genenames.org: the HGNC resources in 2011

The HUGO Gene Nomenclature Committee (HGNC) aims to assign a unique gene symbol and name to every human gene. The HGNC database currently contains almost 30 000 approved gene symbols, over 19 000 of which represent protein-coding genes. The public website, www.genenames.org, displays all approved nomenclature within Symbol Reports that contain data curated by HGNC editors and links to related genomic, phenotypic and proteomic information. Here we describe improvements to our resources, including a new Quick Gene Search, a new List Search, an integrated HGNC BioMart and a new Statistics and Downloads facility

Reliable microsatellite genotyping of the Eurasian badger (Meles meles) using faecal DNA

The potential link between badgers and bovine tuberculosis has made it vital to develop accurate techniques to census badgers. Here we investigate the potential of using genetic profiles obtained from faecal DNA as a basis for population size estimation. After trialling several methods we obtained a high amplification success rate (89%) by storing faeces in 70% ethanol and using the guanidine thiocyanate/silica method for extraction. Using 70% ethanol as a storage agent had the advantage of it being an antiseptic. In order to obtain reliable genotypes with fewer amplification reactions than the standard multiple-tubes approach, we devised a comparative approach in which genetic profiles were compared and replication directed at similar, but not identical, genotypes. This modified method achieved a reduction in polymerase chain reactions comparable with the maximumlikelihood model when just using reliability criteria, and was slightly better when using reliability criteria with the additional proviso that alleles must be observed twice to be considered reliable. Our comparative approach would be best suited for studies that include multiple faeces from each individual. We utilized our approach in a well-studied population of badgers from which individuals had been sampled and reliable genotypes obtained. In a study of 53 faeces sampled from three social groups over 10 days, we found that direct enumeration could not be used to estimate population size, but that the application of mark–recapture models has the potential to provide more accurate results

Next-generation metrics for monitoring genetic erosion within populations of conservation concern

This work was conducted as a part of the Next-generation Genetic Monitoring Working Group at the National Institute for Mathematical and Biological Synthesis, sponsored by the National Science Foundation through NSF Award #DBI-1300426, with additional support from The University of Tennessee, Knoxville. Emma Carrol was supported by a Marie Slodowska Curie Fellowship, (Behaviour-Connect) funded by the EU Horizon2020 program. MWB was supported by a Royal Society Wolfson research merit award. LW was supported by the University of Idaho. This research was supported in part by NSF awards 1355106 and 1357386 to AES.Genetic erosion is a major threat to biodiversity because it can reduce fitness and ultimately contribute to the extinction of populations. Here, we explore the use of quantitative metrics to detect and monitor genetic erosion. Monitoring systems should not only characterize the mechanisms and drivers of genetic erosion (inbreeding, genetic drift, demographic instability, population fragmentation, introgressive hybridization, selection) but also its consequences (inbreeding and outbreeding depression, emergence of large effect detrimental alleles, maladaptation and loss of adaptability). Technological advances in genomics now allow the production of data the can be measured by new metrics with improved precision, increased efficiency and the potential to discriminate between neutral diversity (shaped mainly by population size and gene-flow) and functional/adaptive diversity (shaped mainly by selection), allowing the assessment of management-relevant genetic markers. The requirements of such studies in terms of sample size and marker density largely depend on the kind of population monitored, the questions to be answered and the metrics employed. We discuss prospects for the integration of this new information and metrics into conservation monitoring programmes.Publisher PDFPeer reviewe

Orangutans venture out of the rainforest and into the Anthropocene

Conservation benefits from understanding how adaptability and threat interact to determine a taxon’s vulnerability. Recognizing how interactions with humans have shaped taxa such as the critically endangered orangutan (Pongo spp.) offers insights into this relationship. Orangutans are viewed as icons of wild nature, and most efforts to prevent their extinction have focused on protecting minimally disturbed habitat, with limited success. We synthesize fossil, archeological, genetic, and behavioral evidence to demonstrate that at least 70,000 years of human influence have shaped orangutan distribution, abundance, and ecology and will likely continue to do so in the future. Our findings indicate that orangutans are vulnerable to hunting but appear flexible in response to some other human activities. This highlights the need for a multifaceted, landscape-level approach to orangutan conservation that leverages sound policy and cooperation among government, private sector, and community stakeholders to prevent hunting, mitigate human-orangutan conflict, and preserve and reconnect remaining natural forests. Broad cooperation can be encouraged through incentives and strategies that focus on the common interests and concerns of different stakeholders. Orangutans provide an illustrative example of how acknowledging the long and pervasive influence of humans can improve strategies to preserve biodiversity in the Anthropocene

Diversity, genetic structure and evidence of outcrossing in British populations of the rock fern Adiantum capillus-veneris using microsatellites

Microsatellites were isolated and a marker system was developed in the fern Adiantum capillus-veneris. Polymorphic markers were then used to study the genetic diversity and structure of populations within the UK and Ireland where this species grows at the northern edge of its range, requiring a specific rock habitat and limited to a few scattered populations. Three dinucleotide loci detected a high level of diversity (23 alleles and 28 multilocus genotypes) across the UK and Ireland, with nearly all variation partitioned among rather than within populations. Of 17 populations represented by multiple samples, all except four were monomorphic. Heterozygosity was detected in three populations, all within Glamorgan, Wales (UK), showing evidence of outcrossing. We make inferences on the factors determining the observed levels and patterns of genetic variation and the possible evolutionary history of the populations

