USA
| | - Robert C Thomson
- School of Life Sciences, University of Hawai’i, Honolulu, HI 96822, USA
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160
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Lucek K, Gompert Z, Nosil P. The role of structural genomic variants in population differentiation and ecotype formation in Timema cristinae walking sticks. Mol Ecol 2019; 28:1224-1237. [PMID: 30636326 DOI: 10.1111/mec.15016] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 01/05/2019] [Accepted: 01/07/2019] [Indexed: 12/22/2022]
Abstract
Theory predicts that structural genomic variants such as inversions can promote adaptive diversification and speciation. Despite increasing empirical evidence that adaptive divergence can be triggered by one or a few large inversions, the degree to which widespread genomic regions under divergent selection are associated with structural variants remains unclear. Here we test for an association between structural variants and genomic regions that underlie parallel host-plant-associated ecotype formation in Timema cristinae stick insects. Using mate-pair resequencing of 20 new whole genomes we find that moderately sized structural variants such as inversions, deletions and duplications are widespread across the genome, being retained as standing variation within and among populations. Using 160 previously published, standard-orientation whole genome sequences we find little to no evidence that the DNA sequences within inversions exhibit accentuated differentiation between ecotypes. In contrast, a formerly described large region of reduced recombination that harbours genes controlling colour-pattern exhibits evidence for accentuated differentiation between ecotypes, which is consistent with differences in the frequency of colour-pattern morphs between host-associated ecotypes. Our results suggest that some types of structural variants (e.g., large inversions) are more likely to underlie adaptive divergence than others, and that structural variants are not required for subtle yet genome-wide genetic differentiation with gene flow.
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Affiliation(s)
- Kay Lucek
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | | | - Patrik Nosil
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,Department of Biology, Utah State University, Logan, Utah
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161
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Wang X, Maher KH, Zhang N, Que P, Zheng C, Liu S, Wang B, Huang Q, Chen D, Yang X, Zhang Z, Székely T, Urrutia AO, Liu Y. Demographic Histories and Genome-Wide Patterns of Divergence in Incipient Species of Shorebirds. Front Genet 2019; 10:919. [PMID: 31781152 PMCID: PMC6857203 DOI: 10.3389/fgene.2019.00919] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 08/30/2019] [Indexed: 12/30/2022] Open
Abstract
Understanding how incipient species are maintained with gene flow is a fundamental question in evolutionary biology. Whole genome sequencing of multiple individuals holds great potential to illustrate patterns of genomic differentiation as well as the associated evolutionary histories. Kentish (Charadrius alexandrinus) and the white-faced (C. dealbatus) plovers, which differ in their phenotype, ecology and behavior, are two incipient species and parapatrically distributed in East Asia. Previous studies show evidence of genetic diversification with gene flow between the two plovers. Under this scenario, it is of great importance to explore the patterns of divergence at the genomic level and to determine whether specific regions are involved in reproductive isolation and local adaptation. Here we present the first population genomic analysis of the two incipient species based on the de novo Kentish plover reference genome and resequenced populations. We show that the two plover lineages are distinct in both nuclear and mitochondrial genomes. Using model-based coalescence analysis, we found that population sizes of Kentish plover increased whereas white-faced plovers declined during the Last Glaciation Period. Moreover, the two plovers diverged allopatrically, with gene flow occurring after secondary contact. This has resulted in low levels of genome-wide differentiation, although we found evidence of a few highly differentiated genomic regions in both the autosomes and the Z-chromosome. This study illustrates that incipient shorebird species with gene flow after secondary contact can exhibit discrete divergence at specific genomic regions and provides basis to further exploration on the genetic basis of relevant phenotypic traits.
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Affiliation(s)
- Xuejing Wang
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Kathryn H. Maher
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Nan Zhang
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Pinjia Que
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Chenqing Zheng
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Department of Bioinformatics, Shenzhen Realomics Biological Technology Ltd, Shenzhen, China
| | - Simin Liu
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Biao Wang
- School of Biosciences, University of Melbourne, Parkville, VIC, Australia
| | - Qin Huang
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - De Chen
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Xu Yang
- Department of Bioinformatics, Shenzhen Realomics Biological Technology Ltd, Shenzhen, China
| | - Zhengwang Zhang
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Tamás Székely
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Araxi O. Urrutia
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Yang Liu
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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162
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Lindsay WR, Andersson S, Bererhi B, Höglund J, Johnsen A, Kvarnemo C, Leder EH, Lifjeld JT, Ninnes CE, Olsson M, Parker GA, Pizzari T, Qvarnström A, Safran RJ, Svensson O, Edwards SV. Endless forms of sexual selection. PeerJ 2019; 7:e7988. [PMID: 31720113 PMCID: PMC6839514 DOI: 10.7717/peerj.7988] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 10/04/2019] [Indexed: 12/11/2022] Open
Abstract
In recent years, the field of sexual selection has exploded, with advances in theoretical and empirical research complementing each other in exciting ways. This perspective piece is the product of a "stock-taking" workshop on sexual selection and sexual conflict. Our aim is to identify and deliberate on outstanding questions and to stimulate discussion rather than provide a comprehensive overview of the entire field. These questions are organized into four thematic sections we deem essential to the field. First we focus on the evolution of mate choice and mating systems. Variation in mate quality can generate both competition and choice in the opposite sex, with implications for the evolution of mating systems. Limitations on mate choice may dictate the importance of direct vs. indirect benefits in mating decisions and consequently, mating systems, especially with regard to polyandry. Second, we focus on how sender and receiver mechanisms shape signal design. Mediation of honest signal content likely depends on integration of temporally variable social and physiological costs that are challenging to measure. We view the neuroethology of sensory and cognitive receiver biases as the main key to signal form and the 'aesthetic sense' proposed by Darwin. Since a receiver bias is sufficient to both initiate and drive ornament or armament exaggeration, without a genetically correlated or even coevolving receiver, this may be the appropriate 'null model' of sexual selection. Thirdly, we focus on the genetic architecture of sexually selected traits. Despite advances in modern molecular techniques, the number and identity of genes underlying performance, display and secondary sexual traits remains largely unknown. In-depth investigations into the genetic basis of sexual dimorphism in the context of long-term field studies will reveal constraints and trajectories of sexually selected trait evolution. Finally, we focus on sexual selection and conflict as drivers of speciation. Population divergence and speciation are often influenced by an interplay between sexual and natural selection. The extent to which sexual selection promotes or counteracts population divergence may vary depending on the genetic architecture of traits as well as the covariance between mating competition and local adaptation. Additionally, post-copulatory processes, such as selection against heterospecific sperm, may influence the importance of sexual selection in speciation. We propose that efforts to resolve these four themes can catalyze conceptual progress in the field of sexual selection, and we offer potential avenues of research to advance this progress.
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Affiliation(s)
- Willow R. Lindsay
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Staffan Andersson
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Badreddine Bererhi
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Jacob Höglund
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Arild Johnsen
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Charlotta Kvarnemo
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Erica H. Leder
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Jan T. Lifjeld
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Calum E. Ninnes
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, United States of America
| | - Mats Olsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Geoff A. Parker
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Tommaso Pizzari
- Department of Zoology, Edward Grey Institute, University of Oxford, Oxford, United Kingdom
| | - Anna Qvarnström
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Rebecca J. Safran
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, United States of America
| | - Ola Svensson
- School of Natural Sciences, Technology and Environmental Studies, Södertörn University, Huddinge, Sweden
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, United States of America
- Gothenburg Centre for Advanced Studies in Science and Technology, Chalmers University of Technology, Göteborg, Sweden
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163
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Fruciano C, Meyer A, Franchini P. Divergent Allometric Trajectories in Gene Expression and Coexpression Produce Species Differences in Sympatrically Speciating Midas Cichlid Fish. Genome Biol Evol 2019; 11:1644-1657. [PMID: 31124568 PMCID: PMC6563553 DOI: 10.1093/gbe/evz108] [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] [Accepted: 05/17/2019] [Indexed: 12/19/2022] Open
Abstract
The mechanisms of speciation without geographic isolation (i.e., sympatric speciation) remain debated. This is due in part to the fact that the genomic landscape that could promote or hinder species divergence in the presence of gene flow is still largely unknown. However, intensive research is now centered on understanding the genetic architecture of adaptive traits associated with this process as well as how gene expression might affect these traits. Here, using RNA-Seq data, we investigated gene expression of sympatrically speciating benthic and limnetic Neotropical cichlid fishes at two developmental stages. First, we identified groups of coexpressed genes (modules) at each stage. Although there are a few large and well-preserved modules, most of the other modules are not preserved across life stages. Second, we show that later in development more and larger coexpression modules are associated with divergence between benthic and limnetic fish compared with the earlier life stage. This divergence between benthic and limnetic fish in coexpression mirrors divergence in overall expression between benthic and limnetic fish, which is more pronounced later in life. Our results reveal that already at 1-day posthatch benthic and limnetic fish diverge in (co)expression, and that this divergence becomes more substantial when fish are free-swimming but still unlikely to have divergent swimming and feeding habits. More importantly, our study describes how the coexpression of several genes through development, as opposed to individual genes, is associated with benthic–limnetic species differences, and how two morphogenetic trajectories diverge as fish grow older.
