História evolutiva e dinâmica demográfica de Cavia intermedia (Mammalia: Rodentia) inferida através de abordagem genômica

Abstract

Insular populations have always been the subject of interest for ecological and genetic studies. The insular Cavia intermedia is one of the rarest mammals in the world, with an average census size of about 40 individuals, corroborated by an extremely low genetic diversity and effective population size (Ne). Here, we used restricted site-associated DNA sequencing (RAD-seq) to obtain genome wide sequence data of C. intermedia and its continental sister species, C. magna to study their molecular diversity and demographic history. We have generated approximately 10 millions of useable reads of 300 bp for 20 individuals each of both species. However, both using the Cavia porcellus draft genome as a reference or de novo approaches and applying stringent filters for quality and missing data, only about a hundred loci could be used. This final dataset generated widely different molecular diversity and divergence time values between methods of analyses, some compatible with the previous studies (e.g., Ne ~60 for C. intermedia) but some with significantly larger values. We suggest that to obtain a high quality and very informative dataset it would be necessary to significantly increase the sequence data as well as apply other assembly approaches.