HGNC: The Why and How of Standardised Gene Nomenclature

The HUGO Gene Nomenclature Committee (HGNC) aims to approve a unique gene symbol and gene name for every human gene. Standardisation of gene symbols is necessary to allow researchers and curators to refer to the same gene without ambiguity. Consistent use of gene symbols in publications and across different websites makes it easy for researchers to find all relevant information for a particular gene and facilitates data mining and retrieval. For each gene that we name we curate relevant information including symbol aliases, chromosomal location, locus type, sequence accessions and links to relevant databases. Therefore, our website is a central resource for human genetics. 
 
We endeavour to approve gene symbols that are acceptable to researchers to encourage widespread use of our symbols. In order to achieve this, we contact researchers that work on particular genes for advice before approving symbols and allow researchers to submit gene symbols to us directly for our consideration. We attend conferences to discuss difficult nomenclature matters and to gain community agreement. We interact with annotators of genes and proteins to provide symbols and names that accurately reflect the nature of each gene and its products. We also work with the gene nomenclature committees for other organisms, and aim to approve equivalent gene symbols for orthologous genes in human and other vertebrate species, especially mouse and rat. 
 
We will demonstrate the steps that are required to name a gene, and will show how and where the nomenclature of a particular gene is used. We will also explain the nature of our collaborations with particular journals and other databases in striving to achieve the use of a common gene nomenclature by all

Molecular Biogeography: Towards an Integrated Framework for Conserving Pan-African Biodiversity

BACKGROUND: Biogeographic models partition ecologically similar species assemblages into discrete ecoregions. However, the history, relationship and interactions between these regions and their assemblages have rarely been explored. METHODOLOGY/PRINCIPAL FINDINGS: Here we develop a taxon-based approach that explicitly utilises molecular information to compare ecoregion history and status, which we exemplify using a continentally distributed mammalian species: the African bushbuck (Tragelaphus scriptus). We reveal unprecedented levels of genetic diversity and structure in this species and show that ecoregion biogeographic history better explains the distribution of molecular variation than phenotypic similarity or geography. We extend these data to explore ecoregion connectivity, identify core habitats and infer ecological affinities from them. CONCLUSIONS/SIGNIFICANCE: This analysis defines 28 key biogeographic regions for sub-Saharan Africa, and provides a valuable framework for the incorporation of genetic and biogeographic information into a more widely applicable model for the conservation of continental biodiversity

SNeP: a tool to estimate trends in recent effective population size trajectories using genome-wide SNP data

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Colonization of the Scottish islands via long-distance Neolithic transport of red deer (Cervus elaphus)

Red deer (Cervus elaphus) have played a key role in human societies throughout history, with important cultural significance and as a source of food and materials. This relationship can be traced back to the earliest human cultures and continues to the present day. Humans are thought to be responsible for the movement of a considerable number of deer throughout history, although the majority of these movements are poorly described or understood. Studying such translocations allows us to better understand ancient human–wildlife interactions, and in the case of island colonizations, informs us about ancient human maritime practices. This study uses DNA sequences to characterise red deer genetic diversity across the Scottish islands (Inner and Outer Hebrides and Orkney) and mainland using ancient deer samples, and attempts to infer historical colonization events. We show that deer from the Outer Hebrides and Orkney are unlikely to have originated from mainland Scotland, implying that humans introduced red deer from a greater distance. Our results are also inconsistent with an origin from Ireland or Norway, suggesting long-distance maritime travel by Neolithic people to the outer Scottish Isles from an unknown source. Common haplotypes and low genetic differentiation between the Outer Hebrides and Orkney imply common ancestry and/or gene flow across these islands. Close genetic proximity between the Inner Hebrides and Ireland, however, corroborates previous studies identifying mainland Britain as a source for red deer introductions into Ireland. This study provides important information on the processes that led to the current distribution of the largest surviving indigenous land mammal in the British Isles

High performance computation of landscape genomic models integrating local indices of spatial association

Since its introduction, landscape genomics has developed quickly with the increasing availability of both molecular and topo-climatic data. The current challenges of the field mainly involve processing large numbers of models and disentangling selection from demography. Several methods address the latter, either by estimating a neutral model from population structure or by inferring simultaneously environmental and demographic effects. Here we present Sam$\beta$ada, an integrated approach to study signatures of local adaptation, providing rapid processing of whole genome data and enabling assessment of spatial association using molecular markers. Specifically, candidate loci to adaptation are identified by automatically assessing genome-environment associations. In complement, measuring the Local Indicators of Spatial Association (LISA) for these candidate loci allows to detect whether similar genotypes tend to gather in space, which constitutes a useful indication of the possible kinship relationship between individuals. In this paper, we also analyze SNP data from Ugandan cattle to detect signatures of local adaptation with Sam$\beta$ada, BayEnv, LFMM and an outlier method (FDIST approach in Arlequin) and compare their results. Sam$\beta$ada is an open source software for Windows, Linux and MacOS X available at \url{http://lasig.epfl.ch/sambada}Comment: 1 figure in text, 1 figure in supplementary material The structure of the article was modified and some explanations were updated. The methods and results presented are the same as in the previous versio

