15 Works

Data from: Secondary contact and local adaptation contribute to genome-wide patterns of clinal variation in Drosophila melanogaster

Alan O. Bergland, Ray Tobler, Josefa Gonzalez, Paul Schmidt, Dimitri A. Petrov & Dmitri Petrov
Populations arrayed along broad latitudinal gradients often show patterns of clinal variation in phenotype and genotype. Such population differentiation can be generated and maintained by both historical demographic events and local adaptation. These evolutionary forces are not mutually exclusive and can in some cases produce nearly identical patterns of genetic differentiation among populations. Here, we investigate the evolutionary forces that generated and maintain clinal variation genome-wide among populations of Drosophila melanogaster sampled in North America...

Data from: Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform

Shadi Shokralla, Teresita M. Porter, Joel F. Gibson, Rafal Dobosz, Daniel H. Janzen, Winnie Hallwachs, G. Brian Golding & Mehrdad Hajibabaei
Genetic information is a valuable component of biosystematics, especially specimen identification through the use of species-specific DNA barcodes. Although many genomics applications have shifted to High-Throughput Sequencing (HTS) or Next-Generation Sequencing (NGS) technologies, sample identification (e.g., via DNA barcoding) is still most often done with Sanger sequencing. Here, we present a scalable double dual-indexing approach using an Illumina Miseq platform to sequence DNA barcode markers. We achieved 97.3% success by using half of an Illumina...

Data from: Detecting epistasis from an ensemble of adapting populations

David M. McCandlish, Jakub Otwinowski & Joshua B. Plotkin
The role that epistasis plays during adaptation remains an outstanding problem, which has received considerable attention in recent years. Most of the recent empirical studies are based on ensembles of replicate populations that adapt in a fixed, laboratory controlled condition. Researchers often seek to infer the presence and form of epistasis in the fitness landscape from the time-evolution of various statistics averaged across the ensemble of populations. Here we provide a rigorous analysis of what...

Data from: Spatially varying selection shapes life history clines among populations of Drosophila melanogaster from sub-Saharan Africa

Daniel K. Fabian, Justin B. Lack, Vinayak Mathur, Christian Schlötterer, Paul S. Schmidt, John E. Pool & Thomas Flatt
Clines in life history traits, presumably driven by spatially varying selection, are widespread. Major latitudinal clines have been observed, for example, in Drosophila melanogaster, an ancestrally tropical insect from Africa that has colonized temperate habitats on multiple continents. Yet, how geographic factors other than latitude, such as altitude or longitude, affect life history in this species remains poorly understood. Moreover, most previous work has been performed on derived European, American and Australian populations, but whether...

Data from: Complex disease and phenotype mapping in the domestic dog

Jessica J. Hayward, Marta G. Castelhano, Kyle C. Oliveira, Elizabeth Corey, Cheryl Balkman, Tara L. Baxter, Margret L. Casal, Sharon A. Center, Meiying Fang, Susan J. Garrison, Sara E. Kalla, Pavel Korniliev, Michael I. Kotlikoff, N. Sydney Moise, Laura M. Shannon, Kenneth W. Simpson, Nathan B. Sutter, Rory J. Todhunter & Adam R. Boyko
The domestic dog is becoming an increasingly valuable model species in medical genetics, showing particular promise to advance our understanding of cancer and orthopaedic disease. Here we undertake the largest canine genome-wide association study to date, with a panel of over 4,200 dogs genotyped at 180,000 markers, to accelerate mapping efforts. For complex diseases, we identify loci significantly associated with hip dysplasia, elbow dysplasia, idiopathic epilepsy, lymphoma, mast cell tumour and granulomatous colitis; for morphological...

Data from: The transcriptomic and evolutionary signature of social interactions regulating honey bee caste development

Svjetlana Vojvodic, Brian R. Johnson, Brock A. Harpur, Clement F. Kent, Amro Zayed, Kirk E. Anderson & Timothy A. Linksvayer
The caste fate of developing female honey bee larvae is strictly socially regulated by adult nurse workers. As a result of this social regulation, nurse-expressed genes as well as larval-expressed genes may affect caste expression and evolution. We used a novel transcriptomic approach to identify genes with putative direct and indirect effects on honey bee caste development, and we subsequently studied the relative rates of molecular evolution at these caste-associated genes. We experimentally induced the...

Data from: Predicting optimal outcomes in cognitive therapy or interpersonal psychotherapy for depressed individuals using the Personalized Advantage Index approach

Marcus J. H. Huibers, Zachary D. Cohen, Lotte H. J. M. Lemmens, Arnoud Arntz, Frenk P. M. L. Peeters, Pim Cuijpers & Robert J. DeRubeis
Introduction: Although psychotherapies for depression produce equivalent outcomes, individual patients respond differently to different therapies. Predictors of outcome have been identified in the context of randomized trials, but this information has not been used to predict which treatment works best for the depressed individual. In this paper, we aim to replicate a recently developed treatment selection method, using data from an RCT comparing the effects of cognitive therapy (CT) and interpersonal psychotherapy (IPT). Methods: 134...

Data from: A functional cartography of cognitive systems

Marcelo G. Mattar, Michael W. Cole, Sharon L. Thompson-Schill & Danielle S. Bassett
One of the most remarkable features of the human brain is its ability to adapt rapidly and efficiently to external task demands. Novel and non-routine tasks, for example, are implemented faster than structural connections can be formed. The neural underpinnings of these dynamics are far from understood. Here we develop and apply novel methods in network science to quantify how patterns of functional connectivity between brain regions reconfigure as human subjects perform 64 different tasks....