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Affiliation(s)
- Carmelo Fruciano
- Department of Biology, University of Konstanz, Germany.,Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS UMR 8197, Paris, France
| | - Axel Meyer
- Department of Biology, University of Konstanz, Germany
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164
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Semenov GA, Safran RJ, Smith CC, Turbek SP, Mullen SP, Flaxman SM. Unifying Theoretical and Empirical Perspectives on Genomic Differentiation. Trends Ecol Evol 2019; 34:987-995. [DOI: 10.1016/j.tree.2019.07.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/10/2019] [Accepted: 07/15/2019] [Indexed: 01/17/2023]
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165
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Baniaga AE, Marx HE, Arrigo N, Barker MS. Polyploid plants have faster rates of multivariate niche differentiation than their diploid relatives. Ecol Lett 2019; 23:68-78. [PMID: 31637845 DOI: 10.1111/ele.13402] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/01/2019] [Accepted: 09/16/2019] [Indexed: 01/02/2023]
Abstract
Polyploid speciation entails substantial and rapid postzygotic reproductive isolation of nascent species that are initially sympatric with one or both parents. Despite strong postzygotic isolation, ecological niche differentiation has long been thought to be important for polyploid success. Using biogeographic data from across vascular plants, we tested whether the climatic niches of polyploid species are more differentiated than their diploid relatives and if the climatic niches of polyploid species differentiated faster than those of related diploids. We found that polyploids are often more climatically differentiated from their diploid parents than the diploids are from each other. Consistent with this pattern, we estimated that polyploid species generally have higher rates of multivariate niche differentiation than their diploid relatives. In contrast to recent analyses, our results confirm that ecological niche differentiation is an important component of polyploid speciation and that niche differentiation is often significantly faster in polyploids.
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Affiliation(s)
- Anthony E Baniaga
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Hannah E Marx
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.,Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Nils Arrigo
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
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166
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Zieliński P, Dudek K, Arntzen JW, Palomar G, Niedzicka M, Fijarczyk A, Liana M, Cogǎlniceanu D, Babik W. Differential introgression across newt hybrid zones: Evidence from replicated transects. Mol Ecol 2019; 28:4811-4824. [DOI: 10.1111/mec.15251] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/16/2019] [Accepted: 09/19/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Piotr Zieliński
- Institute of Environmental Sciences Faculty of Biology Jagiellonian University Kraków Poland
| | - Katarzyna Dudek
- Institute of Environmental Sciences Faculty of Biology Jagiellonian University Kraków Poland
| | | | - Gemma Palomar
- Institute of Environmental Sciences Faculty of Biology Jagiellonian University Kraków Poland
| | - Marta Niedzicka
- Institute of Environmental Sciences Faculty of Biology Jagiellonian University Kraków Poland
| | - Anna Fijarczyk
- Département de Biologie Faculté des Sciences et de génie Université Laval Québec QC Canada
| | | | - Dan Cogǎlniceanu
- Faculty of Natural Sciences and Agricultural Sciences University Ovidius Constanţa Constanţa Romania
| | - Wiesław Babik
- Institute of Environmental Sciences Faculty of Biology Jagiellonian University Kraków Poland
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167
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Guðbrandsson J, Kapralova KH, Franzdóttir SR, Bergsveinsdóttir ÞM, Hafstað V, Jónsson ZO, Snorrason SS, Pálsson A. Extensive genetic differentiation between recently evolved sympatric Arctic charr morphs. Ecol Evol 2019; 9:10964-10983. [PMID: 31641448 PMCID: PMC6802010 DOI: 10.1002/ece3.5516] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 07/11/2019] [Accepted: 07/12/2019] [Indexed: 12/22/2022] Open
Abstract
The availability of diverse ecological niches can promote adaptation of trophic specializations and related traits, as has been repeatedly observed in evolutionary radiations of freshwater fish. The role of genetics, environment, and history in ecologically driven divergence and adaptation, can be studied on adaptive radiations or populations showing ecological polymorphism. Salmonids, especially the Salvelinus genus, are renowned for both phenotypic diversity and polymorphism. Arctic charr (Salvelinus alpinus) invaded Icelandic streams during the glacial retreat (about 10,000 years ago) and exhibits many instances of sympatric polymorphism. Particularly, well studied are the four morphs in Lake Þingvallavatn in Iceland. The small benthic (SB), large benthic (LB), planktivorous (PL), and piscivorous (PI) charr differ in many regards, including size, form, and life history traits. To investigate relatedness and genomic differentiation between morphs, we identified variable sites from RNA-sequencing data from three of those morphs and verified 22 variants in population samples. The data reveal genetic differences between the morphs, with the two benthic morphs being more similar and the PL-charr more genetically different. The markers with high differentiation map to all linkage groups, suggesting ancient and pervasive genetic separation of these three morphs. Furthermore, GO analyses suggest differences in collagen metabolism, odontogenesis, and sensory systems between PL-charr and the benthic morphs. Genotyping in population samples from all four morphs confirms the genetic separation and indicates that the PI-charr are less genetically distinct than the other three morphs. The genetic separation of the other three morphs indicates certain degree of reproductive isolation. The extent of gene flow between the morphs and the nature of reproductive barriers between them remain to be elucidated.
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Affiliation(s)
- Jóhannes Guðbrandsson
- Institute of Life and Environmental SciencesUniversity of IcelandReykjavikIceland
- Marine and Freshwater Research InstituteReykjavikIceland
| | - Kalina H. Kapralova
- Institute of Life and Environmental SciencesUniversity of IcelandReykjavikIceland
| | - Sigríður R. Franzdóttir
- Institute of Life and Environmental SciencesUniversity of IcelandReykjavikIceland
- Biomedical CenterUniversity of IcelandReykjavikIceland
| | | | - Völundur Hafstað
- Institute of Life and Environmental SciencesUniversity of IcelandReykjavikIceland
| | - Zophonías O. Jónsson
- Institute of Life and Environmental SciencesUniversity of IcelandReykjavikIceland
- Biomedical CenterUniversity of IcelandReykjavikIceland
| | | | - Arnar Pálsson
- Institute of Life and Environmental SciencesUniversity of IcelandReykjavikIceland
- Biomedical CenterUniversity of IcelandReykjavikIceland
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168
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Marques DA, Lucek K, Sousa VC, Excoffier L, Seehausen O. Admixture between old lineages facilitated contemporary ecological speciation in Lake Constance stickleback. Nat Commun 2019; 10:4240. [PMID: 31534121 PMCID: PMC6751218 DOI: 10.1038/s41467-019-12182-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 08/27/2019] [Indexed: 01/25/2023] Open
Abstract
Ecological speciation can sometimes rapidly generate reproductively isolated populations coexisting in sympatry, but the origin of genetic variation permitting this is rarely known. We previously explored the genomics of very recent ecological speciation into lake and stream ecotypes in stickleback from Lake Constance. Here, we reconstruct the origin of alleles underlying ecological speciation by combining demographic modelling on genome-wide single nucleotide polymorphisms, phenotypic data and mitochondrial sequence data in the wider European biogeographical context. We find that parallel differentiation between lake and stream ecotypes across replicate lake-stream ecotones resulted from recent secondary contact and admixture between old East and West European lineages. Unexpectedly, West European alleles that introgressed across the hybrid zone at the western end of the lake, were recruited to genomic islands of differentiation between ecotypes at the eastern end of the lake. Our results highlight an overlooked outcome of secondary contact: ecological speciation facilitated by admixture variation. Ecological speciation can proceed rapidly, but the origin of genetic variation facilitating it has remained elusive. Here, the authors show that secondary contact and introgression between deeply diverged lineages of stickleback fish facilitated rapid ecological speciation into lake and stream ecotypes in Lake Constance.
