Sebastien Puechmaille | Universität Greifswald (original) (raw)

Papers by Sebastien Puechmaille

Biodiversity data jurnal, Feb 2, 2024

White-nose disease (WND), caused by the psychrophilic fungus Pseudogymnoascus destructans, repres... more White-nose disease (WND), caused by the psychrophilic fungus Pseudogymnoascus destructans, represents one of the greatest threats for North American hibernating bats. Research on molecular data has significantly advanced our knowledge of various aspects of the disease, yet more studies are needed regarding patterns of P. destructans genetic diversity distribution. In the present study, we investigate three sites within the native range of the fungus in detail: two natural hibernacula (karst caves) in Bulgaria, southeastern Europe and one artificial hibernaculum (disused cellar) in Germany, northern Europe, where we conducted intensive surveys between 2014 and 2019. Using 18 microsatellite and two mating type markers, we describe how P. destructans genetic diversity is distributed between and within sites, the latter including differentiation across years and seasons of sampling; across sampling locations within the site; and between bats and hibernaculum walls. We found significant genetic differentiation between hibernacula, but we could not detect any significant differentiation within hibernacula, based on the variables examined. This indicates that most of the pathogen's movement occurs within sites. Genotypic richness of P. destructans varied between sites within the same order of magnitude, being approximately two times higher in the natural caves (Bulgaria) compared to the disused cellar (Germany). Within all sites, the pathogen's genotypic richness was higher in samples collected from hibernaculum walls than in samples collected from bats, ‡ §,| |, §, ¶ © Zhelyazkova V et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. which corresponds with the hypothesis that hibernacula walls represent the environmental reservoir of the fungus. Multiple pathogen genotypes were commonly isolated from a single bat (i.e. from the same swab sample) in all study sites, which might be important to consider when studying disease progression.

Ethology, Aug 16, 2013

ABSTRACT The sensory drive hypothesis of speciation predicts that divergence in communication sys... more ABSTRACT The sensory drive hypothesis of speciation predicts that divergence in communication systems will occur when environments differ and that this sensory divergence can ultimately promote speciation. The factors affecting geographic evolution in acoustic signals remain poorly understood, especially in the contexts of high gene flow. This study investigated variation patterns in peak frequency emitted by the Chinese endemic Myotis davidii on a broad geographic scale by evaluating the relative importance of morphological, environmental, geographic, and genetic variables. Significant variation in peak frequency was observed among regions, but peak frequencies among populations within region had some percentage of similarity. Differences in peak frequency were not associated with morphological difference, genetic structure, and geographic distance among regions, which suggested that peak frequency divergences in M. davidii were not the primary driver of regions&#39; isolation in a context of weak gene flow. Within the Middle East Plain (MEP), one of the regions delineated in this study, peak frequency differences of M. davidii were not significantly correlated with genetic distance and geographic distance among populations, suggesting that peak frequency was not be subject to cultural drift within MEP. Our results provide evidence that geographic variation in echolocation call design may evolve as a consequence of local adaptation to climate conditions.

Emerging infectious diseases rank among the most important threats to human and wildlife health. ... more Emerging infectious diseases rank among the most important threats to human and wildlife health. A comprehensive understanding of the mode of infection and presence of potential reservoirs is critical for the development of effective counter strategies. Fungal pathogens can remain viable in environmental reservoirs for extended periods of time before infecting susceptible individuals. This may be the case for Pseudogymnoascus destructans (Pd), the causative agent of bat white-nose disease. Owing to its cold-loving nature, this fungal pathogen only grows on bats during hibernation, when their body temperature is reduced. Bats only spend part of their life cycle in hibernation and do not typically show signs of infection in summer, raising the question of whether Pd remains viable in hibernacula during this period (roughly six months). If so, this could facilitate the re-infection of bats when they return to the sites the following winter. In a laboratory experiment, we determined the germination rate of Pd spores kept under constant conditions on a wall-like substrate, over the course of two years. Results showed that the seasonal pattern in Pd germination mirrored the life cycle of the bats, with an increased germination rate at times when hibernating bats would naturally be present and lower germination rates during their absence. We suggest that Pd is dependent on the presence of hibernating bats and has therefore coupled its germination rate to host availability. Furthermore, we demonstrate that Pd spores survive extended periods of host absence and can remain viable for at least two years. There is, however, a strong decrease in spore viability between the first and second years (98%). Pd viability for at least two years on a solid mineral-based substrate establishes the potential for environmental reservoirs in hibernacula walls and has strong implications for the efficacy of certain management strategies (e.g. bat culling).

