21 research outputs found
Analysis of two genomic variants of orang-utan hepadnavirus and their relationship to other primate hepatitis B-like viruses
No full textWe recently described orang-utan hepadnavirus (OuHV) (Warren et al., Journal of Virology, 73, 7860–7865, 1999). Phylogenetic analyses indicated that the various isolates of OuHV can be divided into two genomic variants. Two representatives from each genomic cluster were analysed both molecularly and phylogenetically. Their genome organization was highly similar to other hepadnaviruses of apes and humans. The complete genome sequences of the two OuHV types had an overall 5% sequence difference. Research on 25 seropositive Bornean orang-utans showed that, of the 19 animals infected with one variant, 12 originated from East Kalimantan. Phylogenetic analysis was performed using the full-length genomes of various primate hepadnaviruses. The tree topology revealed one cluster of Old World hepadnaviruses that is divided into two subclusters, one consisting of the ape viruses, and the other comprising the human genotypes A–E. These data suggest that the great apes and gibbons have been infected with a common ancestor hepadnavirus
Error bounds for discrete minimizers of the {G}inzburg--{L}andau energy in the high- regime
No full textIn this work, we study discrete minimizers of the Ginzburg–Landau energy in finite element spaces. Special focus is given to the influence of the Ginzburg–Landau parameter . This parameter is of physical interest as large values can trigger the appearance of vortex lattices. Since the vortices have to be resolved on sufficiently fine computational meshes, it is important to translate the size of into a mesh resolution condition, which can be done through error estimates that are explicit with respect to and the spatial mesh width . For that, we first work in an abstract framework for a general class of discrete spaces, where we present convergence results
in a problem-adapted -weighted norm. Afterwards we apply our findings to Lagrangian finite elements and a particular generalized finite element construction. In numerical experiments we confirm that our derived - and -error estimates are indeed optimal in and
Genetic signature of anthropogenic population collapse in orang-utans.
No full textGreat ape populations are undergoing a dramatic decline, which is predicted to result in their extinction in the wild from entire regions in the near future. Recent findings have particularly focused on African apes, and have implicated multiple factors contributing to this decline, such as deforestation, hunting, and disease. Less well-publicised, but equally dramatic, has been the decline in orang-utans, whose distribution is limited to parts of Sumatra and Borneo. Using the largest-ever genetic sample from wild orang-utan populations, we show strong evidence for a recent demographic collapse in North Eastern Borneo and demonstrate that this signature is independent of the mutation and demographic models used. This is the first demonstration that genetic data can detect and quantify the effect of recent, human-induced deforestation and habitat fragmentation on an endangered species. Because current demographic collapses are usually confounded by ancient events, this suggests a much more dramatic decline than demographic data alone and emphasises the need for major conservation efforts
Time since the Population Collapse
No full text<p>The posterior distribution for the time since the population collapse is represented on a logarithmic scale. These distributions have a median around 210 y. Most of their mass is concentrated in recent years with a sharp decrease as time goes back. Indeed, 10%, 20%, 50%, 80%, and 90% of the distribution mass are below 10, 35, 210, 950, and 1,900 y, respectively. The thin and thick lines correspond to S1 and S2, respectively. The prior is shown as a dashed line, its median being 100,000 y ago (see text). The vertical dashed line corresponds to the 95% quantile of the posterior distribution. Arrows correspond to the dates of arrival of the first hunter-gatherers (HG) or farmers (F), or to the start of the forest exploitation (FE).</p
Time since the Population Collapse (in Years)
No full text<p>The two curves represent the posterior distributions for S1 (solid line) and S2 (dashed line) in a natural rather than a logarithmic scale. The two posterior distributions are nearly indistinguishable and clearly show that the orang-utan population collapse most likely started in the last decades. The vertical dashed and dotted lines correspond to the 95% quantile of the posterior distributions for S1 and S2, respectively. The arrows correspond to the dates of arrival of the first farmers (F) or to the start of the forest exploitation (FE). The arrival of the first hunter-gatherers would be far outside this figure on the right, some 40,000 y ago.</p
Population Size Change
No full text<p>Solid curves correspond to the posterior distributions under a model of exponential population size change. Dashed curves were obtained under a model of linear change. Thin and thick lines correspond to results obtained for populations S1 and S2, respectively (see main text for details). <i>r</i> = <i>N<sub>0</sub></i>/<i>N<sub>1</sub></i> represents the ratio of present <i>(N<sub>0</sub>)</i> to past <i>(N<sub>1</sub>)</i> population size. Whichever demographic model or population is used, there is no support for positive values (increase in population size) or values close to zero (no significant change in population size). The prior distribution is shown for comparison (flat dotted line).</p
Ancestral and Present Population Sizes
No full text<p>The posterior distributions are represented in a logarithmic scale and show very little overlap, confirming that <i>N<sub>0</sub></i> is much smaller than <i>N<sub>1</sub></i>. This result holds for the two populations analysed. The thin and thick lines correspond to S1 and S2, respectively. The priors are also shown for <i>N<sub>0</sub></i> (dotted line) and <i>N<sub>1</sub></i> (dashed line).</p
DNA analysis indicates that Asian elephants are native to Borneo and are therefore a high priority for conservation.
No full textThe origin of Borneo's elephants is controversial. Two competing hypotheses argue that they are either indigenous, tracing back to the Pleistocene, or were introduced, descending from elephants imported in the 16th-18th centuries. Taxonomically, they have either been classified as a unique subspecies or placed under the Indian or Sumatran subspecies. If shown to be a unique indigenous population, this would extend the natural species range of the Asian elephant by 1300 km, and therefore Borneo elephants would have much greater conservation importance than if they were a feral population. We compared DNA of Borneo elephants to that of elephants from across the range of the Asian elephant, using a fragment of mitochondrial DNA, including part of the hypervariable d-loop, and five autosomal microsatellite loci. We find that Borneo's elephants are genetically distinct, with molecular divergence indicative of a Pleistocene colonisation of Borneo and subsequent isolation. We reject the hypothesis that Borneo's elephants were introduced. The genetic divergence of Borneo elephants warrants their recognition as a separate evolutionary significant unit. Thus, interbreeding Borneo elephants with those from other populations would be contraindicated in ex situ conservation, and their genetic distinctiveness makes them one of the highest priority populations for Asian elephant conservation
