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Species delimitation is ever more critical for assessing biodiversity in threatened regions of the world, especially when undescribed lineages may be at risk from habitat loss. Mouse lemurs (Microcebus) are an example of a rapid radiation of morphologically cryptic species that are distributed throughout Madagascar in its rapidly vanishing forested habitats. Here, we focus on two pairs of sister lineages that occur in a region in northeastern Madagascar that shows high levels of microendemism. We revisit previous hypotheses of species diversity by filling geographic sampling gaps and by generating new genomic data for three named species, as well as an undescribed lineage previously identified to be of interest due to its highly divergent mtDNA. We analyzed RADseq data with multiple species delimitation methods based on the multispecies coalescent (MSC) model while accounting for introgression. Non-sister lineages occur sympatrically in two instances, despite an estimated divergence time of less than 1 Ma, thus suggesting rapid evolution of reproductive isolation in the mouse lemur clade. We note, however, that the divergence time estimates reported here are based on the MSC and calibrated with pedigree-based primate mutation rates. These dates are considerably more recent than previous analyses that used traditional relaxed clock methods and distant fossil calibrations. One pair of sister lineages passed all species delimitation tests while the other pair failed most, largely due to differences in Ne between the two pairs of lineages. Nevertheless, delimitation results were also supported by differences in levels of gene flow and patterns of isolation-by-distance between the two pairs. We conclude that MSC-based species delimitation methods are valuable tools for evaluating cryptic species, even though these methods can be strongly affected by variable Ne. We suggest that this result has general implications for species delimitation studies of other recently diverged lineages. In the tarball, there are four folders describing analyses, metadata, scripts, and the sequence data. Each folder and their subdirectories have readme files describing the contents.

Background: The extent to which selection determines interspecific patterns of genetic exchanges enlightens the role of adaptation in evolution and speciation. Often reported extensive interspecific introgression could be selection-driven, but also result from demographic processes, especially in cases of invasive species replacements, which can promote introgression at their front. Because invasion and selective sweeps similarly mold variation, population genetics evidence for selection can only be gathered in an explicit demographic framework. The Iberian hare, Lepus granatensis, displays in its northern range extensive mitochondrial DNA introgression from L. timidus, an arctic/boreal species that it replaced locally after the last glacial maximum. We use whole-genome sequencing to infer geographic and genomic patterns of nuclear introgression and fit a neutral model of species replacement with hybridization, allowing us to evaluate how selection influenced introgression genome-wide, including for mtDNA. Results: Although the average nuclear and mtDNA introgression patterns are strongly contrasted, they fit a single neutral model of post-glacial invasive replacement of timidus by granatensis. Outliers of elevated introgression include several genes related to immunity, spermatogenesis, and mitochondrial metabolism. Introgression is reduced on the X-chromosome and in low recombining regions. Conclusion: General nuclear and mtDNA patterns of introgression can be explained by purely demographic processes. Hybrid incompatibilities and interplay between selection and recombination locally modulate levels of nuclear introgression. Selection promoted introgression of some genes involved in conflicts, either interspecific (parasites) or possibly cytonuclear. In the latter case, nuclear introgression could mitigate the potential negative effects of alien mtDNA on mitochondrial metabolism and male-specific traits. Hare (Lepus) pseudo-reference genome built through iterative mapping of sequencing reads from Lepus timidus, Lepus granatensis and Lepus americanus on the European rabbit (Oryctolagus cuniculus) genome template (available from ftp://ftp.ensembl.org/pub/release-80/fasta/oryctolagus_cuniculus/dna/).

Rapid changes in ocean circulation and climate have been observed in marine-sediment and ice cores over the last glacial period and deglaciation, highlighting the non-linear character of the climate system and underlining the possibility of rapid climate shifts in response to anthropogenic greenhouse gas forcing. To date, these rapid changes in climate and ocean circulation are still not fully explained. One obstacle hindering progress in our understanding of the interactions between past ocean circulation and climate changes is the difficulty of accurately dating marine cores. Here, we present a set of 92 marine sediment cores from the Atlantic Ocean for which we have established age-depth models that are consistent with the Greenland GICC05 ice core chronology, and computed the associated dating uncertainties, using a new deposition modeling technique. This is the first set of consistently dated marine sediment cores enabling paleoclimate scientists to evaluate leads/lags between circulation and climate changes over vast regions of the Atlantic Ocean. Moreover, this data set is of direct use in paleoclimate modeling studies.

