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Powell DL, García-Olazábal M, Keegan M, Reilly P, Du K, Díaz-Loyo AP, Banerjee S, Blakkan D, Reich D, Andolfatto P, Rosenthal GG, Schartl M, Schumer M. Natural hybridization reveals incompatible alleles that cause melanoma in swordtail fish. Science 2020; 368:731-736. [PMID: 32409469 PMCID: PMC8074799 DOI: 10.1126/science.aba5216] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 03/27/2020] [Indexed: 12/21/2022]
Abstract
The establishment of reproductive barriers between populations can fuel the evolution of new species. A genetic framework for this process posits that "incompatible" interactions between genes can evolve that result in reduced survival or reproduction in hybrids. However, progress has been slow in identifying individual genes that underlie hybrid incompatibilities. We used a combination of approaches to map the genes that drive the development of an incompatibility that causes melanoma in swordtail fish hybrids. One of the genes involved in this incompatibility also causes melanoma in hybrids between distantly related species. Moreover, this melanoma reduces survival in the wild, likely because of progressive degradation of the fin. This work identifies genes underlying a vertebrate hybrid incompatibility and provides a glimpse into the action of these genes in natural hybrid populations.
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Affiliation(s)
- Daniel L Powell
- Department of Biology, Stanford University and Howard Hughes Medical Institute, Stanford, CA, USA.
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, Mexico
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Mateo García-Olazábal
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, Mexico
- Department of Biology, Texas A&M University, College Station, TX, USA
| | | | - Patrick Reilly
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Kang Du
- Developmental Biochemistry, Biocenter, University of Würzburg, Würzburg, Bavaria, Germany
| | - Alejandra P Díaz-Loyo
- Laboratorio de Ecología de la Conducta, Instituto de Fisiología, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Shreya Banerjee
- Department of Biology, Stanford University and Howard Hughes Medical Institute, Stanford, CA, USA
| | - Danielle Blakkan
- Department of Biology, Stanford University and Howard Hughes Medical Institute, Stanford, CA, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Howard Hughes Medical Institute, and the Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Gil G Rosenthal
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, Mexico
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Manfred Schartl
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, Mexico
- Department of Biology, Texas A&M University, College Station, TX, USA
- Developmental Biochemistry, Biocenter, University of Würzburg, Würzburg, Bavaria, Germany
- Hagler Institute for Advanced Study, Texas A&M University, College Station, TX, USA
- Xiphophorus Genetic Stock Center, Texas State University San Marcos, San Marcos, TX, USA
| | - Molly Schumer
- Department of Biology, Stanford University and Howard Hughes Medical Institute, Stanford, CA, USA.
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Franchini P, Jones JC, Xiong P, Kneitz S, Gompert Z, Warren WC, Walter RB, Meyer A, Schartl M. Long-term experimental hybridisation results in the evolution of a new sex chromosome in swordtail fish. Nat Commun 2018; 9:5136. [PMID: 30510159 PMCID: PMC6277394 DOI: 10.1038/s41467-018-07648-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 11/13/2018] [Indexed: 01/13/2023] Open
Abstract
The remarkable diversity of sex determination mechanisms known in fish may be fuelled by exceptionally high rates of sex chromosome turnovers or transitions. However, the evolutionary causes and genomic mechanisms underlying this variation and instability are yet to be understood. Here we report on an over 30-year evolutionary experiment in which we tested the genomic consequences of hybridisation and selection between two Xiphophorus fish species with different sex chromosome systems. We find that introgression and imposing selection for pigmentation phenotypes results in the retention of an unexpectedly large maternally derived genomic region. During the hybridisation process, the sex-determining region of the X chromosome from one parental species was translocated to an autosome in the hybrids leading to the evolution of a new sex chromosome. Our results highlight the complexity of factors contributing to patterns observed in hybrid genomes, and we experimentally demonstrate that hybridisation can catalyze rapid evolution of a new sex chromosome. Fish have a high diversity of sex-determining systems, but the mechanisms responsible for this are not well understood. Here, Franchini et al. show how hybridization and backcrossing have led to the evolution of a new sex chromosome in swordtail fish during 30 years of experimental evolution.
