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Satomura K, Tamura K. Ancient Male Recombination Shaped Genetic Diversity of Neo-Y Chromosome inDrosophila albomicans. Mol Biol Evol 2015; 33:367-74. [DOI: 10.1093/molbev/msv221] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 10/10/2015] [Indexed: 12/29/2022] Open
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2
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Dufresnes C, Brelsford A, Béziers P, Perrin N. Stronger transferability but lower variability in transcriptomic- than in anonymous microsatellites: evidence from Hylid frogs. Mol Ecol Resour 2014; 14:716-25. [PMID: 24345298 DOI: 10.1111/1755-0998.12215] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 12/03/2013] [Accepted: 12/11/2013] [Indexed: 11/28/2022]
Abstract
A simple way to quickly optimize microsatellites in nonmodel organisms is to reuse loci available in closely related taxa; however, this approach can be limited by the stochastic and low cross-amplification success experienced in some groups (e.g. amphibians). An efficient alternative is to develop loci from transcriptome sequences. Transcriptomic microsatellites have been found to vary in their levels of cross-species amplification and variability, but this has to date never been tested in amphibians. Here, we compare the patterns of cross-amplification and levels of polymorphism of 18 published anonymous microsatellites isolated from genomic DNA vs. 17 loci derived from a transcriptome, across nine species of tree frogs (Hyla arborea and Hyla cinerea group). We established a clear negative relationship between divergence time and amplification success, which was much steeper for anonymous than transcriptomic markers, with half-lives (time at which 50% of the markers still amplify) of 1.1 and 37 My, respectively. Transcriptomic markers are significantly less polymorphic than anonymous loci, but remain variable across diverged taxa. We conclude that the exploitation of amphibian transcriptomes for developing microsatellites seems an optimal approach for multispecies surveys (e.g. analyses of hybrid zones, comparative linkage mapping), whereas anonymous microsatellites may be more informative for fine-scale analyses of intraspecific variation. Moreover, our results confirm the pattern that microsatellite cross-amplification is greatly variable among amphibians and should be assessed independently within target lineages. Finally, we provide a bank of microsatellites for Palaearctic tree frogs (so far only available for H. arborea), which will be useful for conservation and evolutionary studies in this radiation.
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Affiliation(s)
- Christophe Dufresnes
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, Lausanne , 1015, Switzerland
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3
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Berset-Brändli L, Jaquiéry J, Broquet T, Perrin N. Isolation and characterization of microsatellite loci for the European tree frog (Hyla arborea). Mol Ecol Resour 2013; 8:1095-7. [PMID: 21585982 DOI: 10.1111/j.1755-0998.2008.02189.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We developed 11 new microsatellite markers for the European tree frog (Hyla arborea), and tested patterns of polymorphism in 54 adults (27 males and 27 females) from two ponds close to Lausanne (Western Switzerland). One marker was sex linked and two pairs displayed linkage disequilibrium. Comparisons of allele numbers with heterozygosity values support a stepwise-mutation model at neutral equilibrium, with mutation rates spanning nearly two orders of magnitude. These markers will prove useful for population genetic studies and fine-scale investigations requiring genetic assignment techniques.
