Cavefish 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.
We 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.
Although 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.
Abstract
Evolution sometimes proceeds by loss, especially when structures and genes become dispensable after an environmental shift relaxes functional constraints. Subterranean vertebrates are ...outstanding models to analyze this process, and gene decay can serve as a readout. We sought to understand some general principles on the extent and tempo of the decay of genes involved in vision, circadian clock, and pigmentation in cavefishes. The analysis of the genomes of two Cuban species belonging to the genus Lucifuga provided evidence for the largest loss of eye-specific genes and nonvisual opsin genes reported so far in cavefishes. Comparisons with a recently evolved cave population of Astyanax mexicanus and three species belonging to the Chinese tetraploid genus Sinocyclocheilus revealed the combined effects of the level of eye regression, time, and genome ploidy on eye-specific gene pseudogenization. The limited extent of gene decay in all these cavefishes and the very small number of loss-of-function mutations per pseudogene suggest that their eye degeneration may not be very ancient, ranging from early to late Pleistocene. This is in sharp contrast with the identification of several vision genes carrying many loss-of-function mutations in ancient fossorial mammals, further suggesting that blind fishes cannot thrive more than a few million years in cave ecosystems.
In 2020, the world faced the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic that drastically altered people’s lives. Since then, many countries have been forced to suspend ...public gatherings, leading to many conference cancellations, postponements, or reorganizations. Switching from a face-to-face to a remote conference became inevitable and the ultimate solution to sustain scientific exchanges at the national and the international levels. The same year, as a committee, we were in charge of organizing the major French annual conference that covers all computational biology areas: The “Journées Ouvertes en Biologie, Informatique et Mathématiques
”
(JOBIM). Despite the health crisis, we succeeded in changing the conference format from face to face to remote in a very short amount of time. Here, we propose 10 simple rules based on this experience to modify a conference format in an optimized and cost-effective way. In addition to the suggested rules, we decided to emphasize an unexpected benefit of this situation: a significant reduction in greenhouse gas (GHG) emissions related to travel for scientific conference attendance. We believe that even once the SARS-CoV-2 crisis is over, we collectively will have an opportunity to think about the way we approach such scientific events over the longer term.
This article describes the motivation, origin and evolution of the student symposia series organised by the ISCB Student Council. The meeting series started thirteen years ago in Madrid and has ...spread to four continents. The article concludes with the highlights of the most recent edition of annual Student Council Symposium held in conjunction with the 25th Conference on Intelligent Systems for Molecular Biology and the 16th European Conference on Computational Biology, in Prague, in July 2017.
Animals in many phyla are adapted to and thrive in the constant darkness of subterranean environments. To do so, cave animals have presumably evolved mechano- and chemosensory compensations to the ...loss of vision, as is the case for the blind characiform cavefish, Astyanax mexicanus. Here, we systematically assessed the olfactory capacities of cavefish and surface fish of this species in the lab as well as in the wild, in five different caves in northeastern Mexico, using an olfactory setup specially developed to test and record olfactory responses during fieldwork. Overall cavefish showed lower (i.e., better) olfactory detection thresholds than surface fish. However, wild adult cavefish from the Pachón, Sabinos, Tinaja, Chica and Subterráneo caves showed highly variable responses to the three different odorant molecules they were exposed to. Pachón and Subterráneo cavefish showed the highest olfactory capacities, and Chica cavefish showed no response to the odors presented. We discuss these data with regard to the environmental conditions in which these different cavefish populations live. Our experiments in natural settings document the diversity of cave environments inhabited by a single species of cavefish, A. mexicanus, and highlight the complexity of the plastic and genetic mechanisms that underlie cave adaptation.
