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 utilizes 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 geographical spread of ancestry backwards 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 geographical 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 a Antirrhinum majus (snapdragon) flower color hybrid zone, where we do not detect any signal of a strong genome wide barrier to gene flow. KEYWORDS Barriers to Gene Flow; Isolation by Distance; Identity by Descent; Demographic Inference M any populations are distributed across geographically extended habitats that are sometimes interrupted by barriers to gene flow. They can arise due to physical obstacles that reduce migration, but can also be caused by genetic incompatibilities, which reduce gene flow across a hybrid zone (Barton 1979). Barriers can prevent locally adapted populations from being swamped by dispersal, and they can facilitate divergence, ultimately leading to speciation. Therefore, they play a central role not only in conservation, but also in evolutionary biology and ecology. As direct observations of individual movement and reproduction are time-consuming and expensive, and moreover can only give a snapshot in time, there is much interest in indirect methods that infer such barriers from observed geographic genetic structure.Such methods to detect barriers from genetic data can be grouped into two distinct approaches ): Clustering methods, that detect geographic genetic discontinuities between populations by grouping individuals into population units based on genetic similarity (Falush et al. 2003;

Peer Review #2 of "Can secondary contact following range expansion be distinguished from barriers to gene flow? (v0.1)"

“…These converge quickly to their continuous diffusive counterparts, especially in one spatial dimension (Nagylaki, 1988;Barton, 2008;Forien, 2017). Recently, such continuous diffusion models have been applied to scenarios of barriers to gene flow (Ringbauer et al, 2018), as well as secondary contact (Sedghifar et al, 2015). Here, we summarize relevant findings and provide predictions for our simulations where available.…”

“…Manuscript to be reviewed the spread of ancestry (m B /(mσ 2 ) ≪ 1) (Barton, 2008;Ringbauer et al, 2018).…”

Are populations like a circuit? Comparing isolation by resistance to a new coalescent‐based method

“…Furthermore, the likelihood model underlying MAPS is based on coalescent theory, and thus should not be subject to the drawbacks of resistance distance. Ringbauer, Kolesnikov, Field, and Barton () also uses shared haplotype lengths to identify a barrier in a coalescence‐based framework. However, the underlying migration model is symmetric, and haplotype length‐based methods require fairly dense genotyping and a genetic map, something not available for many species.…”

Are populations like a circuit? Comparing isolation by resistance to a new coalescent-based method

“…Furthermore, the likelihood model underlying MAPS is based on coalescent theory, and thus should not be subject to the drawbacks of resistance distance. Ringbauer et al [2018] also uses shared haplotype lengths to identify a barrier in a coalescence-based framework. However, the underlying migration model is symmetric, and haplotype length-based methods require fairly dense genotyping and a genetic map, something not available for many species.…”