Evidence for late Pleistocene origin of Astyanax mexicanus cavefish

Abstract

BackgroundCavefish populations belonging to the Mexican tetra species Astyanax mexicanus are outstanding models to study the tempo and mode of adaptation to a radical environmental change. They are currently assigned to two main groups, the so-called “old” and “new” lineages, which would have populated several caves independently and at different times. However, we do not have yet accurate estimations of the time frames of evolution of these populations.ResultsWe reanalyzed the geographic distribution of mitochondrial and nuclear DNA polymorphisms and we found that these data do not support the existence of two cavefish lineages. Using IMa2, a program that allows dating population divergence in addition to demographic parameters, we found that microsatellite polymorphism strongly supports a very recent origin of cave populations (< 20,000 years). We identified a large number of single-nucleotide polymorphisms (SNPs) in transcript sequences of pools of embryos (Pool-seq) belonging to Pachón cave population and a surface population from Texas. Based on summary statistics that can be computed with this SNP data set together with simulations of evolution of SNP polymorphisms in two recently isolated populations, we looked for sets of demographic parameters that allow the computation of summary statistics with simulated populations that are similar to the ones with the sampled populations. In most simulations for which we could find a good fit between the summary statistics of observed and simulated data, the best fit occurred when the divergence between simulated populations was less than 30,000 years.ConclusionsAlthough it is often assumed that some cave populations have a very ancient origin, a recent origin of these populations is strongly supported by our analyses of independent sets of nuclear DNA polymorphism. Moreover, the observation of two divergent haplogroups of mitochondrial and nuclear genes with different geographic distributions support a recent admixture of two divergent surface populations, before the isolation of cave populations. If cave populations are indeed only several thousand years old, many phenotypic changes observed in cavefish would thus have mainly involved the fixation of genetic variants present in surface fish populations and within a very short period of time.Electronic supplementary materialThe online version of this article (10.1186/s12862-018-1156-7) contains supplementary material, which is available to authorized users.

Phenotypic plasticity as a mechanism of cave colonization and adaptation

“…Recent studies revealed that cavefish lineages are much younger than previously thought, from less than 20,000 [5] to about 200,000 [6] years old, implying that the evolution of numerous cave-related phenotypes may have occurred over relatively short time periods. Furthermore, troglomorphic phenotypes are maintained in A. mexicanus cavefish despite the lack of complete isolation between surface fish and cavefish populations [6][7][8][9].…”

Modulation of DNA Repair Systems in Blind Cavefish during Evolution in Constant Darkness

“…An alternative explanation for the retention of CPD photolyase function in cavefish may relate to the length of time that evolution has occurred in the dark cave environment. In support of this interpretation, recent microsatellite polymorphism analysis has suggested that surface and cave populations of Astyanax that may have diverged less than 20,000 years ago [61] carry no mutations in the photolyase coding sequences ( [25] and AstMex102 database in ENSEMBL vs92). In contrast, geological evidence Figure S5).…”

A new cave locality for Astyanax cavefish in Sierra de El Abra, Mexico

“…Population genetics analyses performed on the Astyanax mexicanus cave and surface system have demonstrated the co-existence in the El Abra region of two mitochondrial haplotypes, A and B, initially defined after the ND2 gene sequence (Dowling et al 2002;Strecker et al 2003Strecker et al , 2004Ornelas-Garcia et al 2008). These mitochondrial DNA data have been used to propose evolving scenarii on the relatedness of Astyanax cave and surface populations in the region (Fumey et al 2018). Here, we used 16S rRNA mitochondrial sequence analysis to start documenting the genetic lineage of the newly discovered Chiquitita cavefish population.…”