Conservation of Human Microsatellites across 450 Million Years of Evolution

Buschiazzo, Emmanuel; Gemmell, Neil J.

doi:10.1093/gbe/evq007

Cited by 41 publications

(57 citation statements)

References 73 publications

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“…22 In contrast, we exploit the Drosophila melanogaster population data set to bridge the gap between SSR micro-and macro-evolution. This gap will shrink further with additional genome sequences being released in the near future, either from very closely related sister species or from separate populations of the same species.…”

Section: Discussionmentioning

confidence: 99%

“…Such an exponential decay has been observed as well for the conservation of human SSR loci in vertebrate genomes and may be a general trend in SSR macroevolution. 22 As mentioned before, SSR mutation rates are much lower in Drosophila than in vertebrates, and reduced mutation rates might partly be attributed to the facts that i) SSRs in D. melanogaster are shorter, 58 and ii) shorter SSRs are less mutable. 2,59 By applying the same SSR identification method used in this study for Drosophilidae to five mammal genomes (human, chimpanzee, mouse, rat, pig), we indeed found that Drosophila SSRs are shorter than mammalian SSRs (on average 26 nt vs. 32 nt; see Supplementary File 1 for details).…”

Section: Overall Macroevolutionary Trend Of Simple Sequence Repeatsmentioning

confidence: 92%

“…that repeat number variation and interrupting mutations in an SSR haves no fitness effect and areis a purely stochastic processes. [20][21][22] The assumed lack of selection pressure on SSR retention suggests that SSRs are not retained over long evolutionary time scales and thus not across different species. Accordingly, the transfer of SSR markers is particularly difficult between distant species.…”

Section: Introductionmentioning

confidence: 99%

“…22 Considering SSR abundance, it is not necessarily surprising to find some SSR loci retained over a long time scale. Mechanistically, mutations in viable SSRs favor their preservation, i.e.…”

Section: Introductionmentioning

confidence: 99%

“…To date, only one study has systematically evaluated the full-genome conservation of SSRs: Buschiazzo and Gemmell studied the conservation of human SSR loci in 11 vertebrate species using fullgenome alignments present in the UCSC Genome Browser. 22,37 They could show that conservation of human SSR loci declines exponentially with increasing divergence time and suggested that the majority of SSRs in genomes are maintained by chance. Accordingly, we here take advantage of the recently published wealth of genomes and address issues associated to the possible stochastic nature and retention of SSRs across species.…”

Section: Introductionmentioning

confidence: 99%

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Evolutionary dynamics of simple sequence repeats across long evolutionary time scale in genus Drosophila

2012

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Repetitive DNA is among the fastest evolving types of genomic DNA, which includes simple sequence repeats (SSRs), short regions of tandemly repeated one to six nucleotides long motifs. SSRs are found most frequently in noncoding regions. Repeat number variation occurs rapidly and is presumably neutral such that polymorphic SSRs are frequently used as genetic markers to characterize and classify populations. Despite their rapid evolution, recent reports suggested that SSR loci can be retained over hundreds of millions of years. We here investigate the dynamics and genomic features of SSR evolution in syntenic regions conserved across twelve Drosophila species and within a D. melanogaster population dataset. We find that SSR loci decay exponentially with time, the percentage of retained SSRs mostly reflects species relationships and correlates well with the sequence similarity of neighboring genes. About 47% of repeat loci within syntenic regions may share common ancestry due to predicted conservation in at least two species from the Drosophila subgenera Sophophora and Drosophila respectively, i.e. after 80 million years of divergence time. Since loci which are highly polymorphic at the population level also decay faster across species, SSR evolution appears to be a gradual process in which conservation pressure may act at relatively constant rates across time scales. A higher proportion of SSR loci are retained among Drosophila subgenus species considering their evolutionary distance and the expected decay rate estimated across all Drosophila species. This prolonged SSR retention might be caused by a higher SSR mutation rate and a lower nucleotide substitution rate in the Drosophila subgenus compared to Sophophora species. SSRs in exons and on autosomes evolve more slowly than SSRs located outside of exons or on the sex chromosome, respectively, both within and across species. SSR variability and phylogenetic conservation thus varies depending on the genomic location. These findings provide new insights into the dynamics of SSRs at both micro-and macro-evolutionary scales. The development of robust models of SSR long-term evolution will facilitate more in-depth analyses in general and the prediction of neutrally evolving SSRs and SSRs evolving under purifying selection, extending our knowledge of the functional impact of SSRs in genome evolution.

