30 Works

Data from: Dating the species network: allopolyploidy and repetitive DNA evolution in American daisies (Melampodium sect. Melampodium, Asteraceae)

Jamie McCann, Tae-Soo Jang, Jiri Macas, Gerald M. Schneeweiss, Nicholas J. Matzke, Petr Novak, Tod F. Stuessy, Jose L. Villaseñor & Hanna Weiss-Schneeweiss
Allopolyploidy has played an important role in the evolution of the flowering plants. Genome mergers are often accompanied by significant and rapid alterations of genome size and structure via chromosomal rearrangements and altered dynamics of tandem and dispersed repetitive DNA families. Recent developments in sequencing technologies and bioinformatic methods allow for a comprehensive investigation of the repetitive component of plant genomes. Interpretation of evolutionary dynamics following allopolyploidization requires both the knowledge of parentage and the...

Data from: Genomewide genotyping of a novel Mexican Chile Pepper collection illuminates the history of landrace differentiation after Capsicum annuum L. domestication

Nathan Taitano, Vivian Bernau, Lev Jardón-Barbolla, Brian Leckie, Michael Mazourek, Kristin Mercer, Leah McHale, Andrew Michel, David Baumler, Michael Kantar, Esther Van Der Knapp & Esther Van Der Knaap
Studies of genetic diversity among phenotypically distinct crop landraces improve our understanding of fruit evolution and genome structure under domestication. Chile peppers (Capsicum spp. L.) are economically valuable and culturally important species, and extensive phenotypic variation among landraces exists in southern Mexico, a center of C. annuum diversity. We collected 103 chile pepper seed accessions from 22 named landraces across 27 locations in southern Mexico. We genotyped these accessions with genotyping-by-sequencing (GBS), yielding 32,623 filtered...

Data from: Local prey community composition and genetic distance predict venom divergence among populations of the northern Pacific rattlesnake (Crotalus oreganus)

Matthew L. Holding, Mark J. Margres, Darin R. Rokyta, H. Lisa Gibbs & H. Lisle Gibbs
Identifying the environmental correlates of divergence in functional traits between populations can provide insights into the evolutionary mechanisms that generate local adaptation. Here, we assess patterns of population differentiation in expressed venom proteins in Northern Pacific rattlesnakes (Crotalus oreganus) from 13 locations across California. We evaluate the relative importance of major biotic (prey species community composition), abiotic (temperature, precipitation, and elevation) and genetic factors (genetic distance based on RADseq loci) as correlates of population divergence...

Data from: How does human motor cortex regulate vocal pitch in singers?

Michel Belyk, Yune S. Lee & Steven Brown
Vocal pitch is used as an important communicative device by humans, as found in the melodic dimension of both speech and song. Vocal pitch is determined by the degree of tension in the vocal folds of the larynx, which itself is influenced by complex and non-linear interactions among the laryngeal muscles. The relationship between these muscles and vocal pitch has been described by a mathematical model in the form of a set of “control rules”....

Data from: Too constrained to converse: the effect of financial constraints on word-of-mouth

Anna Paley, Stephanie M. Tully & Eesha Sharma
Existing research demonstrates that financial constraints are widespread and influence consumer attention, preference, choice, and consumption in a variety of ways. Despite the growing knowledge of how financial constraints affect the consumer decision making process, less is known about its impact on post-purchase behavior. This work examines whether financial constraints impact an important post-purchase behavior—word-of-mouth—and in what direction. Seven studies show that financial constraints reduce purchase-related word-of-mouth. This effect emerges across consumers’ reported frequencies of...

Data from: Fluidigm2PURC: automated processing and haplotype inference for double-barcoded PCR amplicons

Paul D. Blischak, Maribeth Latvis, Diego F. Morales-Briones, Jens C. Johnson, Verónica S. Di Stilio, Andrea D. Wolfe & David C. Tank
Premise of the Study: Targeted enrichment strategies for phylogenomic inference are a time‐ and cost‐efficient way to collect DNA sequence data for large numbers of individuals at multiple, independent loci. Automated and reproducible processing of these data is a crucial step for researchers conducting phylogenetic studies. Methods and Results: We present Fluidigm2PURC, an open source Python utility for processing paired‐end Illumina data from double‐barcoded PCR amplicons. In combination with the program PURC (Pipeline for Untangling...