Handbook of the Mammals of Europe, 2020

Journal of Wildlife Diseases, Oct 1, 2017

BMC Evolutionary Biology, Jan 5, 2017

Background: As bats have recently been described to harbor many different viruses, several studie... more Background: As bats have recently been described to harbor many different viruses, several studies have investigated the genetic co-variation between viruses and different bat species. However, little is known about the genetic co-variation of viruses and different populations of the same bat species, although such information is needed for an understanding of virus transmission dynamics within a given host species. We hypothesized that if virus transmission between host populations depends on events linked to gene flow in the bats, genetic co-variation should exist between host populations and astroviruses. Results: We used 19 nuclear and one mitochondrial microsatellite loci to analyze the genetic population structure of the Natterer's bat (Myotis nattereri) within and among populations at different geographical scales in Germany. Further, we correlated the observed bat population structure to that of partial astrovirus sequences (323-394 nt fragments of the RNA-dependent RNA polymerase gene) obtained from the same bat populations. Our analyses revealed that the studied bat colonies can be grouped into three distinct genetic clusters, corresponding to the three geographic regions sampled. Furthermore, we observed an overall isolation-by-distance pattern, while no significant pattern was observed within a geographic region. Moreover, we found no correlation between the genetic distances among the bat populations and the astrovirus sequences they harbored. Even though high genetic similarity of some of the astrovirus haplotypes found in several different regions was detected, identical astrovirus haplotypes were not shared between different sampled regions. Conclusions: The genetic population structure of the bat host suggests that mating sites where several local breeding colonies meet act as stepping-stones for gene flow. Identical astrovirus haplotypes were not shared between different sampled regions suggesting that astroviruses are mostly transmitted among host colonies at the local scale. Nevertheless, high genetic similarity of some of the astrovirus haplotypes found in several different regions implies that occasional transmission across regions with subsequent mutations of the virus haplotypes does occur.

Journal of Applied Ecology, May 16, 2007

1. Non-invasive genetic data analysed with capture-mark-recapture (CMR) models can be used to est... more 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.

Molecular Ecology Resources, Mar 2, 2016

Inferences of population structure and more precisely the identification of genetically homogeneo... more Inferences of population structure and more precisely the identification of genetically homogeneous groups of individuals are essential to the fields of ecology, evolutionary biology and conservation biology. Such population structure inferences are routinely investigated via the program structure implementing a Bayesian algorithm to identify groups of individuals at Hardy–Weinberg and linkage equilibrium. While the method is performing relatively well under various population models with even sampling between subpopulations, the robustness of the method to uneven sample size between subpopulations and/or hierarchical levels of population structure has not yet been tested despite being commonly encountered in empirical data sets. In this study, I used simulated and empirical microsatellite data sets to investigate the impact of uneven sample size between subpopulations and/or hierarchical levels of population structure on the detected population structure. The results demonstrated that uneven sampling often leads to wrong inferences on hierarchical structure and downward‐biased estimates of the true number of subpopulations. Distinct subpopulations with reduced sampling tended to be merged together, while at the same time, individuals from extensively sampled subpopulations were generally split, despite belonging to the same panmictic population. Four new supervised methods to detect the number of clusters were developed and tested as part of this study and were found to outperform the existing methods using both evenly and unevenly sampled data sets. Additionally, a subsampling strategy aiming to reduce sampling unevenness between subpopulations is presented and tested. These results altogether demonstrate that when sampling evenness is accounted for, the detection of the correct population structure is greatly improved.

Ecology and Evolution, May 15, 2018

The amount of gene flow is an important determinant for genetic differentiation among populations... more The amount of gene flow is an important determinant for genetic differentiation among populations (e.g., Slatkin, 1985). As it can influence effective population size, genetic diversity, local adaptation, and ultimately speciation, gene flow is one of the most important processes in both population genetics and ecology (e.g., Bohonak, 1999). In the absence of this transfer of genetic material between populations, a combination of mutations and genetic drift cause genetic divergence of populations. Gene flow between populations can

Current Opinion in Microbiology, Aug 1, 2021

Hibernation, a period where bats have suppressed immunity and low body temperatures, provides the... more Hibernation, a period where bats have suppressed immunity and low body temperatures, provides the psychrophilic fungus Pseudogymnoascus destructans the opportunity to colonise bat skin, leading to severe disease in susceptible species. Innate immunity, which requires less energy and may remain more active during torpor, can control infections with local inflammation in some bat species that are resistant to infection. If infection is not controlled before emergence from hibernation, ineffective adaptive immune mechanisms are activated, including incomplete Th1, ineffective Th2, and variable Th17 responses. The Th17 and neutrophil responses, normally beneficial antifungal mechanisms, appear to be sources of immunopathology for susceptible bat species, because they are hyperactivated after return to homeothermy. Non-susceptible species show both well-balanced and suppressed immune responses both during and after hibernation.

