Biology subjects

Ben Chehida, Y.

Publications and source records attributed to Ben Chehida, Y..

9 recordsLinked to original sources

bioRxiv2025

Genetic parallelism underpins convergent mimicry coloration across Lepidoptera

Convergent evolution, the repeated evolution of similar phenotypes in response to the same selective pressures across multiple lineages, is widespread in nature. The extent to which the same genetic mechanisms contribute to convergent evolution could reveal whether the pathway towards these optimal endpoints is flexible or constrained to follow a particular route. Although mimicry of aposematic colour patterns is well known in Lepidoptera, our knowledge of the genetic basis of these convergent patterns is mostly restricted to a few closely-related species. Here we study the genetic basis of mimicry across seven species of Ithomiini and Heliconius butterflies and a day-flying Chetone moth, representing lineages that diverged between [~]1-120 Mya, each presenting similar colour pattern switches. In all the butterfly species, the genetic variants most strongly associated with convergent colour pattern switches are similarly located in non-coding regions near the genes ivory and optix. Colour pattern variation in the moth is associated with a [~]1 Mb inversion around ivory paralleling the supergene architecture of the co-mimic Heliconius numata. In contrast to previous studies in Heliconius, there is limited evidence of alleles shared by means of hybridization in convergence among closely-related ithomiine species. Repeated parallel evolution of regulatory switches via reuse of the same two genes suggests that convergent colour pattern evolution is highly constrained, even across large evolutionary timescales.

evolutionary biology↗

bioRxiv2024

SAMPLE: an R package to estimate sampling effort for species' occurrence rates.

Species occurrence rates are the backbone of many ecological studies. Sampling of species occurrence, however, can come with challenges and might prove more difficult than anticipated. Logistical difficulties, limited funds or time, elusiveness or rarity of species and difficult sampling environments are all examples of scenarios that might contribute to (undesired) small sample sizes. In order to help circumvent some of these difficulties and uncertainties, we present SAMPLE, an R package that aims to inform the user whether the amount of sampling conducted is enough to accurately estimate the occurrence rate of species. We use a simulation approach to help verify the accuracy of the package and to help guide the user in choosing the most appropriate values for the available parameters. Moreover, we provide a real data set where we used SAMPLE to estimate the occurrence rate of various coral-dwelling species on their hosts and the minimum number of samples required for an accurate estimation. This provided example data set includes closely related host species, single or multiple symbionts on a single host coral taxon, and data points obtained from different depths to illustrate how occurrence rates can vary depending on the provided input. Due to its simplicity and easiness of use, this package allows for users to run it whilst in the field to estimate if sampling is sufficient or if the sampling approach needs to be adapted for a particular species. We hope that this package proves itself useful to users that need to estimate occurrence or prevalence rates of species and do not always have the possibility to obtain large sample sizes.

ecology↗

bioRxiv2023

Mitochondrial variation in Anopheles gambiae and An. coluzzii: phylogeographic legacy of species isolation and mito-nuclear associations with metabolic resistance to pathogens and insecticides

Mitochondrial DNA (mtDNA) has been a popular marker in phylogeography, phylogeny, and molecular ecology, but its complex evolution is increasingly recognized. Here, we investigated mtDNA variation in An. gambiae and An. coluzzii, in perspective with other species in the Anopheles gambiae complex (AGC), by assembling the mitogenomes of 1219 mosquitoes across Africa. The mtDNA phylogeny of the AGC was consistent with a previously reported highly reticulated evolutionary history, revealing important discordances with the species tree. The three most widespread species (An. gambiae, An. coluzzii, An. arabiensis), known for extensive historical introgression, could not be discriminated based on mitogenomes. Furthermore, a monophyletic clustering of the three salt-water tolerant species (An. merus, An. melas, An. bwambae) in the AGC also suggested that introgression and possibly selection shaped mtDNA evolution. MtDNA variation in An. gambiae and An. coluzzii across Africa revealed significant partitioning among populations and species. A peculiar mtDNA lineage found predominantly in An. coluzzii and in the hybrid taxon of the African "far-west" exhibited divergence comparable to the inter-species divergence in the AGC, with a geographic distribution matching closely An. coluzziis geographic range. This phylogeographic relict of the An. coluzzii and An. gambiae split was associated with population and species structuration, but not with Wolbachia occurrence. The lineage was significantly associated with SNPs in the nuclear genome, particularly in genes associated with pathogen and insecticide resistance. These findings underline the mito-nuclear coevolution history and the role played by mitochondria in shaping metabolic responses to pathogens and insecticide in Anopheles.