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Affiliation(s)
- David A Marques
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.,Department of Fish Ecology and Evolution, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland.,Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland
| | - Kay Lucek
- Department of Environmental Sciences, University of Basel, Schönbeinstrasse 6, CH-4056, Basel, Switzerland
| | - Vitor C Sousa
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.,Centre for Ecology, Evolution and Environmental Changes, University of Lisbon, Campo Grande 016, 1749-016, Lisbon, Portugal
| | - Laurent Excoffier
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.,Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Ole Seehausen
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland. .,Department of Fish Ecology and Evolution, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland.
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169
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Coathup MJ, Osborne OG, Savolainen V. How predictable is genome evolution? eLife 2019; 8:50784. [PMID: 31517601 PMCID: PMC6744270 DOI: 10.7554/elife.50784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 09/11/2019] [Indexed: 11/24/2022] Open
Abstract
Similar patterns of genomic divergence have been observed in the evolution of plant species separated by oceans.
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Affiliation(s)
- Matthew J Coathup
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, United Kingdom
| | - Owen G Osborne
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
| | - Vincent Savolainen
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, United Kingdom
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170
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White NJ, Snook RR, Eyres I. The Past and Future of Experimental Speciation. Trends Ecol Evol 2019; 35:10-21. [PMID: 31522756 DOI: 10.1016/j.tree.2019.08.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 08/08/2019] [Accepted: 08/14/2019] [Indexed: 12/22/2022]
Abstract
Speciation is the result of evolutionary processes that generate barriers to gene flow between populations, facilitating reproductive isolation. Speciation is typically studied via theoretical models and snapshot tests in natural populations. Experimental speciation enables real-time direct tests of speciation theory and has been long touted as a critical complement to other approaches. We argue that, despite its promise to elucidate the evolution of reproductive isolation, experimental speciation has been underutilised and lags behind other contributions to speciation research. We review recent experiments and outline a framework for how experimental speciation can be implemented to address current outstanding questions that are otherwise challenging to answer. Greater uptake of this approach is necessary to rapidly advance understanding of speciation.
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Affiliation(s)
- Nathan J White
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Rhonda R Snook
- Department of Zoology, Stockholm University, Stockholm 106-91, Sweden
| | - Isobel Eyres
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK.
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171
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172
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Ellegren H, Wolf JBW. Parallelism in genomic landscapes of differentiation, conserved genomic features and the role of linked selection. J Evol Biol 2019; 30:1516-1518. [PMID: 28786191 DOI: 10.1111/jeb.13113] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 05/01/2017] [Accepted: 05/03/2017] [Indexed: 01/01/2023]
Affiliation(s)
- H Ellegren
- Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden
| | - J B W Wolf
- Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.,Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
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173
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Lohse K. Come on feel the noise - from metaphors to null models. J Evol Biol 2019; 30:1506-1508. [PMID: 28786185 DOI: 10.1111/jeb.13109] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 04/17/2017] [Accepted: 04/19/2017] [Indexed: 01/03/2023]
Affiliation(s)
- K Lohse
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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174
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Ginsberg PS, Humphreys DP, Dyer KA. Ongoing hybridization obscures phylogenetic relationships in the Drosophila subquinaria species complex. J Evol Biol 2019; 32:1093-1105. [PMID: 31385638 DOI: 10.1111/jeb.13512] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 07/30/2019] [Indexed: 12/28/2022]
Abstract
Inferring evolutionary relationships among recently diverged lineages is necessary to understand how isolating barriers produce independent lineages. Here, we investigate the phylogenetic relationships between three incompletely isolated and closely related mushroom-feeding Drosophila species. These species form the Drosophila subquinaria species complex and consist of one Eurasian species (D. transversa) and two widespread North American species (D. subquinaria and D. recens) that are sympatric in central Canada. Although patterns of pre- and post-mating isolation among these species are well characterized, previous work on their phylogenetic relationships is limited and conflicting. In this study, we generated a multi-locus data set of 29 loci from across the genome sequenced in a population sample from each species, and then, we inferred species relationships and patterns of introgression. We find strong statistical support that D. subquinaria is paraphyletic, showing that samples from the geographic region sympatric with D. recens are most closely related to D. recens, whereas samples from the geographic region allopatric with D. recens are most closely related to D. transversa. We present several lines of evidence that both incomplete lineage sorting and gene flow are causing phylogenetic discordance. We suggest that ongoing gene flow primarily from D. recens into D. subquinaria in the sympatric part of their ranges causes phylogenetic uncertainty in the evolutionary history of these species. Our results highlight how population genetic data can be used to disentangle the sources of phylogenetic discordance among closely related species.
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Affiliation(s)
- Paul S Ginsberg
- Department of Genetics, University of Georgia, Athens, GA, USA
| | | | - Kelly A Dyer
- Department of Genetics, University of Georgia, Athens, GA, USA
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175
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Talla V, Johansson A, Dincă V, Vila R, Friberg M, Wiklund C, Backström N. Lack of gene flow: Narrow and dispersed differentiation islands in a triplet ofLeptideabutterfly species. Mol Ecol 2019; 28:3756-3770. [DOI: 10.1111/mec.15188] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 07/08/2019] [Accepted: 07/12/2019] [Indexed: 01/02/2023]
Affiliation(s)
- Venkat Talla
- Department of Evolutionary Biology Evolutionary Biology Centre (EBC) Uppsala University Uppsala Sweden
| | - Anna Johansson
- Department of Medical Biochemistry and Microbiology Uppsala Biomedical Centre (BMC) Uppsala Sweden
| | - Vlad Dincă
- Department of Ecology and Genetics University of Oulu Oulu Finland
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC‐UPF) Barcelona Spain
| | - Magne Friberg
- Department of Biology, Biodiversity Unit Lund University Lund Sweden
| | - Christer Wiklund
- Division of Ecology Department of Zoology Stockholm University Stockholm Sweden
| | - Niclas Backström
- Department of Evolutionary Biology Evolutionary Biology Centre (EBC) Uppsala University Uppsala Sweden
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176
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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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177
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Dong Y, Chen S, Cheng S, Zhou W, Ma Q, Chen Z, Fu CX, Liu X, Zhao YP, Soltis PS, Wong GKS, Soltis DE, Xiang QYJ. Natural selection and repeated patterns of molecular evolution following allopatric divergence. eLife 2019; 8:45199. [PMID: 31373555 PMCID: PMC6744222 DOI: 10.7554/elife.45199] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 08/01/2019] [Indexed: 11/13/2022] Open
Abstract
Although geographic isolation is a leading driver of speciation, the tempo and pattern of divergence at the genomic level remain unclear. We examine genome-wide divergence of putatively single-copy orthologous genes (POGs) in 20 allopatric species/variety pairs from diverse angiosperm clades, with 16 pairs reflecting the classic eastern Asia-eastern North America floristic disjunction. In each pair, >90% of POGs are under purifying selection, and <10% are under positive selection. A set of POGs are under strong positive selection, 14 of which are shared by 10-15 pairs, and one shared by all pairs; 15 POGs are annotated to biological processes responding to various stimuli. The relative abundance of POGs under different selective forces exhibits a repeated pattern among pairs despite an ~10 million-year difference in divergence time. Species divergence times are positively correlated with abundance of POGs under moderate purifying selection, but negatively correlated with abundance of POGs under strong purifying selection.
