Ambroise Dalecky

Ecophylogenetics: advances and perspectives

Ecophylogenetics can be viewed as an emerging fusion of ecology, biogeography and macroevolution. This new and fast‐growing field is promoting the incorporation of evolution and historical contingencies into the ecological research agenda through the widespread use of phylogenetic data. Including phylogeny into ecological thinking represents an opportunity for biologists from different fields to collaborate and has provided promising avenues of research in both theoretical and empirical ecology, towards a better understanding of the assembly of communities, the functioning of ecosystems and their responses to environmental changes. The time is ripe to assess critically the extent to which the integration of phylogeny into these different fields of ecology has delivered on its promise. Here we review how phylogenetic information has been used to identify better the key components of species interactions with their biotic and abiotic environments, to determine the relationships between diversity and ecosystem functioning and ultimately to establish good management practices to protect overall biodiversity in the face of global change. We evaluate the relevance of information provided by phylogenies to ecologists, highlighting current potential weaknesses and needs for future developments. We suggest that despite the strong progress that has been made, a consistent unified framework is still missing to link local ecological dynamics to macroevolution. This is a necessary step in order to interpret observed phylogenetic patterns in a wider ecological context. Beyond the fundamental question of how evolutionary history contributes to shape communities, ecophylogenetics will help ecology to become a better integrative and predictive science.

Kin associations and direct vs indirect fitness benefits in colonial cooperatively breeding sociable weavers Philetairus socius

Indirect fitness benefits are believed to be an important force behind the evolution of cooperative breeding. However, helpers may associate with their relatives as a result of delayed dispersal, hence, kin associations might be a consequence of demographic viscosity rather than active choice. In addition, recent studies showed that helpers may have access to reproduction therefore direct benefits might also play an important role. Here, we investigate the possible roles of direct genetic benefits and kin associations on helping behavior in the sociable weaver Philetairus socius, a colonial and cooperatively breeding passerine. We used a microsatellite-based genotyping method to describe the genetic structure within nests and colonies. Within a colony, we found considerable genetic structure between males but not females. Sociable weaver colonies have several nests that are simultaneously active, giving individuals a choice of associating with a range of first-order kin to unrelated individuals. Helpers were significantly more related to the young in the helped nests than in other nests of the colony, suggesting an active choice for associating with kin. The helpers were generally offspring or first-order relatives of one (50%) or both (43%) breeders, although more infrequently, seemingly unrelated individuals also helped (7%). We found no supporting evidence of extrapair parentage and hence no direct genetic gains from helping in our population. This strong reproductive skew is contrary to theoretical models predicting conflicts over reproduction in stepfamilies. We discuss whether female decisions and/or other direct benefits of remaining in kin associations or helping might explain the high skew observed.

Genetic structure and invasion history of the house mouse ( Mus musculus domesticus ) in Senegal, West Africa: a legacy of colonial and contemporary times

Knowledge of the genetic make-up and demographic history of invasive populations is critical to understand invasion mechanisms. Commensal rodents are ideal models to study whether complex invasion histories are typical of introductions involving human activities. The house mouse Mus musculus domesticus is a major invasive synanthropic rodent originating from South-West Asia. It has been largely studied in Europe and on several remote islands, but the genetic structure and invasion history of this taxon have been little investigated in several continental areas, including West Africa. In this study, we focussed on invasive populations of M. m. domesticus in Senegal. In this focal area for European settlers, the distribution area and invasion spread of the house mouse is documented by decades of data on commensal rodent communities. Genetic variation at one mitochondrial locus and 16 nuclear microsatellite markers was analysed from individuals sampled in 36 sites distributed across the country. A combination of phylogeographic and population genetics methods showed that there was a single introduction event on the northern coast of Senegal, from an exogenous (probably West European) source, followed by a secondary introduction from northern Senegal into a coastal site further south. The geographic locations of these introduction sites were consistent with the colonial history of Senegal. Overall, the marked microsatellite genetic structure observed in Senegal, even between sites located close together, revealed a complex interplay of different demographic processes occurring during house mouse spatial expansion, including sequential founder effects and stratified dispersal due to human transport along major roads.