Understanding the relationship between habitat quality and population dynamics is fundamental for... more Understanding the relationship between habitat quality and population dynamics is fundamental for long-term management and range predictions in ecology. However, habitat suitability 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 demography 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 500meter 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 nonmigratory 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.

PeerJ, May 10, 2022

Background. The accuracy of predictions of invasive species ranges is dependent on niche similari... more Background. The accuracy of predictions of invasive species ranges is dependent on niche similarity between invasive and native populations and on our ability to identify the niche characteristics. With this work we aimed to compare the niche dynamics of two genetically related invasive populations of Vespa velutina (an effective predator of honeybees and wild pollinators), in two distinct climatic regions, one in central Europe and another one in the northwestern Iberian Peninsula, and hence to identify uninvaded regions susceptible to invasion. Methods. Niche dynamics and shifts of V. velutina were assessed by comparing the environmental niches of the native and of the two invasive populations, using climatic, topographic and land use variables. We also ran reciprocal distribution models using different algorithms and records from both native and invasive ranges to compare model predictions and estimate which regions are at a greater risk of being invaded. Results. An apparent niche shift was detected in the population of the NW of Iberian Peninsula, where the species is living under environmental conditions different from the native niche. In central Europe, large suitable areas remain unoccupied. The fact that both invasive populations are well established, despite occupying environmentally distinct regions indicates that V. velutina has a high ability to successfully invade different environmental envelopes from those existing in its native range. For example, in northwestern Iberian Peninsula the species is now thriving out of its native niche limits. Moreover, the large extent of still unoccupied environmental space with similar

Animal Behaviour, 2017

Sharing resources with conspecifics or heterospecifics can involve costs like increased competiti... more Sharing resources with conspecifics or heterospecifics can involve costs like increased competition or higher pathogen infection risks as well as benefits such as information on the location, quality and availability of resources. Depending on the consequences of sharing resources, the responses of individuals towards resources used by conspecifics and heterospecifics can range from ignoring them through avoidance to attraction. Within bats it is well known that colony members share information about day roosts and roost switching is often coordinated within the colony. However, little is known about roosting interactions between distinct colonies of conspecifics or heterospecifics. In this study, we investigated roosting interactions between five co-occurring bat colonies that belong to three forestliving species (Myotis bechsteinii, Myotis nattereri, Plecotus auritus). Occupied roosts were continuously monitored with an automatic RFID system over three maternity seasons. Furthermore, we used simulations to test whether colonies preferentially occupied recently used roosts of other colonies. We found no evidence that the roosting behaviour of the M. bechsteinii colony was influenced by the co-occurring heterospecific colonies. In contrast, P. auritus and M. nattereri frequently explored roosts of conspecific and heterospecific colonies, respectively. Nevertheless, with largely separated roosting ranges, the three P. auritus colonies avoided occupying roosts that had been inhabited by conspecific colonies. In contrast, M. nattereri specifically occupied recent roosts of all three P. auritus colonies. Our results give evidence that co-occurring colonies of conspecific and heterospecific bats can influence each other's roost usage. Our findings have implications for both our understanding of inter-and intraspecific resource sharing among distinct social groups and the management of forest-living bats that are of conservation concern.

Molecular Ecology Resources, Nov 28, 2017

Monitoring wild populations is crucial for their effective management. Noninvasive genetic method... more Monitoring wild populations is crucial for their effective management. Noninvasive genetic methods provide robust data from individual free-ranging animals, which can be used in capture-mark-recapture (CMR) models to estimate demographic parameters without capturing or disturbing them. However, sex-and status-specific behaviour, which may lead to differences in detection probabilities, is rarely considered in monitoring. Here, we investigated population size, sex ratio, sex-and status-related behaviour in 19 Rhinolophus hipposideros maternity colonies (Northern France) with a noninvasive genetic CMR approach (using faeces) combined with parentage assignments. The use of the DDX3X/Y-Mam sexual marker designed in this study, which shows inter-and intra-chromosomal length polymorphism across placental mammals, together with 8 polymorphic microsatellite markers, produced high quality genetic data with limited genotyping errors and allowed us to reliably distinguish different categories of individuals (males, reproductive and nonreproductive females) and to estimate population sizes. We showed that visual counts represent well adult female numbers and that population composition in maternity colonies changes dynamically during the summer. Before parturition, colonies mainly harbour pregnant and non-pregnant females with a few visiting males whereas after parturition, colonies are mainly composed of mothers and their offspring with a few visiting non-mothers and males. Our approach gives deeper insight into sex-and status-specific behaviour, a prerequisite for understanding population dynamics and developing effective monitoring and management strategies. Provided sufficient samples can be obtained, this approach can be readily applied to a wide range of species.