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Affiliation(s)
- L Berset-Brändli
- Department of Ecology and Evolution University of Lausanne, CH 1015 Lausanne, Switzerland
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4
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Guerrero RF, Kirkpatrick M, Perrin N. Cryptic recombination in the ever‐young sex chromosomes of
H
ylid frogs. J Evol Biol 2012; 25:1947-1954. [DOI: 10.1111/j.1420-9101.2012.02591.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2012] [Revised: 06/22/2012] [Accepted: 07/09/2012] [Indexed: 11/29/2022]
Affiliation(s)
- R. F. Guerrero
- Section of Integrative Biology The University of Texas at Austin Austin TX USA
| | - M. Kirkpatrick
- Section of Integrative Biology The University of Texas at Austin Austin TX USA
| | - N. Perrin
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
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5
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Grossen C, Neuenschwander S, Perrin N. The evolution of XY recombination: sexually antagonistic selection versus deleterious mutation load. Evolution 2012; 66:3155-66. [PMID: 23025605 DOI: 10.1111/j.1558-5646.2012.01661.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recombination arrest between X and Y chromosomes, driven by sexually antagonistic genes, is expected to induce their progressive differentiation. However, in contrast to birds and mammals (which display the predicted pattern), most cold-blooded vertebrates have homomorphic sex chromosomes. Two main hypotheses have been proposed to account for this, namely high turnover rates of sex-determining systems and occasional XY recombination. Using individual-based simulations, we formalize the evolution of XY recombination (here mediated by sex reversal; the "fountain-of-youth" model) under the contrasting forces of sexually antagonistic selection and deleterious mutations. The shift between the domains of elimination and accumulation occurs at much lower selection coefficients for the Y than for the X. In the absence of dosage compensation, mildly deleterious mutations accumulating on the Y depress male fitness, thereby providing incentives for XY recombination. Under our settings, this occurs via "demasculinization" of the Y, allowing recombination in XY (sex-reversed) females. As we also show, this generates a conflict with the X, which coevolves to oppose sex reversal. The resulting rare events of XY sex reversal are enough to purge the Y from its load of deleterious mutations. Our results support the "fountain of youth" as a plausible mechanism to account for the maintenance of sex-chromosome homomorphy.
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Affiliation(s)
- Christine Grossen
- Department of Ecology & Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland.
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6
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Jaquiéry J, Stoeckel S, Rispe C, Mieuzet L, Legeai F, Simon JC. Accelerated evolution of sex chromosomes in aphids, an x0 system. Mol Biol Evol 2011; 29:837-47. [PMID: 21998277 DOI: 10.1093/molbev/msr252] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Sex chromosomes play a role in many important biological processes, including sex determination, genomic conflicts, imprinting, and speciation. In particular, they exhibit several unusual properties such as inheritance pattern, hemizygosity, and reduced recombination, which influence their response to evolutionary factors (e.g., drift, selection, and demography). Here, we examine the evolutionary forces driving X chromosome evolution in aphids, an XO system where females are homozygous (XX) and males are hemizygous (X0) at sex chromosomes. We show by simulations that the unusual mode of transmission of the X chromosome in aphids, coupled with cyclical parthenogenesis, results in similar effective population sizes and predicted levels of genetic diversity for X chromosomes and autosomes under neutral evolution. These results contrast with expectations from standard XX/XY or XX/X0 systems (where the effective population size of the X is three-fourths that of autosomes) and have deep consequences for aphid X chromosome evolution. We then localized 52 microsatellite markers on the X and 351 on autosomes. We genotyped 167 individuals with 356 of these loci and found similar levels of allelic richness on the X and on the autosomes, as predicted by our simulations. In contrast, we detected higher dN and dN/dS ratio for X-linked genes compared with autosomal genes, a pattern compatible with either positive or relaxed selection. Given that both types of chromosomes have similar effective population sizes and that the single copy of the X chromosome of male aphids exposes its recessive genes to selection, some degree of positive selection seems to best explain the higher rates of evolution of X-linked genes. Overall, this study highlights the particular relevance of aphids to study the evolutionary factors driving sex chromosomes and genome evolution.
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Affiliation(s)
- Julie Jaquiéry
- Institut National de Recherche Agronomique (INRA), Unité Mixte de Recherche 1099, Biology of Organisms and Populations Applied to Plant Protection, Le Rheu, France.
