Woodland restoration and forest structure affect nightjar abundance in the Ozark Highlands

Chuck-will's-widow (Antrostomus carolinensis) and eastern whip-poor-will (Antrostomus vociferus) are nightjars in eastern North America that have declined 69% and 67%, respectively, in abundance since 1966, resulting in conservation concerns for these species. We investigated relationships between nightjar abundance and landscape composition, forest structure, and application of tree thinning and prescribed fire because of regional interest in woodland restoration and nightjar conservation. We conducted nocturnal nightjar surveys at 385 points in southern Missouri, USA, in 2014 and 2015 and related counts to pine (Pinus spp.) and hardwood basal area, canopy closure, percent forest cover, and percent of area thinned or burned within 500 m of survey points. We modeled abundance of chuck-will's-widow and eastern whip-poor-will using time-removal models that included a detection process and an abundance process within a hierarchical Bayesian framework. We detected 534 eastern whip-poor-will and 186 chuck-will's-widow during surveys. Our data supported global models that included all 6 vegetation and management variables for both species. Chuck-will's-widow abundance was negatively related to hardwood basal area and peaked at intermediate values of percent area burned and percent forest cover. Eastern whip-poor-will abundance was negatively related to hardwood basal area and canopy cover, positively related to percent forest cover and percent of area burned, and peaked at low to moderate levels of percent of area thinned. Relationships to forest structure and management activities generally supported the conclusion that woodland restoration benefits nightjars and that chuck-will's-widow select landscapes with less forest cover than eastern whip-poor-will.     

A Hybrid Likelihood Model for Sequence-Based Disease Association Studies

In the past few years, case-control studies of common diseases have shifted their focus from single genes to whole exomes. New sequencing technologies now routinely detect hundreds of thousands of sequence variants in a single study, many of which are rare or even novel. The limitation of classical single-marker association analysis for rare variants has been a challenge in such studies. A new generation of statistical methods for case-control association studies has been developed to meet this challenge. A common approach to association analysis of rare variants is the burden-style collapsing methods to combine rare variant data within individuals across or within genes. Here, we propose a new hybrid likelihood model that combines a burden test with a test of the position distribution of variants. In extensive simulations and on empirical data from the Dallas Heart Study, the new model demonstrates consistently good power, in particular when applied to a gene set (e.g., multiple candidate genes with shared biological function or pathway), when rare variants cluster in key functional regions of a gene, and when protective variants are present. When applied to data from an ongoing sequencing study of bipolar disorder (191 cases, 107 controls), the model identifies seven gene sets with nominal p-values0.05, of which one MAPK signaling pathway (KEGG) reaches trend-level significance after correcting for multiple testing.     

Structure of CcmG/DsbE at 1.14 A resolution: high-fidelity reducing activity in an indiscriminately oxidizing environment

CcmG is unlike other periplasmic thioredoxin (TRX)-like proteins in that it has a specific reducing activity in an oxidizing environment and a high fidelity of interaction. These two unusual properties are required for its role in c-type cytochrome maturation. The crystal structure of CcmG reveals a modified TRX fold with an unusually acidic active site and a groove formed from two inserts in the fold. Deletion of one of the groove-forming inserts disrupts c-type cytochrome formation. Two unique structural features of CcmG-an acidic active site and an adjacent groove-appear to be necessary to convert an indiscriminately binding scaffold, the TRX fold, into a highly specific redox protein.     

Evolutionary implications of developmental instability in parthenogenetic drosophila mercatorum. I. Comparison of several strains with different genotypes

Natural populations of sexually reproducing Drosophila mercatorum are capable of a very low rate of parthenogenesis, but this mode of reproduction has apparently never characterized an entirely asexual population in this species. The high abortion rate observed in laboratory parthenogenetic lines suggests that developmental constraints may cause the failure of this trait to spread in nature. To investigate the basis of this developmental instability and how it may affect the evolution of parthenogenesis in natural populations, early embryonic development was compared between one sexual and four parthenogenetic laboratory strains of D. mercatorum. There is a large amount of variation within a given parthenogenetic strain, suggesting that parthenogenesis is associated with a general breakdown of developmental stability. There is relatively little variation among different parthenogenetic strains, suggesting that most abortions are due to a feature inherent to parthenogenetic reproduction rather than a feature of a particular genome. Likewise, there is little variation between parthenogenetic and sexual strains in the causes of abortions, suggesting that the developmental problems encountered by parthenogenetic lineages are not unique to parthenogens. Thus, the failure of parthenogenesis to spread within D. mercatorum can be attributed to no particular developmental constraint per se operating after the initiation of embryogenesis. However, the overall increase in all developmental problems that occurs with the transition from sexual to parthenogenetic development suggests that the high degree of developmental instability associated with parthenogenesis may be considered a developmental constraint in its own right.