Biology subjects

Sgarlata, G. M.

Publications and source records attributed to Sgarlata, G. M..

7 recordsLinked to original sources

bioRxiv2026

Exploring the only known case of sympatry in sportive lemurs: isolation by distance or speciation?

Among Madagascar primates, the sportive lemurs (family Lepilemuridae) have seen their species diversity increase from eight in 2005 to 26 in 2009 mostly by applying the phylogenetic species concept to DNA barcode data. Despite the genus being speciose, only one case of sympatry is known from northern Madagascar, where two sportive lemur species described based on low mtDNA divergence, Lepilemur ankaranensis and Lepilemur milanoii, were found to co-occur at the center of their joint distribution range. Here, to clarify the taxonomy of these two species and examine their sympatry, we apply an integrative taxonomic framework to genomic and morphological data from 84 individuals of L. ankaranensis and L. milanoii, encompassing their entire distribution range and the forest of Analafiana, beyond their southernmost limit. Using clustering, multivariate, and isolation by distance analyses, we find no evidence of a sympatric zone and show that despite clear genetic differentiation between regions, the genomic and morphological diversity of the L. ankaranensis, L. milanoii-Analafiana group is clinal and explained by geographic distance. These results clarify that L. milanoii is a junior synonym of L. ankaranensis and that the Analafiana forest population belongs to L. ankaranensis, extending its distribution. It further implies that the 'sympatric' zone, the Andrafiamena forest, hosts conspecific individuals with slightly differentiated mtDNA backgrounds, rather than slightly differentiated sympatric species. Lastly, we re-evaluate the IUCN conservation metrics of L. ankaranensis, which continue to qualify as Endangered (EN) under the B1ab(i-v) criteria.

evolutionary biology↗

bioRxiv2026

The Genome-Wide Effect of Drift and Selection over a Single Generation

The relative importance of genetic drift versus selection to evolutionary change has long been debated. This debate has mainly focused over long-time-scales (e.g. hundreds of thousands of generations), leaving the question of short-term evolutionary change relatively unaddressed. Our knowledge about the effects of selection on genetic change over short time scales is often based on identifying major allele frequency changes at few loci with large selective advantage. Yet selection often acts on polygenic traits where the short-term response is shaped by small shifts in allele frequency at many loci that will be difficult to distinguish from genetic drift. Here, we quantify the genome-wide effects of polygenic selection over a single generation, using the idea that alleles in stronger genetic correlation (LD) with selected alleles are expected to show greater variance in allele frequency change than expected under genetic drift. We derive expressions relating variation in LD among loci to the variance in allele frequency change due to linked selection and genetic drift and leverage this theory to quantify the contribution of linked selection to a single generation of allele frequency change. To demonstrate our approach, we decompose the genome-wide allele frequency change in the UK Biobank using fitness proxy phenotypes. We show that selection makes a small, but significant, contribution, with genetic drift making up the large majority of the change in allele frequencies. Our framework could be applied to other organisms for which data on number of offspring or allele frequencies over consecutive generations are available, enabling investigations of the short-term, genome-wide effects of polygenic selection across a wide range of species.

evolutionary biology↗

bioRxiv2026

Modelling and Inferring Large-scale Demographic Fluctuations in Structured Populations Through Simulations and PSMC-based Methods.

The climatic oscillations of the Quaternary have likely affected the demographic history of many species, and PSMC (Pairwise Sequentially Markovian Coalescent) has been widely used to investigate these histories. However, it is increasingly acknowledged that PSMC trajectories are difficult to interpret. First, they are influenced by connectivity changes, even without population size changes. Second, most PSMC curves exhibit a few humps when tens of cycles occurred during the Pleistocene. Finally, responses to ancient habitat change have been shown to be species-specific. To address these issues, we simulated structured populations where connectivity (or population size and connectivity) varied according to successive interglacial and glacial periods during the last 2.6 million years. We computed the IICR (Inverse Instantaneous Coalescence Rate), the function that PSMC estimates, and ran PSMC. We further varied the generation length and assumed that some species were positively or negatively affected by glacials. We found that the IICR carries information regarding the demographic oscillations, but that PSMC fails to recover it for times older than 300 ky. For the last 200 ky, PSMC was often able to reproduce qualitatively the demographic oscillations. We also tested SNIF (Structured Non-stationary Inferential Framework), which produced good results using the IICR curve as an input but not when using the PSMC curve. Altogether, our study suggests that the humps older than 300 ky in PSMC histories are unlikely to represent trends of population size or connectivity. However, improving the estimation of the IICR could potentially help reconstruct some of these past demographic changes.

genomics↗

bioRxiv2024

Life history traits influence the dynamics of genetic diversityin a refugium population undergoing expansion andcontraction

Species ranges are dynamic, experiencing expansions, contractions or shifts as a response to habitat changes induced by extrinsic factors such as climate change and, more recently, human activities. While the scientific literature has explored the genetic effects of spatial processes, published studies rarely incorporate life-history traits to study the effect of such changes on species living in the same environments. There is thus a gap in our understanding regarding the variation in genetic diversity patterns among species with distinct life-history traits such as growth rates and generation times, experiencing the same habitat change scenarios. In this study, we first used spatial simulations to investigate the temporal dynamics of genetic diversity within refugium populations experiencing a range expansion followed by a stationary and a contraction period. We explored different scenarios, varying both the speed of contraction and the life-history traits of the simulated species. In addition, we used a simpler panmictic model for which we derived analytical results. Altogether, we identified three temporal dynamics of genetic diversity in the refugium population during the contraction phase: scenarios where genetic diversity i) decreased throughout the contractions, ii) increased for periods that could be greater than thousands of years before plateauing and then decreasing or iii) followed a persistent increasing trend, without any visible effect of the expansion or contraction. We show that these different temporal dynamics can be predicted by comparing the observed expected heterozygosity (He) to the values expected if the species were at equilibrium within the refuge (He refuge) and within the whole landscape (He landscape). We also observe that there are scenarios where a rapid contraction maintains more diversity just at the end of the contraction, as widely believed and as reported in a previous simulation study. However, we also observe the opposite pattern for a wide range of parameters. The widespread idea that observing high diversity levels in a refugium population is due to a recent and rapid habitat loss is thus not necessarily true and will depend on various life history traits and how they relate to habitat change dynamics.

