Can Microsatellites Be Used to Infer Phylogenies? Evidence from Population Affinities of the Western Canary Island Lizard (Gallotia galloti)

Population phylogeographic studies are generally based solely on mtDNA without corroboration, from an independent segregating unit (i.e., nuclear genes), that the mtDNA gene tree represents the organismal phylogeny. This paper attempts to evaluate the utility of microsatellites for this process by use of the Western Canary Island lacertid (Gallotia galloti) as a model. The geological times of island eruptions are known, and well-supported mtDNA phylogenies exist (corroborated as the organismal phylogeny rather than just a gene tree by nuclear random amplified polymorphic DNAs (RAPDs)). The allelic variation in 12 populations from four islands (representing five haplotype lineages) was investigated in five unlinked microsatellite loci. Analysis of molecular variance showed this data to be highly structured. A series of genetic distances among populations was computed based on both the variance in allele frequency (i.e., F_st related) and the variance in repeat numbers (i.e., R_st related). The genetic distances based on the former were more highly correlated with the mtDNA genetic distances than those based on the latter. All trees based on both models supported the primary division shown by mtDNA and RAPDs, which is dated at ca. 2.8 to 5.6 mybp (depending on calibration of the mtDNA clock) and which could, under the evolutionary species concept, be regarded separate species. This was achieved despite theoretical problems posed by the use of few loci, suspected bottlenecks, and large population sizes. The finer details were less consistently represented. Nevertheless, this study demonstrates that even a small number of microsatellites can be useful in corroborating the deeper divisions of a population phylogeny.     

Pursuing glacier retreat: genetic structure of a rapidly expanding Larix decidua population

One of the greatest threats to the long-term viability of migrating plant species is the loss of genetic diversity due to founder effects. Populations can expand as a response to climate change, but it is uncertain if long-lived plant species can maintain sufficient genetic diversity at the leading edge of migrating populations. This study uses an expanding Larix decidua population investigated along a chronosequence at landscape (350 ha) and local (0.8 ha) scales to test whether accelerated migration as a result of climate warming has the potential to intensify genetic erosion. Nine SSR markers revealed similar genetic diversity among eight sub-populations along the chronosequence (overall H(e) = 0.73; SE=0.04). Sub-populations were not genetically differentiated and all sampled individuals (N=730) formed one major genetic cluster indicating homogenizing gene flow despite spatial genetic structure (SGS) up to 80 m. At the local scale, individuals at the leading edge [early successional sub-population (ESSP), N =140] and a sub-population at equilibrium [late successional sub-population (LSSP), N = 290] revealed high genetic diversity in largest-sized cohorts. SGS among juveniles occurred up to 30 m in LSSP but there was no structure in ESSP. Accordingly, a maximum likelihood paternity assignment revealed local gene dispersal in LSSP (2-48 m) and intermediate-to-long distance dispersal into ESSP (115-3132 m). The findings indicate intensive mixing of the genes in this expanding population instead of founder effects and support the view that genetic diversity can be maintained in a long-lived species during rapid population expansion driven by climate warming.     

Broad-scale latitudinal patterns of genetic diversity among native European and introduced house sparrow (Passer domesticus) populations

Introduced species offer unique opportunities to study evolution in new environments, and some provide opportunities for understanding the mechanisms underlying macroecological patterns. We sought to determine how introduction history impacted genetic diversity and differentiation of the house sparrow (Passer domesticus), one of the most broadly distributed bird species. We screened eight microsatellite loci in 316 individuals from 16 locations in the native and introduced ranges. Significant population structure occurred between native than introduced house sparrows. Introduced house sparrows were distinguished into one North American group and a highly differentiated Kenyan group. Genetic differentiation estimates identified a high magnitude of differentiation between Kenya and all other populations, but demonstrated that European and North American samples were differentiated too. Our results support previous claims that introduced North American populations likely had few source populations, and indicate house sparrows established populations after introduction. Genetic diversity also differed among native, introduced North American, and Kenyan populations with Kenyan birds being least diverse. In some cases, house sparrow populations appeared to maintain or recover genetic diversity relatively rapidly after range expansion (<50 years; Mexico and Panama), but in others (Kenya) the effect of introduction persisted over the same period. In both native and introduced populations, genetic diversity exhibited large-scale geographic patterns, increasing towards the equator. Such patterns of genetic diversity are concordant with two previously described models of genetic diversity, the latitudinal model and the species diversity model.     

