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  • 1
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    Extensive copy-number variation of young genes across stickleback populations (2014)
    Public Library of Sciences (PLoS)
    In:  PLOS Genetics, 10 (12). e1004830.
    Details
    Publication Date: 2019-08-08
    Description: Duplicate genes emerge as copy-number variations (CNVs) at the population level, and remain copy-number polymorphic until they are fixed or lost. The successful establishment of such structural polymorphisms in the genome plays an important role in evolution by promoting genetic diversity, complexity and innovation. To characterize the early evolutionary stages of duplicate genes and their potential adaptive benefits, we combine comparative genomics with population genomics analyses to evaluate the distribution and impact of CNVs across natural populations of an eco-genomic model, the three-spined stickleback. With whole genome sequences of 66 individuals from populations inhabiting three distinct habitats, we find that CNVs generally occur at low frequencies and are often only found in one of the 11 populations surveyed. A subset of CNVs, however, displays copy-number differentiation between populations, showing elevated within-population frequencies consistent with local adaptation. By comparing teleost genomes to identify lineage-specific genes and duplications in sticklebacks, we highlight rampant gene content differences among individuals in which over 30% of young duplicate genes are CNVs. These CNV genes are evolving rapidly at the molecular level and are enriched with functional categories associated with environmental interactions, depicting the dynamic early copy-number polymorphic stage of genes during population differentiation.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1371/journal.pgen.1004830
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 2
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    Evolution of MHC class I genes in the endangered loggerhead sea turtle (Caretta caretta) revealed by 454 amplicon sequencing (2013)
    BioMed Central
    In:  BMC Evolutionary Biology, 13 . No. 95.
    Details
    Publication Date: 2019-01-21
    Description: Background: In evolutionary and conservation biology, parasitism is often highlighted as a major selective pressure. To fight against parasites and pathogens, genetic diversity of the immune genes of the major histocompatibility complex (MHC) are particularly important. However, the extensive degree of polymorphism observed in these genes makes it difficult to conduct thorough population screenings. Methods: We utilized a genotyping protocol that uses 454 amplicon sequencing to characterize the MHC class I in the endangered loggerhead sea turtle (Caretta caretta) and to investigate their evolution at multiple relevant levels of organization. Results: MHC class I genes revealed signatures of trans-species polymorphism across several reptile species. In the studied loggerhead turtle individuals, it results in the maintenance of two ancient allelic lineages. We also found that individuals carrying an intermediate number of MHC class I alleles are larger than those with either a low or high number of alleles. Conclusions: Multiple modes of evolution seem to maintain MHC diversity in the loggerhead turtles, with relatively high polymorphism for an endangered species.
    Type: Article , PeerReviewed
    Format: text
    Format: text
    DOI: 10.1186/1471-2148-13-95
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 3
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    Living on the edge: how philopatry maintains adaptive potential (2013)
    Royal Society of London
    In:  Proceedings of the Royal Society B: Biological Sciences, 280 (20130305).
    Details
    Publication Date: 2019-04-05
    Description: Without genetic variation, species cannot cope with changing environments, and evolution does not proceed. In endangered species, adaptive potential may be eroded by decreased population sizes and processes that further reduce gene flow such as philopatry and local adaptations. Here, we focused on the philopatric and endangered loggerhead sea turtle (Caretta caretta) nesting in Cape Verde as a model system to investigate the link between adaptive potential and philopatry. We produced a dataset of three complementary genomic regions to investigate female philopatric behaviour (mitochondrial DNA), male-mediated gene flow (microsatellites) and adaptive potential (major histocompatibility complex, MHC). Results revealed genetically distinct nesting colonies, indicating remarkably small-scale philopatric behaviour of females. Furthermore, these colonies also harboured local pools of MHC alleles, especially at the margins of the population's distribution, which are therefore important reserves of additional diversity for the population. Meanwhile, directional male-mediated gene flow from the margins of distribution sustains the adaptive potential for the entire rookery. We therefore present the first evidence for a positive association between philopatry and locally adapted genomic regions. Contrary to expectation, we propose that philopatry conserves a high adaptive potential at the margins of a distribution, while asymmetric gene flow maintains genetic connectivity with the rest of the population.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1098/rspb.2013.0305
