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Otalora K, Riera JL, Tavecchia G, Rotger A, Igual JM, Trotta JP, Baldo L. Population genetics and phylogeographic history of the insular lizard Podarcis lilfordi (Gunther, 1874) from the Balearic Islands based on genome-wide polymorphic data. Ecol Evol 2024; 14:e11407. [PMID: 38799398 PMCID: PMC11116764 DOI: 10.1002/ece3.11407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/12/2024] [Accepted: 04/30/2024] [Indexed: 05/29/2024] Open
Abstract
Islands provide a great system to explore the processes that maintain genetic diversity and promote local adaptation. We explored the genomic diversity of the Balearic lizard Podarcis lilfordi, an endemic species characterized by numerous small insular populations with large phenotypic diversity. Using the newly available genome for this species, we characterized more than 300,000 SNPs, merging genotyping-by-sequencing (GBS) data with previously published restriction site-associated DNA sequencing (RAD-Seq) data, providing a dataset of 16 island populations (191 individuals) across the range of species distribution (Menorca, Mallorca, and Cabrera). Results indicate that each islet hosts a well-differentiated population (F ST = 0.247 ± 0.09), with no recent immigration/translocation events. Contrary to expectations, most populations harbor a considerable genetic diversity (mean nucleotide diversity, P i = 0.144 ± 0.021), characterized by overall low inbreeding values (F IS < 0.1). While the genetic diversity significantly decreased with decreasing islet surface, maintenance of substantial genetic diversity even in tiny islets suggests variable selection or other mechanisms that buffer genetic drift. Maximum-likelihood tree based on concatenated SNP data confirmed the existence of the two major independent lineages of Menorca and Mallorca/Cabrera. Multiple lines of evidence, including admixture and root testing, robustly placed the origin of the species in the Mallorca Island, rather than in Menorca. Outlier analysis mainly retrieved a strong signature of genome differentiation between the two major archipelagos, especially in the sexual chromosome Z. A set of proteins were target of multiple outliers and primarily associated with binding and catalytic activity, providing interesting candidates for future selection studies. This study provides the framework to explore crucial aspects of the genetic basis of phenotypic divergence and insular adaptation.
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Affiliation(s)
- Katherin Otalora
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Biology FacultyUniversity of Barcelona (UB)BarcelonaSpain
- Fundación FUNMAJO, EBA, RAIEC, Biodiversity BranchTunjaBoyacáColombia
| | - Joan Lluís Riera
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Biology FacultyUniversity of Barcelona (UB)BarcelonaSpain
| | - Giacomo Tavecchia
- Animal Demography and Ecology Unit (GEDA‐IMEDEA, CSIC‐UIB)EsporlesSpain
| | - Andreu Rotger
- Animal Demography and Ecology Unit (GEDA‐IMEDEA, CSIC‐UIB)EsporlesSpain
| | - José Manuel Igual
- Animal Demography and Ecology Unit (GEDA‐IMEDEA, CSIC‐UIB)EsporlesSpain
| | - Jean‐Remi Paul Trotta
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
| | - Laura Baldo
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Biology FacultyUniversity of Barcelona (UB)BarcelonaSpain
- Institute for Research on Biodiversity (IRBio)University of Barcelona (UB)BarcelonaSpain
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Wang Z, Luo W, Ping J, Xia Y, Ran J, Zeng X. Large X-effects are absent in torrent frogs with nascent sex chromosomes. Mol Ecol 2023; 32:5338-5349. [PMID: 37602937 DOI: 10.1111/mec.17113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/23/2023] [Accepted: 08/09/2023] [Indexed: 08/22/2023]
Abstract
Sex chromosomes are popularized as a special role in driving speciation. However, the empirical evidence from natural population processes has been limited to organisms with degenerated sex chromosomes, where hemizygosity is mainly considered to act as the driver of reproductive isolation. Here, we examined several hybrid zones of torrent frog Amolops mantzorum species complex, using an approach by mapping species-diagnostic loci onto the reference genome to compare sex-linked versus autosomal patterns of introgression. We find little support in sex-linked incompatibilities for large X-effects for these populations in hybrid zones with homomorphic sex chromosomes, due to the absence of the hemizygous effects. As expected, the large X-effects were not found in those with heteromorphic but newly evolved sex chromosomes, owing to the absence of strong genetic differences between X and Y chromosomes. The available data so far on amphibians suggest little role for sex-linked genes in speciation. The large X-effects in those with nascent sex chromosomes may not be as ubiquitous as presumed across the animal kingdom.
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Affiliation(s)
- Ziwen Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wei Luo
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | - Jun Ping
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yun Xia
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Jianghong Ran
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xiaomao Zeng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
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Pollmann M, Kuhn D, König C, Homolka I, Paschke S, Reinisch R, Schmidt A, Schwabe N, Weber J, Gottlieb Y, Steidle JLM. New species based on the biological species concept within the complex of Lariophagus distinguendus (Hymenoptera, Chalcidoidea, Pteromalidae), a parasitoid of household pests. Ecol Evol 2023; 13:e10524. [PMID: 37720058 PMCID: PMC10500055 DOI: 10.1002/ece3.10524] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 07/07/2023] [Accepted: 08/30/2023] [Indexed: 09/19/2023] Open
Abstract
The pteromalid parasitoid Lariophagus distinguendus (Foerster) belongs to the Hymenoptera, a megadiverse insect order with high cryptic diversity. It attacks stored product pest beetles in human storage facilities. Recently, it has been shown to consist of two separate species. To further study its cryptic diversity, strains were collected to compare their relatedness using barcoding and nuclear genes. Nuclear genes identified two clusters which agree with the known two species, whereas the barcode fragment determined an additional third Clade. Total reproductive isolation (RI) according to the biological species concept (BSC) was investigated in crossing experiments within and between clusters using representative strains. Sexual isolation exists between all studied pairs, increasing from slight to strong with genetic distance. Postzygotic barriers mostly affected hybrid males, pointing to Haldane's rule. Hybrid females were only affected by unidirectional Spiroplasma-induced cytoplasmic incompatibility and behavioural sterility, each in one specific strain combination. RI was virtually absent between strains separated by up to 2.8% COI difference, but strong or complete in three pairs from one Clade each, separated by at least 7.2%. Apparently, each of these clusters represents one separate species according to the BSC, highlighting cryptic diversity in direct vicinity to humans. In addition, these results challenge the recent 'turbo-taxonomy' practice of using 2% COI differences to delimitate species, especially within parasitic Hymenoptera. The gradual increase in number and strength of reproductive barriers between strains with increasing genetic distance also sheds light on the emergence of barriers during the speciation process in L. distinguendus.
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Affiliation(s)
- Marie Pollmann
- Department of Chemical Ecology 190t, Institute of BiologyUniversity of HohenheimStuttgartGermany
| | - Denise Kuhn
- Department of Entomology 360c, Institute of PhytomedicineUniversity of HohenheimStuttgartGermany
| | - Christian König
- Akademie für Natur‐ und Umweltschutz Baden‐WürttembergStuttgartGermany
| | - Irmela Homolka
- Department of Chemical Ecology 190t, Institute of BiologyUniversity of HohenheimStuttgartGermany
| | - Sina Paschke
- Department of Chemical Ecology 190t, Institute of BiologyUniversity of HohenheimStuttgartGermany
| | - Ronja Reinisch
- Department of Chemical Ecology 190t, Institute of BiologyUniversity of HohenheimStuttgartGermany
| | - Anna Schmidt
- Department of Chemical Ecology 190t, Institute of BiologyUniversity of HohenheimStuttgartGermany
| | - Noa Schwabe
- Plant Evolutionary Biology 190b, Institute of BiologyUniversity of HohenheimStuttgartGermany
| | - Justus Weber
- Department of Chemical Ecology 190t, Institute of BiologyUniversity of HohenheimStuttgartGermany
| | - Yuval Gottlieb
- Robert H. Smith Faculty of Agriculture, Food and Environment, Koret School of Veterinary MedicineHebrew University of JerusalemRehovotIsrael
| | - Johannes Luitpold Maria Steidle
- Department of Chemical Ecology 190t, Institute of BiologyUniversity of HohenheimStuttgartGermany
- KomBioTa – Center of Biodiversity and Integrative TaxonomyUniversity of HohenheimStuttgartGermany
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Bendall EE, Mattingly KM, Moehring AJ, Linnen CR. A Test of Haldane's Rule in Neodiprion Sawflies and Implications for the Evolution of Postzygotic Isolation in Haplodiploids. Am Nat 2023; 202:40-54. [PMID: 37384768 DOI: 10.1086/724820] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2023]
Abstract
AbstractHaldane's rule-a pattern in which hybrid sterility or inviability is observed in the heterogametic sex of an interspecific cross-is one of the most widely obeyed rules in nature. Because inheritance patterns are similar for sex chromosomes and haplodiploid genomes, Haldane's rule may apply to haplodiploid taxa, predicting that haploid male hybrids will evolve sterility or inviability before diploid female hybrids. However, there are several genetic and evolutionary mechanisms that may reduce the tendency of haplodiploids to obey Haldane's rule. Currently, there are insufficient data from haplodiploids to determine how frequently they adhere to Haldane's rule. To help fill this gap, we crossed a pair of haplodiploid hymenopteran species (Neodiprion lecontei and Neodiprion pinetum) and evaluated the viability and fertility of female and male hybrids. Despite considerable divergence, we found no evidence of reduced fertility in hybrids of either sex, consistent with the hypothesis that hybrid sterility evolves slowly in haplodiploids. For viability, we found a pattern opposite to that of Haldane's rule: hybrid females, but not males, had reduced viability. This reduction was most pronounced in one direction of the cross, possibly due to a cytoplasmic-nuclear incompatibility. We also found evidence of extrinsic postzygotic isolation in hybrids of both sexes, raising the possibility that this form or reproductive isolation tends to emerge early in speciation in host-specialized insects. Our work emphasizes the need for more studies on reproductive isolation in haplodiploids, which are abundant in nature but underrepresented in the speciation literature.
