Biology subjects

Mona, S.

Publications and source records attributed to Mona, S..

3 recordsLinked to original sources

bioRxiv2025

Performance of Sequential Markovian Coalescence Methods when Populations are Structured

Sequentially Markovian Coalescent (SMC) methods are widely used to reconstruct demographic histories from genomic data, yet their accuracy in the presence of population structure has not been systematically evaluated. Here we assessed the performance of two popular SMC based algorithms (PSMC and SMC++) in retrieving the inverse instantaneous coalescent rate (IICR) simulated under two structured equilibrium scenarios, namely the finite island (FIM) and the two-dimensional stepping-stone (2D-SST). Looking backward in time, the IICR of a couple of lineages collected in a deme is characterized by a short period of constant value (the scattering phase) followed by an increase over time (the transition phase) up to a plateau (the collecting phase). Both algorithms recovered the IICR at the collecting phase but significantly deviated from the values expected during the transition phase under specific parameters combination. Specifically, the total error increased with the number of demes and the abruptness of the transition phase, which in turn is related to the extent of between demes connectivity. Moreover, each algorithm displayed a specific bias, corresponding backward in time to an artificial expansion either at the beginning of the collecting phase (PSMC) or of the transition phase (SMC++). Our results demonstrate that the observed systematic biases carry information about metapopulation dynamics, rather than being simple artefacts. Moreover, combining the results obtained from the two algorithms will increase our understanding of the historical demography of the metapopulations and help to put forward specific evolutionary scenarios to be tested with model-based algorithms using SFS or LD statistics.

evolutionary biology↗

bioRxiv2025

Combining population genomics with ancient DNA to understand island colonization history of the Madagascar turtle dove

The Mascarene archipelago (Mauritius, Reunion and Rodrigues), characterized by first human arrival being recent, offers a unique setting to study species colonization. Here we use a combination of modern and ancient DNA data as a case study to investigate the recent colonization history of a species of concern in relation to conservation programs - the Madagascar turtle dove (Nesoenas picturata) on Mauritius and Reunion. We generated a reference genome and re-sequenced genomes from contemporary N. picturata populations, as well as genome-wide data from relevant subfossils. A combination of model-free inferences, site frequency spectrum (SFS) based demographic modelling, and analyses of population structure including that of subfossils indicate that N. picturata colonized both islands independently and naturally from Madagascar, long before human arrival. Summary statistics and SFS-based modeling reveal large effective population sizes (Ne) and high genetic diversity in island populations, conflicting with historical accounts of human-induced demographic collapse. Based on goodness-of-fit, genetic structure and diversity indices do not discriminate between two solutions, one of which posits large recent Ne and negligible translocation rates, while the other supports recent severe bottlenecks followed by high post-human translocation from Madagascar. Nonetheless, linkage disequilibrium provides stronger evidence for the latter scenario, which may also explain high genetic diversity. Both modern and ancient DNA data sources independently support the classification of N. picturata as native to both islands. Our findings highlight the importance of validating demographic models with multiple summary statistics, and potential of using a combination of different data sources to resolve colonization history in recent time.

evolutionary biology↗

bioRxiv2019

Demographic history of a remote ichthyofauna assemblage reveals common processes driving colonization and persistence in endemic coral reef fishes

Elucidating demographic history during the settlement of ecological communities is crucial for properly inferring the mechanisms that shape patterns of species diversity and their persistence through time. Here, we used genomic data and coalescent-based approaches to elucidate for the first time the demographic dynamics associated with the settlement by endemic reef fish fauna of one of the most remote peripheral islands of the Pacific Ocean, Rapa Nui (Easter Island). We compared the demographic history of nine endemic species in order to explore their demographic responses to Pleistocene climatic fluctuations. We found that Rapa Nui endemic species share a common demographic history as signatures of population expansions were retrieved for almost all of the species studied here, and synchronous demographic expansions initiated during the last glacial period were recovered for more than half of the studied species. These results suggest that eustatic fluctuations associated with Milankovitch cycles have played a central role in species demographic histories and in the final stage of the community assembly of many Rapa Nui reef fishes. Specifically, sea level low stands resulted in the maximum reef habitat extension for Rapa Nui endemic species; we discuss the potential role of seamounts in allowing endemic species to cope with Pleistocene climatic fluctuations, and we highlight the importance of local historical processes over regional ones. Overall, our results shed light on the mechanisms by which endemism arises and is maintained in peripheral reef fish fauna.

genomics↗