Eric J. Petit

Landscape connectivity influences gene flow in a roe deer population inhabiting a fragmented landscape: an individual-based approach

Changes in agricultural practices and forest fragmentation can have a dramatic effect on landscape connectivity and the dispersal of animals, potentially reducing gene flow within populations. In this study, we assessed the influence of woodland connectivity on gene flow in a traditionally forest‐dwelling species — the European roe deer — in a fragmented landscape. From a sample of 648 roe deer spatially referenced within a study area of 55 × 40 km, interindividual genetic distances were calculated from genotypes at 12 polymorphic microsatellite loci. We calculated two geographical distances between each pair of individuals: the Euclidean distance (straight line) and the ‘least cost distance’ (the trajectory that maximizes the use of wooded corridors). We tested the correlation between genetic pairwise distances and the two types of geographical pairwise distance using Mantel tests. The correlation was better using the least cost distance, which takes into account the distribution of wooded patches, especially for females (the correlation was stronger but not significant for males). These results suggest that in a fragmented woodland area roe deer dispersal is strongly linked to wooded structures and hence that gene flow within the roe deer population is influenced by the connectivity of the landscape.

Quantifying genotyping errors in noninvasive population genetics

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.

Noninvasive population genetics: a review of sample source, diet, fragment length and microsatellite motif effects on amplification success and genotyping error rates

Noninvasive population genetics has found many applications in ecology and conservation biology. However, the technical difficulties inherent to the analysis of low quantities of DNA generally tend to limit the efficiency of this approach. The nature of samples and loci used in noninvasive population genetics are important factors that may help increasing the potential success of case studies. Here we reviewed the effects of the source of DNA (hair vs. faeces), the diet of focal species, the length of mitochondrial DNA fragments, and the length and repeat motif of nuclear microsatellite loci on genotyping success (amplification success and rate of allelic dropout). Locus-specific effects appeared to have the greatest impact, amplification success decreasing with both mitochondrial and microsatellite fragments’ length, while error rates increase with amplicons’ length. Dinucleotides showed best amplification success and lower error rates compared to longer repeat units. Genotyping success did not differ between hair- versus faeces-extracted DNA, and success in faeces-based analyses was not consistently influenced by the diet of focal species. While the great remaining variability among studies implies that other unidentified parameters are acting, results show that the careful choice of genetic markers may allow optimizing the success of noninvasive approaches.

Genetic isolation by distance and landscape connectivity in the American marten (Martes americana)

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.

Extreme sex-biased dispersal in the communally breeding, nonmigratory Bechstein's bat (Myotis bechsteinii).

Maternity colonies of the communally breeding, nonmigratory Bechsteins bat consist of closely related females that live together with unrelated females, and average colony relatedness is low despite the absence of immigration. We compared the genetic structure of both nuclear and mitochondrial microsatellites in order to quantify sex‐specific dispersal rates. More specifically, we aimed at testing whether male dispersal is able to balance the genetic effect of strong (absolute) female philopatry. Absolute female philopatry, indicated by an extreme mitochondrial DNA population differentiation of 96%, was indeed opposed by strong (possibly complete) male dispersal. Based on our knowledge of the biology of Myotis bechsteinii, we conclude that inbreeding avoidance is likely to be the crucial factor driving male dispersal in this species.

NO EVIDENCE OF BOTTLENECK IN THE POSTGLACIAL RECOLONIZATION OF EUROPE BY THE NOCTULE BAT (NYCTALUS NOCTULA )

During the Pleistocene, the habitat of the noctule bat (Nyctalus noctula) was limited to small refuge areas located in Southern Europe, whereas the species is now widespread across this continent. Using mtDNA (control region and ND1 gene) polymorphisms, we asked whether this recolonization occurred through bottlenecks and whether it was accompanied by population growth. Sequences of the second hypervariable domain of the control region were obtained from 364 noctule bats representing 18 colonies sampled across Europe. This yielded 108 haplotypes that were depicted on a minimum spanning tree that showed a starlike structure with two long branches. Additional sequences obtained from the ND1 gene confirmed that the different parts of the MST correspond to three clades which diverged before the Last Glacial Maximum (18,000 yrC14 BP), leading to the conclusion that the noctule bat survived in several isolated refugia. Partitioning populations into coherent geographical groups divided our samples (φCT = 0.17; P = 0.01) into a group of highly variable nursing colonies from central and eastern Europe and less variable, isolated colonies from western and southern Europe. Demographic analyses suggest that populations of the former group underwent demographic expansions either after the Younger Dryas (11,000–10,000 yrC14 BP), assuming a fast mutation rate for HV II, or during the Pleistocene, assuming a conventional mutation rate. We discuss the fact that the high genetic variability (h = 0.69–0.96; π = 0.006–0.013) observed in nursing colonies that are located some distance from potential Pleistocene refugia is probably due to the combined effect of rapid evolution of the control region in growing populations and a range shift of noctule populations parallel to the recovery of forests in Europe after the last glaciations.

Sex-biased dispersal in a migratory bat: a characterization using sex-specific demographic parameters.

Abstract We studied the noctule bat (Nyctalus noctula), in which the mitochondrial FST 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 (FST= 0.6%).

Sex-biased dispersal in western lowland gorillas (Gorilla gorilla gorilla).

We explored two hypotheses related to potential differences between sexes in dispersal behaviour in western lowland gorillas (Gorilla gorilla gorilla). Direct observations suggest that immature females have more opportunities to move between breeding groups than immature males. The distribution of kin dyadic relationships within and between groups does not, however, support this hypothesis. At larger geographical scales, dispersal is likely to be easier for males than females because of the solitary phase most blackbacks experience before founding their own breeding group. However, previous work indicates that males settle preferentially close to male kin. By specifically tracing female and male lineages with mitochondrial and Y‐chromosomal genetic markers, we found that male gorillas in the 6000 km2 area we surveyed form a single population whereas females are restricted to the individual sites we sampled and do not freely move around this area. These differences are more correctly described as differences in dispersal distances, rather than differences in dispersal rates between sexes (both sexes emigrate from their natal group in this species). Differences in resource competition and dispersal costs between female and male gorillas are compatible with the observed pattern, but more work is needed to understand if these ultimate causes are responsible for sex‐biased dispersal distances in western lowland gorillas.

A population genetic analysis of migration: the case of the noctule bat (Nyctalus noctula)

Although rarely assessed, the population genetics of hibernating colonies can help to understand some aspects of population structure, even when samples from nursery or mating colonies are not available, or in studies of migration when both types of samples are available and can be compared. Here we illustrate both points in a survey of mitochondrial DNA (mtDNA) control region sequences used to study the population genetics of hibernating colonies of a migrating species, the noctule bat (Nyctalus noctula). Lacking samples from Scandinavian nursery colonies, we use a North European hibernacula to suggest that Scandinavian populations are isolated from Central and East European colonies. Then, we compare genetic diversities of nursery and hibernating colonies. We find a significantly higher haplotype diversity in hibernacula, confirming that they consist of individuals from different nursery colonies. Finally, we show that pairwise comparisons of the haplotype frequencies of nursery and hibernating colonies contain some information on the migration direction of the noctule bat.

Dispersal and genetic structure in the American marten, Martes americana

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 FST 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 (σ2) inferred both from the genetic pattern of IBD and from the radio‐tracking survey showed that most juveniles make little contribution to gene flow.