The characiform fish
Astyanaxmexicanus
comes in two forms, a surface-dwelling morph which lives in the rivers of North and Central America and a blind, depigmented cave-dwelling morph which inhabits ...caves in Mexico. In recent years, this species has arguably become among the most influential model system for the study of evolutionary development and genomics in cave biology. While recent articles have analysed in great detail
Astyanax
genetics, development, physiology, phylogeny and behaviour, there have been comparatively few recent studies concerning its ecology and in particular its biogeography. Mitchell et al. (1977) reported the species inhabiting 29 caves in the Sierra de El Abra region. Despite the elapsing of over 40 years and the latest surge of interest in the model, not a single new cave locality had been described for the species. We describe here a new and 30
th
cave locality, Chiquitita Cave, inhabited by troglomorphic
A.mexicanus
. Their morphology, eye histology, 16S rRNA DNA sequence, and smelling capabilities are analysed. This cave represents the southernmost extension for the cave morph’s habitat within the Sierra de El Abra. Its name, Chiquitita Cave (Tiny Cave), was chosen in reference to a potential hydrologic connection to “Chica Cave” (small cave), which is among the most studied populations of
Astyanax
.
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•Mutations at the Doa locus resulted in modified CHC profiles in males and females.•In trans-heterozygote Doa females, the amount of tricosene+pentacosene was doubled.•Doa male ...courtship behavior was severely affected.
Mutations at the Darkener of Apricot (Doa) locus of Drosophila melanogaster alter sexual differentiation by disrupting sex-specific splicing of doublesex pre-mRNA, a key regulator of sex determination. Here, we study the effect of seven Doa alleles and several trans-heterozygous combinations on pheromones and courtship behavior. The cuticular hydrocarbon (CHC) profile was slightly masculinized in females, with an accumulation of shorter compounds (C23 and C25) and a reduction in longer compounds (C27 and C29). The profile was feminized in males. Female cuticular profiles showed fewer dienes and female pheromones in six alleles and in the trans-heterozygotes and showed more male pheromones (tricosene and pentacosene) in three alleles (DEM, E786 and HD) and in all trans-heterozygotes.
Courtship was severely affected in Doa males; in particular, males made fewer copulation attempts and copulated less with both control and Doa females.
These results suggest that Doa could modulate pheromone production and sex behavior by altering sexual differentiation in the cuticle and the nervous system.
In 2020, the world faced the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic that drastically altered people's lives. Since then, many countries have been forced to suspend ...public gatherings, leading to many conference cancellations, postponements, or reorganizations. Switching from a face-to-face to a remote conference became inevitable and the ultimate solution to sustain scientific exchanges at the national and the international levels. The same year, as a committee, we were in charge of organizing the major French annual conference that covers all computational biology areas: The "Journées Ouvertes en Biologie, Informatique et Mathématiques" (JOBIM). Despite the health crisis, we succeeded in changing the conference format from face to face to remote in a very short amount of time. Here, we propose 10 simple rules based on this experience to modify a conference format in an optimized and cost-effective way. In addition to the suggested rules, we decided to emphasize an unexpected benefit of this situation: a significant reduction in greenhouse gas (GHG) emissions related to travel for scientific conference attendance. We believe that even once the SARS-CoV-2 crisis is over, we collectively will have an opportunity to think about the way we approach such scientific events over the longer term.
The sizes of
blind cavefish populations of North-East Mexico are demographic parameters of great importance for investigating a variety of ecological, evolutionary, and conservation issues. However, ...few estimates have been obtained. For these mobile animals living in an environment difficult to explore as a whole, methods based on capture-mark-recapture are appropriate, but their feasibility and interpretation of results depend on several assumptions that must be carefully examined. Here, we provide evidence that minimally invasive genetic identification from captures at different time intervals (three days and three years) can give insights into cavefish population size dynamics as well as other important demographic parameters of interest. We also provide tools to calibrate sampling and genotyping efforts necessary to reach a given level of precision. Our results suggest that the El Pachón cave population is currently very small, of an order of magnitude of a few hundreds of individuals, and is distributed in a relatively isolated area. The probable decline in population size in the El Pachón cave since the last census in 1971 raises serious conservation issues.
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