1
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Bohutínská M, Peichel CL. Divergence time shapes gene reuse during repeated adaptation. Trends Ecol Evol 2024; 39:396-407. [PMID: 38155043 DOI: 10.1016/j.tree.2023.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 11/15/2023] [Accepted: 11/20/2023] [Indexed: 12/30/2023]
Abstract
When diverse lineages repeatedly adapt to similar environmental challenges, the extent to which the same genes are involved (gene reuse) varies across systems. We propose that divergence time among lineages is a key factor driving this variability: as lineages diverge, the extent of gene reuse should decrease due to reductions in allele sharing, functional differentiation among genes, and restructuring of genome architecture. Indeed, we show that many genomic studies of repeated adaptation find that more recently diverged lineages exhibit higher gene reuse during repeated adaptation, but the relationship becomes less clear at older divergence time scales. Thus, future research should explore the factors shaping gene reuse and their interplay across broad divergence time scales for a deeper understanding of evolutionary repeatability.
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Affiliation(s)
- Magdalena Bohutínská
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, 3012, Switzerland; Department of Botany, Faculty of Science, Charles University, Prague, 12800, Czech Republic.
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, 3012, Switzerland
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2
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Feller AF, Peichel CL, Seehausen O. Testing for a role of postzygotic incompatibilities in rapidly speciated Lake Victoria cichlids. Evolution 2024; 78:652-664. [PMID: 38288653 DOI: 10.1093/evolut/qpae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/22/2023] [Accepted: 01/29/2024] [Indexed: 03/27/2024]
Abstract
Intrinsic postzygotic hybrid incompatibilities are usually due to negative epistatic interactions between alleles from different parental genomes. While such incompatibilities are thought to be uncommon in speciation with gene flow, they may be important if such speciation results from a hybrid population. Here we aimed to test this idea in the endemic cichlid fishes of Lake Victoria. Hundreds of species have evolved within the lake in <15k years from hybrid progenitors. While the importance of prezygotic barriers to gene flow is well established in this system, the possible relevance of postzygotic genetic incompatibilities is unknown. We inferred the presence of negative epistatic interactions from systematic patterns of genotype ratio distortions in experimental crosses and wild samples. We then compared the positions of putative incompatibility loci to regions of high genetic differentiation between sympatric sister species and between members of clades that may have arisen in the early history of this radiation, and further determined if the loci showed fixed differences between the closest living relatives of the lineages ancestral to the hybrid progenitors. Overall, we find little evidence for a major role of intrinsic postzygotic incompatibilities in the Lake Victoria radiation. However, we find putative incompatibility loci significantly more often coinciding with islands of genetic differentiation between species that separated early in the radiation than between the younger sister species, consistent with the hypothesis that such variants segregated in the hybrid swarm and were sorted between species in the early speciation events.
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Affiliation(s)
- Anna F Feller
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, Eawag Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
- Arnold Arboretum of Harvard University, Boston, MA, United States
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Ole Seehausen
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, Eawag Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
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3
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Berdan EL, Barton NH, Butlin R, Charlesworth B, Faria R, Fragata I, Gilbert KJ, Jay P, Kapun M, Lotterhos KE, Mérot C, Durmaz Mitchell E, Pascual M, Peichel CL, Rafajlović M, Westram AM, Schaeffer SW, Johannesson K, Flatt T. How chromosomal inversions reorient the evolutionary process. J Evol Biol 2023; 36:1761-1782. [PMID: 37942504 DOI: 10.1111/jeb.14242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 09/13/2023] [Accepted: 10/05/2023] [Indexed: 11/10/2023]
Abstract
Inversions are structural mutations that reverse the sequence of a chromosome segment and reduce the effective rate of recombination in the heterozygous state. They play a major role in adaptation, as well as in other evolutionary processes such as speciation. Although inversions have been studied since the 1920s, they remain difficult to investigate because the reduced recombination conferred by them strengthens the effects of drift and hitchhiking, which in turn can obscure signatures of selection. Nonetheless, numerous inversions have been found to be under selection. Given recent advances in population genetic theory and empirical study, here we review how different mechanisms of selection affect the evolution of inversions. A key difference between inversions and other mutations, such as single nucleotide variants, is that the fitness of an inversion may be affected by a larger number of frequently interacting processes. This considerably complicates the analysis of the causes underlying the evolution of inversions. We discuss the extent to which these mechanisms can be disentangled, and by which approach.
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Affiliation(s)
- Emma L Berdan
- Bioinformatics Core, Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Nicholas H Barton
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Roger Butlin
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
- Ecology and Evolutionary Biology, School of Bioscience, The University of Sheffield, Sheffield, UK
| | - Brian Charlesworth
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Rui Faria
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Inês Fragata
- CHANGE - Global Change and Sustainability Institute/Animal Biology Department, cE3c - Center for Ecology, Evolution and Environmental Changes, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | | | - Paul Jay
- Center for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
| | - Martin Kapun
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
- Central Research Laboratories, Natural History Museum of Vienna, Vienna, Austria
| | - Katie E Lotterhos
- Department of Marine and Environmental Sciences, Northeastern University, Boston, Massachusetts, USA
| | - Claire Mérot
- UMR 6553 Ecobio, Université de Rennes, OSUR, CNRS, Rennes, France
| | - Esra Durmaz Mitchell
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Functional Genomics & Metabolism Research Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Marta Pascual
- Departament de Genètica, Microbiologia i Estadística, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Marina Rafajlović
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
- Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
| | - Anja M Westram
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Stephen W Schaeffer
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Kerstin Johannesson
- Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
- Tjärnö Marine Laboratory, Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden
| | - Thomas Flatt
- Department of Biology, University of Fribourg, Fribourg, Switzerland
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4
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Rodríguez-Ramírez CE, Hiltbrunner M, Saladin V, Walker S, Urrutia A, Peichel CL. Molecular mechanisms of Eda-mediated adaptation to freshwater in threespine stickleback. Mol Ecol 2023. [PMID: 37194086 DOI: 10.1111/mec.16989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/12/2023] [Accepted: 04/26/2023] [Indexed: 05/18/2023]
Abstract
A main goal of evolutionary biology is to understand the genetic basis of adaptive evolution. Although the genes that underlie some adaptive phenotypes are now known, the molecular pathways and regulatory mechanisms mediating the phenotypic effects of those genes often remain a black box. Unveiling this black box is necessary to fully understand the genetic basis of adaptive phenotypes, and to understand why particular genes might be used during phenotypic evolution. Here, we investigated which genes and regulatory mechanisms are mediating the phenotypic effects of the Eda haplotype, a locus responsible for the loss of lateral plates and changes in the sensory lateral line of freshwater threespine stickleback (Gasterosteus aculeatus) populations. Using a combination of RNAseq and a cross design that isolated the Eda haplotype on a fixed genomic background, we found that the Eda haplotype affects both gene expression and alternative splicing of genes related to bone development, neuronal development and immunity. These include genes in conserved pathways, like the BMP, netrin and bradykinin signalling pathways, known to play a role in these biological processes. Furthermore, we found that differentially expressed and differentially spliced genes had different levels of connectivity and expression, suggesting that these factors might influence which regulatory mechanisms are used during phenotypic evolution. Taken together, these results provide a better understanding of the mechanisms mediating the effects of an important adaptive locus in stickleback and suggest that alternative splicing could be an important regulatory mechanism mediating adaptive phenotypes.
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Affiliation(s)
- Carlos E Rodríguez-Ramírez
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Melanie Hiltbrunner
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Verena Saladin
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Stephanie Walker
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Araxi Urrutia
- Department of Biology and Biochemistry, and Milner Centre for Evolution, University of Bath, Bath, UK
- Institute of Ecology, UNAM, Mexico City, Mexico
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
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5
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Poore HA, Stuart YE, Rennison DJ, Roesti M, Hendry AP, Bolnick DI, Peichel CL. Repeated genetic divergence plays a minor role in repeated phenotypic divergence of lake-stream stickleback. Evolution 2023; 77:110-122. [PMID: 36622692 DOI: 10.1093/evolut/qpac025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 09/22/2022] [Accepted: 11/15/2022] [Indexed: 01/10/2023]
Abstract
Recent studies have shown that the repeated evolution of similar phenotypes in response to similar ecological conditions (here "parallel evolution") often occurs through mutations in the same genes. However, many previous studies have focused on known candidate genes in a limited number of systems. Thus, the question of how often parallel phenotypic evolution is due to parallel genetic changes remains open. Here, we used quantitative trait locus (QTL) mapping in F2 intercrosses between lake and stream threespine stickleback (Gasterosteus aculeatus) from four independent watersheds on Vancouver Island, Canada to determine whether the same QTL underlie divergence in the same phenotypes across, between, and within watersheds. We find few parallel QTL, even in independent crosses from the same watershed or for phenotypes that have diverged in parallel. These findings suggest that different mutations can lead to similar phenotypes. The low genetic repeatability observed in these lake-stream systems contrasts with the higher genetic repeatability observed in other stickleback systems. We speculate that differences in evolutionary history, gene flow, and/or the strength and direction of selection might explain these differences in genetic parallelism and emphasize that more work is needed to move beyond documenting genetic parallelism to identifying the underlying causes.
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Affiliation(s)
- Hilary A Poore
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Divisions of Basic Sciences and Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Yoel E Stuart
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States.,Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Diana J Rennison
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Division of Biological Sciences, University of California at San Diego, La Jolla, CA, United States
| | - Marius Roesti
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Andrew P Hendry
- Redpath Museum and Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Daniel I Bolnick
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States.,Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Divisions of Basic Sciences and Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
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6
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Singh P, Taborsky M, Peichel CL, Sturmbauer C. Genomic basis of Y-linked dwarfism in cichlids pursuing alternative reproductive tactics. Mol Ecol 2023; 32:1592-1607. [PMID: 36588349 DOI: 10.1111/mec.16839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 12/08/2022] [Accepted: 12/19/2022] [Indexed: 01/03/2023]
Abstract
Sexually antagonistic selection, which favours different optima in males and females, is predicted to play an important role in the evolution of sex chromosomes. Body size is a sexually antagonistic trait in the shell-brooding cichlid fish Lamprologous callipterus, as "bourgeois" males must be large enough to carry empty snail shells to build nests whereas females must be small enough to fit into shells for breeding. In this species, there is also a second male morph: smaller "dwarf" males employ an alternative reproductive strategy by wriggling past spawning females into shells to fertilize eggs. L. callipterus male morphology is passed strictly from father to son, suggesting Y-linkage. However, sex chromosomes had not been previously identified in this species, and the genomic basis of size dimorphism was unknown. Here we used whole-genome sequencing to identify a 2.4-Mb sex-linked region on scaffold_23 with reduced coverage and single nucleotide polymorphism density in both male morphs compared to females. Within this sex region, distinct Y-haplotypes delineate the two male morphs, and candidate genes for body size (GHRHR, a known dwarfism gene) and sex determination (ADCYAP1R1) are in high linkage disequilibrium. Because differences in body size between females and males are under strong selection in L. callipterus, we hypothesize that sexual antagonism over body size initiated early events in sex chromosome evolution, followed by Y divergence to give rise to bourgeois and dwarf male reproductive strategies. Our results are consistent with the hypothesis that sexually antagonistic traits should be linked to young sex chromosomes.
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Affiliation(s)
- Pooja Singh
- Institute of Biology, University of Graz, Graz, Austria.,Aquatic Ecology Division, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
| | - Michael Taborsky
- Behavioural Ecology Division, Institute of Ecology and Evolution, University of Bern, Switzerland.,Max Planck Institute of Animal Behavior, Constance, Germany.,Institute for Advanced Study (Wissenschaftskolleg) Berlin, Berlin, Germany
| | - Catherine L Peichel
- Evolutionary Ecology Division, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
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7
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Roesti M, Groh JS, Blain SA, Huss M, Rassias P, Bolnick DI, Stuart YE, Peichel CL, Schluter D. Species divergence under competition and shared predation. Ecol Lett 2023; 26:111-123. [PMID: 36450600 DOI: 10.1111/ele.14138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/28/2022] [Accepted: 10/03/2022] [Indexed: 12/02/2022]
Abstract
Species competing for resources also commonly share predators. While competition often drives divergence between species, the effects of shared predation are less understood. Theoretically, competing prey species could either diverge or evolve in the same direction under shared predation depending on the strength and symmetry of their interactions. We took an empirical approach to this question, comparing antipredator and trophic phenotypes between sympatric and allopatric populations of threespine stickleback and prickly sculpin fish that all live in the presence of a trout predator. We found divergence in antipredator traits between the species: in sympatry, antipredator adaptations were relatively increased in stickleback but decreased in sculpin. Shifts in feeding morphology, diet and habitat use were also divergent but driven primarily by stickleback evolution. Our results suggest that asymmetric ecological character displacement indirectly made stickleback more and sculpin less vulnerable to shared predation, driving divergence of antipredator traits between sympatric species.