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Affiliation(s)
- Paolo Franchini
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Julia C Jones
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany.,Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, 75123, Sweden
| | - Peiwen Xiong
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Susanne Kneitz
- Physiological Chemistry, Biozentrum, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | | | - Wesley C Warren
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, 63108, MO, USA
| | - Ronald B Walter
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, 78666-4616, TX, USA
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany. .,Radcliffe Institute for Advanced Study, Harvard University, 9 Garden Street, Cambridge, MA, 02139, USA.
| | - Manfred Schartl
- Physiological Chemistry, Biozentrum, University of Würzburg, Am Hubland, 97074, Würzburg, Germany. .,Comprehensive Cancer Centre, University Clinic Würzburg, Josef Schneider Straße 6, 97074, Würzburg, Germany. .,Hagler Institute for Advanced Study and Department of Biology, Texas A&M University, College Station, TX, 77843, USA.
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Jones JC, Fruciano C, Keller A, Schartl M, Meyer A. Evolution of the elaborate male intromittent organ of Xiphophorus fishes. Ecol Evol 2016; 6:7207-7220. [PMID: 27891216 PMCID: PMC5114703 DOI: 10.1002/ece3.2396] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 07/26/2016] [Accepted: 08/01/2016] [Indexed: 11/08/2022] Open
Abstract
Internally fertilizing animals show a remarkable diversity in male genital morphology that is associated with sexual selection, and these traits are thought to be evolving particularly rapidly. Male fish in some internally fertilizing species have "gonopodia," highly modified anal fins that are putatively important for sexual selection. However, our understanding of the evolution of genital diversity remains incomplete. Contrary to the prediction that male genital traits evolve more rapidly than other traits, here we show that gonopodial traits and other nongonopodial traits exhibit similar evolutionary rates of trait change and also follow similar evolutionary models in an iconic genus of poeciliid fish (Xiphophorus spp.). Furthermore, we find that both mating and nonmating natural selection mechanisms are unlikely to be driving the diverse Xiphophorus gonopodial morphology. Putative holdfast features of the male genital organ do not appear to be influenced by water flow, a candidate selective force in aquatic habitats. Additionally, interspecific divergence in gonopodial morphology is not significantly higher between sympatric species, than between allopatric species, suggesting that male genitals have not undergone reproductive character displacement. Slower rates of evolution in gonopodial traits compared with a subset of putatively sexually selected nongenital traits suggest that different selection mechanisms may be acting on the different trait types. Further investigations of this elaborate trait are imperative to determine whether it is ultimately an important driver of speciation.
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Affiliation(s)
- Julia C Jones
- Lehrstuhl für Zoologie und Evolutionsbiologie Department of Biology University of Konstanz Universitätstraße 10 78457 Konstanz Germany; Zukunftskolleg University of Konstanz Konstanz Germany; Present address: Evolution, Behaviour and Environment School of Life Sciences University of Sussex Brighton UK
| | - Carmelo Fruciano
- Lehrstuhl für Zoologie und Evolutionsbiologie Department of Biology University of Konstanz Universitätstraße 10 78457 Konstanz Germany; School of Earth, Environmental & Biological Sciences Queensland University of Technology Brisbane Qld 4000 Australia
| | - Anja Keller
- Lehrstuhl für Zoologie und Evolutionsbiologie Department of Biology University of Konstanz Universitätstraße 10 78457 Konstanz Germany
| | - Manfred Schartl
- Physiological Chemistry, Biozentrum University of Würzburg Am Hubland 97074 Würzburg Germany; Comprehensive Cancer Centre University Clinic Würzburg Josef Schneider Straße 697074 Würzburg Germany
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie Department of Biology University of Konstanz Universitätstraße 10 78457 Konstanz Germany
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Hulsey CD, Bell KL, García-de-León FJ, Nice CC, Meyer A. Do relaxed selection and habitat temperature facilitate biased mitogenomic introgression in a narrowly endemic fish? Ecol Evol 2016; 6:3684-3698. [PMID: 27186367 PMCID: PMC4853310 DOI: 10.1002/ece3.2121] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/14/2016] [Accepted: 03/21/2016] [Indexed: 12/19/2022] Open
Abstract
Introgression might be exceptionally common during the evolution of narrowly endemic species. For instance, in the springs of the small and isolated Cuatro Ciénegas Valley, the mitogenome of the cichlid fish Herichthys cyanoguttatus could be rapidly introgressing into populations of the trophically polymorphic H. minckleyi. We used a combination of genetic and environmental data to examine the factors associated with this mitochondrial introgression. A reduced representation library of over 6220 single nucleotide polymorphisms (SNPs) from the nuclear genome showed that mitochondrial introgression into H. minckleyi is biased relative to the amount of nuclear introgression. SNP assignment probabilities also indicated that cichlids with more hybrid ancestry are not more commonly female providing no support for asymmetric backcrossing or hybrid‐induced sex‐ratio distortion in generating the bias in mitochondrial introgression. Smaller effective population size in H. minckleyi inferred from the SNPs coupled with sequences of all 13 mitochondrial proteins suggests that relaxed selection on the mitogenome could be facilitating the introgression of “H. cyanoguttatus” haplotypes. Additionally, we showed that springs with colder temperatures had greater amounts of mitochondrial introgression from H. cyanoguttatus. Relaxed selection in H. minckleyi coupled with temperature‐related molecular adaptation could be facilitating mitogenomic introgression into H. minckleyi.
