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Chikhi, L.

Publications and source records attributed to Chikhi, L..

At least 19 recordsLinked to original sources
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↗
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↗
bioRxiv2024

Extending the IICR to complex non-stationary structured models

Population genetic studies use genetic data to understand aspects of the evolutionary history of species, particularly to infer their demography. Here, we extend the non-stationary structured coalescent framework to complex models where the parameters of the model, and thus the state space, change between stationary periods. To do this, we introduce glue matrices that allow us to map one state space to another, hence enabling the computation of the Inverse Instantaneous Coalescence Rate (IICR) using Q-matrices of different dimensions. This approach allows us to study models where the number of demes changes due to extinction or foundation. Our analysis confirms that interpreting IICR curves as indicators of population size changes can be misleading. However, we also show that there are cases where new deme foundations can generate an increase in the IICR (forward in time). We explore the impact of changes in migration rates, timing of deme creation or deletion, and sampling strategies on the IICR, identifying several counter-intuitive results. For instance, we find that the IICR starts to decrease several generations before any change in the number of demes, as if the population "knew" something was about to happen. It is particularly unexpected when a deme is founded and the population is only increasing. Our results underscore the need for careful interpretation of PSMC and similar curves, which are often used and interpreted as population size changes. By presenting examples of IICRs for various transitions and sampling scenarios, we emphasize the importance of nuanced approaches in population genetic studies.

evolutionary biology↗
bioRxiv2024

Estimating the effective population size across space and time in the Critically Endangered western chimpanzee in Guinea-Bissau: challenges and implications for conservation management

Effective population size (Ne) is a key concept in evolutionary and conservation biology. The western chimpanzee (Pan troglodytes verus) is a Critically Endangered taxon. In Guinea-Bissau, chimpanzees are mainly threatened by habitat loss, hunting and diseases. Guinea-Bissau is considered a key area for its conservation. Genetic tools have not yet been applied to inform management and no estimates of Ne have been obtained. In this study, we use countrys range-wide microsatellite data and five whole-genome sequences to estimate several Ne and infer the recent and ancient demographic history of populations using different methods. We also aim to integrate the different Ne estimates to improve our understanding of the evolutionary history and current demography of this great ape and to discuss strengths and limitations of each estimator and their complementarity in informing conservation decisions. Results from the PSMC method suggest a large ancestral Ne, likely due to ancient structure over the whole subspecies distribution until approximately 10-15,000 years ago. After that, a change in connectivity, a real decrease in size or a combination of both occurred, which reduced the then still large ancestral population to a smaller size (MSVAR: [~]10,000 decreasing to 1,000-6,000 individuals), possibly indicating a fragmentation into coastal and inner subpopulations. In the most recent past, contemporary Ne is below or close to 500 (GONE: 116-580, NeEstimator: 107-549), suggesting a high risk of extinction. The populations at coastal Parks may have been small or isolated for several generations whereas the Boe Park one exhibit higher long-term Ne estimates and can be considered a stronghold of chimpanzee conservation. Through combining different types of molecular markers and analytical methodologies, we try to overcome the limitations of obtaining high quality DNA sampling from wild threatened populations and estimate Ne at different temporal and spatial scales, which is crucial information to make informed conservation decisions at local and regional scales.

genomics↗
bioRxiv2024

Mitochondrial Dysfunction alters Early Endosome Distribution and Cargo Trafficking via ROS-Mediated Microtubule Reorganization

Mitochondria are essential for bioenergetic functions and various cellular processes, including differentiation and immunity, their dysfunction leading to several pathologies. While these pathologies have traditionally been associated with ATP deficits, mitochondrial dysfunction also leads to reactive oxygen species (ROS) generation, inflammation, and alterations the function of other organelles. While the negative impact of mitochondrial dysfunction on lysosomal activity has been established, the relationship between mitochondria and the rest of the endocytic compartment remains poorly understood. Here, we show that inhibiting mitochondrial activity through genetic and chemical approaches causes early endosome (EE) perinuclear aggregation and impairs cargo delivery to lysosomes. This impairment is due to altered microtubule architecture and centrosome dynamics, mediated by ROS. Antioxidants can rescue these EE defects, underlying the pivotal role of mitochondria in maintaining cellular activities through ROS regulation of microtubule networks. Our findings highlight the significance of mitochondria beyond ATP production, emphasizing their critical involvement in endocytic trafficking and cellular homeostasis. These insights emphasize mitochondrias critical involvement in cellular activities and suggest novel targets for therapies to mitigate the effects of mitochondrial dysfunction.

