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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 symmetricaln-island is then processed to arrive at a ready-to-use demographic parameters inference framework.

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 theHomo sapienslineage 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 andHomo sapiensneeds 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 ancestralHomo sapienspopulations 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.

Throughout Earth’s 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.

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 forest’s 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 betweenpatch-sizeandedge-effecton 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.

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 (Eliurusspp.) 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 theEliurusgenus a suitable model for investigating species adaptation to new environments, as well as response to HL&F (dryvshumid). In the present study, we investigatedEliurusspp. 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 124Eliurusindividuals sampled in poorly studied forests of northern Madagascar, we identified an undescribedEliurustaxon (Eliurus sp. nova). We tested the hypothesis of a newEliurusspecies 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) thead-hoctest of isolation-by-distance withinversusbetween 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 thatEliurus 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 ofEliurusspecies evolution and diversification, and use the distribution of northernEliurusspecies as a proxy for reconstructing past changes in forest cover and vegetation type in northern Madagascar.

Genotyping-by-sequencing methods such as RADseq are popular for generating genomic and population-scale data sets from a diverse range of organisms. These often lack a usable reference genome, restricting users to RADseq specific software for processing. However, these come with limitations compared to generic next generation sequencing (NGS) toolkits. Here, we describe and test a simple pipeline for reference-free RADseq data processing that blends de novo elements from STACKS with the full suite of state-of-the art NGS tools. Specifically, we use the de novo RADseq assembly employed by STACKS to create a catalogue of RAD loci that serves as a reference for read mapping, variant calling and site filters. Using RADseq data from 28 zebra sequenced to ~8x depth-of-coverage we evaluate our approach by comparing the site frequency spectra (SFS) to those from alternative pipelines. Most pipelines yielded similar SFS at 8x depth, but only a genotype likelihood based pipeline performed similarly at low sequencing depth (2-4x). We compared the RADseq SFS with medium-depth (~13x) shotgun sequencing of eight overlapping samples, revealing that the RADseq SFS was persistently slightly skewed towards rare and invariant alleles. Using simulations and human data we confirm that this is expected when there is allelic dropout (AD) in the RADseq data. AD in the RADseq data caused a heterozygosity deficit of ~16%, which dropped to ~5% after filtering AD. Hence, AD was the most important source of bias in our RADseq data.

Duke Lemur Centre publication #1510; International audience; Madagascar's Central Highlands are largely composed of grasslands, interspersed with patches of forest. The historical perspective was that Madagascar's grasslands had anthropogenic origins, but emerging evidence suggests that grasslands were a component of the pre-human Central Highlands vegetation. Consequently, there is now vigorous debate regarding the extent to which these grasslands have expanded due to anthropogenic pressures. Here, we shed light on the temporal dynamics of Madagascar's vegetative composition by conducting a population genomic investigation of Goodman's mouse lemur (Microcebus lehilahytsara; Cheirogaleidae). These small-bodied primates occur both in Madagascar's eastern rainforests and in the Central Highlands, making them a valuable indicator species. Population divergences among forest-dwelling mammals will reflect changes to their habitat, including fragmentation, whereas patterns of post-divergence gene flow can reveal formerly wooded migration corridors. To explore these patterns, we used RADseq data to infer population genetic structure, demographic models of post-divergence gene flow, and population size change through time. The results offer evidence that open habitats are an ancient component of the Central Highlands, and that widespread forest fragmentation occurred naturally during a period of decreased precipitation near the last glacial maximum. Models of gene flow suggest that migration across the Central Highlands has been possible from the Pleistocene through the recent Holocene via riparian corridors. Though our findings support the hypothesis that Central Highland grasslands predate human arrival, we also find evidence for human-mediated population declines. This highlights the extent to which species imminently threatened by human-mediated deforestation may already be vulnerable from paleoclimatic conditions.

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.