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Affiliation(s)
- Marius Roesti
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Zoology Department and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jeffrey S Groh
- Zoology Department and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.,Center for Population Biology and Department of Evolution and Ecology, University of California, Davis, California, USA
| | - Stephanie A Blain
- Zoology Department and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Magnus Huss
- Zoology Department and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Aquatic Resources, Swedish University of Agricultural Sciences, Öregrund, Sweden
| | - Peter Rassias
- Zoology Department and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Daniel I Bolnick
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Yoel E Stuart
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Dolph Schluter
- Zoology Department and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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8
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Dagilis AJ, Sardell JM, Josephson MP, Su Y, Kirkpatrick M, Peichel CL. Searching for signatures of sexually antagonistic selection on stickleback sex chromosomes. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210205. [PMID: 35694749 PMCID: PMC9189504 DOI: 10.1098/rstb.2021.0205] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Intralocus sexually antagonistic selection occurs when an allele is beneficial to one sex but detrimental to the other. This form of selection is thought to be key to the evolution of sex chromosomes but is hard to detect. Here we perform an analysis of phased young sex chromosomes to look for signals of sexually antagonistic selection in the Japan Sea stickleback (Gasterosteus nipponicus). Phasing allows us to date the suppression of recombination on the sex chromosome and provides unprecedented resolution to identify sexually antagonistic selection in the recombining region of the chromosome. We identify four windows with elevated divergence between the X and Y in the recombining region, all in or very near genes associated with phenotypes potentially under sexually antagonistic selection in humans. We are unable, however, to rule out the alternative hypothesis that the peaks of divergence result from demographic effects. Thus, although sexually antagonistic selection is a key hypothesis for the formation of supergenes on sex chromosomes, it remains challenging to detect. This article is part of the theme issue ‘Genomic architecture of supergenes: causes and evolutionary consequences’.
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Affiliation(s)
- Andrius J Dagilis
- Department of Integrative Biology, University of Texas, Austin TX 78712, USA.,Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jason M Sardell
- Department of Integrative Biology, University of Texas, Austin TX 78712, USA
| | - Matthew P Josephson
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Yiheng Su
- Department of Computer Science, University of Texas, Austin TX 78712, USA
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas, Austin TX 78712, USA
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
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9
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Jeffries DL, Mee JA, Peichel CL. Identification of a candidate sex determination gene in Culaea inconstans suggests convergent recruitment of an Amh duplicate in two lineages of stickleback. J Evol Biol 2022; 35:1683-1695. [PMID: 35816592 PMCID: PMC10083969 DOI: 10.1111/jeb.14034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/07/2022] [Accepted: 05/19/2022] [Indexed: 11/29/2022]
Abstract
Sex chromosomes vary greatly in their age and levels of differentiation across the tree of life. This variation is largely due to the rates of sex chromosome turnover in different lineages; however, we still lack an explanation for why sex chromosomes are so conserved in some lineages (e.g. mammals, birds) but so labile in others (e.g. teleosts, amphibians). To identify general mechanisms driving transitions in sex determination systems or forces which favour their conservation, we first require empirical data on sex chromosome systems from multiple lineages. Stickleback fishes are a valuable model lineage for the study of sex chromosome evolution due to variation in sex chromosome systems between closely-related species. Here, we identify the sex chromosome and a strong candidate for the master sex determination gene in the brook stickleback, Culaea inconstans. Using whole-genome sequencing of wild-caught samples and a lab cross, we identify AmhY, a male specific duplication of the gene Amh, as the candidate master sex determination gene. AmhY resides on Chromosome 20 in C. inconstans and is likely a recent duplication, as both AmhY and the sex-linked region of Chromosome 20 show little sequence divergence. Importantly, this duplicate AmhY represents the second independent duplication and recruitment of Amh as the sex determination gene in stickleback and the eighth example known across teleosts. We discuss this convergence in the context of sex chromosome turnovers and the role that the Amh/AmhrII pathway, which is crucial for sex determination, may play in the evolution of sex chromosomes in teleosts.
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Affiliation(s)
- Daniel L Jeffries
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Jonathan A Mee
- Department of Biology, Mount Royal University, Calgary, Alberta, Canada
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
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10
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Kirkpatrick M, Sardell JM, Pinto BJ, Dixon G, Peichel CL, Schartl M. Evolution of the canonical sex chromosomes of the guppy and its relatives. G3 (Bethesda) 2022; 12:6472354. [PMID: 35100353 PMCID: PMC9335935 DOI: 10.1093/g3journal/jkab435] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/03/2021] [Indexed: 11/14/2022]
Abstract
The sex chromosomes of the guppy, Poecilia reticulata, and its close relatives are of particular interest: they are much younger than the highly degenerate sex chromosomes of model systems such as humans and Drosophila melanogaster, and they carry many of the genes responsible for the males' dramatic coloration. Over the last decade, several studies have analyzed these sex chromosomes using a variety of approaches including sequencing genomes and transcriptomes, cytology, and linkage mapping. Conflicting conclusions have emerged, in particular concerning the history of the sex chromosomes and the evolution of suppressed recombination between the X and Y. Here, we address these controversies by reviewing the evidence and reanalyzing data. We find no evidence of a nonrecombining sex-determining region or evolutionary strata in P. reticulata. Furthermore, we find that the data most strongly support the hypothesis that the sex-determining regions of 2 close relatives of the guppy, Poecilia wingei and Micropoecilia picta, evolved independently after their lineages diverged. We identify possible causes of conflicting results in previous studies and suggest best practices going forward.
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Affiliation(s)
- Mark Kirkpatrick
- Department of Integrative Biology, University of Texas, Austin, TX 78712, USA
| | - Jason M Sardell
- Department of Integrative Biology, University of Texas, Austin, TX 78712, USA
| | - Brendan J Pinto
- Department of Integrative Biology, University of Texas, Austin, TX 78712, USA.,Milwaukee Public Museum, Milwaukee, WI 53233, USA
| | - Groves Dixon
- Department of Integrative Biology, University of Texas, Austin, TX 78712, USA
| | - Catherine L Peichel
- Institute of Ecology and Evolution, University of Bern, Bern 3012, Switzerland
| | - Manfred Schartl
- Developmental Biochemistry, University of Würzburg, Würzburg97074, Germany.,Department of Chemistry and Biochemistry, The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX 78666, USA
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11
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Rennison DJ, Peichel CL. Pleiotropy facilitates parallel adaptation in sticklebacks. Mol Ecol 2022; 31:1476-1486. [PMID: 34997980 PMCID: PMC9306781 DOI: 10.1111/mec.16335] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 10/27/2021] [Accepted: 12/20/2021] [Indexed: 11/27/2022]
Abstract
Highly pleiotropic genes are predicted to be used less often during adaptation, as mutations in these loci are more likely to have negative fitness consequences. Following this logic, we tested whether pleiotropy impacts the probability that a locus will be used repeatedly in adaptation. We used two proxies to estimate pleiotropy: number of phenotypic traits affected by a given genomic region and gene connectivity. We first surveyed 16 independent stream‐lake and three independent benthic‐limnetic ecotype pairs of threespine stickleback to estimate genome‐wide patterns in parallel genomic differentiation. Our analysis revealed parallel divergence across the genome; 30%–37% of outlier regions were shared between at least two independent pairs in either the stream‐lake or benthic‐limnetic comparisons. We then tested whether parallel genomic regions are less pleiotropic than nonparallel regions. Counter to our a priori prediction, parallel genomic regions contained genes with significantly more pleiotropy; that is, influencing a greater number of traits and more highly connected. The increased pleiotropy of parallel regions could not be explained by other genomic factors, as there was no significant difference in mean gene count, mutation or recombination rates between parallel and nonparallel regions. Interestingly, although nonparallel regions contained genes that were less connected and influenced fewer mapped traits on average than parallel regions, they also tended to contain the genes that were predicted to be the most pleiotropic. Taken together, our findings are consistent with the idea that pleiotropy only becomes constraining at high levels and that low or intermediate levels of pleiotropy may be beneficial for adaptation.
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Affiliation(s)
- Diana J Rennison
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012, Bern, Switzerland
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012, Bern, Switzerland
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12
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Thompson KA, Peichel CL, Rennison DJ, McGee MD, Albert AYK, Vines TH, Greenwood AK, Wark AR, Brandvain Y, Schumer M, Schluter D. Analysis of ancestry heterozygosity suggests that hybrid incompatibilities in threespine stickleback are environment dependent. PLoS Biol 2022; 20:e3001469. [PMID: 35007278 PMCID: PMC8746713 DOI: 10.1371/journal.pbio.3001469] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 11/04/2021] [Indexed: 12/25/2022] Open
Abstract
Hybrid incompatibilities occur when interactions between opposite ancestry alleles at different loci reduce the fitness of hybrids. Most work on incompatibilities has focused on those that are "intrinsic," meaning they affect viability and sterility in the laboratory. Theory predicts that ecological selection can also underlie hybrid incompatibilities, but tests of this hypothesis using sequence data are scarce. In this article, we compiled genetic data for F2 hybrid crosses between divergent populations of threespine stickleback fish (Gasterosteus aculeatus L.) that were born and raised in either the field (seminatural experimental ponds) or the laboratory (aquaria). Because selection against incompatibilities results in elevated ancestry heterozygosity, we tested the prediction that ancestry heterozygosity will be higher in pond-raised fish compared to those raised in aquaria. We found that ancestry heterozygosity was elevated by approximately 3% in crosses raised in ponds compared to those raised in aquaria. Additional analyses support a phenotypic basis for incompatibility and suggest that environment-specific single-locus heterozygote advantage is not the cause of selection on ancestry heterozygosity. Our study provides evidence that, in stickleback, a coarse-albeit indirect-signal of environment-dependent hybrid incompatibility is reliably detectable and suggests that extrinsic incompatibilities can evolve before intrinsic incompatibilities.
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Affiliation(s)
- Ken A. Thompson
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Canada
| | - Catherine L. Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Diana J. Rennison
- Division of Biological Sciences, University of California San Diego, San Diego, California, United States of America
| | - Matthew D. McGee
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | | | - Timothy H. Vines
- DataSeer Research Data Services, Vancouver, British Columbia, Canada
| | | | - Abigail R. Wark
- Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - Yaniv Brandvain
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Molly Schumer
- Department of Biology, Stanford University, Stanford, California, United States of America
- Howard Hughes Medical Institute, Maryland, United States of America
| | - Dolph Schluter
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Canada
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13
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Liu Z, Roesti M, Marques D, Hiltbrunner M, Saladin V, Peichel CL. Chromosomal fusions facilitate adaptation to divergent environments in threespine stickleback. Mol Biol Evol 2021; 39:6462204. [PMID: 34908155 PMCID: PMC8826639 DOI: 10.1093/molbev/msab358] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Chromosomal fusions are hypothesized to facilitate adaptation to divergent environments, both by bringing together previously unlinked adaptive alleles and by creating regions of low recombination that facilitate the linkage of adaptive alleles; but, there is little empirical evidence to support this hypothesis. Here, we address this knowledge gap by studying threespine stickleback (Gasterosteus aculeatus), in which ancestral marine fish have repeatedly adapted to freshwater across the northern hemisphere. By comparing the threespine and ninespine stickleback (Pungitius pungitius) genomes to a de novo assembly of the fourspine stickleback (Apeltes quadracus) and an outgroup species, we find two chromosomal fusion events involving the same chromosomes have occurred independently in the threespine and ninespine stickleback lineages. On the fused chromosomes in threespine stickleback, we find an enrichment of quantitative trait loci underlying traits that contribute to marine versus freshwater adaptation. By comparing whole-genome sequences of freshwater and marine threespine stickleback populations, we also find an enrichment of regions under divergent selection on these two fused chromosomes. There is elevated genetic diversity within regions under selection in the freshwater population, consistent with a simulation study showing that gene flow can increase diversity in genomic regions associated with local adaptation and our demographic models showing gene flow between the marine and freshwater populations. Integrating our results with previous studies, we propose that these fusions created regions of low recombination that enabled the formation of adaptative clusters, thereby facilitating freshwater adaptation in the face of recurrent gene flow between marine and freshwater threespine sticklebacks.