Population genetic structure and the effect of founder events on the genetic variability of moose, Alces alces, in Canada

Moose, Alces alces, occur naturally throughout most of Canada but successful introductions of known numbers of animals have been made to the islands of Newfoundland and Cape Breton. Five microsatellite loci were used to investigate the population genetic structure and any change in genetic variability due to founder events of moose in Canada. Comparisons of allele frequencies for moose from 11 regions of the country suggested that there are at least seven genetically distinct populations (P < 0.05) in North America, namely Alberta, eastern Ontario, New Brunswick, Cape Breton, Labrador, western Newfoundland, and the Avalon Peninsula of Newfoundland. The average population heterozygosity was approximately 33% (range from 22 to 41%). UPGMA analysis of Nei's genetic distances produced phenograms similar to what would be expected when geographical location and population history are considered. The loss of heterozygosity due to a single founder event (n = 3; two introductions and a natural colonization) ranged from 14 to 30%, and the cumulative loss of heterozygosity due to two successive founder events (an introduction followed by a natural colonization) was 46%. In these examples loss of genetic variability has not been associated with any known phenotypic deviances, suggesting that populations may be established from a small number of founders. However, the viability of these founded populations over evolutionary timescales cannot be determined and is highly dependent upon chance.     

When North and South don’t mix: genetic connectivity of a recently endangered oceanic cycad,Cycas micronesica,in Guam using EST‐microsatellites

Subject to environmental changes and recurrent isolation in the last ca. 250 Ma, cycads are often described as relicts of a previously common lineage, with populations characterized by low genetic variation and restricted gene flow. We found that on the island of Guam, the endemic Cycas micronesica has most of the genetic variation of 14 EST‐microsatellites distributed within each of 18 genetic populations, from 24 original sampling sites. There were high levels of genetic variation in terms of total number of alleles and private alleles, and moderate levels of inbreeding. Restricted but ongoing gene flow among populations within Guam reveals a genetic mosaic, probably more typical of cycads than previously assumed. Contiguous cycad populations in the north of Guam had higher self‐recruitment rates compared to fragmented populations in the south, with no substantial connection between them except for one population. Guam’s genetic mosaic may be explained by the influence of forest continuity, seed size, edaphic differences, and human transport of cycads. Also important are the extent of synchrony among flushes of reproductive female seed‐bearing sporophylls and restricted pollen movement by an obligate mutualist and generalist insects. An NADH EST‐locus under positive selection may reflect pressure from edaphic differences across Guam. This and three other loci are ideal candidates for ecological genomic studies. Given this species’ vulnerability due to the recent introduction of the cycad aulacaspis scale, we also identify priority populations for ex situ conservation, and provide a genetic baseline for understanding the effects of invasive species on cycads in the Western Pacific, and islands in general.     

Admixture and sexual bias in the population settlement of La Réunion Island (Indian Ocean)

La Réunion, one of the three Mascarene islands located in the Indian Ocean, remained devoid of inhabitants until it was first colonized by the French in the middle of the 17th century. The continuous flow of foreign-born slaves and immigrant workers from Africa, India, Southeast Asia, and China to work on coffee and sugar cane plantations led to the island becoming a melting pot of people of multiple ethnic origins. To establish the impact of the different incoming ethnic groups on the present Reunionese gene pool, we have sequenced both hypervariable regions I and II of the mitochondrial DNA molecule, the 9 bp COII/tRNA(Lys) deletion, and four SNPs located in the coding region in a total of 41 samples of the general population, and a further 18 STRs and 35 SNPs on the Y chromosome in 26 of these samples. Our results show that there was a strong sexual bias (asymmetrical gene flow) in the peopling of La Réunion, where admixture events were mainly between male settlers and females from the incoming slave groups. Most of the Y-chromosome gene pool is of European/Middle Eastern ancestry (85%), whereas the mtDNA gene pool is mainly of Indian and East Asian ancestry (70%). The absence of genetic diversity within these two major components of the mtDNA gene pool suggests these populations may have witnessed strong founder effects during the colonization process.     

