Meeting Abstract
Adaptation and speciation are key processes in the evolution of biodiversity. Elucidating the genomic basis of traits involved in these processes remains a major task for the field, especially in non-model organisms. High-throughput sequencing allows for a comparative genomic approach to identify molecular changes in organisms currently undergoing ecological speciation. Here, we studied genetic changes underlying adaptation using genetically distinct and locally adapted populations of extremophile fishes (Poecilia mexicans) living in toxic, hydrogen sulfide-rich springs and caves. The recent divergence of ecotypes inhabiting different habitats and the contrasting environmental conditions makes this system ideal for studying the genetic basis of adaptation and speciation. We used RNA-sequencing to assemble and annotate transcriptomes of Poecilia mexicana based on transcripts from 16 wild-caught individuals with four individuals and four tissue types per ecotype (non-sulfidic surface, sulfidic surface, non-sulfidic cave, and sulfidic cave). Transcripts from each organ type were mapped against the de novo assembled reference transcriptome to call single nucleotide polymorphisms (SNPs) and estimate gene expression variation. We quantified coding changes in transcribed genes among ecotypes by identifying FST outliers to test for SNPs under selection. We identified variation in gene expression patterns between ecotypes and tissues by using the EdgeR package to identify genes that are differentially expressed. We find variation, both in gene expression and coding changes, across the ecotypes examined, thus making the P. mexicana transcriptome a valuable genomic resource for studying the underlying genetics of adaption and speciation.
