Molecular ecology and evolution of the porpoises

Although quite common in terrestrial environments, population differentiation across contiguous geographical areas due to vicariance processes or geographical barriers are far less frequent in the marine environment. Movements in pelagic species such as cetaceans are potentially unrestricted over vast distances. This raises the question of how populations become genetically differentiated, what factors drive individual dispersal, and how speciation occurs in marine pelagic species. The present thesis aimed to investigate how these processes occur at two different evolutionary scales: within (micro-evolution) and between (macro-evolution) species. Combining phylogenetic, phylogeographic, and population genetic approaches complemented with ecological modelling, this thesis investigates the evolution of a group of small cetaceans: the porpoise family (Phocoenidae). The study of the phylogenetic relationships between porpoises as well as their biogeography showed that the seven extant porpoise species radiated during the last 5 million years in response to past environmental changes. At the more recent evolutionary scale within the harbor and finless porpoise species, I investigated the processes partitioning the genetic variation among populations, ecotypes, or subspecies. Analysis of empirical and simulated genetic data shed light on past changes in population size and connectivity, while suitable habitat modelling provided insights into the environmental context in which these demographic events happened. Results revealed that all within species subdivisions arose during the last million years and were strongly influenced by the environmental changes occurring during the Last Glacial Maximum (~26-19 kilo years). The results of this thesis provide a framework for the management and conservation of porpoises

Genetic homogeneity in the face of morphological heterogeneity in the harbor porpoise from the Black Sea and adjacent waters (<i>Phocoena phocoena relicta</i>)

Absence of genetic differentiation is usually taken as an evidence of panmixia, but can also reflect other situations, including even nearly complete demographic independence among large-sized populations. Deciphering which situation applies has major practical implications (e.g., in conservation biology). The endangered harbor porpoises in the Black Sea illustrates this point well. While morphological heterogeneity suggested that population differentiation may exist between individuals from the Black and Azov seas, no genetic study provided conclusive evidence or covered the entire subspecies range. Here, we assessed the genetic structure at ten microsatellite loci and a 3904 base-pairs mitochondrial fragment in 144 porpoises across the subspecies range (i.e., Aegean, Marmara, Black, and Azov seas). Analyses of the genetic structure, including F ST, Bayesian clustering, and multivariate analyses revealed a nearly complete genetic homogeneity. Power analyses rejected the possibility of underpowered analyses (power to detect F ST ≥ 0.008 at microsatellite loci). Simulations under various demographic models, evaluating the evolution of F ST, showed that a time-lag effect between demographic and genetic subdivision is also unlikely. With a realistic effective population size of 1000 individuals, the expected “gray zone” would be at most 20 generations under moderate levels of gene flow (≤10 migrants per generation). After excluding alternative hypotheses, panmixia remains the most likely hypothesis explaining the genetic homogeneity in the Black Sea porpoises. Morphological heterogeneity may thus reflect other processes than population subdivision (e.g., plasticity, selection). This study illustrates how combining empirical and theoretical approaches can contribute to understanding patterns of weak population structure in highly mobile marine species. </p

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

Impact of climate change is expected to be especially noticeable at the edges of a species' distribution, where they meet suboptimal habitat conditions. In Mauritania and Iberia, two genetically differentiated populations of harbor porpoises (Phocoena phocoena) form an ecotype adapted to local upwelling conditions and distinct from other ecotypes further north on the NE Atlantic continental shelf and in the Black Sea. By analyzing the evolution of mitochondrial genetic variation in the Iberian population between two temporal cohorts (1990–2002 vs. 2012–2015), we report a substantial decrease in genetic diversity. Phylogenetic analyses including neighboring populations identified two porpoises in southern Iberia carrying a divergent haplotype closely related to those from the Mauritanian population, yet forming a distinct lineage. This suggests that Iberian porpoises may not be as isolated as previously thought, indicating possible dispersion from Mauritania or an unknown population in between, but none from the northern ecotype. Demo-genetic scenario testing by approximate Bayesian computation showed that the rapid decline in the Iberian mitochondrial diversity was not simply due to the genetic drift of a small population, but models support instead a substantial decline in effective 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 Iberian waters.</p

Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum

Historical variation in food resources is expected to be a major driver of cetacean evolution, especially for the smallest species like porpoises. Despite major conservation issues among porpoise species (e.g., vaquita and finless), their evolutionary history remains understudied. Here, we reconstructed their evolutionary history across the speciation continuum. Phylogenetic analyses of 63 mitochondrial genomes suggest that porpoises radiated during the deep environmental changes of the Pliocene. However, all intra-specific subdivisions were shaped during the Quaternary glaciations. We observed analogous evolutionary patterns in both hemispheres associated with convergent evolution to coastal versus oceanic environments. This suggests that similar mechanisms are driving species diversification in northern (harbor and Dall's) and southern species (spectacled and Burmeister's). In contrast to previous studies, spectacled and Burmeister's porpoises shared 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 since the last 5,000 years. Cryptic lineages within Dall's, spectacled and Pacific harbor porpoises suggest a richer evolutionary history than previously suspected. These results provide a new perspective on the mechanisms driving diversification in porpoises and an evolutionary framework for their conservation

Ce que l’étude des protéines du fluide séminal de drosophile nous apprend sur l’évolution de la reproduction

Au cours des dernières décennies, une baisse drastique de la fertilité mâle a été observée, révélant des troubles importants dans la qualité et la quantité des spermatozoïdes. Cependant, les causes d’infertilité peuvent être également attribuées à la qualité et à la quantité du fluide séminal transmis à la femelle lors de l’accouplement. Les travaux présentés ici renseignent sur la composition du fluide séminal et ses conséquences sur les spermatozoïdes, ainsi que sur ses effets sur la physiologie et le comportement reproducteur des femelles. Ils soulignent l’importance du fluide séminal dans les interactions sexuelles postcopulatoires et illustrent ses effets en tant que pression de sélection dans la coévolution mâle-femelle

Determinants of dispersal and phylogeographic history of a highly mobile cetacean species:The North Atlantic harbour porpoise.

Understanding the determinants of individual dispersal, population structure, and evolutionary history can provide insights about how species will evolve with climate change. However, such a task is complex for highly mobile marine species such as cetaceans for which it is intuitively difficult to infer what could limit their dispersal. The harbor porpoise (Phocoena phococena) is widely distributed in the North Atlantic. Its biogeographic history has been shaped by environmental variation during the last Glaciations with the divergence of three ecotypes (or sub-species) in the Eastern North Atlantic (ENA). However, we still do not know the degree to which populations in the ENA are connected to those in the Western North Atlantic (WNA), what environmental determinants drive the dispersal of porpoises, and whether distinct ecotypes exist in the WNA. Here we analyze the genetic diversity of 10 microsatellite loci and one-quarter of the mitogenome for an unprecedented sampling of 1,533 individuals. Using spatially explicit population genetics approaches, we investigated fine-scale population structure over the entire North Atlantic. Our study suggests that porpoises from the WNA and ENA are part of the same “continental shelf ecotype” that stretches from the northern Bay of Biscay to the WNA. We identified a clear signal of restricted dispersal in the mitogenome data supporting previous evidence of female philopatry. We also discovered a cryptic divergent mitochondrial lineage in one individual from Western Greenland suggesting a fourth distinct ecotype may exist. Finally, we reconstructed the phylogeographic history of these porpoises using coalescent simulations of population evolution, shedding light on the likely scenarios that shaped the current pattern of genetic diversity. These results provide key insights into the factors and processes shaping population structure in this species and will help model its evolution in the forecasted climate changes

Microbiome composition is shaped by geography and population structure in the parasitic wasp Asobara japonica , but not in the presence of the endosymbiont Wolbachia

International audienceThe microbial community composition is crucial for diverse life-history traits in many organisms. However, we still lack a sufficient understanding of how the host microbiome is acquired and maintained, a pressing issue in times of global environmental change. Here we investigated to what extent host genotype, environmental conditions, and the endosymbiont Wolbachia influence the bacterial communities in the parasitic wasp Asobara japonica. We sampled multiple wasp populations across ten locations in their natural distribution range in Japan and sequenced the host genome (whole genome sequencing) and microbiome (16S rRNA gene). We compared the host population structure and bacterial community composition of wasps that reproduce sexually and are uninfected with Wolbachia with wasps that reproduce asexually and carry Wolbachia. The bacterial communities in asexual wasps were highly similar due to a strong effect of Wolbachia rather than host genomic structure. In contrast, in sexual wasps, bacterial communities appear primarily shaped by a combination of population structure and environmental conditions. Our research highlights that multiple factors shape the bacterial communities of an organism and that the presence of a single endosymbiont can strongly alter their compositions. This information is crucial to understanding how organisms and their associated microbiome will react in the face of environmental change