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Extra-organismal DNA (eoDNA) from material left behind by organisms (noninvasive DNA, e.g., feces, hair) or from environmental samples (eDNA, e.g., water, soil) is a valuable source of genetic information. However, the relatively low quality and quantity of eoDNA, which can be further degraded by environmental factors, results in reduced amplification and sequencing success. This is often compensated for through cost- and time-intensive replications of genotyping/sequencing procedures. Therefore, system- and site-specific quantifications of environmental degradation are needed to maximize sampling efficiency (e.g., fewer replicates, shorter sampling durations), and to improve species detection and abundance estimates. Using 10 environmentally diverse bat roosts as a case study, we developed a robust modeling pipeline to quantify the environmental factors degrading eoDNA, predict eoDNA quality, and estimate sampling-site-specific ideal exposure duration. Maximum humidity was the strongest eoDNA-degrading factor, followed by exposure duration and then maximum temperature. We also found a positive effect when hottest days occurred later. The strength of this effect fell between the strength of the effects of exposure duration and maximum temperature. With those predictors and information on sampling period (before or after offspring were born), we reliably predicted mean eoDNA quality per sampling visit at new sites with a mean squared error of 0.0349. Site-specific simulations revealed that reducing exposure duration to 2–8 days could substantially improve eoDNA quality for future sampling. Our pipeline identified high humidity and temperature as strong drivers of eoDNA degradation even in the absence of rain and direct sunlight. Furthermore, we outline the pipeline's utility for other systems and study goals, such as estimating sample age, improving eDNA-based species detection, and increasing the accuracy of abundance estimates.

Projecting future response of biological systems to global change requires a mechanistic understanding of how climate and ecology jointly drive species demography and range dynamics. Such knowledge is particularly crucial when it comes to invasive species, which expansion may have far-reaching consequences for recipient ecosystems. Here, we use mark-recapture in replicated outdoor mesocosms to examine how survival and dispersal, two key drivers of population and range dynamics, respond to climate and ecology in the invasive red swamp crayfish (Procambarus clarkii) along an invasion gradient. We show that crayfish survival probability increased with (i) increasing body size at high (but not low) crayfish density and (ii) with warmer temperatures, and decreased (i) with increasing body condition and (ii) under higher crayfish density. Overland dispersal probability by crayfish increased with increasing (i) body-size, (ii) body condition and (iii) temperatures. In contrast, crayfish from range-edge and range-core habitats had similar survival and overland dispersal probabilities, suggesting no evolution of the crayfish expansion potential along the invasion gradient. Our results highlight that species population dynamics and range shifts in a changing world are driven by joint contributions from both climate and ecology. In P. clarkii, global warming will simultaneously promote both a demographic increase and a geographic range expansion, especially in populations dominated by large-bodied individuals.

The development of methods for individual identification in wild species and the refinement of Capture-Mark-Recapture (CMR) models during the past decades has greatly improved the assessment of population demographic rates to answer ecological and conservation questions. In particular, multistate models, with their flexibility for the analysis of complex study systems, have become popular in the ecological community. However, despite the extensive use of these models, little attention has been paid to the effect of common violations of the CMR model assumptions, such as mark loss and the often-associated recycling of remarked individuals.To explore this knowledge gap we used a wide range of simulation scenarios reflecting frequently encountered real case studies inspired from the survival rates of 700 vertebrates’ species. We estimated the effects of mark loss and recycled individuals on parameter estimates using a multi-state Cormack-Jolly-Seber (MSCJS) framework. We explored parameter bias through simulations of a metapopulation system with different capture and survival rates. We also illustrated how mark loss can be easily estimated and accounted for using an empirical long-term (10 years) CMR dataset of bats, individually identified using both PIT tag technology as marks that can be lost, and multi-locus genotypes as ‘permanent marks’.The results from our simulated scenarios demonstrated that the occurrence of bias and the parameters concerned were highly dependent on the study system, and no general rules on parameter behaviour can be established a priori. The model structure and the interdependency among parameters make it challenging to predict how bias could affect estimates.Our results highlight the need to assess the effect of mark loss when using MSCJS models. Ignoring such violations of model assumptions can have important implications for ecological inferences and conservation policies. In general, the use of permanent marks (e.g. genotype), should always be preferred when modelling of population dynamics and if not possible, combining two types of temporary marks (e.g. PIT tags, bands) should be considered.

Some species are difficult to observe and others, need to be not disturbed because of their vulnerability. In response to the difficulty of studying the dispersal behaviors of these species, some areas of biology have been combined in order to access the information despite practical limitations. Here we present the combination of several methodologies from landscape ecology to non- invasive population genetics that allow us to obtain important information onRinolophus hipposideros, a vulnerable European bat. We genotyped 18 georeferrenced colonies in Brittany (France) from droppings collected in their refuges. We used 6 microsatellite markers in order to obtain the genetic distances between them. On the other hand we calculated Euclidian distances between the refuges occupied by these colonies and some ecological distances with the Pathmatrix module of ArcGis 3.2. We tested hypothesis about the difficulty of dispersal of the species in areas without forest cover or with a low density of hedges. Thanks to the Monmonier algorithm we could infer possible genetic barriers between the colonies and we could compare their location to the presence of landscape barriers (areas with little tree cover). We detected a pattern of isolation by distance that reveals limited dispersal capacities in the species but no pattern linked to ecological distances. We found that some of the neighboring colonies with greater genetic distances between them were located in areas with low density of hedges which could suggest an impact of this landscape element in their movements. Finer studies should allow us to conclude on the need or not of forest cover in the dispersal of this species.Abstract Figure

International audience; In forest-specialist mammals, forest loss may induce resistance to animal movement and reduce gene flow between populations, and thereby increase genetic erosion and extinction risks for populations. Understanding how landscape features affect gene flow is of critical importance for conservation. Using landscape genetic tools at multiple spatial scales, we assessed the effects of landscape heterogeneity (in particular the presence of wide open or rural habitats) on gene flow in an endangered forest-specialist species – the Barbary macaque (Macaca sylvanus) –, in its major forest site in Morocco. We genotyped 248 individuals from 23 macaque groups using 11 microsatellite loci. We modelled different scenarios of isolation by landscape resistance. We further tested the relationships between genetic distance and isolation by resistance, after controlling for the effect of isolation by distance. Our results revealed a significant genetic structure and a disruption of gene flow even in geographic proximity. Whatever the spatial scale, remoteness from the forest edge beyond 1km acted as a barrier to macaque movements. In addition, at a fine scale, human-dominated areas were also detected as a barrier. The detection of private alleles in each population suggests an ongoing process of isolation. The preservation of the Barbary macaque implies 1) strictly avoiding all silvicultural practices (in particular clear-cutting of holm oak forests) that could contribute to increase distances between forest patches, 2) restoring corridors between forests, 3) and preserving key small forest patches as potential stepping stones facilitating macaque dispersal.