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7
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Stöck M, Horn A, Grossen C, Lindtke D, Sermier R, Betto-Colliard C, Dufresnes C, Bonjour E, Dumas Z, Luquet E, Maddalena T, Sousa HC, Martinez-Solano I, Perrin N. Ever-young sex chromosomes in European tree frogs. PLoS Biol 2011; 9:e1001062. [PMID: 21629756 PMCID: PMC3100596 DOI: 10.1371/journal.pbio.1001062] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Accepted: 04/06/2011] [Indexed: 11/23/2022] Open
Abstract
Non-recombining sex chromosomes are expected to undergo evolutionary decay,
ending up genetically degenerated, as has happened in birds and mammals. Why are
then sex chromosomes so often homomorphic in cold-blooded vertebrates? One
possible explanation is a high rate of turnover events, replacing master
sex-determining genes by new ones on other chromosomes. An alternative is that
X-Y similarity is maintained by occasional recombination events, occurring in
sex-reversed XY females. Based on mitochondrial and nuclear gene sequences, we
estimated the divergence times between European tree frogs (Hyla
arborea, H. intermedia, and H.
molleri) to the upper Miocene, about 5.4–7.1 million years
ago. Sibship analyses of microsatellite polymorphisms revealed that all three
species have the same pair of sex chromosomes, with complete absence of X-Y
recombination in males. Despite this, sequences of sex-linked loci show no
divergence between the X and Y chromosomes. In the phylogeny, the X and Y
alleles cluster according to species, not in groups of gametologs. We conclude
that sex-chromosome homomorphy in these tree frogs does not result from a recent
turnover but is maintained over evolutionary timescales by occasional X-Y
recombination. Seemingly young sex chromosomes may thus carry old-established
sex-determining genes, a result at odds with the view that sex chromosomes
necessarily decay until they are replaced. This raises intriguing perspectives
regarding the evolutionary dynamics of sexually antagonistic genes and the
mechanisms that control X-Y recombination. Non-recombining sex chromosomes, such as the Y chromosome, are expected to
degenerate over evolutionary times because they accumulate deleterious mutations
that cannot be corrected by recombination with a pristine copy. In most
cold-blooded vertebrates, such as frogs, however, sex chromosomes are
undifferentiated. Why is that so? On the one hand, the
“high-turnover” hypothesis holds that these sex chromosomes are
regularly replaced before they had time to decay. On the other hand, the
“fountain-of-youth” hypothesis posits that they are regularly
rejuvenated by X-Y recombination in sex-reversed XY females. Here, we show that
three species of tree frogs that diverged more than 5.4 million years ago share
the same pair of undifferentiated sex chromosomes. Although male recombination
stopped before species divergence, X and Y alleles show no differentiation, and
cluster by species, not gametologs. We conclude that their sex chromosome
homomorphy is not due to a recent turnover but is maintained over long
evolutionary times by occasional recombination. Such rare episodes of X-Y
recombination are expected to have long-lasting consequences on the evolution of
sex chromosomes and sex antagonistic genes.
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Affiliation(s)
- Matthias Stöck
- Department of Ecology and Evolution, University of Lausanne, Lausanne,
Switzerland
| | - Agnès Horn
- Department of Ecology and Evolution, University of Lausanne, Lausanne,
Switzerland
| | - Christine Grossen
- Department of Ecology and Evolution, University of Lausanne, Lausanne,
Switzerland
| | - Dorothea Lindtke
- Department of Ecology and Evolution, University of Lausanne, Lausanne,
Switzerland
- Department of Biology, University of Fribourg, Fribourg,
Switzerland
| | - Roberto Sermier
- Department of Ecology and Evolution, University of Lausanne, Lausanne,
Switzerland
| | | | - Christophe Dufresnes
- Department of Ecology and Evolution, University of Lausanne, Lausanne,
Switzerland
| | - Emmanuel Bonjour
- Department of Ecology and Evolution, University of Lausanne, Lausanne,
Switzerland
| | - Zoé Dumas
- Department of Ecology and Evolution, University of Lausanne, Lausanne,
Switzerland
- Umweltmikrobiologie, EAWAG, Dübendorf, Switzerland
| | - Emilien Luquet
- UMR 5023 Ecology of Fluvial Hydrosystems, Bât. Darwin C,
Université Lyon, Villeurbanne, France
| | | | - Helena Clavero Sousa
- Department of Ecology and Evolution, University of Lausanne, Lausanne,
Switzerland
- Perpetuo Socorro, Puerto Santa María (Cádiz),
Spain
| | - Iñigo Martinez-Solano
- Instituto de Investigación en Recursos Cinegéticos
(UCLM-CSIC-JCCM), Ciudad Real, Spain
| | - Nicolas Perrin
