Covert deformed wing virus infections have long-term deleterious effects on honeybee foraging and survival

Several studies have suggested that covert stressors can contribute to bee colony declines. Here we provide a novel case study and show using radio-frequency identification (RFID) tracking technology that covert deformed wing virus (DWV) infections in adult honeybee workers seriously impact longterm foraging and survival under natural foraging conditions. In particular, our experiments show that adult workers injected with low doses of DWV experienced increased mortality rates, that DWV caused workers to start foraging at a premature age, and that the virus reduced the workers’ total activity span as foragers. Altogether, these results demonstrate that covert deformed wing virus infections have strongly deleterious effects on honey bee foraging and survival. These results are consistent with previous studies that suggested DWV to be an important contributor to the ongoing bee declines in Europe and the US. Overall, our study underlines the strong impact that covert pathogen infections can have on individual and group-level performance in bees

The Y-Chromosome Tree Bursts into Leaf: 13,000 High-Confidence SNPs Covering the Majority of Known Clades

Many studies of human populations have used the male-specific region of the Y chromosome (MSY) as a marker, but MSY sequence variants have traditionally been subject to ascertainment bias. Also, dating of haplogroups has relied on Y-specific short tandem repeats (STRs), involving problems of mutation rate choice, and possible long-term mutation saturation. Next-generation sequencing can ascertain single nucleotide polymorphisms (SNPs) in an unbiased way, leading to phylogenies in which branch-lengths are proportional to time, and allowing the times-to-most-recent-common-ancestor (TMRCAs) of nodes to be estimated directly. Here we describe the sequencing of 3.7 Mb of MSY in each of 448 human males at a mean coverage of 51x, yielding 13,261 high-confidence SNPs, 65.9% of which are previously unreported. The resulting phylogeny covers the majority of the known clades, provides date estimates of nodes, and constitutes a robust evolutionary framework for analyzing the history of other classes of mutation. Different clades within the tree show subtle but significant differences in branch lengths to the root. We also apply a set of 23 Y-STRs to the same samples, allowing SNP- and STR-based diversity and TMRCA estimates to be systematically compared. Ongoing purifying selection is suggested by our analysis of the phylogenetic distribution of nonsynonymous variants in 15 MSY single-copy genes

Whole-genome sequencing for an enhanced understanding of genetic variation among South Africans

The Southern African Human Genome Programme is a national initiative that aspires to unlock the unique genetic character of southern African populations for a better understanding of human genetic diversity. In this pilot study the Southern African Human Genome Programme characterizes the genomes of 24 individuals (8 Coloured and 16 black southeastern Bantu-speakers) using deep whole-genome sequencing. A total of ~16 million unique variants are identified. Despite the shallow time depth since divergence between the two main southeastern Bantu-speaking groups (Nguni and Sotho-Tswana), principal component analysis and structure analysis reveal significant (p < 10−6) differentiation, and FST analysis identifies regions with high divergence. The Coloured individuals show evidence of varying proportions of admixture with Khoesan, Bantu-speakers, Europeans, and populations from the Indian sub-continent. Whole-genome sequencing data reveal extensive genomic diversity, increasing our understanding of the complex and region-specific history of African populations and highlighting its potential impact on biomedical research and genetic susceptibility to disease

DNA Methods to Identify Missing Persons

Human identification by DNA analysis in missing person cases typically involves comparison of two categories of sample: a reference sample, which could be obtained from intimate items of the person in question or from family members, and the questioned sample from the unknown person-usually derived from the bones, teeth, or soft tissues of human remains. Exceptions include the analysis of archived tissues, such as those held by hospital pathology departments, and the analysis of samples relating to missing, but living persons. DNA is extracted from the questioned and reference samples and well-characterized regions of the genetic code are amplified from each source using the Polymerase Chain Reaction (PCR), which generates sufficient copies of the target region for visualization and comparison of the genetic sequences obtained from each sample. If the DNA sequences of the questioned and reference samples differ, this is normally sufficient for the questioned DNA to be excluded as having come from the same source. If the sequences are identical, statistical analysis is necessary to determine the probability that the match is a consequence of the questioned sequence coming from the same individual who provided the reference sample or from a randomly occurring individual in the general population. Match probabilities that are currently achievable are frequently greater than 1 in 1 billion, allowing identity to be assigned with considerable confidence in many cases

