Genomic data reveal a loss of diversity in two species of tuco-tucos (genus Ctenomys) following a volcanic eruption

Jeremy L Hsu,Uma Ramakrishnan,Eileen A Lacey,Elizabeth A Hadly,Mauro N Tammone,Jeremy Chase Crawford

doi:10.1038/s41598-017-16430-1

Abstract

Marked reductions in population size can trigger corresponding declines in genetic variation. Understanding the precise genetic consequences of such reductions, however, is often challenging due to the absence of robust pre- and post-reduction datasets. Here, we use heterochronous genomic data from samples obtained before and immediately after the 2011 eruption of the Puyehue-Cordón Caulle volcanic complex in Patagonia to explore the genetic impacts of this event on two parapatric species of rodents, the colonial tuco-tuco (Ctenomys sociabilis) and the Patagonian tuco-tuco (C. haigi). Previous analyses using microsatellites revealed no post-eruption changes in genetic variation in C. haigi, but an unexpected increase in variation in C. sociabilis. To explore this outcome further, we used targeted gene capture to sequence over 2,000 putatively neutral regions for both species. Our data revealed that, contrary to the microsatellite analyses, the eruption was associated with a small but significant decrease in genetic variation in both species. We suggest that genome-level analyses provide greater power than traditional molecular markers to detect the genetic consequences of population size changes, particularly changes that are recent, short-term, or modest in size. Consequently, genomic analyses promise to generate important new insights into the effects of specific environmental events on demography and genetic variation.

Highlights

Significant reductions in population size can substantially impact patterns of genetic variation and potentially alter the evolutionary trajectories of affected organisms
Our sequence alignment resulted in a mean per-individual depth of coverage of 11.46 for C. sociabilis and 11.41 for C. haigi, with greater than 99.9% cover per individual of targeted areas for both species
The final data set consisted of 531 Single nucleotide polymorphisms (SNPs) for C. sociabilis and 449 SNPs for C. haigi

Summary

Introduction

Significant reductions in population size (i.e. population bottlenecks1) can substantially impact patterns of genetic variation and potentially alter the evolutionary trajectories of affected organisms. Most analyses that have used genomic data to assess the impacts of reductions in population size have focused on demographic changes associated with agricultural activities such as domestication of plants and animals[3,6,7,8] The relevance of these analyses to wild populations is unclear, as domesticated species have typically been subject to strong artificial selection that may confound signals of other evolutionary forces such as drift, mutation, migration, and gene flow[3]. Previous analyses based on microsatellite markers[16] suggested that this event was associated with a significant post-eruption increase in genetic variation in C. sociabilis but not in C. haigi To explore this unexpected outcome in greater detail, we employed targeted sequence capture to generate a large number of genome-wide markers for each study species. Our analyses of the effects of the Puyehue-Cordón Caulle eruption should generate important new insights into the role of demographic processes in shaping short-term genomic responses to pronounced reductions in population size

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Conclusion