238 Works

Data from: Key players and hierarchical organization of prairie dog social networks

Jennifer L. Verdolin, Robert R. Dunn & Amanda L. Traud
The use of social network theory in evaluating animal social groups has gained traction in recent years. Despite the utility of social network analysis in describing attributes of social groups, it remains unclear how comparable this approach is to traditional behavioral observational studies. Using data on Gunnison’s prairie dog (Cynomys gunnisoni) social interactions we describe social networks from three populations. We then compare those social networks to groups identified by traditional behavioral approaches and explore...

Data from: When should species richness be energy limited, and how would we know?

Allen H. Hurlbert & James C. Stegen
Energetic constraints are fundamental to ecology and evolution, and empirical relationships between species richness and estimates of available energy (i.e. resources) have led some to suggest that richness is energetically constrained. However, the mechanism linking energy with richness is rarely specified and predictions of secondary patterns consistent with energy-constrained richness are lacking. Here, we lay out the necessary and sufficient assumptions of a causal relationship linking energy gradients to richness gradients. We then describe an...

Data from: Effects on population divergence of within-generational learning about prospective mates

Maria R. Servedio & Reuven Dukas
Although learned mate preferences are suspected to have important effects during speciation, theoretical models have largely neglected the effects on speciation and population divergence of within-generational learning, that is, learning based upon prior experience with potential mates. Here we use population genetic models to address this deficit. Focussing on the situation of secondary contact between populations that still hybridize, we consider models of learning by females and by males under polygyny. We assess the effects...

Add Health Wave V Documentation: Cardiovascular Measures

Eric A. Whistsel, Robert Angel, Rick O'Hara, Lixin Qu, Kathryn Carrier & Kathleen Mullan Harris
This document summarizes the rationale, equipment, measurement, protocol and data cleaning procedures for each of the cardiovascular measures collected at the Wave V home exam. It also documents how constructed variables were derived from the cardiovascular measures collected in the field. Whenever possible, data collection and methods in Wave V mirrored those of Wave IV to ensure comparability of data between waves. This document is one in a set of Wave V user guides. User...

Data from: Human endometrial transcriptome and progesterone receptor cistrome reveal important pathways and epithelial regulators

Ru-Pin Alicia Chi, Tianyuan Wang, Nyssa Adams, San-Pin Wu, Steven Young, Thomas Spencer & Francesco DeMayo
Context. Poor uterine receptivity is one major factor leading to pregnancy loss and infertility. Understanding the molecular events governing successful implantation is hence critical in combating infertility. Objective. To define PGR-regulated molecular mechanisms and epithelial roles in receptivity. Design. RNA-seq and PGR-ChIP-seq were conducted in parallel to identify PGR-regulated pathways during the WOI in endometrium of fertile women. Setting. Endometrial biopsies from the proliferative and mid-secretory phases were analyzed. Patients or Other Participants. Participants were...

Mutation of CFAP57, a protein required for the asymmetric targeting of a subset of inner dynein arms in Chlamydomonas, causes primary ciliary dyskinesia

Susan Dutcher, Ximena Bustamante-Marin, Amjad Horani, Mihaela Stoyanova, Wu-Lin Charng, Mathieu Bottier, Patrick Sears, Wei-Ning Yin, Leigh Anne Daniels, Hailey Bowen, Donald Conrad, Michael Knowles, Lawrence Ostrowski & Maimoona Zariwala
Primary ciliary dyskinesia (PCD) is characterized by chronic airway disease, reduced fertility, and randomization of the left/right body axis. It is caused by defects of motile cilia and sperm flagella. We screened a cohort of affected individuals that lack an obvious axonemal defect for pathogenic variants using whole exome capture, next generation sequencing, and bioinformatic analysis assuming an autosomal recessive trait. We identified one subject with an apparently homozygous nonsense variant [(c.1762C>T), p.(Arg588*)] in the...

Data from: A stochastic model for predicting age and mass at maturity of insects

Geoffrey Legault & Joel Kingsolver
Variation in age and mass at maturity is commonly observed in populations, even among individuals with the same genetic and environmental backgrounds. Accounting for such individual variation with a stochastic model is important for estimating optimal evolutionary strategies and for understanding potential trade-offs among life history traits. However, most studies employ stochastic models that are either phenomenological or account for variation in only one life history trait. We propose a model based on the developmental...

