P. Galbusera

A comparison of microsatellite‐based pairwise relatedness estimators

Studies of inbreeding depression or kin selection require knowledge of relatedness between individuals. If pedigree information is lacking, one has to rely on genotypic information to infer relatedness. In this study we investigated the performance (absolute and relative) of 10 marker‐based relatedness estimators using allele frequencies at microsatellite loci obtained from natural populations of two bird species and one mammal species. Using Monte Carlo simulations we show that many factors affect the performance of estimators and that different sets of loci promote the use of different estimators: in general, there is no single best‐performing estimator. The use of locus‐specific weights turns out to greatly improve the performance of estimators when marker loci are used that differ strongly in allele frequency distribution. Microsatellite‐based estimates are expected to explain between 25 and 79% of variation in true relatedness depending on the microsatellite dataset and on the population composition (i.e. the frequency distribution of relationship in the population). We recommend performing Monte Carlo simulations to decide which estimator to use in studies of pairwise relatedness.

Genetic structure of the forest herb Primula elatior in a changing landscape

To investigate whether changes in land use and associated forest patch turnover affected genetic diversity and structure of the forest herb Primula elatior, historical data on landscape changes were combined with a population genetic analysis using dominant amplified fragment length polymorphism markers. Based on nine topographic maps, landscape history was reconstructed and forest patches were assigned to two age classes: young (less than 35 years) and old (more than 35 years). The level of differentiation among Primula populations in recently established patches was compared with the level of differentiation among populations in older patches. Genetic diversity was independent of population size (P > 0.05). Most genetic variation was present within populations. Within‐population diversity levels tended to be higher for populations located in older forests compared with those for populations located in young forests (Hj = 0.297 and 0.285, respectively). Total gene diversity was also higher for old than for young populations (Ht = 0.2987 and 0.2828, respectively). The global fixation index FST averaged over loci was low, but significant. Populations in older patches were significantly more differentiated from each other than were populations in recently established patches and they showed significant isolation by distance. In contrast, no significant correlations between pairwise geographical distance and FST were found for populations in recently established patches. The location of young and old populations in the studied system and altered gene flow because of increased population density and decreased inter‐patch distances between extant populations may explain the observed lower genetic differentiation in the younger populations. This study exemplifies the importance of incorporating data on historical landscape changes in population genetic research at the landscape scale.

Geographical distance and physical barriers shape the genetic structure of Eurasian red squirrels (Sciurus vulgaris) in the Italian Alps

Red squirrels (Sciurus vulgaris) are widely distributed throughout Eurasia, occurring in many types of coniferous and mixed‐deciduous forests. In fragmented landscapes, small and partly isolated populations with low immigration rates show reduced genetic diversity, but reforestation can increase gene flow and restore levels of genetic variation in a few decades. No studies have so far investigated the genetic structure of red squirrel in large, continuous forests. The Italian Alps are presently characterized by almost continuous, recently reconnected forest habitats, that were affected by deep landscape changes during last glaciations but remained mostly unchanged between 10 000 and 200 years bp, when forest cover was heavily reduced. In this study we analyse patterns of genetic variability of red squirrels in and between seven sites distributed over 250 km of Alpine habitat, using mitochondrial DNA (mtDNA) and microsatellites. We use isolation‐by‐distance (IBD) models to investigate the relative importance that past (Pleistocene glaciations) and recent (fragmentation, bottlenecks) events had on the present genetic situation. Both nuclear and mtDNA data indicate a significant differentiation among study sites and a significant correlation between genetic and geographical distance only over a large scale. No recent bottlenecks are recorded through microsatellites and demographic models strongly support equilibrium between gene flow and drift; however, mtDNA suggests that there may have been local demographic crashes, probably in correspondence with the 19th‐century forest fragmentation. These findings indicate that local landscape factors other than geographical distance per se, such as barriers of unsuitable habitat, affect gene flow and determine differentiation.

Genetic signature of population fragmentation varies with mobility in seven bird species of a fragmented Kenyan cloud forest.

Habitat fragmentation can restrict geneflow, reduce neighbourhood effective population size, and increase genetic drift and inbreeding in small, isolated habitat remnants. The extent to which habitat fragmentation leads to population fragmentation, however, differs among landscapes and taxa. Commonly, researchers use information on the current status of a species to predict population effects of habitat fragmentation. Such methods, however, do not convey information on species‐specific responses to fragmentation. Here, we compare levels of past population differentiation, estimated from microsatellite genotypes, with contemporary dispersal rates, estimated from multi‐strata capture–recapture models, to infer changes in mobility over time in seven sympatric, forest‐dependent bird species of a Kenyan cloud forest archipelago. Overall, populations of sedentary species were more strongly differentiated and clustered compared to those of vagile ones, while geographical patterning suggested an important role of landscape structure in shaping genetic variation. However, five of seven species with broadly similar levels of genetic differentiation nevertheless differed substantially in their current dispersal rates. We conclude that post‐fragmentation levels of vagility, without reference to past population connectivity, may not be the best predictor of how forest fragmentation affects the life history of forest‐dependent species. As effective conservation strategies often hinge on accurate prediction of shifts in ecological and genetic relationships among populations, conservation practices based solely upon current population abundances or movements may, in the long term, prove to be inadequate.

