A year ago, we published a study showing a reduced nucleotide diversity and efficacy of natural selection against slightly deleterious mutations in insular species using a large set of whole-genome sequences, as expected under the nearly neutral theory. Lukáš Kratochvíl & Michail Rovatsos recently question the use of ratios in biology, and specifically here the use of ratios of diversity at the non-synonymous and synonymous sites (πN/πS).
With Benoit Nabholz, we took the opportunity of the response to go deeper in the analysis. First, we explain more clearly that πN and πS are highly correlated under both a nearly and a strictly neutral model because πS = 2cNeμ and πN = 2cNeμf, where c is the ploidy level and f depnds on the theory considered. Under a strict neutral model f is a constant, while under a nearly neutral model, the value changes depending on Ne. When πN is plotted against πS, we observed a better fit for a non-linear model than a linear model, as expected assuming the nearly neutral theory. We also observed that the distributions of fitness effects of mutation are different between mainland and island species, with higher proportion of weakly and mildly deleterious mutations in island species, which is congruent with a reduction of the efficacy of selection in island species.
More details: Leroy et al. Island songbirds as windows into evolution in small populations Current Biology 2021
Leroy & Nabholz Response to Kratochvíl and Rovatsos (The pros, cons and alternatives to the use of πN/πS ratio in pop genomics) Current Biology 2022.
Using a large whole-genome pooled sequencing project, we studied changes in allele covariances in age-structured cohorts of three national oak forests in France dating back to up to 1680. Based on these data and analyses, we provide support for adaptive evolution of long-lived species during recent climatic changes and in particular at genes related to drought and disease resistance. This study is important since the pace of tree microevolution during Anthropocene warming is largely unknown. In addition, this work has practical implications for forest management to climate change.
More details: Saleh*, Chen* et al. Genome-wide evolutionary response of European oaks during the Anthropocene Evolution Letters
Press release:Evolution follows climate: oaks adapted rapidly to climate change in the Anthropocene - INRAE.
I am a population geneticist, employed as permanent researcher (CRCN) at INRAE, Toulouse, France. My research is focused on the study of evolutionary forces: gene flow, drift, mutation and selection and their relative importance in divergence and speciation. My main model is honey bees but I continue to work on some other models through collaborations, including some models I studied over the last decade (plants: oaks, cereals, Populus, Bromeliads etc; animals: passerine birds, salmon etc). My interests also include genomics - in its broader sense - and statistical methods for population genetics.