Correction to: Heredity https://doi.org/10.1038/s41437-021-00426-9, published online 12 April 2021.The author originally listed as Camille Noûs on this article [1] is fictitious (http://www.cogitamus.fr/indexen.html) and as such does not fulfil the requirements for authorship. The correct authorship list is: Armando Arredondo, Beatriz Mourato, Khoa Nguyen, Simon Boitard, Willy Rodríguez, Olivier Mazet & Lounès Chikhi. This has been corrected.; International audience; 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.

Mouse 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. mittermeieriandM. lehilahytsarais 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.

The geographic distribution of a species can provide insights into its population size, ecology, evolution, and how it responded to past (and may respond to future) environmental change. Improving our knowledge of the distribution of threatened species thus is a high priority in assessing their conservation status. However, there are few data available for many recently described yet understudied and potentially threatened primate taxa, making their conservation difficult. Here, we investigated the distribution of the Montagne d’Ambre fork-marked lemur, Phaner electromontis, a threatened nocturnal primate endemic to northern Madagascar and classified as Endangered by the IUCN. Because fork-marked lemurs are highly vocal, we used acoustic surveys to assess the species’ presence-absence and relative population density within 66 distinct forest survey sites in northern Madagascar. Further, we compared data among five forest types within the study area and investigated the relationship between relative population density and climate variables. We report the presence of P. electromontis in 22 study sites; several of these populations were unknown previously. Although we found P. electromontis most frequently in dry-transitional forests, our results suggest that geography (spatial autocorrelation) rather than environmental variables explains the species’ distribution. We hypothesize that environmental unpredictability and gummivory, combined with the presence of several distinct Phaner species in the studied area, could explain the observed distribution.

Note S1. Brief description of the Iberian native cattle breeds sampled in our study. Table S1. Iberian breeds databases. Table S2. Individual sample information. The Y-chromosome haplogroups in bold were determined in this study (n.a.: not applicable). Table S3. FST values between taurine breeds. The highest value is shown in bold and the lowest in italic. Figure S1. Average error rate per sample. Figure S2. Population structure plots determined by NGSadmix; each individual is represented by a stacked column for 3, 4, 6 and 8 proportions. Other K values are shown in Fig. 1b. Figure S3. Principal component analysis done with PCAngsd (components 1 and 2 are shown in Fig. 1c). Variance explained by each component is shown in parenthesis. Figure S4. Differences in Tajima’s D between autosomes and sex chromosome X (calculated using only the female individuals). Figure S5. D-statistics determined as in [4] using genome-wide data. Positive values indicate an excess of derived alleles shared by the breeds in H2 (ANG: Angus; HOL: Holstein; JER: Jersey) and the British Aurochs [5], as indicated by the tree depicted above. Figure S6. Approximately-maximum-likelihood phylogeny of cattle Y-chromosome sequences (sites with a minimum of two minor alleles) determined in FastTree [6] which uses the Jukes-Cantor distance [7]. Labels for the Iberian cattle are according to Table S2. JER: Jersey; ANG: Angus; BOR: Borana; KEN: Kenana. 50% missing data was allowed. The taurine haplogroups Y1 and Y2 are shown in green and red, respectively, and the indicine Y3 in grey. Figure S7. FST per chromosome for all pairwise comparisons within Iberian cattle and between Iberian cattle and the African taurine N’Dama and the African indicine Ogaden. The proportion of shared variation oscillates throughout the genome, reaching extreme values for chromosome 21 (the largest between Iberian and African taurine cattle) and sex chromosome X (shows the lowest differentiation within taurine breeds, while having a relatively large FST between Iberian and the African indicine cattle). (DOCX 1909 kb)