International audience; Within-species genetic diversity is crucial for the persistence and integrity of populations and ecosystems. Conservation actions require an understanding of factors influencing genetic diversity, especially in the context of global change. Both population size and connectivity are factors greatly influencing genetic diversity; the relative importance of these factors can, however, change through time. Hence, quantifying the degree to which population size or genetic connectivity are shaping genetic diversity, and at which ecological time scale (past or present), is challenging, yet essential for the development of efficient conservation strategies. In this study, we estimated the genetic diversity of 42 colonies of Rhinolophus hipposideros, a long-lived mammal vulnerable to global change, sampling locations spanning its continental northern range. Here, we present an integrative approach that disentangles and quantifies the contribution of different connectivity measures in addition to contemporary colony size and historic bottlenecks in shaping genetic diversity. In our study, the best model explained 64% of the variation in genetic diversity. It included historic bottlenecks, contemporary colony size, connectivity and a negative interaction between the latter two. Contemporary connectivity explained most genetic diversity when considering a 65 km radius around the focal colonies, emphasizing the large geographic scale at which the positive impact of connectivity on genetic diversity is most profound and hence, the minimum scale at which conservation should be planned. Our results highlight that the relative importance of the two main factors shaping genetic diversity varies through time, emphasizing the relevance of disentangling them to ensure appropriate conservation strategies.

International audience; Recent theoretical and experimental models have revealed the role played by evolution during species spread, and in particular have questioned the influence of genetic drift at range edges. By investigating the spread of an aquatic invader in patchy habitats, we quantified genetic drift and explored its consequences for genetic diversity and fitness. We examined the interplay of gene flow and genetic drift in 36 populations of the red swamp crayfish, Procambarus clarkii, in a relatively recently invaded wetland area (30 years, Brière, northwest France). Despite the small spatial scale of our study (15 km ), populations were highly structured according to the strong barrier of land surfaces and revealed a clear pattern of colonization through watercourses. Isolated populations exhibited small effective sizes and low dispersal rates that depended on water connectivity, suggesting that genetic drift dominated in the evolution of allele frequencies in these populations. We also observed a significant decrease in the genetic diversity of isolated populations over only a 2-year period, but failed to demonstrate an associated fitness cost using fluctuating asymmetry. This study documents the possible strong influence of genetic drift during the spread of a species, and such findings provide critical insights into the current context of profound rearrangements in species distributions due to global change.

Bats are the longest-lived mammals, given their body size. However, the underlying molecular mechanisms of their extended healthspans are poorly understood. To address this question we carried out an eight-year longitudinal study of ageing in long-lived bats (Myotis myotis). We deep-sequenced ~1.7 trillion base pairs of RNA from 150 blood samples collected from known aged bats to ascertain the age-related transcriptomic shifts and potential microRNA-directed regulation that occurred. We also compared ageing transcriptomic profiles between bats and other mammals by analysis of 298 longitudinal RNA sequencing datasets. Bats did not show the same transcriptomic changes with age as commonly observed in humans and other mammals, but rather exhibited a unique, age-related gene expression pattern associated with DNA repair, autophagy, immunity and tumour suppression that may drive their extended healthspans. We show that bats have naturally evolved transcriptomic signatures that are known to extend lifespan in model organisms, and identify novel genes not yet implicated in healthy ageing. We further show that bats’ longevity profiles are partially regulated by microRNA, thus providing novel regulatory targets and pathways for future ageing intervention studies. These results further disentangle the ageing process by highlighting which ageing pathways contribute most to healthy ageing in mammals. RNA-Seq analysis of an 8-year longitudinal study of long-lived bats reveals unique transcriptomic signatures and novel candidate genes associated with healthy ageing.

International audience; 1.One of the major planning tools to respond to urban landscape fragmentation is the development of ecological corridors, that is, interconnected networks of urban green and blue spaces. Least‐cost paths (LCP) appear to be an easy and appropriate resistance‐based modelling method to respond to urban planners’ needs. However, the ecological validation of urban corridors using LCP is rarely performed and needs to be generalized to different species, habitats and cities.2.We developed an experimental design to test the efficiency of LCP predictions to detect highly connecting landscape contexts that facilitate individual movements compared to movements in less connecting landscape contexts. We deliberately assigned LCP analysis parameters based on the scientific literature and expert knowledge to test a method potentially easy to use for urban stakeholders. To extend the validation, we applied our LCP model to two biological taxa with different habitat requirements: grassland‐dwelling moths and forest‐dwelling passerines, and to two medium‐sized cities.3.We used mark–release–recapture (MRR) methods for moths and playback recall protocols for passerines to compare the patterns of individual movement between two contrasted connectivity contexts determined by the presence and absence of modelled LCPs. MRR protocol estimated movement rates between herbaceous patches and the two contrasted connectivity contexts. Playback recall protocol consisted in attracting individuals from wooded patches to the two contrasted connectivity contexts. A movement was considered facilitated, when displacement was rapidly engaged and individuals moved a long distance from their wooded patch.4.Moth and passerine movement patterns differed between the two connectivity contexts: moth recapture rates were higher in highly connecting contexts than in less connecting contexts. For passerine birds, responses to playback recalls were faster and movement distance longer in highly connecting contexts. All results support the hypothesis that both taxa were more prone to move in corridors modelled by LCP.5.Synthesis and applications. The convergence of the results for different biological models and across cities strengthens the relevance of LCP analysis for planning urban greenways and provides guidelines for landscape planners in the development of these corridors to favour the movement and survival of multiple urban species.

Marine organisms show population structure at a relatively fine spatial scale, even in open habitats. The tools commonly used to assess subtle patterns of connectivity have diverse levels of resolution and can complement each other to inform on population structure. We assessed and compared the discriminatory power of genetic markers and otolith shape to reveal the population structure on evolutionary and ecological time scales of the common sole (Solea solea), living in the Eastern English Channel (EEC) stock off France and the UK. First, we genotyped fish with Single Nucleotide Polymorphisms to assess population structure at an evolutionary scale. Then, we tested for spatial segregation of the subunits using otolith shape as an integrative tracer of life history. Finally, a supervised machine learning framework was applied to genotypes and otolith phenotypes to probabilistically assign adults to subunits and assess the discriminatory power of each approach. Low but significant genetic differentiation was found among subunits. Moreover, otolith shape appeared to vary spatially, suggesting spatial population structure at fine spatial scale. However, results of the supervised discriminant analyses failed to discriminate among subunits, especially for otolith shape. We suggest that the degree of population segregation may not be strong enough to allow for robust fish assignments. Finally, this study revealed a weak yet existing metapopulation structure of common sole at the fine spatial scale of the EEC based on genotypes and otolith shape, with one subunit being more isolated. Our study argues for the use of complementary tracers to investigate marine population structure. ispartof: PLOS ONE vol:15 issue:11 ispartof: location:United States status: published