- Department of Ecology and Evolution, University of Lausanne, Lausanne,
Switzerland
- * E-mail:
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Dufresnes C, Luquet E, Plenet S, Stöck M, Perrin N. Polymorphism at a Sex-Linked Transcription Cofactor in European Tree Frogs (Hyla arborea): Sex-Antagonistic Selection or Neutral Processes? Evol Biol 2011. [DOI: 10.1007/s11692-011-9114-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Broquet T, Angelone S, Jaquiery J, Joly P, Lena JP, Lengagne T, Plenet S, Luquet E, Perrin N. Genetic bottlenecks driven by population disconnection. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2010; 24:1596-1605. [PMID: 20666803 DOI: 10.1111/j.1523-1739.2010.01556.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Connectivity among populations plays a crucial role in maintaining genetic variation at a local scale, especially in small populations affected strongly by genetic drift. The negative consequences of population disconnection on allelic richness and gene diversity (heterozygosity) are well recognized and empirically established. It is not well recognized, however, that a sudden drop in local effective population size induced by such disconnection produces a temporary disequilibrium in allelic frequency distributions that is akin to the genetic signature of a demographic bottleneck. To document this effect, we used individual-based simulations and empirical data on allelic richness and gene diversity in six pairs of isolated versus well-connected (core) populations of European tree frogs. In our simulations, population disconnection depressed allelic richness more than heterozygosity and thus resulted in a temporary excess in gene diversity relative to mutation drift equilibrium (i.e., signature of a genetic bottleneck). We observed a similar excess in gene diversity in isolated populations of tree frogs. Our results show that population disconnection can create a genetic bottleneck in the absence of demographic collapse.
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Affiliation(s)
- Thomas Broquet
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland.
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11
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Abstract
Sex chromosomes have evolved multiple times in many taxa. The recent explosion in the availability of whole genome sequences from a variety of organisms makes it possible to investigate sex chromosome evolution within and across genomes. Comparative genomic studies have shown that quite distant species may share fundamental properties of sex chromosome evolution, while very similar species can evolve unique sex chromosome systems. Furthermore, within-species genomic analyses can illuminate chromosome-wide sequence and expression polymorphisms. Here, we explore recent advances in the study of vertebrate sex chromosomes achieved using genomic analyses.
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Affiliation(s)
- Melissa A Wilson
- Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
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Broquet T, Jaquiéry J, Perrin N. Opportunity for sexual selection and effective population size in the lek-breeding European treefrog (Hyla arborea). Evolution 2009; 63:674-83. [PMID: 19087183 DOI: 10.1111/j.1558-5646.2008.00586.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Sexual selection in lek-breeding species might drastically lower male effective population size, with potentially important consequences for evolutionary and conservation biology. Using field-monitoring and parental-assignment methods, we analyzed sex-specific variances in breeding success in a population of European treefrogs, to (1) help understanding the dynamics of genetic variance at sex-specific loci, and (2) better quantify the risk posed by genetic drift in this species locally endangered by habitat fragmentation. The variance in male mating success turned out to be markedly lower than values obtained from other amphibian species with polygamous mating systems. The ratio of effective breeding size to census breeding size was only slightly lower in males (0.44) than in females (0.57), in line with the patterns of genetic diversity previously reported from H. arborea sex chromosomes. Combining our results with data on age at maturity and adult survival, we show that the negative effect of the mating system is furthermore compensated by the effect of delayed maturity, so that the estimated instantaneous effective size broadly corresponded to census breeding size. We conclude that the lek-breeding system of treefrogs impacts only weakly the patterns of genetic diversity on sex-linked genes and the ability of natural populations to resist genetic drift.