Data from: Large birds travel farther in homogeneous environments

Marlee A. Tucker, Olga Alexandrou, , Keith L. Bildstein, Katrin Böhning-Gaese, Chloe Bracis, John N. Brzorad, Evan R. Buechley, David Cabot, Justin M. Calabrese, Carlos Carrapato, André Chiaradia, Lisa C. Davenport, Sarah C. Davidson, Mark Desholm, Christopher R. DeSorbo, Robert Domenech, Peter Enggist, William F. Fagan, Nina Farwig, Wolfgang Fiedler, Christen H. Fleming, Alastair Franke, John M. Fryxell, Clara García-Ripollés … & João Paulo Silva
Aim: Animal movement is an important determinant of individual survival, population dynamics, and ecosystem structure and function. Yet it is still unclear how local movements are related to resource availability and the spatial arrangement of resources. Using resident bird species and migratory bird species outside of the migratory period, we examined how the distribution of resources affect the movement patterns of both large terrestrial birds (e.g., raptors, bustards, hornbills) and waterbirds (e.g., cranes, storks, ducks,...

Data from: Using host-associated differentiation to track source population and dispersal distance among insect vectors of plant pathogens

Gina M. Angelella, Andy P. Michel, Ian Kaplan, G.M. Angelella & A.P. Michel
Small, mobile insects are notoriously challenging to track across landscapes and manage in agricultural fields. However, genetic differentiation among insect populations and host-plants acquired through host-associated differentiation could be exploited to infer movement within crop systems and damage potential. Although many insects exhibit host-associated differentiation, management strategies for insect vectors of plant pathogens assume a homogenous population. Nevertheless, phenotypic changes derived from host-associated differentiation could manifest in altered behavior or physiology affecting the likelihood of...

Data from: Risk factors for suicidality in Huntington's disease: an analysis of the 2CARE clinical trial

Andrew J. McGarry, Michael P. McDermott, Karl Kieburtz, Wai Lun Alan Fung, Elizabeth Anne McCusker, Jing Peng, Elisabeth A. De Blieck & Merit E. Cudkowicz
Most suicidality literature in HD is based on natural history studies or retrospective reviews, but reports on risk factors from clinical trials are limited. We analyzed 609 participants from 2CARE, a randomized, double-blind, placebo controlled clinical trial with up to 5 years of follow-up, for risk factors related to suicidality. The primary outcome variable was the time from randomization until the first occurrence of either suicidal ideation or attempt. We also considered time from randomization...

Data from: The Sarracenia alata pitcher plant system and obligate arthropod inquilines should be considered an evolutionary community

Jordan D. Satler & Bryan C. Carstens
Aim: The Sarracenia alata pitcher plant and inquiline species comprise an ecological community. These inquilines span the continuum in their ecological association with the host pitcher plant, from species that contain little-to-no interaction with the plant to species that are completely dependent on the plant for their entire life cycle. We are interested in testing if degree of ecological dependence is positively correlated with a shared evolutionary history, and in identifying members of this community...

Data from: Transcriptome profiles of sunflower reveal the potential role of microsatellites in gene expression divergence

Chathurani Ranathunge, Gregory L. Wheeler, Melody E. Chimahusky, Meaghan M. Kennedy, Jesse I. Morrison, Brian S. Baldwin, Andy D. Perkins & Mark E. Welch
The mechanisms by which natural populations generate adaptive genetic variation are not well understood. Some studies propose that microsatellites can function as drivers of adaptive variation. Here we tested a potentially adaptive role for transcribed microsatellites with natural populations of the common sunflower (Helianthus annuus L.) by assessing the enrichment of microsatellites in genes that show expression divergence across latitudes. Seeds collected from six populations at two distinct latitudes in Kansas and Oklahoma were planted...

Data from: Using phylogenomic data to explore the effects of relaxed clocks and calibration strategies on divergence time estimation: primates as a test case

Mario Dos Reis, Gregg F. Gunnell, Jose Barba-Montoya, Alex Wilkins, Ziheng Yang & Anne D. Yoder
Primates have long been a test case for the development of phylogenetic methods for divergence time estimation. Despite a large number of studies, however, the timing of origination of crown Primates relative to the K-Pg boundary and the timing of diversification of the main crown groups remain controversial. Here we analysed a dataset of 372 taxa (367 Primates and 5 outgroups, 3.4 million aligned base pairs) that includes nine primate genomes. We systematically explore the...