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Dufresnes C, Crochet PA. Sex chromosomes as supergenes of speciation: why amphibians defy the rules? Philos Trans R Soc Lond B Biol Sci 2022; 377:20210202. [PMID: 35694748 PMCID: PMC9189495 DOI: 10.1098/rstb.2021.0202] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
As reflected by the two rules of speciation (Haldane's rule and the large X-/Z-effect), sex chromosomes are expected to behave like supergenes of speciation: they recombine only in one sex (XX females or ZZ males), supposedly recruit sexually antagonistic genes and evolve faster than autosomes, which can all contribute to pre-zygotic and post-zygotic isolation. While this has been mainly studied in organisms with conserved sex-determining systems and highly differentiated (heteromorphic) sex chromosomes like mammals, birds and some insects, these expectations are less clear in organismal groups where sex chromosomes repeatedly change and remain mostly homomorphic, like amphibians. In this article, we review the proposed roles of sex-linked genes in isolating nascent lineages throughout the speciation continuum and discuss their support in amphibians given current knowledge of sex chromosome evolution and speciation modes. Given their frequent recombination and lack of differentiation, we argue that amphibian sex chromosomes are not expected to become supergenes of speciation, which is reflected by the rarity of empirical studies consistent with a 'large sex chromosome effect' in frogs and toads. The diversity of sex chromosome systems in amphibians has a high potential to disentangle the evolutionary mechanisms responsible for the emergence of sex-linked speciation genes in other organisms. This article is part of the theme issue 'Genomic architecture of supergenes: causes and evolutionary consequences'.
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Affiliation(s)
- Christophe Dufresnes
- LASER, College of Biology and Environment, Nanjing Forestry University, Nanjing 210037, People's Republic of China
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6
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Kulikova IV, Shedko SV, Zhuravlev YN, Lavretsky P, Peters JL. Z‐chromosome outliers as diagnostic markers to discriminate Mallard and Chinese Spot‐billed Duck (Anatidae). ZOOL SCR 2022. [DOI: 10.1111/zsc.12540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Irina V. Kulikova
- Federal Scientific Center of the East Asia Terrestrial Biodiversity Far Eastern Branch of the Russian Academy of Sciences Vladivostok Russia
| | - Sergei V. Shedko
- Federal Scientific Center of the East Asia Terrestrial Biodiversity Far Eastern Branch of the Russian Academy of Sciences Vladivostok Russia
| | - Yury N. Zhuravlev
- Federal Scientific Center of the East Asia Terrestrial Biodiversity Far Eastern Branch of the Russian Academy of Sciences Vladivostok Russia
| | - Philip Lavretsky
- Department of Biological Sciences University of Texas El Paso Texas USA
| | - Jeffrey L. Peters
- Department of Biological Sciences Wright State University Dayton Ohio USA
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Integrating Cytogenetics and Population Genomics: Allopatry and Neo-Sex Chromosomes May Have Shaped the Genetic Divergence in the Erythrinus erythrinus Species Complex (Teleostei, Characiformes). BIOLOGY 2022; 11:biology11020315. [PMID: 35205181 PMCID: PMC8869172 DOI: 10.3390/biology11020315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/13/2022] [Accepted: 02/15/2022] [Indexed: 11/18/2022]
Abstract
Simple Summary Fish present astonishing diversity, comprising more species than the combined total of all other vertebrates. Here, we integrated cytogenetic and genomic data to investigate how the evolution of multiple sex chromosomes together with allopatry is linked to genetic diversity and speciation in the fish species Erythrinus erythrinus. We hypothesized that the presence of multiple sex chromosomes has contributed to the genetic differentiation of populations, which could have potentially accelerated speciation. Abstract Diversity found in Neotropical freshwater fish is remarkable. It can even hinder a proper delimitation of many species, with the wolf fish Erythrinus erythrinus (Teleostei, Characiformes) being a notable example. This nominal species shows remarkable intra-specific variation, with extensive karyotype diversity found among populations in terms of different diploid chromosome numbers (2n), karyotype compositions and sex chromosome systems. Here, we analyzed three distinct populations (one of them cytogenetically investigated for the first time) that differed in terms of their chromosomal features (termed karyomorphs) and by the presence or absence of heteromorphic sex chromosomes. We combined cytogenetics with genomic approaches to investigate how the evolution of multiple sex chromosomes together with allopatry is linked to genetic diversity and speciation. The results indicated the presence of high genetic differentiation among populations both from cytogenetic and genomic aspects, with long-distance allopatry potentially being the main agent of genetic divergence. One population showed a neo-X1X2Y sexual chromosome system and we hypothesize that this system is associated with enhanced inter-population genetic differentiation which could have potentially accelerated speciation compared to the effect of allopatry alone.
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Burton RS. The role of mitonuclear incompatibilities in allopatric speciation. Cell Mol Life Sci 2022; 79:103. [PMID: 35091831 PMCID: PMC11072163 DOI: 10.1007/s00018-021-04059-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 11/19/2021] [Accepted: 11/25/2021] [Indexed: 11/03/2022]
Abstract
Aerobic metabolism in eukaryotic cells requires extensive interactions between products of the nuclear and mitochondrial genomes. Rapid evolution of the mitochondrial genome, including fixation of both adaptive and deleterious mutations, creates intrinsic selection pressures favoring nuclear gene mutations that maintain mitochondrial function. As this process occurs independently in allopatry, the resulting divergence between conspecific populations can subsequently be manifest in mitonuclear incompatibilities in inter-population hybrids. Such incompatibilities, mitonuclear versions of Bateson-Dobzhansky-Muller incompatibilities that form the standard model for allopatric speciation, can potentially restrict gene flow between populations, ultimately resulting in varying degrees of reproductive isolation. The potential role of mitonuclear incompatibilities in speciation is further enhanced where mtDNA substitution rates are elevated compared to the nuclear genome and where population structure maintains allopatry for adequate time to evolve multiple mitonuclear incompatibilities. However, the fact that mitochondrial introgression occurs across species boundaries has raised questions regarding the efficacy of mitonuclear incompatibilities in reducing gene flow. Several scenarios now appear to satisfactorily explain this phenomenon, including cases where differences in mtDNA genetic load may drive introgression or where co-introgression of coadapted nuclear genes may support the function of introgressed mtDNA. Although asymmetries in reproductive isolation between taxa are consistent with mitonuclear incompatibilities, interactions between autosomes and sex chromosomes yield similar predictions that are difficult to disentangle. With regard to establishing reproductive isolation while in allopatry, existing studies clearly suggest that mitonuclear incompatibilities can contribute to the evolution of barriers to gene flow. However, there is to date relatively little definitive evidence supporting a primary role for mitonuclear incompatibilities in the speciation process.
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Affiliation(s)
- Ronald S Burton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093-0202, USA.
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9
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Yano CF, Sember A, Kretschmer R, Bertollo LAC, Ezaz T, Hatanaka T, Liehr T, Ráb P, Al-Rikabi A, Viana PF, Feldberg E, de Oliveira EA, Toma GA, de Bello Cioffi M. Against the mainstream: exceptional evolutionary stability of ZW sex chromosomes across the fish families Triportheidae and Gasteropelecidae (Teleostei: Characiformes). Chromosome Res 2021; 29:391-416. [PMID: 34694531 DOI: 10.1007/s10577-021-09674-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 09/20/2021] [Accepted: 09/22/2021] [Indexed: 10/20/2022]
Abstract
Teleost fishes exhibit a breath-taking diversity of sex determination and differentiation mechanisms. They encompass at least nine sex chromosome systems with often low degree of differentiation, high rate of inter- and intra-specific variability, and frequent turnovers. Nevertheless, several mainly female heterogametic systems at an advanced stage of genetic differentiation and high evolutionary stability have been also found across teleosts, especially among Neotropical characiforms. In this study, we aim to characterize the ZZ/ZW sex chromosome system in representatives of the Triportheidae family (Triportheus auritus, Agoniates halecinus, and the basal-most species Lignobrycon myersi) and its sister clade Gasteropelecidae (Carnegiella strigata, Gasteropelecus levis, and Thoracocharax stellatus). We applied both conventional and molecular cytogenetic approaches including chromosomal mapping of 5S and 18S ribosomal DNA clusters, cross-species chromosome painting (Zoo-FISH) with sex chromosome-derived probes and comparative genomic hybridization (CGH). We identified the ZW sex chromosome system for the first time in A. halecinus and G. levis and also in C. strigata formerly reported to lack sex chromosomes. We also brought evidence for possible mechanisms underlying the sex chromosome differentiation, including inversions, repetitive DNA accumulation, and exchange of genetic material. Our Zoo-FISH experiments further strongly indicated that the ZW sex chromosomes of Triportheidae and Gasteropelecidae are homeologous, suggesting their origin before the split of these lineages (approx. 40-70 million years ago). Such extent of sex chromosome stability is almost exceptional in teleosts, and hence, these lineages afford a special opportunity to scrutinize unique evolutionary forces and pressures shaping sex chromosome evolution in fishes and vertebrates in general.
