June 2021 – Urine DNA (uDNA) as a non‐lethal method for endoparasite biomonitoring: Development and validation
We used the host-parasite system brown trout – Tetracapsuloides bryosalmonae (an emerging myxozoan parasite of salmonids) to non-lethally detect endoparasite DNA from fish urine. We showed that uDNA diagnostic test was sensitive enough to assess host infection status (90% of successful diagnostic) as well as parasite load.
Duval, E., Blanchet, S., Quéméré, E., Jacquin, L., Veyssière, C., Lautraite, A., … & Loot, G. (2021). Urine DNA (uDNA) as a non‐lethal method for endoparasite biomonitoring: Development and validation. Environmental DNA.
June 2021 – Pathogen-mediated selection favours the maintenance of innate immunity gene polymorphism in a widespread wild ungulate
As we showed in a previous work, innate immunity-related gene such as Toll-Like receptor genes (Tlr) exhibit similarly high levels of genetic diversity as genes of the Major Histocompatibility Complex (MHC), and signatures of contemporary balancing selection in roe deer.
We investigated the evolutionary mechanisms by which pathogen-mediated selection could shape this innate immunity genetic diversity in roe deer by examining the relationships between Tlr (Tlr2, Tlr4 and Tlr5) genotypes and infections with Toxoplasma and Chlamydia, two widespread intracellular pathogens known to cause reproductive failure in ungulates. We showed that the two pathogens, whose exposure vary significantly across year and landscape structure, exert antagonistic selective pressures on toll-like receptors gene polymorphism.
Quéméré, E., Hessenauer, P., Galan, M., Fernandez, M., Merlet, J., Chaval, Y., … & Charbonnel, N. (2021). Pathogen‐mediated selection favours the maintenance of innate immunity gene polymorphism in a widespread wild ungulate. Journal of Evolutionary Biology.
May 2021 – Unravelling the dietary diversity of neotropical top predators using scat DNA metabarcoding: a case study on the elusive Giant Otter
We developed a multi-marker DNA metabarcoding approach to analyze the dietary diversity of giant otters (Pteronura brasiliensis) from fecal DNA while controlling predator species identity. Most prey are identified at the species level and the dietary profiles provided independently by the two markers are highly similar, whether in terms of list of prey or frequency of occurrences, hence validating the approach. We detected a higher number of rare fish prey with the 12S primers that amplified solely Teleost species while the degenerate COI primers revealed non-fish prey (e.g., amphibians, snakes, birds, and earthworms) and confirmed predator species identity.
Quéméré, E., Aucourd, M., Troispoux, V., Brosse, S., Murienne, J., Covain, R., … & Galan, M. (2021). Unraveling the dietary diversity of Neotropical top predators using scat DNA metabarcoding: A case study on the elusive Giant Otter. Environmental DNA.
August 2020 –
Genetic consequences of social structure in the golden-crowned sifaka
Nearly 15 years ago, during my Phd supervised by Lounès Chikhi, I headed toward northern Madagascar to assess the conservation and genetic status of the critically endangered golden-crowned sifaka (Propithecus tattersalli), one the most emblematic lemur species. I used non-invasive DNA (extraction from faecal material) to study the impact of habitat loss and fragmentation in the evolution of the genetic diversity of this species. With my fied assistants, we were able to obtain a large collection of fecal samples across the entire species range. With Bárbara Parreira and collegues from The Instituto Gulbenkian of Ciencia, we recently went back to this awesome dataset and used simulations to investigate the effect of fine-scale social structure on the genetic diversity of species at different organisational level (individual, social group, sampling site, forest fragment).
Contrary to the widely shared idea that small social groups should drift and accumulate inbreeding, we demonstrated that social structure maintained high levels of genotypic diversity within social units. In orther words, when the data were analysed at the level of the social unit, rather than at the level of the forest fragment, outbreeding seemed the rule, rather than the exception. This article published this month in the journal Heredity is the outcome of a fruitful talk between theory and applied genetics, and shows the importance of social structure in maintaining genotypic diversity in an endangered species that lives in a highly fragmented region. Link for the paper is here.
Parreira, B., Quéméré, E., Vanpé, C., Carvalho, I., & Chikhi, L. (2020). Genetic consequences of social structure in the golden-crowned sifaka. Heredity, 1-12
August 2020 – Demography and adaptation promoting evolutionary transitions in a mammalian genus that diversified during the Pleistocene
Roe deer (Capreolus spp.) are a little odd. They are one of only a few placental mammals—and the only genus among even‐toed ungulates—capable of putting embryonic development “on ice”, also known as embryonic diapause. It would seem such an unusual trait is probably the product of natural selection, but a big question is, how does selection for important traits, such as diapause, interact with the historical demography of a species? In a ‘From the Cover’ article in this issue of Molecular Ecology , de Jong et al. (2020) demonstrate that selection is acting on genes associated with reproductive biology in roe deer, despite heightened genetic drift due to reduced effective population size through the Pleistocene.
De Jong M, Li Zhipeng, Qin Y, Quéméré E, Baker K, Wang W, Hoelzel R (2020).Demography and adaptation promoting evolutionary transitions in a mammalian genus that diversified during the Pleistocene. Molecular Ecology. 29(15):2777-2792
June 2020 – During her Phd Viva, my student Laura Gervais discuss about how biologging and genome-wide data can help to expand the study of evolutionary potential in wild populations.
Marsh 2020 – Genetic epidemiology of the Alpine ibex reservoir of persistent and virulent brucellosis outbreak
We investigated immunogenetic diversity of the Alpine ibex (Capra ibex) population of the Bargy massif, reservoir of a virulent outbreak of brucellosis. We analysed the polymorphism and associations with disease resistance of the MHC Class II Drb gene and several non-MHC genes (Toll-like receptor genes, Slc11A1) involved in the innate immune response to Brucella in domestic ungulates. We found a very low neutral genetic diversity and a unique MHC Drb haplotype in this population founded few decades ago from a small number of individuals. By contrast, other immunity-related genes have maintained polymorphism and some showed significant associations with the brucellosis infection status hence suggesting a predominant role of pathogen-mediated selection in their recent evolutionary trajectory.
Quéméré E, Rossi S, Petit E, Marchand P, Merlet J, Game Y, Galan M, Gilo-Fromont E (2020) Genetic epidemiology of the Alpine ibex reservoir of persistent and virulent brucellosis outbreak. Scientific Reports (10):4400. https://www.nature.com/articles/s41598-020-61299-2
January 2020 – Pedigree‐free quantitative genetic approach provides evidence for heritability of movement tactics
We combined intensive biologging technology with genome‐wide data and a pedigree‐free quantitative genetic approach to quantify repeatability, heritability and evolvability for a suite of behaviours related to the risk avoidance‐resource acquisition trade‐off in a wild roe deer (Capreolus capreolus ) population inhabiting a heterogeneous, human‐dominated landscape.
Gervais, L., Hewison, A. J., Morellet, N., Bernard, M., Merlet, J., Cargnelutti, B., Chaval, Y., Pujol, B., Quemere, E. (2020). Pedigree-free quantitative genetic approach provides evidence for heritability of movement tactics in wild roe deer. Journal of Evolutionary Biology 33(5):595-607. https://doi.org/10.1111/jeb.13594