International audience; ge-related telomere shortening is considered a hallmark of the ageing process. However, a recent cross-sectional ageing study of relative telomere length (rTL) in bats failed to detect a relationship between rTL and age in the long-lived genus Myotis (M. myotis and M. bechsteinii), suggesting some other factors are responsible for driving telomere dynamics in these species. Here, we test if longitudinal rTL data show signatures of age-associated telomere attrition in M. myotis and differentiate which intrinsic or extrinsic factors are likely to drive telomere length dynamics. Using quantitative polymerase chain reaction, rTL was measured in 504 samples from a marked population, from Brittany, France, captured between 2013 and 2016. These represent 174 individuals with an age range of 0 to 7+ years. We find no significant relationship between rTL and age (p = .762), but demonstrate that within-individual rTL is highly variable from year to year. To investigate the heritability of rTL, a population pedigree (n = 1744) was constructed from genotype data generated from a 16-microsatellite multiplex, designed from an initial, low-coverage, Illumina genome for M. myotis. Heritability was estimated in a Bayesian, mixed model framework, and showed that little of the observed variance in rTL is heritable (h(2) = 0.01-0.06). Rather, correlations of first differences, correlating yearly changes in telomere length and weather variables, demonstrate that, during the spring transition, average temperature, minimum temperature, rainfall and windspeed correlate with changes in longitudinal telomere dynamics. As such, rTL may represent a useful biomarker to quantify the physiological impact of various environmental stressors in bats.

Understanding the relationship between habitat quality and population dynamics is fundamental for long-term management and range predictions in ecology. However, habitat quality is generally only investigated at the individual scale, as it is the case for the lesser horseshoe bat (Rhinolophus hipposideros), a species of conservation concern. Using a statistical modelling approach and census data of 94 lesser horseshoe bat colonies located in Brittany (France), we analysed the effect of landscape composition and configuration on the demographic components of surveyed maternity colonies (i.e. colony size, fecundity and growth rate), and compared our result to those provided by individual-based studies. Our results validated that the landscape in a 500-meter buffer around colonies (core foraging area) is crucial for population size and dynamics, and confirmed the positive influence of broadleaved woodland proportion on bat colony size. We revealed a positive effect of lakeshores and riverbanks on colony size and growth rate, underlying the importance of these habitats for the long-term conservation of this non-migratory forest species. Importantly, our results refine previous knowledge concerning the threat posed by the intensification of human activities (e.g. urbanization, agriculture, habitat fragmentation), and highlight the negative effect of large and regular patches of artificial and crop lands and of open land patches shape complexity on all demographic variables investigated. While our results support the dependence of population dynamics and associated conservation management to individual behaviour and sensitivity, environmental responses differed between the population metrics investigated, showing that efficient range prediction will require to fully grasp the complexity of the interaction between landscape and the different population dynamic parameters.

International audience; Landscape connectivity promotes dispersal and other types of movement, including foraging activity; consequently, the inclusion of connectivity concept is a priority in conservation and landscape planning in response to fragmentation. Urban planners expect the scientific community to provide them with an easy, but scientifically rigorous, method to identify highly connecting contexts in landscapes. The least-cost paths (LCP) method is one of the simplest resistance-based models that could be a good candidate to spatially identify areas where movement is potentially favored in a given landscape. We tested the efficiency of LCP predictions to detect highly connecting landscape contexts facilitating individual movements compared to those performed in un-connecting landscape contexts. We used a landscape-level behavioral experiment based on a translocation protocol and individual repeated measures. In the city of Rennes (France), 30 male hedgehogs (Erinaceus europaeus) were translocated and radio-tracked in both highly connecting and un-connecting contexts, respectively, which were determined by the presence and absence of modelled LCPs. Individual movement patterns were compared between the two predicted contexts. Individuals travelled longer distances, moved faster, and were more active in the highly connecting contexts compared to the un-connecting contexts. Moreover, in highly connecting contexts, hedgehog movement followed LCP orientation, with individuals using more wooded habitats than other land cover class. By using a rigorous experimental design, this study validated the ecological relevance of LCP analysis to identify highly connecting areas, and could be easily implemented by urban landscape planners.

The effective size of a population is the size of an ideal population which would undergo genetic drift at the same rate as the real population. The balance between selection and genetic drift depends on the effective population size (Ne), rather than the real numbers of individuals in the population (N). The objectives of the present study were to estimateNein the potato cyst nematodeGlobodera pallidaand to explore the causes of a lowNe/Nratio in cyst nematodes using artificial populations. Using a temporal analysis of 24 independent populations, the medianNewas 58 individuals (minNe= 25 and maxNe= 228).Neis commonly lower thanNbut in the case of cyst nematodes, theNe/Nratio was extremely low. Using artificial populations showed that this low ratio did not result from migration, selection and overlapping generations, but could be explain by the fact thatG. pallidapopulations deviate in structure from the assumptions of the ideal population by having unequal sex ratios, high levels of inbreeding and a high variance in family sizes. The consequences of a lowNe, resulting in a strong intensity of genetic drift, could be important for their control becauseG. pallidapopulations will have a low capacity to adapt to changing environments.

The speed and dynamics of range expansions shape species distributions and community composition. Despite the critical impact of population growth rates for range expansion, they are neglected in existing empirical studies, which focus on the investigation of selected life-history traits. Here, we present an approach based on non-invasive genetic capture–mark–recapture data for the estimation of adult survival, fecundity and juvenile survival, which determine population growth. We demonstrate the reliability of our method with simulated data, and use it to investigate life-history changes associated with range expansion in 35 colonies of the bat species Rhinolophus hipposideros . Comparing the demographic parameters inferred for 19 of those colonies which belong to an expanding population with those inferred for the remaining 16 colonies from a non-expanding population reveals that range expansion is associated with higher net reproduction. Juvenile survival was the main driver of the observed reproduction increase in this long-lived bat species with low per capita annual reproductive output. The higher average growth rate in the expanding population was not associated with a trade-off between increased reproduction and survival, suggesting that the observed increase in reproduction stems from a higher resource acquisition in the expanding population. Environmental conditions in the novel habitat hence seem to have an important influence on range expansion dynamics, and warrant further investigation for the management of range expansion in both native and invasive species.

International audience; The arrival of non-native species in a community can be deleterious for native species. The joint investigation of several descriptors of native populations susceptible to invaders, under different invasion contexts, may help in predicting the outcome of their co-occurrence with invasive species. Moreover, empirical studies seldom document the relative importance of the effects of invasive species on native species compared with other factors. Using survey data, we evaluated whether reproduction (larval density) and distribution of breeding sites of three amphibian species (Rana dalmatina, Lissotriton helveticus, and Triturus marmoratus) were related to the presence of invasive red swamp crayfish Procambarus clarkii, compared to other native predators, habitat, and landscape features, in two pond networks that differed in invasion intensity. The red swamp crayfish was only negatively associated with the larval density of one amphibian species studied. Its effect size was similar to that of some native predators, and much smaller than that of the canopy cover of ponds. Amphibians were widespread in the two pond networks. The occupancy of only one species in each network was negatively related to crayfish presence, while the occupancy of all species was negatively related to fish presence. The distribution of amphibian breeding sites was positively associated with aquatic vegetation cover. Negative associations between amphibians and red swamp crayfish were detected only in a few cases, even in the most invaded area, and thus results were less alarming than in previous studies. Differences in ecological traits of native amphibians and interactions with other environmental factors may explain the variable effects of red swamp crayfish on native amphibian populations.