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Affiliation(s)
- Cassia Fernanda Yano
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rod. Washington Luiz km 235, Sao Carlos, SP, 13565-905, Brazil
| | - Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Libechov, 277 21, Czech Republic.
| | - Rafael Kretschmer
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rod. Washington Luiz km 235, Sao Carlos, SP, 13565-905, Brazil
| | - Luiz Antônio Carlos Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rod. Washington Luiz km 235, Sao Carlos, SP, 13565-905, Brazil
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, Australia
| | - Terumi Hatanaka
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rod. Washington Luiz km 235, Sao Carlos, SP, 13565-905, Brazil
| | - Thomas Liehr
- Jena University Hospital, Institute of Human Genetics, Am Klinikum 1, 07747, Jena, Germany
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Libechov, 277 21, Czech Republic
| | - Ahmed Al-Rikabi
- Jena University Hospital, Institute of Human Genetics, Am Klinikum 1, 07747, Jena, Germany
| | - Patrik Ferreira Viana
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo 2936, Petropolis, Manaus, AM, Brazil
| | - Eliana Feldberg
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo 2936, Petropolis, Manaus, AM, Brazil
| | - Ezequiel Aguiar de Oliveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rod. Washington Luiz km 235, Sao Carlos, SP, 13565-905, Brazil
| | - Gustavo Akira Toma
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rod. Washington Luiz km 235, Sao Carlos, SP, 13565-905, Brazil
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rod. Washington Luiz km 235, Sao Carlos, SP, 13565-905, Brazil
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Stöck M, Dedukh D, Reifová R, Lamatsch DK, Starostová Z, Janko K. Sex chromosomes in meiotic, hemiclonal, clonal and polyploid hybrid vertebrates: along the 'extended speciation continuum'. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200103. [PMID: 34304588 PMCID: PMC8310718 DOI: 10.1098/rstb.2020.0103] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2021] [Indexed: 12/15/2022] Open
Abstract
We review knowledge about the roles of sex chromosomes in vertebrate hybridization and speciation, exploring a gradient of divergences with increasing reproductive isolation (speciation continuum). Under early divergence, well-differentiated sex chromosomes in meiotic hybrids may cause Haldane-effects and introgress less easily than autosomes. Undifferentiated sex chromosomes are more susceptible to introgression and form multiple (or new) sex chromosome systems with hardly predictable dominance hierarchies. Under increased divergence, most vertebrates reach complete intrinsic reproductive isolation. Slightly earlier, some hybrids (linked in 'the extended speciation continuum') exhibit aberrant gametogenesis, leading towards female clonality. This facilitates the evolution of various allodiploid and allopolyploid clonal ('asexual') hybrid vertebrates, where 'asexuality' might be a form of intrinsic reproductive isolation. A comprehensive list of 'asexual' hybrid vertebrates shows that they all evolved from parents with divergences that were greater than at the intraspecific level (K2P-distances of greater than 5-22% based on mtDNA). These 'asexual' taxa inherited genetic sex determination by mostly undifferentiated sex chromosomes. Among the few known sex-determining systems in hybrid 'asexuals', female heterogamety (ZW) occurred about twice as often as male heterogamety (XY). We hypothesize that pre-/meiotic aberrations in all-female ZW-hybrids present Haldane-effects promoting their evolution. Understanding the preconditions to produce various clonal or meiotic allopolyploids appears crucial for insights into the evolution of sex, 'asexuality' and polyploidy. 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)
- 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
| | - Dmitrij Dedukh
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, 277 21 Libechov, Czech Republic
| | - Radka Reifová
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, Prague 2, 128 00, Czech Republic
| | - Dunja K. Lamatsch
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Zuzana Starostová
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, Prague 2, 128 00, Czech Republic
| | - Karel Janko
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, 277 21 Libechov, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 701 03 Ostrava, Czech Republic
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Mass of genes rather than master genes underlie the genomic architecture of amphibian speciation. Proc Natl Acad Sci U S A 2021; 118:2103963118. [PMID: 34465621 DOI: 10.1073/pnas.2103963118] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genetic architecture of speciation, i.e., how intrinsic genomic incompatibilities promote reproductive isolation (RI) between diverging lineages, is one of the best-kept secrets of evolution. To directly assess whether incompatibilities arise in a limited set of large-effect speciation genes, or in a multitude of loci, we examined the geographic and genomic landscapes of introgression across the hybrid zones of 41 pairs of frog and toad lineages in the Western Palearctic region. As the divergence between lineages increases, phylogeographic transitions progressively become narrower, and larger parts of the genome resist introgression. This suggests that anuran speciation proceeds through a gradual accumulation of multiple barrier loci scattered across the genome, which ultimately deplete hybrid fitness by intrinsic postzygotic isolation, with behavioral isolation being achieved only at later stages. Moreover, these loci were disproportionately sex linked in one group (Hyla) but not in others (Rana and Bufotes), implying that large X-effects are not necessarily a rule of speciation with undifferentiated sex chromosomes. The highly polygenic nature of RI and the lack of hemizygous X/Z chromosomes could explain why the speciation clock ticks slower in amphibians compared to other vertebrates. The clock-like dynamics of speciation combined with the analytical focus on hybrid zones offer perspectives for more standardized practices of species delimitation.
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12
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Ávila Herrera IM, Král J, Pastuchová M, Forman M, Musilová J, Kořínková T, Šťáhlavský F, Zrzavá M, Nguyen P, Just P, Haddad CR, Hiřman M, Koubová M, Sadílek D, Huber BA. Evolutionary pattern of karyotypes and meiosis in pholcid spiders (Araneae: Pholcidae): implications for reconstructing chromosome evolution of araneomorph spiders. BMC Ecol Evol 2021; 21:75. [PMID: 33941079 PMCID: PMC8091558 DOI: 10.1186/s12862-021-01750-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 01/25/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Despite progress in genomic analysis of spiders, their chromosome evolution is not satisfactorily understood. Most information on spider chromosomes concerns the most diversified clade, entelegyne araneomorphs. Other clades are far less studied. Our study focused on haplogyne araneomorphs, which are remarkable for their unusual sex chromosome systems and for the co-evolution of sex chromosomes and nucleolus organizer regions (NORs); some haplogynes exhibit holokinetic chromosomes. To trace the karyotype evolution of haplogynes on the family level, we analysed the number and morphology of chromosomes, sex chromosomes, NORs, and meiosis in pholcids, which are among the most diverse haplogyne families. The evolution of spider NORs is largely unknown. RESULTS Our study is based on an extensive set of species representing all major pholcid clades. Pholcids exhibit a low 2n and predominance of biarmed chromosomes, which are typical haplogyne features. Sex chromosomes and NOR patterns of pholcids are diversified. We revealed six sex chromosome systems in pholcids (X0, XY, X1X20, X1X2X30, X1X2Y, and X1X2X3X4Y). The number of NOR loci ranges from one to nine. In some clades, NORs are also found on sex chromosomes. CONCLUSIONS The evolution of cytogenetic characters was largely derived from character mapping on a recently published molecular phylogeny of the family. Based on an extensive set of species and mapping of their characters, numerous conclusions regarding the karyotype evolution of pholcids and spiders can be drawn. Our results suggest frequent autosome-autosome and autosome-sex chromosome rearrangements during pholcid evolution. Such events have previously been attributed to the reproductive isolation of species. The peculiar X1X2Y system is probably ancestral for haplogynes. Chromosomes of the X1X2Y system differ considerably in their pattern of evolution. In some pholcid clades, the X1X2Y system has transformed into the X1X20 or XY systems, and subsequently into the X0 system. The X1X2X30 system of Smeringopus pallidus probably arose from the X1X20 system by an X chromosome fission. The X1X2X3X4Y system of Kambiwa probably evolved from the X1X2Y system by integration of a chromosome pair. Nucleolus organizer regions have frequently expanded on sex chromosomes, most probably by ectopic recombination. Our data suggest the involvement of sex chromosome-linked NORs in achiasmatic pairing.