Kinship and intragroup social dynamics in two sympatric African Colobus species

SFRH/BPD/87396/2012 UID/ANT/04038/2013Kinship has been described as a major factor shaping primates’ social dynamics, with individuals biasing their affiliative interactions to their related counterparts. However, it has also been demonstrated that, under certain circumstances, social bonding can be established in the absence of kin. The fact that Colobus polykomos (western black-and-white colobus) and Procolobus badius temminckii (Temminck’s red colobus) often live in sympatry (subject to the same ecological/anthropogenic pressures) but exhibit contrasting social systems makes them good models to test which factors shape their social systems. We investigated the influence of kinship on intragroup social dynamics of one focal group of each species present in Cantanhez National Park, Guinea-Bissau. Between October 2008 and June 2009 we used focal sampling to collect information on the individuals’ nearest neighbors and ad libitum sampling to collect data on intragroup social interactions. We estimated pairwise relatedness using fecal DNA from 9 individuals of Colobus polykomos and 15 individuals of Procolobus badius temminckii genotyped at 15 microsatellite loci. We found that, in the focal group of Colobus polykomos, individuals showed no preference to interact or be spatially closer to related partners. Moreover, mainly unrelated females and related males composed the focal group of Procolobus badius temminckii but grooming was most frequent among female dyads and only rarely involved male dyads. We conclude that kinship is not an important factor determining the social bonding in either study species, suggesting that other factors, e.g., anthropogenic, ecological, may be at play shaping these groups’ social bonding.authorsversionpublishe

A Qualitative Assessment of Guinea-Bissau’s Hunting History and Culture - and Their Implications for Primate Conservation

Illegal hunting and trade threaten the high biodiversity of Guinea-Bissau (GB) in West Africa, particularly for nonhuman primates (NHP). Primate carcasses are sold at bushmeat markets and at restaurants and the primate pet trade is active. Traditional medicine practitioners also use NHP body-parts further promoting the commerce of NHP skins. A better understanding of hunting and related trade activities, including the profile of hunters and their motivations, would improve NHP conservation in GB. However, information on commercial hunting is incomplete due to a general unwillingness to describe illegal activities by the local communities. Here, we investigated aspects of hunting practice and related commercial activities targeting NHP in GB by collecting qualitative ethnographic information using semi-structured interviews. Participants were asked about hunted species, techniques and hunting locations, their motivations to hunt wild NHP, uses of carcasses, and their perceptions on the demographic trajectory of hunted species. Eight participants in the study listed species hunted in GB, which included a total of seven NHP. Hunting areas described were spread across southern GB and included locations within the limits of national protected areas and formalized ecological corridors. Participants mentioned the trade in NHP meat at bushmeat restaurants as the primary motivation for primate-targeted hunting, with the exception of western chimpanzees, which are specifically targeted for the exotic pet trade. Several strategies are used in hunting NHP, including traps, firearms, and hunting dogs. The majority of hunted NHP were perceived as having declined in population size during recent decades. Episodes when military groups hunted NHP intensively using more sophisticated weapons and methods in the 1980s were also described. This study highlights how hunting and related activities are complex and multi-dimensional and illustrates the use of ethnographic methods to improve knowledge about illegal and concealed practices impacting NHP conservation. Our results suggest an urgent need to raise awareness of local communities and subsistence hunters living within protected areas about the environmental and social impacts of hunting.info:eu-repo/semantics/publishedVersio

Demography and rapid local adaptation shape Creole cattle genome diversity in the tropics

The introduction of Iberian cattle in the Americas after Columbus’ arrival imposed high selection pressures on a limited number of animals over a brief period of time. Knowledge of the genomic regions selected during this process may help in enhancing climatic resilience and sustainable animal production. We first determined taurine and indicine contributions to the genomic structure of modern Creole cattle. Second, we inferred their demographic history using approximate Bayesian computation (ABC), linkage disequilibrium (LD), and Ne Slope (NeS) analysis. Third, we performed whole genome scans for selection signatures based on cross‐population extended haplotype homozygosity (XP‐EHH) and population differentiation (FST) to disentangle the genetic mechanisms involved in adaptation and phenotypic change by a rapid and major environmental transition. To tackle these questions, we combined SNP array data (~54,000 SNPs) in Creole breeds with their modern putative Iberian ancestors. Reconstruction of the population history of Creoles from the end of the 15th century indicated a major demographic expansion until the introduction of zebu and commercial breeds into the Americas ~180 years ago, coinciding with a drastic Ne contraction. NeS analysis provided insights into short‐term complexity in population change and depicted a decrease/expansion episode at the end of the ABC‐inferred expansion, as well as several additional fluctuations in Ne with the attainment of the current small Ne only towards the end of the 20th century. Selection signatures for tropical adaptation pinpointed the thermoregulatory slick hair coat region, identifying a new candidate gene (GDNF), as well as novel candidate regions involved in immune function, behavioural processes, iron metabolism and adaptation to new feeding conditions. The outcomes from this study will help in future‐proofing farm animal genetic resources (FAnGR) by providing molecular tools that allow selection for improved cattle performance, resilience and welfare under climate change