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Affiliation(s)
- Yibo Dong
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, United States.,Plant Biology Division, Noble Research Institute, Ardmore, United States
| | - Shichao Chen
- Florida Museum of Natural History, University of Florida, Gainesville, United States.,Department of Biology, University of Florida, Gainesville, United States.,School of Life Sciences and Technology, Tongji University, Shanghai, China
| | | | - Wenbin Zhou
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, United States
| | - Qing Ma
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, United States
| | - Zhiduan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Cheng-Xin Fu
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xin Liu
- Beijing Genomics Institute, Shenzhen, China
| | - Yun-Peng Zhao
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, United States
| | - Gane Ka-Shu Wong
- Beijing Genomics Institute, Shenzhen, China.,Department of Biological Sciences, University of Alberta, Edmonton, Canada.,Department of Medicine, University of Alberta, Edmonton, Canada
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, United States.,Department of Biology, University of Florida, Gainesville, United States
| | - Qiu-Yun Jenny Xiang
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, United States
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178
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Bourgeois Y, Ruggiero RP, Manthey JD, Boissinot S. Recent Secondary Contacts, Linked Selection, and Variable Recombination Rates Shape Genomic Diversity in the Model Species Anolis carolinensis. Genome Biol Evol 2019; 11:2009-2022. [PMID: 31134281 PMCID: PMC6681179 DOI: 10.1093/gbe/evz110] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2019] [Indexed: 12/14/2022] Open
Abstract
Gaining a better understanding on how selection and neutral processes affect genomic diversity is essential to gain better insights into the mechanisms driving adaptation and speciation. However, the evolutionary processes affecting variation at a genomic scale have not been investigated in most vertebrate lineages. Here, we present the first population genomics survey using whole genome resequencing in the green anole (Anolis carolinensis). Anoles have been intensively studied to understand mechanisms underlying adaptation and speciation. The green anole in particular is an important model to study genome evolution. We quantified how demography, recombination, and selection have led to the current genetic diversity of the green anole by using whole-genome resequencing of five genetic clusters covering the entire species range. The differentiation of green anole's populations is consistent with a northward expansion from South Florida followed by genetic isolation and subsequent gene flow among adjacent genetic clusters. Dispersal out-of-Florida was accompanied by a drastic population bottleneck followed by a rapid population expansion. This event was accompanied by male-biased dispersal and/or selective sweeps on the X chromosome. We show that the interaction between linked selection and recombination is the main contributor to the genomic landscape of differentiation in the anole genome.
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Affiliation(s)
| | | | - Joseph D Manthey
- New York University Abu Dhabi, United Arab Emirates
- Department of Biological Sciences, Texas Tech University
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179
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Stankowski S, Chase MA, Fuiten AM, Rodrigues MF, Ralph PL, Streisfeld MA. Widespread selection and gene flow shape the genomic landscape during a radiation of monkeyflowers. PLoS Biol 2019; 17:e3000391. [PMID: 31339877 PMCID: PMC6660095 DOI: 10.1371/journal.pbio.3000391] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 07/26/2019] [Accepted: 07/03/2019] [Indexed: 12/12/2022] Open
Abstract
Speciation genomic studies aim to interpret patterns of genome-wide variation in light of the processes that give rise to new species. However, interpreting the genomic "landscape" of speciation is difficult, because many evolutionary processes can impact levels of variation. Facilitated by the first chromosome-level assembly for the group, we use whole-genome sequencing and simulations to shed light on the processes that have shaped the genomic landscape during a radiation of monkeyflowers. After inferring the phylogenetic relationships among the 9 taxa in this radiation, we show that highly similar diversity (π) and differentiation (FST) landscapes have emerged across the group. Variation in these landscapes was strongly predicted by the local density of functional elements and the recombination rate, suggesting that the landscapes have been shaped by widespread natural selection. Using the varying divergence times between pairs of taxa, we show that the correlations between FST and genome features arose almost immediately after a population split and have become stronger over time. Simulations of genomic landscape evolution suggest that background selection (BGS; i.e., selection against deleterious mutations) alone is too subtle to generate the observed patterns, but scenarios that involve positive selection and genetic incompatibilities are plausible alternative explanations. Finally, tests for introgression among these taxa reveal widespread evidence of heterogeneous selection against gene flow during this radiation. Combined with previous evidence for adaptation in this system, we conclude that the correlation in FST among these taxa informs us about the processes contributing to adaptation and speciation during a rapid radiation.
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Affiliation(s)
- Sean Stankowski
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Madeline A. Chase
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Allison M. Fuiten
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Murillo F. Rodrigues
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Peter L. Ralph
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Matthew A. Streisfeld
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
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180
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Wang X, Que P, Heckel G, Hu J, Zhang X, Chiang CY, Zhang N, Huang Q, Liu S, Martinez J, Pagani-Núñez E, Dingle C, Leung YY, Székely T, Zhang Z, Liu Y. Genetic, phenotypic and ecological differentiation suggests incipient speciation in two Charadrius plovers along the Chinese coast. BMC Evol Biol 2019; 19:135. [PMID: 31248363 PMCID: PMC6598359 DOI: 10.1186/s12862-019-1449-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 05/29/2019] [Indexed: 02/01/2023] Open
Abstract
Background Speciation with gene flow is an alternative to the nascence of new taxa in strict allopatric separation. Indeed, many taxa have parapatric distributions at present. It is often unclear if these are secondary contacts, e.g. caused by past glaciation cycles or the manifestation of speciation with gene flow, which hampers our understanding of how different forces drive diversification. Here we studied genetic, phenotypic and ecological aspects of divergence in a pair of incipient shorebird species, the Kentish (Charadrius alexandrinus) and the White-faced Plovers (C. dealbatus), shorebirds with parapatric breeding ranges along the Chinese coast. We assessed divergence based on molecular markers with different modes of inheritance and quantified phenotypic and ecological divergence in aspects of morphometric, dietary and climatic niches. Results Our integrative analyses revealed small to moderate levels of genetic and phenotypic distinctiveness with symmetric gene flow across the contact area at the Chinese coast. The two species diverged approximately half a million years ago in dynamic isolation with secondary contact occurring due to cycling sea level changes between the Eastern and Southern China Sea in the mid-late Pleistocene. We found evidence of character displacement and ecological niche differentiation between the two species, invoking the role of selection in facilitating divergence despite gene flow. Conclusion These findings imply that ecology can indeed counter gene flow through divergent selection and thus contributes to incipient speciation in these plovers. Furthermore, our study highlights the importance of using integrative datasets to reveal the evolutionary history and assist the inference of mechanisms of speciation. Electronic supplementary material The online version of this article (10.1186/s12862-019-1449-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xuejing Wang
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.,Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012, Bern, Switzerland
| | - Pinjia Que
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012, Bern, Switzerland.,Swiss Institute of Bioinformatics, Genopode, 1015, Lausanne, Switzerland
| | - Junhua Hu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xuecong Zhang
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Chung-Yu Chiang
- Department of Environmental Science, Tunhai University, Taichun, Taiwan
| | - Nan Zhang
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Qin Huang
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Simin Liu
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | | | - Emilio Pagani-Núñez
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Caroline Dingle
- School of Biological Sciences, The University of Hong Kong, Hong Kong, SAR, China
| | - Yu Yan Leung
- School of Biological Sciences, The University of Hong Kong, Hong Kong, SAR, China
| | - Tamás Székely
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.,Milner Center for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, BA1 7AY, UK
| | - Zhengwang Zhang
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yang Liu
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
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181
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Lewis JJ, Reed RD. Genome-Wide Regulatory Adaptation Shapes Population-Level Genomic Landscapes in Heliconius. Mol Biol Evol 2019; 36:159-173. [PMID: 30452724 PMCID: PMC6340471 DOI: 10.1093/molbev/msy209] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Cis-regulatory evolution is an important engine of organismal diversification. Although recent studies have looked at genomic patterns of regulatory evolution between species, we still have a poor understanding of the magnitude and nature of regulatory variation within species. Here, we examine the evolution of regulatory element activity over wing development in three Heliconius erato butterfly populations to determine how regulatory variation is associated with population structure. We show that intraspecific divergence in chromatin accessibility and regulatory activity is abundant, and that regulatory variants are spatially clustered in the genome. Regions with strong population structure are highly enriched for regulatory variants, and enrichment patterns are associated with developmental stage and gene expression. We also found that variable regulatory elements are particularly enriched in species-specific genomic regions and long interspersed nuclear elements. Our findings suggest that genome-wide selection on chromatin accessibility and regulatory activity is an important force driving patterns of genomic divergence within Heliconius species. This work also provides a resource for the study of gene regulatory evolution in H. erato and other heliconiine butterflies.