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Section: Discussionmentioning

confidence: 99%

Section: Overall Macroevolutionary Trend Of Simple Sequence Repeatsmentioning

confidence: 92%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Evolutionary dynamics of simple sequence repeats across long evolutionary time scale in genus Drosophila

2012

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Challenges in analysis and interpretation of microsatellite data for population genetic studies

Putman

Carbone

2014

Ecology and Evolution

328

252

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Advancing technologies have facilitated the ever-widening application of genetic markers such as microsatellites into new systems and research questions in biology. In light of the data and experience accumulated from several years of using microsatellites, we present here a literature review that synthesizes the limitations of microsatellites in population genetic studies. With a focus on population structure, we review the widely used fixation (FST) statistics and Bayesian clustering algorithms and find that the former can be confusing and problematic for microsatellites and that the latter may be confounded by complex population models and lack power in certain cases. Clustering, multivariate analyses, and diversity-based statistics are increasingly being applied to infer population structure, but in some instances these methods lack formalization with microsatellites. Migration-specific methods perform well only under narrow constraints. We also examine the use of microsatellites for inferring effective population size, changes in population size, and deeper demographic history, and find that these methods are untested and/or highly context-dependent. Overall, each method possesses important weaknesses for use with microsatellites, and there are significant constraints on inferences commonly made using microsatellite markers in the areas of population structure, admixture, and effective population size. To ameliorate and better understand these constraints, researchers are encouraged to analyze simulated datasets both prior to and following data collection and analysis, the latter of which is formalized within the approximate Bayesian computation framework. We also examine trends in the literature and show that microsatellites continue to be widely used, especially in non-human subject areas. This review assists with study design and molecular marker selection, facilitates sound interpretation of microsatellite data while fostering respect for their practical limitations, and identifies lessons that could be applied toward emerging markers and high-throughput technologies in population genetics.

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Strategies for determining kinship in wild populations using genetic data

Städele

Vigilant

2016

Ecology and Evolution

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Knowledge of kin relationships between members of wild animal populations has broad application in ecology and evolution research by allowing the investigation of dispersal dynamics, mating systems, inbreeding avoidance, kin recognition, and kin selection as well as aiding the management of endangered populations. However, the assessment of kinship among members of wild animal populations is difficult in the absence of detailed multigenerational pedigrees. Here, we first review the distinction between genetic relatedness and kinship derived from pedigrees and how this makes the identification of kin using genetic data inherently challenging. We then describe useful approaches to kinship classification, such as parentage analysis and sibship reconstruction, and explain how the combined use of marker systems with biparental and uniparental inheritance, demographic information, likelihood analyses, relatedness coefficients, and estimation of misclassification rates can yield reliable classifications of kinship in groups with complex kin structures. We outline alternative approaches for cases in which explicit knowledge of dyadic kinship is not necessary, but indirect inferences about kinship on a group‐ or population‐wide scale suffice, such as whether more highly related dyads are in closer spatial proximity. Although analysis of highly variable microsatellite loci is still the dominant approach for studies on wild populations, we describe how the long‐awaited use of large‐scale single‐nucleotide polymorphism and sequencing data derived from noninvasive low‐quality samples may eventually lead to highly accurate assessments of varying degrees of kinship in wild populations.

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Conservation of Human Microsatellites across 450 Million Years of Evolution

Cited by 41 publications

References 73 publications

Evolutionary dynamics of simple sequence repeats across long evolutionary time scale in genus Drosophila

Evolutionary dynamics of simple sequence repeats across long evolutionary time scale in genus Drosophila

Challenges in analysis and interpretation of microsatellite data for population genetic studies

Strategies for determining kinship in wild populations using genetic data

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