Data from: Competitively mediated changes in male toad calls can depend on call structure

Rebecca Stirman & Karin S. Pfennig
Many species of males aggregate in large groups where they signal to attract females. These large aggregations create intense competition for mates, and the simultaneous signaling by many individuals can impair any given male’s ability to attract females. In response to this situation, male signals can be modified, either evolutionarily or facultatively, such that the detectability of the signal is enhanced. The way in which signals are modified varies among even closely related species, yet...

Data from: The mouse universal genotyping array: from substrains to subspecies

Andrew Parker Morgan, Chen-Ping Fu, Chia-Yu Kao, Catherine E. Welsh, John P. Didion, Liran Yadgary, Leeanna Hyacinth, Martin T. Ferris, Timothy A. Bell, Darla R. Miller, Paola Giusti-Rodriguez, Randal J. Nonneman, Kevin D. Cook, Jason K. Whitmire, Lisa E. Gralinski, Mark P. Keller, Alan D. Attie, Gary A. Churchill, Petko Petkov, Patrick F. Sullivan, Jennifer R. Brennan, Leonard McMillan & Fernando Pardo-Manuel De Villena
Genotyping microarrays are an important resource for genetic mapping, population genetics, and monitoring of the genetic integrity of laboratory stocks. We have developed the third generation of the Mouse Universal Genotyping Array (MUGA) series, GigaMUGA, a 143,259-probe Illumina Infinium II array for the house mouse (Mus musculus). The bulk of the content of GigaMUGA is optimized for genetic mapping in the Collaborative Cross and Diversity Outbred populations, and for substrain-level identification of laboratory mice. In...

Data from: Natural selection on floral morphology depends on climate

Diane R. Campbell & John M. Powers
Climate has the potential to influence evolution, but how it influences the strength or direction of natural selection is largely unknown. We quantified the strength of selection on four floral traits of the subalpine herb Ipomopsis sp. in 10 years that differed in precipitation, causing extreme temporal variation in the date of snowmelt in the Colorado Rocky Mountains. The chosen floral traits were under selection by hummingbird and hawkmoth pollinators, with hawkmoth abundance highly variable...

Data from: Hypothesis: a plastically-produced phenotype predicts host specialization and can precede subsequent mutations in bacteriophage

Colin S. Maxwell
The role of phenotypic plasticity in the evolution of new traits is controversial due to a lack of direct evidence. Phage host range becomes plastic in the presence of restriction-modification (R-M) systems in their hosts. I modeled the evolution of phage host range in the presence of R-M systems. The model makes two main predictions. The first prediction is that the offspring of the first phage to gain a new methylation pattern by infecting a...

Data from: Genomic scans reveal multiple mito‐nuclear incompatibilities in population crosses of the copepod Tigriopus californicus

Thiago G. Lima, Ronald S. Burton & Christopher Scott Willett
The evolution of intrinsic postzygotic isolation can be explained by the accumulation of Dobzhansky-Muller incompatibilities (DMI). Asymmetries in the levels of hybrid inviability and hybrid sterility are commonly observed between reciprocal crosses, a pattern that can result from the involvement of uniparentally inherited factors. The mitochondrial genome is one such factor that appears to participate in DMI in some crosses but the frequency of its involvement versus biparentally inherited factors is unclear. Here we assess...

Data from: A convolutional neural network for detecting sea turtles in drone imagery

Patrick C. Gray, Abram B. Fleishman, David J. Klein, Matthew W. McKown, Vanessa S. Bézy, Kenneth J. Lohmann & David W. Johnston
1. Marine megafauna are difficult to observe and count because many species travel widely and spend large amounts of time submerged. As such, management programs seeking to conserve these species are often hampered by limited information about population levels. 2. Unoccupied aircraft systems (UAS, aka drones) provide a potentially useful technique for assessing marine animal populations, but a central challenge lies in analyzing the vast amounts of data generated in the images or video acquired...

