Revision of Madagascar's Dwarf Lemurs (Cheirogaleidae:Cheirogaleus): Designation of Species, Candidate Species Status and Geographic Boundaries Based on Molecular and Morphological Data

The genus Cheirogaleus, the dwarf lemurs, is a radiation of strepsirrhine primates endemic to the island of Madagascar. The dwarf lemurs are taxonomically grouped in the family Cheirogaleidae (Infraorder: Lemuriformes) along with the genera Microcebus, Mirza, Allocebus, and Phaner. The taxonomic history of the genus Cheirogaleus has been controversial since its inception due to a paucity of evidence in support of some proposed species. In this study, we addressed this issue by expanding the geographic breadth of samples by 91 individuals and built upon existing mitochondrial (cytb and COII) and nuclear (FIBA and vWF) DNA datasets to better resolve the phylogeny of Cheirogaleus. The mitochondrial gene fragments D-loop and PAST as well as the CFTR-PAIRB nuclear loci were also sequenced. In agreement with previous genetic studies, numerous deep divergences were resolved in the C. major, C. minor and C. medius lineages. Four of these lineages were segregated as new species, seven were identified as confirmed candidate species, and four were designated as unconfirmed candidate species based on comparative mitochondrial DNA sequence data gleaned from the literature or this study. Additionally, C. thomasi was resurrected. Given the widespread distribution of the genus Cheirogaleus throughout Madagascar, the methodology employed in this study combined all available lines of evidence to standardize investigative procedures in a genus with limited access to type material and a lack of comprehensive sampling across its total distribution. Our results highlighted lineages that likely represent new species and identified localities that may harbor an as-yet undescribed cryptic species diversity pending further field and laboratory work.We are most grateful to the Ahmanson Foundation, the Theodore F. and Claire M. Hubbard Family Foundation, the Primate Action Fund / Conservation International, the Margot Marsh Biodiversity Foundation, and the National Geographic Society, for financial assistance

The Unintended Consequences of a Ban on the Humane Slaughter (Processing) of Horses in the United States

Federal legislation has been proposed to amend the Horse Protection Act to prohibit the shipping, transporting, moving, delivering, receiving, possessing, purchasing, selling, or donation of horses and other equines to be humanely slaughtered (processed) for human consumption, and for other purposes. The intent of the legislation is to enact a ban in the United States on processing horses for human consumption. The legislation does not provide fiscal support that would likely be needed to respond to an ever increasing number of unwanted, neglected, and abused horses. Often times horse neglect and abuse cases originate from a lack of economic resources needed to adequately maintain a horse’s health. While everyone fully supports and is committed to the humane treatment of all horses, there are unintended consequences of banning horse processing. The purpose of this paper is to identify and review the unintended consequences of a ban in the United States on the processing of horses for human consumption: 1. The potential for a large number of abandoned or unwanted horses is substantial. 2. Public animal rescue facilities are currently saturated with unwanted horses. No funding has been allocated to manage a large increase in horses that will likely become the responsibility of these facilities. 3. Cost of maintaining unwanted horses accumulates over time: A conservative estimate of the total cost of caring for unwanted horses, based upon 2005 statistics, is $220 million; Cumulative annual maintenance costs of otherwise processed horses, since the year 2000, would have exceeded more than$513 million in 2005. 4. The export value of horse meat for human consumption was approximately $26 million. A ban on processing would eliminate these annual revenues. 5. The option of rendering equine carcasses is decreasing. Private-land burial and disposal in landfills have a negative impact on the environment. 6. The Bureau of Land Management’s Wild Horse and Burro Adoption Program may be negatively impacted by a ban on horse processing. BLM horses and an increasing number of unwanted horses will be competing for adoption homes. Horse processing facilities offer a humane end-of-life option for approximately 1% of the United States horse population. Tens of thousands of horses could be neglected or abandoned if a processing ban were imposed. The direct economic impact and future unintended–and currently unaccounted for–economic impact of banning horse processing for human consumption are substantial. Proponents have not addressed the inevitable costs of such a ban. Horse owners will realize a direct impact from lower horse sale prices. Local and state governments will be adversely impacted by increased costs of regulation and care of unwanted or neglected horses

PhyloMarker—A Tool for Mining Phylogenetic Markers Through Genome Comparison: Application of the Mouse Lemur (Genus Microcebus) Phylogeny

Molecular phylogeny is a fundamental tool to understanding the evolution of all life forms. One common issue faced by molecular phylogeny is the lack of sufficient molecular markers. Here, we present PhyloMarker, a phylogenomic tool designed to find nuclear gene markers for the inference of phylogeny through multiple genome comparison. Around 800 candidate markers were identified by PhyloMarker through comparison of partial genomes of Microcebus and Otolemur. In experimental tests of 20 randomly selected markers, nine markers were successfully amplified by PCR and directly sequenced in all 17 nominal Microcebus species. Phylogenetic analyses of the sequence data obtained for 17 taxa and nine markers confirmed the distinct lineage inferred from previous mtDNA data. PhyloMarker has also been used by other projects including the herons (Ardeidae, Aves) phylogeny and the Wood mice (Muridae, Mammalia) phylogeny. All source code and sample data are made available at http://bioinfo-srv1.awh.unomaha.edu/phylomarker/

Does sorting by color using visible and high‐energy violet light improve classification of taxa in honey bee pollen pellets?