cell biology↗
bioRxiv2024

Extending the IICR to multiple genomes and identification of limitations of some demographic inferential methods

Reconstructing the demographic history of populations and species is one of the greatest challenges facing population geneticists. [50] introduced, for a sample of size k = 2 haploid genomes, a time- and sample-dependent parameter which they called the IICR (inverse instantaneous coalescence rate). Here we extend their work to larger sample sizes and focus on Tk, the time to the first coalescence event in a haploid sample of size k where k [≥] 2. We define the IICRk as the Inverse Instantaneous Coalescence Rate among k lineages. We show that (i) under a panmictic population [Formula] is equivalent to Ne, (ii) the IICRk can be obtained by either simulating Tk values or by using the Q-matrix approach of [61] and we provide the corresponding Python and R scripts. We then study the properties of the [Formula] under a limited set of n-island and stepping-stone models. We show that (iii) in structured models the [Formula] is dependent on the sample size and on the sampling scheme, even when the genomes are sampled in the same deme. For instance, we find that [Formula] plots for individuals sampled in the same deme will be shifted towards recent times with a lower plateau as k increases. We thus show that (iv) the [Formula] cannot be used to represent "the demographic history" in a general sense, (v) the [Formula] can be estimated from real or simulated genomic data using the PSMC/MSMC methods [44, 65] (vi) the MSMC2 method produces smoother curves that infer something that is not the [Formula], but are close to the [Formula] in the recent past when all samples are obtained from the same deme. Altogether we argue that the PSMC, MSMC and MSMC2 plots are not expected to be identical even when the genomes are sampled from the same deme, that none can be said to represent the "demographic history of populations" and that they should be interpreted with care. We suggest that the PSMC, MSMC and MSMC2 could be used together with the [Formula] to identify the signature of population structure, and to develop new strategies for model choice.

evolutionary biology↗
bioRxiv2024

On the demographic history of chimpanzees and some consequences of integrating population structure in chimpanzees and other great apes

Reconstructing the evolutionary history of great apes is of particular importance for our understanding of the demographic history of humans. The reason for this is that modern humans and their hominin ancestors evolved in Africa and thus shared the continent with the ancestors of chimpanzees and gorillas. Common chimpanzees (Pan troglodytes) are our closest relatives with bonobos (Pan paniscus) and most of what we know about their evolutionary history comes from genetic and genomic studies. Most evolutionary studies of common chimpanzees have assumed that the four currently recognised subspecies can be modelled using simple tree models where each subspecies is panmictic and represented by one branch of the evolutionary tree. However, several studies have identified the existence of significant population structure, both within and between subspecies, with evidence of isolation-by-distance (IBD) patterns. This suggests that demographic models integrating population structure may be necessary to improve our understanding of their evolutionary history. Here we propose to use n-island models within each subspecies to infer a demographic history integrating population structure and changes in connectivity (i.e. gene flow). For each subspecies, we use SNIF (structured non-stationary inference framework), a method developed to infer a piecewise stationary n-island model using PSMC (pairwise sequentially Markovian coalescent) curves as summary statistics. We then propose a general model integrating the four subspecies metapopulations within a phylogenetic tree. We find that this model correctly predicts estimates of within subspecies genetic diversity and differentiation, but overestimates genetic differentiation between subspecies as a consequence of the tree structure. We argue that spatial models integrating gene flow between subspecies should improve the prediction of between subspecies differentiation and IBD patterns. We also use a simple spatially structured model for bonobos and chimpanzees (without admixture) and find that it explains signals of admixture between the two species that have been reported and could thus be spurious. This may have implications for our understanding of the evolutionary history of the Homo genus.

evolutionary biology↗
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↗
bioRxiv2023

African bush pigs exhibit porous species boundaries and appeared in Madagascar concurrently with human arrival