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Affiliation(s)
- Zuyao Liu
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Marius Roesti
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - David Marques
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland.,Natural History Museum Basel, Basel, Switzerland
| | - Melanie Hiltbrunner
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Verena Saladin
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
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14
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Abstract
How consistent are the evolutionary trajectories of sex chromosomes shortly after they form? Insights into the evolution of recombination, differentiation, and degeneration can be provided by comparing closely related species with homologous sex chromosomes. The sex chromosomes of the threespine stickleback (Gasterosteus aculeatus) and its sister species, the Japan Sea stickleback (G. nipponicus), have been well characterized. Little is known, however, about the sex chromosomes of their congener, the blackspotted stickleback (G. wheatlandi). We used pedigrees to obtain experimentally phased whole genome sequences from blackspotted stickleback X and Y chromosomes. Using multispecies gene trees and analysis of shared duplications, we demonstrate that Chromosome 19 is the ancestral sex chromosome and that its oldest stratum evolved in the common ancestor of the genus. After the blackspotted lineage diverged, its sex chromosomes experienced independent and more extensive recombination suppression, greater X-Y differentiation, and a much higher rate of Y degeneration than the other two species. These patterns may result from a smaller effective population size in the blackspotted stickleback. A recent fusion between the ancestral blackspotted stickleback Y chromosome and Chromosome 12, which produced a neo-X and neo-Y, may have been favored by the very small size of the recombining region on the ancestral sex chromosome. We identify six strata on the ancestral and neo-sex chromosomes where recombination between the X and Y ceased at different times. These results confirm that sex chromosomes can evolve large differences within and between species over short evolutionary timescales.
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Affiliation(s)
- Jason M Sardell
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | | | - Anne C Dalziel
- Department of Biology, Saint Mary’s University, Halifax, NS, Canada
| | | | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
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15
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Kratochvíl L, Stöck M, Rovatsos M, Bullejos M, Herpin A, Jeffries DL, Peichel CL, Perrin N, Valenzuela N, Pokorná MJ. Expanding the classical paradigm: what we have learnt from vertebrates about sex chromosome evolution. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200097. [PMID: 34304593 PMCID: PMC8310716 DOI: 10.1098/rstb.2020.0097] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2021] [Indexed: 12/15/2022] Open
Abstract
Until recently, the field of sex chromosome evolution has been dominated by the canonical unidirectional scenario, first developed by Muller in 1918. This model postulates that sex chromosomes emerge from autosomes by acquiring a sex-determining locus. Recombination reduction then expands outwards from this locus, to maintain its linkage with sexually antagonistic/advantageous alleles, resulting in Y or W degeneration and potentially culminating in their disappearance. Based mostly on empirical vertebrate research, we challenge and expand each conceptual step of this canonical model and present observations by numerous experts in two parts of a theme issue of Phil. Trans. R. Soc. B. We suggest that greater theoretical and empirical insights into the events at the origins of sex-determining genes (rewiring of the gonadal differentiation networks), and a better understanding of the evolutionary forces responsible for recombination suppression are required. Among others, crucial questions are: Why do sex chromosome differentiation rates and the evolution of gene dose regulatory mechanisms between male versus female heterogametic systems not follow earlier theory? Why do several lineages not have sex chromosomes? And: What are the consequences of the presence of (differentiated) sex chromosomes for individual fitness, evolvability, hybridization and diversification? We conclude that the classical scenario appears too reductionistic. Instead of being unidirectional, we show that sex chromosome evolution is more complex than previously anticipated and principally forms networks, interconnected to potentially endless outcomes with restarts, deletions and additions of new genomic material. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.
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Affiliation(s)
- Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague, Czech Republic
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries - IGB (Forschungsverbund Berlin), Müggelseedamm 301, 12587 Berlin, Germany
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague, Czech Republic
| | - Mónica Bullejos
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Las Lagunillas Campus S/N, 23071 Jaén, Spain
| | - Amaury Herpin
- INRAE, LPGP, 35000 Rennes, France
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, People's Republic of China
| | - Daniel L. Jeffries
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Catherine L. Peichel
- Institute of Ecology and Evolution, University of Bern, CH-3012 Bern, Switzerland
| | - Nicolas Perrin
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Martina Johnson Pokorná
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague, Czech Republic
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
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16
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Archambeault SL, Durston DJ, Wan A, El-Sabaawi RW, Matthews B, Peichel CL. Phosphorus limitation does not drive loss of bony lateral plates in freshwater stickleback (Gasterosteus aculeatus). Evolution 2020; 74:2088-2104. [PMID: 32537747 PMCID: PMC7773418 DOI: 10.1111/evo.14044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/30/2020] [Accepted: 06/06/2020] [Indexed: 11/29/2022]
Abstract
Connecting the selective forces that drive the evolution of phenotypes to their underlying genotypes is key to understanding adaptation, but such connections are rarely tested experimentally. Threespine stickleback (Gasterosteus aculeatus) are a powerful model for such tests because genotypes that underlie putatively adaptive traits have been identified. For example, a regulatory mutation in the Ectodysplasin (Eda) gene causes a reduction in the number of bony armor plates, which occurs rapidly and repeatedly when marine sticklebacks invade freshwater. However, the source of selection on plate loss in freshwater is unknown. Here, we tested whether dietary reduction of phosphorus can account for selection on plate loss due to a growth advantage of low-plated fish in freshwater. We crossed marine fish heterozygous for the 16 kilobase freshwater Eda haplotype and compared the growth of offspring with different genotypes under contrasting levels of dietary phosphorus in both saltwater and freshwater. Eda genotype was not associated with growth differences in any treatment, or with mechanisms that could mitigate the impacts of phosphorus limitation, such as differential phosphorus deposition, phosphorus excretion, or intestine length. This study highlights the importance of experimentally testing the putative selective forces acting on phenotypes and their underlying genotypes in the wild.
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Affiliation(s)
- Sophie L. Archambeault
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, Washington, USA
- Divisions of Basic Sciences and Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Alex Wan
- Aquaculture Nutrition and Aquafeed Research Unit (ANARU), Carna Research Station, Ryan Institute, NUI Galway, Ireland
| | | | - Blake Matthews
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland
| | - Catherine L. Peichel
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, Washington, USA
- Divisions of Basic Sciences and Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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17
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Archambeault SL, Bärtschi LR, Merminod AD, Peichel CL. Adaptation via pleiotropy and linkage: Association mapping reveals a complex genetic architecture within the stickleback Eda locus. Evol Lett 2020; 4:282-301. [PMID: 32774879 PMCID: PMC7403726 DOI: 10.1002/evl3.175] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 04/04/2020] [Accepted: 04/29/2020] [Indexed: 11/26/2022] Open
Abstract
Genomic mapping of the loci associated with phenotypic evolution has revealed genomic "hotspots," or regions of the genome that control multiple phenotypic traits. This clustering of loci has important implications for the speed and maintenance of adaptation and could be due to pleiotropic effects of a single mutation or tight genetic linkage of multiple causative mutations affecting different traits. The threespine stickleback (Gasterosteus aculeatus) is a powerful model for the study of adaptive evolution because the marine ecotype has repeatedly adapted to freshwater environments across the northern hemisphere in the last 12,000 years. Freshwater ecotypes have repeatedly fixed a 16 kilobase haplotype on chromosome IV that contains Ectodysplasin (Eda), a gene known to affect multiple traits, including defensive armor plates, lateral line sensory hair cells, and schooling behavior. Many additional traits have previously been mapped to a larger region of chromosome IV that encompasses the Eda freshwater haplotype. To identify which of these traits specifically map to this adaptive haplotype, we made crosses of rare marine fish heterozygous for the freshwater haplotype in an otherwise marine genetic background. Further, we performed fine-scale association mapping in a fully interbreeding, polymorphic population of freshwater stickleback to disentangle the effects of pleiotropy and linkage on the phenotypes affected by this haplotype. Although we find evidence that linked mutations have small effects on a few phenotypes, a small 1.4-kb region within the first intron of Eda has large effects on three phenotypic traits: lateral plate count, and both the number and patterning of the posterior lateral line neuromasts. Thus, the Eda haplotype is a hotspot of adaptation in stickleback due to both a small, pleiotropic region affecting multiple traits as well as multiple linked mutations affecting additional traits.
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Affiliation(s)
- Sophie L. Archambeault
- Institute of Ecology and EvolutionUniversity of BernBern3012Switzerland
- Graduate Program in Molecular and Cellular BiologyUniversity of WashingtonSeattleWashington98195
- Divisions of Basic Sciences and Human BiologyFred Hutchinson Cancer Research CenterSeattleWashington98109
| | - Luis R. Bärtschi
- Institute of Ecology and EvolutionUniversity of BernBern3012Switzerland
| | | | - Catherine L. Peichel
- Institute of Ecology and EvolutionUniversity of BernBern3012Switzerland
- Graduate Program in Molecular and Cellular BiologyUniversity of WashingtonSeattleWashington98195
- Divisions of Basic Sciences and Human BiologyFred Hutchinson Cancer Research CenterSeattleWashington98109
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18
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Peichel CL, McCann SR, Ross JA, Naftaly AFS, Urton JR, Cech JN, Grimwood J, Schmutz J, Myers RM, Kingsley DM, White MA. Assembly of the threespine stickleback Y chromosome reveals convergent signatures of sex chromosome evolution. Genome Biol 2020; 21:177. [PMID: 32684159 PMCID: PMC7368989 DOI: 10.1186/s13059-020-02097-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 07/08/2020] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Heteromorphic sex chromosomes have evolved repeatedly across diverse species. Suppression of recombination between X and Y chromosomes leads to degeneration of the Y chromosome. The progression of degeneration is not well understood, as complete sequence assemblies of heteromorphic Y chromosomes have only been generated across a handful of taxa with highly degenerate sex chromosomes. Here, we describe the assembly of the threespine stickleback (Gasterosteus aculeatus) Y chromosome, which is less than 26 million years old and at an intermediate stage of degeneration. Our previous work identified that the non-recombining region between the X and the Y spans approximately 17.5 Mb on the X chromosome. RESULTS We combine long-read sequencing with a Hi-C-based proximity guided assembly to generate a 15.87 Mb assembly of the Y chromosome. Our assembly is concordant with cytogenetic maps and Sanger sequences of over 90 Y chromosome BAC clones. We find three evolutionary strata on the Y chromosome, consistent with the three inversions identified by our previous cytogenetic analyses. The threespine stickleback Y shows convergence with more degenerate sex chromosomes in the retention of haploinsufficient genes and the accumulation of genes with testis-biased expression, many of which are recent duplicates. However, we find no evidence for large amplicons identified in other sex chromosome systems. We also report an excellent candidate for the master sex-determination gene: a translocated copy of Amh (Amhy). CONCLUSIONS Together, our work shows that the evolutionary forces shaping sex chromosomes can cause relatively rapid changes in the overall genetic architecture of Y chromosomes.
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Affiliation(s)
- Catherine L. Peichel
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
| | - Shaugnessy R. McCann
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
| | - Joseph A. Ross
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195 USA
| | | | - James R. Urton
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195 USA
| | - Jennifer N. Cech
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195 USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806 USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806 USA
| | - Richard M. Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806 USA
| | - David M. Kingsley
- Department of Developmental Biology and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Michael A. White
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
- Department of Genetics, University of Georgia, Athens, GA 30602 USA
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19
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Feller AF, Haesler MP, Peichel CL, Seehausen O. Genetic architecture of a key reproductive isolation trait differs between sympatric and non-sympatric sister species of Lake Victoria cichlids. Proc Biol Sci 2020; 287:20200270. [PMID: 32259470 PMCID: PMC7209058 DOI: 10.1098/rspb.2020.0270] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
One hallmark of the East African cichlid radiations is the rapid evolution of reproductive isolation that is robust to full sympatry of many closely related species. Theory predicts that species persistence and speciation in sympatry with gene flow are facilitated if loci of large effect or physical linkage (or pleiotropy) underlie traits involved in reproductive isolation. Here, we investigate the genetic architecture of a key trait involved in behavioural isolation, male nuptial coloration, by crossing two sister species pairs of Lake Victoria cichlids of the genus Pundamilia and mapping nuptial coloration in the F2 hybrids. One is a young sympatric species pair, representative of an axis of colour motif differentiation, red-dorsum versus blue, that is highly recurrent in closely related sympatric species. The other is a species pair representative of colour motifs, red-chest versus blue, that are common in allopatric but uncommon in sympatric closely related species. We find significant quantitative trait loci (QTLs) with moderate to large effects (some overlapping) for red and yellow in the sympatric red-dorsum × blue cross, whereas we find no significant QTLs in the non-sympatric red-chest × blue cross. These findings are consistent with theory predicting that large effect loci or linkage/pleiotropy underlying mating trait differentiation could facilitate speciation and species persistence with gene flow in sympatry.
