Fine-scale genetic structure and dispersal in the common vole (Microtus arvalis)

The genetic structure and demography of local populations is tightly linked to the rate and scale of dispersal. Dispersal parameters are notoriously difficult to determine in the field, and remain often completely unknown for smaller organisms. In this study, we investigate spatial and temporal genetic structure in relation to dispersal patterns among local populations of the probably most abundant European mammals, the common vole (Microtus arvalis). Voles were studied in six natural populations at distances of 0.4-2.5 km in three different seasons (fall, spring, summer) corresponding to different life-history stages. Field observations provided no direct evidence for movements of individuals between populations. The analysis of 10 microsatellite markers revealed a persistent overall genetic structure among populations of 2.9%, 2.5% and 3% FST in the respective season. Pairwise comparisons showed that even the closest populations were significantly differentiated from each other in each season, but there was no evidence for temporal differentiation within populations or isolation by distance among populations. Despite significant genetic structure, assignment analyses identified a relatively high proportion of individuals as being immigrants for the population where they were captured. The immigration rate was not significantly lower for females than for males. We suggest that a generally low and sex-dependent effective dispersal rate as the consequence of only few immigrants reproducing successfully in the new populations together with the social structure within populations may explain the maintenance of genetic differentiation among populations despite migration.

Genetic variation and demographic history of the Haplochromis laparogramma group of Lake Victoria-An analysis based on SINEs and mitochondrial DNA

More than 500 endemic haplochromine cichlid species inhabit Lake Victoria. This striking species diversity is a classical example of recent explosive adaptive radiation thought to have happened within the last similar to 15,000 years. In this study, we examined the population structure and historical demography of 3 pelagic haplochromine cichlid species that resemble in morphology and have similar niche, Haplochromis (Yssichromis) laparogramma, Haplochromis (Y.) pyrrhocephalus, and Haplochromis (Y.) sp. "glaucocephalus". We investigated the sequences of the mitochondrial DNA control region and the insertion patterns of short interspersed elements (SINEs) of 759 individuals. We show that sympatric forms are genetically differentiated in 4 of 6 cases, but we also found apparent weakening of the genetic differentiation in areas with turbid water. We estimated the timings of population expansion and species divergence to coincide with the refilling of the lake at the Pleistocene/Holocene boundary. We also found that estimates can be altered significantly by the choice of the shape of the molecular clock. If we employ the nonlinear clock model of evolutionary rates in which the rates are higher towards the recent, the population expansion was dated at around the event of desiccation of the lake ca. 17,000 YBP. Thus, we succeeded in clarifying the species and population structure of closely related Lake Victoria cichlids and in showing the importance of applying appropriate clock calibrations in elucidating recent evolutionary events. (C) 2009 Elsevier B.V. All rights reserved.

The scaling of genetic diversity in a changing and fragmented world

Most species do not live in a constant environment over space or time. Their environment is often heterogeneous with a huge variability in resource availability and exposure to pathogens or predators, which may affect the local densities of the species. Moreover, the habitat might be fragmented, preventing free and isotropic migrations between local sub-populations (demes) of a species, making some demes more isolated than others. For example, during the last ice age populations of many species migrated towards refuge areas from which re-colonization originated when conditions improved. However, populations that could not move fast enough or could not adapt to the new environmental conditions faced extinctions. Populations living in these types of dynamic environments are often referred to as metapopulations and modeled as an array of subdivisions (or demes) that exchange migrants with their neighbors. Several studies have focused on the description of their demography, probability of extinction and expected patterns of diversity at different scales. Importantly, all these evolutionary processes may affect genetic diversity, which can affect the chance of populations to persist. In this chapter we provide an overview on the consequences of fragmentation, long-distance dispersal, range contractions and range shifts on genetic diversity. In addition, we describe new methods to detect and quantify underlying evolutionary processes from sampled genetic data.

Long distance dispersal shaped patterns of human genetic diversity in Eurasia

Most previous attempts at reconstructing the past history of human populations did not explicitly take geography into account, or considered very simple scenarios of migration and ignored environmental information. However, it is likely that the Last Glacial Maximum (LGM) affected the demography and the range of many species, including our own. Moreover, long-distance dispersal (LDD) may have been an important component of human migrations, allowing fast colonization of new territories and preserving high levels of genetic diversity. Here, we use a high-quality microsatellite dataset genotyped in 22 populations to estimate the posterior probabilities of several scenarios for the settlement of the Old World by modern humans. We considered models ranging from a simple spatial expansion to others including LDD and a LGM-induced range contraction, as well as Neolithic demographic expansions. We find that scenarios with LDD are much better supported by data than models without LDD. Nevertheless, we show evidence that LDD events to empty habitats were strongly prevented during the settlement of Eurasia. This unexpected absence of LDD ahead of the colonization wave front could have been caused by an Allee effect, either due to intrinsic causes such as an inbreeding depression built during the expansion, or to extrinsic causes such as direct competition with archaic humans. Overall, our results suggest only a relatively limited effect of the LGM-contraction on current patterns of human diversity. This is in clear contrast with the major role of LDD migrations, which have potentially contributed to the intermingled genetic structure of Eurasian populations.