Several African mammals exhibit a phylogeographic pattern where closely related taxa are split between West/Central and East/Southern Africa, but their evolutionary relationships and histories remain controversial. Bushpigs (Potamochoerus larvatus) and red river hogs (P. porcus) are recognised as separate species due to morphological distinctions, a perceived lack of interbreeding at contact, and putatively old divergence times, but historically, they were considered conspecific. Moreover, the presence of Malagasy bushpigs as the sole large terrestrial mammal shared with the African mainland raises intriguing questions about its origin and arrival in Madagascar. Analyses of 67 whole genomes revealed a genetic continuum between the two species, with putative signatures of historical gene flow, variable FST values, and a recent divergence time (<500,000 years). Thus, our study challenges key arguments for splitting Potamochoerus into two species and suggests their speciation might be incomplete. Our findings also indicate that Malagasy bushpigs diverged from southern African populations and underwent a limited bottleneck 1,000-5,000 years ago, concurrent with human arrival in Madagascar. These results shed new light on the evolutionary history of an iconic and widespread African genus and provide insight into the longstanding biogeographic puzzle surrounding the bushpigs presence in Madagascar.

evolutionary biology↗
bioRxiv2023

Exact calculation of the expected SFS in structured populations

The Site Frequency Spectrum (SFS), summary statistic of the distribution of derived allele frequencies in a sample of DNA sequences, provides information about genetic variation and can be used to make population inferences. The exact calculation of the expected SFS in panmictic population has been derived in the Markovian coalescent theory for decades, but its generalization to the structured coalescent is hampered by the almost exponential growth of the states space. We propose here a complete algorithmic procedure, from how to build a suitable state space and sort it, to how to take advantage of the sparsity of the rate matrix and to solve numerically the linear system by an iterative method. The simplest case of the symmetrical n-island is then processed to arrive at a ready-to-use demographic parameters inference framework.

genetics↗
bioRxiv2023

Questioning Neanderthal admixture: on models, robustness and consensus in human evolution

Genomic and ancient DNA data have revolutionized palaeoanthropology and our vision of human evolution, with indisputable landmarks like the sequencing of Neanderthal and Denisovan genomes. Yet, using genetic data to identify, date and quantify evolutionary events--like ancient bottlenecks or admixture--is not straightforward, as inferences may depend on model assumptions. In the last two decades, the idea that Neanderthals and members of the Homo sapiens lineage interbred has gained momentum. From the status of unlikely theory, it has reached consensus among human evolutionary biologists. This theory is mainly supported by statistical approaches that depend on demographic models minimizing or ignoring population structure, despite its widespread occurrence and the fact that when ignored, population structure can lead to infer spurious demographic events. We simulated genomic data under a structured and admixture-free model of human evolution, and found that all the tested admixture approaches identified long Neanderthal fragments in our simulated genomes and an admixture event that never took place. We also observed that several published admixture models failed to predict important empirical diversity or admixture statistics, and that our model was best at predicting these statistics jointly. Our results suggest that models accounting for population structure are fundamental to improve our understanding of human evolution, and that admixture between Neanderthals and Homo sapiens needs to be re-evaluated in the light of structured models. Beyond the Neanderthal case, we argue that ancient hybridization events, which are increasingly documented in many species, including with other hominins, may also benefit from such reevaluation. Significance statementThe idea that Neanderthals and some ancestral Homo sapiens populations interbred has gained momentum in the last two decades. Yet, this theory is mainly supported by statistical approaches that assume highly simplified models of hominin evolution. A major issue is that these methods have been poorly tested in the context of population structure, despite its widespread occurrence in many vertebrate species. We simulated data under a structured model and found that all tested methods identified spurious admixture events, suggesting a lack of robustness to population structure. Besides, our structured model was better at predicting several key genomic statistics than the tested admixture models. This suggests that admixture should be re-evaluated in the light of population structure, in hominins and beyond.

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↗
bioRxiv2021

Heterogeneity in effective size across the genome: effects on the Inverse Instantaneous Coalescence Rate (IICR) and implications for demographic inference under linked selection.

The relative contribution of selection and neutrality in shaping species genetic diversity is one of the most central and controversial questions in evolutionary theory. Genomic data provide growing evidence that linked selection, i.e. the modification of genetic diversity at neutral sites through linkage with selected sites, might be pervasive over the genome. Several studies proposed that linked selection could be modelled as first approximation by a local reduction (e.g. purifying selection, selective sweeps) or increase (e.g. balancing selection) of effective population size (Ne). At the genome-wide scale, this leads to variations of Ne from one region to another, reflecting the heterogeneity of selective constraints and recombination rates between regions. We investigate here the consequences of such genomic variations of Ne on the genome-wide distribution of coalescence times. The underlying motivation concerns the impact of linked selection on demographic inference, because the distribution of coalescence times is at the heart of several important demographic inference approaches. Using the concept of Inverse Instantaneous Coalescence Rate, we demonstrate that in a panmictic population, linked selection always results in a spurious apparent decrease of Ne along time. Balancing selection has a particularly large effect, even when it concerns a very small part of the genome. We also study more general models including genuine population size changes, population structure or transient selection and find that the effect of linked selection can be significantly reduced by that of population structure. The models and conclusions presented here are also relevant to the study of other biological processes generating apparent variations of Ne along the genome.