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Affiliation(s)
| | - Katherine L Bell
- Department of Biology Texas State University, San Marcos 601 University Drive 78666 San Marcos Texas
| | - Francisco J García-de-León
- Laboratorio de Genética para la Conservación Centro de Investigaciones Biológicas del Noroeste PO Box 128 La Paz B.C.S. Mexico
| | - Chris C Nice
- Department of Biology Texas State University, San Marcos 601 University Drive 78666 San Marcos Texas
| | - Axel Meyer
- Department of Biology University of Konstanz Universitätstraße 10 78457 Konstanz Germany
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Schumer M, Cui R, Powell DL, Rosenthal GG, Andolfatto P. Ancient hybridization and genomic stabilization in a swordtail fish. Mol Ecol 2016; 25:2661-79. [DOI: 10.1111/mec.13602] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 01/06/2016] [Accepted: 01/06/2016] [Indexed: 01/13/2023]
Affiliation(s)
- Molly Schumer
- Department of Ecology and Evolutionary Biology Princeton University Princeton NJ 08544 USA
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca” 16 de Septiembre 392 Calnali Hidalgo 43230 Mexico
| | - Rongfeng Cui
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca” 16 de Septiembre 392 Calnali Hidalgo 43230 Mexico
- Department of Biology Texas A&M University TAMU College Station TX 77843 USA
- Max Planck Institute for the Biology of Aging D‐50931 Cologne Germany
| | - Daniel L. Powell
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca” 16 de Septiembre 392 Calnali Hidalgo 43230 Mexico
- Department of Biology Texas A&M University TAMU College Station TX 77843 USA
| | - Gil G. Rosenthal
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca” 16 de Septiembre 392 Calnali Hidalgo 43230 Mexico
- Department of Biology Texas A&M University TAMU College Station TX 77843 USA
| | - Peter Andolfatto
- Department of Ecology and Evolutionary Biology Princeton University Princeton NJ 08544 USA
- Lewis‐Sigler Institute for Integrative Genomics Princeton University Princeton NJ 08544 USA
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Culumber ZW, Tobler M. Ecological divergence and conservatism: spatiotemporal patterns of niche evolution in a genus of livebearing fishes (Poeciliidae: Xiphophorus). BMC Evol Biol 2016; 16:44. [PMID: 26895994 PMCID: PMC4761163 DOI: 10.1186/s12862-016-0593-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 01/13/2016] [Indexed: 01/23/2023] Open
Abstract
Background Ecological factors often have a strong impact on spatiotemporal patterns of biodiversity. The integration of spatial ecology and phylogenetics allows for rigorous tests of whether speciation is associated with niche conservatism (constraints on ecological divergence) or niche divergence. We address this question in a genus of livebearing fishes for which the role of sexual selection in speciation has long been studied, but in which the potential role of ecological divergence during speciation has not been tested. Results By combining reconstruction of ancestral climate tolerances and disparity indices, we show that the earliest evolutionary split in Xiphophorus was associated with significant divergence for temperature variables. Niche evolution and present day niches were most closely associated with each species’ geographic distribution relative to a biogeographic barrier, the Trans-Mexican Volcanic Belt. Tests for similarity of the environmental backgrounds of closely related species suggested that the relative importance of niche conservatism and divergence during speciation varied among the primary clades of Xiphophorus. Closely related species in the two swordtail clades exhibited higher levels of niche overlap than expected given environmental background similarity indicative of niche conservatism. In contrast, almost all species of platyfish had significantly divergent niches compared to environmental backgrounds, which is indicative of niche divergence. Conclusion The results suggest that the relative importance of niche conservatism and divergence differed among the clades of Xiphophorus and that traits associated with niche evolution may be more evolutionarily labile in the platyfishes. Our results ultimately suggest that the taxonomic scale of tests for conservatism and divergence could greatly influence inferences of their relative importance in the speciation process. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0593-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zachary W Culumber
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA.
