20 Works

Habitat transitions alter the adaptive landscape and shape phenotypic evolution in needlefishes (Belonidae)

Matthew Kolmann, Michael D. Burns, Justin Y. K. Ng, Nathan R. Lovjoy & Devin D. Bloom
Habitat occupancy can have a profound influence on macroevolutionary dynamics, and a switch in major habitat type may alter the evolutionary trajectory of a lineage. In this study we investigate how evolutionary transitions between marine and freshwater habitats affect macroevolutionary adaptive landscapes, using needlefishes (Belonidae) as a model system. We examined the evolution of body shape and size in marine and freshwater needlefishes and tested for phenotypic change in response to transitions between habitats. Using...

The geometry of resource constraint: an empirical study of the golden snub-nosed monkey

Rong Hou, Colin Chapman, Jessica Rothman, He Zhang, Kang Huang, Songtao Guo, Baoguo Li & David Raubenheimer
1. Apposite conceptualization and measurement of resource variation is critical for understanding many issues in ecology, including ecological niches, persistence and distribution of populations, the structure of communities, and population resilience to perturbations. 2. We apply the nutritional geometry framework to conceptualise and quantify the responses of a temperate-living primate, the golden snub-nosed monkey (Rhinopithecus roxellana) to variation in resource quality and quantity and in nutrient requirements associated with seasonal environments. 3. We present a...

Incipient speciation and secondary contact in a fossorial island endemic, the São Tomé caecilian

Kyle O'Connell, Ivan Prates, Lauren Scheinberg, Kevin Mulder & Rayna Bell
Secondary contact of lineages in the early stages of divergence can result in lineage fusion or promote reproductive isolation through reinforcement. While these processes are well studied in many taxonomic groups, we know little about their contribution to diversification of the secretive and enigmatic caecilians (Amphibia: Gymnophiona). Here, we combine genetic (mtDNA and genome-wide SNPs) and phenotypic data to investigate the divergence history of caecilians endemic to the oceanic island of São Tomé in the...

Assessing the feasibility of a rapid, high-volume cervical cancer screening program using HPV self-sampling and digital colposcopy in rural regions of Yunnan, China

Andrew Goldstein, Lena Goldstein, Roberta Lipson, Sarah Bedell, Jue Wang, Sarah Stamper, Gal Brenner, Gail Goldstein, Karen O'Keefe, S O'Keefe, McKenna O'Keefe, Tierney O'Keefe, Amelia Goldstein & Anna Zhao
Objective: Implementation of a novel, rapid, high-volume, see-and-treat cervical cancer screening program utilizing self-swab HPV testing and digital colposcopy in underserved regions of Yunnan China. Design: 500-1000 women per day self-swabbed for high-risk HPV (hrHPV+). Four careHPVTM machines (Qiagen) were run simultaneously to test the specimens. All hrHPV+ patients were contacted the same day and digital colposcopy (DC) was performed with the EVA system (MobileODT). Digital images were obtained, and all suspected lesions were biopsied...

Data from: Spatiotemporal dynamics of the ant community in a dry forest differ by vertical strata but not by successional stage

Frederico Neves, Reuber Antoniazzi, Flávio Camarota, Fábio Pacelhe & Scott Powell
Ants are diverse and ecologically important organisms in tropical forests, where their spatiotemporal distribution can be highly complex. This complexity arises mainly from marked differences in microclimatic conditions and resource availability through space and time that is even more evident in highly seasonal environments, such as tropical dry forests. However, it is unclear how seasonality interacts with other factors that might shape temporal variation of ant composition (β-diversity), like vertical strata and habitat disturbance. Our...

Data from: Cold and hungry: combined effects of low temperature and resource scarcity on an edge-of-range temperate primate, the golden snub-nose monkey

Rong Hou, Colin A. Chapman, Ollie Jay, Songtao Guo, Baoguo Li & David Raubenheimer
Both biotic and abiotic factors play important roles in influencing ecological distributions and niche limits. Where biotic and abiotic stressors co-occur in space and time, homeostatic systems face a different category of challenge in which stressors compound to impose a challenge that is greater than the sum of the separate factors. We studied the homeostatic strategies of the golden snub-nosed monkey (Rhinopithecus roxellana), a species living in temperate deciduous forests at the edge of the...

Gregariousness, foraging effort, and social interactions in lactating bonobos and chimpanzees

Sean Lee, Gottfried Hohmann, Elizabeth Lonsdorf, Barbara Fruth & Carson Murray
Fission-fusion dynamics have evolved in a broad range of animal taxa and are thought to allow individuals to mitigate feeding competition. While this is the principal benefit of fission-fusion, few studies have evaluated its costs. We compared gregariousness, foraging budgets, and social budgets between lactating bonobos and chimpanzees from wild populations to evaluate such costs. Both species exhibit fission-fusion dynamics, but chimpanzees, particularly in East African populations, appear to experience higher feeding competition than bonobos....