Premise: Pollen collected by honey bees from different plant species often differs in color, and this has been used as a basis for plant identification. The objective of this study was to develop a new, low-cost protocol to sort pollen pellets by color using high-energy violet light and visible light to determine whether pollen pellet color is associated with variations in plant species identity.
 Methods and Results: We identified 35 distinct colors and found that 52% of pollen subsamples (n = 200) were dominated by a single taxon. Among these near-pure pellets, only one color consistently represented a single pollen taxon (Asteraceae: Cichorioideae). Across the spectrum of colors spanning yellows, oranges, and browns, similarly colored pollen pellets contained pollen from multiple plant families ranging from two to 13 families per color.
 Conclusions: Sorting pollen pellets illuminated under high-energy violet light lit from four directions within a custom-made light box aided in distinguishing pellet composition, especially in pellets within the same color

Injury Rates, Mechanisms, Risk Factors and Prevention Strategies in Youth Rugby Union: What’s All the Ruck-Us About? A Systematic Review and Meta-analysis

Background: Rugby Union is a collision team sport played globally. Despite this, significant concerns have been raised regarding the sport’s safety, particularly in youth players. Given this, a review of injury rates, risk factors and prevention strategies is required across different youth age groups as well as in males and females. Objective: The objective of this systematic review (SR) and meta-analysis was to investigate injury and concussion rates, risk factors and primary prevention strategies in youth rugby. Methods: To be included, studies were required to report either rates, risk factors or prevention strategies in youth rugby and to have a randomised controlled trial, quasi-experimental, cohort, case control, or ecological study design. Exclusion criteria included non-peer-reviewed grey literature, conference abstracts, case studies, previous systematic reviews and studies not written in English. Nine databases were searched. The full search strategy and list of sources are available and pre-registered on PROSPERO (Ref: CRD42020208343). Each study was assessed for risk of bias using the Downs and Black quality assessment tool. Meta-analyses were conducted using a DerSimonian Laird random effect model for each age group and sex. Results: Sixty-nine studies were included in this SR. The match injury rates (using a 24-h time-loss definition) were 40.2/1000 match hours (95% CI 13.9–66.5) in males and 69.0/1000 match hours (95% CI 46.8–91.2) in females. Concussion rates were 6.2/1000 player-hours (95% CI 5.0–7.4) for males and 33.9/1000 player-hours (95% CI: 24.1–43.7) for females. The most common injury site was lower extremity (males) and the head/neck (females). The most common injury type was ligament sprain (males) and concussion (females). The tackle was the most common event associated with injury in matches (55% male, 71% females). Median time loss was 21 days for males and 17 days for females. Twenty-three risk factors were reported. The risk factors with the strongest evidence were higher levels of play and increasing age. Primary injury prevention strategies were the focus of only eight studies and included law changes (n = 2), equipment (n = 4), education (n = 1) and training (n = 1). The prevention strategy with the most promising evidence was neuromuscular training. The primary limitations included a broad range of injury definitions (n = 9) and rate denominators (n = 11) used, as well as a limited number of studies which could be included in the meta-analysis for females (n = 2). Conclusion: A focus on high-quality risk factor and primary prevention evaluation should be considered in future studies. Targeting primary prevention and stakeholder education remain key strategies in the prevention, recognition and management of injuries and concussions in youth rugby

Injury Rates, Mechanisms, Risk Factors and Prevention Strategies in Youth Rugby Union: What’s All the Ruck-Us About? A Systematic Review and Meta-analysis

