Biology subjects

Casane, D.

Publications and source records attributed to Casane, D..

10 recordsLinked to original sources

bioRxiv2022

Genetic identification and reiterated captures suggests that the Astyanax mexicanus El Pachon cavefish population is closed and declining

The size of Astyanax mexicanus blind cavefish populations of North-East Mexico is a demographic parameter of great importance for investigating a variety of ecological, evolutionary and conservation issues. However, very 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 the feasibility of such approach and the interpretation of the 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 can give insights on 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 Pachon 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 Pachon cave since the last census in 1971 raises serious conservation issues.

zoology↗

bioRxiv2022

Ancient and nonuniform loss of olfactory receptor expression renders the shark nose a de facto vomeronasal organ

Cartilaginous fishes are renowned for a keen sense of smell, a reputation based on behavioral observations and supported by the presence of large and morphologically complex olfactory organs. At the molecular level, genes belonging to the four families coding for most olfactory receptors in other vertebrates have been identified in a chimera and a shark, but it was unknown whether they actually code for olfactory receptors in these species. Here we describe the evolutionary dynamics of these gene families in cartilaginous fishes using genomes of a chimera, a skate, a sawfish and eight sharks. The number of putative OR, TAAR and V1R/ORA receptors is very low and stable whereas the number of putative V2R/OlfC receptors is higher and much more dynamic. In the catshark Scyliorhinus canicula, we show that many V2R/OlfC receptors are expressed in the olfactory epithelium in the sparsely distributed pattern characteristic for olfactory receptors. In contrast, the other three vertebrate olfactory receptor families are either not expressed (OR) or only represented with a single receptor (V1R/ORA and TAAR). The complete overlap of markers of microvillous olfactory sensory neurons with panneuronal marker HuC in the olfactory organ suggests the same cell type specificity of V2R/OlfC expression as for bony fishes, i.e. in microvillous neurons. The relatively low number of olfactory receptors in cartilaginous fishes compared to bony fishes could be the result of an ancient and constant selection in favor of a high olfactory sensitivity at the expense of a high discrimination capability.

evolutionary biology↗

bioRxiv2022

Acoustic signatures in cavefish populations inhabiting different caves

Complex patterns of acoustic communication exist throughout the animal kingdom, including underwater. The river-dwelling and the Pachon cave-adapted morphs of the fish Astyanax mexicanus share a repertoire of sounds, but their trigger, use and meaning has changed in cavefish after their recent colonization of the subterranean environment. Here, we explored whether and how sounds produced by blind cavefishes inhabiting different Mexican caves may have evolved, too. We compared acoustic parameters of sounds produced by wild cavefish, recorded in their natural settings, in six different caves located in three mountains ranges in North-East Mexico. Multi-parametric analyses show that the six cavefish populations sampled present cave-specific acoustic signatures, as well as possible individual signatures. The variations in acoustic parameters do not seem related to fish phenotypes, phylogeography or ecological conditions. We propose that the evolution of such acoustic signatures would be neutral and occur by drift, progressively leading to the differentiation of local accents that may prevent interbreeding and thus contribute to speciation.

animal behavior and cognition↗

bioRxiv2021

Coevolution of the olfactory organ and its receptor repertoire in ray-finned fishes

Ray-finned fishes (Actinopterygii) perceive their environment through a range of sensory modalities, including olfaction 1,2. Anatomical diversity of the olfactory organ suggests that olfaction is differentially important among species 1,3,4. To explore this topic, we studied the evolutionary dynamics of the four main gene families (OR, TAAR, ORA/VR1 and OlfC/VR2) 5 coding for olfactory receptors in 185 species of ray-finned fishes. The large variation in the number of functional genes, between 28 in the Ocean Sunfish Mola mola and 1317 in the Reedfish Erpetoichthys calabaricus, is the result of parallel expansions and contractions of the four main gene families. Several ancient and independent simplifications of the olfactory organ are associated with massive gene losses. In contrast, polypteriforms, which have a unique and complex olfactory organ, have almost twice as many olfactory receptor genes as any other ray-finned fish. These observations suggest a functional link between morphology of the olfactory organ and richness of the olfactory receptor repertoire. Further, our results demonstrate that the genomic underpinning of olfaction in ray-finned fishes is heterogeneous and presents a dynamic pattern of evolutionary expansions, simplifications and reacquisitions.