Data from: The Lyme disease pathogen has no effect on the survival of its rodent reservoir host

Maarten J. Voordouw, Shelly Lachish & Marc C. Dolan
Zoonotic pathogens that cause devastating morbidity and mortality in humans may be relatively harmless in their natural reservoir hosts. The tick-borne bacterium Borrelia burgdorferi causes Lyme disease in humans but few studies have investigated whether this pathogen reduces the fitness of its reservoir hosts under natural conditions. We analyzed four years of capture-mark-recapture (CMR) data on a population of white-footed mice, Peromyscus leucopus, to test whether B. burgdorferi and its tick vector affect the survival...

Data from: Seasonal variation in life history traits in two Drosophila species

Emily L. Behrman, Samuel S. Watson, Katherine R. O'Brien, Shane M. Heschel & Paul S. Schmidt
Seasonal environmental heterogeneity is cyclic, persistent and geographically widespread. In species that reproduce multiple times annually, environmental changes across seasonal time may create different selection regimes that may shape the population ecology and life history adaptation in these species. Here, we investigate how two closely related species of Drosophila in a temperate orchard respond to environmental changes across seasonal time. Natural populations of Drosophila melanogaster and D. simulans were sampled at four timepoints from June...

Data from: Genes associated with ant social behavior show distinct transcriptional and evolutionary patterns

Timothy Linksvayer, Alexander Mikheyev, Timothy A Linksvayer & Alexander S Mikheyev
MySQL database for gene expression analysisMySQL database for the transcriptional, network connectedness, molecular evolution, and GO term analysismonomorium_2014-12-08.sql.gzData tables from MySQL database for gene expression analysisseparated data tables from MySQL database as zipped .csv files for the transcriptional, network connectedness, molecular evolution, and GO term analysismonomorium tables.zipdata summary by genesummary of data listed by M. pharaonis gene in comma deliminated (.csv) format. Header line with variables: gene is the M. pharaonis gene name; SINV homolog...

Data from: Comparative analyses of clinical and environmental populations of Cryptococcus neoformans in Botswana

Yuan Chen, Anastasia P. Litvintseva, Aubrey E. Frazzitta, Miriam R. Haverkamp, Liuyang Wang, Charles Fang, Charles Muthoga, Thomas G. Mitchell & John R. Perfect
Cryptococcus neoformans var. grubii (Cng) is the most common cause of fungal meningitis, and its prevalence is highest in sub-Saharan Africa. Patients become infected by inhaling airborne spores or desiccated yeast cells from the environment, where the fungus thrives in avian droppings, trees and soil. To investigate the prevalence and population structure of Cng in southern Africa, we analysed isolates from 77 environmental samples and 64 patients. We detected significant genetic diversity among isolates and...

Data from: A novel method to analyze social transmission in chronologically sequenced assemblages, implemented on cultural inheritance of the art of cooking

Sven Isaksson, Alexander Funcke, Ida Envall, Magnus Enquist & Patrik Lindenfors
Here we present an analytical technique for the measurement and evaluation of changes in chronologically sequenced assemblages. To illustrate the method, we studied the cultural evolution of European cooking as revealed in seven cook books dispersed over the past 800 years. We investigated if changes in the set of commonly used ingredients were mainly gradual or subject to fashion fluctuations. Applying our method to the data from the cook books revealed that overall, there is...

Data from: Comparative population genomics of latitudinal variation in D. simulans and D. melanogaster

Heather E. Machado, Alan O. Bergland, Emily L. Behrman, Katherine R. O'Brien, Paul S. Schmidt & Dmitri A. Petrov
Examples of clinal variation in phenotypes and genotypes across latitudinal transects have served as important models for understanding how spatially varying selection and demographic forces shape variation within species. Here we examine the selective and demographic contributions to latitudinal variation through the largest comparative genomic study to date of Drosophila simulans and D. melanogaster, with genomic sequence data from 382 individual fruit flies, collected across a spatial transect of 19 degrees latitude and at multiple...

Data from: Altered fronto-temporal functional connectivity in individuals at ultra-high-risk of developing psychosis

Youngwoo Bryan Yoon, Je-Yeon Yun, Wi Hoon Jung, Kang Ik K. Cho, Sung Nyun Kim, Tae Young Lee, Hye Yoon Park & Jun Soo Kwon
Background: The superior temporal gyrus (STG) is one of the key regions implicated in psychosis, given that abnormalities in this region are associated with an increased risk of conversion from an at-risk mental state to psychosis. However, inconsistent results regarding the functional connectivity strength of the STG have been reported, and the regional heterogeneous characteristics of the STG should be considered. Methods: To investigate the distinctive functional connection of each subregion in the STG, we...

Registration Year

  • 2015
    15

Resource Types

  • Dataset
    15

Affiliations

  • University of Pennsylvania
    15
  • Stanford University
    2
  • University of Veterinary Medicine Vienna
    2
  • VU University Amsterdam
    1
  • Duke University
    1
  • University of Lausanne
    1
  • Australian National University
    1
  • University of Guelph
    1
  • University of Wisconsin-Madison
    1
  • McMaster University
    1