BackgroundCave animals converge evolutionarily on a suite of troglomorphic traits, the best known of which are eyelessness and depigmentation. We studied 11 cave and 10 surface populations of Astyanax mexicanus in order to better understand the evolutionary origins of the cave forms, the basic genetic structuring of both cave and surface populations, and the degree to which present day migration among them affects their genetic divergence.ResultsTo assess the genetic structure within populations and the relationships among them we genotyped individuals at 26 microsatellite loci. We found that surface populations are similar to one another, despite their relatively large geographic separation, whereas the cave populations are better differentiated. The cave populations we studied span the full range of the cave forms in three separate geographic regions and have at least five separate evolutionary origins. Cave populations had lower genetic diversity than surface populations, correlated with their smaller effective population sizes, probably the result of food and space limitations. Some of the cave populations receive migrants from the surface and exchange migrants with one another, especially when geographically close. This admixture results in significant heterozygote deficiencies at numerous loci due to Wahlund effects. Cave populations receiving migrants from the surface contain small numbers of individuals that are intermediate in both phenotype and genotype, affirming at least limited gene flow from the surface.ConclusionsCave populations of this species are derived from two different surface stocks denoted "old" and "new." The old stock colonized caves at least three times independently while the new stock colonized caves at least twice independently. Thus, the similar cave phenotypes found in these caves are the result of repeated convergences. These phenotypic convergences have occurred in spite of gene flow from surface populations suggesting either strong natural or sexual selection for alleles responsible for the cave phenotype in the cave environment.

Evolution depends on genetic variation generated by mutation or recombination from standing genetic variation. In sexual organisms, little is known about the molecular population genetics of adaptation and reverse evolution. We carry out 50 generations of experimental reverse evolution in populations of Drosophila melanogaster, previously differentiated by forward evolution, and follow changes in the frequency of SNPs in both arms of the third chromosome. We characterize the effects of sampling finite population sizes and natural selection at the genotype level. We demonstrate that selection has occurred at several loci and further that there is no general loss or gain of allele diversity. We also observe that despite the complete convergence to ancestral levels of adaptation, allele frequencies only show partial return.

Background: Trichomonias is the most common non-viral STI among women worldwide and is associated with serious reproductive morbidity, poor birth outcomes and amplified HIV transmission. Single-dose metronidazole therapy has been the treatment of choice for over three decades. There is mounting evidence, however, of high rates of repeat positives following single-dose metronidazole, and among HIVinfected women, bacterial vaginosis (BV) was found to alter treatment efficacy. The purpose of this study was to examine the effectiveness of single-dose metronidazole compared to 7 day-dose metronidazole for the treatment of trichomoniasis among HIV-uninfected, non-pregnant women and to determine if this effect was modified by BV. Methods: This was a randomized, parallel, multi-site, open-label trial of single-dose (2 g one-time) versus 7 day-dose (500 mg twice daily) for the treatment of trichomoniasis. The primary outcome was T. vaginalis infection by arm, per nucleic acid amplification test or culture, four weeks post-completion of treatment, in intentto-treat analyses. This analysis was also stratified by BV status. Findings: Of 623 women randomized, those in the 7 day-dose arm were less likely to be T. vaginalis positive at test-of-cure compared to those in the single-dose arm [34/312 (10.9%) vs. 58/311 (18.6%), p=0·001] [R.R. 0.55 (95% C.I. 0.34–0.70)]. Risk was similar by BV status (p=0·17). Self-reported adherence in both arms was > 95%. Side effects were similar by arm. Interpretation: In this sample of HIV-uninfected, non-pregnant women with trichomoniasis, compared to single-dose, 7 day-dose metronidazole treatment resulted in 45% fewer treatment failures. The 7 day-dose metronidazole should be the preferred treatment for trichomoniasis among women.

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.