The Population Genomics of Repeated Evolution in the Blind Cavefish Astyanax mexicanus

Abstract

Distinct populations of Astyanax mexicanus cavefish offer striking examples of repeatable convergence or parallelism in their independent evolutions from surface to cave phenotypes. However, the extent to which the repeatability of evolution occurred at the genetic level remains poorly understood. To address this, we first characterized the genetic diversity of 518 single-nucleotide polymorphisms (SNPs), obtained through RAD tag sequencing and distributed throughout the genome, in seven cave and three groups of surface populations. The cave populations represented two distinct lineages (old and new). Thirty-one SNPs were significantly differentiated between surface and old cave populations, two SNPs were differentiated between surface and new cave populations, and 44 SNPs were significantly differentiated in both old and new cave populations. In addition, we determined whether these SNPs map to the same locations of previously described quantitative trait loci (QTL) between surface and cave populations. A total of 25 differentiated SNPs co-map with several QTL, such as one containing a fibroblast growth factor gene (Fgf8) involved in eye development and lens size. Further, the identity of many SNPs that co-mapped with QTL was the same in independently derived cave populations. These conclusions were further confirmed by haplotype analyses of SNPs within QTL regions. Our findings indicate that the repeatability of evolution at the genetic level is substantial, suggesting that ancestral standing genetic variation significantly contributed to the population genetic variability used in adaptation to the cave environment.

Relaxed selective constraints drove functional modifications in peripheral photoreception of the cavefish P. andruzzii and provide insight into the time of cave colonization

“…We cannot exclude that the fixation of the LOF predates the colonization of the subterranean environment, but this alternative scenario seems quite unlikely. Conversely, no line of evidence from this and previous studies on this species support multiple independent colonization events of the dark environment, as observed in other species (Strecker et al, 2012;Bradic et al, 2013).…”

Insulin resistance in cavefish as an adaptation to a nutrient-limited environment

“…Tinaja and Pachón cavefish originated from a more ancient surface population compared to Molino cavefish 7 .…”

The Evolution of Sensory Adaptation in Astyanax mexicanus

“…ensembl.org), available embryology techniques that up-and down-regulate genes (Gross et al, 2009;Hinaux et al, 2014;Yamamoto and Jeffery, 2000;Yamamoto et al, 2004Yamamoto et al, , 2009, defined embryonic and larval stages (Hinaux et al, 2011), transcriptome datasets (Gross et al, 2013;Hinaux et al, 2013), and defined evolutionary relationships among populations (Bradic et al, 2012(Bradic et al, , 2013Coghill et al, 2014;Gross, 2012;Ornelas-García et al, 2008). ensembl.org), available embryology techniques that up-and down-regulate genes (Gross et al, 2009;Hinaux et al, 2014;Yamamoto and Jeffery, 2000;Yamamoto et al, 2004Yamamoto et al, , 2009, defined embryonic and larval stages (Hinaux et al, 2011), transcriptome datasets (Gross et al, 2013;Hinaux et al, 2013), and defined evolutionary relationships among populations (Bradic et al, 2012(Bradic et al, , 2013Coghill et al, 2014;Gross, 2012;Ornelas-García et al, 2008).…”