Data From: TERRA-REF, An open reference data set from high resolution genomics, phenomics, and imaging sensors

David LeBauer, Burnette Maxwell, Jeffrey Demieville, Noah Fahlgren, Andrew French, Roman Garnett, Zhenbin Hu, Kimberly Huynh, Rob Kooper, Zongyang Li, Maitiniyazi Maimaitijiang, Jerome Mao, Todd Mockler, Geoffrey Morris, Maria Newcomb, Michael Ottman, Philip Ozersky, Sidike Paheding, Duke Pauli, Robert Pless, Wei Qin, Kristina Riemer, Gareth Rohde, William Rooney, Vasit Sagan … & Charles Zender
The ARPA-E funded TERRA-REF project is generating open-access reference datasets for the study of plant sensing, genomics, and phenomics. Sensor data were generated by a field scanner sensing platform that captures color, thermal, hyperspectral, and active flourescence imagery as well as three dimensional structure and associated environmental measurements. This dataset is provided alongside data collected using traditional field methods in order to support calibration and validation of algorithms used to extract plot level phenotypes from...

Allometric escape from acoustic constraints in frog calls is rare

Joao Filipe Tonini, Diogo Provete, Natan Maciel, Alessandro Morais, Sandra Goutte, Felipe Toledo & R. Alexander Pyron
Allometric constraint is a product of natural selection, particularly with respect to body size and traits constrained by physical properties thereof, such as metabolism, longevity, and vocal frequency. Parameters describing allometric relationships are conserved across most lineages, indicating that physical constraints dictate scaling patterns in deep time, despite substantial genetic and ecological divergence among organisms. Acoustic allometry (sound frequency ~ body size) is conserved across frogs, in defiance of massive variation in both body size...

Genetic algorithm-based personalized models of human cardiac action potential

Roman Syunyaev, Igor Efimov, Kedar Aras, Anna Gams, Aaron Koppel, Oleg Gusev, Andrey Pikunov & Ruslan Deviatiiarov
We present a novel modification of genetic algorithm (GA) which determines personalized parameters of cardiomyocyte electrophysiology model based on set of experimental human action potential (AP) recorded at different heart rates. In order to find the steady state solution, the optimized algorithm performs simultaneous search in the parametric and slow variables spaces. We demonstrate that several GA modifications are required for effective convergence. Firstly, we used a mutation operator, based on Cauchy amplitude distribution along...

Data from: Phylogenomic data reveal reticulation and incongruence among mitochondrial candidate species in Dusky Salamanders (Desmognathus)

Robert Alexander Pyron, Kyle A. O'Connell, Emily Moriarty Lemmon, Alan R. Lemmon & David A. Beamer
Gene flow between evolutionarily distinct lineages is increasingly recognized as a common occurrence. Such processes distort our ability to diagnose and delimit species, as well as confound attempts to estimate phylogenetic relationships. A conspicuous example is Dusky Salamanders (Desmognathus), a common model-system for ecology, evolution, and behavior. Only 22 species are described; 7 in the last 40 years. However, mitochondrial datasets indicate the presence of up to 45 “candidate species” presenting a complex history of...

Detection of prey odors underpins dietary specialization in a Neotropical top-predator: how army ants find their ant prey

John Manubay & Scott Powell
1. Deciphering the mechanisms that underpin dietary specialization and niche partitioning is crucial to understanding the maintenance of biodiversity. New world army ants live in species-rich assemblages throughout the Neotropics and are voracious predators of other arthropods. They are therefore an important and potentially informative group for addressing how diverse predator assemblages partition available prey resources. 2. New World army ants are largely specialist predators of other ants, with each species specializing on different ant...

Data from: Convergent evolution of broadband reflectors underlies metallic colorations in butterflies

Christopher Day, Anna Ren, Arnaud Martin & Joseph Hanly
Supplementary Files for Ren, Day et al. 2020 : Convergent evolution of broadband reflectors underlies metallic coloration in butterflies

Data from: Integration of genomics and transcriptomics predicts diabetic retinopathy susceptibility genes

Andrew Skol, Segun Jung, Ana Marija Sokovic, Siquan Chen, Sarah Fazal, Olukayode Sosina, Poulami Borkar, Amy Lin, Maria Sverdlov, Dingcai Cao, Anand Swaroop, Ionut Bebu, Barbara Stranger & Michael Grassi
We determined differential gene expression in response to high glucose in lymphoblastoid cell lines derived from matched individuals with type 1 diabetes with and without retinopathy. Those genes exhibiting the largest difference in glucose response were assessed for association to diabetic retinopathy in a genome-wide association study meta-analysis. Expression Quantitative Trait Loci (eQTLs) of the glucose response genes were tested for association with diabetic retinopathy. We detected an enrichment of the eQTLs from the glucose...

