Bernard Kaufmann

Optimizing the trade‐off between spatial and genetic sampling efforts in patchy populations: towards a better assessment of functional connectivity using an individual‐based sampling scheme

Genetic data are increasingly used in landscape ecology for the indirect assessment of functional connectivity, that is, the permeability of landscape to movements of organisms. Among available tools, matrix correlation analyses (e.g. Mantel tests or mixed models) are commonly used to test for the relationship between pairwise genetic distances and movement costs incurred by dispersing individuals. When organisms are spatially clustered, a population‐based sampling scheme (PSS) is usually performed, so that a large number of genotypes can be used to compute pairwise genetic distances on the basis of allelic frequencies. Because of financial constraints, this kind of sampling scheme implies a drastic reduction in the number of sampled aggregates, thereby reducing sampling coverage at the landscape level. We used matrix correlation analyses on simulated and empirical genetic data sets to investigate the efficiency of an individual‐based sampling scheme (ISS) in detecting isolation‐by‐distance and isolation‐by‐barrier patterns. Provided that pseudo‐replication issues are taken into account (e.g. through restricted permutations in Mantel tests), we showed that the use of interindividual measures of genotypic dissimilarity may efficiently replace interpopulation measures of genetic differentiation: the sampling of only three or four individuals per aggregate may be sufficient to efficiently detect specific genetic patterns in most situations. The ISS proved to be a promising methodological alternative to the more conventional PSS, offering much flexibility in the spatial design of sampling schemes and ensuring an optimal representativeness of landscape heterogeneity in data, with few aggregates left unsampled. Each strategy offering specific advantages, a combined use of both sampling schemes is discussed.

Skin swabbing as a new efficient DNA sampling technique in amphibians, and 14 new microsatellite markers in the alpine newt (Ichthyosaura alpestris)

This study introduces a novel DNA sampling method in amphibians using skin swabs. We assessed the relevancy of skin swabs relevancy for genetic studies by amplifying a set of 17 microsatellite markers in the alpine newt Ichthyosaura alpestris, including 14 new polymorphic loci, and a set of 11 microsatellite markers in Hyla arborea, from DNA collected with buccal swabs (the standard swab method), dorsal skin swabs and ventral skin swabs. We tested for quality and quantity of collected DNA with each method by comparing electrophoresis migration patterns. The consistency between genotypes obtained from skin swabs and buccal swabs was assessed. Dorsal swabs performed better than ventral swabs in both species, possibly due to differences in skin structure. Skin swabbing proved to be a useful alternative to buccal swabbing for small or vulnerable animals: by drastically limiting handling, this method may improve the trade‐off between the scientific value of collected data, individual welfare and species conservation. In addition, the 14 new polymorphic microsatellites for the alpine newt will increase the power of genetic studies in this species. In four populations from France (n = 19–25), the number of alleles per locus varied from 2 to 16 and expected heterozygosities ranged from 0.04 to 0.91. Presence of null alleles was detected in two markers and two pairs displayed gametic disequilibrium. No locus appeared to be sex‐linked.

Invasiveness of an introduced species: the role of hybridization and ecological constraints

Introduced species are confronted with new environments to which they need to adapt. However, the ecological success of an introduced species is generally difficult to predict, especially when hybridizations may be involved in the invasion success. In western Europe, the lake frog Pelophylax ridibundus appears to be particularly successful. A reason for this species’ success might be the presence of the invader’s genetic material prior to the introduction in the form of a hybrid between P. ridibundus and a second indigenous water frog species. These hybrids reproduce by hybridogenesis, only transmitting the ridibundus genome to gametes and backcrossing with the indigenous species (i.e. P. lessonae). This reproductive system allows the hybrid to be independent from P. ridibundus, and allows the ridibundus genome to be more widely spread than the species itself. Matings among hybrids produce newly formed P. ridibundus offspring (N), if the genomes are compatible. Therefore, we hypothesize that hybridogenesis increases the invasiveness of P. ridibundus (1) by enhancing propagule pressure through N individuals, and/or (2) by increasing adaptation of invaders to the native water frogs’ habitat through hybrid-derived ridibundus genomes that are locally adapted. We find support for the first hypothesis because a notable fraction of N tadpoles is viable. However, in our semi-natural experiments they did not outperform ridibundus tadpoles in the native water frogs’ habitat, nor did they differ physiologically. This does not support the second hypothesis and highlights ecological constraints on the invasion. However, we cannot rule out that these constraints may fall with ongoing selection, making a replacement of indigenous species highly probable in the future.

