Coprolites as a source of information on the genome and diet of the cave hyena

We performed high-throughput sequencing of DNA from fossilized faeces to evaluate this material as a source of information on the genome and diet of Pleistocene carnivores. We analysed coprolites derived from the extinct cave hyena (Crocuta crocuta spelaea), and sequenced 90 million DNA fragments from two specimens. The DNA reads enabled a reconstruction of the cave hyena mitochondrial genome with up to a 158-fold coverage. This genome, and those sequenced from extant spotted (Crocuta crocuta) and striped (Hyaena hyaena) hyena specimens, allows for the establishment of a robust phylogeny that supports a close relationship between the cave and the spotted hyena. We also demonstrate that high-throughput sequencing yields data for cave hyena multi-copy and single-copy nuclear genes, and that about 50 per cent of the coprolite DNA can be ascribed to this species. Analysing the data for additional species to indicate the cave hyena diet, we retrieved abundant sequences for the red deer (Cervus elaphus), and characterized its mitochondrial genome with up to a 3.8-fold coverage. In conclusion, we have demonstrated the presence of abundant ancient DNA in the coprolites surveyed. Shotgun sequencing of this material yielded a wealth of DNA sequences for a Pleistocene carnivore and allowed unbiased identification of diet.     

广州地区艾滋病患者中人类疱疹病毒8感染及部分序列的检测

检测广州地区艾滋病患者中人类疱疹病毒8(HHV-8)的感染状况并完成部分序列的测序,从而了解HHV-8感染相关的Kaposi’s肉瘤在本地区艾滋患者中可能的罹患风险,并初步探讨HHV-8在本地区是否存在基因序列的变异。使用n-PCR法检测患者唾液中的HHV-8 DNA,PCR产物经ABI3100系统直接测序。结果显示在广州地区艾滋病患者中唾液HHV-8 DNA阳性率为20.0%,而在作为对照的健康组的阳性率为0.0%,艾滋病患者组与健康对照组间具非常显著性差异;检测的部分碱基序列未发现变异。提示在广州地区的艾滋病患者中存在较高的HHV-8感染。     

Long-term survival despite low genetic diversity in the critically endangered Madagascar fish-eagle

The critically endangered Madagascar fish-eagle ( Haliaeetus vociferoides ) is considered to be one of the rarest birds of prey globally and at significant risk of extinction. In the most recent census, only 222 adult individuals were recorded with an estimated total breeding population of no more than 100–120 pairs. Here, levels of Madagascar fish-eagle population genetic diversity based on 47 microsatellite loci were compared with its sister species, the African fish-eagle ( Haliaeetus vocifer ), and 16 of these loci were also characterized in the white-tailed eagle ( Haliaeetus albicilla ) and the bald eagle ( Haliaeetus leucocephalus ). Overall, extremely low genetic diversity was observed in the Madagascar fish-eagle compared to other surveyed Haliaeetus species. Determining whether this low diversity is the result of a recent bottleneck or a more historic event has important implications for their conservation. Using a Bayesian coalescent-based method, we show that Madagascar fish-eagles have maintained a small effective population size for hundreds to thousands of years and that its low level of neutral genetic diversity is not the result of a recent bottleneck. Therefore, efforts made to prevent Madagascar fish-eagle extinction should place high priority on maintenance of habitat requirements and reducing direct and indirect human persecution. Given the current rate of deforestation in Madagascar, we further recommend that the population be expanded to occupy a larger geographical distribution. This will help the population persist when exposed to stochastic factors (e.g. climate and disease) that may threaten a species consisting of only 200 adult individuals while inhabiting a rapidly changing landscape.     

Goose hybrids, captive breeding and restocking of the Fennoscandian populations of the Lesser White-fronted goose (Anser erythropus)

The lesser white-fronted goose (Anser erythropus) isthe most threatened of the Palearctic goose species with a decliningpopulation trend throughout its distributional range. The currentestimate of the Fennoscandian subpopulation size is 30–50 breedingpairs, whereas it still numbered more than 10000 individuals at thebeginning of the last century. Reintroduction and restocking have beencarried out in Sweden and Finland using captive lesser white-frontedgoose stock with unknown origins. We have carried out a study of thegenetic composition of captive-bred stock by sequencing a 221 bphypervariable fragment of the mitochondrial DNA (mtDNA) control regionfrom 15 individuals from the Hailuoto farm, Finland. Two out of thethree maternal lineages detected in the captive stock are also presentin wild populations. The third maternal lineage among the captive lesserwhite-fronted geese originates from the closely related greaterwhite-fronted goose (Anser albifrons). None of the investigatedwild lesser white-fronted goose individuals carried the mtDNA of thegreater white-fronted goose. The presence of greater white-fronted goosemtDNA in the lesser white-fronted goose captive stock suggests thathybridization has occurred during captive propagation.     

Molecular Characterization of Phytoplasma Associated with Rose Witches'-Broom in China

In 2005, rose plants (Rosa rugosa cv. ‘Plena’) exhibiting typical phytoplasma disease symptoms of stunting, yellowing, witches’‐broom and dieback were observed in Pingyin, Shandong Province, China. The disease, rose witches’‐broom (RoWB), is progressively destructive and can be graft‐transmitted. Polymerase chain reaction (PCR), sequencing of PCR products and electron microscopy were used to investigate the possible association of phytoplasma with RoWB. All results indicated that presence of phytoplasma in the symptomatic rose plants. Sequence alignment of 16S rRNA gene, tuf gene and rp gene confirmed that the phytoplasma associated with RoWB is the causal agent of Paulownia witches’‐broom disease, which might be transmitted from the paulownia tree that is several meters away. To our knowledge, this is the first report of the molecular characterization of phytoplasma infecting rose in China.