Data from: Bioprinted liver provides early insight into the role of Kupffer cells in TGF-β1 and methotrexate-induced fibrogenesis

Leah M. Norona, Deborah G. Nguyen, David A. Gerber, Sharon C. Presnell, Merrie Mosedale & Paul B. Watkins
Hepatic fibrosis develops from a series of complex interactions among resident and recruited cells making it a challenge to replicate using standard in vitro approaches. While studies have demonstrated the importance of macrophages in fibrogenesis, the role of Kupffer cells (KCs) in modulating the initial response remains elusive. Previous work demonstrated utility of 3D bioprinted liver to recapitulate basic fibrogenic features following treatment with fibrosis-associated agents. In the present study, culture conditions were modified to...

Data from: Using collision cones to assess biological deconfliction methods

Natalie L. Brace, Tyson L. Hedrick, Diane H. Theriault, Nathan W. Fuller, Zheng Wu, Margrit Betke, Julia K. Parrish, Daniel Grünbaum & Kristi A. Morgansen
Biological systems consistently outperform autonomous systems governed by engineered algorithms in their ability to reactively avoid collisions. To better understand this discrepancy, a collision avoidance algorithm was applied to frames of digitized video trajectory data from bats, swallows and fish (Myotis velifer, Petrochelidon pyrrhonota and Danio aequipinnatus). Information available from visual cues, specifically relative position and velocity, was provided to the algorithm which used this information to define collision cones that allowed the algorithm to...

Data from: An experimental investigation of how intraspecific competition and phenotypic plasticity can promote the evolution of novel, complex phenotypes

Nicholas Levis
Intraspecific competition has long been considered a key driver of evolutionary diversification, but whether it can also promote evolutionary innovation is less clear. We examined the interplay between competition and phenotypic plasticity in fueling the origins of a novel, complex phenotype––a distinctive carnivore morph found in spadefoot toad tadpoles (genus Spea) that specializes on fairy shrimp. We specifically sought to explore the possible origins of this phenotype by providing shrimp to Scaphiopus holbrookii tadpoles (the...

Temperature-dependent competitive outcomes between the fruit flies Drosophila santomea and D. yakuba

Aaron Comeault & Daniel Matute
We use these data to test whether temperature can indirectly affect the fitness of Drosophila santomea and D. yakuba by altering interspecific competitive outcomes. We show that, when raised in isolation, both D. santomea and D. yakuba display similar variation in relative fitness across temperatures of 18°C, 22°C, and 25°C. However, D. santomea has higher fitness than D. yakuba when experiencing interspecific competition at 18°C, while the inverse is true at 25°C. Patterns of fitness...

Data from: Challenges and solutions for analyzing dual RNA-seq data for non-model host/pathogen systems

Kayleigh R. O'Keeffe & Corbin D. Jones
1. Dual RNA-seq simultaneously profiles the transcriptomes of a host and pathogen during infection and may reveal the mechanisms underlying host-pathogen interactions. Dual RNA-seq is inherently a mixture of transcripts from at least two species (host and pathogen), so this mixture must be computationally sorted into host and pathogen components. Sorting relies on aligning reads to respective reference genomes, which may be unavailable for both species in non-model host-pathogen pairs. This lack of genomic resources...

Data from: A maladaptive combination of traits contributes to the maintenance of a Drosophila hybrid zone

Brandon S. Cooper, Alisa Sedghifar, W. Thurston Nash, Aaron A. Comeault & Daniel R. Matute
Drosophila teissieri and D. yakuba diverged approximately 3 mya and are thought to share a large, ancestral, African range [1, 2, 3]. These species now co-occur in parts of continental Africa and in west Africa on the island of Bioko [1, 4]. While D. yakuba is a human commensal, D. teissieri seems to be associated with Parinari fruits, restricting its range to forests [4, 5, 6]. Genome data indicate introgression, despite no evidence of contemporary...

Growth, stress and acclimation responses to fluctuating temperatures in field and domesticated populations of Manduca sexta

Joel Kingsolver, Joel Kingsolver, Megan Moore, Christina Hill & Kate Augustine
Diurnal fluctuations in temperature are ubiquitous in terrestrial environments, and insects and other ectotherms have evolved to tolerate or acclimate to such fluctuations. Few studies have examined whether ectotherms acclimate to diurnal temperature fluctuations, or how natural and domesticated populations differ in their responses to diurnal fluctuations. We examine how diurnally fluctuating temperatures during development affect growth, acclimation and stress responses for two populations of Manduca sexta: a field population that typically experiences wide variation...