genetics↗
bioRxiv2020

Inferring number of populations and changes in connectivity under the n-island model

Inferring the demographic history of species is one of the greatest challenges in populations genetics. This history is often represented as a history of size changes, thus ignoring population structure. Alternatively, structure is defined a priori as a population tree and not inferred. Here we propose a framework based on the IICR (Inverse Instantaneous Coalescence Rate), which can be estimated using the PSMC method of Li and Durbin (2011) for a single diploid individual. For an isolated population, the IICR matches the population size history, which is how the PSMC outputs are generally interpreted. However, it is increasingly acknowledged that the IICR is a function of the demographic model and sampling scheme. Our automated method fits observed IICR curves of diploid individuals with IICR curves obtained under piecewise-stationary symmetrical island models, in which we assume a fixed number of time periods during which gene flow is constant. We infer the number of islands, their sizes, the periods at which connectivity changes and the corresponding rates of connectivity. Validation with simulated data showed that the method can accurately recover most of the scenario parameters. Our application to a set of five human PSMCs yielded demographic histories that are in agreement with previous studies using similar methods and with recent research suggesting ancient human structure. They are in contrast with the widely accepted view of human evolution consisting of one ancestral population branching into three large continental and panmictic populations with varying degrees of connectivity and no population structure within each continent.

evolutionary biology↗
bioRxiv2020

Mitochondria-Derived Vesicles prevent inflammation by controlling the inclusion of mitochondrial proteins into extracellular vesicles

Most cells constitutively secrete mitochondrial DNA and proteins in extracellular vesicles (EVs), small vesicles that allow the transfer of material between cells. While under pro-inflammatory conditions, this mitochondrial content can further enhance inflammation, its role in the absence of inflammation remains elusive. Here, we demonstrate that cells actively prevent the packaging of pro-inflammatory, oxidized mitochondrial proteins into EVs. Importantly, the distinction between material to be included into EVs and damaged mitochondrial content to be excluded was dependent on their selective targeting to one of two distinct Mitochondria-Derived Vesicles (MDVs) pathways, MDVs being small vesicles carrying material between mitochondria and other organelles. Sorting nexin 9 (Snx9)-dependent MDVs were required to target mitochondrial proteins into EVs, while the Parkinsons disease related protein Parkin blocked this process by targeting damaged mitochondrial content to lysosomes. Our results thus provide important insight into the interplay between mitochondrial quality control mechanisms and mitochondria driven immune responses.

cell biology↗
bioRxiv2019

Complex processes of cryptic speciation in mouse lemurs from a micro-endemism hotspot in Madagascar

AO_SCPLOWBSTRACTC_SCPLOWMouse lemurs (Microcebus) are a radiation of morphologically cryptic primates distributed throughout Madagascar for which the number of recognized species has exploded in the past two decades. This taxonomic explosion has prompted understandable concern that there has been substantial oversplitting in the mouse lemur clade. Here, we take an integrative approach to investigate species diversity in two pairs of sister lineages that occur in a region in northeastern Madagascar with high levels of microendemism and predicted habitat loss. We analyzed RADseq data with multispecies coalescent (MSC) species delimitation methods for three named species and an undescribed lineage previously identified to have divergent mtDNA. Marked differences in effective population sizes, levels of gene flow, patterns of isolation-by-distance, and species delimitation results were found among them. Whereas all tests support the recognition of the presently undescribed lineage as a separate species, the species-level distinction of two previously described species, M. mittermeieri and M. lehilahytsara is not supported - a result that is particularly striking when using the genealogical discordance index (gdi). Non-sister lineages occur sympatrically in two of the localities sampled for this study, despite an estimated divergence time of less than 1 Ma. This suggests rapid evolution of reproductive isolation in the focal lineages, and in the mouse lemur clade generally. The divergence time estimates reported here are based on the MSC and calibrated with pedigree-based mutation rates and are considerably more recent than previously published fossil-calibrated concatenated likelihood estimates, however. We discuss the possible explanations for this discrepancy, noting that there are theoretical justifications for preferring the MSC estimates in this case.

evolutionary biology↗