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 4
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    Genomic Dynamics of Transposable Elements in the Western Clawed Frog (Silurana tropicalis) (2013)
    Oxford University Press
    Details
    Publication Date: 2013-05-16
    Description: Transposable elements (TEs) are repetitive DNA sequences that can make new copies of themselves that are inserted elsewhere in a host genome. The abundance and distributions of TEs vary considerably among phylogenetically diverse hosts. With the aim of exploring the basis of this variation, we evaluated correlations between several genomic variables and the presence of TEs and non-TE repeats in the complete genome sequence of the Western clawed frog ( Silurana tropicalis ). This analysis reveals patterns of TE insertion consistent with gene disruption but not with the insertional preference model. Analysis of non-TE repeats recovered unique features of their genome-wide distribution when compared with TE repeats, including no strong correlation with exons and a particularly strong negative correlation with GC content. We also collected polymorphism data from 25 TE insertion sites in 19 wild-caught S. tropicalis individuals. DNA transposon insertions were fixed at eight of nine sites and at a high frequency at one of nine, whereas insertions of long terminal repeat (LTR) and non-LTR retrotransposons were fixed at only 4 of 16 sites and at low frequency at 12 of 16. A maximum likelihood model failed to attribute these differences in insertion frequencies to variation in selection pressure on different classes of TE, opening the possibility that other phenomena such as variation in rates of replication or duration of residence in the genome could play a role. Taken together, these results identify factors that sculpt heterogeneity in TE distribution in S. tropicalis and illustrate that genomic dynamics differ markedly among TE classes and between TE and non-TE repeats.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    A Large Pseudoautosomal Region on the Sex Chromosomes of the Frog Silurana tropicalis (2013)
    Oxford University Press
    Details
    Publication Date: 2013-06-15
    Description: Sex chromosome divergence has been documented across phylogenetically diverse species, with amphibians typically having cytologically nondiverged ("homomorphic") sex chromosomes. With an aim of further characterizing sex chromosome divergence of an amphibian, we used "RAD-tags" and Sanger sequencing to examine sex specificity and heterozygosity in the Western clawed frog Silurana tropicalis (also known as Xenopus tropicalis ). Our findings based on approximately 20 million genotype calls and approximately 200 polymerase chain reaction-amplified regions across multiple male and female genomes failed to identify a substantially sized genomic region with genotypic hallmarks of sex chromosome divergence, including in regions known to be tightly linked to the sex-determining region. We also found that expression and molecular evolution of genes linked to the sex-determining region did not differ substantially from genes in other parts of the genome. This suggests that the pseudoautosomal region, where recombination occurs, comprises a large portion of the sex chromosomes of S. tropicalis . These results may in part explain why African clawed frogs have such a high incidence of polyploidization, shed light on why amphibians have a high rate of sex chromosome turnover, and raise questions about why homomorphic sex chromosomes are so prevalent in amphibians.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    Spontaneous Mutation Accumulation in Daphnia pulex in Selection-Free vs. Competitive Environments (2017)
    Oxford University Press
    Details
    Publication Date: 2017-01-05
    Description: Understanding the rates, spectra, and fitness effects of spontaneous mutations is fundamental to answering key questions in evolution, molecular biology, disease genetics, and conservation biology. To estimate mutation rates and evaluate the effect of selection on new mutations, we propagated mutation accumulation (MA) lines of Daphnia pulex for more than 82 generations and maintained a non-MA population under conditions where selection could act. Both experiments were started with the same obligate asexual progenitor clone. By sequencing 30 genomes and implementing a series of validation steps that informed the bioinformatic analyses, we identified a total of 477 single nucleotide mutations (SNMs) in the MA lines, corresponding to a mutation rate of 2.30 x 10 –9 (95% CI 1.90–2.70 x 10 –9 ) per nucleotide per generation. The high overall rate of loss of heterozygosity (LOH) of 4.82 x 10 –5 per site per generation was due to a large ameiotic recombination event spanning an entire arm of a chromosome (~6 Mb) and several hemizygous deletion events spanning ~2 kb each. In the non-MA population, we found significantly fewer mutations than expected based on the rate derived from the MA experiment, indicating purifying selection was likely acting to remove new deleterious mutations. We observed a surprisingly high level of genetic variability in the non-MA population, which we propose to be driven by balancing selection. Our findings suggest that both positive and negative selection on new mutations is powerful and effective in a strictly clonal population.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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