Dataset Information

Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns.

ABSTRACT: In continuous populations with local migration, nearby pairs of individuals have on average more similar genotypes than geographically well-separated pairs. A barrier to gene flow distorts this classical pattern of isolation by distance. Genetic similarity is decreased for sample pairs on different sides of the barrier and increased for pairs on the same side near the barrier. Here, we introduce an inference scheme that uses this signal to detect and estimate the strength of a linear barrier to gene flow in two dimensions. We use a diffusion approximation to model the effects of a barrier on the geographic spread of ancestry backward in time. This approach allows us to calculate the chance of recent coalescence and probability of identity by descent. We introduce an inference scheme that fits these theoretical results to the geographic covariance structure of bialleleic genetic markers. It can estimate the strength of the barrier as well as several demographic parameters. We investigate the power of our inference scheme to detect barriers by applying it to a wide range of simulated data. We also showcase an example application to an Antirrhinum majus (snapdragon) flower-color hybrid zone, where we do not detect any signal of a strong genome-wide barrier to gene flow.

SUBMITTER: Ringbauer H

PROVIDER: S-EPMC5844333 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature

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Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns.

Ringbauer Harald H Kolesnikov Alexander A Field David L DL Barton Nicholas H NH

Genetics 20180108 3

In continuous populations with local migration, nearby pairs of individuals have on average more similar genotypes than geographically well-separated pairs. A barrier to gene flow distorts this classical pattern of isolation by distance. Genetic similarity is decreased for sample pairs on different sides of the barrier and increased for pairs on the same side near the barrier. Here, we introduce an inference scheme that uses this signal to detect and estimate the strength of a linear barrier to ...[more]

PMID: 29311149

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Project description:BackgroundUnderstanding and identifying the factors responsible for genetic differentiation is of fundamental importance for efficient utilization and conservation of traditional rice landraces. In this study, we examined the spatial genetic differentiation of 594 individuals sampled from 28 locations in Yunnan Province, China, covering a wide geographic distribution and diverse growing conditions. All 594 accessions were studied using ten unlinked target genes and 48 microsatellite loci, and the representative 108 accessions from the whole collection were sampled for resequencing.ResultsThe genetic diversity of rice landraces was quite different geographically and exhibited a geographical decline from south to north in Yunnan, China. Population structure revealed that the rice landraces could be clearly differentiated into japonica and indica groups, respectively. In each group, the rice accessions could be further differentiated corresponded to their geographic locations, including three subgroups from northern, southern and middle locations. We found more obvious internal geographic structure in the japonica group than in the indica group. In the japonica group, we found that genetic and phenotypic differentiation were strongly related to geographical distance, suggesting a pattern of isolation by distance (IBD); this relationship remained highly significant when we controlled for environmental effects, where the likelihood of gene flow is inversely proportional to the distance between locations. Moreover, the gene flow also followed patterns of isolation by environment (IBE) whereby gene flow rates are higher in similar environments. We detected 314 and 216 regions had been differentially selected between Jap-N and Jap-S, Ind-N and Ind-S, respectively, and thus referred to as selection signatures for different geographic subgroups. We also observed a number of significant and interesting associations between loci and environmental factors, which implies adaptation to local environment.ConclusionsOur findings highlight the influence of geographical isolation and environmental heterogeneity on the pattern of the gene flow, and demonstrate that both geographical isolation and environment drives adaptive divergence play dominant roles in the genetic differentiation of the rice landraces in Yunnan, China as a result of limited dispersal.

Dataset Information

Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns.

Publications

Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns.

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