Data from: Moving in the Anthropocene: global reductions in terrestrial mammalian movements

Marlee A. Tucker, Katrin Böhning-Gaese, William F. Fagan, John M. Fryxell, Bram Van Moorter, Susan C. Alberts, Abdullahi H. Ali, Andrew M. Allen, Nina Attias, Tal Avgar, Hattie Bartlam-Brooks, Buuveibaatar Bayarbaatar, Jerrold L. Belant, Alessandra Bertassoni, Dean Beyer, Laura Bidner, Floris M. Van Beest, Stephen Blake, Niels Blaum, Chloe Bracis, Danielle Brown, P. J. Nico De Bruyn, Francesca Cagnacci, Justin M. Calabrese, Constança Camilo-Alves … & Thomas Mueller
Animal movement is fundamental for ecosystem functioning and species survival, yet the effects of the anthropogenic footprint on animal movements have not been estimated across species. Using a unique GPS-tracking database of 803 individuals across 57 species, we found that movements of mammals in areas with a comparatively high human footprint were on average one-half to one-third the extent of their movements in areas with a low human footprint. We attribute this reduction to behavioral...

Data from: Genetic signatures of small effective population sizes and demographic declines in an endangered rattlesnake, Sistrurus catenatus

Michael Sovic, Anthony Fries, Scott A. Martin & H. Lisle Gibbs
Endangered species that exist in small isolated populations are at elevated risk of losing adaptive variation due to genetic drift. Analyses that estimate short-term effective population sizes, characterize historical demographic processes, and project the trajectory of genetic variation into the future are useful for predicting how levels of genetic diversity may change. Here, we use data from two independent types of genetic markers (single nucleotide polymorphisms [SNPs] and microsatellites) to evaluate genetic diversity in 17...

Data from: The effect of gene flow on coalescent-based species-tree inference

Colby Long & Laura Kubatko
Most current methods for inferring species-level phylogenies under the coalescent model assume that no gene flow occurs following speciation. Several studies have examined the impact of gene flow (e.g., Eckert and Carstens (2008); Chung and Ane (2011); Leache et al. (2014); Solis-Lemus et al. (2016)) and of ancestral population structure (DeGeorgio and Rosenberg, 2016) on the performance of species-level phylogenetic inference, and analytic results have been proven for network models of gene flow (e.g., Solis-Lemus...

Data from: Archaeopedological analysis of colluvial deposits in favourable and unfavourable areas: reconstruction of land use dynamics in SW Germany

Jessica Henkner, Jan Ahlrichs, Sean Downey, Markus Fuchs, Bruce James, Andrea Junge, Thomas Knopf, Thomas Scholten & Peter Kühn
Colluvial deposits, as the correlate sediments of human induced soil erosion, depict an excellent archive of land use and landscape history as representatives of human-environment interactions. This study establishes a chronostratigraphy of colluvial deposits and reconstructs past land use dynamics in the Swabian Jura, the Baar and the Black Forest in SW Germany. In the agriculturally favourable Baar area multiple main phases of colluvial deposition, and thus intensified land use, can be identified from the...

Data from: Artificial lighting at night alters aquatic-riparian invertebrate food webs

S. Mažeika P. Sullivan, Katie Hossler & Lars A. Meyer
Artificial lighting at night (ALAN) is a global phenomenon that can be detrimental to organisms at individual and population levels, yet potential consequences for communities and ecosystem functions are less resolved. Riparian systems may be particularly vulnerable to ALAN. We investigated the impacts of ALAN on invertebrate community composition and food-web characteristics for linked aquatic-terrestrial ecosystems. We focused on food-chain length (FCL) - a central property of ecological communities that can influence their structure, function...

Data from: Mutations in bacterial genes induce unanticipated changes in the relationship between bacterial pathogens in experimental otitis media

Vinal Lakhani, Tan Li, Sayak Mukherjee, William C.L. Stewart, W. Edward Sword & Jayajit Das
Otitis media (OM) is a common polymicrobial infection of the middle ear in children under the age of fifteen years. A widely used experimental strategy to analyze roles of specific phenotypes of bacterial pathogens of OM is to study changes in co-infection kinetics of bacterial populations in animal models when a wild type bacterial strain is replaced by a specific isogenic mutant strain in the co-inoculating mixtures. Since relationships between the OM bacterial pathogens within...

Data from: Walking crowds on a shaky surface: stable walkers discover Millennium Bridge oscillations with and without pedestrian synchrony

Varun Joshi & Manoj Srinivasan
Why did the London Millennium Bridge shake when there was a big enough crowd walking on it? What features of human walking dynamics when coupled to a shaky surface produce such shaking? Here, we use a simple biped model capable of walking stably in 3D to examine these questions. We simulate multiple such stable bipeds walking simultaneously on a bridge, showing that they naturally synchronize under certain conditions, but that synchronization is not required to...