HAL (Le Centre pour la Communication Scientifique Directe), Mar 22, 2008

National audienc

Conservation Genetics, May 13, 2016

The New Zealand long-tailed bat (Chalinolobus tuberculatus) is an endemic species threatened with... more The New Zealand long-tailed bat (Chalinolobus tuberculatus) is an endemic species threatened with extinction. Since the arrival of humans, massive deforestation has occurred and invasive mammalian predators were introduced. As a result, C. tuberculatus' distribution shrank dramatically and became fragmented. To aid the management of the remaining populations, two Evolutionary Significant Units (ESUs) were designated: one on each of New Zealand's main islands. We utilised mitochondrial sequence data (cytb, 703 bp) and 10 nuclear DNA microsatellite loci to reconstruct the demographic history of this species, to characterise the level of genetic diversity in remaining populations, and to assess the current connectivity between them. Our results indicate that the North Island, with the highest genetic diversity, served as a glacial refuge, with a loss of diversity following the path recolonization to the south of the South Island. However, our data are also consistent with continued, or at least very recent, genetic exchange between colonies across the species distribution. The only exception is the Hanging Rock colony on the east coast of the South Island, which appears to be isolated. Thus, there was no support for the previously designated ESUs. Signatures of past population declines were found in three colonies, the most extreme of which was found in Hanging Rock. Consequently, we recommend that it be genetically rescued via translocation from a donor population. In general, future management priorities should treat Chalinolobus tuberculatus as a single unit, focusing on maintaining connectivity between remaining populations, together with continued roost protection and pest control.

HAL (Le Centre pour la Communication Scientifique Directe), 2007

... sample quality, with bat droppings collected from humid places potentially harbouring more de... more ... sample quality, with bat droppings collected from humid places potentially harbouring more degraded DNA (Wasser et al., 1997; Taberlet et al ... Farcy, Roland Jamault, Yann Le Bris, Arnaud Le Houedec, Arnaud Le Mouël, Ludovic Morlier, Pierre-Yves Pasco and Jacques Ros for ...

HAL (Le Centre pour la Communication Scientifique Directe), 2007

Molecular Ecology, Nov 1, 2015

The white-nose syndrome (WNS), caused by the fungal pathogen Pseudogymnoascus destructans, is thr... more 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.

Molecular Ecology Notes, Dec 1, 2005

Fourteen polymorphic microsatellites isolated in the lesser horseshoe bat, Rhinolophus hipposider... more Fourteen polymorphic microsatellites isolated in the lesser horseshoe bat, Rhinolophus hipposideros , are described. A subset of eight loci successfully coamplified in a multiplex polymerase chain reaction (PCR), and allowed to confirm that expected heterozygosity was relatively high for the eight loci (0.56-0.83). This set of eight microsatellites indeed permits to build genetic tags that distinguish all individuals in colonies consisting of up to more than 1000 individuals.

Biodiversity data jurnal, Feb 2, 2024

Ethology, Aug 16, 2013

Handbook of the Mammals of Europe, 2020

Journal of Wildlife Diseases, Oct 1, 2017

BMC Evolutionary Biology, Jan 5, 2017

Journal of Applied Ecology, May 16, 2007

Molecular Ecology Resources, Mar 2, 2016

Ecology and Evolution, May 15, 2018

Current Opinion in Microbiology, Aug 1, 2021

PeerJ, May 10, 2022

Animal Behaviour, 2017

Molecular Ecology Resources, Nov 28, 2017

HAL (Le Centre pour la Communication Scientifique Directe), Mar 22, 2008

National audienc

Conservation Genetics, May 13, 2016

HAL (Le Centre pour la Communication Scientifique Directe), 2007

Molecular Ecology, Nov 1, 2015

Molecular Ecology Notes, Dec 1, 2005