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Affiliation(s)
- James J Lewis
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY
| | - Robert D Reed
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY
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182
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Wang B, Mojica JP, Perera N, Lee CR, Lovell JT, Sharma A, Adam C, Lipzen A, Barry K, Rokhsar DS, Schmutz J, Mitchell-Olds T. Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta. Genome Biol 2019; 20:126. [PMID: 31227026 PMCID: PMC6587263 DOI: 10.1186/s13059-019-1729-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 06/04/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Genomic variation is widespread, and both neutral and selective processes can generate similar patterns in the genome. These processes are not mutually exclusive, so it is difficult to infer the evolutionary mechanisms that govern population and species divergence. Boechera stricta is a perennial relative of Arabidopsis thaliana native to largely undisturbed habitats with two geographic and ecologically divergent subspecies. Here, we delineate the evolutionary processes driving the genetic diversity and population differentiation in this species. RESULTS Using whole-genome re-sequencing data from 517 B. stricta accessions, we identify four genetic groups that diverged around 30-180 thousand years ago, with long-term small effective population sizes and recent population expansion after the Last Glacial Maximum. We find three genomic regions with elevated nucleotide diversity, totaling about 10% of the genome. These three regions of elevated nucleotide diversity show excess of intermediate-frequency alleles, higher absolute divergence (dXY), and lower relative divergence (FST) than genomic background, and significant enrichment in immune-related genes, reflecting long-term balancing selection. Scattered across the genome, we also find regions with both high FST and dXY among the groups, termed FST-islands. Population genetic signatures indicate that FST-islands with elevated divergence, which have experienced directional selection, are derived from divergent sorting of ancient polymorphisms. CONCLUSIONS Our results suggest that long-term balancing selection on disease resistance genes may have maintained ancestral haplotypes across different geographical lineages, and unequal sorting of balanced polymorphisms may have generated genomic regions with elevated divergence. This study highlights the importance of ancestral balanced polymorphisms as crucial components of genome-wide variation.
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Affiliation(s)
- Baosheng Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- Department of Biology, Duke University, Box 90338, Durham, NC, 27708, USA.
| | - Julius P Mojica
- Department of Biology, Duke University, Box 90338, Durham, NC, 27708, USA
| | - Nadeesha Perera
- Department of Biology, Duke University, Box 90338, Durham, NC, 27708, USA
| | - Cheng-Ruei Lee
- Institute of Ecology and Evolutionary Biology and Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan, ROC
| | - John T Lovell
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Aditi Sharma
- Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Catherine Adam
- Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Anna Lipzen
- Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Daniel S Rokhsar
- Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
- Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
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183
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Zeng K, Jackson BC, Barton HJ. Methods for Estimating Demography and Detecting Between-Locus Differences in the Effective Population Size and Mutation Rate. Mol Biol Evol 2019; 36:423-433. [PMID: 30428070 PMCID: PMC6409433 DOI: 10.1093/molbev/msy212] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
It is known that the effective population size (Ne) and the mutation rate (u) vary across the genome. Here, we show that ignoring this heterogeneity may lead to biased estimates of past demography. To solve the problem, we develop new methods for jointly inferring past changes in population size and detecting variation in Ne and u between loci. These methods rely on either polymorphism data alone or both polymorphism and divergence data. In addition to inferring demography, we can use the methods to study a variety of questions: 1) comparing sex chromosomes with autosomes (for finding evidence for male-driven evolution, an unequal sex ratio, or sex-biased demographic changes) and 2) analyzing multilocus data from within autosomes or sex chromosomes (for studying determinants of variability in Ne and u). Simulations suggest that the methods can provide accurate parameter estimates and have substantial statistical power for detecting difference in Ne and u. As an example, we use the methods to analyze a polymorphism data set from Drosophila simulans. We find clear evidence for rapid population expansion. The results also indicate that the autosomes have a higher mutation rate than the X chromosome and that the sex ratio is probably female-biased. The new methods have been implemented in a user-friendly package.
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Affiliation(s)
- Kai Zeng
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Benjamin C Jackson
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Henry J Barton
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
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184
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Li MR, Wang HY, Ding N, Lu T, Huang YC, Xiao HX, Liu B, Li LF. Rapid Divergence Followed by Adaptation to Contrasting Ecological Niches of Two Closely Related Columbine Species Aquilegia japonica and A. oxysepala. Genome Biol Evol 2019; 11:919-930. [PMID: 30793209 PMCID: PMC6433176 DOI: 10.1093/gbe/evz038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2019] [Indexed: 12/20/2022] Open
Abstract
Elucidating the mechanisms underlying the genetic divergence between closely related species is crucial to understanding the origin and evolution of biodiversity. The genus Aquilegia L. has undergone rapid adaptive radiation, generating about 70 well-recognized species that are specialized to distinct habitats and pollinators. In this study, to address the underlying evolutionary mechanisms that drive the genetic divergence, we analyzed the whole genomes of two ecologically isolated Aquilegia species, A. oxysepala and A. japonica as well as their putative hybrid. Our comparative genomic analyses reveal that while the two species diverged only recently and experienced recurrent gene flow, a high level of genetic divergence is observed in their nuclear genomes. In particular, candidate genomic regions that show signature of selection differ dramatically between the two species. Given that the splitting time of the two species is broadly matched with the decrease in effective population sizes, we propose that allopatric isolation together with natural selection have preceded the interspecific gene flow in the process of speciation. The observed high genetic divergence is likely an outcome of combined effects of natural selection, genetic drift and divergent sorting of ancestral polymorphisms. Our study provides a genome-wide view of how genetic divergence has evolved between closely related species.
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Affiliation(s)
- Ming-Rui Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Hua-Ying Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Ning Ding
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Tianyuan Lu
- McGill University and Genome Quebec Innovation Center, Montreal, Quebec, Canada
| | - Ye-Chao Huang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Hong-Xing Xiao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Lin-Feng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
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185
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Shen Y, Wang L, Fu J, Xu X, Yue GH, Li J. Population structure, demographic history and local adaptation of the grass carp. BMC Genomics 2019; 20:467. [PMID: 31174480 PMCID: PMC6555922 DOI: 10.1186/s12864-019-5872-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 05/31/2019] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Genetic diversity within a species reflects population evolution, ecology, and ability to adapt. Genome-wide population surveys of both natural and introduced populations provide insights into genetic diversity, the evolutionary processes and the genetic basis underlying local adaptation. Grass carp is the most important freshwater foodfish species for food and water weed control. However, there is as yet no overall picture on genetic variations and population structure of this species, which is important for its aquaculture. RESULTS We used 43,310 SNPs to infer the population structure, evidence of local adaptation and sources of introduction. The overall genetic differentiation of this species was low. The native populations were differentiated into three genetic clusters, corresponding to the Yangtze, Pearl and Heilongjiang River Systems, respectively. The populations in Malaysia, India and Nepal were introduced from both the Yangtze and Pearl River Systems. Loci and genes involved in putative local selection for native locations were identified. Evidence of both positive and balancing selection was found in the introduced locations. Genes associated with loci under putative selection were involved in many biological functions. Outlier loci were grouped into clusters as genomic islands within some specific genomic regions, which likely agrees with the divergence hitchhiking scenario of divergence-with-gene-flow. CONCLUSIONS This study, for the first time, sheds novel insights on the population differentiation of the grass carp, genetics of its strong ability in adaption to diverse environments and sources of some introduced grass carp populations. Our data also suggests that the natural populations of the grass carp have been affected by the aquaculture besides neutral and adaptive forces.
