Simian immunodeficiency viruses (SIVs) have been discovered in over 45 primate species; however, the pathogenic potential of most SIV strains remains unknown due to difficulties inherent in observing wild populations. Because those SIV infections that are pathogenic have been shown to induce changes in the host's gut microbiome, monitoring the microbiota present in faecal samples can provide a noninvasive means for studying the effects of SIV infection on the health of wild-living primates. Here, we...
Data from: Mapping the fitness landscape of gene expression uncovers the cause of antagonism and sign epistasis between adaptive mutationsHsin-Hung Chou, Nigel F. Delaney, Jeremy A. Draghi & Christopher J. Marx
How do adapting populations navigate the tensions between the costs of gene expression and the benefits of gene products to optimize the levels of many genes at once? Here we combined independently-arising beneficial mutations that altered enzyme levels in the central metabolism of Methylobacterium extorquens to uncover the fitness landscape defined by gene expression levels. We found strong antagonism and sign epistasis between these beneficial mutations. Mutations with the largest individual benefit interacted the most...
Molecular analyses of turtle relationships have overturned prevailing morphological hypotheses and prompted the development of a new taxonomy. Here we provide the first genome-scale analysis of turtle phylogeny. We sequenced 2,381 ultraconserved element (UCE) loci representing a total of 1,718,154 bp of aligned sequence. Our sampling includes 32 turtle taxa representing all 14 recognized turtle families and an additional six outgroups. Maximum likelihood, Bayesian, and species tree methods produce a single resolved phylogeny. This robust...
Data from: Population structure of the Chagas disease vector Triatoma infestans in an urban environmentCamilo E. Khatchikian, Erica A. Foley, Corentin M. Barbu, Josephine Hwang, Jenny Ancca-Juárez, Katty Borrini-Mayori, Victor R. Quıspe-Machaca, Cesar Naquira, Dustin Brisson & Michael Z. Levy
Chagas disease is a vector-borne disease endemic in Latin America. Triatoma infestans, a common vector of this disease, has recently expanded its range into rapidly developing cities of Latin America. We aim to identify the environmental features that affect the colonization and dispersal of T. infestans in an urban environment. We amplified 13 commonly used microsatellites from 180 T. infestans samples collected from a sampled transect in the city of Arequipa, Peru, in 2007 and...
Data from: Next-generation DNA barcoding: using next-generation sequencing to enhance and accelerate DNA barcode capture from single specimensShadi Shokralla, Joel F. Gibson, Hamid Nikbakht, Daniel H. Janzen, Winnie Hallwachs & Mehrdad Hajibabaei
DNA barcoding is an efficient method to identify specimens and to detect undescribed/cryptic species. Sanger sequencing of individual specimens is the standard approach in generating large-scale DNA barcode libraries and identifying unknowns. However, the Sanger sequencing technology is, in some respects, inferior to next-generation sequencers, which are capable of producing millions of sequence reads simultaneously. Additionally, direct Sanger sequencing of DNA barcode amplicons, as practiced in most DNA barcoding procedures, is hampered by the need...
Data from: A molecular phylogeny of Eumorpha (Lepidoptera: Sphingidae) and the evolution of anti-predator larval eyespotsFrancesca V. Ponce, Jesse W. Breinholt, Thomas Hossie, Jesse R. Barber, Daniel H. Janzen, Winnie Hallwachs & Akito Y. Kawahara
Many insects possess conspicuous external circular ring markings that resemble the eye of a vertebrate. These ‘eyespots’ typically function to startle or otherwise deter predators, but few studies have examined how eyespots have evolved. We study the evolution of the posterior larval eyespot in the charismatic New World hawkmoth genus Eumorpha. While Eumorpha has a range of posterior larval eyespot shapes and sizes, little is known of how this trait has evolved because phylogenetic relationships...
Data from: A highly pleiotropic amino acid polymorphism in the Drosophila insulin receptor contributes to life history adaptationAnnalise B. Paaby, Alan O. Bergland, Emily L. Behrman & Paul S. Schmidt
Finding the specific nucleotides that underlie adaptive variation is a major goal in evolutionary biology, but polygenic traits pose a challenge because the complex genotype-phenotype relationship can obscure the effects of individual alleles. However, natural selection working in large wild populations can shift allele frequencies and indicate functional regions of the genome. Previously, we showed that the two most common alleles of a complex amino acid insertion-deletion polymorphism in the Drosophila insulin receptor show independent,...
In sexually reproducing animals, male and female reproductive strategies often conflict. In some species, males use aggression to overcome female choice, but debate persists over the extent to which this strategy is successful. Previous studies of male aggression toward females among wild chimpanzees have yielded contradictory results about the relationship between aggression and mating behavior. Critically, however, copulation frequency in primates is not always predictive of reproductive success. We analyzed a 17-year sample of behavioral...
Data from: More than just two sexes: the neural correlates of voice gender perception in gender dysphoriaJessica Junger, Ute Habel, Sabine Bröhr, Josef Neulen, Christiane Neuschaefer-Rube, Peter Birkholz, Christian Kohler, Frank Schneider, Birgit Derntl & Katharina Pauly
Gender dysphoria (also known as “transsexualism”) is characterized as a discrepancy between anatomical sex and gender identity. Research points towards neurobiological influences. Due to the sexually dimorphic characteristics of the human voice, voice gender perception provides a biologically relevant function, e.g. in the context of mating selection. There is evidence for a better recognition of voices of the opposite sex and a differentiation of the sexes in its underlying functional cerebral correlates, namely the prefrontal...
Data from: Genomic evidence of rapid and stable adaptive oscillations over seasonal time scales in DrosophilaAlan O. Bergland, Emily L. Behrman, Katherine R. O'Brien, Paul S. Schmidt & Dmitri A. Petrov
In many species, genomic data have revealed pervasive adaptive evolution indicated by the fixation of beneficial alleles. However, when selection pressures are highly variable along a species' range or through time adaptive alleles may persist at intermediate frequencies for long periods. So called “balanced polymorphisms” have long been understood to be an important component of standing genetic variation, yet direct evidence of the strength of balancing selection and the stability and prevalence of balanced polymorphisms...
Nonhealing diabetic foot ulcers (DFUs) are a common and costly complication of diabetes. Microbial burden, or "bioburden," is believed to underlie delayed healing, although little is known of those clinical factors that may influence microbial load, diversity, and/or pathogenicity. We profiled the microbiomes of neuropathic nonischemic DFUs without clinical evidence of infection in 52 individuals using high-throughput sequencing of the bacterial 16S ribosomal RNA gene. Comparatively, wound cultures, the standard diagnostic in the clinic, vastly...
University of Pennsylvania11
National Institutes of Health2
The University of Texas at Austin1
University of California System1
University of Georgia1
Stanford University School of Medicine1
Institut de Recherche pour le Développement1
New York University1