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Affiliation(s)
- Ivalú M. Ávila Herrera
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech Republic
| | - Jiří Král
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech Republic
| | - Markéta Pastuchová
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech Republic
| | - Martin Forman
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech Republic
| | - Jana Musilová
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech Republic
- Research Team of Plant Stress Biology and Biotechnology, Division of Crop Genetics and Breeding, Crop Research Institute, Drnovská 507/73, 161 00 Prague 6, Czech Republic
| | - Tereza Kořínková
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech Republic
- Prague 1, Czech Republic
| | - František Šťáhlavský
- Invertebrate Zoology Unit, Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44 Prague 2, Czech Republic
| | - Magda Zrzavá
- Laboratory of Molecular Cytogenetics, Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
- Laboratory of Molecular Cytogenetics, Department of Molecular Biology and Genetics, Institute of Entomology, Biology Centre CAS, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Petr Nguyen
- Laboratory of Molecular Cytogenetics, Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
- Laboratory of Molecular Cytogenetics, Department of Molecular Biology and Genetics, Institute of Entomology, Biology Centre CAS, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Pavel Just
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech Republic
- Invertebrate Zoology Unit, Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44 Prague 2, Czech Republic
| | - Charles R. Haddad
- Research Group of Arachnid Systematics and Ecology, Department of Zoology and Entomology, Faculty of Natural and Agricultural Sciences, University of the Free State, P.O. Box 339, Bloemfontein, 9300 Republic of South Africa
| | - Matyáš Hiřman
- Invertebrate Zoology Unit, Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44 Prague 2, Czech Republic
| | - Martina Koubová
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech Republic
| | - David Sadílek
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech Republic
- Invertebrate Zoology Unit, Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44 Prague 2, Czech Republic
| | - Bernhard A. Huber
- Arachnida Section, Alexander Koenig Zoological Research Museum, Adenauerallee 160, 53113 Bonn, Germany
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13
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Hill P, Wapstra E, Ezaz T, Burridge CP. Pleistocene divergence in the absence of gene flow among populations of a viviparous reptile with intraspecific variation in sex determination. Ecol Evol 2021; 11:5575-5583. [PMID: 34026030 PMCID: PMC8131762 DOI: 10.1002/ece3.7458] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 02/21/2021] [Accepted: 02/25/2021] [Indexed: 12/26/2022] Open
Abstract
Polymorphisms can lead to genetic isolation if there is differential mating success among conspecifics divergent for a trait. Polymorphism for sex-determining system may fall into this category, given strong selection for the production of viable males and females and the low success of heterogametic hybrids when sex chromosomes differ (Haldane's rule). Here we investigated whether populations exhibiting polymorphism for sex determination are genetically isolated, using the viviparous snow skink Carinascincus ocellatus. While a comparatively high elevation population has genotypic sex determination, in a lower elevation population there is an additional temperature component to sex determination. Based on 11,107 SNP markers, these populations appear genetically isolated. "Isolation with Migration" analysis also suggests these populations diverged in the absence of gene flow, across a period encompassing multiple Pleistocene glaciations and likely greater geographic proximity of populations. However, further experiments are required to establish whether genetic isolation may be a cause or consequence of differences in sex determination. Given the influence of temperature on sex in one lineage, we also discuss the implications for the persistence of this polymorphism under climate change.
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Affiliation(s)
- Peta Hill
- Discipline of Biological SciencesUniversity of TasmaniaSandy BayTas.Australia
| | - Erik Wapstra
- Discipline of Biological SciencesUniversity of TasmaniaSandy BayTas.Australia
| | - Tariq Ezaz
- Institute for Applied EcologyUniversity of CanberraBruceACTAustralia
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14
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Matute DR, Cooper BS. Comparative studies on speciation: 30 years since Coyne and Orr. Evolution 2021; 75:764-778. [PMID: 33491225 PMCID: PMC8247902 DOI: 10.1111/evo.14181] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/16/2020] [Accepted: 12/22/2020] [Indexed: 12/28/2022]
Abstract
Understanding the processes of population divergence and speciation remains a core question in evolutionary biology. For nearly a hundred years evolutionary geneticists have characterized reproductive isolation (RI) mechanisms and specific barriers to gene flow required for species formation. The seminal work of Coyne and Orr provided the first comprehensive comparative analysis of speciation. By combining phylogenetic hypotheses and species range data with estimates of genetic divergence and multiple mechanisms of RI across Drosophila, Coyne and Orr's influential meta-analyses answered fundamental questions and motivated new analyses that continue to push the field forward today. Now 30 years later, we revisit the five questions addressed by Coyne and Orr, identifying results that remain well supported and others that seem less robust with new data. We then consider the future of speciation research, with emphasis on areas where novel methods and data motivate potential progress. While the literature remains biased towards Drosophila and other model systems, we are enthusiastic about the future of the field.
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Affiliation(s)
- Daniel R. Matute
- Biology DepartmentUniversity of North CarolinaChapel HillNorth Carolina27510
| | - Brandon S. Cooper
- Division of Biological SciencesUniversity of MontanaMissoulaMontana59812
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15
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Melander SL, Mueller RL. Comprehensive Analysis of Salamander Hybridization Suggests a Consistent Relationship between Genetic Distance and Reproductive Isolation across Tetrapods. COPEIA 2020. [DOI: 10.1643/ch-19-319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Scott Lucas Melander
- Department of Biology, Colorado State University, 251 W Pitkin Street, Fort Collins, Colorado 80523; (SLM) ; and (RLM) . Send reprint requests to SLM
| | - Rachel Lockridge Mueller
- Department of Biology, Colorado State University, 251 W Pitkin Street, Fort Collins, Colorado 80523; (SLM) ; and (RLM) . Send reprint requests to SLM
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16
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Zheng XL. Unveiling mosquito cryptic species and their reproductive isolation. INSECT MOLECULAR BIOLOGY 2020; 29:499-510. [PMID: 32741005 PMCID: PMC7754467 DOI: 10.1111/imb.12666] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 07/04/2020] [Accepted: 07/18/2020] [Indexed: 06/11/2023]
Abstract
Mosquitoes are major vectors of many infectious pathogens or parasites. Understanding cryptic species and the speciation of disease vectors has important implications for vector management, evolution and host-pathogen and/or host-parasite interactions. Currently, mosquito cryptic species have been reported in many studies, most of which focus on the reproductive isolation of cryptic species and mainly on Anopheles gambiae sensu lato complex. Emerging species within the primary malaria vector Anopheles gambiae show different ecological preferences and significant prezygotic reproductive isolation, while Aedes mariae and Aedes zammitii show postmating reproductive isolation. However, data reporting the reproductive isolation in Culex and Aedes albopictus mosquito cryptic species is absent. The lack of systematic studies leaves many questions open, such as whether cryptic species are more common in particular habitats, latitudes or taxonomic groups; what mosquito cryptic species evolutionary processes bring about reproductive isolation in the absence of morphological differentiation? How does Wolbachia infection affect in mosquitoes' reproductive isolation? In this review, we provide a summary of recent advances in the discovery and identification of sibling or cryptic species within mosquito genera.
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Affiliation(s)
- XL. Zheng
- Department of Pathogen Biology, School of Public HealthSouthern Medical UniversityGuangzhouChina
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17
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Dufresnes C, Litvinchuk SN, Rozenblut-Kościsty B, Rodrigues N, Perrin N, Crochet PA, Jeffries DL. Hybridization and introgression between toads with different sex chromosome systems. Evol Lett 2020; 4:444-456. [PMID: 33014420 PMCID: PMC7523563 DOI: 10.1002/evl3.191] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 01/26/2023] Open
Abstract
The growing interest in the lability of sex determination in non‐model vertebrates such as amphibians and fishes has revealed high rates of sex chromosome turnovers among closely related species of the same clade. Can such lineages hybridize and admix with different sex‐determining systems, or could the changes have precipitated their speciation? We addressed these questions in incipient species of toads (Bufonidae), where we identified a heterogametic transition and characterized their hybrid zone with genome‐wide markers (RADseq). Adult and sibship data confirmed that the common toad B. bufo is female heterogametic (ZW), while its sister species the spined toad B. spinosus is male heterogametic (XY). Analysis of a fine scale transect across their parapatric ranges in southeastern France unveiled a narrow tension zone (∼10 km), with asymmetric mitochondrial and nuclear admixture over hundreds of kilometers southward and northward, respectively. The geographic extent of introgression is consistent with an expansion of B. spinosus across B. bufo’s former ranges in Mediterranean France, as also suggested by species distribution models. However, widespread cyto‐nuclear discordances (B. spinosus backrosses carrying B. bufo mtDNA) run against predictions from the dominance effects of Haldane's rule, perhaps because Y and W heterogametologs are not degenerated. Common and spined toads can thus successfully cross‐breed despite fundamental differences in their sex determination mechanisms, but remain partially separated by reproductive barriers. Whether and how the interactions of their XY and ZW genes contribute to these barriers shall provide novel insights on the debated role of labile sex chromosomes in speciation.