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Affiliation(s)
- Yubang Shen
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, 201306, China.,Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Republic of Singapore
| | - Le Wang
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Republic of Singapore
| | - Jianjun Fu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Xiaoyan Xu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, 201306, China
| | - Gen Hua Yue
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Republic of Singapore. .,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Republic of Singapore. .,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore.
| | - Jiale Li
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, 201306, China. .,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China.
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186
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Aguirre-Liguori JA, Gaut BS, Jaramillo-Correa JP, Tenaillon MI, Montes-Hernández S, García-Oliva F, Hearne SJ, Eguiarte LE. Divergence with gene flow is driven by local adaptation to temperature and soil phosphorus concentration in teosinte subspecies (Zea mays parviglumis and Zea mays mexicana). Mol Ecol 2019; 28:2814-2830. [PMID: 30980686 DOI: 10.1111/mec.15098] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 03/27/2019] [Accepted: 04/08/2019] [Indexed: 01/03/2023]
Abstract
Patterns of genomic divergence between hybridizing taxa can be heterogeneous along the genome. Both differential introgression and local adaptation may contribute to this pattern. Here, we analysed two teosinte subspecies, Zea mays ssp. parviglumis and ssp. mexicana, to test whether their divergence has occurred in the face of gene flow and to infer which environmental variables have been important drivers of their ecological differentiation. We generated 9,780 DArTseqTM SNPs for 47 populations, and used an additional data set containing 33,454 MaizeSNP50 SNPs for 49 populations. With these data, we inferred features of demographic history and performed genome wide scans to determine the number of outlier SNPs associated with climate and soil variables. The two data sets indicate that divergence has occurred or been maintained despite continuous gene flow and/or secondary contact. Most of the significant SNP associations were to temperature and to phosphorus concentration in the soil. A large proportion of these candidate SNPs were located in regions of high differentiation that had been identified previously as putative inversions. We therefore propose that genomic differentiation in teosintes has occurred by a process of adaptive divergence, with putative inversions contributing to reduced gene flow between locally adapted populations.
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Affiliation(s)
- Jonás A Aguirre-Liguori
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California
| | - Juan Pablo Jaramillo-Correa
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Maud I Tenaillon
- Génétique Quantitative et Evolution- Le Moulon, INRA, Gif-sur-Yvette, France
| | - Salvador Montes-Hernández
- Campo Experimental Bajío, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Celaya, México
| | - Felipe García-Oliva
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Morelia, México
| | - Sarah J Hearne
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, México
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
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187
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Marques DA, Meier JI, Seehausen O. A Combinatorial View on Speciation and Adaptive Radiation. Trends Ecol Evol 2019; 34:531-544. [DOI: 10.1016/j.tree.2019.02.008] [Citation(s) in RCA: 162] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 02/07/2019] [Accepted: 02/13/2019] [Indexed: 01/28/2023]
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188
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Pértille F, Da Silva VH, Johansson AM, Lindström T, Wright D, Coutinho LL, Jensen P, Guerrero-Bosagna C. Mutation dynamics of CpG dinucleotides during a recent event of vertebrate diversification. Epigenetics 2019; 14:685-707. [PMID: 31070073 PMCID: PMC6557589 DOI: 10.1080/15592294.2019.1609868] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
DNA methylation in CpGs dinucleotides is associated with high mutability and disappearance of CpG sites during evolution. Although the high mutability of CpGs is thought to be relevant for vertebrate evolution, very little is known on the role of CpG-related mutations in the genomic diversification of vertebrates. Our study analysed genetic differences in chickens, between Red Junglefowl (RJF; the living closest relative to the ancestor of domesticated chickens) and domesticated breeds, to identify genomic dynamics that have occurred during the process of their domestication, focusing particularly on CpG-related mutations. Single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) between RJF and these domesticated breeds were assessed in a reduced fraction of their genome. Additionally, DNA methylation in the same fraction of the genome was measured in the sperm of RJF individuals to identify possible correlations with the mutations found between RJF and the domesticated breeds. Our study shows that although the vast majority of CpG-related mutations found relate to CNVs, CpGs disproportionally associate to SNPs in comparison to CNVs, where they are indeed substantially under-represented. Moreover, CpGs seem to be hotspots of mutations related to speciation. We suggest that, on the one hand, CpG-related mutations in CNV regions would promote genomic ‘flexibility’ in evolution, i.e., the ability of the genome to expand its functional possibilities; on the other hand, CpG-related mutations in SNPs would relate to genomic ‘specificity’ in evolution, thus, representing mutations that would associate with phenotypic traits relevant for speciation.
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Affiliation(s)
- Fábio Pértille
- a Avian Behavioral Genomics and Physiology Group, IFM Biology , Linköping University , Linköping , Sweden.,b Animal Biotechnology Laboratory, Animal Science Department , University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ) , Piracicaba , São Paulo , Brazil
| | - Vinicius H Da Silva
- c Animal Breeding and Genomics Centre , Wageningen University & Research , Wageningen , The Netherlands.,d Department of Animal Ecology (AnE) , Netherlands Institute of Ecology (NIOO-KNAW) , Wageningen , The Netherlands.,e Department of Animal Breeding and Genetics , Swedish University of Agricultural Sciences , Uppsala , Sweden
| | - Anna M Johansson
- e Department of Animal Breeding and Genetics , Swedish University of Agricultural Sciences , Uppsala , Sweden
| | - Tom Lindström
- f Division of Theoretical Biology, IFM , Linköping University , Linköping , Sweden
| | - Dominic Wright
- a Avian Behavioral Genomics and Physiology Group, IFM Biology , Linköping University , Linköping , Sweden
| | - Luiz L Coutinho
- b Animal Biotechnology Laboratory, Animal Science Department , University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ) , Piracicaba , São Paulo , Brazil
| | - Per Jensen
- a Avian Behavioral Genomics and Physiology Group, IFM Biology , Linköping University , Linköping , Sweden
| | - Carlos Guerrero-Bosagna
- a Avian Behavioral Genomics and Physiology Group, IFM Biology , Linköping University , Linköping , Sweden
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189
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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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190
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Haselhorst MSH, Parchman TL, Buerkle CA. Genetic evidence for species cohesion, substructure and hybrids in spruce. Mol Ecol 2019; 28:2029-2045. [DOI: 10.1111/mec.15056] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 02/10/2019] [Accepted: 02/11/2019] [Indexed: 12/18/2022]
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191
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McFarlane SE, Pemberton JM. Detecting the True Extent of Introgression during Anthropogenic Hybridization. Trends Ecol Evol 2019; 34:315-326. [DOI: 10.1016/j.tree.2018.12.013] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 12/10/2018] [Accepted: 12/18/2018] [Indexed: 10/27/2022]
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192
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193
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Galtier N. Delineating species in the speciation continuum: A proposal. Evol Appl 2019; 12:657-663. [PMID: 30976300 PMCID: PMC6439491 DOI: 10.1111/eva.12748] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 11/08/2018] [Indexed: 12/18/2022] Open
Abstract
Delineating species is a difficult and seemingly uninteresting issue that is still essential to address. Taxonomic methodology is heterogeneous according to the taxa and scientists involved due to the disparate data quality and quantity and disagreements over the species concept. This has negative impacts on basic and applied research. Genomic data substantially enhance our understanding of the speciation process but do not provide a ubiquitous solution to the species problem. The relevance of comparative approaches in speciation research has nevertheless recently been demonstrated. I suggest moving towards a more unified taxonomic classification through a reference-based decision procedure.