Developmental instability and inbreeding in natural bird populations exposed to different levels of habitat disturbance

As habitat disturbance and inbreeding increasingly stress natural populations, ecologists are in urgent need of simple estimators to measure their impact. It has been argued that developmental instability (DI) could be such a measure. Observed associations between DI and environmental or genetic stress, however, are largely inconsistent. We here test whether an interaction between habitat disturbance and inbreeding could, at least partly, explain these discordant patterns. We therefore studied individual estimates of fluctuating asymmetry (FA) and of inbreeding in three populations of the critically endangered Taita thrush that are differentially exposed to habitat disturbance following severe forest fragmentation. As predicted, the relationship between DI and inbreeding was pronounced under high levels of disturbance, but weak or nonexistent under less disturbed conditions. Examining this relationship with mean d2, an allelic distance estimator assumed to reflect ancestral inbreeding, did not reveal any significant trend, hence suggesting that inbreeding effects in the Taita thrush are fairly recent.

Cross-species amplification of microsatellite primers in passerine birds

Developing species specific microsatellite primers can be avoidedby using existing markers which amplify across species. However,for passerines, such ‘cross-species’ markers are mostly lackingand few guidelines exist for selecting them from the wide rangeof existing markers. Here cross-species amplification tests of 40microsatellite primers in 13 passerine species show an increasein probability of amplification and polymorphism with decreasingphylogenetic distance. Primers which successfully amplified inmany species had a higher chance to be polymorphic. However,since the amplification success, across a broad range of species,of particular primersets remains difficult to predict it iscrucial to identify such markers empirically. Here we describesuch widely applicable bird (passerines) microsatellite markers.

Genetic variability and gene flow in the globally, critically-endangered Taita Thrush

Analysis of 155 individuals with seven polymorphicmicrosatellite DNA markers showed significant genetic differentiationbetween the only three remaining subpopulations of the globally,critically-endangered Taita thrush. Small, recently-disturbedsubpopulations such as studied here may violate the assumptions ofmutation-drift and gene flow-drift equilibrium inherent to mostpopulation genetic tools that estimate gene flow. We thereforeidentified putative dispersers using two recently-developed assignmenttests based on individual genotypes. Previous-generation and currentmigration rates between any two subpopulations were estimated at one andzero individuals per generation, respectively. Strong congruence withnon-genetic estimates of between-fragment dispersal provided indirectevidence for the accuracy of the assignment test. From a conservationperspective, the available demographic and genetic data suggest asubstantial threat to the long-term survival of at least the smallestsubpopulation.

Bringing genetic diversity to the forefront of conservation policy and management

In this essay we explore questions on how to increase the visibility and utility of genetic information for biodiversity managers and policy makers. This is discussed in the light of Aichi CBD Target 13, which for the first time impels signatories to minimise genetic erosion and safeguard genetic diversity. Drawing on qualitative results from a questionnaire sent to European conservation professionals by the ConGRESS Framework 7 Support Action (www.congressgenetics.eu), we summarise our preliminary findings on the attitudes and experiences of European conservation professionals in using genetics. We then discuss the implications of these findings for academics involved in conservation genetics and suggest that a much closer partnership between academic conservation geneticists and conservation practitioners is necessary if the full potential of genetic tools in conservation is to be realised.

Genetic equilibrium despite habitat fragmentation in an Afrotropical bird.

We examined the effects of habitat fragmentation of the white‐starred robin Pogonocichla stellata metapopulation in the Taita Hills archipelago, a hotspot for biodiversity which was fragmented ~40 years ago. Using seven microsatellite markers, we analysed the robins genetic structure and tested for equilibrium between migration and drift (testing the probability of decreased dispersal) as well as between mutation and drift (test for recent reduction in effective population size, i.e. bottlenecks). This metapopulation was found to retain relatively high levels of genetic variability (HE between 0.63 and 0.71) and to be in migration–drift equilibrium, suggesting that increased isolation between fragments did not have much effect on the dispersal between them. Furthermore, this equilibrium test greatly enhanced the interpretation of parameters (e.g. FST) assumed to have reached an equilibrium value. In contrast to previous findings on the related and sympatric Taita thrush Turdus helleri (which is critically endangered), there were no indications for recent bottlenecks in any of the robin subpopulations. This difference can be attributed to the higher dispersal capacity of the robin compared with the thrush (deduced from both the genetic and capture–recapture data). Our results stress the importance of sustained dispersal for species conservation.

Gene flow in a direct-developing, leaf litter frog between isolated mountains in the Taita Hills, Kenya

Amphibians are in decline worldwide, and high altitude tropical areas appear to be the worst affected. This is in stark contrast with current information we have on gene flow in amphibian populations which focus on temperate pond breeding species. Using AFLP markers, we show that a small, direct-developing, leaf litter frog from the Taita Hills in south–west Kenya (Schoutedenella xenodactyloides) has extended populations covering large areas (>3.5 km) of fragmented, forest habitat, uncharacteristic of typical amphibian models. Further, we demonstrate high levels of gene flow (FST < 0.065) through unsuitable dry savannah habitat which might otherwise be considered a barrier to dispersal. Landscape genetic analysis demonstrates a strong link between hydrologic features, and further highlights links between sites through specific catchments. We propose a model of passive-active dispersal for the Dwarf Squeaker, S. xenodactyloides, which features passive downhill and active uphill movements over large areas, contrasting with limited cross slope movements. Our study highlights the importance of the diverse reproductive strategies of the Amphibia when considering dispersal and gene flow, and hence conservation management.