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Affiliation(s)
- Christophe Dufresnes
- LASER College of Biology and the Environment Nanjing Forestry University Nanjing People's Republic of China.,Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom
| | - Spartak N Litvinchuk
- Institute of Cytology Russian Academy of Sciences Saint Petersburg Russia.,Dagestan State University Makhachkala Russia
| | - Beata Rozenblut-Kościsty
- Department of Evolutionary Biology and Conservation of Vertebrates Faculty of Biological Sciences University of Wrocław Wrocław Poland
| | - Nicolas Rodrigues
- Department of Ecology & Evolution University of Lausanne Lausanne Switzerland
| | - Nicolas Perrin
- Department of Ecology & Evolution University of Lausanne Lausanne Switzerland
| | - Pierre-André Crochet
- CEFE Univ. Montpellier, CNRS, EPHE, IRD Univ Paul Valéry Montpellier 3 Montpellier France
| | - Daniel L Jeffries
- Department of Ecology & Evolution University of Lausanne Lausanne Switzerland
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18
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Wedell N. Selfish genes and sexual selection: the impact of genomic parasites on host reproduction. J Zool (1987) 2020. [DOI: 10.1111/jzo.12780] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- N. Wedell
- Biosciences University of Exeter, Penryn Campus Penryn UK
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19
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Bourgeois YXC, Bertrand JAM, Delahaie B, Holota H, Thébaud C, Milá B. Differential divergence in autosomes and sex chromosomes is associated with intra-island diversification at a very small spatial scale in a songbird lineage. Mol Ecol 2020; 29:1137-1153. [PMID: 32107807 DOI: 10.1111/mec.15396] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 02/12/2020] [Accepted: 02/20/2020] [Indexed: 12/16/2022]
Abstract
Recently diverged taxa showing marked phenotypic and ecological diversity provide optimal systems to understand the genetic processes underlying speciation. We used genome-wide markers to investigate the diversification of the Reunion grey white-eye (Zosterops borbonicus) on the small volcanic island of Reunion (Mascarene archipelago), where this species complex exhibits four geographical forms that are parapatrically distributed across the island and differ strikingly in plumage colour. One form restricted to the highlands is separated by a steep ecological gradient from three distinct lowland forms which meet at narrow hybrid zones that are not associated with environmental variables. Analyses of genomic variation based on single nucleotide polymorphism data from genotyping-by-sequencing and pooled RAD-seq approaches show that signatures of selection associated with elevation can be found at multiple regions across the genome, whereas most loci associated with the lowland forms are located on the Z sex chromosome. We identified TYRP1, a Z-linked colour gene, as a likely candidate locus underlying colour variation among lowland forms. Tests of demographic models revealed that highland and lowland forms diverged in the presence of gene flow, and divergence has progressed as gene flow was restricted by selection at loci across the genome. This system holds promise for investigating how adaptation and reproductive isolation shape the genomic landscape of divergence at multiple stages of the speciation process.
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Affiliation(s)
- Yann X C Bourgeois
- School of Biological Sciences, University of Portsmouth, Portsmouth, UK.,Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université Paul Sabatier, Toulouse, France
| | - Joris A M Bertrand
- Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université Paul Sabatier, Toulouse, France.,Laboratoire Génome & Développement des Plantes, UMR 5096, Université de Perpignan Via Domitia, Perpignan, France
| | - Boris Delahaie
- Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université Paul Sabatier, Toulouse, France.,Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Hélène Holota
- Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université Paul Sabatier, Toulouse, France
| | - Christophe Thébaud
- Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université Paul Sabatier, Toulouse, France
| | - Borja Milá
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
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20
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Genomic Data Reveal Conserved Female Heterogamety in Giant Salamanders with Gigantic Nuclear Genomes. G3-GENES GENOMES GENETICS 2019; 9:3467-3476. [PMID: 31439718 PMCID: PMC6778777 DOI: 10.1534/g3.119.400556] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Systems of genetic sex determination and the homology of sex chromosomes in different taxa vary greatly across vertebrates. Much progress remains to be made in understanding systems of genetic sex determination in non-model organisms, especially those with homomorphic sex chromosomes and/or large genomes. We used reduced representation genome sequencing to investigate genetic sex determination systems in the salamander family Cryptobranchidae (genera Cryptobranchus and Andrias), which typifies both of these inherent difficulties. We tested hypotheses of male- or female-heterogamety by sequencing hundreds of thousands of anonymous genomic regions in a panel of known-sex cryptobranchids and characterized patterns of presence/absence, inferred zygosity, and depth of coverage to identify sex-linked regions of these 56 gigabase genomes. Our results strongly support the hypothesis that all cryptobranchid species possess homologous systems of female heterogamety, despite maintenance of homomorphic sex chromosomes over nearly 60 million years. Additionally, we report a robust, non-invasive genetic assay for sex diagnosis in Cryptobranchus and Andrias which may have great utility for conservation efforts with these endangered salamanders. Co-amplification of these W-linked markers in both cryptobranchid genera provides evidence for long-term sex chromosome stasis in one of the most divergent salamander lineages. These findings inform hypotheses about the ancestral mode of sex determination in salamanders, but suggest that comparative data from other salamander families are needed. Our results further demonstrate that massive genomes are not necessarily a barrier to effective genome-wide sequencing and that the resulting data can be highly informative about sex determination systems in taxa with homomorphic sex chromosomes.
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21
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Amancio AP, Duarte SSM, Silva RC, da Cruz AS, Silva DC, da Silva CC, da Cruz AD. Banded karyotype of Nelore cattle ( Bos taurus indicus Linnaeus, 1758). COMPARATIVE CYTOGENETICS 2019; 13:265-275. [PMID: 31558984 PMCID: PMC6728309 DOI: 10.3897/compcytogen.v13i3.36449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 08/04/2019] [Indexed: 06/10/2023]
Abstract
Chromosome banding techniques were applied and standardized to obtain karyotype characteristics for the first time in Brazil of Nelore cattle - Bos taurus indicus Linnaeus, 1758 - (bovine subspecies most prominent in Brazilian livestock). Blood samples were collected from the animals of the School of Agrarian and Biological Sciences of the Pontifical Catholic University of Goiás, two males and two females of pure breed. These samples were submitted to the cell culture method to study metaphase chromosomes. Chromosome banding techniques (C, G and NOR) revealed the karyotype architecture of Nelore cattle common with that of other breeds of zebu cattle formerly karyotyped. The diploid chromosome number was invariably normal, 2n = 60. C-banding revealed C-positive heterochromatin in centromeric regions almost in all chromosomes. G-banding presented the expected band pattern in the respective chromosome pairs in correspondence with the established chromosomal patterns for the species. Ag-staining for nucleolus organizer regions (AgNOR) was identified on the telomeric end of the long arm in 7 autosomal chromosomes. In this study we found more regions in chromosomes with staining than presented in the literature for the Bos indicus group (BIN). These NOR regions were repeated on the same chromosomes for the 4 animals studied.
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Affiliation(s)
- Andréia Pires Amancio
- PhD Program in Biotechnology and Biodiversity, Federal University of Goiás, Rede Centro Oeste de Pós-Graduação de Pesquisa e Inovação, Rua 235, n. 40, Setor Leste Universitário, Goiânia, GO 74605-050, Brazil
- Replicon Research Group, Genetics Master’s Program, School of Agrarian and Biological Sciences, Pontifical Catholic University of Goiás, Rua 235, n. 40, Setor Leste Universitário, Goiânia, GO 74605-050, Brazil
| | - Sabrina Sara Moreira Duarte
- Replicon Research Group, Genetics Master’s Program, School of Agrarian and Biological Sciences, Pontifical Catholic University of Goiás, Rua 235, n. 40, Setor Leste Universitário, Goiânia, GO 74605-050, Brazil
- Genetics and Molecular Biology Master’s and PhD Program, Federal University of Goias, Avenida Esperança, s/n., Campus Samambaia, Goiânia, GO 74690-900, Brazil
| | - Rafael Carneiro Silva
- Replicon Research Group, Genetics Master’s Program, School of Agrarian and Biological Sciences, Pontifical Catholic University of Goiás, Rua 235, n. 40, Setor Leste Universitário, Goiânia, GO 74605-050, Brazil
| | - Alex Silva da Cruz
- Replicon Research Group, Genetics Master’s Program, School of Agrarian and Biological Sciences, Pontifical Catholic University of Goiás, Rua 235, n. 40, Setor Leste Universitário, Goiânia, GO 74605-050, Brazil
| | - Danilo Conrado Silva
- Replicon Research Group, Genetics Master’s Program, School of Agrarian and Biological Sciences, Pontifical Catholic University of Goiás, Rua 235, n. 40, Setor Leste Universitário, Goiânia, GO 74605-050, Brazil
| | - Claudio Carlos da Silva
- PhD Program in Biotechnology and Biodiversity, Federal University of Goiás, Rede Centro Oeste de Pós-Graduação de Pesquisa e Inovação, Rua 235, n. 40, Setor Leste Universitário, Goiânia, GO 74605-050, Brazil
- Replicon Research Group, Genetics Master’s Program, School of Agrarian and Biological Sciences, Pontifical Catholic University of Goiás, Rua 235, n. 40, Setor Leste Universitário, Goiânia, GO 74605-050, Brazil
- Human Cytogenetics and Molecular Genetics Laboratory, Health Secretary of Goias State Goiânia, GO, Brazil
- State University of Goiás, Campus Eseffego, Goiânia, GO, Brazil
| | - Aparecido Divino da Cruz
- PhD Program in Biotechnology and Biodiversity, Federal University of Goiás, Rede Centro Oeste de Pós-Graduação de Pesquisa e Inovação, Rua 235, n. 40, Setor Leste Universitário, Goiânia, GO 74605-050, Brazil
- Replicon Research Group, Genetics Master’s Program, School of Agrarian and Biological Sciences, Pontifical Catholic University of Goiás, Rua 235, n. 40, Setor Leste Universitário, Goiânia, GO 74605-050, Brazil
- Genetics and Molecular Biology Master’s and PhD Program, Federal University of Goias, Avenida Esperança, s/n., Campus Samambaia, Goiânia, GO 74690-900, Brazil
- Human Cytogenetics and Molecular Genetics Laboratory, Health Secretary of Goias State Goiânia, GO, Brazil
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22
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Pinto BJ, Titus-McQuillan J, Daza JD, Gamble T. Persistence of a Geographically-Stable Hybrid Zone in Puerto Rican Dwarf Geckos. J Hered 2019; 110:523-534. [PMID: 30859222 DOI: 10.1093/jhered/esz015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 03/08/2019] [Indexed: 12/14/2022] Open
Abstract
Determining the mechanisms that create and maintain biodiversity is a central question in ecology and evolution. Speciation is the process that creates biodiversity. Speciation is mediated by incompatibilities that lead to reproductive isolation between divergent populations and these incompatibilities can be observed in hybrid zones. Gecko lizards are a speciose clade possessing an impressive diversity of behavioral and morphological traits. In geckos, however, our understanding of the speciation process is negligible. To address this gap, we used genetic sequence data (both mitochondrial and nuclear markers) to revisit a putative hybrid zone between Sphaerodactylus nicholsi and Sphaerodactylus townsendi in Puerto Rico, initially described in 1984. First, we addressed discrepancies in the literature on the validity of both species. Second, we sampled a 10-km-wide transect across the putative hybrid zone and tested explicit predictions about its dynamics using cline models. Third, we investigated potential causes for the hybrid zone using species distribution modeling and simulations; namely, whether unique climatic variables within the hybrid zone might elicit selection for intermediate phenotypes. We find strong support for the species-level status of each species and no evidence of movement, or unique climatic variables near the hybrid zone. We suggest that this narrow hybrid zone is geographically stable and is maintained by a combination of dispersal and selection. Thus, this work has identified an extant model system within geckos that that can be used for future investigations detailing genetic mechanisms of reproductive isolation in an understudied vertebrate group.