Data from: An ecological approach to measuring the evolutionary consequences of gene flow from crops to wild or weedy relatives

Lesley G. Campbell, David Lee, Kruti Shukla, Thomas A. Waite, Detlef Bartsch & Norman C. Ellstrand
Premise of the study: Agricultural practices routinely create opportunities for crops to hybridize with wild relatives, leading to crop gene introgression into wild genomes. Conservationists typically worry this introgression could lead to genetic homogenization of wild populations, over and above the central concern of transgene escape. Alternatively, viewing introgression as analogous to species invasion, we suggest that increased genetic diversity may likewise be an undesirable outcome. Methods: Here, we compare the sensitivity of conventional population...

Data from: HyDe: a Python package for genome-scale hybridization detection

Paul D. Blischak, Julia Chifman, Andrea D. Wolfe & Laura S. Kubatko
The analysis of hybridization and gene flow among closely related taxa is a common goal for researchers studying speciation and phylogeography. Many methods for hybridization detection use simple site pattern frequencies from observed genomic data and compare them to null models that predict an absence of gene flow. The theory underlying the detection of hybridization using these site pattern probabilities exploits the relationship between the coalescent process for gene trees within population trees and the...

Data from: Optimizing prevention of HIV mother to child transmission: duration of antiretroviral therapy and viral suppression at delivery among pregnant Malawian women

Maganizo B. Chagomerana, William C. Miller, Jennifer H. Tang, Irving F. Hoffman, Bryan C. Mthiko, Jacob Phulusa, Mathias John, Allan Jumbe & Mina C. Hosseinipour
Background: Effective antiretroviral therapy during pregnancy minimizes the risk of vertical HIV transmission. Some women present late in their pregnancy for first antenatal visit; whether these women achieve viral suppression by delivery and how suppression varies with time on ART is unclear. Methods: We conducted a prospective cohort study of HIV-infected pregnant women initiating antiretroviral therapy for the first time from June 2015 to November 2016. Multivariable Poisson models with robust variance estimators were used...

Data from: Total duplication of the small single copy region in the angiosperm plastome: rearrangement and inverted repeat instability in Asarum

Brandon Tyler Sinn, Dylan D. Sedmak, Lawrence M. Kelly & John V. Freudenstein
Premise of the Study: As more plastomes are assembled, it is evident that rearrangements, losses, intergenic spacer expansion and contraction, and syntenic breaks within otherwise functioning plastids are more common than was thought previously, and such changes have developed independently in disparate lineages. However, to date, the magnoliids remain characterized by their highly conserved plastid genomes (plastomes). Methods: Illumina HiSeq and MiSeq platforms were used to sequence the plastomes of Saruma henryi and those of...

Data from: Habitat structure modifies microclimate: an approach for mapping fine-scale thermal refuge

Charlotte R. Milling, Janet L. Rachlow, Peter J. Olsoy, Mark A. Chappell, Timothy R. Johnson, Jennifer S. Forbey, Lisa A. Shipley & Daniel H. Thornton
1. Contemporary techniques predicting habitat suitability under climate change projections often underestimate availability of thermal refuges. Habitat structure contributes to thermal heterogeneity at a variety of spatial scales, but quantifying microclimates at organism‐relevant resolutions remains a challenge. Landscapes that appear homogeneous at large scales may offer patchily distributed thermal refuges at finer scales. 2. We quantified the relationship between vegetation structure and the thermal environment at a scale relevant to small, terrestrial animals using a...

Data from: Dominant and subordinate outside options alter help and eviction in a pay-to-stay negotiation model

Jennifer K. Hellmann & Ian M. Hamilton
In several cooperatively breeding species, subordinates that do not help sufficiently are punished or evicted from the group by dominant individuals. The credibility of dominant eviction threats may vary with the social context beyond the group level: when subordinates can easily breed in a neighboring territory, dominant may be less able to demand help from subordinates. Further, dominant ability to enforce subordinate cooperation may be reduced when it is difficult to replace evicted subordinates or...

Registration Year

  • 2018
    30

Resource Types

  • Dataset
    30

Affiliations

  • The Ohio State University
    30
  • Max Planck Institute for Ornithology
    2
  • Duke University
    2
  • Université Paul-Valéry Montpellier
    2
  • University of Georgia
    2
  • University of Alberta
    2
  • University of Minnesota
    2
  • North Carolina Museum of Natural Sciences
    2
  • University College London
    2
  • University of British Columbia
    2