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Affiliation(s)
- Nicolas Galtier
- UMR 5554 – Institut des Sciences de l'EvolutionCNRS – University of Montpellier – IRD – EPHEMontpellierFrance
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194
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Conte MA, Joshi R, Moore EC, Nandamuri SP, Gammerdinger WJ, Roberts RB, Carleton KL, Lien S, Kocher TD. Chromosome-scale assemblies reveal the structural evolution of African cichlid genomes. Gigascience 2019; 8:giz030. [PMID: 30942871 PMCID: PMC6447674 DOI: 10.1093/gigascience/giz030] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 01/11/2019] [Accepted: 03/07/2019] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND African cichlid fishes are well known for their rapid radiations and are a model system for studying evolutionary processes. Here we compare multiple, high-quality, chromosome-scale genome assemblies to elucidate the genetic mechanisms underlying cichlid diversification and study how genome structure evolves in rapidly radiating lineages. RESULTS We re-anchored our recent assembly of the Nile tilapia (Oreochromis niloticus) genome using a new high-density genetic map. We also developed a new de novo genome assembly of the Lake Malawi cichlid, Metriaclima zebra, using high-coverage Pacific Biosciences sequencing, and anchored contigs to linkage groups (LGs) using 4 different genetic maps. These new anchored assemblies allow the first chromosome-scale comparisons of African cichlid genomes. Large intra-chromosomal structural differences (∼2-28 megabase pairs) among species are common, while inter-chromosomal differences are rare (<10 megabase pairs total). Placement of the centromeres within the chromosome-scale assemblies identifies large structural differences that explain many of the karyotype differences among species. Structural differences are also associated with unique patterns of recombination on sex chromosomes. Structural differences on LG9, LG11, and LG20 are associated with reduced recombination, indicative of inversions between the rock- and sand-dwelling clades of Lake Malawi cichlids. M. zebra has a larger number of recent transposable element insertions compared with O. niloticus, suggesting that several transposable element families have a higher rate of insertion in the haplochromine cichlid lineage. CONCLUSION This study identifies novel structural variation among East African cichlid genomes and provides a new set of genomic resources to support research on the mechanisms driving cichlid adaptation and speciation.
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Affiliation(s)
- Matthew A Conte
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Rajesh Joshi
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, PO Box 5003, Ås, Norway
| | - Emily C Moore
- Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27695, USA
| | | | | | - Reade B Roberts
- Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Karen L Carleton
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, PO Box 5003, Ås, Norway
| | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, MD 20742, USA
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195
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Knief U, Bossu CM, Saino N, Hansson B, Poelstra J, Vijay N, Weissensteiner M, Wolf JBW. Epistatic mutations under divergent selection govern phenotypic variation in the crow hybrid zone. Nat Ecol Evol 2019; 3:570-576. [PMID: 30911146 PMCID: PMC6445362 DOI: 10.1038/s41559-019-0847-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 02/18/2019] [Indexed: 12/22/2022]
Abstract
The evolution of genetic barriers opposing inter-specific gene flow is key to the origin of new species. Drawing from information of over 400 admixed genomes sourced from replicate transects across the European hybrid zone between all-black carrion crows and grey-coated hooded crows, we decipher the interplay between phenotypic divergence and selection at the molecular level. Over 68% of plumage variation was explained by epistasis between the gene NDP and a ~2.8 Mb region on chromosome 18 with suppressed recombination. Both pigmentation loci showed evidence for divergent selection resisting introgression. This study reveals how few, large-effect loci can govern prezygotic isolation and shield phenotypic divergence from gene flow.
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Affiliation(s)
- Ulrich Knief
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Munich, Germany
| | - Christen M Bossu
- Science for Life Laboratories and Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.,Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden.,Institute of the Environment and Sustainability, Center for Tropical Research, University of California, Los Angeles, CA, USA
| | - Nicola Saino
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
| | - Bengt Hansson
- Department of Biology, Lund University, Lund, Sweden
| | - Jelmer Poelstra
- Science for Life Laboratories and Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.,Biology Department, Duke University, Durham, NC, USA
| | - Nagarjun Vijay
- Science for Life Laboratories and Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.,Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
| | - Matthias Weissensteiner
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Munich, Germany.,Science for Life Laboratories and Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden
| | - Jochen B W Wolf
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Munich, Germany. .,Science for Life Laboratories and Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.
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196
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Barth JMI, Villegas-Ríos D, Freitas C, Moland E, Star B, André C, Knutsen H, Bradbury I, Dierking J, Petereit C, Righton D, Metcalfe J, Jakobsen KS, Olsen EM, Jentoft S. Disentangling structural genomic and behavioural barriers in a sea of connectivity. Mol Ecol 2019; 28:1394-1411. [PMID: 30633410 PMCID: PMC6518941 DOI: 10.1111/mec.15010] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 12/21/2018] [Accepted: 12/27/2018] [Indexed: 12/17/2022]
Abstract
Genetic divergence among populations arises through natural selection or drift and is counteracted by connectivity and gene flow. In sympatric populations, isolating mechanisms are thus needed to limit the homogenizing effects of gene flow to allow for adaptation and speciation. Chromosomal inversions act as an important mechanism maintaining isolating barriers, yet their role in sympatric populations and divergence with gene flow is not entirely understood. Here, we revisit the question of whether inversions play a role in the divergence of connected populations of the marine fish Atlantic cod (Gadus morhua), by exploring a unique data set combining whole‐genome sequencing data and behavioural data obtained with acoustic telemetry. Within a confined fjord environment, we find three genetically differentiated Atlantic cod types belonging to the oceanic North Sea population, the western Baltic population and a local fjord‐type cod. Continuous behavioural tracking over 4 year revealed temporally stable sympatry of these types within the fjord. Despite overall weak genetic differentiation consistent with high levels of gene flow, we detected significant frequency shifts of three previously identified inversions, indicating an adaptive barrier to gene flow. In addition, behavioural data indicated that North Sea cod and individuals homozygous for the LG12 inversion had lower fitness in the fjord environment. However, North Sea and fjord‐type cod also occupy different depths, possibly contributing to prezygotic reproductive isolation and representing a behavioural barrier to gene flow. Our results provide the first insights into a complex interplay of genomic and behavioural isolating barriers in Atlantic cod and establish a new model system towards an understanding of the role of genomic structural variants in adaptation and diversification.
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Affiliation(s)
- Julia M I Barth
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.,Zoological Institute, University of Basel, Basel, Switzerland
| | - David Villegas-Ríos
- Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies, IMEDEA CSIC-UIB, Esporles, Spain.,Department of Ecology and Marine Resources, Institute of Marine Research, (IIM CSIC), Vigo, Spain
| | - Carla Freitas
- Institute for Marine Research, Flødevigen, Norway.,Centre for Coastal Research, University of Agder, Agder, Norway.,Oceanic Observatory of Madeira, Funchal, Portugal
| | - Even Moland
- Institute for Marine Research, Flødevigen, Norway.,Centre for Coastal Research, University of Agder, Agder, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Carl André
- Department of Marine Sciences - Tjärnö, University of Gothenburg, Gothenburg, Sweden
| | - Halvor Knutsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.,Institute for Marine Research, Flødevigen, Norway.,Centre for Coastal Research, University of Agder, Agder, Norway
| | - Ian Bradbury
- Science Branch, Fisheries and Oceans Canada, St. John's, Newfoundland and Labrador, Canada
| | - Jan Dierking
- GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | | | - David Righton
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Lowestoft, UK
| | - Julian Metcalfe
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Lowestoft, UK
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Esben M Olsen
- Institute for Marine Research, Flødevigen, Norway.,Centre for Coastal Research, University of Agder, Agder, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
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197
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How Linked Selection Shapes the Diversity Landscape in Ficedula Flycatchers. Genetics 2019; 212:277-285. [PMID: 30872320 PMCID: PMC6499528 DOI: 10.1534/genetics.119.301991] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 03/07/2019] [Indexed: 12/19/2022] Open
Abstract
There is an increasing awareness that selection affecting linked neutral sites strongly influences on how diversity is distributed across the genome. In particular, linked selection is likely involved in the formation of heterogenous landscapes of genetic diversity, including genomic regions with locally reduced effective population sizes that manifest as dips in diversity, and "islands" of differentiation between closely related populations or species. Linked selection can be in the form of background selection or selective sweeps, and a long-standing quest in population genetics has been to unveil the relative importance of these processes. Here, we analyzed the theoretically expected reduction of diversity caused by linked selection in the collared flycatcher (Ficedula albicollis) genome and compared this with population genomic data on the distribution of diversity across the flycatcher genome. By incorporating data on recombination rate variation and the density of target sites for selection (including both protein-coding genes and conserved noncoding elements), we found that background selection can explain most of the observed baseline variation in genetic diversity. However, positive selection was necessary to explain the pronounced local diversity dips in the collared flycatcher genome. We confirmed our analytical findings by comprehensive simulations. Therefore, our study demonstrates that even though both background selection and selective sweeps contribute to the heterogeneous diversity landscape seen in this avian system, they play different roles in shaping it.