Habitat loss and fragmentation are major threats to biodiversity worldwide. Madagascar is among the top biodiversity hotspots and in the past 100 years several species became endangered on the island as a consequence of anthropogenic activities. In this study, we assessed the levels of genetic diversity and variation of a population of mouse lemurs (Microcebus tavaratra) inhabiting the degraded forests of the Loky-Manambato region (Northern Madagascar). We used a panel of 15 microsatellite markers to genotype 149 individuals. Our aim was to understand if the elements contributing to the heterogeneity of the landscape, such as forest fragmentation, roads, rivers and open habitat, influence the genetic structure of this population. The results showed that geographic distance along with open habitat, vegetation type and, to some extent, the Manankolana River, seem to be the main factors responsible for M. tavaratra population structure in this region. We found that this species still maintains substantial levels of genetic diversity within each forest patch and at the overall population, with low genetic differentiation observed between patches. This seems to suggest that the still existing riparian forest network connecting the different forest patches in this region, facilitates dispersal and maintains high levels of gene flow. We highlight that special efforts targeting riparian forest maintenance and reforestation might be a good strategy to reduce the effect of habitat fragmentation on the genetic diversity of extant M. tavaratra populations.

Forest loss, fragmentation, and anthropization threaten the survival of forest species all over the world. Shifting agriculture is one of these threatening processes in Madagascar. However, when its cycle is halted and the land is left to regenerate, the resulting growth of secondary forest may provide a viable habitat for folivorous and omnivorous lemur species. We aimed to identify the response of nocturnal lemurs to different successional stages of regenerating secondary, degraded mature, and mature forest across a mosaic-type landscape. We surveyed four nocturnal lemur species (Avahi laniger, Microcebus cf. simmonsi, Allocebus trichotis, and Daubentonia madagascariensis) in four forest types of varying habitat disturbance in northeastern Madagascar. We estimated densities in mature and regenerating secondary forest for the eastern woolly lemur (Avahi laniger) and mouse lemur (Microcebus cf. simmonsi), two sympatric species with folivorous and omnivorous diets respectively. We did not estimate densities of Allocebus trichotis and Daubentonia madagascariensis owing to small sample size; however, we observed both species exclusively in mature forest. We found higher population densities of A. laniger and M. cf. simmonsi in secondary than in mature forest, showing the potential of regenerating secondary forest for lemur conservation. Several environmental factors influenced the detectability of the two lemur species. While observer and habitat type influenced detection of the eastern woolly lemur, canopy height and vine density influenced detection of mouse lemurs. Understanding how different species with different diets interact with anthropogenically impacted habitat will aid future management decisions for the conservation of primate species.

Phylogeographic barriers, together with habitat loss and fragmentation, contribute to the evolution of a species’ genetic diversity by limiting gene flow and increasing genetic differentiation among populations. Changes in connectivity can thus affect the genetic diversity of populations, which may influence the evolutionary potential of species and the survival of populations in the long term. We studied the genetic diversity of the little known Northern rufous mouse lemur (Microcebus tavaratra), endemic to Northern Madagascar. We focused on the population of M. tavaratra in the Loky–Manambato region, Northern Madagascar, a region delimited by two permanent rivers and characterized by a mosaic of fragmented forests. We genotyped 148 individuals at three mitochondrial loci (D-loop, cytb, and cox2) in all the major forests of the study region. Our analyses suggest that M. tavaratra holds average genetic diversity when compared to other mouse lemur species, and we identified two to four genetic clusters in the study region, a pattern similar to that observed in another lemur endemic to the region (Propithecus tattersalli). The main cluster involved samples from the two mountain forests in the study region, which were connected until recently. However, the river crossing the study region does not appear to be a strict barrier to gene flow in M. tavaratra. Finally, the inferred demographic history of M. tavaratra suggests no detectable departure from stationarity over the last millennia. Comparisons with codistributed species (P. tattersalli and two endemic rodents, Eliurus spp.) suggest both differences and similarities in the genetic clusters identified (i.e., barriers to species dispersal) and in the inferred demographic history. These comparisons suggest that studies of codistributed species are important to understand the effects of landscape features on species and to reconstruct the history of habitat changes in a region.