Towards a consensus Y-chromosomal phylogeny and Y-SNP set in forensics in the next-generation sequencing era

Currently, several different Y-chromosomal phylogenies and haplogroup nomenclatures are presented in scientific literature and at conferences demonstrating the present diversity in Y-chromosomal phylogenetic trees and Y-SNP sets used within forensic and anthropological research. This situation can be ascribed to the exponential growth of the number of Y-SNPs discovered due to mostly next-generation sequencing (NGS) studies. As Y-SNPs and their respective phylogenetic positions are important in forensics, such as for male lineage characterization and paternal bio-geographic ancestry inference, there is a need for forensic geneticists to know how to deal with these newly identified Y-SNPs and phylogenies, especially since these phylogenies are often created with other aims than to carry out forensic genetic research. Therefore, we give here an overview of four categories of currently used Y-chromosomal phylogenies and the associated Y-SNP sets in scientific research in the current NGS era. We compare these categories based on the construction method, their advantages and disadvantages, the disciplines wherein the phylogenetic tree can be used, and their specific relevance for forensic geneticists. Based on this overview, it is clear that an up-to-date reduced tree with a consensus Y-SNP set and a stable nomenclature will be the most appropriate reference resource for forensic research. Initiatives to reach such an international consensus are therefore highly recommended. (C) 2014 Elsevier Ireland Ltd. All rights reserved

Track-a-Forager: a program for the automated analysis of RFID tracking data to reconstruct foraging behaviour

Behavioural studies make increasingly use of the passive radio-frequency identification (RFID) technology to monitor the foraging behaviour and activity patterns of individual animals over extended periods of time. Central place foragers, such as social insects, birds and many rodents have proved particularly well suited for this technology. As yet, however, there is no standardized methodology to filter and postprocess the data resulting from RFID scanners. Here we present a new user-friendly, publically available Java program named "Track-a-Forager" to analyse and rigorously filter RFID animal tracking data. The program is particularly suited and has special features to analyse social insect behaviour, but it is generic enough to analyse data obtained from any species. The implemented filtering algorithm consists of several well-defined steps to cluster multiple temporally clustered RFID scans of the same individual, determine events of leaving and entering the nest and/or feeder and reconstruct foraging trips for each individual. Track-a-Forager analyses RFID data independent of the used scanner system for eight different types of standard experimental setups that are common in foraging behaviour research. These setups differ with respect to whether or not foraging at an artificial feeder is monitored and the specific placement of the RFID scanners at the nest or feeder. As a real-life example, we show how Track-a-Forager enables one to reconstruct 75 % more foraging trips compared to if one were to use the raw data

Seeing the Wood for the Trees: A Minimal Reference Phylogeny for the Human Y Chromosome

During the last few decades, a wealth of studies dedicated to the human Y chromosome and its DNA variation, in particular Y-chromosome single-nucleotide polymorphisms (Y-SNPs), has led to the construction of a well-established Y-chromosome phylogeny. Since the recent advent of new sequencing technologies, the discovery of additional Y-SNPs is exploding and their continuous incorporation in the phylogenetic tree is leading to an ever higher resolution. However, the large and increasing amount of information included in the complete Y-chromosome phylogeny, which now already includes many thousands of identified Y-SNPs, can be overwhelming and complicates its understanding as well as the task of selecting suitable markers for genotyping purposes in evolutionary, demographic, anthropological, genealogical, medical, and forensic studies. As a solution, we introduce a concise reference phylogeny whereby we do not aim to provide an exhaustive tree that includes all known Y-SNPs but, rather, a quite stable reference tree aiming for optimal global discrimination capacity based on a strongly reduced set that includes only the most resolving Y-SNPs. Furthermore, with this reference tree, we wish to propose a common standard for Y-marker as well as Y-haplogroup nomenclature. The current version of our tree is based on a core set of 417 branch-defining Y-SNPs and is available online at http://www.phylotree.org/Y. (C) 2013 Wiley Periodicals, Inc

Recent Radiation within Y-chromosomal Haplogroup R-M269 Resulted in High Y-STR Haplotype Resemblance

Genomics, epigenetics, population genetics and bioinformatic