evolutionary biology↗

bioRxiv2021

Harbor porpoise losing its edges: genetic time series suggests a rapid population decline in Iberian waters over the last 30 years

Impact of climate changes on species is expected to be especially visible at the extremities of the species distribution, where they meet sub-optimal conditions. In Mauritania and Iberia, two genetically isolated populations of harbor porpoises form a distinct ecotype and are presumably locally adapted to the upwelling waters. By analyzing the evolution of mitochondrial genetic variation in the Iberian population between two temporal cohorts (1990-2002 vs. 2012-2015), we report a dramatic decrease in genetic diversity. Phylogenetic analyses including neighboring populations identified two porpoises in southern Iberia carrying a divergent haplotype close to the Mauritanian population, yet forming a distinctive lineage. This suggests that Iberian porpoises may not be as isolated as previously thought with immigration from Mauritania or an unknown population in between, but none from the northern ecotype. The rapid decline in the Iberian mitochondrial diversity may be driven by either genetic drift, or by a dramatic decline in census population size possibly resulting from environmental stochasticity, prey depletion, or acute fishery bycatches. These results illustrate the value of genetics time series to inform demographic trends and emphasize the urgent need for conservation measures to ensure the viability of this small harbor porpoise population in Iberia.

evolutionary biology↗

bioRxiv2020

No leading-edge effect in North Atlantic harbor porpoises: Evolutionary and conservation implications

Understanding a species response to past environmental changes can help forecast how they will cope with ongoing climate changes. Harbor porpoises are widely distributed in the North Atlantic and were deeply impacted by the Pleistocene changes with the split of three sub-species. Despite major impacts of fisheries on natural populations, little is known about population connectivity and dispersal, how they reacted to the Pleistocene changes and how they will evolve in the future. Here, we used phylogenetics, population genetics, and predictive habitat modelling to investigate population structure and phylogeographic history of the North Atlantic porpoises. A total of 925 porpoises were characterized at 10 microsatellite loci and one-quarter of the mitogenome (mtDNA). A highly divergent mtDNA lineage was uncovered in one porpoise off Western Greenland, suggesting that a cryptic group may occur and could belong to a recently discovered mesopelagic ecotype off Greenland. Aside from it and the southern sub-species, spatial genetic variation showed that porpoises from both sides of the North Atlantic form a continuous system belonging to the same subspecies (Phocoena phocoena phoceona). Yet, we identified important departures from random mating and restricted intergenerational dispersal forming a highly significant isolation-by-distance (IBD) at both mtDNA and nuclear markers. A ten times stronger IBD at mtDNA compared to nuclear loci supported previous evidence of female philopatry. Together with the lack of spatial trends in genetic diversity, this IBD suggests that migration-drift equilibrium has been reached, erasing any genetic signal of a leading-edge effect that accompanied the predicted recolonization of the northern habitats freed from Pleistocene ice. These results illuminate the processes shaping porpoise population structure and provide a framework for designing conservation strategies and forecasting future population evolution.

evolutionary biology↗

bioRxiv2019

Evolutionary history of the porpoises (Phocoenidae) across the speciation continuum: a mitogenome phylogeographic perspective

Historical changes affecting food resources are a major driver of cetacean evolution. Small cetaceans like porpoises (Phocoenidae) are among the most metabolically challenged marine mammals and are particularly sensitive to changes in their food resources. The seven species of this family inhabit mostly temperate waters and constitute a textbook example of antitropical distribution. Yet, their evolutionary history remains poorly known despite major conservation issues threatening the survival of some porpoises (e.g., vaquita and Yangzte finless porpoises). Here, we reconstructed their evolutionary history across the speciation continuum, from intraspecific subdivisions to species divergence. Phylogenetic analyses of 63 mitochondrial genomes suggest that, like other toothed whales, porpoises radiated during the Pliocene in response to deep environmental changes. However, all intra-specific phylogeographic patterns were shaped during the Quaternary Glaciations. We observed analogous evolutionary patterns in both hemispheres associated with convergent adaptations to coastal versus oceanic environments. This result suggests that the mechanism(s) driving species diversification in the relatively well-known species from the northern hemisphere may apply also to the poorly-known southern species. In contrast to previous studies, we showed that the spectacled and Burmeisters porpoises share a more recent common ancestor than with the vaquita that diverged from southern species during the Pliocene. The low genetic diversity observed in the vaquita carried signatures of a very low population size throughout at least the last 5,000 years, leaving one single relict mitochondrial lineage. Finally, we observed unreported subspecies level divergence within Dalls, spectacled and Pacific harbor porpoises, suggesting a richer evolutionary history than previously suspected. These results provide a new perspective on the mechanism driving the adaptation and speciation processes involved in the diversification of cetacean species. This knowledge can illuminate their demographic trends and provide an evolutionary framework for their conservation.