Data on assessing the effects of genetic divergence and morphology on Anolis lizard mating

Emmanuel D'Agostino, Colin Donihue, Jonathan Losos & Anthony Geneva
The brown anole (Anolis sagrei) is a widespread neotropical lizard found on many islands in the West Indies as well as the coast of Central America. Across their range, brown anole populations show extensive ecomorphological trait variation and substantial genetic divergence. It is unclear, however, whether this genetic and morphological divergence results in reproductive isolation between populations. We investigated variation in mating behavior across populations by analyzing four hours of video of each of 234...

Data from: Folding wings like a cockroach: a review of transverse wing folding ensign wasps (Hymenoptera: Evaniidae: Afrevania and Trissevania)

István Mikó, Robert S. Copeland, James P. Balhoff, Matthew J. Yoder & Andrew R. Deans
We revise two relatively rare ensign wasp genera, whose species are restricted to Sub-Saharan Africa: Afrevania and Trissevania. Afrevania longipetiolata sp. nov., Trissevania heatherae sp. nov., T. hugoi sp. nov., T. mrimaensis sp. nov. and T. slideri sp. nov. are described, males and females of T. anemotis and Afrevania leroyi are redescribed, and an identification key for Trissevaniini is provided. We argue that Trissevania mrimaensis sp. nov. and T. heatherae sp. nov. populations are vulnerable,...

Data from: Metapopulation dominance and genomic-island acquisition of Bradyrhizobium with superior catabolic capabilities

Amanda C. Hollowell, John U. Regus, David Turissini, Kelsey A. Gano-Cohen, Roxanne Bantay, Andrew Bernardo, Devora Moore, Jonathan Pham & Joel L. Sachs
Root nodule forming rhizobia exhibit a bipartite lifestyle, replicating in soil and also within plant cells where they fix nitrogen for legume hosts. Host control models posit that legume hosts act as a predominant selective force on rhizobia, but few studies have examined rhizobial fitness in natural populations. Here, we genotyped and phenotyped Bradyrhizobium isolates across >800km of the native Acmispon strigosus host range. We sequenced chromosomal genes expressed under free-living conditions and accessory symbiosis...

Data from: Female and male life tables for seven wild primate species

Anne M. Bronikowski, Marina Cords, Susan C. Alberts, Jeanne Altmann, Diane K. Brockman, Linda M. Fedigan, Anne Pusey, Tara Stoinski, Karen B. Strier & William F. Morris
We provide male and female census count data, age-specific survivorship, and female age-specific fertility estimates for populations of seven wild primates that have been continuously monitored for at least 29 years: sifaka (Propithecus verreauxi) in Madagascar; muriqui (Brachyteles hypoxanthus) in Brazil; capuchin (Cebus capucinus) in Costa Rica; baboon (Papio cynocephalus) and blue monkey (Cercopithecus mitis) in Kenya; chimpanzee (Pan troglodytes) in Tanzania; and gorilla (Gorilla beringei) in Rwanda. Using one-year age-class intervals, we computed point...

Data from: High throughput functional genomics identifies modulators of TCE metabolite genotoxicity and candidate susceptibility genes

Vanessa Y. De La Rosa, Jonathan Asfaha, Michael Fasullo, Alex Loguinov, Peng Li, Lee E. Moore, Nathaniel Rothman, Jun Nakamura, James A. Swenberg, Ghislaine Scelo, Luoping Zhang, Martyn T. Smith & Chris D. Vulpe
Trichloroethylene (TCE), an industrial chemical and environmental contaminant, is a human carcinogen. Reactive metabolites are implicated in renal carcinogenesis associated with TCE exposure, yet the toxicity mechanisms of these metabolites and their contribution to cancer and other adverse effects remain unclear. We employed an integrated functional genomics approach that combined functional profiling studies in yeast and avian DT40 cell models to provide new insights into the specific mechanisms contributing to toxicity associated with TCE metabolites....

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