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Affiliation(s)
- Brendan J Pinto
- Department of Biological Sciences, Marquette University, Milwaukee, WI
| | | | - Juan D Daza
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX
| | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, WI.,Bell Museum of Natural History, University of Minnesota, Saint Paul, MN.,Milwaukee Public Museum, Milwaukee, WI
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23
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Nascimento J, Lima JD, Suárez P, Baldo D, Andrade GV, Pierson TW, Fitzpatrick BM, Haddad CFB, Recco-Pimentel SM, Lourenço LB. Extensive Cryptic Diversity Within the Physalaemus cuvieri- Physalaemus ephippifer Species Complex (Amphibia, Anura) Revealed by Cytogenetic, Mitochondrial, and Genomic Markers. Front Genet 2019; 10:719. [PMID: 31475033 PMCID: PMC6702337 DOI: 10.3389/fgene.2019.00719] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 07/09/2019] [Indexed: 01/03/2023] Open
Abstract
Previous cytogenetic and phylogenetic analyses showed a high variability in the frog taxa Physalaemus cuvieri and Physalaemus ephippifer and suggested the presence of undescribed diversity in this species complex. Here, by 1) adding specimens from the Brazilian Amazon region, 2) employing sequence-based species delimitation approaches, and 3) including RADseq-style markers, we demonstrate that the diversity in the P. cuvieri-P. ephippifer species complex is even greater than previously suspected. Specimens from Viruá and Western Pará, located at the Guiana Amazonian area of endemism, were recovered as distinct from all previously identified lineages by the phylogenetic analyses based on mitochondrial DNA and RAD markers, a PCA from RAD data, and cytogenetic analysis. The sequence-based species delimitation analyses supported the recognition of one or two undescribed species among these Amazonian specimens and also supported the recognition of at least three other species in the P. cuvieri-P. ephippifer species complex. These new results reinforce the need for a comprehensive taxonomic revision.
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Affiliation(s)
- Juliana Nascimento
- Laboratório de Estudos Cromossômicos (LabEsC), Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas, São Paulo, Brazil
| | - Jucivaldo D. Lima
- Núcleo de Biodiversidade (NUBIO), Instituto de Pesquisas Científicas e Tecnológicas do Estado do Amapá, Zoologia, Campus da Fazendinha, Macapá, Brazil
| | - Pablo Suárez
- Instituto de Biología Subtropical (CONICET-UNaM), Puerto Iguazú, Argentina
| | - Diego Baldo
- Laboratorio de Genética Evolutiva, Instituto de Biología Subtropical (CONICET-UNaM), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Posadas, Argentina
| | - Gilda V. Andrade
- Departamento de Biologia, Centro de Ciências Biológicas e da Saúde, Universidade Federal do Maranhão-UFMA, São Luís, Brazil
| | - Todd W. Pierson
- Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville, TN, United States
| | - Benjamin M. Fitzpatrick
- Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville, TN, United States
| | - Célio F. B. Haddad
- Departamento de Zoologia and Centro de Aquicultura (CAUNESP), Instituto de Biociências, Universidade Estadual Paulista, São Paulo, Brazil
| | - Shirlei M. Recco-Pimentel
- Laboratório de Estudos Cromossômicos (LabEsC), Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas, São Paulo, Brazil
| | - Luciana Bolsoni Lourenço
- Laboratório de Estudos Cromossômicos (LabEsC), Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas, São Paulo, Brazil
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24
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Carabajal Paladino LZ, Provazníková I, Berger M, Bass C, Aratchige NS, López SN, Marec F, Nguyen P. Sex Chromosome Turnover in Moths of the Diverse Superfamily Gelechioidea. Genome Biol Evol 2019; 11:1307-1319. [PMID: 31028711 PMCID: PMC6486803 DOI: 10.1093/gbe/evz075] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2019] [Indexed: 01/22/2023] Open
Abstract
Sex chromosomes play a central role in genetics of speciation and their turnover was suggested to promote divergence. In vertebrates, sex chromosome-autosome fusions resulting in neo-sex chromosomes occur frequently in male heterogametic taxa (XX/XY), but are rare in groups with female heterogamety (WZ/ZZ). We examined sex chromosomes of seven pests of the diverse lepidopteran superfamily Gelechioidea and confirmed the presence of neo-sex chromosomes in their karyotypes. Two synteny blocks, which correspond to autosomes 7 (LG7) and 27 (LG27) in the ancestral lepidopteran karyotype exemplified by the linkage map of Biston betularia (Geometridae), were identified as sex-linked in the tomato leafminer, Tuta absoluta (Gelechiidae). Testing for sex-linkage performed in other species revealed that while LG7 fused to sex chromosomes in a common ancestor of all Gelechioidea, the second fusion between the resulting neo-sex chromosome and the other autosome is confined to the tribe Gnoreschemini (Gelechiinae). Our data accentuate an emerging pattern of high incidence of neo-sex chromosomes in Lepidoptera, the largest clade with WZ/ZZ sex chromosome system, which suggest that the paucity of neo-sex chromosomes is not an intrinsic feature of female heterogamety. Furthermore, LG7 contains one of the major clusters of UDP-glucosyltransferases, which are involved in the detoxification of plant secondary metabolites. Sex chromosome evolution in Gelechioidea thus supports an earlier hypothesis postulating that lepidopteran sex chromosome-autosome fusions can be driven by selection for association of Z-linked preference or host-independent isolation genes with larval performance and thus can contribute to ecological specialization and speciation of moths.
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Affiliation(s)
- Leonela Z Carabajal Paladino
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
- The Pirbright Institute, Surrey, United Kingdom
| | - Irena Provazníková
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
- University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic
| | - Madeleine Berger
- Rothamsted Research, Department of Biointeractions and Crop Protection, Herts, United Kingdom
| | - Chris Bass
- University of Exeter, College of Life and Environmental Sciences, Biosciences, Penryn, Cornwall, United Kingdom
| | - Nayanie S Aratchige
- Coconut Research Institute of Sri Lanka, Crop Protection Division, Bandirippuwa Estate, Lunuwila, Sri Lanka
| | - Silvia N López
- Instituto Nacional de Tecnología Agropecuaria, Instituto de Microbiología y Zoología Agrícola, Hurlingham, Buenos Aires, Argentina
| | - František Marec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
| | - Petr Nguyen
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
- University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic
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25
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Danzmann RG, Norman JD, Rondeau EB, Messmer AM, Kent MP, Lien S, Igboeli O, Fast MD, Koop BF. A genetic linkage map for the salmon louse (Lepeophtheirus salmonis): evidence for high male:female and inter-familial recombination rate differences. Mol Genet Genomics 2018; 294:343-363. [PMID: 30460550 DOI: 10.1007/s00438-018-1513-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 10/15/2018] [Indexed: 01/28/2023]
Abstract
A salmon louse (Lepeophtheirus salmonis salmonis) genetic linkage map was constructed to serve as a genomic resource for future investigations into the biology of this important marine parasitic copepod species, and to provide insights into the inheritance patterns of genetic markers in this species. SNP genotyping of 8 families confirmed the presence of 15 linkage groups based upon the assignment of 93,773 markers. Progeny sample size weight adjusted map sizes in males (with the exception of SL12 and SL15) ranged in size from 96.50 cM (SL11) to 134.61 cM (SL06), and total combined map steps or bins ranged from 143 (SL09) to 203 (SL13). The SL12 male map was the smallest linkage group with a weight-averaged size of 3.05 cM with 6 recombination bins. Male:female specific recombination rate differences are 10.49:1 and represent one of the largest reported sex-specific differences for any animal species. Recombination ratio differences (M:F) ranged from 1.0 (SL12) to 29:1 (SL15). The number of markers exhibiting normal Mendelian segregation within the sex linkage group SL15 was extremely low (N = 80) in comparison to other linkage groups genotyped [range: 1459 (SL12)-10206 markers (SL05)]. Re-evaluation of Mendelian inheritance patterns of markers unassigned to any mapping parent according to hemizygous segregation patterns (models presented) identified matches for many of these markers to hemizygous patterns. The greatest proportion of these markers assigned to SL15 (N increased to 574). Inclusion of the hemizygous markers revised SL15 sex-specific recombination rate differences to 28:1. Recombination hot- and coldspots were identified across all linkage groups with all linkage groups possessing multiple peaks. Nine of 13 linkage groups evaluated possessed adjacent domains with hot-coldspot transitional zones. The most common pattern was for one end of the linkage to show elevated recombination in addition to internal regions. For SL01 and SL06, however, a terminal region with high recombination was not evident while a central domain possessing extremely high-recombination levels was present. High levels of recombination were weakly coupled to higher levels of SNP variation within domains, but this association was very strong for the central domains of SL01 and SL06. From the pooled paternal half-sib lots (several virgin females placed with 1 male), only 1 or two surviving family lots were obtained. Surviving families possessed parents where both the male and female possessed either inherently low or high recombination rates. This study provides insight into the organization of the sea louse genome, and describes large differences in recombination rate that exist among individuals of the same sex, and between the sexes. These differences in recombination rate may be coupled to the capabilities of this species to adapt to environmental and pharmaceutical treatments, given that family survivorship appears to be enhanced when parents have similar recombination levels.