Attempts to identify a ‘homeland’ for our species from genetic data are widespread in the academic literature. However, even when putting aside the question of whether a ‘homeland’ is a useful concept, there are a number of inferential pitfalls in attempting to identify the geographic origin of a species from contemporary patterns of genetic variation. These include making strong claims from weakly informative data, treating genetic lineages as representative of populations, assuming a high degree of regional population continuity over hundreds of thousands of years, and using circumstantial observations as corroborating evidence without considering alternative hypotheses on an equal footing, or formally evaluating any hypothesis. In this commentary we review the recent publication that claims to pinpoint the origins of ‘modern humans’ to a very specific region in Africa (Chan et al., 2019), demonstrate how it fell into these inferential pitfalls, and discuss how this can be avoided.

International audience; Several inferential methods using genomic data have been proposed to quantify and date population size changes in the history of species. At the same time an increasing number of studies have shown that population structure can generate spurious signals of population size change. Recently, Mazet et al. (2016) introduced, for a sample size of two, a time-dependent parameter, which they called the IICR (inverse instantaneous coalescence rate). The IICR is equivalent to a population size in panmictic models, but not necessarily in structured models. It is characterised by a temporal trajectory that suggests population size changes, as a function of the sampling scheme, even when the total population size was constant. Here, we extend the work of Mazet et al. (2016) by (i) showing how the IICR can be computed for any demographic model of interest, under the coalescent, (ii) applying this approach to models of population structure (1D and 2D stepping stone, split models, two-and three-island asymmetric gene flow, continent-island models), (iii) stressing the importance of the sampling strategy in generating different histories, (iv) arguing that IICR plots can be seen as summaries of genomic information that can thus be used for model choice or model exclusion (v) applying this approach to the question of admixture between humans and Neanderthals. Altogether these results are potentially important given that the widely used PSMC (pairwise sequentially Markovian coalescent) method of Li and Durbin (2011) estimates the IICR of the sample, not necessarily the history of the populations.

SummaryPairwise measures of neutral genetic differentiation are supposed to contain information about past and on-going dispersal events and are thus often used as dependent variables in correlative analyses to elucidate how neutral genetic variation is affected by landscape connectivity. However, spatial heterogeneity in the intensity of genetic drift, stemming from variations in population sizes, may inflate variance in measures of genetic differentiation and lead to erroneous or incomplete interpretations in terms of connectivity. Here, we tested the efficiency of two distance-based metrics designed to capture the unique influence of spatial heterogeneity in local drift on genetic differentiation. These metrics are easily computed from estimates of effective population sizes or from environmental proxies for local carrying capacities, and allow us to introduce the hypothesis of Spatial-Heterogeneity-in-Effective-Population-Sizes (SHNe). SHNe can be tested in a way similar to isolation-by-distance or isolation-by-resistance within the classical landscape genetics hypothesis-testing framework.We used simulations under various models of population structure to investigate the reliability of these metrics to quantify the unique contribution of SHNe in explaining patterns of genetic differentiation. We then applied these metrics to an empirical genetic dataset obtained for a freshwater fish (Gobio occitaniae).Simulations showed that SHNe explained up to 60% of variance in genetic differentiation (measured asFst) in the absence of gene flow, and up to 20% when migration rates were as high as 0.10. Furthermore, one of the two metrics was particularly robust to uncertainty in the estimation of effective population sizes (or proxies for carrying capacity). In the empirical dataset, the effect of SHNe on spatial patterns ofFstwas five times higher than that of isolation-by-distance, uniquely contributing to 41% of variance in pairwiseFst. Taking the influence of SHNe into account also allowed decreasing the signal-to-noise ratio, and improving the upper estimate of effective dispersal distance.We conclude that the use of SHNe metrics in landscape genetics will substantially improve the understanding of evolutionary drivers of genetic variation, providing substantial information as to the actual drivers of patterns of genetic differentiation in addition to traditional measures of Euclidean distance or landscape resistance.