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Affiliation(s)
- Anna F Feller
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
| | - Marcel P Haesler
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Ole Seehausen
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
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20
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Ishikawa A, Kabeya N, Ikeya K, Kakioka R, Cech JN, Osada N, Leal MC, Inoue J, Kume M, Toyoda A, Tezuka A, Nagano AJ, Yamasaki YY, Suzuki Y, Kokita T, Takahashi H, Lucek K, Marques D, Takehana Y, Naruse K, Mori S, Monroig O, Ladd N, Schubert CJ, Matthews B, Peichel CL, Seehausen O, Yoshizaki G, Kitano J. A key metabolic gene for recurrent freshwater colonization and radiation in fishes. Science 2019; 364:886-889. [PMID: 31147520 DOI: 10.1126/science.aau5656] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 04/17/2019] [Indexed: 01/10/2023]
Abstract
Colonization of new ecological niches has triggered large adaptive radiations. Although some lineages have made use of such opportunities, not all do so. The factors causing this variation among lineages are largely unknown. Here, we show that deficiency in docosahexaenoic acid (DHA), an essential ω-3 fatty acid, can constrain freshwater colonization by marine fishes. Our genomic analyses revealed multiple independent duplications of the fatty acid desaturase gene Fads2 in stickleback lineages that subsequently colonized and radiated in freshwater habitats, but not in close relatives that failed to colonize. Transgenic manipulation of Fads2 in marine stickleback increased their ability to synthesize DHA and survive on DHA-deficient diets. Multiple freshwater ray-finned fishes also show a convergent increase in Fads2 copies, indicating its key role in freshwater colonization.
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Affiliation(s)
- Asano Ishikawa
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan.,Department of Genetics, Graduate University for Advanced Studies (SOKENDAI), Shizuoka, Japan
| | - Naoki Kabeya
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan.,Department of Aquatic Bioscience, The University of Tokyo, Tokyo, Japan
| | - Koki Ikeya
- Gifu World Freshwater Aquarium, Gifu, Japan
| | - Ryo Kakioka
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Jennifer N Cech
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Naoki Osada
- Graduate School of Bioengineering and Bioinformatics, Hokkaido University, Sapporo, Japan
| | - Miguel C Leal
- Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland
| | - Jun Inoue
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Manabu Kume
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Ayumi Tezuka
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, Japan
| | | | - Yo Y Yamasaki
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Yuto Suzuki
- Department of Marine Bioscience, Fukui Prefectural University, Obama, Fukui, Japan
| | - Tomoyuki Kokita
- Department of Marine Bioscience, Fukui Prefectural University, Obama, Fukui, Japan
| | - Hiroshi Takahashi
- Department of Applied Aquabiology, National Fisheries University, Shimonoseki, Yamaguchi, Japan
| | - Kay Lucek
- Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland.,Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - David Marques
- Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland.,Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Yusuke Takehana
- Laboratory of Bioresources, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Kiyoshi Naruse
- Laboratory of Bioresources, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Seiichi Mori
- Biological Laboratory, Gifu Kyoritsu University, Ogaki, Gifu, Japan
| | - Oscar Monroig
- Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Ribera de Cabanes, Castellón, Spain
| | - Nemiah Ladd
- Department of Surface Waters-Research and Management, Eawag Swiss Federal Institute of Aquatic Science and Technology, Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland.,Department of Earth Sciences, ETH-Zurich, Zurich Switzerland
| | - Carsten J Schubert
- Department of Surface Waters-Research and Management, Eawag Swiss Federal Institute of Aquatic Science and Technology, Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland
| | - Blake Matthews
- Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland.,Department of Aquatic Ecology, Eawag Swiss Federal Institute of Aquatic Science and Technology, Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland
| | - Catherine L Peichel
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Ole Seehausen
- Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland.,Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Goro Yoshizaki
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan. .,Department of Genetics, Graduate University for Advanced Studies (SOKENDAI), Shizuoka, Japan
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21
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Drinnenberg IA, Berger F, Elsässer SJ, Andersen PR, Ausió J, Bickmore WA, Blackwell AR, Erwin DH, Gahan JM, Gaut BS, Harvey ZH, Henikoff S, Kao JY, Kurdistani SK, Lemos B, Levine MT, Luger K, Malik HS, Martín-Durán JM, Peichel CL, Renfree MB, Rutowicz K, Sarkies P, Schmitz RJ, Technau U, Thornton JW, Warnecke T, Wolfe KH. EvoChromo: towards a synthesis of chromatin biology and evolution. Development 2019; 146:146/19/dev178962. [PMID: 31558570 DOI: 10.1242/dev.178962] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Over the past few years, interest in chromatin and its evolution has grown. To further advance these interests, we organized a workshop with the support of The Company of Biologists to debate the current state of knowledge regarding the origin and evolution of chromatin. This workshop led to prospective views on the development of a new field of research that we term 'EvoChromo'. In this short Spotlight article, we define the breadth and expected impact of this new area of scientific inquiry on our understanding of both chromatin and evolution.
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Affiliation(s)
- Ines A Drinnenberg
- Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique UMR 3664, Paris 75005, France
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Simon J Elsässer
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Peter R Andersen
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohrgasse 3, 1030 Vienna, Austria
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 3P6, Canada
| | - Wendy A Bickmore
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | | | - Douglas H Erwin
- Department of Paleobiology, MRC-121, National Museum of Natural History, Washington, DC 20013-7012, USA
| | - James M Gahan
- Sars Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgt. 55, 5008 Bergen, Norway
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Zachary H Harvey
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Steven Henikoff
- Division of Basic Sciences and Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Joyce Y Kao
- Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY 10003, USA.,Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Siavash K Kurdistani
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Bernardo Lemos
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Mia T Levine
- Department of Biology, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Karolin Luger
- Howard Hughes Medical Institute and Department of Biochemistry, CU Boulder, Boulder, CO 80303, USA
| | - Harmit S Malik
- Division of Basic Sciences and Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - José M Martín-Durán
- Queen Mary University of London, School of Biological and Chemical Sciences, Mile End Road, London E1 4NS, UK
| | - Catherine L Peichel
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Marilyn B Renfree
- School of BioSciences, The University of Melbourne, Melbourne, 3010 VIC, Australia
| | - Kinga Rutowicz
- Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, 8092 Zürich, Switzerland
| | - Peter Sarkies
- MRC London Institute of Medical Sciences and Institute of Clinical Sciences, IMperial College London, Du Cane Road, London W12 0NN, UK
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Ulrich Technau
- Department for Molecular Evolution and Development, Centre of Organismal Systems Biology, University of Vienna, Vienna A-1090, Austria
| | - Joseph W Thornton
- Department of Human Genetics, and Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637 USA
| | - Tobias Warnecke
- MRC London Institute of Medical Sciences and Institute of Clinical Sciences, IMperial College London, Du Cane Road, London W12 0NN, UK
| | - Kenneth H Wolfe
- Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland
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22
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Rennison DJ, Stuart YE, Bolnick DI, Peichel CL. Ecological factors and morphological traits are associated with repeated genomic differentiation between lake and stream stickleback. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180241. [PMID: 31154970 PMCID: PMC6560272 DOI: 10.1098/rstb.2018.0241] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2018] [Indexed: 12/24/2022] Open
Abstract
The repeated evolution of similar phenotypes in independent populations (i.e. parallel or convergent evolution) provides an opportunity to identify genetic and ecological factors that influence the process of adaptation. Threespine stickleback fish ( Gasterosteus aculeatus) are an excellent model for such studies, as they have repeatedly adapted to divergent habitats across the Northern hemisphere. Here, we use genomic, ecological and morphological data from 16 independent pairs of stickleback populations adapted to divergent lake and stream habitats. We combine a population genomic approach to identify regions of the genome that are likely under selection in these divergent habitats with an association mapping approach to identify regions of the genome that underlie variation in ecological factors and morphological traits. Over 37% of genomic windows are repeatedly differentiated across lake-stream pairs. Similarly, many genomic windows are associated with variation in abiotic factors, diet items and morphological phenotypes. Both the highly differentiated windows and candidate trait windows are non-randomly distributed across the genome and show some overlap. However, the overlap is not significant on a genome-wide scale. Together, our data suggest that adaptation to divergent food resources and predation regimes are drivers of differentiation in lake-stream stickleback, but that additional ecological factors are also important. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.
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Affiliation(s)
- Diana J. Rennison
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Yoel E. Stuart
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Daniel I. Bolnick
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
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23
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Pennell MW, Mank JE, Peichel CL. Transitions in sex determination and sex chromosomes across vertebrate species. Mol Ecol 2018; 27:3950-3963. [PMID: 29451715 PMCID: PMC6095824 DOI: 10.1111/mec.14540] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 01/30/2018] [Accepted: 02/06/2018] [Indexed: 12/14/2022]
Abstract
Despite the prevalence of sexual reproduction across eukaryotes, there is a remarkable diversity of sex-determination mechanisms. The underlying causes of this diversity remain unclear, and it is unknown whether there are convergent trends in the directionality of turnover in sex-determination mechanisms. We used the recently assembled Tree of Sex database to assess patterns in the evolution of sex-determination systems in the remarkably diverse vertebrate clades of teleost fish, squamate reptiles and amphibians. Contrary to theoretical predictions, we find no evidence that the evolution of separate sexes is irreversible, as transitions from separate sexes to hermaphroditism occur at higher rates than the reverse in fish. We also find that transitions from environmental sex determination to genetic sex determination occur at higher rates than the reverse in both squamates and fish, suggesting that genetic sex determination is more stable. However, our data are not consistent with the hypothesis that heteromorphic sex chromosomes are an "evolutionary trap." Rather, we find similar transition rates between homomorphic and heteromorphic sex chromosomes in both fish and amphibians, and to environmental sex determination from heteromorphic vs. homomorphic sex chromosome systems in fish. Finally, we find that transitions between male and female heterogamety occur at similar rates in amphibians and squamates, while transitions to male heterogamety occur at higher rates in fish. Together, these results provide the most comprehensive view to date of the evolution of vertebrate sex determination in a phylogenetic context, providing new insight into long-standing questions about the evolution of sexual reproduction.
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Affiliation(s)
- Matthew W. Pennell
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Judith E. Mank
- Department of Genetics, Evolution and Environment, University College London, London, UK
- Department of Organismal Biology, Uppsala University, Sweden
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24
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Affiliation(s)
- Catherine L Peichel
- From the Divisions of Basic Sciences and Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109; and Institute of Ecology and Evolution, University of Bern, CH-3012 Bern, Switzerland.
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25
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Peichel CL, Marques DA. The genetic and molecular architecture of phenotypic diversity in sticklebacks. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2015.0486. [PMID: 27994127 DOI: 10.1098/rstb.2015.0486] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2016] [Indexed: 11/12/2022] Open
Abstract
A major goal of evolutionary biology is to identify the genotypes and phenotypes that underlie adaptation to divergent environments. Stickleback fish, including the threespine stickleback (Gasterosteus aculeatus) and the ninespine stickleback (Pungitius pungitius), have been at the forefront of research to uncover the genetic and molecular architecture that underlies phenotypic diversity and adaptation. A wealth of quantitative trait locus (QTL) mapping studies in sticklebacks have provided insight into long-standing questions about the distribution of effect sizes during adaptation as well as the role of genetic linkage in facilitating adaptation. These QTL mapping studies have also provided a basis for the identification of the genes that underlie phenotypic diversity. These data have revealed that mutations in regulatory elements play an important role in the evolution of phenotypic diversity in sticklebacks. Genetic and molecular studies in sticklebacks have also led to new insights on the genetic basis of repeated evolution and suggest that the same loci are involved about half of the time when the same phenotypes evolve independently. When the same locus is involved, selection on standing variation and repeated mutation of the same genes have both contributed to the evolution of similar phenotypes in independent populations.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.