| | - Michael Tobler
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
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Shen Y, Chalopin D, Garcia T, Boswell M, Boswell W, Shiryev SA, Agarwala R, Volff JN, Postlethwait JH, Schartl M, Minx P, Warren WC, Walter RB. X. couchianus and X. hellerii genome models provide genomic variation insight among Xiphophorus species. BMC Genomics 2016; 17:37. [PMID: 26742787 PMCID: PMC4705583 DOI: 10.1186/s12864-015-2361-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 12/30/2015] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Xiphophorus fishes are represented by 26 live-bearing species of tropical fish that express many attributes (e.g., viviparity, genetic and phenotypic variation, ecological adaptation, varied sexual developmental mechanisms, ability to produce fertile interspecies hybrids) that have made attractive research models for over 85 years. Use of various interspecies hybrids to investigate the genetics underlying spontaneous and induced tumorigenesis has resulted in the development and maintenance of pedigreed Xiphophorus lines specifically bred for research. The recent availability of the X. maculatus reference genome assembly now provides unprecedented opportunities for novel and exciting comparative research studies among Xiphophorus species. RESULTS We present sequencing, assembly and annotation of two new genomes representing Xiphophorus couchianus and Xiphophorus hellerii. The final X. couchianus and X. hellerii assemblies have total sizes of 708 Mb and 734 Mb and correspond to 98 % and 102 % of the X. maculatus Jp 163 A genome size, respectively. The rates of single nucleotide change range from 1 per 52 bp to 1 per 69 bp among the three genomes and the impact of putatively damaging variants are presented. In addition, a survey of transposable elements allowed us to deduce an ancestral TE landscape, uncovered potential active TEs and document a recent burst of TEs during evolution of this genus. CONCLUSIONS Two new Xiphophorus genomes and their corresponding transcriptomes were efficiently assembled, the former using a novel guided assembly approach. Three assembled genome sequences within this single vertebrate order of new world live-bearing fishes will accelerate our understanding of relationship between environmental adaptation and genome evolution. In addition, these genome resources provide capability to determine allele specific gene regulation among interspecies hybrids produced by crossing any of the three species that are known to produce progeny predisposed to tumor development.
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Affiliation(s)
- Yingjia Shen
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA.
- Key Laboratory of Coastal and Wetland Ecosystems, Ministry of Education, A316 Environment and Ecology Bldg., Xiamen, Fujian, 361102, China.
| | - Domitille Chalopin
- Institut de Génomique Fonctionnelle de Lyon, Unité Mixte de Recherche 5242, Centre National de la Recherche Scientifique, Université de Lyon I, Ecole Normale Supérieure de Lyon, Lyon, France.
| | - Tzintzuni Garcia
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA.
| | - Mikki Boswell
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA.
| | - William Boswell
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA.
| | - Sergey A Shiryev
- The National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA.
| | - Richa Agarwala
- The National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA.