evolutionary biology↗

bioRxiv2021

Genomic evidence that blind cavefishes are not wrecks of ancient life

Cavefishes often have modified eyes, from small but otherwise functional, to highly degenerate structures embedded in a connective tissue and covered by skin. Darwin assumed that these animals are wrecks of ancient life, but several genomic studies suggests they are not ancient. The most radical dating shift is for populations of a Mexican cavefish, Astyanax mexicanus, that have been recently estimated to be at the most a few tens of thousands years old. Despite having highly degenerate eyes, the eye-specific genes of A. mexicanus have low levels of decay. Other blind cavefishes we have examined so far are even older, but also can be dated to the Pleistocene. Here, we estimated the age of blindness of two additional fish species by the level of decay of eye-specific genes. Many pseudogenes were identified in the amblyopsid Typhlichthys subterraneus, suggesting that blindness evolved a few million years ago. In contrast, the blind cichlid Lamprologus lethops appears to be a new case of very recent and rapid eye regression, which occurred in deep river water, an environment similar to caves. Genome-wide analyses support the hypothesis that blindness in cavefishes is never very ancient, and ranges from the Early Pliocene to Late Pleistocene. Together with the description of hundreds of cavefish species, our results suggest that surface fishes were able to recurrently and rapidly adapt to caves and similar small dark ecosystems but the resulting highly specialized blind species with a limited distribution may be evolutionary dead-ends in a relatively short time.

evolutionary biology↗

bioRxiv2021

Evolutionary dynamics of the OR gene repertoire in teleost fishes: evidence of an association with changes in olfactory epithelium shape

Teleost fishes perceive their environment through a range of sensory modalities, among which olfaction often plays an important role. Richness of the olfactory repertoire depends on the diversity of receptors coded by homologous genes classified into four families: OR, TAAR, VR1 and VR2. Herein, we focus on the OR gene repertoire. While independent large contractions of the OR gene repertoire associated with ecological transitions have been found in mammals, little is known about the diversity of the OR gene repertoire and its evolution within teleost fishes, a group that includes more than 34,000 living species. We analyzed genomes of 163 species representing diversity in this large group. We found a large range of variation in the number of functional OR genes, from 15 in Syngnathus typhle and Mola mola, to 429 in Mastacembelus armatus. The number of OR genes was higher in species with an extensively folded olfactory epithelium, that is, for example, when a multi-lamellar rosette was present in the olfactory organ. Moreover, the number of lamellae was correlated with the richness of the OR gene repertoire. While a slow and balanced birth-and-death process generally drives evolution of the OR gene repertoire, we inferred several episodes of high rates of gene loss, sometimes followed by large gains in the number of OR genes. These gains coincide with morphological changes of the olfactory organ and suggest a strong functional association between changes in the morphology and the evolution of the OR gene repertoire.

evolutionary biology↗

bioRxiv2020

Contrasted gene decay in subterranean vertebrates: insights from cavefishes and fossorial mammals

Evolution sometimes proceeds by loss, especially when structures and genes become dispensable after an environmental shift relaxing functional constraints. Gene decay can serve as a read-out of this evolutionary process. Animals living in the dark are outstanding models, in particular cavefishes as hundreds of species evolved independently during very different periods of time in absence of light. Here, we sought to understand some general principals on the extent and tempo of decay of several gene sets in cavefishes. The analysis of the genomes of two Cuban species belonging to the genus Lucifuga provides evidence for the most massive loss of eye genes reported so far in cavefishes. Comparisons with a recently-evolved cave population of Astyanax mexicanus and three species belonging to the tetraploid Chinese genus Sinocyclocheilus revealed the combined effects of the level of eye regression, time and genome ploidy on the number of eye pseudogenes. In sharp contrast, most circadian clock and pigmentation genes appeared under strong selection. In cavefishes for which complete genomes are available, the limited extent of eye gene decay and the very small number of loss of function (LoF) mutations per pseudogene suggest that eye degeneration is never very ancient, ranging from early to late Pleistocene. This is in sharp contrast with the identification of several eye pseudogenes carrying many LoF mutations in ancient fossorial mammals. Our analyses support the hypothesis that blind fishes cannot thrive more than a few millions of years in cave ecosystems.