Data from: Specialized breeding in plants affects diversification trajectories in Neotropical frogs

Joao Filipe Tonini, Rodrigo Ferreira & R. Alexander Pyron
Many animals breed exclusively in plants that accumulate rainwater (phytotelma; e.g., bromeliad, bamboo, fruit husk, and tree hole), to which they are either physiologically or behaviorally specialized for this microhabitat. Of the numerous life-history modes observed in frogs, few are as striking or potentially consequential as the transition from pond- or stream-breeding to the deposition of eggs or larvae in phytotelmata. Such specialization can increase offspring survivorship due to reduced competition and predation, representing potential...

Data from: Does facial hair greying in chimpanzees provide a salient progressive cue of aging?

Elizabeth Tapanes, Jason Kamilar, Brenda Bradley & Stephanie Anestis
The greying of human head hair is arguably the most salient marker of human aging. In wild mammal populations, greying can change with life history or environmental factors (e.g., sexual maturity in silverback gorillas). Yet, whether humans are unique in our pattern of age-related hair depigmentation is unclear. We examined the relationship between pigmentation loss in facial hair (greying) to age, population, and sex in wild and captive chimpanzees (Pan troglodytes). Digital facial photographs representing...

Data from: Hemiptera phylogenomic resources: tree-based orthology prediction and conserved exon identification

Christopher Owen, David Stern, Sarah Hilton & Keith Crandall
High-throughput sequencing of transcriptomes and targeted genomic regions are advancing our knowledge of The Tree of Life. Building phylogenies with regions of the genome requires 1-to-1 ortholog resources of genes and non-coding loci. One organismal group that has received little attention in this area is the Hemiptera, the fifth largest insect order represented by approximately 103,590 named species. Here, we present a set of 3,872 Hemiptera 1-to-1 orthogroups based on tree-based orthology inference of 8...

Active modification of cavity nest-entrances is a common strategy in arboreal ants

Flávio Camarota, Galen V. Priest, Flávio Camarota, Heraldo Vasconcelos, Scott Powell & Robert J. Marquis.
The majority of tropical arboreal ant species nest in tree cavities. These cavities, often produced initially by wood-boring beetles, can be in live or dead wood and represent long-lasting and highly defensible nesting resources. Yet the size of cavity entrances can constrain their use. Active entrance modification may be an effective way to overcome this constraint. Here, we conduct the first systematic study of nest-entrance modification in an arboreal ant community. Using field experiments deployed...

How female × male and male × male interactions influence competitive fertilization in Drosophila melanogaster

Stefan Lüpold, Jonathan Reil, Mollie Manier, Valérian Zeender, John Belote & Scott Pitnick
How males and females contribute to joint reproductive success has been a long-standing question in sexual selection. Under postcopulatory sexual selection (PSS), paternity success is predicted to derive from complex interactions among females engaging in cryptic female choice and males engaging in sperm competition. Such interactions have been identified as potential sources of genetic variation in sexually selected traits but are also expected to inhibit trait diversification. To date, studies of interactions between females and...

Factors associated with attitudes toward HIV cure research among transgender women and travestis: a cross-sectional survey in São Paulo, Brazil

Robert Wozniak, Cerqueira Natalia, Dantas Maria, Bianca Mahafe, Daniel Barros, Edmilson Alves De Medeiros, Ana Soares De Oliveira, Thiago Sabino, Albert Roggenbuck, Vivian Avelino-Silva, Carrie Johnston, Jez Marston, Sebastian Bidegain, Manya Magnus, Esper Kallas, Douglas Nixon & Camila Donini
Objective: Characterizing the perceptions of groups most affected by HIV is fundamental in establishing guidelines for biomedical advancement. Although Brazil has successfully fought HIV/AIDS through several measures, transgender women still have a likelihood of HIV infection 55 times higher than the general population. This study aimed to better understand the perception and awareness of HIV cure research among the trans-identifying population in São Paulo, Brazil, and to determine factors that motivate or discourage participation in...

Registration Year

  • 2020

Resource Types

  • Dataset


  • George Washington University
  • Northwest University
  • Agricultural Research Service
  • University of Sydney
  • Harvard University
  • Universidade Federal de Viçosa
  • Donald Danforth Plant Science Center
  • Northwestern University
  • Universidade Federal de Goiás
  • City University of New York