Population divergence with or without admixture: selecting models using an ABC approach

Abstract

Genetic data have been widely used to reconstruct the demographic history of populations, including the estimation of migration rates, divergence times and relative admixture contribution from different populations. Recently, increasing interest has been given to the ability of genetic data to distinguish alternative models. One of the issues that has plagued this kind of inference is that ancestral shared polymorphism is often difficult to separate from admixture or gene flow. Here, we applied an approximate Bayesian computation (ABC) approach to select the model that best fits microsatellite data among alternative splitting and admixture models. We performed a simulation study and showed that with reasonably large data sets (20 loci) it is possible to identify with a high level of accuracy the model that generated the data. This suggests that it is possible to distinguish genetic patterns due to past admixture events from those due to shared polymorphism (population split without admixture). We then apply this approach to microsatellite data from an endangered and endemic Iberian freshwater fish species, in which a clustering analysis suggested that one of the populations could be admixed. In contrast, our results suggest that the observed genetic patterns are better explained by a population split model without admixture.

Evolutionary history and population genetics of a cyprinid fish (Iberochondrostoma olisiponensis) endangered by introgression from a more abundant relative

“…Both species show additional evidence of small effective population sizes as indicated by high and significant inbreeding indices. These results are qualitatively concordant with previous findings in I. lusitanicum indicating a genetically depauperate, highly fragmented species that experienced severe demographic crashes in historical times (Alves and Coelho 1994;Robalo et al 2007b;Sousa et al 2008Sousa et al , 2012. Relative to previous studies we found higher levels of population differentiation in both nuclear and mitochondrial markers, perhaps due to the use of sequence data instead of microsatellites from additional populations.…”

“…I. lusitanicum has shown drastic population crashes over the last decades (Sousa et al 2008) and is listed as Critically Endangered both in the Portuguese Red Data book (Cabral et al 2005) and in the IUCN Red List of Threatened Species (Crivelli 2006). Levels of genetic diversity and population fragmentation also followed these demographic trends, indicating a genetically depauperate, highly fragmented species (Alves and Coelho 1994;Robalo et al 2007b;Sousa et al 2008Sousa et al , 2012. The rarer and much less known C. olisiponensis is listed in the IUCN Red List of Threatened Species also as Critically Endangered (Gante et al 2012).…”

Multispecies genetic structure and hybridization in the Betula genus across Eurasia

“…If the admixture‐like genetic pattern in Pop2 was not generated by admixture but by ancestral polymorphism, as suggested by Sousa et al . () and Tsuda et al . (), this scenario could be expected to be the most likely.…”

Divergence history of the Carpathian and smooth newts modelled in space and time

“…ABC methods are useful for differentiating between various models of species divergence, for instance, between speciation models allowing or ruling out the postdivergence gene flow (Sousa et al . ; Sousa & Hey ).…”