Complex phylogeographic history of central African forest elephants and its implications for taxonomy

Background: Previous phylogenetic analyses of African elephants have included limited numbers of forest elephant samples. A large-scale assessment of mitochondrial DNA diversity in forest elephant populations here reveals a more complex evolutionary history in African elephants as a whole than two-taxon models assume. Results: We analysed hypervariable region 1 of the mitochondrial control region for 71 new central African forest elephants and the mitochondrial cytochrome b gene from 28 new samples and compare these sequences to other African elephant data. We find that central African forest elephant populations fall into at least two lineages and that west African elephants (both forest and savannah) share their mitochondrial history almost exclusively with central African forest elephants. We also find that central African forest populations show lower genetic diversity than those in savannahs, and infer a recent population expansion. Conclusion: Our data do not support the separation of African elephants into two evolutionary lineages. The demographic history of African elephants seems more complex, with a combination of multiple refugial mitochondrial lineages and recurrent hybridization among them rendering a simple forest/savannah elephant split inapplicable to modern African elephant populations

Country-wide genetic monitoring over 21 years reveals lag in genetic recovery despite spatial connectivity, in an expanding carnivore (Eurasian otter, Lutra lutra) population

Numerous terrestrial mammal species have experienced extensive population declines during past centuries, due largely to anthropogenic pressures. For some species, including the Eurasian otter (Lutra lutra), environmental and legal protection has more recently led to population growth and recolonization of parts of their historic ranges. While heralded as conservation success, only few such recoveries have been examined from a genetic perspective, i.e. whether genetic variability and connectivity have been restored. We here use large-scale and long-term genetic monitoring data from UK otters, whose population underwent a well-documented population decline between the 1950s and 1970s, to explore the dynamics of a population re-expansion over a 21-year period. We genotyped otters from across Wales and England at five time points between 1994 and 2014 using 15 microsatellite loci. We used this combination of long-term temporal and large-scale spatial sampling to evaluate 3 hypotheses relating to genetic recovery that (i) gene flow between subpopulations would increase over time, (ii) genetic diversity of previously isolated populations would increase and that (iii) genetic structuring would weaken over time. Although we found an increase in inter-regional gene flow and admixture levels among subpopulations, there was no significant temporal change in either heterozygosity or allelic richness. Genetic structuring among the main subpopulations hence remained strong and showed a clear historical continuity. These findings highlight an underappreciated aspect of population recovery of endangered species: that genetic recovery may often lag behind the processes of spatial and demographic recovery. In other words, the restoration of the physical connectivity of populations does not necessarily lead to genetic connectivity. Our findings emphasize the need for genetic data as an integral part of conservation monitoring, to enable the potential vulnerability of populations to be evaluated

The coalition for conservation genetics: working across organizations to build capacity and achieve change in policy and practice

The Coalition for Conservation Genetics (CCG) brings together four eminentorganizations with the shared goal of improving the integration of geneticinformation into conservation policy and practice. We provide a historicalcontext of conservation genetics as a field and reflect on current barriers toconserving genetic diversity, highlighting the need for collaboration acrosstraditional divides, international partnerships, and coordinated advocacy. Wethen introduce the CCG and illustrate through examples how a coalitionapproach can leverage complementary expertise and improve the organiza-tional impact at multiple levels. The CCG has proven particularly successfulat implementing large synthesis-type projects, training early-career scientists,and advising policy makers. Achievements to date highlight the potential forthe CCG to make effective contributions to practical conservation policy andmanagement that no one“parent”organization could achieve on its own.Finally, we reflect on the lessons learned through forming the CCG, and ourvision for the futur

Global distribution and diversity of ovine-associated Staphylococcus aureus

Staphylococcus aureus is an important pathogen of many species, including sheep, and impacts on both human and animal health, animal welfare, and farm productivity. Here we present the widest global diversity study of ovine-associated S. aureus to date. We analysed 97 S. aureus isolates from sheep and sheep products from the UK, Turkey, France, Norway, Australia, Canada and the USA using multilocus sequence typing (MLST) and spa typing. These were compared with 196 sheep isolates from Europe (n = 153), Africa (n = 28), South America (n = 14) and Australia (n = 1); 172 bovine, 68 caprine and 433 human S. aureus profiles. Overall there were 59 STs and 87 spa types in the 293 ovine isolates; in the 97 new ovine isolates there were 22 STs and 37 spa types, including three novel MLST alleles, four novel STs and eight novel spa types. Three main CCs (CC133, CC522 and CC700) were detected in sheep and these contained 61% of all isolates. Four spa types (t002, t1534, t2678 and t3576) contained 31% of all isolates and were associated with CC5, CC522, CC133 and CC522 respectively. spa types were consistent with MLST CCs, only one spa type (t1403) was present in multiple CCs. The three main ovine CCs have different but overlapping patterns of geographical dissemination that appear to match the location and timing of sheep domestication and selection for meat and wool production. CC133, CC522 and CC700 remained ovine-associated following the inclusion of additional host species. Ovine isolates clustered separately from human and bovine isolates and those from sheep cheeses, but closely with caprine isolates. As with cattle isolates, patterns of clonal diversification of sheep isolates differ from humans, indicative of their relatively recent host-jump