Genetic variation and inference of demographic histories in non-model species

Both long-term environmental changes such as those driven by the glacial cycles and more recent anthropogenic impacts have had major effects on the past demography in wild organisms. Within species, these changes are reflected in the amount and distribution of neutral genetic variation. In this thesis, mitochondrial and microsatellite DNA was analysed to investigate how environmental and anthropogenic factors have affected genetic diversity and structure in four ecologically different animal species. Paper I describes the post-glacial recolonisation history of the speckled-wood butterfly (Pararge aegeria) in Northern Europe. A decrease in genetic diversity with latitude and a marked population structure were uncovered, consistent with a hypothesis of repeated founder events during the postglacial recolonisation. Moreover, Approximate Bayesian Computation analyses indicate that the univoltine populations in Scandinavia and Finland originate from recolonisations along two routes, one on each side of the Baltic. Paper II aimed to investigate how past sea-level rises affected the population history of the convict surgeonfish (Acanthurus triostegus) in the Indo-Pacific. Assessment of the species’ demographic history suggested a population expansion that occurred approximately at the end of the last glaciation. Moreover, the results demonstrated an overall lack of phylogeographic structure, probably due to the high dispersal rates associated with the species’ pelagic larval stage. Populations at the species’ eastern range margin were significantly differentiated from other populations, which likely is a consequence of their geographic isolation. In Paper III, we assessed the effect of human impact on the genetic variation of European moose (Alces alces) in Sweden. Genetic analyses revealed a spatial structure with two genetic clusters, one in northern and one in southern Sweden, which were separated by a narrow transition zone. Moreover, demographic inference suggested a recent population bottleneck. The inferred timing of this bottleneck coincided with a known reduction in population size in the 19th and early 20th century due to high hunting pressure. In Paper IV, we examined the effect of an indirect but well-described human impact, via environmental toxic chemicals (PCBs), on the genetic variation of Eurasian otters (Lutra lutra) in Sweden. Genetic clustering assignment revealed differentiation between otters in northern and southern Sweden, but also in the Stockholm region. ABC analyses indicated a decrease in effective population size in both northern and southern Sweden. Moreover, comparative analyses of historical and contemporary samples demonstrated a more severe decline in genetic diversity in southern Sweden compared to northern Sweden, in agreement with the levels of PCBs found.

Impact of selection and demography on the diffusion of lactase persistence.

The lactase enzyme allows lactose digestion in fresh milk. Its activity strongly decreases after the weaning phase in most humans, but persists at a high frequency in Europe and some nomadic populations. Two hypotheses are usually proposed to explain the particular distribution of the lactase persistence phenotype. The gene-culture coevolution hypothesis supposes a nutritional advantage of lactose digestion in pastoral populations. The calcium assimilation hypothesis suggests that carriers of the lactase persistence allele(s) (LCT*P) are favoured in high-latitude regions, where sunshine is insufficient to allow accurate vitamin-D synthesis. In this work, we test the validity of these two hypotheses on a large worldwide dataset of lactase persistence frequencies by using several complementary approaches. Methodology We first analyse the distribution of lactase persistence in various continents in relation to geographic variation, pastoralism levels, and the genetic patterns observed for other independent polymorphisms. Then we use computer simulations and a large database of archaeological dates for the introduction of domestication to explore the evolution of these frequencies in Europe according to different demographic scenarios and selection intensities. Conclusions Our results show that gene-culture coevolution is a likely hypothesis in Africa as high LCT*P frequencies are preferentially found in pastoral populations. In Europe, we show that population history played an important role in the diffusion of lactase persistence over the continent. Moreover, selection pressure on lactase persistence has been very high in the North-western part of the continent, by contrast to the South-eastern part where genetic drift alone can explain the observed frequencies. This selection pressure increasing with latitude is highly compatible with the calcium assimilation hypothesis while the gene-culture coevolution hypothesis cannot be ruled out if a positively selected lactase gene was carried at the front of the expansion wave during the Neolithic transition in Europe.