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Affiliation(s)
- Roy G Danzmann
- Department of Integrative Biology, College of Biological Sciences, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.
| | - Joseph D Norman
- Department of Integrative Biology, College of Biological Sciences, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.,The Hospital for Sick Children, 686 Bay St., Toronto, ON, M5G 0A4, Canada
| | - Eric B Rondeau
- Department of Biology, Centre for Biomedical Research, University of Victoria, 3800 Finnerty Road, Victoria, BC, V8W 3N5, Canada
| | - Amber M Messmer
- Department of Biology, Centre for Biomedical Research, University of Victoria, 3800 Finnerty Road, Victoria, BC, V8W 3N5, Canada
| | - Matthew P Kent
- Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences, 1432, As, Norway
| | - Sigbjørn Lien
- Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences, 1432, As, Norway
| | - Okechukwu Igboeli
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave., Charlottetown, PEI, C1A 4P3, Canada
| | - Mark D Fast
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave., Charlottetown, PEI, C1A 4P3, Canada
| | - Ben F Koop
- Department of Biology, Centre for Biomedical Research, University of Victoria, 3800 Finnerty Road, Victoria, BC, V8W 3N5, Canada
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26
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Gerchen JF, Dufresnes C, Stöck M. Introgression across Hybrid Zones Is Not Mediated by Large X-Effects in Green Toads with Undifferentiated Sex Chromosomes. Am Nat 2018; 192:E178-E188. [DOI: 10.1086/699162] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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27
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Janoušek V, Fischerová J, Mořkovský L, Reif J, Antczak M, Albrecht T, Reifová R. Postcopulatory sexual selection reduces Z-linked genetic variation and might contribute to the large Z effect in passerine birds. Heredity (Edinb) 2018; 122:622-635. [PMID: 30374041 DOI: 10.1038/s41437-018-0161-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/20/2018] [Accepted: 10/12/2018] [Indexed: 12/19/2022] Open
Abstract
The X and Z sex chromosomes play a disproportionately large role in intrinsic postzygotic isolation. The underlying mechanisms of this large X/Z effect are, however, still poorly understood. Here we tested whether faster rates of molecular evolution caused by more intense positive selection or genetic drift on the Z chromosome could contribute to the large Z effect in two closely related passerine birds, the Common Nightingale (Luscinia megarhynchos) and the Thrush Nightingale (L. luscinia). We found that the two species differ in patterns of molecular evolution on the Z chromosome. The Z chromosome of L. megarhynchos showed lower levels of within-species polymorphism and an excess of non-synonymous polymorphisms relative to non-synonymous substitutions. This is consistent with increased levels of genetic drift on this chromosome and may be attributed to more intense postcopulatory sexual selection acting on L. megarhynchos males as was indicated by significantly longer sperm and higher between-male variation in sperm length in L. megarhynchos compared to L. luscinia. Interestingly, analysis of interspecific gene flow on the Z chromosome revealed relatively lower levels of introgression from L. megarhynchos to L. luscinia than vice versa, indicating that the Z chromosome of L. megarhynchos accumulated more hybrid incompatibilities. Our results are consistent with the view that postcopulatory sexual selection may reduce the effective population size of the Z chromosome and thus lead to stronger genetic drift on this chromosome in birds. This can result in relatively faster accumulation of hybrid incompatibilities on the Z and thus contribute to the large Z effect.
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Affiliation(s)
- Václav Janoušek
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, Prague 2, 128 00, Czech Republic
| | - Jitka Fischerová
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, Prague 2, 128 00, Czech Republic
| | - Libor Mořkovský
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, Prague 2, 128 00, Czech Republic
| | - Jiří Reif
- Institute for Environmental Studies, Faculty of Science, Charles University, Benátská 2, Prague 2, 128 01, Czech Republic
| | - Marcin Antczak
- Department of Behavioural Ecology, Adam Mickiewicz University, Umultowska 89, Poznań, 61-614, Poland
| | - Tomáš Albrecht
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, Prague 2, 128 00, Czech Republic.,Institute of Vertebrate Biology, The Czech Academy of Sciences, Květná 8, Brno, 603 65, Czech Republic
| | - Radka Reifová
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, Prague 2, 128 00, Czech Republic.
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28
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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: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [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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29
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Barreto FS, Watson ET, Lima TG, Willett CS, Edmands S, Li W, Burton RS. Genomic signatures of mitonuclear coevolution across populations of Tigriopus californicus. Nat Ecol Evol 2018; 2:1250-1257. [DOI: 10.1038/s41559-018-0588-1] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Accepted: 05/21/2018] [Indexed: 12/19/2022]
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30
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Campbell CR, Poelstra JW, Yoder AD. What is Speciation Genomics? The roles of ecology, gene flow, and genomic architecture in the formation of species. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly063] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
| | - J W Poelstra
- Department of Biology, Duke University, Durham, NC, USA
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC, USA
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31
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Filatov DA. The two "rules of speciation" in species with young sex chromosomes. Mol Ecol 2018; 27:3799-3810. [PMID: 29781541 DOI: 10.1111/mec.14721] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 04/24/2018] [Accepted: 05/02/2018] [Indexed: 01/17/2023]
Abstract
The two "rules of speciation," Haldane's rule (HR) and the large-X effect (LXE), are thought to be caused by recessive species incompatibilities exposed in the phenotype due to the hemizygosity of X-linked genes in the heterogametic sex. Thus, the reports of HR and the LXE in species with recently evolved non- or partially degenerate Y-chromosomes, such as Silene latifolia and its relatives, were surprising. Here, I argue that rapid species-specific degeneration of Y-linked genes and associated adjustment of expression of X-linked gametologs (dosage compensation) may lead to rapid evolution of sex-linked species incompatibilities. This process is likely to be too slow in species with old degenerate Y-chromosomes (e.g., in mammals), but Y-degeneration in species with young gene-rich sex chromosomes may be fast enough to play a significant role in speciation. To illustrate this point, I report the analysis of Y-degeneration and the associated evolution of gene expression on the X-chromosome of S. latifolia and Silene dioica, a close relative that shares the same recently evolved sex chromosomes. Despite the recent (≤1MY) divergence of the two species, ~7% of Y-linked genes have undergone degeneration in one but not the other species. This species-specific degeneration appears to drive faster expression divergence of X-linked genes, which may account for HR and the LXE reported for these species. Furthermore, I suggest that "exposure" of autosomal or sex-linked recessive species incompatibilities in the haploid plant gametophyte may mimic the presence of HR in plants. Both haploid expression and species-specific Y-degeneration need to receive more attention if we are to understand the role of these processes in speciation.
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32
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Ghenu AH, Blanckaert A, Butlin RK, Kulmuni J, Bank C. Conflict between heterozygote advantage and hybrid incompatibility in haplodiploids (and sex chromosomes). Mol Ecol 2018; 27:3935-3949. [PMID: 29328538 DOI: 10.1111/mec.14482] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 12/19/2017] [Accepted: 12/22/2017] [Indexed: 01/08/2023]
Abstract
In many diploid species, the sex chromosomes play a special role in mediating reproductive isolation. In haplodiploids, where females are diploid and males haploid, the whole genome behaves similarly to the X/Z chromosomes of diploids. Therefore, haplodiploid systems can serve as a model for the role of sex chromosomes in speciation and hybridization. A previously described population of Finnish Formica wood ants displays genome-wide signs of ploidally and sexually antagonistic selection resulting from hybridization. Here, hybrid females have increased survivorship but hybrid males are inviable. To understand how the unusual hybrid population may be maintained, we developed a mathematical model with hybrid incompatibility, female heterozygote advantage, recombination and assortative mating. The rugged fitness landscape resulting from the co-occurrence of heterozygote advantage and hybrid incompatibility results in a sexual conflict in haplodiploids, which is caused by the ploidy difference. Thus, whereas heterozygote advantage always promotes long-term polymorphism in diploids, we find various outcomes in haplodiploids in which the population stabilizes either in favour of males, females or via maximizing the number of introgressed individuals. We discuss these outcomes with respect to the potential long-term fate of the Finnish wood ant population and provide approximations for the extension of the model to multiple incompatibilities. Moreover, we highlight the general implications of our results for speciation and hybridization in haplodiploids versus diploids and how the described fitness relationships could contribute to the outstanding role of sex chromosomes as hotspots of sexual antagonism and genes involved in speciation.