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198
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Wu CC, Klaesson A, Buskas J, Ranefall P, Mirzazadeh R, Söderberg O, Wolf JBW. In situ quantification of individual mRNA transcripts in melanocytes discloses gene regulation of relevance to speciation. J Exp Biol 2019; 222:jeb194431. [PMID: 30718374 PMCID: PMC6650291 DOI: 10.1242/jeb.194431] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 01/31/2019] [Indexed: 01/12/2023]
Abstract
Functional validation of candidate genes involved in adaptation and speciation remains challenging. Here, we exemplify the utility of a method quantifying individual mRNA transcripts in revealing the molecular basis of divergence in feather pigment synthesis during early-stage speciation in crows. Using a padlock probe assay combined with rolling circle amplification, we quantified cell-type-specific gene expression in the histological context of growing feather follicles. Expression of Tyrosinase Related Protein 1 (TYRP1), Solute Carrier Family 45 member 2 (SLC45A2) and Hematopoietic Prostaglandin D Synthase (HPGDS) was melanocyte-limited and significantly reduced in follicles from hooded crow, explaining the substantially lower eumelanin content in grey versus black feathers. The central upstream Melanocyte Inducing Transcription Factor (MITF) only showed differential expression specific to melanocytes - a feature not captured by bulk RNA-seq. Overall, this study provides insight into the molecular basis of an evolutionary young transition in pigment synthesis, and demonstrates the power of histologically explicit, statistically substantiated single-cell gene expression quantification for functional genetic inference in natural populations.
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Affiliation(s)
- Chi-Chih Wu
- Science of Life Laboratories and Department of Evolutionary Biology, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Axel Klaesson
- Department of Pharmaceutical Biosciences, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Julia Buskas
- Science of Life Laboratories and Department of Evolutionary Biology, Uppsala University, SE-752 36 Uppsala, Sweden
- Department of Physics, Chemistry and Biology (IFM), Linköping University, SE-581 83 Linköping, Sweden
| | - Petter Ranefall
- Science of Life Laboratories and Department of Information Technology, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Reza Mirzazadeh
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm SE-17165, Sweden
| | - Ola Söderberg
- Department of Pharmaceutical Biosciences, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Jochen B W Wolf
- Science of Life Laboratories and Department of Evolutionary Biology, Uppsala University, SE-752 36 Uppsala, Sweden
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, D-82152 Planegg-Martinsried, Germany
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199
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Inter-chromosomal coupling between vision and pigmentation genes during genomic divergence. Nat Ecol Evol 2019; 3:657-667. [PMID: 30833758 DOI: 10.1038/s41559-019-0814-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 01/11/2019] [Indexed: 12/30/2022]
Abstract
Recombination between loci underlying mate choice and ecological traits is a major evolutionary force acting against speciation with gene flow. The evolution of linkage disequilibrium between such loci is therefore a fundamental step in the origin of species. Here, we show that this process can take place in the absence of physical linkage in hamlets-a group of closely related reef fishes from the wider Caribbean that differ essentially in colour pattern and are reproductively isolated through strong visually-based assortative mating. Using full-genome analysis, we identify four narrow genomic intervals that are consistently differentiated among sympatric species in a backdrop of extremely low genomic divergence. These four intervals include genes involved in pigmentation (sox10), axial patterning (hoxc13a), photoreceptor development (casz1) and visual sensitivity (SWS and LWS opsins) that develop islands of long-distance and inter-chromosomal linkage disequilibrium as species diverge. The relatively simple genomic architecture of species differences facilitates the evolution of linkage disequilibrium in the presence of gene flow.
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200
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Takuno S, Miyagi R, Onami JI, Takahashi-Kariyazono S, Sato A, Tichy H, Nikaido M, Aibara M, Mizoiri S, Mrosso HDJ, Mzighani SI, Okada N, Terai Y. Patterns of genomic differentiation between two Lake Victoria cichlid species, Haplochromis pyrrhocephalus and H. sp. 'macula'. BMC Evol Biol 2019; 19:68. [PMID: 30832572 PMCID: PMC6399900 DOI: 10.1186/s12862-019-1387-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 02/12/2019] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND The molecular basis of the incipient stage of speciation is still poorly understood. Cichlid fish species in Lake Victoria are a prime example of recent speciation events and a suitable system to study the adaptation and reproductive isolation of species. RESULTS Here, we report the pattern of genomic differentiation between two Lake Victoria cichlid species collected in sympatry, Haplochromis pyrrhocephalus and H. sp. 'macula,' based on the pooled genome sequences of 20 individuals of each species. Despite their ecological differences, population genomics analyses demonstrate that the two species are very close to a single panmictic population due to extensive gene flow. However, we identified 21 highly differentiated short genomic regions with fixed nucleotide differences. At least 15 of these regions contained genes with predicted roles in adaptation and reproductive isolation, such as visual adaptation, circadian clock, developmental processes, adaptation to hypoxia, and sexual selection. The nonsynonymous fixed differences in one of these genes, LWS, were reported as substitutions causing shift in absorption spectra of LWS pigments. Fixed differences were found in the promoter regions of four other differentially expressed genes, indicating that these substitutions may alter gene expression levels. CONCLUSIONS These diverged short genomic regions may have contributed to the differentiation of two ecologically different species. Moreover, the origins of adaptive variants within the differentiated regions predate the geological formation of Lake Victoria; thus Lake Victoria cichlid species diversified via selection on standing genetic variation.
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Affiliation(s)
- Shohei Takuno
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Shonan Village, Hayama, Kanagawa, 240-0193 Japan
| | - Ryutaro Miyagi
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501 Japan
- Department of Biological sciences, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo, 197-0397 Japan
| | - Jun-ichi Onami
- JST (Japan Science and Technology Agency), NBDC (National Bioscience Database Center), 5-3, Yonbancho, Chiyoda-ku, Tokyo, 102-0081 Japan
| | - Shiho Takahashi-Kariyazono
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Shonan Village, Hayama, Kanagawa, 240-0193 Japan
| | - Akie Sato
- Department of Anatomy and Cytohistology, School of Dental Medicine, Tsurumi University, 2-1-3 Tsurumi, Tsurumi-ku, Yokohama, 230-8501 Japan
| | - Herbert Tichy
- Max-Planck-Institut für Biologie, Abteilung Immungenetik, Corrensstrasse 42, D-72076 Tübingen, Germany
| | - Masato Nikaido
- School of Life Science and Technology, Department of Life Science and Technology, Tokyo Institute of Technology (Tokyo Tech), 2-12-1, Ookayama, Meguro ward, Tokyo, Japan
| | - Mitsuto Aibara
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501 Japan
| | - Shinji Mizoiri
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501 Japan
| | | | - Semvua I. Mzighani
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501 Japan
- Tanzania Fisheries Research Institute (TAFIRI), Mwanza, Tanzania
| | - Norihiro Okada
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501 Japan
- Department of Life Sciences, National Cheng Kung University, 701 Tainan, Taiwan
- Foundation for Advancement of International Science (FAIS), Tsukuba, Japan
| | - Yohey Terai
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Shonan Village, Hayama, Kanagawa, 240-0193 Japan
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501 Japan
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