evolutionary biology↗

bioRxiv2019

Phylogeographic evidence that the distribution of cryptic euryhaline species in the Gambusia punctata species group in Cuba was shaped by the archipelago geological history

The main drivers of diversification of freshwater fishes in Cuba are not yet well understood. For example, salt tolerance was thought as the main factor involved in the diversification of Gambusia punctata species group in this archipelago. However, evidence from a recent DNA barcoding survey suggested the presence of cryptic species and no correlation between species delimitation and level of salinity. In this study, we analyzed the cryptic diversification of G. punctata species group in Cuba, based on a comprehensive sampling of its distribution and including habitats with different salinity levels. We evaluated the patterns of molecular divergence of the samples by sequencing a set of mitochondrial DNA (mtDNA) regions and genotyping nine nuclear microsatellite loci. We also used cytochrome b gene (cytb) partial sequences and these microsatellite loci to analyze population structure inside putative species. Five mtDNA well-differentiated haplogroups were found, four of them also identified by the analysis of the microsatellite polymorphism which corresponds to two already recognized species, G. punctata, and G. rhizophorae, and three putative new species. The extent of hybrid zones between these groups is also described. In each group, populations inhabiting environments with contrasting salinity levels were identified, indicating a generalized trait not specific to G. rhizophorae. The geographic distribution of the groups suggested a strong association with major relict territories of the Cuban Archipelago that was periodically joined or split-up by changes in seawater levels and land uplifts. Salinity tolerance might have facilitated sporadic and long-distance oversea dispersal but did not prevent speciation in the Cuban archipelago.

evolutionary biology↗

bioRxiv2019

Diachronic monitoring of snow leopards at Sarychat-Ertash State Reserve (Kyrgyzstan) through scat genotyping: a pilot study

Snow leopards (Panthera uncia) are a keystone species of Central Asias high mountain ecosystem. The species is listed as vulnerable and is elusive, preventing accurate population assessments that could inform conservation actions. Non-invasive genetic monitoring conducted by citizen scientists offers avenues to provide key data on this species that would otherwise be inaccessible. From 2011 to 2015, OSI-Panthera citizen science expeditions tracked signs of presence of snow leopards along transects in the main valleys and crests of the Sarychat-Ertash State Reserve (Kyrgyzstan). Scat samples were genotyped at seven autosomal microsatellite loci and at a X/Y locus for sex identification, which allowed estimating a minimum of 11 individuals present in the reserve from 2011 to 2015. The genetic recapture of 7 of these individuals enabled diachronic monitoring, providing indications of individuals movements throughout the reserve. We found putative family relationships between several individuals. Our results demonstrate the potential of this citizen science program to get a precise description of a snow leopard population through time.

genetics↗

bioRxiv2016

Evidence of Late Pleistocene origin of Astyanax mexicanus cavefish

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 share similar phenotypic changes such as blindness and depigmentation resulting from independent and convergent evolution. As such they allow examining whether their evolution involved the fixation of preexisting standing genetic variations and/or de novo mutations. Cavefish populations 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.\n\nResultsFirst, 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, neither the ancient origin of the \"old\" lineage. Using IMa2, a program based on a method that does not assume that populations are at mutation/migration/drift equilibrium and thus allows dating population divergence in addition to demographic parameters, we found that microsatellite polymorphism strongly supports a very recent origin of cave populations (i.e. less than 20,000 years). Second, we identified a large number of single-nucleotide polymorphisms (SNPs) in transcript sequences of pools of embryos (Pool-seq) belonging to the \"old\" Pachon cave population and a surface population from Texas. Pachon cave population has accumulated more neutral substitutions than the surface population and we showed that it could be another signature of its recent origin. 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.\n\nConclusionsAlthough it is often assumed that some cave populations such as Pachon cavefish have a very ancient origin, within the range of the late Miocene to the middle Pleistocene, a recent origin of these populations is strongly supported by our analyses of two independent sets of nuclear DNA polymorphism using two very different methods of analysis. 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.

evolutionary biology↗