A Species-Level Phylogeny of Extant Snakes with Description of a New Colubrid Subfamily and Genus

Background With over 3,500 species encompassing a diverse range of morphologies and ecologies, snakes make up 36% of squamate diversity. Despite several attempts at estimating higherlevel snake relationships and numerous assessments of generic- or species-level phylogenies, a large-scale species-level phylogeny solely focusing on snakes has not been completed. Here, we provide the largest-yet estimate of the snake tree of life using maximum likelihood on a supermatrix of 1745 taxa (1652 snake species + 7 outgroup taxa) and 9,523 base pairs from 10 loci (5 nuclear, 5 mitochondrial), including previously unsequenced genera (2) and species (61). Results Increased taxon sampling resulted in a phylogeny with a new higher-level topology and corroborate many lower-level relationships, strengthened by high nodal support values (\u3e 85%) down to the species level (73.69% of nodes). Although the majority of families and subfamilies were strongly supported as monophyletic with \u3e 88% support values, some families and numerous genera were paraphyletic, primarily due to limited taxon and loci sampling leading to a sparse supermatrix and minimal sequence overlap between some closely-related taxa. With all rogue taxa and incertae sedis species eliminated, higher-level relationships and support values remained relatively unchanged, except in five problematic clades. Conclusion Our analyses resulted in new topologies at higher- and lower-levels; resolved several previous topological issues; established novel paraphyletic affiliations; designated a new subfamily, Ahaetuliinae, for the genera Ahaetulla, Chrysopelea, Dendrelaphis, and Dryophiops;and appointed Hemerophis (Coluber) zebrinus to a new genus, Mopanveldophis. Although we provide insight into some distinguished problematic nodes, at the deeper phylogenetic scale, resolution of these nodes may require sampling of more slowly-evolving nuclear genes

Using the Conservation Planning Tool to Effectively Recover Northern Bobwhites: An Example for States to Effectively Step-Down the NBCI Plan

The National Bobwhite Conservation Initiative (NBCI) 2.0 provides a sound foundation for recovering northern bobwhites (Colinus virginianus) range-wide, regionally and, to some extent, even locally. However, the NBCI does not provide detailed guidance to states on how to step-down the plan for efficacious delivery of on-the-ground management actions prescribed via biologists within the plan itself. States often must incorporate multiple planning efforts (e.g., state wildlife action plans) and geospatial layers not directly included in the NBCI plan (see NBCI Appendix in these Proceedings) to make tenable decisions which best guide allocation of resources and benefit multiple species of greatest conservation concern. The Conservation Planning Tool (CPT), developed as part of NBCI 2.0, provides the infrastructure for states and conservation organizations to capture biologist information coalesced in the plan while incorporating other data (e.g., species emphasis areas, current CRP implementation, etc.) germane to conservation planning. We use 3 states (Kansas, Florida, and Virginia) to demonstrate the utility of the CPT and to develop a step-down implementation plan, via creation of a habitat prioritization model, for recovery of bobwhites in each state. We explore the implications associated with creation of focal areas with respect to high versus medium ranked areas and underscore the importance of inclusion of major land-use opportunities and constraints prescribed within the plan to garner successful bobwhite recovery. We propose a framework for the integration of monitoring efforts into the step-down model to assess bird response and evaluate NBCI success through estimating bobwhite population density

Effect of scavenger receptor BI antagonist ITX5061 in patients with hepatitis C virus infection undergoing liver transplantation

Hepatitis C virus (HCV) entry inhibitors have been hypothesized to prevent infection of the liver after transplantation. ITX5061 is a Scavenger Receptor B-I (SR-BI) antagonist that blocks HCV entry and infection in vitro. We assessed the safety and efficacy of ITX5061 to limit HCV infection of the graft. The study included 23 HCV infected patients undergoing liver transplantation. The first 13 "control" patients did not receive drug. The subsequent 10 patients received ITX5061 150 mg immediately pre- and post-transplant, and daily for 1 week thereafter. ITX5061 pharmacokinetics and plasma HCV RNA were quantified. Viral genetic diversity was measured by ultradeep pyrosequencing. ITX5061 was well tolerated with measurable plasma concentrations during therapy. Whilst the median HCV RNA reduction was greater in ITX treated patients at all time points in the first week after transplantation there was no difference in the overall change in the area over the HCV RNA curve in the 7-day treatment period. However, in genotype 1 infected patients treatment was associated with a sustained reduction in HCV RNA levels compared to the control group (area over the HCV RNA curve analysis, p=0.004). Ultradeep pyrosequencing revealed a complex and evolving pattern of HCV variants infecting the graft during the first week. ITX5061 significantly limited viral evolution where the median divergence between day 0 and day 7 was 3.5% in the control group compared to 0.1% in the treated group.CONCLUSIONS: ITX5061 reduces plasma HCV RNA post transplant notably in genotype 1 infected patients and slows viral evolution. Following liver transplantation the likely contribution of extrahepatic reservoirs of HCV necessitates combining entry inhibitors such as ITX5061 with inhibitors of replication in future studies. Clinicaltrials.gov NCT01292824. This article is protected by copyright. All rights reserved.</p

Species-level phylogeny on final dataset of 1652 snake species.

<p>Maximum-likelihood phylogenetic estimate based on 10 concatenated genes. Node values represent SHL support values. Seven outgroup taxa are not shown. Colors of clades indicate their position in the overall tree, shown at left. Newly sequenced taxa are highlighted in bold. Skeleton of the species tree is displayed on the left with displayed subfamilies/families highlighted. Letters denoted by i and ii represent parts of the tree where external branches do not connect to the part of the tree immediately preceding it. A) Anomalepididae, Epictinae, Leptotyphlopinae, Gerrhopilidae, Xenotyphlopidae, and Typhlopinae. B) Asiatyphlopinae I, Afrotyphlopinae; Madatyphlopinae, and Asiatyphlopinae II.</p

Number of taxa sampled per family or subfamily.

<p>Families are listed in order according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0161070#pone.0161070.g001" target="_blank">Fig 1</a>. For the taxonomy of families and subfamilies, we use Adalsteinsson <i>et al</i>, [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0161070#pone.0161070.ref026" target="_blank">26</a>] for Anomalepididae and Leptotyphlopidae, Pyron and Wallach [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0161070#pone.0161070.ref029" target="_blank">29</a>] for Gerrhopilidae, Typhlopidae, and Xenotyphlopidae, Pyron et al [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0161070#pone.0161070.ref030" target="_blank">30</a>] for Booidea, and Pyron <i>et al</i> [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0161070#pone.0161070.ref015" target="_blank">15</a>] for Alethinophidia. The number of species per clade was taken from The Reptile Database (<a href="http://www.reptile-database.org/" target="_blank">http://www.reptile-database.org/</a>) on 10/01/2015. Percentages of the number of species sampled do not include taxa not assigned to species status. Paraphyletic taxa are included under their traditional family and/or subfamily. In the Total cell for total number of species, the number not in parentheses equals the sum of the values in the table and the number in the parentheses equals the number returned when a search for Serpentes is conducted in The Reptile Database. Percentage for total number of species sampled is based on 3566 species.</p

Phylogenetic tree of Serpentes continued.

<p>A) Colubrinae continued. B) Colubrinae continued.</p