Biology subjects

Thumloup, J.

Publications and source records attributed to Thumloup, J..

4 recordsLinked to original sources

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

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↗