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Affiliation(s)
- Catherine L Peichel
- Divisions of Basic Sciences and Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - David A Marques
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Department of Fish Ecology and Evolution, Eawag, Swiss Federal Institute for Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
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26
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Thompson CJ, Ahmed NI, Veen T, Peichel CL, Hendry AP, Bolnick DI, Stuart YE. Many-to-one form-to-function mapping weakens parallel morphological evolution. Evolution 2017; 71:2738-2749. [PMID: 28881442 DOI: 10.1111/evo.13357] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 07/28/2017] [Accepted: 08/15/2017] [Indexed: 01/05/2023]
Abstract
Evolutionary ecologists aim to explain and predict evolutionary change under different selective regimes. Theory suggests that such evolutionary prediction should be more difficult for biomechanical systems in which different trait combinations generate the same functional output: "many-to-one mapping." Many-to-one mapping of phenotype to function enables multiple morphological solutions to meet the same adaptive challenges. Therefore, many-to-one mapping should undermine parallel morphological evolution, and hence evolutionary predictability, even when selection pressures are shared among populations. Studying 16 replicate pairs of lake- and stream-adapted threespine stickleback (Gasterosteus aculeatus), we quantified three parts of the teleost feeding apparatus and used biomechanical models to calculate their expected functional outputs. The three feeding structures differed in their form-to-function relationship from one-to-one (lower jaw lever ratio) to increasingly many-to-one (buccal suction index, opercular 4-bar linkage). We tested for (1) weaker linear correlations between phenotype and calculated function, and (2) less parallel evolution across lake-stream pairs, in the many-to-one systems relative to the one-to-one system. We confirm both predictions, thus supporting the theoretical expectation that increasing many-to-one mapping undermines parallel evolution. Therefore, sole consideration of morphological variation within and among populations might not serve as a proxy for functional variation when multiple adaptive trait combinations exist.
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Affiliation(s)
- Cole J Thompson
- Department of Integrative Biology, One University Station C0990, University of Texas at Austin, Austin, Texas
| | - Newaz I Ahmed
- Department of Integrative Biology, One University Station C0990, University of Texas at Austin, Austin, Texas.,Department of Internal Medicine, University of Texas-Southwestern, Dallas, Texas
| | - Thor Veen
- Department of Integrative Biology, One University Station C0990, University of Texas at Austin, Austin, Texas.,Department of Life Sciences, Quest University, Squamish, BC, Canada
| | - Catherine L Peichel
- Divisions of Basic Sciences and Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Current Address: Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | | | - Daniel I Bolnick
- Department of Integrative Biology, One University Station C0990, University of Texas at Austin, Austin, Texas
| | - Yoel E Stuart
- Department of Integrative Biology, One University Station C0990, University of Texas at Austin, Austin, Texas
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27
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Bay RA, Arnegard ME, Conte GL, Best J, Bedford NL, McCann SR, Dubin ME, Chan YF, Jones FC, Kingsley DM, Schluter D, Peichel CL. Genetic Coupling of Female Mate Choice with Polygenic Ecological Divergence Facilitates Stickleback Speciation. Curr Biol 2017; 27:3344-3349.e4. [PMID: 29056455 DOI: 10.1016/j.cub.2017.09.037] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 08/12/2017] [Accepted: 09/15/2017] [Indexed: 11/28/2022]
Abstract
Ecological speciation with gene flow is widespread in nature [1], but it presents a conundrum: how are associations between traits under divergent natural selection and traits that contribute to assortative mating maintained? Theoretical models suggest that genetic mechanisms inhibiting free recombination between loci underlying these two types of traits (hereafter, "genetic coupling") can facilitate speciation [2-4]. Here, we perform a direct test for genetic coupling by mapping both divergent traits and female mate choice in a classic model of ecological speciation: sympatric benthic and limnetic threespine stickleback (Gasterosteus aculeatus). By measuring mate choice in F2 hybrid females, we allowed for recombination between loci underlying assortative mating and those under divergent ecological selection. In semi-natural mating arenas in which females had access to both benthic and limnetic males, we found that F2 females mated with males similar to themselves in body size and shape. In addition, we found two quantitative trait loci (QTLs) associated with female mate choice that also predicted female morphology along the benthic-limnetic trait axis. Furthermore, a polygenic genetic model that explains adaptation to contrasting benthic and limnetic feeding niches [5] also predicted F2 female mate choice. Together, these results provide empirical evidence that genetic coupling of assortative mating with traits under divergent ecological selection helps maintain species in the face of gene flow, despite a polygenic basis for adaptation to divergent environments.
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Affiliation(s)
- Rachael A Bay
- Biodiversity Research Centre and Zoology Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada; Institute of the Environment and Sustainability, University of California, Los Angeles, 619 Charles E. Young Drive #300, Los Angeles, CA 90024, USA
| | - Matthew E Arnegard
- Biodiversity Research Centre and Zoology Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada; Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Gina L Conte
- Biodiversity Research Centre and Zoology Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Jacob Best
- Biodiversity Research Centre and Zoology Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Nicole L Bedford
- Biodiversity Research Centre and Zoology Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Shaugnessy R McCann
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Matthew E Dubin
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Yingguang Frank Chan
- Department of Developmental Biology and Howard Hughes Medical Institute, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA
| | - Felicity C Jones
- Department of Developmental Biology and Howard Hughes Medical Institute, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA
| | - David M Kingsley
- Department of Developmental Biology and Howard Hughes Medical Institute, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA
| | - Dolph Schluter
- Biodiversity Research Centre and Zoology Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Catherine L Peichel
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA.
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28
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Peichel CL, Sullivan ST, Liachko I, White MA. Improvement of the Threespine Stickleback Genome Using a Hi-C-Based Proximity-Guided Assembly. J Hered 2017; 108:693-700. [PMID: 28821183 DOI: 10.1093/jhered/esx058] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 07/05/2017] [Indexed: 11/13/2022] Open
Abstract
Scaffolding genomes into complete chromosome assemblies remains challenging even with the rapidly increasing sequence coverage generated by current next-generation sequence technologies. Even with scaffolding information, many genome assemblies remain incomplete. The genome of the threespine stickleback (Gasterosteus aculeatus), a fish model system in evolutionary genetics and genomics, is not completely assembled despite scaffolding with high-density linkage maps. Here, we first test the ability of a Hi-C based proximity-guided assembly (PGA) to perform a de novo genome assembly from relatively short contigs. Using Hi-C based PGA, we generated complete chromosome assemblies from a distribution of short contigs (20-100 kb). We found that 96.40% of contigs were correctly assigned to linkage groups (LGs), with ordering nearly identical to the previous genome assembly. Using available bacterial artificial chromosome (BAC) end sequences, we provide evidence that some of the few discrepancies between the Hi-C assembly and the existing assembly are due to structural variation between the populations used for the 2 assemblies or errors in the existing assembly. This Hi-C assembly also allowed us to improve the existing assembly, assigning over 60% (13.35 Mb) of the previously unassigned (~21.7 Mb) contigs to LGs. Together, our results highlight the potential of the Hi-C based PGA method to be used in combination with short read data to perform relatively inexpensive de novo genome assemblies. This approach will be particularly useful in organisms in which it is difficult to perform linkage mapping or to obtain high molecular weight DNA required for other scaffolding methods.
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Affiliation(s)
- Catherine L Peichel
- Divisons of Basic Sciences and Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA,Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | | | | | - Michael A White
- Department of Genetics, University of Georgia, 120 Green Street, Athens, GA 30602
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29
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Stuart YE, Veen T, Weber JN, Hanson D, Ravinet M, Lohman BK, Thompson CJ, Tasneem T, Doggett A, Izen R, Ahmed N, Barrett RDH, Hendry AP, Peichel CL, Bolnick DI. Contrasting effects of environment and genetics generate a continuum of parallel evolution. Nat Ecol Evol 2017; 1:158. [DOI: 10.1038/s41559-017-0158] [Citation(s) in RCA: 155] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 04/07/2017] [Indexed: 12/25/2022]
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30
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Jiang Y, Peichel CL, Torrance L, Rizvi Z, Thompson S, Palivela VV, Pham H, Ling F, Bolnick DI. Sensory trait variation contributes to biased dispersal of threespine stickleback in flowing water. J Evol Biol 2017; 30:681-695. [PMID: 28029723 DOI: 10.1111/jeb.13035] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 12/16/2016] [Accepted: 12/20/2016] [Indexed: 12/13/2022]
Abstract
Gene flow is widely thought to homogenize spatially separate populations, eroding effects of divergent selection. The resulting theory of 'migration-selection balance' is predicated on a common assumption that all genotypes are equally prone to dispersal. If instead certain genotypes are disproportionately likely to disperse, then migration can actually promote population divergence. For example, previous work has shown that threespine stickleback (Gasterosteus aculeatus) differ in their propensity to move up- or downstream ('rheotactic response'), which may facilitate genetic divergence between adjoining lake and stream populations of stickleback. Here, we demonstrate that intraspecific variation in a sensory system (superficial neuromast lines) contributes to this variation in swimming behaviour in stickleback. First, we show that intact neuromasts are necessary for a typical rheotactic response. Next, we showed that there is heritable variation in the number of neuromasts and that stickleback with more neuromasts are more likely to move downstream. Variation in pectoral fin shape contributes to additional variation in rheotactic response. These results illustrate how within-population quantitative variation in sensory and locomotor traits can influence dispersal behaviour, thereby biasing dispersal between habitats and favouring population divergence.
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Affiliation(s)
- Y Jiang
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - C L Peichel
- Divisions of Basic Sciences and Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - L Torrance
- Texas A&M University, Corpus Christi, TX, USA
| | - Z Rizvi
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - S Thompson
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - V V Palivela
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - H Pham
- University of Texas Health Science Center, Houston, TX, USA
| | - F Ling
- Department of Fisheries Science, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - D I Bolnick
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
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31
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Cech JN, Peichel CL. Centromere inactivation on a neo-Y fusion chromosome in threespine stickleback fish. Chromosome Res 2016; 24:437-450. [PMID: 27553478 DOI: 10.1007/s10577-016-9535-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 08/14/2016] [Accepted: 08/16/2016] [Indexed: 02/07/2023]
Abstract
Having one and only one centromere per chromosome is essential for proper chromosome segregation during both mitosis and meiosis. Chromosomes containing two centromeres are known as dicentric and often mis-segregate during cell division, resulting in aneuploidy or chromosome breakage. Dicentric chromosome can be stabilized by centromere inactivation, a process which reestablishes monocentric chromosomes. However, little is known about this process in naturally occurring dicentric chromosomes. Using a combination of fluorescence in situ hybridization (FISH) and immunofluorescence combined with FISH (IF-FISH) on metaphase chromosome spreads, we demonstrate that centromere inactivation has evolved on a neo-Y chromosome fusion in the Japan Sea threespine stickleback fish (Gasterosteus nipponicus). We found that the centromere derived from the ancestral Y chromosome has been inactivated. Our data further suggest that there have been genetic changes to this centromere in the two million years since the formation of the neo-Y chromosome, but it remains unclear whether these genetic changes are a cause or consequence of centromere inactivation.
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Affiliation(s)
- Jennifer N Cech
- Divisions of Basic Sciences and Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave North, Mailstop C2-023, Seattle, WA, 98109, USA
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA, 98195, USA
| | - Catherine L Peichel
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012, Bern, Switzerland.
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32
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Cech JN, Peichel CL. Identification of the centromeric repeat in the threespine stickleback fish (Gasterosteus aculeatus). Chromosome Res 2015; 23:767-79. [PMID: 26424612 DOI: 10.1007/s10577-015-9495-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 09/11/2015] [Accepted: 09/17/2015] [Indexed: 01/09/2023]
Abstract
Centromere sequences exist as gaps in many genome assemblies due to their repetitive nature. Here we take an unbiased approach utilizing centromere protein A (CENP-A) chomatin immunoprecipitation followed by high-throughput sequencing to identify the centromeric repeat sequence in the threespine stickleback fish (Gasterosteus aculeatus). A 186-bp, AT-rich repeat was validated as centromeric using both fluorescence in situ hybridization (FISH) and immunofluorescence combined with FISH (IF-FISH) on interphase nuclei and metaphase spreads. This repeat hybridizes strongly to the centromere on all chromosomes, with the exception of weak hybridization to the Y chromosome. Together, our work provides the first validated sequence information for the threespine stickleback centromere.