I’m not like everybody else: urbanization factors shaping spatial distribution of native and invasive ants are species-specific

Urbanization is a major global change inducing complex and multiple modifications of landscapes and ecosystems. The spatial distributions of organisms experiencing these modifications will likely shift specifically, depending on each species’ response to each environmental modification induced by urbanization. We sampled two ant genera (Lasius and Tetramorium) at 1248 locations along an urbanization gradient in Lyon, France and used high resolution spatial layers for 18 spatial (e.g., open habitat fragmentation, bioclimatic data and surface temperatures) and temporal (e.g., comparison of Normalized Difference Vegetation Index between 1986 and 2015) environmental variables associated with urbanization. Coupling two different analytical methods (Outlying Mean Index and Boosted Regression Trees), we showed that each species’ distribution was influenced by its own combination of environmental factors. Two morphologically cryptic Tetramorium species (T. sp.E and T. sp.U2) were both highly abundant but with opposite responses to urbanization: while T. sp.E was favored by urbanized habitat, T. sp.U2 avoided urbanized areas. Among Lasius species, we detected 63 occurrences of the invasive ant Lasius neglectus, the distribution of which was favored only by embankments along roads. We found that, even at this reduced spatial scale, climatic effects influenced most species and interacted with urbanization factors.

Characterization and PCR multiplexing of 14 new polymorphic microsatellite loci for the invasive subantarctic carabid Merizodus soledadinus (Coleoptera: Carabidae)

Seventeen novel microsatellite markers were characterized from an enriched DNA library for the invasive carabid beetle Merizodus soledadinus. Loci were tested, as parts of two multiplex sets in 48 M. soledadinus from 2 populations. 14 loci gave reliable amplification, and genetic diversity ranged from 2 to 6 alleles per locus. In other species of the supertribe trechitae, 8 loci reliably amplified in Eotachys bistriatus, whereas all failed for Trechisibus antarcticus and Trechus obtusus.

Microsatellite Development and First Population Size Estimates for the Groundwater Isopod Proasellus walteri

Effective population size (N e) is one of the most important parameters in, ecology, evolutionary and conservation biology; however, few studies of N e in surface freshwater organisms have been published to date. Even fewer studies have been carried out in groundwater organisms, although their evolution has long been considered to be particularly constrained by small N e. In this study, we estimated the contemporary effective population size of the obligate groundwater isopod: Proaselluswalteri (Chappuis, 1948). To this end, a genomic library was enriched for microsatellite motifs and sequenced using 454 GS-FLX technology. A total of 54,593 reads were assembled in 10,346 contigs or singlets, of which 245 contained candidate microsatellite sequences with suitable priming sites. Ninety-six loci were tested for amplification, polymorphism and multiplexing properties, of which seven were finally selected for N e estimation. Linkage disequilibrium and approximate Bayesian computation methods revealed that N e in this small interstitial groundwater isopod could reach large sizes (> 585 individuals). Our results suggest that environmental conditions in groundwater, while often referred to as extreme, are not necessarily associated with small N e.

Range limits in sympatric cryptic species: a case study in Tetramorium pavement ants (Hymenoptera: Formicidae) across a biogeographical boundary

In the context of climate changes, factors that determine the distribution patterns of European species of the ubiquitous ant genus Tetramorium were investigated. The study took place along a steep North‐South climatic gradient across the boundary between the European Continental and Mediterranean biogeographical regions spanning 460 km along the Rhône valley, France. Ants from 1690 Tetramorium colonies were collected in 19 sampling zones. Species were identified using an integrative approach based on a two‐step process combining nuclear DNA (14 microsatellite markers), morphological examination and mitochondrial DNA cytochrome oxidase I sequencing. The impact of climate on species distribution patterns was tested using bioclimatic variables. Species discrimination was successful, despite a complex situation with cryptic species, inter‐specific hybridisation and uneven sampling across species. Our results showed a strong effect of latitude, temperature and rainfall on the distribution of three of four species. Tetramorium semilaeve was found only south of the boundary, in warmer and dryer sites; Tetramorium caespitum extended north and 70 km south of the boundary and favoured colder sites with strong seasonal variation. Tetramorium immigrans was absent from the northernmost sampling zones and favoured warmer and wetter sites. Tetramorium moravicum was mostly found close to the boundary, but without significant climatic preferences. The fundamental role of climate as a factor limiting the ranges of these species at a major biogeographical boundary is confirmed. Monitoring range limits of these strongly climate‐dependant species may offer exciting insights on the impact of climate changes on species distributions.

Relatedness predicts male mating success in a pond-breeding amphibian

When deciding to mate, it is assumed that females choose males bearing genes that will improve the genetic quality of their offspring, which is affected by both additive and nonadditive genetic variation. In this context, a ‘compatible genes’ model has been put forward to explain female mating decisions. According to this model, females are assumed to increase the genetic quality of their offspring by choosing mates on the basis of interactions between maternal and paternal genomes. Yet, this model is mainly supported by empirical data in endotherm vertebrates. Few studies have investigated this issue in terrestrial ectotherms like amphibians. These organisms often live in spatially structured populations characterized by small subpopulations and a high degree of philopatry, leading to striking reduction in gene flow, high genetic drift and relatively high inbreeding levels. In such a situation, one might expect that natural selection should favour mating tactics limiting the risk of inbreeding depression. In this paper, using an experimental approach controlling for the reproductive state of males, we examined how genetic compatibility may affect mating behaviour in an anuran, the yellow-bellied toad, Bombina variegata. First, our analyses confirmed a high degree of inbreeding in the studied population. Yet, we did not find any mating tactic that reduced the risk of inbreeding depression. Contrary to our expectations, males more closely related to the female had the higher mating success. We discuss the ecological and evolutionary implications of these results.