Spatial Inference of Admixture Proportions and Secondary Contact Zones

Abstract

Genetic admixture of distinct gene pools is the consequence of complex spatiotemporal processes that could have involved massive migration and local mating during the history of a species. However, current methods for estimating individual admixture proportions lack the incorporation of such a piece of information. Here, we extend Bayesian clustering algorithms by including global trend surfaces and spatial autocorrelation in the prior distribution on individual admixture coefficients. We test our algorithm by using spatially explicit and realistic coalescent simulations of colonization followed by secondary contact. By coupling our multiscale spatial analyses with a Bayesian evaluation of model complexity and fit, we show that the algorithm provides a correct description of smooth clinal variation, while still detecting zones of sharp variation when they are present in the data. We also apply our approach to understand the population structure of the killifish, Fundulus heteroclitus, for which the algorithm uncovers a presumed contact zone in the Atlantic coast of North America.

Historical isolation and hydrodynamically constrained gene flow in declining populations of the South-African abalone, Haliotis midae

“…The latter was also consistent with a secondary contact zone between western and eastern populations. It should be noted that the DIC values were not used to test the applicability of a clinal model to our data but did show the steepest decrease from K max = 2 to K max = 3, similarly to what was found for killifish where a contact zone best explained the data using spatial analysis together with DIC evaluation (Durand et al 2009). …”

Extraordinarily rapid life-history divergence between Cryptasterina sea star species

“…Geographical locations of individuals and microsatellite genotypes were used to infer significant clusters of individuals over genetic and physical space in C. pentagona [44,45]. Four significant clusters were found (figure 4) and they largely correlate with geographical distance, suggesting that contemporary gene flow in this species is restricted to only local levels.…”

“…The program TESS [44,45] estimated genetic clusters from microsatellite genotypes and geographical locations of individuals using a 100 000 step burn-in and 1 000 000 sweeps of the CAR model with spatial interaction optimization using mean distance.…”

Population Genomics of Marine Fishes: Next-Generation Prospects and Challenges

“…in the Northern Atlantic (Roques et al, 2001), and coral reef fishes in the Indo-Pacific (Hobbs et al, 2009). Moreover, several well-characterized intra-specific hybrid zones also provide valuable model systems for evolutionary studies in marine fishes (Nielsen et al, 2003(Nielsen et al, , 2004Durand et al, 2009). These could be used to identify genomic regions of reduced introgression that are potentially involved in maintaining reproductive isolation between parental populations (Gompert and Buerkle, 2011).…”