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Affiliation(s)
- Jennifer N Cech
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave North, Mailstop C2-023, Seattle, WA, 98109, USA.,Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA, 98195, USA
| | - Catherine L Peichel
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave North, Mailstop C2-023, Seattle, WA, 98109, USA.
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33
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Jiang Y, Torrance L, Peichel CL, Bolnick DI. Differences in rheotactic responses contribute to divergent habitat use between parapatric lake and stream threespine stickleback. Evolution 2015. [DOI: 10.1111/evo.12740] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Yuexin Jiang
- Department of Integrative Biology; University of Texas at Austin; One University Station C0990 Austin Texas 78712
- Department of Environmental Science and Policy; University of California at Davis; One Shields Avenue Davis California 95616
| | | | - Catherine L. Peichel
- Divisions of Human Biology and Basic Sciences; Fred Hutchinson Cancer Research Center; 1100 Fairview Ave. N. Seattle Washington 98109
| | - Daniel I. Bolnick
- Department of Integrative Biology; University of Texas at Austin; One University Station C0990 Austin Texas 78712
- Howard Hughes Medical Institute; University of Texas at Austin; One University Station C0990 Austin Texas 78712
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34
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White MA, Kitano J, Peichel CL. Purifying Selection Maintains Dosage-Sensitive Genes during Degeneration of the Threespine Stickleback Y Chromosome. Mol Biol Evol 2015; 32:1981-95. [PMID: 25818858 DOI: 10.1093/molbev/msv078] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Sex chromosomes are subject to unique evolutionary forces that cause suppression of recombination, leading to sequence degeneration and the formation of heteromorphic chromosome pairs (i.e., XY or ZW). Although progress has been made in characterizing the outcomes of these evolutionary processes on vertebrate sex chromosomes, it is still unclear how recombination suppression and sequence divergence typically occur and how gene dosage imbalances are resolved in the heterogametic sex. The threespine stickleback fish (Gasterosteus aculeatus) is a powerful model system to explore vertebrate sex chromosome evolution, as it possesses an XY sex chromosome pair at relatively early stages of differentiation. Using a combination of whole-genome and transcriptome sequencing, we characterized sequence evolution and gene expression across the sex chromosomes. We uncovered two distinct evolutionary strata that correspond with known structural rearrangements on the Y chromosome. In the oldest stratum, only a handful of genes remain, and these genes are under strong purifying selection. By comparing sex-linked gene expression with expression of autosomal orthologs in an outgroup, we show that dosage compensation has not evolved in threespine sticklebacks through upregulation of the X chromosome in males. Instead, in the oldest stratum, the genes that still possess a Y chromosome allele are enriched for genes predicted to be dosage sensitive in mammals and yeast. Our results suggest that dosage imbalances may have been avoided at haploinsufficient genes by retaining function of the Y chromosome allele through strong purifying selection.
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Affiliation(s)
- Michael A White
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Catherine L Peichel
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
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Greenwood AK, Ardekani R, McCann SR, Dubin ME, Sullivan A, Bensussen S, Tavaré S, Peichel CL. Genetic mapping of natural variation in schooling tendency in the threespine stickleback. G3 (Bethesda) 2015; 5:761-9. [PMID: 25717151 PMCID: PMC4426364 DOI: 10.1534/g3.114.016519] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 02/23/2015] [Indexed: 02/06/2023]
Abstract
Although there is a heritable basis for many animal behaviors, the genetic architecture of behavioral variation in natural populations remains mostly unknown, particularly in vertebrates. We sought to identify the genetic basis for social affiliation in two populations of threespine sticklebacks (Gasterosteus aculeatus) that differ in their propensity to school. Marine sticklebacks from Japan school strongly whereas benthic sticklebacks from a lake in Canada are more solitary. Here, we expanded on our previous efforts to identify quantitative trait loci (QTL) for differences in schooling tendency. We tested fish multiple times in two assays that test different aspects of schooling tendency: 1) the model school assay, which presents fish with a school of eight model sticklebacks; and 2) the choice assay, in which fish are given a choice between the model school and a stationary artificial plant. We found low-to-moderate levels of repeatability, ranging from 0.1 to 0.5, in schooling phenotypes. To identify the genomic regions that contribute to differences in schooling tendency, we used QTL mapping in two types of crosses: benthic × marine backcrosses and an F2 intercross. We found two QTL for time spent with the school in the model school assay, and one QTL for number of approaches to the school in the choice assay. These QTL were on three different linkage groups, not previously linked to behavioral differences in sticklebacks. Our results highlight the importance of using multiple crosses and robust behavioral assays to uncover the genetic basis of behavioral variation in natural populations.
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Affiliation(s)
- Anna K Greenwood
- Divisions of Basic Sciences and Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
| | - Reza Ardekani
- Program in Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089
| | - Shaugnessy R McCann
- Divisions of Basic Sciences and Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
| | - Matthew E Dubin
- Divisions of Basic Sciences and Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
| | - Amy Sullivan
- Divisions of Basic Sciences and Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
| | - Seth Bensussen
- Divisions of Basic Sciences and Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
| | - Simon Tavaré
- Program in Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089
| | - Catherine L Peichel
- Divisions of Basic Sciences and Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
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Bachtrog D, Mank JE, Peichel CL, Kirkpatrick M, Otto SP, Ashman TL, Hahn MW, Kitano J, Mayrose I, Ming R, Perrin N, Ross L, Valenzuela N, Vamosi JC. Sex determination: why so many ways of doing it? PLoS Biol 2014; 12:e1001899. [PMID: 24983465 PMCID: PMC4077654 DOI: 10.1371/journal.pbio.1001899] [Citation(s) in RCA: 698] [Impact Index Per Article: 69.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Sexual reproduction is an ancient feature of life on earth, and the familiar X and Y chromosomes in humans and other model species have led to the impression that sex determination mechanisms are old and conserved. In fact, males and females are determined by diverse mechanisms that evolve rapidly in many taxa. Yet this diversity in primary sex-determining signals is coupled with conserved molecular pathways that trigger male or female development. Conflicting selection on different parts of the genome and on the two sexes may drive many of these transitions, but few systems with rapid turnover of sex determination mechanisms have been rigorously studied. Here we survey our current understanding of how and why sex determination evolves in animals and plants and identify important gaps in our knowledge that present exciting research opportunities to characterize the evolutionary forces and molecular pathways underlying the evolution of sex determination.
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Affiliation(s)
- Doris Bachtrog
- University of California, Berkeley, Department of Integrative Biology, Berkeley, California, United States of America
| | - Judith E. Mank
- University College London, Department of Genetics, Evolution and Environment, London, United Kingdom
| | - Catherine L. Peichel
- Fred Hutchinson Cancer Research Center, Divisions of Human Biology and Basic Sciences, Seattle, Washington, United States of America
| | - Mark Kirkpatrick
- University of Texas, Department of Integrative Biology, Austin, Texas, United States of America
| | - Sarah P. Otto
- University of British Columbia, Department of Zoology, Vancouver, British Columbia, Canada
| | - Tia-Lynn Ashman
- University of Pittsburgh, Department of Biological Sciences, Pittsburgh, Pennsylvania, United States of America
| | - Matthew W. Hahn
- Indiana University, Department of Biology, Bloomington Indiana, United States of America
| | - Jun Kitano
- National Institute of Genetics, Ecological Genetics Laboratory, Mishima, Shizuoka, Japan
| | - Itay Mayrose
- Tel Aviv University, Department of Molecular Biology and Ecology of Plants, Tel Aviv, Israel
| | - Ray Ming
- University of Illinois, Department of Plant Biology, Urbana-Champaign, Illinois, United States of America
| | - Nicolas Perrin
- University of Lausanne, Department of Ecology and Evolution, Lausanne, Switzerland
| | - Laura Ross
- University of Oxford, Department of Zoology, Oxford, United Kingdom
| | - Nicole Valenzuela
- Iowa State University, Department of Ecology, Evolution and Organismal Biology, Ames, Iowa, United States of America
| | - Jana C. Vamosi
- University of Calgary, Department of Biological Sciences, Calgary, Alberta, Canada
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Arnegard ME, McGee MD, Matthews B, Marchinko KB, Conte GL, Kabir S, Bedford N, Bergek S, Chan YF, Jones FC, Kingsley DM, Peichel CL, Schluter D. Genetics of ecological divergence during speciation. Nature 2014; 511:307-11. [PMID: 24909991 PMCID: PMC4149549 DOI: 10.1038/nature13301] [Citation(s) in RCA: 199] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 04/01/2014] [Indexed: 01/15/2023]
Abstract
Ecological differences often evolve early in speciation as divergent natural selection drives adaptation to distinct ecological niches, leading ultimately to reproductive isolation. Although this process is a major generator of biodiversity, its genetic basis is still poorly understood. Here we investigate the genetic architecture of niche differentiation in a sympatric species pair of threespine stickleback fish by mapping the environment-dependent effects of phenotypic traits on hybrid feeding and performance under semi-natural conditions. We show that multiple, unlinked loci act largely additively to determine position along the major niche axis separating these recently diverged species. We also find that functional mismatch between phenotypic traits reduces the growth of some stickleback hybrids beyond that expected from an intermediate phenotype, suggesting a role for epistasis between the underlying genes. This functional mismatch might lead to hybrid incompatibilities that are analogous to those underlying intrinsic reproductive isolation but depend on the ecological context.
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Affiliation(s)
- Matthew E Arnegard
- 1] Fred Hutchinson Cancer Research Center, Human Biology and Basic Sciences Divisions, 1100 Fairview Avenue North, Seattle, Washington 98109, USA [2] University of British Columbia, Biodiversity Research Centre and Zoology Department, 6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
| | - Matthew D McGee
- University of California at Davis, Department of Evolution and Ecology, One Shields Avenue, Davis, California 95616, USA
| | - Blake Matthews
- EAWAG, Department of Aquatic Ecology, Center for Ecology, Evolution, and Biogeochemistry, Seestrasse 79, 6047 Kastanienbaum, Switzerland
| | - Kerry B Marchinko
- University of British Columbia, Biodiversity Research Centre and Zoology Department, 6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
| | - Gina L Conte
- University of British Columbia, Biodiversity Research Centre and Zoology Department, 6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
| | - Sahriar Kabir
- University of British Columbia, Biodiversity Research Centre and Zoology Department, 6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
| | - Nicole Bedford
- University of British Columbia, Biodiversity Research Centre and Zoology Department, 6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
| | - Sara Bergek
- 1] Uppsala University, Department of Animal Ecology, Evolutionary Biology Centre (EBC), Norbyvägen 18D, SE-75236 Uppsala, Sweden [2] Swedish University of Agricultural Sciences, Department of Aquatic Resources, Stångholmsvägen 2, SE-17893 Drottningholm, Sweden
| | - Yingguang Frank Chan
- Stanford University School of Medicine, Department of Developmental Biology and Howard Hughes Medical Institute, 279 Campus Drive, Stanford, California 94305, USA
| | - Felicity C Jones
- Stanford University School of Medicine, Department of Developmental Biology and Howard Hughes Medical Institute, 279 Campus Drive, Stanford, California 94305, USA
| | - David M Kingsley
- Stanford University School of Medicine, Department of Developmental Biology and Howard Hughes Medical Institute, 279 Campus Drive, Stanford, California 94305, USA
| | - Catherine L Peichel
- Fred Hutchinson Cancer Research Center, Human Biology and Basic Sciences Divisions, 1100 Fairview Avenue North, Seattle, Washington 98109, USA
| | - Dolph Schluter
- University of British Columbia, Biodiversity Research Centre and Zoology Department, 6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
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Miller CT, Glazer AM, Summers BR, Blackman BK, Norman AR, Shapiro MD, Cole BL, Peichel CL, Schluter D, Kingsley DM. Modular skeletal evolution in sticklebacks is controlled by additive and clustered quantitative trait Loci. Genetics 2014; 197:405-20. [PMID: 24652999 PMCID: PMC4012497 DOI: 10.1534/genetics.114.162420] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 02/22/2014] [Indexed: 11/18/2022] Open
Abstract
Understanding the genetic architecture of evolutionary change remains a long-standing goal in biology. In vertebrates, skeletal evolution has contributed greatly to adaptation in body form and function in response to changing ecological variables like diet and predation. Here we use genome-wide linkage mapping in threespine stickleback fish to investigate the genetic architecture of evolved changes in many armor and trophic traits. We identify >100 quantitative trait loci (QTL) controlling the pattern of serially repeating skeletal elements, including gill rakers, teeth, branchial bones, jaws, median fin spines, and vertebrae. We use this large collection of QTL to address long-standing questions about the anatomical specificity, genetic dominance, and genomic clustering of loci controlling skeletal differences in evolving populations. We find that most QTL (76%) that influence serially repeating skeletal elements have anatomically regional effects. In addition, most QTL (71%) have at least partially additive effects, regardless of whether the QTL controls evolved loss or gain of skeletal elements. Finally, many QTL with high LOD scores cluster on chromosomes 4, 20, and 21. These results identify a modular system that can control highly specific aspects of skeletal form. Because of the general additivity and genomic clustering of major QTL, concerted changes in both protective armor and trophic traits may occur when sticklebacks inherit either marine or freshwater alleles at linked or possible "supergene" regions of the stickleback genome. Further study of these regions will help identify the molecular basis of both modular and coordinated changes in the vertebrate skeleton.