Differential immune gene expression associated with contemporary range expansion of two invasive rodents in Senegal

Biological invasions are major anthropogenic changes associated with threats to biodiversity and health. What determines the successful establishment and spread of introduced populations still remains unsolved. Here, we explore the assertion that invasion success relies on immune phenotypic traits that would be advantageous in recently invaded sites. We compared gene expression profiles between anciently and recently established populations of two major invading species, the house mouse Mus musculus domesticus and the black rat Rattus rattus, in Senegal (West Africa). Transcriptome analyses revealed respectively 364 and 83 differentially expressed genes between anciently and recently established mouse and rat populations. Among them, 20.0% and 10.6% were annotated with functions related to immunity. All immune-related genes detected along the mouse invasion route were over-expressed in recently invaded sites. Genes of the complement activation pathway were over-represented. Results were less straightforward for the black rat as no particular immunological process was over-represented. We revealed changes in transcriptome profiles along invasion routes, although specific patterns differed between the two invasive species. These changes could potentially be driven by increased infection risks in recently invaded sites for the house mouse and stochastic events associated with colonization history for the black rat. These results provide a first step in identifying the immune eco-evolutionary processes potentially involved in invasion success.

Leishmania major and Trypanosoma lewisi infection in invasive and native rodents in Senegal

Bioinvasion is a major public health issue because it can lead to the introduction of pathogens in new areas and favours the emergence of zoonotic diseases. Rodents are prominent invasive species, and act as reservoirs in many zoonotic infectious diseases. The aim of this study was to determine the link between the distribution and spread of two parasite taxa (Leishmania spp. and Trypanosoma lewisi) and the progressive invasion of Senegal by two commensal rodent species (the house mouse Mus musculus domesticus and the black rat Rattus rattus). M. m. domesticus and R. rattus have invaded the northern part and the central/southern part of the country, respectively. Native and invasive rodents were caught in villages and cities along the invasion gradients of both invaders, from coastal localities towards the interior of the land. Molecular diagnosis of the two trypanosomatid infections was performed using spleen specimens. In the north, neither M. m. domesticus nor the native species were carriers of these parasites. Conversely, in the south, 17.5% of R. rattus were infected by L. major and 27.8% by T. lewisi, while very few commensal native rodents were carriers. Prevalence pattern along invasion gradients, together with the knowledge on the geographical distribution of the parasites, suggested that the presence of the two parasites in R. rattus in Senegal is of different origins. Indeed, the invader R. rattus could have been locally infected by the native parasite L. major. Conversely, it could have introduced the exotic parasite T. lewisi in Senegal, the latter appearing to be poorly transmitted to native rodents. Altogether, these data show that R. rattus is a carrier of both parasites and could be responsible for the emergence of new foci of cutaneous leishmaniasis, or for the transmission of atypical human trypanosomiasis in Senegal.

Biological invasions in rodent communities: from ecological interactions to zoonotic bacterial infection issues

Several hypotheses (such as ‘enemy release’, ‘novel weapon’, ‘spillback’ and ‘dilution/density effect’) suggest changes in host-parasite ecological interactions during biological invasion events. Such changes can impact both invasion process outcome and the dynamics of exotic and/or endemic zoonotic diseases. To evaluate these predictions, we investigated the ongoing invasions of the house mouse Mus musculus domesticus, and the black rat, Rattus rattus, in Senegal (West Africa). We focused on zoonotic bacterial communities depicted using 16S rRNA amplicon sequencing approach in both invasive and native rodents sampled along two well-defined invasion routes. Overall, this study provided new ecological evidence connecting parasitism and rodent invasion process, with diverse potential roles of zoonotic bacteria in the invasion success. Our results also highlighted the main factors that lie behind bacterial community structure in commensal rodents. Further experimental studies as well as comparative spatio-temporal surveys are necessary to decipher the actual role of zoonotic bacteria in these invasions. Our data also gave new support for the difficulty to predict the direction in which the relationship between biodiversity changes and disease risk could go. These results should be used as a basis for public health prevention services to design reservoir monitoring strategies based on multiple pathogen surveillance.