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Affiliation(s)
- Thomas Broquet
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland.
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Berset-Brändli L, Jaquiéry J, Broquet T, Ulrich Y, Perrin N. Extreme heterochiasmy and nascent sex chromosomes in European tree frogs. Proc Biol Sci 2008; 275:1577-85. [PMID: 18426748 DOI: 10.1098/rspb.2008.0298] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We investigated sex-specific recombination rates in Hyla arborea, a species with nascent sex chromosomes and male heterogamety. Twenty microsatellites were clustered into six linkage groups, all showing suppressed or very low recombination in males. Seven markers were sex linked, none of them showing any sign of recombination in males (r=0.00 versus 0.43 on average in females). This opposes classical models of sex chromosome evolution, which envision an initially small differential segment that progressively expands as structural changes accumulate on the Y chromosome. For autosomes, maps were more than 14 times longer in females than in males, which seems the highest ratio documented so far in vertebrates. These results support the pleiotropic model of Haldane and Huxley, according to which recombination is reduced in the heterogametic sex by general modifiers that affect recombination on the whole genome.
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Affiliation(s)
- Laura Berset-Brändli
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
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14
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A key transcription cofactor on the nascent sex chromosomes of European tree frogs (Hyla arborea). Genetics 2008; 179:1721-3. [PMID: 18622030 DOI: 10.1534/genetics.108.090746] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We show that MED15, a key component of the transcription complex Mediator, lies within the nonrecombining segment of nascent sex chromosomes in the male-heterogametic Hyla arborea. Both X and Y alleles are expressed during embryonic development and differ by three frame-preserving indels (eight amino acids in total) within their glutamine-rich central part. These changes have the potential to affect the conformation of the Mediator complex and to activate genes in a sex-specific way and might thus represent the first steps toward the acquisition of a male-specific function. Alternatively, they might result from an ancestral neutral polymorphism, with different alleles picked by chance on the X and Y chromosomes when MED15 was trapped in the nonrecombining segment.
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15
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Matsuba C, Miura I, Merilä J. Disentangling genetic vs. environmental causes of sex determination in the common frog, Rana temporaria. BMC Genet 2008; 9:3. [PMID: 18182101 PMCID: PMC2265737 DOI: 10.1186/1471-2156-9-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Accepted: 01/08/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Understanding of sex ratio dynamics in a given species requires understanding its sex determination system, as well as access for reliable tools for sex identification at different life stages. As in the case of many other amphibians, the common frogs (Rana temporaria) do not have well differentiated sex chromosomes, and an identification of individuals' genetic sex may be complicated by sex reversals. Here, we report results of studies shedding light on the sex determination system and sex ratio variation in this species. RESULTS A microsatellite locus RtSB03 was found to be sex-linked in four geographically disparate populations, suggesting male heterogamy in common frogs. However, in three other populations examined, no or little evidence for sex-linkage was detected suggesting either ongoing/recent recombination events, and/or frequent sex-reversals. Comparison of inheritance patterns of alleles in RtSB03 and phenotypic sex within sibships revealed a mixed evidence for sex-linkage: all individuals with male phenotype carried a male specific allele in one population, whereas results were more mixed in another population. CONCLUSION These results make sense only if we assume that the RtSB03 locus is linked to male sex determination factor in some, but not in all common frog populations, and if phenotypic sex-reversals - for which there is earlier evidence from this species - are frequently occurring.
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Affiliation(s)
- Chikako Matsuba
- Ecological Genetics Research Unit, Department of Biological and Environmental Sciences, PO Box 65, University of Helsinki, FI-00014 Helsinki, Finland
| | - Ikuo Miura
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Japan
| | - Juha Merilä
- Ecological Genetics Research Unit, Department of Biological and Environmental Sciences, PO Box 65, University of Helsinki, FI-00014 Helsinki, Finland
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