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Tropical forests harbor extremely high levels of biological diversity and are quickly disappearing. Despite the increasingly recognized high rate of habitat loss, it is expected that new species will be discovered as more effort is put to document tropical biodiversity. Exploring under-studied regions is particularly urgent if we consider the rapid changes in habitat due to anthropogenic activities. Madagascar is known for its extraordinary biological diversity and endemicity. It is also threatened by habitat loss and fragmentation. It holds more than 100 endemic primate species (lemurs). Among these, Microcebus (mouse lemurs) is one of the more diverse genera. We sampled mouse lemurs from several sites across northern Madagascar, including forests never sampled before. We obtained morphological data from 99 Microcebus individuals; we extracted DNA from tissue samples of 42 individuals and amplified two mitochondrial loci (cytb and cox2) commonly used for species identification. Our findings update the distribution of three species (Microcebus tavaratra, Microcebus arnholdi, and Microcebus mamiratra), including a major increase in the distribution area of M. arnholdi. We also report the discovery of a new Microcebus lineage genetically related to M. arnholdi. Several complementary approaches suggest that the newly identified Microcebus lineage might correspond to a new putative species, to be confirmed or rejected with additional data. In addition, morphological analyses showed (a) clear phenotypic differences between M. tavaratra and M. arnholdi, but no clear differences between the new Microcebus lineage and the sister species M. arnholdi; and (b) a significant correlation between climatic variables and morphology, suggesting a possible relationship between species identity, morphology, and environment. By integrating morphological, climatic, genetic, and spatial data of two northern Microcebus species, we show that the spatial distribution of forest-dwelling species may be used as a proxy to reconstruct the past spatial changes in forest cover and vegetation type.

We investigated the genetic, composition of six Canis remains from western Iberia, directly radiocarbon dated to 7,903-7,570 years (cal BP). They were identified as dogs via their qrchaeological and depositional context, osteometry, and a high percentage of aquatic diet shared with humans. For comparison, genetic data were obtained from an additional 37 Iberian dog remains from the Neolithic to Late Antiquity, as well as two Palaeolithic anda a Chalcolithic Canis identified as wolves. Previous data indicated that dog mtDNA haplogroup A (HgA) is prevalent in extant European dogs (>50%), in the Near East and Asia, but rare or absent (

Note S1. Brief description of the Iberian native cattle breeds sampled in our study. Table S1. Iberian breeds databases. Table S2. Individual sample information. The Y-chromosome haplogroups in bold were determined in this study (n.a.: not applicable). Table S3. FST values between taurine breeds. The highest value is shown in bold and the lowest in italic. Figure S1. Average error rate per sample. Figure S2. Population structure plots determined by NGSadmix; each individual is represented by a stacked column for 3, 4, 6 and 8 proportions. Other K values are shown in Fig. 1b. Figure S3. Principal component analysis done with PCAngsd (components 1 and 2 are shown in Fig. 1c). Variance explained by each component is shown in parenthesis. Figure S4. Differences in Tajima’s D between autosomes and sex chromosome X (calculated using only the female individuals). Figure S5. D-statistics determined as in [4] using genome-wide data. Positive values indicate an excess of derived alleles shared by the breeds in H2 (ANG: Angus; HOL: Holstein; JER: Jersey) and the British Aurochs [5], as indicated by the tree depicted above. Figure S6. Approximately-maximum-likelihood phylogeny of cattle Y-chromosome sequences (sites with a minimum of two minor alleles) determined in FastTree [6] which uses the Jukes-Cantor distance [7]. Labels for the Iberian cattle are according to Table S2. JER: Jersey; ANG: Angus; BOR: Borana; KEN: Kenana. 50% missing data was allowed. The taurine haplogroups Y1 and Y2 are shown in green and red, respectively, and the indicine Y3 in grey. Figure S7. FST per chromosome for all pairwise comparisons within Iberian cattle and between Iberian cattle and the African taurine N’Dama and the African indicine Ogaden. The proportion of shared variation oscillates throughout the genome, reaching extreme values for chromosome 21 (the largest between Iberian and African taurine cattle) and sex chromosome X (shows the lowest differentiation within taurine breeds, while having a relatively large FST between Iberian and the African indicine cattle). (DOCX 1909 kb)