Background The distinction between lineages of neotropical bats from the Pteronotus parnellii species complex has been previously made according to mitochondrial DNA, and especially morphology and acoustics, in order to separate them into two species. In these studies, either sample sizes were too low when genetic and acoustic or morphological data were gathered on the same individuals, or genetic and other data were collected on different individuals. In this study, we intensively sampled bats in 4 caves and combined all approaches in order to analyse genetic, morphologic, and acoustic divergence between these lineages that live in the same caves in French Guiana. Results A multiplex of 20 polymorphic microsatellite markers was developed using the 454-pyrosequencing technique to investigate for the first time the extent of reproductive isolation between the two lineages and the population genetic structure within lineages. We genotyped 748 individuals sampled between 2010 and 2015 at the 20 nuclear microsatellite loci and sequenced a portion of the cytochrome c oxydase I gene in a subset of these. Two distinct, non-overlapping haplogroups corresponding to cryptic species P. alitonus and P. rubiginosus were revealed, in accordance with previous findings. No spatial genetic structure between caves was detected for both species. Hybridization appeared to be quite limited (0.1–4%) using microsatellite markers whereas introgression was more common (7.5%) and asymmetric for mitochondrial DNA (mtDNA). Conclusions The extremely low rate of hybridization could be explained by differences in life cycle phenology between species as well as morphological and acoustical distinction between sexes in one or the other species. Taken together, these results add to our growing understanding of the nature of species boundaries in Pteronotus parnelli, but deserve more in-depth studies to understand the evolutionary processes underlying asymmetric mtDNA introgression in this group of cryptic species. Electronic supplementary material The online version of this article (10.1186/s12862-018-1289-8) contains supplementary material, which is available to authorized users.

International audience; Empirical studies of landscape connectivity are limited by the difficulty of directly measuring animal movement. ‘Indirect' approaches involving genetic analyses provide a complementary tool to ‘direct' methods such as capture–recapture or radio-tracking. Here the effect of landscape on dispersal was investigated in a forest-dwelling species, the American marten (Martes americana) using the genetic model of isolation by distance (IBD). This model assumes isotropic dispersal in a homogeneous environment and is characterized by increasing genetic differentiation among individuals separated by increasing geographic distances. The effect of landscape features on this genetic pattern was used to test for a departure from spatially homogeneous dispersal. This study was conducted on two populations in homogeneous vs. heterogeneous habitat in a harvested boreal forest in Ontario (Canada). A pattern of IBD was evidenced in the homogeneous landscape whereas no such pattern was found in the near-by harvested forest. To test whether landscape structure may be accountable for this difference, we used effective distances that take into account the effect of landscape features on marten movement instead of Euclidean distances in the model of isolation by distance. Effective distances computed using least-cost modeling were better correlated to genetic distances in both landscapes, thereby showing that the interaction between landscape features and dispersal in Martes americana may be detected through individual-based analyses of spatial genetic structure. However, the simplifying assumptions of genetic models and the low proportions in genetic differentiation explained by these models may limit their utility in quantifying the effect of landscape structure.

The recent advent of high throughput sequencing and genotyping technologies enables the comparison of patterns of polymorphisms at a very large number of markers. While the characterization of genetic structure from individual sequencing data remains expensive for many non-model species, it has been shown that sequencing pools of individual DNAs (Pool-seq) represents an attractive and cost-effective alternative. However, analyzing sequence read counts from a DNA pool instead of individual genotypes raises statistical challenges in deriving correct estimates of genetic differentiation. In this article, we provide a method-of-moments estimator ofFSTfor Pool-seq data, based on an analysis-of-variance framework. We show, by means of simulations, that this new estimator is unbiased, and outperforms previously proposed estimators. We evaluate the robustness of our estimator to model misspecification, such as sequencing errors and uneven contributions of individual DNAs to the pools. Last, by reanalyzing published Pool-seq data of different ecotypes of the prickly sculpinCottus asper, we show how the use of an unbiasedFSTestimator may question the interpretation of population structure inferred from previous analyses.

Telomeres do not shorten with age in longest-lived bats., Understanding aging is a grand challenge in biology. Exceptionally long-lived animals have mechanisms that underpin extreme longevity. Telomeres are protective nucleotide repeats on chromosome tips that shorten with cell division, potentially limiting life span. Bats are the longest-lived mammals for their size, but it is unknown whether their telomeres shorten. Using >60 years of cumulative mark-recapture field data, we show that telomeres shorten with age in Rhinolophus ferrumequinum and Miniopterus schreibersii, but not in the bat genus with greatest longevity, Myotis. As in humans, telomerase is not expressed in Myotis myotis blood or fibroblasts. Selection tests on telomere maintenance genes show that ATM and SETX, which repair and prevent DNA damage, potentially mediate telomere dynamics in Myotis bats. Twenty-one telomere maintenance genes are differentially expressed in Myotis, of which 14 are enriched for DNA repair, and 5 for alternative telomere-lengthening mechanisms. We demonstrate how telomeres, telomerase, and DNA repair genes have contributed to the evolution of exceptional longevity in Myotis bats, advancing our understanding of healthy aging.

Multispecies population genetics is an emerging field that provides insight relevant to conservation biology and community ecology. However, to date, this approach is limited to species with available genetic resources. The use of thousands of single-nucleotide polymorphism (SNP) markers developed from recent genotyping-by-sequencing (GBS) technologies is a roadmap for the study of nonmodel species, but remains cost prohibitive when several, distantly related species are involved. We aimed to overcome this issue using a single HiSeq3000 run of restriction-site associated DNA sequencing (RAD-Seq) to retrieve SNP markers for 40 diverse species including plants, invertebrates, fish, and mammals. We developed a Python-based pipeline to isolate c. 100–500 high-quality SNP markers for each species that could be genotyped through classical PCR amplification methods. To assess the quality of these markers, we validated our approach on c. 160 of the characterized SNPs for each of 18 Neotropical fish species from the river Maroni (French Guiana, South America), using the MassARRAY iPLEX platform from Agena Bioscience (San Diego, CA, USA). A run of the pipeline applying stringent filtering parameters enabled the successful design of between 130 and 3,492 SNP markers for 30 of the 40 study species. Relaxing pipeline parameters allows for an increase in the number of detected SNPs. Across the 18 species from French Guiana, an average of 85% of markers were successfully amplified, polymorphic, and scored in ≥90% of individuals (c. 200 individuals per species). The great majority (>98%) of these markers were at Hardy–Weinberg equilibrium in each sampling site from the river Maroni. This SNP discovery was performed at the cost of c. $US110 for each of the 40 species. Genotyping was performed at the cost of c. $US6000 for each of the 18 fish species with an average of 200 individuals per species. This strategy was found cost-and-time efficient to develop hundreds of SNP markers for a large range of nonmodel species, which can be used to investigate ecological and evolutionary questions that do not require whole-genome coverage.