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Unité Mixte de Recherche 5242, Centre National de la Recherche Scientifique, Université de Lyon I, Ecole Normale Supérieure de Lyon, Lyon, France.
| | - John H Postlethwait
- Institute of Neuroscience, University of Oregon, 1425 E. 13th Avenue, Eugene, OR, 97403, USA.
| | - Manfred Schartl
- Universität Würzburg, Physiologische Chemie I, Biozentrum, Am Hubland, and Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, D-97074, Würzburg, Germany.
| | - Patrick Minx
- Genome Sequencing Center, Washington University School of Medicine, 4444 Forest Park Blvd., St Louis, MO, 63108, USA.
| | - Wesley C Warren
- Genome Sequencing Center, Washington University School of Medicine, 4444 Forest Park Blvd., St Louis, MO, 63108, USA.
| | - Ronald B Walter
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA.
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Kang JH, Manousaki T, Franchini P, Kneitz S, Schartl M, Meyer A. Transcriptomics of two evolutionary novelties: how to make a sperm-transfer organ out of an anal fin and a sexually selected "sword" out of a caudal fin. Ecol Evol 2015; 5:848-64. [PMID: 25750712 PMCID: PMC4338968 DOI: 10.1002/ece3.1390] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 12/10/2014] [Accepted: 12/12/2014] [Indexed: 01/09/2023] Open
Abstract
Swords are exaggerated male ornaments of swordtail fishes that have been of great interest to evolutionary biologists ever since Darwin described them in the Descent of Man (1871). They are a novel sexually selected trait derived from modified ventral caudal fin rays and are only found in the genus Xiphophorus. Another phylogenetically more widespread and older male trait is the gonopodium, an intromittent organ found in all poeciliid fishes, that is derived from a modified anal fin. Despite many evolutionary and behavioral studies on both traits, little is known so far about the molecular mechanisms underlying their development. By investigating transcriptomic changes (utilizing a RNA-Seq approach) in response to testosterone treatment in the swordtail fish, Xiphophorus hellerii, we aimed to better understand the architecture of the gene regulatory networks underpinning the development of these two evolutionary novelties. Large numbers of genes with tissue-specific expression patterns were identified. Among the "sword genes" those involved in embryonic organ development, sexual character development and coloration were highly expressed, while in the gonopodium rather more morphogenesis-related genes were found. Interestingly, many genes and genetic pathways are shared between both developing novel traits derived from median fins: the sword and the gonopodium. Our analyses show that a larger set of gene networks was co-opted during the development and evolution of the "older" gonopodium than in the "younger," and morphologically less complex trait, the sword. We provide a catalog of candidate genes for future efforts to dissect the development of those sexually selected exaggerated male traits in swordtails.
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Affiliation(s)
- Ji Hyoun Kang
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of KonstanzUniversitätsstraβe 10, 78457, Konstanz, Germany
- Konstanz Research School Chemical Biology, University of KonstanzKonstanz, Germany
| | - Tereza Manousaki
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of KonstanzUniversitätsstraβe 10, 78457, Konstanz, Germany
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine ResearchHeraklion, Greece
| | - Paolo Franchini
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of KonstanzUniversitätsstraβe 10, 78457, Konstanz, Germany
| | - Susanne Kneitz
- Physiological Chemistry, Biozentrum, University of WürzburgAm Hubland, Würzburg, Germany
| | - Manfred Schartl
- Physiological Chemistry, Biozentrum, University of WürzburgAm Hubland, Würzburg, Germany
- Comprehensive Cancer Center, University Clinic WürzburgJosef Schneider Straβe 6, 97074, Würzburg, Germany
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of KonstanzUniversitätsstraβe 10, 78457, Konstanz, Germany
- Konstanz Research School Chemical Biology, University of KonstanzKonstanz, Germany
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Choleva L, Musilova Z, Kohoutova-Sediva A, Paces J, Rab P, Janko K. Distinguishing between incomplete lineage sorting and genomic introgressions: complete fixation of allospecific mitochondrial DNA in a sexually reproducing fish (Cobitis; Teleostei), despite clonal reproduction of hybrids. PLoS One 2014; 9:e80641. [PMID: 24971792 PMCID: PMC4074047 DOI: 10.1371/journal.pone.0080641] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2012] [Accepted: 10/15/2013] [Indexed: 11/19/2022] Open
Abstract
Distinguishing between hybrid introgression and incomplete lineage sorting causing incongruence among gene trees in that they exhibit topological differences requires application of statistical approaches that are based on biologically relevant models. Such study is especially challenging in hybrid systems, where usual vectors mediating interspecific gene transfers--hybrids with Mendelian heredity--are absent or unknown. Here we study a complex of hybridizing species, which are known to produce clonal hybrids, to discover how one of the species, Cobitis tanaitica, has achieved a pattern of mito-nuclear mosaic genome over the whole geographic range. We appplied three distinct methods, including the method using solely the information on gene tree topologies, and found that the contrasting mito-nuclear signal might not have resulted from the retention of ancestral polymorphism. Instead, we found two signs of hybridization events related to C. tanaitica; one concerning nuclear gene flow and the other suggested mitochondrial capture. Interestingly, clonal inheritance (gynogenesis) of contemporary hybrids prevents genomic introgressions and non-clonal hybrids are either absent or too rare to be detected among European Cobitis. Our analyses therefore suggest that introgressive hybridizations are rather old episodes, mediated by previously existing hybrids whose inheritance was not entirely clonal. Cobitis complex thus supports the view that the type of resulting hybrids depends on a level of genomic divergence between sexual species.