evolutionary biology↗

bioRxiv2022

The effect of habitat loss and fragmentation on isolation-by-distance and time

Throughout Earths natural history, habitats have undergone drastic changes in quality and extent, influencing the distribution of species and their diversity. In the last few hundred years, human activities have destroyed natural habitats at an unprecedent rate, converting continuous habitat into fragmented and isolated patches. Recent global metanalyses suggest that habitat loss and fragmentation (HL&F) has negatively impacted the genetic diversity of many taxa across the world. These conclusions have been drawn by comparing present-day genetic patterns from populations occurring in continuous and fragmented landscapes. In this work, we attempted to go beyond pattern and investigate through simulations some of the processes that influence genetic variation in the context of HL&F. Since most species have a geographically restricted dispersal (known as "isolation-by-distance", IBD), we studied the impact of HL&F on isolation-by-distance. We characterised the behaviour of IBD in the case of i) instantaneous HL&F, ii) gradual (two-steps) HL&F, and iii) instantaneous HL&F following range expansion. In addition, we propose a spatially-explicit theoretical framework by modifying the original theoretical results on isolation-by-distance (Slatkin, 1991; Slatkin, 1993) and apply them to a toroidal stepping-stone model in the context of HL&F. Our results suggest that isolation-by-distance can be maintained for relatively long time after HL&F, thus pointing to the long-term importance of spatial genetic structure in species genetic diversity. In addition, our results may explain why present-day fragmented population still show significant IBD pattern although being disconnected.

evolutionary biology↗

bioRxiv2022

On the genetic consequences of habitat contraction: edge effects and habitat loss

Natural climate change and recent anthropogenic activities have largely contributed to habitat loss and fragmentation across the world, leading to 70% of worldwide remaining forests to be within 1 km of forests edges (Haddad et al., 2015). Ecological studies have shown that edge-effect influences ecological communities, species richness and abundance across many taxa, contributing to worldwide decline in biodiversity. Since edge-effect reduces species abundance and connectivity, it is also expected to negatively influence species genetic variation. In fact, previous theoretical studies had showed that populations closer to the edges of a finite stepping-stone model tends to have shorter coalescence times, and therefore, lower genetic diversity, than central populations. However, predicting the impact of edge effect on local genetic diversity remains challenging in realistic and more complex habitat fragments, where the additive effect of multiple edges is expected to take place. In the present study we explore the genetic consequence of habitat loss at the scale of a habitat fragment (patch-scale), looking at the interplay between patch-size and edge-effect on spatial genetic diversity. We propose a statistical approach to estimate edge-impacted effective population size from habitat cover information and use this measure to predict spatial genetic diversity in both equilibrium and non-equilibrium populations. We address these questions using spatially-explicit simulations and propose a spatially-explicit analytical framework able to model spatio-temporal changes in genetic diversity due to edge-effect and habitat loss.

evolutionary biology↗

bioRxiv2022

The Genomic Diversity of the Eliurus genus in northern Madagascar with a Putative New Species

Madagascar exhibits extraordinarily high level of species richness and endemism, while being severely threatened by habitat loss and fragmentation (HL&F). In front of such threat to biodiversity, conservation effort can be directed, for instance, in the documentation of species that are still unknown to science, or in investigating how species respond to HL&F. The tufted-tail rats genus (Eliurus spp.) is the most speciose genus of endemic rodents in Madagascar, with 13 described species, which occupy two major habitat types: dry or humid forests. The large species diversity and association to specific habitat types make the Eliurus genus a suitable model for investigating species adaptation to new environments, as well as response to HL&F (dry vs humid). In the present study, we investigated Eliurus spp. genomic diversity across northern Madagascar, a region covered by both dry and humid fragmented forests. From the mitochondrial DNA (mtDNA) and nuclear genomic (RAD-seq) data of 124 Eliurus individuals sampled in poorly studied forests of northern Madagascar, we identified an undescribed Eliurus taxon (Eliurus sp. nova). We tested the hypothesis of a new Eliurus species using several approaches: i) DNA barcoding; ii) phylogenetic inferences; iii) species delimitation tests based on the Multi-Species Coalescent (MSC) model, iv) genealogical discordance index (gdi); v) the ad-hoc test of isolation-by-distance within versus between sister-taxa, vi) comparisons of %GC content patterns and vii) morphological analyses. All analyses support the recognition of the undescribed lineage as a distinct species. In addition, we show that Eliurus myoxinus, a species known from the dry forests of western Madagascar, is, surprisingly, found mostly in humid forests in northern Madagascar. In conclusion, we discuss the implications of such findings in the context of Eliurus species evolution and diversification, and use the distribution of northern Eliurus species as a proxy for reconstructing past changes in forest cover and vegetation type in northern Madagascar.

evolutionary biology↗