SummaryThe effective size of a population is the size of an ideal population which would drift at the same rate as the real population. The balance between selection and genetic drift depends on the population size expressed as the genetically effective population size (Ne), rather than the real numbers of individuals in the population (N).The objectives of the present study were to estimate Nein the potato cyst nematodeGlobodera pallidausing artificial populations and to explore the link between Neand the durability of plant resistances.Using a temporal method on 24 independent pairs of initial and final populations, the median Newas 58 individuals.Neis commonly lower than N but in our case the Ne/N ratio was extremely low becauseG. pallidapopulations deviate in structure from the assumptions of the ideal population by having unequal sex-ratios, high levels of inbreeding and a high variance in family sizes. The consequences of a low Necould be important for the control of phytoparasitic nematodes becauseG. pallidapopulations will have a low capacity to adapt to changing environments unless selection intensity is very strong, which could be greatly beneficial for long-term use of plant resistances.

International audience; There is a growing literature on the detection of species-specific DNA fragments in water to reveal animals' presence in aquatic environments. Analysis of Rees etal. (Journal of Applied Ecology, 2014, 51, 1450) and additional publications highlight the downside of the method and suggest that some conclusions have to be toned down. Non-detection of species-specific DNA fragments in a water sample does not automatically imply the absence of the target species. A positive signal does not necessarily mean the species is present because the environmental DNA (eDNA) could have been transported or preserved after an animal's death. Detection of aquatic invertebrates is weakly documented. The effect of species abundance on detection efficiency is not always established.Synthesis and applications. Before successfully becoming an efficient tool to assist proper management policies for monitoring of aquatic species, eDNA surveys must implement sampling strategies that allow estimating detection rates and scaling up information from water samples to larger spatial areas. The effects of discharge variations and dendritic organization in running waters require particular consideration. Before successfully becoming an efficient tool to assist proper management policies for monitoring of aquatic species, eDNA surveys must implement sampling strategies that allow estimating detection rates and scaling up information from water samples to larger spatial areas. The effects of discharge variations and dendritic organization in running waters require particular consideration.

International audience; A general pattern in animal behavior is that group-living species tend to bias their sociopositive behavior toward genetic relatives. In nonhuman primates, kin-biased social bonds have been reported in large multimale, multifemale macaque and baboon groups, but little is known for other species. We addressed this with a comparative study on the genetic and social organization of two sympatric forest guenons, Diana (Cercopithecus diana) and Campbell’s monkeys (Cercopithecus campbelli). We conducted long-term observations of social interactions in two groups of each species in their natural West African forest habitat and collected fecal samples for subsequent microsatellite genetic analyses. We found that both formed female-bonded, egalitarian social organizations. We then compared patterns of genetic relatedness, spatial proximity, and key social behaviors and found that females consistently targeted individuals other than their closest relatives to form social bonds. The fact that females did not preferentially favor genetic relatives contributes to a growing literature showing that social bonds, or “friendships,” among unrelated individuals plays a key role in primate social organizations.

The ontogeny and heritability of echolocation, an important sense in echolocating bats, is still not completely understood. Intraspecific variation in echolocation calls can be high, although the importance of possible explanatory variables (e.g. age, sex, social groups) remains largely unknown. Echolocation pulse features may vary among maternity roosts and this can theoretically be caused either by intercolony genetic differences or by vocal dialects learned during ontogeny within a roost (or a combination of both). In the present study, we analyzed intraspecific variation in echolocation parameters in relation to genetic structure at bi-parentally inherited microsatellites and maternally inherited mitochondrial (mt)DNA in maternal colonies of Pipistrellus pipistrellus in Central Europe. We found that individual colonies differ significantly in mtDNA, whereas the structure on nuclear markers is almost absent. This suggests a typical temperate bat social structure pattern, with strong sex-biased dispersal (i.e. philopatric females and dispersing males) (up to 92% of males leave their birth place according to our results). However, we show for the first time that genetic differentiation among mtDNA matrilines is associated with significant intercolony echolocation parameter differences. Because the genetic component of echolocation is not likely to be encoded by mtDNA, the results support the hypothesis of maternal echolocation dialect transmission to offspring, and the role of learning in this process is discussed.

International audience; Climatic variables are often considered when studying environmental impacts on population dynamics of terrestrial species. However, the temporal resolution considered varies depending on studies, even among studies of the same taxa. Most studies interested in climatic impacts on populations tend to average climatic data across timeframes covering life cycle periods of the organism in question or longer, even though most climatic databases provide at least a monthly resolution. We explored the impact of climatic variables on lesser horseshoe bat (Rhinolophus hipposideros) demography based on count data collected at 94 maternity colonies from 2000 to 2014 in Britanny, France. Meteorological data were considered using different time resolutions (month, life cycle period and year) to investigate their adequacy. Model averaging was used to detect significant predictors for each temporal resolution. Our results show that the finest temporal resolution, e.g. month, was more informative than coarser ones. Precipitation predictors were particularly decisive, with a negative impact on colony sizes when rainfall occurred in October, and a positive impact for June precipitations. Fecundity was influenced by April weather. This highlights the strong impact of climatic conditions during crucial but short time periods on the population dynamics of bats. We demonstrate the importance of choosing an appropriate time resolution and suggest that analogous studies should consider fine-scale temporal resolution (e.g. month) to better grasp the relationship between population dynamics and climatic conditions.