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Affiliation(s)
- Craig T. Miller
- Molecular and Cell Biology Department, University of California, Berkeley, California 94720
- Department of Developmental Biology and Howard Hughes Medical Institute, Stanford University, Stanford, California 94305
| | - Andrew M. Glazer
- Molecular and Cell Biology Department, University of California, Berkeley, California 94720
| | - Brian R. Summers
- Department of Developmental Biology and Howard Hughes Medical Institute, Stanford University, Stanford, California 94305
| | - Benjamin K. Blackman
- Department of Developmental Biology and Howard Hughes Medical Institute, Stanford University, Stanford, California 94305
| | - Andrew R. Norman
- Department of Developmental Biology and Howard Hughes Medical Institute, Stanford University, Stanford, California 94305
| | - Michael D. Shapiro
- Department of Developmental Biology and Howard Hughes Medical Institute, Stanford University, Stanford, California 94305
| | - Bonnie L. Cole
- Department of Developmental Biology and Howard Hughes Medical Institute, Stanford University, Stanford, California 94305
| | - Catherine L. Peichel
- Department of Developmental Biology and Howard Hughes Medical Institute, Stanford University, Stanford, California 94305
| | - Dolph Schluter
- Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - David M. Kingsley
- Department of Developmental Biology and Howard Hughes Medical Institute, Stanford University, Stanford, California 94305
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39
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Seehausen O, Butlin RK, Keller I, Wagner CE, Boughman JW, Hohenlohe PA, Peichel CL, Saetre GP, Bank C, Brännström A, Brelsford A, Clarkson CS, Eroukhmanoff F, Feder JL, Fischer MC, Foote AD, Franchini P, Jiggins CD, Jones FC, Lindholm AK, Lucek K, Maan ME, Marques DA, Martin SH, Matthews B, Meier JI, Möst M, Nachman MW, Nonaka E, Rennison DJ, Schwarzer J, Watson ET, Westram AM, Widmer A. Genomics and the origin of species. Nat Rev Genet 2014; 15:176-92. [PMID: 24535286 DOI: 10.1038/nrg3644] [Citation(s) in RCA: 583] [Impact Index Per Article: 58.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Speciation is a fundamental evolutionary process, the knowledge of which is crucial for understanding the origins of biodiversity. Genomic approaches are an increasingly important aspect of this research field. We review current understanding of genome-wide effects of accumulating reproductive isolation and of genomic properties that influence the process of speciation. Building on this work, we identify emergent trends and gaps in our understanding, propose new approaches to more fully integrate genomics into speciation research, translate speciation theory into hypotheses that are testable using genomic tools and provide an integrative definition of the field of speciation genomics.
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Affiliation(s)
- Ole Seehausen
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; and Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Roger K Butlin
- Department of Animal and Plant Sciences, the University of Sheffield, Sheffield S10 2TN, UK; and the Sven Lovén Centre - Tjärnö, University of Gothenburg, S-452 96 Strömstad, Sweden
| | - Irene Keller
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; the Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland; and the Institute of Integrative Biology, ETH Zürich, ETH Zentrum CHN, 8092 Zürich, Switzerland
| | - Catherine E Wagner
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; and the Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Janette W Boughman
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; and the Department of Zoology; Ecology, Evolutionary Biology and Behavior Program; BEACON Center, Michigan State University, 203 Natural Sciences, East Lansing, Michigan 48824, USA
| | - Paul A Hohenlohe
- Department of Biological Sciences, Institute of Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho 83844-3051, USA
| | - Catherine L Peichel
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Glenn-Peter Saetre
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, PO BOX 1066, Blindern, N-0316 Oslo, Norway
| | - Claudia Bank
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Ake Brännström
- Integrated Science Laboratory and the Department of Mathematics and Mathematical Statistics, Umeå University, 90187 Umeå, Sweden
| | - Alan Brelsford
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland
| | | | - Fabrice Eroukhmanoff
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, PO BOX 1066, Blindern, N-0316 Oslo, Norway
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556-0369 USA
| | - Martin C Fischer
- Institute of Integrative Biology, ETH Zürich, ETH Zentrum CHN, 8092 Zürich, Switzerland
| | - Andrew D Foote
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark. Present address: the Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Paolo Franchini
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Felicity C Jones
- Friedrich Miescher Laboratory of the Max Planck Society, 72076 Tübingen, Germany
| | - Anna K Lindholm
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, CH-8057 Zurich, Switzerland
| | - Kay Lucek
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; and the Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Martine E Maan
- Behavioural Biology Group, Centre for Behaviour and Neurosciences, University of Groningen, PO BOX 11103, 9700 CC Groningen, The Netherlands
| | - David A Marques
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; the Division of Aquatic Ecology and Evolution, and the Computational and Molecular Population Genetics Laboratory, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Simon H Martin
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Blake Matthews
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland
| | - Joana I Meier
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; the Division of Aquatic Ecology and Evolution, and the Computational and Molecular Population Genetics Laboratory, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Markus Möst
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK; and the Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Michael W Nachman
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, California 94720-3160, USA
| | - Etsuko Nonaka
- Integrated Science Laboratory and Department of Ecology and Environmental Science, Umeå University, 90187 Umeå, Sweden
| | - Diana J Rennison
- Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Julia Schwarzer
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; the Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland; and Zoologisches Forschungsmuseum Alexander Koenig, 53113 Bonn, Germany
| | - Eric T Watson
- Department of Biology, The University of Texas at Arlington, 76010-0498 Texas, USA
| | - Anja M Westram
- Department of Animal and Plant Sciences, the University of Sheffield, Sheffield S10 2TN, UK
| | - Alex Widmer
- Institute of Integrative Biology, ETH Zürich, ETH Zentrum CHN, 8092 Zürich, Switzerland
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Yoshida K, Makino T, Yamaguchi K, Shigenobu S, Hasebe M, Kawata M, Kume M, Mori S, Peichel CL, Toyoda A, Fujiyama A, Kitano J. Sex chromosome turnover contributes to genomic divergence between incipient stickleback species. PLoS Genet 2014; 10:e1004223. [PMID: 24625862 PMCID: PMC3953013 DOI: 10.1371/journal.pgen.1004223] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 01/22/2014] [Indexed: 12/30/2022] Open
Abstract
Sex chromosomes turn over rapidly in some taxonomic groups, where closely related species have different sex chromosomes. Although there are many examples of sex chromosome turnover, we know little about the functional roles of sex chromosome turnover in phenotypic diversification and genomic evolution. The sympatric pair of Japanese threespine stickleback (Gasterosteus aculeatus) provides an excellent system to address these questions: the Japan Sea species has a neo-sex chromosome system resulting from a fusion between an ancestral Y chromosome and an autosome, while the sympatric Pacific Ocean species has a simple XY sex chromosome system. Furthermore, previous quantitative trait locus (QTL) mapping demonstrated that the Japan Sea neo-X chromosome contributes to phenotypic divergence and reproductive isolation between these sympatric species. To investigate the genomic basis for the accumulation of genes important for speciation on the neo-X chromosome, we conducted whole genome sequencing of males and females of both the Japan Sea and the Pacific Ocean species. No substantial degeneration has yet occurred on the neo-Y chromosome, but the nucleotide sequence of the neo-X and the neo-Y has started to diverge, particularly at regions near the fusion. The neo-sex chromosomes also harbor an excess of genes with sex-biased expression. Furthermore, genes on the neo-X chromosome showed higher non-synonymous substitution rates than autosomal genes in the Japan Sea lineage. Genomic regions of higher sequence divergence between species, genes with divergent expression between species, and QTL for inter-species phenotypic differences were found not only at the regions near the fusion site, but also at other regions along the neo-X chromosome. Neo-sex chromosomes can therefore accumulate substitutions causing species differences even in the absence of substantial neo-Y degeneration.
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Affiliation(s)
- Kohta Yoshida
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Takashi Makino
- Division of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Miyagi, Japan
| | - Katsushi Yamaguchi
- NIBB Core Research Facilities, National Institute for Basic Biology, Myodaiji, Okazaki, Japan
| | - Shuji Shigenobu
- NIBB Core Research Facilities, National Institute for Basic Biology, Myodaiji, Okazaki, Japan
- School of Life Science, The Graduate University for Advanced Studies, Okazaki, Japan
| | - Mitsuyasu Hasebe
- School of Life Science, The Graduate University for Advanced Studies, Okazaki, Japan
- Division of Evolutionary Biology, National Institute for Basic Biology, Myodaiji, Okazaki, Japan
| | - Masakado Kawata
- Division of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Miyagi, Japan
| | - Manabu Kume
- Biological Laboratories, Gifu-keizai-University, Gifu, Japan
| | - Seiichi Mori
- Biological Laboratories, Gifu-keizai-University, Gifu, Japan
| | - Catherine L. Peichel
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Asao Fujiyama
- Comparative Genomics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan
- PRESTO, Japan Science and Technology Agency, Saitama, Japan
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41
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Mills MG, Greenwood AK, Peichel CL. Pleiotropic effects of a single gene on skeletal development and sensory system patterning in sticklebacks. EvoDevo 2014; 5:5. [PMID: 24499504 PMCID: PMC3976036 DOI: 10.1186/2041-9139-5-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 11/20/2013] [Indexed: 11/10/2022] Open
Abstract
Background Adaptation to a new environment can be facilitated by co-inheritance of a suite of phenotypes that are all advantageous in the new habitat. Although experimental evidence demonstrates that multiple phenotypes often map to the same genomic regions, it is challenging to determine whether phenotypes are associated due to pleiotropic effects of a single gene or to multiple tightly linked genes. In the threespine stickleback fish (Gasterosteus aculeatus), multiple phenotypes are associated with a genomic region around the gene Ectodysplasin (Eda), but only the presence of bony lateral plates has been conclusively shown to be caused by Eda. Results Here, we ask whether pleiotropy or linkage is responsible for the association between lateral plates and the distribution of the neuromasts of the lateral line. We first identify a strong correlation between plate appearance and changes in the spatial distribution of neuromasts through development. We then use an Eda transgene to induce the formation of ectopic plates in low plated fish, which also results in alterations to neuromast distribution. Our results also show that other loci may modify the effects of Eda on plate formation and neuromast distribution. Conclusions Together, these results demonstrate that Eda has pleiotropic effects on at least two phenotypes, highlighting the role of pleiotropy in the genetic basis of adaptation.
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Affiliation(s)
| | | | - Catherine L Peichel
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle WA, 98109, USA.