evolutionary biology↗

bioRxiv2019

The rapid divergence of the Antarctic crinoid species Promachocrinus kerguelensis

Climatic oscillations in Antarctica caused a succession of expansion and reduction of the ice sheets covering the continental shelf of the Southern Ocean. For marine invertebrates, these successions are suspected to have driven allopatric speciation, endemism and the prevalence of cryptic species, leading to the so-called Antarctic biodiversity pump hypothesis. Here we took advantage of the recent sampling effort influenced by the International Polar Year (2007-8) to test for the validity of this hypothesis for 1,797 samples of two recognized crinoid species: Promachocrinus kerguelensis and Florometra mawsoni. Species delimitation analysis identified seven phylogroups. As previously suggested, Promachocrinus kerguelensis forms a complex of six cryptic species. Conversely, despite the morphological differences, our results show that Florometra mawsoni is a lineage nested within Promachocrinus kerguelensis. It suggests that Florometra mawsoni and Promachocrinus kerguelensis belong to the same complex of species. Furthermore, this study indicates that over time and space the different sectors of the Southern Ocean show a remarkable rapid turn-over in term of phylogroups composition and also of genetic variants within phylogroups. We argue that strong \"apparent\" genetic drift causes this rapid genetic turn-over. Finally, we dated the last common ancestor of all phylogroups at less than 1,000 years, raising doubts on the relevance of the Antarctic \"biodiversity pump\" for this complex of species. This work is a first step towards a better understanding of how life is diversifying in the Southern Ocean.

evolutionary biology↗

bioRxiv2019

Genetic homogeneity in face of morphological heterogeneity in the harbor porpoises from the Black Sea and adjacent waters

Isolated from North Atlantic populations, the Black Sea harbor porpoise (Phocoena phocoena relicta) is listed as Endangered due to the massive population decline triggered by historical hunting, and subsequently through fisheries bycatch, and other human activities. Of paramount importance for its conservation, is the characterization of the population structure. While morphological heterogeneity suggested population subdivision, previous genetic studies have failed to find any differences. Here, we investigated the population genetic structure of 144 harbor porpoises sampled opportunistically from across the entire subspecies range including the Aegean, Marmara, Black, and Azov Seas. Genetic variation of across one-fourth of the mitochondrial genome, in combination with the analysis of ten microsatellite loci revealed a nearly complete genetic homogeneity. While simulations show that this inability to reject panmixia does not stem from a lack of power (power to detect FST of 0.008). A genetic time-lag effect limiting our ability to detect population subdivision is also unlikely when effective population size is low, as is the case here. For now, genetic panmixia among porpoises of the Black Sea and adjacent waters cannot be rejected. Population subdivision may well exist, but conclusive evidence would require an improved sampling providing suitable contrasts (e.g., age, sex, season). Also, a genome scale study providing access to neutral and selected genetic variation may reveal cryptic differentiation indicative of ecologically subdivisions. As a precautionary approach, definition of management units should be based on evidence of population heterogeneity obtained from multidisciplinary approaches rather than just genetics.

evolutionary biology↗

bioRxiv2016

Genetic footprint of population fragmentation and contemporary collapse in a freshwater cetacean

Understanding demographic trends and patterns of gene flow in an endangered species is crucial for devising conservation strategies. Here, we examined the extent of population structure and recent evolution of the critically endangered Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis). By analysing genetic variation at the mitochondrial and nuclear microsatellite loci for 148 individuals, we identified three populations along the Yangtze River, each one connected to a group of admixed ancestry. Each population displayed extremely low genetic diversity, consistent with extremely small effective size ([≤]92 individuals). Habitat degradation and distribution gaps correlated with highly asymmetric gene-flow that was inefficient in maintaining connectivity between populations. Genetic inferences of historical demography revealed that the populations in the Yangtze descended from a small number of founders colonizing the river from the sea during the last Ice Age. The colonization was followed by a rapid population split during the last millennium predating the Chinese Modern Economy Development. However, genetic diversity showed a clear footprint of population contraction over the last 50 years leaving only ~2% of the pre-collapsed size, consistent with the population collapses reported from field studies. This genetic perspective provides background information for devising mitigation strategies to prevent this species from extinction.

evolutionary biology↗