Museum DNA reveals the demographic history of the endangered Seychelles warbler

The importance of evolutionary conservation – how understanding evolutionary forces can help guide conservation decisions – is widely recognized. However, the historical demography of many endangered species is unknown, despite the fact that this can have important implications for contemporary ecological processes and for extinction risk. Here, we reconstruct the population history of the Seychelles warbler (Acrocephalus sechellensis) – an ecological model species. By the 1960s, this species was on the brink of extinction, but its previous history is unknown. We used DNA samples from contemporary and museum specimens spanning 140 years to reconstruct bottleneck history. We found a 25% reduction in genetic diversity between museum and contemporary populations, and strong genetic structure. Simulations indicate that the Seychelles warbler was bottlenecked from a large population, with an ancestral Ne of several thousands falling to <50 within the last century. Such a rapid decline, due to anthropogenic factors, has important implications for extinction risk in the Seychelles warbler, and our results will inform conservation practices. Reconstructing the population history of this species also allows us to better understand patterns of genetic diversity, inbreeding and promiscuity in the contemporary populations. Our approaches can be applied across species to test ecological hypotheses and inform conservation

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 &gt; 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 &gt; 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

Does asymmetric gene flow among matrilines maintain the evolutionary potential of the European eel?

Using evolutionary theory to predict the dynamics of populations is one of the aims of evolutionary conservation. In endangered species, with geographic range extending over continuous areas, the predictive capacity of evolutionary-based conservation measures greatly depends on the accurate identification of reproductive units. The endangered European eel (Anguilla anguilla) is a highly migratory fish species with declining population due to a steep recruitment collapse in the beginning of the 1980s. Despite punctual observations of genetic structure, the population is viewed as a single panmictic reproductive unit. To understand the possible origin of the detected structure in this species, we used a combination of mitochondrial and nuclear loci to indirectly evaluate the possible existence of cryptic demes. For that, 403 glass eels from three successive cohorts arriving at a single location were screened for phenotypic and genetic diversity, while controlling for possible geographic variation. Over the 3 years of sampling, we consistently identified three major matrilines which we hypothesized to represent demes. Interestingly, not only we found that population genetic models support the existence of those matriline-driven demes over a completely panmictic mode of reproduction, but also we found evidence for asymmetric gene flow amongst those demes. We uphold the suggestion that the detection of demes related to those matrilines reflect a fragmented spawning ground, a conceptually plausible consequence of the low abundance that the European eel has been experiencing for three decades. Furthermore, we suggest that this cryptic organization may contribute to the maintenance of the adaptive potential of the species

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

Inferring introduction routes of invasive species using approximate Bayesian computation on microsatellite data

Determining the routes of introduction provides not only information about the history of an invasion process, but also information about the origin and construction of the genetic composition of the invading population. It remains difficult, however, to infer introduction routes from molecular data because of a lack of appropriate methods. We evaluate here the use of an approximate Bayesian computation (ABC) method for estimating the probabilities of introduction routes of invasive populations based on microsatellite data. We considered the crucial case of a single source population from which two invasive populations originated either serially from a single introduction event or from two independent introduction events. Using simulated datasets, we found that the method gave correct inferences and was robust to many erroneous beliefs. The method was also more efficient than traditional methods based on raw values of statistics such as assignment likelihood or pairwise F(ST). We illustrate some of the features of our ABC method, using real microsatellite datasets obtained for invasive populations of the western corn rootworm, Diabrotica virgifera virgifera. Most computations were performed with the DIYABC program (http://www1.montpellier.inra.fr/CBGP/diyabc/)

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

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

Peer reviewe

Gene flow at the leading range edge: the long-term consequences of isolation in European Beech (Fagus sylvatica L. Kuhn)

Aim Isolation is expected to lead to negative impacts on populations due to a reduction in effective population size and gene flow, exacerbating the effects of genetic drift, which might be stronger in peripheral and fragmented populations. Fagus sylvatica (European beech) in southern Sweden presents a gradient of isolation towards the leading range edge of the species. We sought to determine the impact of long‐term isolation on genetic diversity and population genetic structure within populations of this species. Location Samples were obtained from 14 sites towards the northern edge of the native range of beech in Sweden. Taxon Fagaceae. Methods Using historical sources, we obtained area‐ and distance‐based measures of isolation. We measured genetic diversity and structure by using nuclear microsatellite marker data, and performed parentage analysis to estimate external pollen‐mediated gene flow. We implemented a partial least squares regression to determine the effects of isolation on each of the genetic diversity estimators and the measures of external pollen‐mediated gene flow. Results Long‐term isolation generally had a negative impact on genetic diversity, which is exacerbated over time, further affecting progeny and suggesting that isolated populations are subject to strong genetic drift, possibly due to the combination of founder events and persistent small population sizes. Bayesian cluster analysis revealed that isolation was also acting as a barrier to gene flow in the north‐eastern distribution of beech. Main conclusions Isolation at the leading range edge of beech in Sweden has created gradients of contemporary gene flow within the species. The long‐term cumulative effects of isolation on this wind‐pollinated tree species and its negative impacts on genetic diversity and gene flow, could lead to inbreeding depression and higher extinction risk where populations remain small and isolated

Lineage Divergence and Historical Gene Flow in the Chinese Horseshoe Bat (Rhinolophus sinicus)

PMCID: PMC3581519This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

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