BackgroundIberian primitive breeds exhibit a remarkable phenotypic diversity over a very limited geographical space. While genomic data are accumulating for most commercial cattle, it is still lacking for these primitive breeds. Whole genome data is key to understand the consequences of historic breed formation and the putative role of earlier admixture events in the observed diversity patterns.ResultsWe sequenced 48 genomes belonging to eight Iberian native breeds and found that the individual breeds are genetically very distinct with FST values ranging from 4 to 16% and have levels of nucleotide diversity similar or larger than those of their European counterparts, namely Jersey and Holstein. All eight breeds display significant gene flow or admixture from African taurine cattle and include mtDNA and Y‐chromosome haplotypes from multiple origins. Furthermore, we detected a very low differentiation of chromosome X relative to autosomes within all analyzed taurine breeds, potentially reflecting male‐biased gene flow.ConclusionsOur results show that an overall complex history of admixture resulted in unexpectedly high levels of genomic diversity for breeds with seemingly limited geographic ranges that are distantly located from the main domestication center for taurine cattle in the Near East. This is likely to result from a combination of trading traditions and breeding practices in Mediterranean countries. We also found that the levels of differentiation of autosomes vs sex chromosomes across all studied taurine and indicine breeds are likely to have been affected by widespread breeding practices associated with male-biased gene flow.

The Bornean elephant population in Sabah, with only 2000 individuals, is currently mainly restricted to a limited number of forest reserves. The main threats to the species' survival are population fragmentation and isolation of the existing herds. To support and help monitor future conservation and management measures, we assessed the genetic diversity and population structure of Bornean elephants using mitochondrial DNA, microsatellites and single nucleotide polymorphisms. Our results confirmed a previously reported lack of mitochondrial control region diversity, characterized by a single widespread haplotype. However, we found low but significant degree of genetic differentiation among populations and marked variation in genetic diversity with the other two types of markers among Bornean elephants. Microsatellite data showed that Bornean elephants from the Lower Kinabatangan and North Kinabatangan ranges are differentiated and perhaps isolated from the main elephant populations located in the Central Forest and Tabin Wildlife Reserve. The pairwise FST values between these sites ranged from 0.08 to 0.14 (p

Genetic data can be combined with ecological data to study the demographic history of a species, identify landscape features that influence migration patterns, and guide conservation efforts. Perrier’s sifaka (Propithecus perrieri) is a Critically Endangered, rare, and elusive social lemur living in a very restricted, fragmented landscape. To assess the effect of habitat loss and fragmentation on the genetic diversity of the Perrier’s sifaka population we examined 24 microsatellite markers genotyped for 67 samples corresponding to 42 individuals. Perrier’s sifaka shows a low current effective population size (ca. 52–105) and a strong heterozygosity excess, suggesting a historically large but dwindling population. Moreover, we identified a pattern of isolation by distance, typical of continuous habitat, suggesting that sifakas were still able to cross the grasslands between forest fragments in the recent past. Our study calls for a unified conservation plan covering the two protected areas where the species is still present, if not the whole area of its past distribution. Further studies inferring the past demographic history of Perrier’s sifaka may confirm the population decline and shed light on its potential causes.

