Population history, gene flow, and bottlenecks in island populations of a secondary seed disperser, the southern grey shrike (Lanius meridionalis koenigi)

Studying the population history and demography of organisms with important ecological roles can aid understanding of evolutionary processes at the community level and inform conservation. We screened genetic variation (mtDNA and microsatellite) across the populations of the southern grey shrike (Lanius meridionalis koenigi) in the Canary Islands, where it is an endemic subspecies and an important secondary seed disperser. We show that the Canarian subspecies is polyphyletic with L. meridionalis elegans from North Africa and that shrikes have colonized the Canary Islands from North Africa multiple times. Substantial differences in genetic diversity exist across islands, which are most likely the product of a combination of historical colonization events and recent bottlenecks. The Eastern Canary Islands had the highest overall levels of genetic diversity and have probably been most recently and/or frequently colonized from Africa. Recent or ongoing bottlenecks were detected in three of the islands and are consistent with anecdotal evidence of population declines due to human disturbance. These findings are troubling given the shrike's key ecological role in the Canary Islands, and further research is needed to understand the community-level consequences of declines in shrike populations. Finally, we found moderate genetic differentiation among populations, which largely reflected the shrike's bottleneck history; however, a significant pattern of isolation-by-distance indicated that some gene flow occurs between islands. This study is a useful first step toward understanding how secondary seed dispersal operates over broad spatial scales

European wildcat populations are subdivided into five main biogeographic groups: consequences of Pleistocene climate changes or recent anthropogenic fragmentation?

Extant populations of the European wildcat are fragmented across the continent, the likely consequence of recent extirpations due to habitat loss and over-hunting. However, their underlying phylogeographic history has never been reconstructed. For testing the hypothesis that the European wildcat survived the Ice Age fragmented in Mediterranean refuges, we assayed the genetic variation at 31 microsatellites in 668 presumptive European wildcats sampled in 15 European countries. Moreover, to evaluate the extent of subspecies/population divergence and identify eventual wild × domestic cat hybrids, we genotyped 26 African wildcats from Sardinia and North Africa and 294 random-bred domestic cats. Results of multivariate analyses and Bayesian clustering confirmed that the European wild and the domestic cats (plus the African wildcats) belong to two well-differentiated clusters (average Ф ST = 0.159, r st = 0.392, P > 0.001; Analysis of molecular variance [AMOVA]). We identified from c. 5% to 10% cryptic hybrids in southern and central European populations. In contrast, wild-living cats in Hungary and Scotland showed deep signatures of genetic admixture and introgression with domestic cats. The European wildcats are subdivided into five main genetic clusters (average Ф ST = 0.103, r st = 0.143, P > 0.001; AMOVA) corresponding to five biogeographic groups, respectively, distributed in the Iberian Peninsula, central Europe, central Germany, Italian Peninsula and the island of Sicily, and in north-eastern Italy and northern Balkan regions (Dinaric Alps). Approximate Bayesian Computation simulations supported late Pleistocene-early Holocene population splittings (from c. 60 k to 10 k years ago), contemporary to the last Ice Age climatic changes. These results provide evidences for wildcat Mediterranean refuges in southwestern Europe, but the evolution history of eastern wildcat populations remains to be clarified. Historical genetic subdivisions suggest conservation strategies aimed at enhancing gene flow through the restoration of ecological corridors within each biogeographic units. Concomitantly, the risk of hybridization with free-ranging domestic cats along corridor edges should be carefully monitored

Reliability assessment of null allele detection: inconsistencies between and within different methods

Microsatellite loci are widely used in population genetic studies, but the presence of null alleles may lead to biased results. Here we assessed five methods that indirectly detect null alleles, and found large inconsistencies among them. Our analysis was based on 20 microsatellite loci genotyped in a natural population of Microtus oeconomus sampled during 8 years, together with 1200 simulated populations without null alleles, but experiencing bottlenecks of varying duration and intensity, and 120 simulated populations with known null alleles. In the natural population, 29% of positive results were consistent between the methods in pairwise comparisons, and in the simulated dataset this proportion was 14%. The positive results were also inconsistent between different years in the natural population. In the null-allele-free simulated dataset, the number of false positives increased with increased bottleneck intensity and duration. We also found a low concordance in null allele detection between the original simulated populations and their 20% random subsets. In the populations simulated to include null alleles, between 22% and 42% of true null alleles remained undetected, which highlighted that detection errors are not restricted to false positives. None of the evaluated methods clearly outperformed the others when both false positive and false negative rates were considered. Accepting only the positive results consistent between at least two methods should considerably reduce the false positive rate, but this approach may increase the false negative rate. Our study demonstrates the need for novel null allele detection methods that could be reliably applied to natural population

Calibration of centre-of-mass energies at LEP 2 for a precise measurement of the W boson mass