This study was funded by the Agence Francaise pour la Biodiversite (research program supervised by J.M.P.) and the Ministere de l'Education Nationale, de l'Enseignement Superieur et de la Recherche (Ph.D. grant to N.B.). This work was carried out under the licenses 08/2015 and 07/2016 delivered by the Prefecture de la Loire-Atlantique. We thank the Parc Natural Regional de Briere, notably J.P. Damien, for supporting our research activities on amphibian ecology. The authors declare that they have no conflict of interest. We are also grateful to two anonymous reviewers for their constructive comments on an earlier version of the manuscript.; International audience; Stable isotope analyses (SIA) are now widely used in ecology research to quantify the trophic implications of a large range of ecological processes. Non-destructive sampling methods have been successfully developed for most vertebrates, but the validation of such methods is missing in amphibians. Filling this methodological gap is critical to reduce the significant lack of knowledge on the trophic ecology of this imperilled group. The relevance of tail fin as a surrogate for muscle, a tissue routinely used for SIA, was assessed in four amphibian species, including tadpoles and adult newts, by (1) testing the link between the isotope ratios of carbon and nitrogen in fin and muscle, and addressing the additional practical issues of (2) the effects of a topical anaesthetic on isotope ratios, and (3) the minimum quantities of fin needed for SIA to limit the severity of sampling. The isotope ratios were highly correlated between the two tissues in all four species. Equations were provided to predict muscle estimates from fin values for each species separately and grouped by their taxonomic order (anurans or urodeles), which represent a valuable solution for any other species. Topical anaesthetics had little influence on isotope ratios, and the surface of tail fin needed for SIA was small. We conclude that the tail fin of amphibians can be used as a non-lethal surrogate for muscle in SIA, and this offers promising prospects for research on the trophic ecology of amphibians, and potentially on their conservation.; Les analyses d'isotopes stables (AIS) sont maintenant largement utilisées en recherche en écologie pour quantifier les implications trophiques d'une large gamme de processus écologiques. Des méthodes d'échantillonnage non-létales ont été développées chez la plupart des vertébrés, mais une telle validation est absente chez les amphibiens. Il est essentiel de combler cette lacune de façon à réduire le manque de connaissances sur l'écologie trophique de ce groupe menacé. La pertinence de la nageoire caudale comme substitut au muscle, un tissu régulièrement utilisé pour les AIS, a été évaluée chez quatre espèces d'amphibiens, incluant des têtards et des tritons, (1) en testant le lien entre les ratios isotopiques du carbone et de l'azote du muscle et de la nageoire, et en répondant à des questions pratiques comme (2) l'effet d'un anesthésique local sur les ratios isotopiques, et (3) les quantités minimales de nageoire nécessaires aux analyses isotopiques, dans le but de limiter la sévérité de l'échantillonnage. Les ratios isotopiques étaient hautement corrélés entre les deux tissus chez les quatre espèces. Des équations ont été fournies pour prédire les valeurs du muscle à partir de celles de la nageoire en considérant chaque espèce séparément et en les regroupant selon leur ordre taxonomique (anoures ou urodèles) ce qui représente une solution intéressante pour d'autres espèces. L'anesthésique topique a eu une faible influence sur les ratios isotopiques, et la surface de nageoire nécessaire pour les AIS était faible. Nous concluons que la nageoire caudale des amphibiens peut être utilisée en tant que substitut au muscle pour conduire des AIS, ce qui offre des perspectives prometteuses pour la recherche en écologie trophique des amphibiens, et potentiellement pour leur conservation.

International audience; The sustainability of modern agriculture relies on strategies that can control the ability of pathogens to overcome chemicals or genetic resistances through natural selection. This evolutionary potential, which depends partly on effective population size (Ne), is greatly influenced by human activities. In this context, wild pathogen populations can provide valuable information for assessing the long-term risk associated with crop pests. In this study, we estimated the effective population size of the beet cyst nematode, Heterodera schachtii, by sampling 34 populations infecting the sea beet Beta vulgaris spp. maritima twice within a one-year period. Only 20 populations produced enough generations to analyze the variation in allele frequencies, with the remaining populations showing a high mortality rate of the host plant after only one year. The 20 analyzed populations showed surprisingly low effective population sizes, with most having Ne close to 85 individuals. We attribute these low values to the variation in population size through time, systematic inbreeding, and unbalanced sex- ratios. Our results suggest that H. schachtii has low evolutionary potential in natural environments. Pest control strategies in which populations on crops mimic wild populations may help prevent parasite adaptation to host resistance.

International audience; Studying wild pathogen populations in natural ecosystems offers the opportunity to better understand the evolutionary dynamics of biotic diseases in crops and to enhance pest control strategies. We used simulations and genetic markers to investigate the spatial and temporal population genetic structure of wild populations of the beet cyst nematode Heterodera schachtii on a wild host plant species, the sea beet (Beta vulgaris spp. maritima), the wild ancestor of cultivated beets. Our analysis of the variation of eight microsatellite loci across four study sites showed that (i) wild H. schachtii populations displayed fine-scaled genetic structure with no evidence of substantial levels of gene flow beyond the scale of the host plant, and comparisons with simulations indicated that (ii) genetic drift substantially affected the residual signals of isolation-by-distance processes, leading to departures from migration–drift equilibrium. In contrast to what can be suspected for (crop) field populations, this showed that wild cyst nematodes have very low dispersal capabilities and are strongly disconnected from each other. Our results provide some key elements for designing pest control strategies , such as decreasing passive dispersal events to limit the spread of virulence among field nematode populations.

Dispersal barriers have demographic, evolutionary, and ecosystem-wide consequences. With ongoing changes in the environment, some dispersal bar riers will likely disappear while new ones will appear, and it is crucial to understand these dynamics to forecast species’ distributions and adaptive potential. Here we review recent literature on the ecological and evolutionary aspects of dispersal to highlight key dynamics of dispersal barriers in the face of global change. After defining dispersal barriers, we explain that a better understanding of their dynamics requires identifying the barrier types that are most susceptible to change and predicting species’ responses. This knowledge is a prerequisite for designing management strategies to increase or reduce connectivity, and maintain adaptive potential. Our intent is to motivate researchers to explicitly consider dispersal barriers in order to better forecast the dynamics of species and ecosystems subject to global change.

Animal societies certainly count among the most complex structures that emerged on earth, the latest of the 'major transitions' in evolution. Their study necessarily involves a wide panel of disciplines and a large diversity of approaches. The field is expanding at a rapid pace, which, however, is not going without some turbulence, as testified by recent fierce controversies regarding the concept of inclusive fitness. These battles elicited appeals for 'more cooperation among altruism researchers' (Okasha 2010). In this spirit, we recently organized at the University of Rennes (10-15 October 2010) a workshop on mammalian social systems. The idea was to bring together 'social scientists' working on a diversity of animal models (from bats to elephants and from hyenas to whales) and using a diversity of approaches (from demography to population genetics and from game-theoretical models to behavioural experiments), with the aim of evaluating how key processes (e.g. inclusive fitness and kin selection, versus cooperation and reciprocity, or the interplay between inbreeding, kin competition and kin recognition) might differently affect the emergence and evolution of social systems in a diversity of mammalian lineages, depending on ecological settings or other constraints. This diversity of complementary approaches explains why the several contributions to the workshop collected in the present Special Issue are not all 'pure' molecular ecology.

