Dataset Information

Are microsatellite fragment lengths useful for population-level studies? The case of Polygala lewtonii (Polygalaceae).

ABSTRACT:

Premise of the study

Microsatellites, despite being commonly used population-level markers, contain biases because scoring relies solely on fragment length. Their complexity can lead to homoplasy, the effects of which are poorly understood. We investigated the impact of using fragment lengths, repeats, or flanking region sequences on common population-level analyses.

Methods

Five polymorphic microsatellite markers amplified across the central Florida scrub endemic Polygala lewtonii (Polygalaceae) and its close, widespread congener P. polygama. We genotyped 147 individuals of P. lewtonii and 156 of P. polygama, and sequenced the amplicons of four markers across all individuals. We ran basic statistics, spatial clustering analysis, historical demographics, and migration tests.

Results

One population of intermediate morphology was genetically clearly identified as P. polygama, making it the southernmost population of this species. Statistics were comparable between the fragment length and repeat numbers, with some notable differences. Flanking regions exhibited surprisingly high polymorphism between species, and between geographically distant conspecific populations.

Discussion

The increasing use of markers developed in one species and amplified in another is only a good practice if precautions are taken, notably the sequencing of the fragments between species and populations. Flanking region sequences are a useful marker at the interspecific level.

SUBMITTER: Germain-Aubrey CC

PROVIDER: S-EPMC4760751 | biostudies-literature | 2016 Feb

REPOSITORIES: biostudies-literature

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Publications

Are microsatellite fragment lengths useful for population-level studies? The case of Polygala lewtonii (Polygalaceae).

Germain-Aubrey Charlotte C CC Nelson Cory C Soltis Douglas E DE Soltis Pamela S PS Gitzendanner Matthew A MA

Applications in plant sciences 20160215 2

<h4>Premise of the study</h4>Microsatellites, despite being commonly used population-level markers, contain biases because scoring relies solely on fragment length. Their complexity can lead to homoplasy, the effects of which are poorly understood. We investigated the impact of using fragment lengths, repeats, or flanking region sequences on common population-level analyses.<h4>Methods</h4>Five polymorphic microsatellite markers amplified across the central Florida scrub endemic Polygala lewtoni ...[more]

PMID: 26949579

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Project description: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 (F ST) 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.

Dataset Information

Are microsatellite fragment lengths useful for population-level studies? The case of Polygala lewtonii (Polygalaceae).

Premise of the study

Methods

Results

Discussion

Publications

Are microsatellite fragment lengths useful for population-level studies? The case of Polygala lewtonii (Polygalaceae).

Similar Datasets

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