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Affiliation(s)
- Lukas Choleva
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, AS CR, v.v.i., Libechov, Czech Republic
- Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland
- * E-mail:
| | - Zuzana Musilova
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, AS CR, v.v.i., Libechov, Czech Republic
- Zoological Institute, Evolutionary Biology, University of Basel, Basel, Switzerland
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Alena Kohoutova-Sediva
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, AS CR, v.v.i., Libechov, Czech Republic
- Institute of Zoology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jan Paces
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, AS CR, v.v.i., Libechov, Czech Republic
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the ASCR, v.v.i., Prague, Czech Republic
| | - Petr Rab
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, AS CR, v.v.i., Libechov, Czech Republic
| | - Karel Janko
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, AS CR, v.v.i., Libechov, Czech Republic
- Life Science Research Centre, Department of Biology and Ecology, Faculty of Natural Sciences, University of Ostrava, Ostrava, Czech Republic
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Carson EW, Espinosa-Pérez H, Souza V. Low Mitochondrial Dna Sequence Variation in the Microendemic Cuatro Ciénegas PlatyfishXiphophorus gordoni. WEST N AM NATURALIST 2013. [DOI: 10.3398/064.073.0212] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Jones JC, Fan S, Franchini P, Schartl M, Meyer A. The evolutionary history of Xiphophorus fish and their sexually selected sword: a genome-wide approach using restriction site-associated DNA sequencing. Mol Ecol 2013; 22:2986-3001. [PMID: 23551333 DOI: 10.1111/mec.12269] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Revised: 01/10/2013] [Accepted: 01/15/2013] [Indexed: 11/27/2022]
Abstract
Next-generation sequencing (NGS) techniques are now key tools in the detection of population genomic and gene expression differences in a large array of organisms. However, so far few studies have utilized such data for phylogenetic estimations. Here, we use NGS data obtained from genome-wide restriction site-associated DNA (RAD) (∼66000 SNPs) to estimate the phylogenetic relationships among all 26 species of swordtail and platyfish (genus Xiphophorus) from Central America. Past studies, both sequence and morphology-based, have differed in their inferences of the evolutionary relationships within this genus, particularly at the species-level and among monophyletic groupings. We show that using a large number of markers throughout the genome, we are able to infer the phylogenetic relationships with unparalleled resolution for this genus. The relationships among all three major clades and species within each of them are highly resolved and consistent under maximum likelihood, Bayesian inference and maximum parsimony. However, we also highlight the current cautions with this data type and analyses. This genus exhibits a particularly interesting evolutionary history where at least two species may have arisen through hybridization events. Here, we are able to infer the paternal lineages of these putative hybrid species. Using the RAD-marker-based tree we reconstruct the evolutionary history of the sexually selected sword trait and show that it may have been present in the common ancestor of the genus. Together our results highlight the outstanding capacity that RAD sequencing data has for resolving previously problematic phylogenetic relationships, particularly among relatively closely related species.