The determination of the centre-of-mass energies for all LEP 2 running is presented. Accurate knowledge of these energies is of primary importance to set the absolute energy scale for the measurement of the W boson mass. The beam energy between 80 and 104 GeV is derived from continuous measurements of the magnetic bending field by 16 NMR probes situated in a number of the LEP dipoles. The relationship between the fields measured by the probes and the beam energy is defined in the NMR model, which is calibrated against precise measurements of the average beam energy between 41 and 61 GeV made using the resonant depolarisation technique. The validity of the NMR model is verified by three independent methods: the flux-loop, which is sensitive to the bending field of all the dipoles of LEP; the spectrometer, which determines the energy through measurements of the deflection of the beam in a magnet of known integrated field; and an analysis of the variation of the synchrotron tune with the total RF voltage. To obtain the centre-of-mass energies, corrections are then applied to account for sources of bending field external to the dipoles, and variations in the local beam energy at each interaction point. The relative error on the centre-of-mass energy determination for the majority of LEP 2 running is 1.2 x 10^{-4}, which is sufficiently precise so as not to introduce a dominant uncertainty on the W mass measurement.Comment: 79 pages, 45 figures, submitted to EPJ

How much of the invader’s genetic variability can slip between our fingers? A case study of secondary dispersal of Poa annua on King George Island (Antarctica)

We studied an invasion of Poa annua on King George Island (Maritime Antarctic). The remoteness of this location, its geographic isolation, and its limited human traffic provided an opportunity to trace the history of an invasion of the species. Poa annua was recorded for the first time at H. Arctowski Polish Antarctic Station in the austral summer of 1985/6. In 2008/9, the species was observed in a new locality at the Ecology Glacier Forefield (1.5 km from “Arctowski”). We used AFLP to analyze the genetic differences among three populations of P. annua: the two mentioned above (Station and Forefield) and the putative origin of the introduction, Warsaw (Poland). There was 38% genetic variance among the populations. Pairwise ФPT was 0.498 between the Forefield and Warsaw populations and 0.283 between Warsaw and Station. There were 15 unique bands in the Warsaw population (frequency from 6% to 100%) and one in the Station/Forefield populations (which appears in all analyzed individuals from both populations). The Δ(K) parameter indicated two groups of samples: Warsaw/Station and Forefield. As indicated by Fu’s Fs statistics and an analysis of mismatch distribution, the Forefield population underwent a bottleneck and/or founder effect. The Forefield population was likely introduced by secondary dispersal from the Station population

Genetic consequences of selection cutting on sugar maple (Acer saccharum Marshall)

Selection cutting is a treatment that emulates tree-by-tree replacement for forests with uneven-age structures. It creates small openings in large areas and often generates a more homogenous forest structure (fewer large leaving trees and defective trees) that differs from old-growth forest. In this study, we evaluated whether this type of harvesting has an impact on genetic diversity of sugar maple (Acer saccharum Marshall). Genetic diversity among seedlings, saplings, and mature trees was compared between selection cut and old-growth forest stands in Québec, Canada. We found higher observed heterozygosity and a lower inbreeding coefficient in mature trees than in younger regeneration cohorts of both forest types. We detected a recent bottleneck in all stands undergoing selection cutting. Other genetic indices of diversity (allelic richness, observed and expected heterozygosity, and rare alleles) were similar between forest types. We concluded that the effect of selection cutting on the genetic diversity of sugar maple was recent and no evidence of genetic erosion was detectable in Québec stands after one harvest. However, the cumulative effect of recurring applications of selection cutting in bottlenecked stands could lead to fixation of deleterious alleles, and this highlights the need for adopting better forest management practices

Genetic evidence challenges the native status of a threatened freshwater fish (Carassius carassius) in England.

A fundamental consideration for the conservation of a species is the extent of its native range, that is, regions naturally colonized. However, both natural processes and human-mediated introductions can drive species distribution shifts. Ruling out the human-mediated introduction of a species into a given region is vital for its conservation, but remains a significant challenge in most cases. The crucian carp Carassius carassius (L.) is a threatened freshwater fish thought to be native to much of Europe. However, its native status in England is based only on anecdotal evidence. Here, we devise an approach that can be used to empirically test the native status of English fauna. We use this approach, along with 13 microsatellite loci, population structure analyses, and Approximate Bayesian Computation (ABC), to test hypotheses for the origins of C. carassius in England. Contrary to the current consensus, we find strong support for the human-mediated introduction of C. carassius into England during the 15th century. This result stimulates an interesting and timely debate surrounding motivations for the conservation of species. We discuss this topic, and the potential for continued conservation of C. carassius in England, despite its non-native origins

Contrasting patterns of genetic and phenotypic differentiation in two invasive salmonids in the southern hemisphere

Peer reviewe

Stratified dispersal and increasing genetic variation during the invasion of Central Europe by the western corn rootworm, Diabrotica virgifera virgifera

Invasive species provide opportunities for investigating evolutionary aspects of colonization processes, including initial foundations of populations and geographic expansion. Using microsatellite markers and historical information, we characterized the genetic patterns of the invasion of the western corn rootworm (WCR), a pest of corn crops, in its largest area of expansion in Europe: Central and South-Eastern (CSE) Europe. We found that the invaded area probably corresponds to a single expanding population resulting from a single introduction of WCR and that gene flow is geographically limited within the population. In contrast to what is expected in classical colonization processes, an increase in genetic variation was observed from the center to the edge of the outbreak. Control measures against WCR at the center of the outbreak may have decreased effective population size in this area which could explain this observed pattern of genetic variation. We also found that small remote outbreaks in southern Germany and north-eastern Italy most likely originated from long-distance dispersal events from CSE Europe. We conclude that the large European outbreak is expanding by stratified dispersal, involving both continuous diffusion and discontinuous long-distance dispersal. This latter mode of dispersal may accelerate the expansion of WCR in Europe in the future