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42
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Hendry AP, Kaeuffer R, Crispo E, Peichel CL, Bolnick DI. Evolutionary inferences from the analysis of exchangeability. Evolution 2013; 67:3429-41. [PMID: 24299398 PMCID: PMC3852416 DOI: 10.1111/evo.12160] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2012] [Accepted: 04/15/2013] [Indexed: 01/11/2023]
Abstract
Evolutionary inferences are usually based on statistical models that compare mean genotypes or phenotypes (or their frequencies) among populations. An alternative is to use the full distribution of genotypes and phenotypes to infer the "exchangeability" of individuals among populations. We illustrate this approach by using discriminant functions on principal components to classify individuals among paired lake and stream populations of threespine stickleback in each of six independent watersheds. Classification based on neutral and nonneutral microsatellite markers was highest to the population of origin and next highest to populations in the same watershed. These patterns are consistent with the influence of historical contingency (separate colonization of each watershed) and subsequent gene flow (within but not between watersheds). In comparison to this low genetic exchangeability, ecological (diet) and morphological (trophic and armor traits) exchangeability was relatively high-particularly among populations from similar habitats. These patterns reflect the role of natural selection in driving parallel adaptive changes when independent populations colonize similar habitats. Importantly, however, substantial nonparallelism was also evident. Our results show that analyses based on exchangeability can confirm inferences based on statistical analyses of means or frequencies, while also refining insights into the drivers of-and constraints on-evolutionary diversification.
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Affiliation(s)
- Andrew P Hendry
- Redpath Museum and Department of Biology, McGill University, 859 Sherbrooke St. W., Montreal, Quebec, Canada, H3A 0C4.
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Abstract
Pigment pattern variation across species or populations offers a tractable framework in which to investigate the evolution of development. Juvenile threespine sticklebacks (Gasterosteus aculeatus) from marine and freshwater environments exhibit divergent pigment patterns that are associated with ecological differences. Juvenile marine sticklebacks have a silvery appearance, whereas sticklebacks from freshwater environments exhibit a pattern of vertical bars. We investigated both the developmental and molecular basis of this population-level variation in pigment pattern. Time course imaging during the transition from larval to juvenile stages revealed differences between marine and freshwater fish in spatial patterns of chromatophore differentiation as well as in pigment amount and dispersal. In freshwater fish, melanophores appear primarily within dark bars whereas iridophores appear within light bars. By contrast, in marine fish, these chromatophores are interspersed across the flank. In addition to spatially segregated chromatophore differentiation, pigment amount and dispersal within melanophores varies spatially across the flank of freshwater, but not marine fish. To gain insight into the molecular pathways that underlie the differences in pigment pattern development, we evaluated differential gene expression in the flanks of developing fish using high-throughput cDNA sequencing (RNA-seq) and quantitative PCR. We identified several genes that were differentially expressed across dark and light bars of freshwater fish, and between freshwater and marine fish. Together, these experiments begin to shed light on the process of pigment pattern evolution in sticklebacks.
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Affiliation(s)
- Anna K Greenwood
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
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Abstract
Genomic and genetic methods allow investigation of how frequently the same genes are used by different populations during adaptive evolution, yielding insights into the predictability of evolution at the genetic level. We estimated the probability of gene reuse in parallel and convergent phenotypic evolution in nature using data from published studies. The estimates are surprisingly high, with mean probabilities of 0.32 for genetic mapping studies and 0.55 for candidate gene studies. The probability declines with increasing age of the common ancestor of compared taxa, from about 0.8 for young nodes to 0.1–0.4 for the oldest nodes in our study. Probability of gene reuse is higher when populations begin from the same ancestor (genetic parallelism) than when they begin from divergent ancestors (genetic convergence). Our estimates are broadly consistent with genomic estimates of gene reuse during repeated adaptation to similar environments, but most genomic studies lack data on phenotypic traits affected. Frequent reuse of the same genes during repeated phenotypic evolution suggests that strong biases and constraints affect adaptive evolution, resulting in changes at a relatively small subset of available genes. Declines in the probability of gene reuse with increasing age suggest that these biases diverge with time.
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Affiliation(s)
- Gina L Conte
- Biodiversity Research Centre and Zoology Department, University of British Columbia, Vancouver, British Columbia, Canada.
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Malek TB, Boughman JW, Dworkin I, Peichel CL. Admixture mapping of male nuptial colour and body shape in a recently formed hybrid population of threespine stickleback. Mol Ecol 2012; 21:5265-79. [PMID: 22681397 DOI: 10.1111/j.1365-294x.2012.05660.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Despite recent progress, we still know relatively little about the genetic architecture that underlies adaptation to divergent environments. Determining whether the genetic architecture of phenotypic adaptation follows any predictable patterns requires data from a wide variety of species. However, in many organisms, genetic studies are hindered by the inability to perform genetic crosses in the laboratory or by long generation times. Admixture mapping is an approach that circumvents these issues by taking advantage of hybridization that occurs between populations or species in the wild. Here, we demonstrate the utility of admixture mapping in a naturally occurring hybrid population of threespine sticklebacks (Gasterosteus aculeatus) from Enos Lake, British Columbia. Until recently, this lake contained two species of sticklebacks adapted to divergent habitats within the lake. This benthic-limnetic species pair diverged in a number of phenotypes, including male nuptial coloration and body shape, which were previously shown to contribute to reproductive isolation between them. However, recent ecological disturbance has contributed to extensive hybridization between the species, and there is now a single, admixed population within Enos Lake. We collected over 500 males from Enos Lake and found that most had intermediate nuptial colour and body shape. By genotyping males with nuptial colour at the two extremes of the phenotypic distribution, we identified seven genomic regions on three chromosomes associated with divergence in male nuptial colour. These genomic regions are also associated with variation in body shape, suggesting that tight linkage and/or pleiotropy facilitated adaptation to divergent environments in benthic-limnetic species pairs.
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Affiliation(s)
- Tiffany B Malek
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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Otto SP, Pannell JR, Peichel CL, Ashman TL, Charlesworth D, Chippindale AK, Delph LF, Guerrero RF, Scarpino SV, McAllister BF. About PAR: the distinct evolutionary dynamics of the pseudoautosomal region. Trends Genet 2012; 27:358-67. [PMID: 21962971 DOI: 10.1016/j.tig.2011.05.001] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 05/03/2011] [Accepted: 05/04/2011] [Indexed: 01/05/2023]
Abstract
Sex chromosomes differ from other chromosomes in the striking divergence they often show in size, structure, and gene content. Not only do they possess genes controlling sex determination that are restricted to either the X or Y (or Z or W) chromosomes, but in many taxa they also include recombining regions. In these 'pseudoautosomal regions' (PARs), sequence homology is maintained by meiotic pairing and exchange in the heterogametic sex. PARs are unique genomic regions, exhibiting some features of autosomes, but they are also influenced by their partial sex linkage. Here we review the distribution and structure of PARs among animals and plants, the theoretical predictions concerning their evolutionary dynamics, the reasons for their persistence, and the diversity and content of genes that reside within them. It is now clear that the evolution of the PAR differs in important ways from that of genes in either the non-recombining regions of sex chromosomes or the autosomes.
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Affiliation(s)
- Sarah P Otto
- Department of Zoology, 6270 University Boulevard, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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Abstract
Closely related species of fishes often have different sex chromosome systems. Such rapid turnover of sex chromosomes can occur by several mechanisms, including fusions between an existing sex chromosome and an autosome. These fusions can result in a multiple sex chromosome system, where a species has both an ancestral and a neo-sex chromosome. Although this type of multiple sex chromosome system has been found in many fishes, little is known about the mechanisms that select for the formation of neo-sex chromosomes, or the role of neo-sex chromosomes in phenotypic evolution and speciation. The identification of closely related, sympatric species pairs in which one species has a multiple sex chromosome system and the other has a simple sex chromosome system provides an opportunity to study sex chromosome turnover. Recently, we found that a population of threespine stickleback (Gasterosteus aculeatus) from Japan has an X1X2Y multiple sex chromosome system resulting from a fusion between the ancestral Y chromosome and an autosome, while a sympatric threespine stickleback population has a simple XY sex chromosome system. Furthermore, we demonstrated that the neo-X chromosome (X2) plays an important role in phenotypic divergence and reproductive isolation between these sympatric stickleback species pairs. Here, we review multiple sex chromosome systems in fishes, as well as recent advances in our understanding of the evolutionary role of sex chromosome turnover in stickleback speciation.
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Affiliation(s)
- Jun Kitano
- Ecological Genetics Laboratory and JST PRESTO, Center for Frontier Research, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411–8540 Japan
| | - Catherine L. Peichel
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109–1024 USA
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Abstract
Sexual dimorphism in geometric body shape and external morphology was compared between marine and stream-resident forms of three-spined stickleback Gasterosteus aculeatus collected from North America and Japan. Some aspects of sexual dimorphism were shared between ecotypes: males had larger heads than females with no significant effect of ecotype on the magnitude of sexual dimorphism. By contrast, a significant sex-by-ecotype interaction was found for body depth. Males tended to have deeper bodies than females in both forms, but the magnitude of sexual dimorphism was reduced in stream-resident forms. Although females were generally larger in standard length and had larger pelvic girdles, significant sexual dimorphism in these traits was not consistently found across populations or ecotypes. These results suggest that some aspects of sexual dimorphism were shared between ecotypes, while others were unique to each population. The results further suggest that ecology may influence the evolution of sexual dimorphism in some external morphological traits, such as body depth.
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Affiliation(s)
- J Kitano
- Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan.
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Kitano J, Kawagishi Y, Mori S, Peichel CL, Makino T, Kawata M, Kusakabe M. Divergence in sex steroid hormone signaling between sympatric species of Japanese threespine stickleback. PLoS One 2011; 6:e29253. [PMID: 22216225 PMCID: PMC3247238 DOI: 10.1371/journal.pone.0029253] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Accepted: 11/23/2011] [Indexed: 11/19/2022] Open
Abstract
Sex steroids mediate the expression of sexually dimorphic or sex-specific traits that are important both for mate choice within species and for behavioral isolation between species. We investigated divergence in sex steroid signaling between two sympatric species of threespine stickleback (Gasterosteus aculeatus): the Japan Sea form and the Pacific Ocean form. These sympatric forms diverge in both male display traits and female mate choice behaviors, which together contribute to asymmetric behavioral isolation in sympatry. Here, we found that plasma levels of testosterone and 17β-estradiol differed between spawning females of the two sympatric forms. Transcript levels of follicle-stimulating hormone-β (FSHβ) gene were also higher in the pituitary gland of spawning Japan Sea females than in the pituitary gland of spawning Pacific Ocean females. By contrast, none of the sex steroids examined were significantly different between nesting males of the two forms. However, combining the plasma sex steroid data with testis transcriptome data suggested that the efficiency of the conversion of testosterone into 11-ketotestosterone has likely diverged between forms. Within forms, plasma testosterone levels in males were significantly correlated with male body size, a trait important for female mate choice in the two sympatric species. These results demonstrate that substantial divergence in sex steroid signaling can occur between incipient sympatric species. We suggest that investigation of the genetic and ecological mechanisms underlying divergence in hormonal signaling between incipient sympatric species will provide a better understanding of the mechanisms of speciation in animals.
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Affiliation(s)
- Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan.
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Kaeuffer R, Peichel CL, Bolnick DI, Hendry AP. Parallel and nonparallel aspects of ecological, phenotypic, and genetic divergence across replicate population pairs of lake and stream stickleback. Evolution 2011; 66:402-18. [PMID: 22276537 DOI: 10.1111/j.1558-5646.2011.01440.x] [Citation(s) in RCA: 172] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Parallel (or convergent) evolution provides strong evidence for a deterministic role of natural selection: similar phenotypes evolve when independent populations colonize similar environments. In reality, however, independent populations in similar environments always show some differences: some nonparallel evolution is present. It is therefore important to explicitly quantify the parallel and nonparallel aspects of trait variation, and to investigate the ecological and genetic explanations for each. We performed such an analysis for threespine stickleback (Gasterosteus aculeatus) populations inhabiting lake and stream habitats in six independent watersheds. Morphological traits differed in the degree to which lake-stream divergence was parallel across watersheds. Some aspects of this variation were correlated with ecological variables related to diet, presumably reflecting the strength and specifics of divergent selection. Furthermore, a genetic scan revealed some markers that diverged between lakes and streams in many of the watersheds and some that diverged in only a few watersheds. Moreover, some of the lake-stream divergence in genetic markers was associated within some of the lake-stream divergence in morphological traits. Our results suggest that parallel evolution, and deviations from it, are primarily the result of natural selection, which corresponds in only some respects to the dichotomous habitat classifications frequently used in such studies.
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Affiliation(s)
- Renaud Kaeuffer
- Redpath Museum and Department of Biology, McGill University, Montreal, Canada, H3A 2K6.
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