Genomic admixture increases fitness during a biological invasion

Abstract During biological invasions, multiple introductions can provide opportunities for admixture among genetically distinct lineages. Admixture is predicted to contribute to invasion success by directly increasing fitness through hybrid vigour or by enhancing evolutionary potential within populations . Here, we demonstrate genome‐wide admixture during an invasion that substantially boosted fitness in the cosmopolitan weed, Silene vulgaris. We identified three divergent demes in the native European range that expanded from glacial refugia and experienced historical admixture in a well‐known suture zone. During recent invasion of North America, multiple introductions created additional opportunities for admixture. In common garden experiments, recombinant genotypes from North America experienced a two‐fold increase in fitness relative to nonrecombinants, whereas recombinant genotypes from Europe showed no lasting fitness benefits. This contrast implicates hybrid vigour behind the boost in fitness and supports the hypothesis that admixture can lead to fitness increases that may catapult invasion into a new range.     

Does local adaptation to resources explain genetic differentiation among Daphnia populations?

Substantial genetic differentiation is frequently observed among populations of cyclically parthenogenetic zooplankton despite their high dispersal capabilities and potential for gene flow. Local adaptation has been invoked to explain population genetic differentiation despite high dispersal, but several neutral models that account for basic life history features also predict high genetic differentiation. Here, we study genetic differentiation among four populations of Daphnia pulex in east central Illinois. As with other studies of Daphnia, we demonstrate substantial population genetic differentiation despite close geographic proximity (<50 km; mean θ = 0.22). However, we explicitly tested and failed to find evidence for, the hypothesis that local adaptation to food resources occurs in these populations. Recognizing that local adaptation can occur in traits unrelated to resources, we estimated contemporary migration rates (m) and tested for admixture to evaluate the hypothesis that observed genetic differentiation is consistent with local adaptation to other untested ecological factors. Using Bayesian assignment methods, we detected migrants in three of the four study populations including substantial evidence for successful reproduction by immigrants in one pond, allowing us to reject the hypothesis that local adaptation limits gene flow for at least this population. Thus, we suggest that local adaptation does not explain genetic differentiation among these Daphnia populations and that other factors related to extinction/colonization dynamics, a long approach to equilibrium F_ST or substantial genetic drift due to a low number of individuals hatching from the egg bank each season may explain genetic differentiation.     

Ancient vs. recent processes as factors shaping the genetic variation of the European wild boar: are the effects of the last glaciation still detectable?

The European wild boar is an important game species, subjected to local extinctions and translocations in the past, and currently enormously and worryingly expanding in some areas where management is urgently required. Understanding the relative roles of ancient and recent events in shaping the genetic structure of this species is therefore not only an interesting scientific issue, but it represents also the basis for addressing future management strategies. In addition, several pig breeds descend from the European wild boar, but the geographical location of the domestication area(s) and the possible introgression of pig genomes into wild populations are still open questions. Here, we analysed the genetic variation in different wild boar populations in Europe. Ten polymorphic microsatellites were typed in 252 wild boars and the mtDNA control region was sequenced in a subset of 145 individuals. Some samples from different pig breeds were also analysed. Our results, which were obtained considering also 612 published mtDNA sequences, suggest that (i) most populations are similarly differentiated, but the major discontinuity is found along the Alps; (ii) except for the Italian populations, European wild boars show the signature of a postglacial demographic expansion; (iii) Italian populations seem to preserve a high proportion of preglaciation diversity; (iv) the demographic decline which occurred in some areas in the last few centuries did not produce a noticeable reduction of genetic variation; (v) signs of human-mediated gene flow among populations are weak, although in some regions the effects of translocations are detectable and a low degree of pig introgression can be identified; (vi) the hypothesis of an independent domestication centre in Italy is not supported by our data, which in turn confirm that Central European wild boar might have represented an important source for domestic breeds. We can therefore conclude that recent human activities had a limited effect on the wild boar genetic structure. It follows that areas with high variation and differentiation represent natural reservoirs of genetic diversity to be protected avoiding translocations. In this context controlling some populations by hunting is not expected to affect significantly genetic variation in this species.