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Affiliation(s)
- Julia C Jones
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasße 10, 78457, Konstanz, Germany
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Schumer M, Cui R, Boussau B, Walter R, Rosenthal G, Andolfatto P. An evaluation of the hybrid speciation hypothesis for Xiphophorus clemenciae based on whole genome sequences. Evolution 2013; 67:1155-68. [PMID: 23550763 PMCID: PMC3621027 DOI: 10.1111/evo.12009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Once thought rare in animal taxa, hybridization has been increasingly recognized as an important and common force in animal evolution. In the past decade, a number of studies have suggested that hybridization has driven speciation in some animal groups. We investigate the signature of hybridization in the genome of a putative hybrid species, Xiphophorus clemenciae, through whole genome sequencing of this species and its hypothesized progenitors. Based on analysis of this data, we find that X. clemenciae is unlikely to have been derived from admixture between its proposed parental species. However, we find significant evidence for recent gene flow between Xiphophorus species. Although we detect genetic exchange in two pairs of species analyzed, the proportion of genomic regions that can be attributed to hybrid origin is small, suggesting that strong behavioral premating isolation prevents frequent hybridization in Xiphophorus. The direction of gene flow between species is potentially consistent with a role for sexual selection in mediating hybridization.
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Affiliation(s)
- Molly Schumer
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08544, USA.
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Kang JH, Schartl M, Walter RB, Meyer A. Comprehensive phylogenetic analysis of all species of swordtails and platies (Pisces: Genus Xiphophorus) uncovers a hybrid origin of a swordtail fish, Xiphophorus monticolus, and demonstrates that the sexually selected sword originated in the ancestral lineage of the genus, but was lost again secondarily. BMC Evol Biol 2013; 13:25. [PMID: 23360326 PMCID: PMC3585855 DOI: 10.1186/1471-2148-13-25] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 01/22/2013] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Males in some species of the genus Xiphophorus, small freshwater fishes from Meso-America, have an extended caudal fin, or sword - hence their common name "swordtails". Longer swords are preferred by females from both sworded and - surprisingly also, non-sworded (platyfish) species that belong to the same genus. Swordtails have been studied widely as models in research on sexual selection. Specifically, the pre-existing bias hypothesis was interpreted to best explain the observed bias of females in presumed ancestral lineages of swordless species that show a preference for assumed derived males with swords over their conspecific swordless males. However, many of the phylogenetic relationships within this genus still remained unresolved. Here we construct a comprehensive molecular phylogeny of all 26 known Xiphophorus species, including the four recently described species (X. kallmani, X. mayae, X. mixei and X. monticolus). We use two mitochondrial and six new nuclear markers in an effort to increase the understanding of the evolutionary relationships among the species in this genus. Based on the phylogeny, the evolutionary history and character state evolution of the sword was reconstructed and found to have originated in the common ancestral lineage of the genus Xiphophorus and that it was lost again secondarily. RESULTS We estimated the evolutionary relationships among all known species of the genus Xiphophorus based on the largest set of DNA markers so far. The phylogeny indicates that one of the newly described swordtail species, Xiphophorus monticolus, is likely to have arisen through hybridization since it is placed with the southern platyfish in the mitochondrial phylogeny, but with the southern swordtails in the nuclear phylogeny. Such discordance between these two types of markers is a strong indication for a hybrid origin. Additionally, by using a maximum likelihood approach the possession of the sexually selected sword trait is shown to be the most likely ancestral state for the genus Xiphophorus. Further, we provide a well supported estimation of the phylogenetic relationships between the previously unresolved northern swordtail groups. CONCLUSIONS This comprehensive molecular phylogeny of the entire genus Xiphophorus provides evidence that a second swordtail species, X. monticolus, arose through hybridization. Previously, we demonstrated that X. clemenciae, another southern swordtail species, arose via hybridization. These findings highlight the potential key role of hybridization in the evolution of this genus and suggest the need for further investigations into how hybridization contributes to speciation more generally.
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Affiliation(s)
- Ji Hyoun Kang
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstraße 10, Konstanz 78457, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Manfred Schartl
- Physiological Chemistry, Biozentrum, University of Würzburg, Am Hubland, Würzburg, 97074, Germany
| | - Ronald B Walter
- Department of Chemistry and Biochemistry, Texas State University-San Marcos, 601 University Dr, San Marcos, TX, 78666, USA
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstraße 10, Konstanz 78457, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
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