The impact of ecology and social organization on genetic structure at landscape spatial scales, where gene dynamics shape evolution as well as determine susceptibility to habitat fragmentation, is poorly understood. Attempts to assess these effects must take into account the potentially confounding effects of history. We used microsatellites to compare genetic structure in seven bat species with contrasting patterns of roosting ecology and social organization, all of which are codistributed in an ancient forest habitat that has been exceptionally buffered from radical habitat shifts. Over one thousand individuals were captured at foraging sites and genotyped at polymorphic microsatellite loci. Analyses of spatially explicit genotype data revealed interspecies differences in the extent of movement and gene flow and genetic structure across continuous intact forest. Highest positive genetic structure was observed in tree-roosting taxa that roost either alone or in small groups. By comparison, a complete absence of genetic autocorrelation was noted in the cave-roosting colonial species across the study area. Our results thus reveal measurable interspecies differences in the natural limits of gene flow in an unmodified habitat, which we attribute to contrasting roosting ecology and social organization. The consequences of ecology and behaviour for gene flow have important implications for conservation. In particular, tree-roosting species characterized by lower vagility and thus gene flow will be disproportionally impacted by landscape-scale forest clearance and habitat fragmentation, which are prevalent in the study region. Our method also highlights the usefulness of rapid sampling of foraging bats for assaying genetic structure, particularly where roosting sites are not always known.

The potential for parallel impacts of habitat change on multiple biodiversity levels has important conservation implications. We report on the first empirical test of the 'species-genetic diversity correlation' across co-distributed taxa with contrasting ecological traits in the context of habitat fragmentation. In a rainforest landscape undergoing conversion to oil palm, we show that depauperate species richness in fragments is mirrored by concomitant declines in population genetic diversity in the taxon predicted to be most susceptible to fragmentation. This association, not seen in the other species, relates to fragment area rather than isolation. While highlighting the over-simplification of extrapolating across taxa, we show that fragmentation presents a double jeopardy for some species. For these, conserving genetic diversity at levels of pristine forest could require sites 15-fold larger than those needed to safeguard species numbers. Importantly, however, each fragment contributes to regional species richness, with larger ones tending to contain more species.

Summary 1 Non-invasive genetic data analysed with capture–mark–recapture (CMR) models can be used to estimate population size, particularly for elusive and endangered species. Data generated from non-invasive genetic sampling are different, however, from conventional CMR data because individuals can be contacted several times within a single sampling session. Two methods have been proposed recently to accommodate this type of data, but no study has attempted to compare their estimates and evaluate their reliability compared with independent estimates of population size. 2 We investigated the reliability and accuracy of estimating the abundance of lesser horseshoe bats Rhinolophus hipposideros by genotyping DNA from droppings collected non-invasively at three colonies over 2 consecutive years. The number of times that each individual was ‘contacted’ (i.e. the number of droppings per individual) was used to estimate population size with two different published methods: a maximum likelihood and a Bayesian estimator. 3 Among the 586 samples extracted, 534 provided a complete genotype at six to eight microsatellite loci, which enabled a reliable discrimination of 165 individuals. Statistical estimates of colony sizes often included independent estimates obtained from visual counts, validating the method. Discrepancies appeared when capture heterogeneity was not taken into account while it occurred. 4 Synthesis and applications. We have taken a first step towards improving methods of estimating numbers of bats by demonstrating that genetic data produced from bat faecal DNA are of high quality and can provide accurate estimates of population size even when samples are taken during only one sampling session. Such protocols provide valuable management tools for elusive and rare species in general. The method is relatively easy and cost-efficient because only one sampling session is required.

We studied the noctule bat (Nyctalus noctula), in which the mitochondrial F(ST) is about 10 times that revealed by nuclear markers, to address two questions. We first verified whether random dispersal of one sex is compatible with highly contrasted mitochondrial and nuclear population structures. Using computer simulations, we then assessed the power of multilocus population differentiation tests when the expected population structure departs only slightly from panmixia. Using an island model with sex-specific demographic parameters, we found that random male dispersal is consistent with the population structure observed in the noctule. However, other parameter combinations are also compatible with the data. We computed the minimum sex bias in dispersal (at least 69% of the dispersing individuals are males), a result that would not be available if we had used more classical population genetic models. The power of multilocus population differentiation tests was unexpectedly high, the tests being significant in almost 100% of the replicates, although the observed population structure infered from nuclear markers was extremely low (F(ST) = 0.6%).

Amplification of a mitochondrial DNA fragment was used to compare the efficiency of five methods for extracting DNA from bat droppings. The Qiagen DNA Stool Kit, which yielded > 90% mtDNA amplification success, was chosen to extract DNA from 586 samples taken over two years in three French colonies of the lesser horseshoe bat (Rhinolophus hipposideros). Samples, for which mtDNA amplification was successful, were subject to the multiplex amplification of eight microsatellite loci. This resulted in > 95% amplification success over 12,592 PCRs. Allelic dropout (ADO) and false allele (FA) rates were low, and consequently, sample and locus quality indexes (QI) were high. These results demonstrate that large scale noninvasive studies of bat colonies are possible.

The demographic history of Rhinolophus hipposideros (lesser horseshoe bat) was recon- structed across its European, North African and Middle-Eastern distribution prior to, during and following the most recent glaciations by generating and analysing a multi- marker data set. This data set consisted of an X-linked nuclear intron (Bgn; 543 bp), mitochondrial DNA(cytb-tRNA-control region; 1630 bp) and eight variable microsatel- lite loci for up to 373 individuals from 86 localities. Using this data set of diverse markers, it was possible to determine the species’ demography at three temporal stages. Nuclear intron data revealed early colonization into Europe from the east, which pre-dates the Quaternary glaciations. The mtDNA data supported multiple glacial refugia across the Mediterranean, the largest of which were found in the Ibero- Maghreb region and an eastern location (Anatolia/Middle East)–that were used by R. hipposideros during the most recent glacial cycles. Finally, microsatellites provided the most recent information on these species’ movements since the Last Glacial Maxi- mumand suggested that lineages that had diverged into glacial refugia, such as in the Ibero-Maghreb region, have remained isolated. These findings should be used to inform future conservation management strategies for R. hipposideros and show the power of using a multimarker data set for phylogeographic studies.

International audience; Deviations of genotypic frequencies from Hardy-Weinberg equilibrium (HWE) expectations could reveal important aspects of the biology of populations. Deviations from HWE due to heterozygote deficits have been recorded for three plant-parasitic nematode species. However, it has never been determined whether the observed deficits were due (i) to the presence of null alleles, (ii) to a high level of consanguinity and/or (iii) to a Wahlund effect. The aim of the present work was, while taking into the possible confounding effect of null alleles, to disentangle consanguinity and Wahlund effect in natural populations of those three economically important cyst nematodes using microsatellite markers: Globodera pallida, G. tabacum and Heterodera schachtii, pests of potato, tobacco and sugar beet, respectively. The results show a consistent pattern of heterozygote deficiency in the three nematode species sampled at the spatial scale of the host plant. We demonstrate that the prevalence of null alleles is weak and that heterozygote deficits do not have a single origin. Our results suggested that it is restricted dispersal that leads to heterozygote deficits through both consanguinity and substructure, which effects can be linked to soil movement, cyst density, and the number of generations per year. We discuss potential implications for the durability of plant resistances that are used to protect crops against parasites in which mating between relatives occur. While consanguineous mating leads to homozygosity at all loci, including loci governing avirulence/virulence, which favours the expression of virulence when recessive, the Wahlund effect is expected to have no particular effect on the adaptation of nematodes to resistances.