Raw_sequences_Plate_1Raw Illumina reads from the first plate of our sequencing run. A map of the plate is in the file Plate_map_for_Illumina to match individuals and populations with wells on the plates.Raw_sequences_Plate_2Raw Illumina reads from the second plate of our sequencing run. A map of the plate is in the file Plate_map_for_Illumina to match individuals and populations with wells on the plates.Raw_Sequences_Plate_3Raw Illumina reads from the third plate of our sequencing run. A map of the plate is in the file Plate_map_for_Illumina to match individuals and populations with wells on the plates.Plate_map_for_IlluminaDescription of the amplicons included in our sequencing run, with information about the Plate (1, 2, or 3, corresponding to 1 of the three raw sequencing files), Population, marker, and other information.Corallium_rubrum_genotypesMicrosatellite genotypes of Corallium rubrum used in analyses.Crubrum genotypes for Dryad.csvParamuricea_clavata_genotypesMicrosatellite genotypes for Paramuricea clavata used in our analyses. This file contains only those genotypes not previously published (see publication for information).Pclavata genotypes for Dryad.csvAlignment_Amphipholis_squamata_16SArlequin-formatted file of alignment of 16S sequences from Amphipholis squamata used in this publication, with population information.Alignment_Amphipholis_squamata.arpAlignment_Echinocardium_cordatum_16SArlequin-formatted file of alignment of 16S sequences from Echinocardium cordatum used in this publication, with population information.Alignment_Echinocardium_cordatum.arpAlignment_Hemimysis_margalefi_COIArlequin-formatted file of alignment of COI sequences from Hemimysis margalefi used in this publication, with population information.Alignment_Hemimysis_margalefi.arpAlignment_Myriapora_truncata_COIArlequin-formatted file of alignment of COI sequences from Myriapora truncata used in this publication, with population information.Alignment_Myriapora_truncata.arpAlignment_Ophioderma_longicauda_COIArlequin-formatted file of alignment of COI sequences from Ophioderma longicauda used in this publication, with population information.Alignment_Paracentrotus_lividus_COIArlequin-formatted file of alignment of COI sequences from Paracentrotus lividus used in this publication, with population information.Alignment_Paracentrotus_lividus.arpAlignment_Patella_caerulea_COIArlequin-formatted file of alignment of COI sequences from Patella caerulea used in this publication, with population information.Alignment_Patella_caerulea.arpAlignment_Ophioderma_longicauda_1972Arlequin-formatted file of alignment of the diploid nuclear locus 1972 from Ophioderma longicauda as used in this publication, with population information.Alignment_Ophioderma_longicauda_55384Arlequin-formatted file of alignment of the diploid nuclear locus 55384 from Ophioderma longicauda as used in this publication, with population information.Alignment_Ophioderma_longicauda_79905Arlequin-formatted file of alignment of the diploid nuclear locus 79905 from Ophioderma longicauda as used in this publication, with population information.Alignment_Ophioderma_longicauda_147510Arlequin-formatted file of alignment of the diploid nuclear locus 147510 from Ophioderma longicauda as used in this publication, with population information. Genetic diversity is crucial for species’ maintenance and persistence, yet is often overlooked in conservation studies. Species diversity is more often reported due to practical constraints, but it is unknown if these measures of diversity are correlated. In marine invertebrates, adults are often sessile or sedentary and populations exchange genes via dispersal of gametes and larvae. Species with a larval period are expected to have more connected populations than those without larval dispersal. We assessed the relationship between measures of species and genetic diversity, and between dispersal ability and connectivity. We compiled data on genetic patterns and life history traits in nine species across five phyla. Sampling sites spanned 600 km in the northwest Mediterranean Sea and focused on a 50 km area near Marseilles, France. Comparative population genetic approaches yielded three main results. (1) Species without larvae showed higher levels of genetic structure than species with free-living larvae but the role of larval type (lecithotrophic or planktotrophic) was negligible. (2) A narrow area around Marseilles, subject to offshore advection, limited genetic connectivity in most species. (3) We identified sites with significant positive contributions to overall genetic diversity across all species, corresponding with areas near low human population densities. In contrast, high levels of human activity corresponded with a negative contribution to overall genetic diversity. Genetic diversity within species was positively and significantly linearly related with local species diversity. Our study suggests that local contribution to overall genetic diversity should be taken into account for future conservation strategies.

Gene flow is usually thought to reduce genetic divergence and impede local adaptation by homogenising gene pools between populations. However, evidence for local adaptation and phenotypic differentiation in highly mobile species, experiencing high levels of gene flow, is emerging. Assessing population genetic structure at different spatial scales is thus a crucial step towards understanding mechanisms underlying intraspecific differentiation and diversification. Here, we studied the population genetic structure of a highly mobile species – the great tit Parus major – at different spatial scales. We analysed 884 individuals from 30 sites across Europe including 10 close-by sites (< 50 km), using 22 microsatellite markers. Overall we found a low but significant genetic differentiation among sites (FST = 0.008). Genetic differentiation was higher, and genetic diversity lower, in south-western Europe. These regional differences were statistically best explained by winter temperature. Overall, our results suggest that great tits form a single patchy metapopulation across Europe, in which genetic differentiation is independent of geographical distance and gene flow may be regulated by environmental factors via movements related to winter severity. This might have important implications for the evolutionary trajectories of sub-populations, especially in the context of climate change, and calls for future investigations of local differences in costs and benefits of philopatry at large scales. Genetic data for 30 populations of great tits across EuropeThis file contains the combined dataset collected on great tits (Parus major) from 30 sites in Europe. Provided are individual data for microsatellites (GenData) and environmental data by site (EnvData)Lemoineetal_BJLS4237.R1.xlsx