In the last years, a wide range of methods allowing to reconstruct past population size changes from genome-wide data have been developed. At the same time, there has been an increasing recognition that population structure can generate genetic data similar to those produced under models of population size change. Recently, Mazet et al. (2016) showed that, for any model of population structure, it is always possible to find a panmictic model with a particular function of population size changes, having exactly the same distribution ofT2(the coalescence time for a sample of size two) to that of the structured model. They called this function IICR (Inverse Instantaneous Coalescence Rate) and showed that it does not necessarily correspond to population size changes under non panmictic models. Besides, most of the methods used to analyse data under models of population structure tend to arbitrarily fix that structure and to minimise or neglect population size changes. Here we extend the seminal work of Herbots (1994) on the structured coalescent and propose a new framework, the Non-Stationary Structured Coalescent (NSSC) that incorporates demographic events (changes in gene flow and/or deme sizes) to models of nearly any complexity. We show how to compute the IICR under a wide family of stationary and non-stationary models. As an example we address the question of human and Neanderthal evolution and discuss how the NSSC framework allows to interpret genomic data under this new perspective.Author summaryGenomic data are becoming available for a rapidly increasing number of species, and contain information about their recent evolutionary history. If we wish to understand how they expanded, contracted or admixed as a consequence of recent and ancient environmental changes, we need to develop general inferential methods. Currently, demographic inference is either done assuming that a species is a single panmictic population or using arbitrary structured models. We use the concept of IICR (Inverse of the Instantaneous Coalescence Rate) together with Markov chains theory to develop a general inferential framework which we call the Non-Stationary Structured Coalescent and apply it to explain human and Neanderthal genomic data in a single structured model.

In the last years, a wide range of methods allowing to reconstruct past population size changes from genome-wide data have been developed. At the same time, there has been an increasing recognition that population structure can generate genetic data similar to those produced under models of population size change. Recently, Mazet et al. (Heredity 116:362–371, 2016) showed that, for any model of population structure, it is always possible to find a panmictic model with a particular function of population size changes, having exactly the same distribution ofT2(the coalescence time for a sample of size two) as that of the structured model. They called this function IICR (Inverse Instantaneous Coalescence Rate) and showed that it does not necessarily correspond to population size changes under non-panmictic models. Besides, most of the methods used to analyse data under models of population structure tend to arbitrarily fix that structure and to minimise or neglect population size changes. Here, we extend the seminal work of Herbots (PhD thesis, University of London, 1994) on the structured coalescent and propose a new framework, the Non-Stationary Structured Coalescent (NSSC) that incorporates demographic events (changes in gene flow and/or deme sizes) to models of nearly any complexity. We show how to compute the IICR under a wide family of stationary and non-stationary models. As an example we address the question of human and Neanderthal evolution and discuss how the NSSC framework allows to interpret genomic data under this new perspective.

The crowned sifaka (Propithecus coronatus) is Endangered. It has a large but highly fragmented distribution; its known range extends from the Betsiboka River in the north of Madagascar, to the Mahavavy River in the north-west, and down to the Tsiribihina River in the south-west. The species lives in forest habitats that are highly and increasingly fragmented and are continuously suffering perturbations and destruction. In order to carry out effective conservation measures targeting P. coronatus, its conservation status needs to be updated so that measures can be taken before anthropogenic or natural environmental changes lead to the extirpation of the species in most of its forests. We (i) identified forest fragments where the species is still present and (ii) using the line-transect “Distance” sampling method, estimated the population size and density in the principal remaining forest fragments in the northern part of its range, including both protected and unprotected areas. We visited most of the forests in the northern part of its range in order to update the current area of occupancy, and to rate the state of its forests using a qualitative “forest quality index.” Our survey results have shown that (i) a large number of forests have disappeared or decreased in size in the last 10 years, and (ii) population densities vary considerably among forest fragments (ranging from 49 to 309 individuals per km²), with some very high densities in forests located along the Mahavavy River and in the Antrema area. Their abundance in the area surveyed is likely to be between 4,226 and 36,672 individuals, and most probably above 10,000. It is difficult to extrapolate from these estimates to the total abundance across the species’ entire range, but we estimate that it is likely to be large, probably between 130,000 and 220,000 individuals. Unfortunately, many field observations suggest that its populations continue to decline at a high rate due to habitat loss and hunting, and we argue for the re-evaluation of the conservation status from Endangered A2cd to Endangered A4acd, and the need to survey the rest of the range of P.coronatus. FCT grant: (SFRH/BD/64875/2009), Institut Français de la Biodiversité, Programme Biodiversité de l’Océan Indien (ref.CD-AOOI-07-003), the GDRI Madagascar, the "Laboratoire d’Excellence" (LABEX) entitled TULIP: (ANR -10-LABX-41), Instituto Gulbenkian de Ciência, “Optimus Alive!” Biodiversity grant, University of Mahajanga, Département de Biologie Animale et Ecologie, Fanamby NGO.