International audience; In the Chinese Hainan Island, Amynthas and Metaphire are two dominated pheretimoid earthworm species belonging to the family Megascolecidae. They differ from earthworms in the adjacent regions in their morphology and at the molecular level, which could have occurred due to the unique geography of Hainan Island. Hainan Island is made of two tectonic parts linked to South China and Indochina blocks, respectively. In addition, there is an apparent complicated link between Hainan Island and mainland China because of the different plate movements and sea level changes. In order to understand the evolution of pheretimoid earthworms in Hainan Island, we first investigated the earthworm biodiversity here. Bayesian phylogenetic tree was then constructed from 3511 base pairs from five mitochondrial genes: COI, COII, 16S, 12S, and ND1. Their divergent time was finally traced based on the molecular clock of 2.0-2.4% substitutions/Ma. The results showed three species differentiations between Hainan and Guangdong earthworm species. According to the paleogeography of Asiatic regions (including Hainan Island itself), we hypothesized that the Hainan pheretimoid earthworms might originate from Southeast Asia, and then they dispersed to the south and finally arrived at South China and Hainan Island. Meanwhile, due to the geology movement of the adjacent plates, there was also the migration of earthworms among adjacent regions. Furthermore, we also considered that the relationship between genera Metaphire and Amynthas might be re-considered as one genus.

The white-nose syndrome (WNS), caused by the fungal pathogen Pseudogymnoascus destructans, is threatening the cave-dwelling bat fauna of North America by killing individuals by the thousands in hibernacula each winter since its appearance in New York State less than ten years ago. Epidemiological models predict that WNS will reach the western coast of the USA by 2035, potentially eliminating most populations of susceptible bat species in its path (Frick et al. 2015; O'Regan et al. 2015). These models were built and validated using distributional data from the early years of the epidemic, which spread throughout eastern North America following a route driven by cave density and winter severity (Maher et al. 2012). In this issue of Molecular Ecology, Wilder et al. (2015) refine these findings by showing that connectivity among host populations, as assessed by population genetic markers, is crucial in determining the spread of the pathogen. Because host connectivity is much reduced in the hitherto disease free western half of North America, Wilder et al. make the reassuring prediction that the disease will spread more slowly west of the Great Plains.

Natal dispersal in a vagile carnivore, the American marten (Martes americana), was studied by comparing radio-tracking data and microsatellite genetic structure in two populations occupying contrasting habitats. The genetic differentiation determined among groups of individuals using F(ST) indices appeared to be weak in both landscapes, and showed no increase with geographical distance. Genetic structure investigated using pairwise genetic distances between individuals conversely showed a pattern of isolation by distance (IBD), but only in the population occurring in a homogeneous high-quality habitat, therefore showing the advantage of individual-based analyses in detecting within-population processes and local landscape effects. The telemetry study of juveniles revealed a leptokurtic distribution of dispersal distances in both populations, and estimates of the mean squared parent-offspring axial distance (sigma2) inferred both from the genetic pattern of IBD and from the radio-tracking survey showed that most juveniles make little contribution to gene flow.

Estimating population size of elusive and rare species is challenging. The difficulties in catching such species has triggered the use of samples collected noninvasively, such as feces or hair; from which genetic analysis yields data similar to capture-mark-recapture (CMR) data. There are, however two differences between classical CMR and noninvasive CMR. First, capture and recapture data are gathered over multiple sampling sessions in classical CMR, whereas in noninvasive CMR they can be obtained from a single sampling session. Second, because of genotyping errors and unlike classical CMR, there is no simple relationship between (genetic) marks and individuals in noninvasive CMR. We evaluated, through simulations, the reliability of population size estimates based on noninvasive CMR. For equal sampling efforts, we compared estimates of population size N obtained from accumulation curves, a maximum likelihood, and a Bayesian estimator. For a closed population and without sampling heterogeneity, estimates obtained from noninvasive CMR were as reliable as estimates from classical CMR. The sampling structure (single or multiple session) did not alter the results, the Bayesian estimator in the case of a single sampling session presented the best compromise between low mean squared error and a 95% confidence interval encompassing the parametric value of N in most simulations. Finally, when suitable field and lab protocols were used, genotyping errors did not substantially bias population size estimates (bias < 3.5% in all simulations). The ability to reliably estimate population size from noninvasive samples taken during a single session offers a new and useful technique for the management and conservation of elusive and rare species.

Metapopulation genetic models consider that colonization and dispersal are distinct behaviours. However, whether colonization and dispersal indeed reflect different biological processes in nature is unclear. One possibility to test this assumption is to assess patterns of autosomal and mitochondrial genetic structure in species with strict female philopatry, such as the communally breeding Bechstein's bat. In this species, mitochondrial DNA can spread only when females establish new colonies, and autosomal DNA is transmitted among colonies only when females mate with solitary males born in foreign colonies. Investigating the genetic structure among 37 colonies, we found that autosomal genes followed an island model on a regional scale and a model of isolation by distance on a larger geographical scale. In contrast, mitochondrial genetic structure revealed no pattern of isolation by distance at a large scale but exhibited an effect of ecological barriers on a regional scale. Our results provide strong empirical evidence that colonization and dispersal do not follow the same behavioural rules in this bat, supporting the assumption of metapopulation genetic models.

The use of noninvasively collected samples greatly expands the range of ecological issues that may be investigated through population genetics. Furthermore, the difficulty of obtaining reliable genotypes with samples containing low quantities of amplifiable DNA may be overcome by designing optimal genotyping schemes. Such protocols are mainly determined by the rates of genotyping errors caused by false alleles and allelic dropouts. These errors may not be avoided through laboratory procedure and hence must be quantified. However, the definition of genotyping error rates remains elusive and various estimation methods have been reported in the literature. In this paper we proposed accurate codification for the frequencies of false alleles and allelic dropouts. We then reviewed other estimation methods employed in hair- or faeces-based population genetics studies and modelled the bias associated with erroneous methods. It is emphasized that error rates may be substantially underestimated when using an erroneous approach. Genotyping error rates may be important determinants of the outcome of noninvasive studies and hence should be carefully computed and reported.

The distribution of mitochondrial control region-sequence polymorphism was investigated in 15 populations of Crocidura russula along an altitudinal gradient in western Switzerland. High-altitude populations are smaller, sparser and appear to undergo frequent bottlenecks. Accordingly, they showed a loss of rare haplotypes, but unexpectedly, were less differentiated than lowland populations. Furthermore, the major haplotypes segregated significantly with altitude. The results were inconsistent with a simple model of drift and dispersal. They suggested instead a role for historical patterns of colonization, or, alternatively, present-day selective forces acting on one of the mitochondrial genes involved in metabolic pathways.