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Affiliation(s)
| | | | - Roger K Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Jonna Kulmuni
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Claudia Bank
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.,Kavli Institute for Theoretical Physics, University of California at Santa Barbara, Santa Barbara, CA, USA
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33
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Fraïsse C, Gunnarsson PA, Roze D, Bierne N, Welch JJ. The genetics of speciation: Insights from Fisher's geometric model. Evolution 2016; 70:1450-64. [PMID: 27252049 DOI: 10.1111/evo.12968] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 05/22/2016] [Indexed: 12/13/2022]
Abstract
Research in speciation genetics has uncovered many robust patterns in intrinsic reproductive isolation, and fitness landscape models have been useful in interpreting these patterns. Here, we examine fitness landscapes based on Fisher's geometric model. Such landscapes are analogous to models of optimizing selection acting on quantitative traits, and have been widely used to study adaptation and the distribution of mutational effects. We show that, with a few modifications, Fisher's model can generate all of the major findings of introgression studies (including "speciation genes" with strong deleterious effects, complex epistasis and asymmetry), and the major patterns in overall hybrid fitnesses (including Haldane's Rule, the speciation clock, heterosis, hybrid breakdown, and male-female asymmetry in the F1). We compare our approach to alternative modeling frameworks that assign fitnesses to genotypes by identifying combinations of incompatible alleles. In some cases, the predictions are importantly different. For example, Fisher's model can explain conflicting empirical results about the rate at which incompatibilities accumulate with genetic divergence. In other cases, the predictions are identical. For example, the quality of reproductive isolation is little affected by the manner in which populations diverge.
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Affiliation(s)
- Christelle Fraïsse
- Université Montpellier, Institut des Sciences de l'Évolution, UMR 5554, Montpellier Cedex 05, France.,CNRS, Institut des Sciences de l'Évolution, UMR 5554, OREME Station Marine, Sète, France.,Department of Genetics, University of Cambridge, Downing Street, Cambridge, United Kingdom
| | - P Alexander Gunnarsson
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, United Kingdom
| | - Denis Roze
- CNRS, UMI 3614, Evolutionary Biology and Ecology of Algae, Roscoff, France.,Sorbonne Universités, UPMC University Paris VI, Roscoff, France
| | - Nicolas Bierne
- Université Montpellier, Institut des Sciences de l'Évolution, UMR 5554, Montpellier Cedex 05, France.,CNRS, Institut des Sciences de l'Évolution, UMR 5554, OREME Station Marine, Sète, France
| | - John J Welch
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, United Kingdom.
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34
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Payseur BA, Rieseberg LH. A genomic perspective on hybridization and speciation. Mol Ecol 2016; 25:2337-60. [PMID: 26836441 PMCID: PMC4915564 DOI: 10.1111/mec.13557] [Citation(s) in RCA: 292] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 01/18/2016] [Accepted: 01/25/2016] [Indexed: 12/13/2022]
Abstract
Hybridization among diverging lineages is common in nature. Genomic data provide a special opportunity to characterize the history of hybridization and the genetic basis of speciation. We review existing methods and empirical studies to identify recent advances in the genomics of hybridization, as well as issues that need to be addressed. Notable progress has been made in the development of methods for detecting hybridization and inferring individual ancestries. However, few approaches reconstruct the magnitude and timing of gene flow, estimate the fitness of hybrids or incorporate knowledge of recombination rate. Empirical studies indicate that the genomic consequences of hybridization are complex, including a highly heterogeneous landscape of differentiation. Inferred characteristics of hybridization differ substantially among species groups. Loci showing unusual patterns - which may contribute to reproductive barriers - are usually scattered throughout the genome, with potential enrichment in sex chromosomes and regions of reduced recombination. We caution against the growing trend of interpreting genomic variation in summary statistics across genomes as evidence of differential gene flow. We argue that converting genomic patterns into useful inferences about hybridization will ultimately require models and methods that directly incorporate key ingredients of speciation, including the dynamic nature of gene flow, selection acting in hybrid populations and recombination rate variation.
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Affiliation(s)
- Bret A. Payseur
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Loren H. Rieseberg
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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35
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Willett CS, Lima TG, Kovaleva I, Hatfield L. Chromosome-Wide Impacts on the Expression of Incompatibilities in Hybrids of Tigriopus californicus. G3 (BETHESDA, MD.) 2016; 6:1739-49. [PMID: 27172190 PMCID: PMC4889669 DOI: 10.1534/g3.116.028050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 04/06/2016] [Indexed: 11/18/2022]
Abstract
Chromosome rearrangements such as inversions have been recognized previously as contributing to reproductive isolation by maintaining alleles together that jointly contribute to deleterious genetic interactions and postzygotic reproductive isolation. In this study, an impact of potential incompatibilities merely residing on the same chromosome was found in crosses of populations of the copepod Tigriopus californicus When genetically divergent populations of this copepod are crossed, hybrids show reduced fitness, and deviations from expected genotypic ratios can be used to determine regions of the genome involved in deleterious interactions. In this study, a set of markers was genotyped for a cross of two populations of T. californicus, and these markers show widespread deviations from Mendelian expectations, with entire chromosomes showing marked skew. Despite the importance of mtDNA/nuclear interactions in incompatibilities in this system in previous studies, in these crosses the expected patterns stemming from these interactions are not widely apparent. Females lack recombination in this species, and a striking difference is observed between male and female backcrosses. This suggests that the maintenance of multiple loci on individual chromosomes can enable some incompatibilities, perhaps playing a similar role in the initial rounds of hybridization to chromosomal rearrangements in preserving sets of alleles together that contribute to incompatibilities. Finally, it was observed that candidate pairs of incompatibility regions are not consistently interacting across replicates or subsets of these crosses, despite the repeatability of the deviations at many of the single loci themselves, suggesting that more complicated models of Dobzhansky-Muller incompatibilities may need to be considered.
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Affiliation(s)
- Christopher S Willett
- Department of Biology, University of North Carolina at Chapel Hill, North Carolina 27599-3280
| | - Thiago G Lima
- Department of Biology, University of North Carolina at Chapel Hill, North Carolina 27599-3280
| | - Inna Kovaleva
- Department of Biology, University of North Carolina at Chapel Hill, North Carolina 27599-3280
| | - Lydia Hatfield
- Department of Biology, University of North Carolina at Chapel Hill, North Carolina 27599-3280
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Pereira RJ, Barreto FS, Pierce NT, Carneiro M, Burton RS. Transcriptome-wide patterns of divergence during allopatric evolution. Mol Ecol 2016; 25:1478-93. [DOI: 10.1111/mec.13579] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 12/03/2015] [Accepted: 01/06/2016] [Indexed: 01/22/2023]
Affiliation(s)
- Ricardo J. Pereira
- Marine Biology Research Division; Scripps Institution of Oceanography; University of California, San Diego; La Jolla CA 92093-0202 USA
- Centre for GeoGenetics; Natural History Museum of Denmark; University of Copenhagen; Øster Voldgade 5-7 1350 Copenhagen Denmark
| | - Felipe S. Barreto
- Marine Biology Research Division; Scripps Institution of Oceanography; University of California, San Diego; La Jolla CA 92093-0202 USA
- Department of Integrative Biology; Oregon State University; Corvallis OR 97331 USA
| | - N. Tessa Pierce
- Marine Biology Research Division; Scripps Institution of Oceanography; University of California, San Diego; La Jolla CA 92093-0202 USA
| | - Miguel Carneiro
- CIBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos; Campus Agrário de Vairão 4485-661 Vairão Portugal
| | - Ronald S. Burton
- Marine Biology Research Division; Scripps Institution of Oceanography; University of California, San Diego; La Jolla CA 92093-0202 USA
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37
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Empirical evidence for large X-effects in animals with undifferentiated sex chromosomes. Sci Rep 2016; 6:21029. [PMID: 26868373 PMCID: PMC4751523 DOI: 10.1038/srep21029] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 01/15/2016] [Indexed: 02/03/2023] Open
Abstract
Reproductive isolation is crucial for the process of speciation to progress. Sex chromosomes have been assigned a key role in driving reproductive isolation but empirical evidence from natural population processes has been restricted to organisms with degenerated sex chromosomes such as mammals and birds. Here we report restricted introgression at sex-linked compared to autosomal markers in a hybrid zone between two incipient species of European tree frog, Hyla arborea and H. orientalis, whose homologous X and Y sex chromosomes are undifferentiated. This large X-effect cannot result from the dominance or faster-X aspects of Haldane's rule, which are specific to degenerated sex chromosomes, but rather supports a role for faster-heterogametic-sex or faster-male evolutionary processes. Our data suggest a prominent contribution of undifferentiated sex chromosomes to speciation.
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