Madagascar is known for its unique biodiversity including its endemic primates, the lemurs. This biodiversity is threatened by deforestation, forest degradation and anthropogenic disturbances. Several mouse lemurs (genus Microcebus) have been shown to cope with habitat disturbances and degradation. However, there are 24 recognized mouse lemur species living in very different habitats, and it is not clear whether all these species respond similarly to forest degradation. Here, we review the literature on mouse lemur use of degraded habitat. We further question whether mouse lemurs show variation in degraded habitat use, with respect to forest type, conservation status and distribution range. We show that data on degraded forest (DF) use is available for 14 species and geographically aggregated in a few locations. However, data are scarce for most species, and lacking for almost half of the currently recognized species. Our results however confirm that most mouse lemur species are able to cope with, but do not necessarily respond positively to habitat degradation. We found no variation in degraded habitat use, with respect to forest type, conservation status and distribution range. However, we identified food resources availability, understory structure, predation, and tree hole availability to be the most frequently invoked factors potentially influencing DF use. The relative frequency of these four factors vary among forest types suggesting that differences may exist but still require research efforts for ecological and environmental differences among regions to be fully understood.RESEARCH HIGHLIGHTSLittle differences in the use of degraded forest (DF) between forest types, distribution ranges or conservation status.Varying factors potentially affecting DF use, such as food resources, forest structure, tree hole availability and predation.

The relative effect of past climate fluctuations and anthropogenic activities on current biome distribution is subject to increasing attention, notably in biodiversity hotspots. In Madagascar, where humans arrived in the last ~4-5,000 years, the exact causes of the demise of large vertebrates that cohabited with humans is yet unresolved. The prevailing narrative holds that Madagascar was covered with forest before human arrival, and that the expansion of grasslands was the result of human driven deforestation. However, recent studies have shown that vegetation and fauna structure substantially fluctuated during the Holocene. Here we study the Holocene history of habitat fragmentation in the north of Madagascar using a population genetics approach. To do so we infer the demographic history of two northern Madagascar neighboring, congeneric, and critically endangered forest dwelling lemur species - Propithecus tattersalli and P. perrieri - using population genetic analyses. Our results highlight the necessity to consider population structure and changes in connectivity in demographic history inferences. We show that both species underwent demographic fluctuations which most likely occured after the mid-Holocene transition. While mid-Holocene climate change probably triggered major demographic changes in the two lemur species range and connectivity, human settlements that expanded over the last four millennia in northern Madagascar likely played a role in the loss and fragmentation of the forest cover. This article is protected by copyright. All rights reserved.

For decades, chromosomal inversions have been regarded as fascinating evolutionary elements as they are expected to suppress recombination between chromosomes with opposite orientations, leading to the accumulation of genetic differences between the two configurations over time. Here, making use of publicly available population genotype data for the largest polymorphic inversion in the human genome (8p23-inv), we assessed whether this inhibitory effect of inversion rearrangements led to significant differences in the recombination landscape of two homologous DNA segments, with opposite orientation. Our analysis revealed that the accumulation of genetic differentiation is positively correlated with the variation in recombination profiles. The observed recombination dissimilarity between inversion types is consistent across all populations analyzed and surpasses the effects of geographic structure, suggesting that both structures (orientations) have been evolving independently over an extended period of time, despite being subjected to the very same demographic history. Aside this mainly independent evolution, we also identified a short segment (350 kb