BackgroundRugby Union is a collision team sport played globally. Despite this, significant concerns have been raised regarding the sport’s safety, particularly in youth players. Given this, a review of injury rates, risk factors and prevention strategies is required across different youth age groups as well as in males and females.ObjectiveThe objective of this systematic review (SR) and meta-analysis was to investigate injury and concussion rates, risk factors and primary prevention strategies in youth rugby.MethodsTo be included, studies were required to report either rates, risk factors or prevention strategies in youth rugby and to have a randomised controlled trial, quasi-experimental, cohort, case control, or ecological study design. Exclusion criteria included non-peer-reviewed grey literature, conference abstracts, case studies, previous systematic reviews and studies not written in English. Nine databases were searched. The full search strategy and list of sources are available and pre-registered on PROSPERO (Ref: CRD42020208343). Each study was assessed for risk of bias using the Downs and Black quality assessment tool. Meta-analyses were conducted using a DerSimonian Laird random effect model for each age group and sex.ResultsSixty-nine studies were included in this SR. The match injury rates (using a 24-h time-loss definition) were 40.2/1000 match hours (95% CI 13.9–66.5) in males and 69.0/1000 match hours (95% CI 46.8–91.2) in females. Concussion rates were 6.2/1000 player-hours (95% CI 5.0–7.4) for males and 33.9/1000 player-hours (95% CI: 24.1–43.7) for females. The most common injury site was lower extremity (males) and the head/neck (females). The most common injury type was ligament sprain (males) and concussion (females). The tackle was the most common event associated with injury in matches (55% male, 71% females). Median time loss was 21 days for males and 17 days for females. Twenty-three risk factors were reported. The risk factors with the strongest evidence were higher levels of play and increasing age. Primary injury prevention strategies were the focus of only eight studies and included law changes (n = 2), equipment (n = 4), education (n = 1) and training (n = 1). The prevention strategy with the most promising evidence was neuromuscular training. The primary limitations included a broad range of injury definitions (n = 9) and rate denominators (n = 11) used, as well as a limited number of studies which could be included in the meta-analysis for females (n = 2).ConclusionA focus on high-quality risk factor and primary prevention evaluation should be considered in future studies. Targeting primary prevention and stakeholder education remain key strategies in the prevention, recognition and management of injuries and concussions in youth rugby

Individual common variants exert weak effects on the risk for autism spectrum disorders.

While it is apparent that rare variation can play an important role in the genetic architecture of autism spectrum disorders (ASDs), the contribution of common variation to the risk of developing ASD is less clear. To produce a more comprehensive picture, we report Stage 2 of the Autism Genome Project genome-wide association study, adding 1301 ASD families and bringing the total to 2705 families analysed (Stages 1 and 2). In addition to evaluating the association of individual single nucleotide polymorphisms (SNPs), we also sought evidence that common variants, en masse, might affect the risk. Despite genotyping over a million SNPs covering the genome, no single SNP shows significant association with ASD or selected phenotypes at a genome-wide level. The SNP that achieves the smallest P-value from secondary analyses is rs1718101. It falls in CNTNAP2, a gene previously implicated in susceptibility for ASD. This SNP also shows modest association with age of word/phrase acquisition in ASD subjects, of interest because features of language development are also associated with other variation in CNTNAP2. In contrast, allele scores derived from the transmission of common alleles to Stage 1 cases significantly predict case status in the independent Stage 2 sample. Despite being significant, the variance explained by these allele scores was small (Vm< 1%). Based on results from individual SNPs and their en masse effect on risk, as inferred from the allele score results, it is reasonable to conclude that common variants affect the risk for ASD but their individual effects are modest

An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding

Regulatory proteins can bind to different sets of genomic targets in various cell types or conditions. To reliably characterize such condition-specific regulatory binding we introduce MultiGPS, an integrated machine learning approach for the analysis of multiple related ChIP-seq experiments. MultiGPS is based on a generalized Expectation Maximization framework that shares information across multiple experiments for binding event discovery. We demonstrate that our framework enables the simultaneous modeling of sparse condition-specific binding changes, sequence dependence, and replicate-specific noise sources. MultiGPS encourages consistency in reported binding event locations across multiple-condition ChIP-seq datasets and provides accurate estimation of ChIP enrichment levels at each event. MultiGPS's multi-experiment modeling approach thus provides a reliable platform for detecting differential binding enrichment across experimental conditions. We demonstrate the advantages of MultiGPS with an analysis of Cdx2 binding in three distinct developmental contexts. By accurately characterizing condition-specific Cdx2 binding, MultiGPS enables novel insight into the mechanistic basis of Cdx2 site selectivity. Specifically, the condition-specific Cdx2 sites characterized by MultiGPS are highly associated with pre-existing genomic context, suggesting that such sites are pre-determined by cell-specific regulatory architecture. However, MultiGPS-defined condition-independent sites are not predicted by pre-existing regulatory signals, suggesting that Cdx2 can bind to a subset of locations regardless of genomic environment. A summary of this paper appears in the proceedings of the RECOMB 2014 conference, April 2–5.National Science Foundation (U.S.) (Graduate Research Fellowship under Grant 0645960)National Institutes of Health (U.S.) (grant P01 NS055923)Pennsylvania State University. Center for Eukaryotic Gene Regulatio