422 Works

Data from: Phylogenomic delineation of Physcomitrium (Bryophyta: Funariaceae) based on targeted sequencing of nuclear exons and their flanking regions rejects the retention of Physcomitrella, Physcomitridium and Aphanorrhegma

Rafael Medina, Matthew G. Johnson, Yang Liu, Norman J. Wickett, A. Jonathan Shaw & Bernard Goffinet
Selection on spore dispersal mechanisms in mosses is thought to shape the transformation of the sporophyte. The majority of extant mosses develop a sporangium that dehisces through the loss of an operculum, and regulates spore release through the movement of articulate teeth, the peristome, lining the capsule mouth. Such complexity was acquired by the Mesozoic Era, but was lost in some groups during subsequent diversification events, challenging the resolution of the affinities for taxa with...

Data from: Eulerian videography technology improves classification of sleep architecture in primates

Emilie M. Melvin, David R. Samson & Charles L. Nunn
Sleep is a critically important dimension of primate behavior, ecology, and evolution, yet primate sleep is under-studied because current methods of analyzing sleep are expensive, invasive, and time-consuming. In contrast to electroencephalography (EEG) and actigraphy, videography is a cost-effective and non-invasive method to study sleep architecture in animals. With video data, however, it is challenging to score subtle changes that occur in different sleep states, and technology has lagged behind innovations in EEG and actigraphy....

Notochord vacuoles absorb compressive bone growth during zebrafish spine formation

Jennifer Bagwell, James Norman, Kathryn Ellis, Brianna Peskin, James Hwang, Xiaoyan Ge, Stacy Nguyen, Sarah McMenamin, Didier Stanier & Michel Bagnat
The vertebral column or spine assembles around the notochord rod which contains a core made of large vacuolated cells. Each vacuolated cell possesses a single fluid-filled vacuole, and loss or fragmentation of these vacuoles in zebrafish leads to spine kinking. Here, we identified a mutation in the kinase gene dstyk that causes fragmentation of notochord vacuoles and a severe congenital scoliosis-like phenotype in zebrafish. Live imaging revealed that Dstyk regulates fusion of membranes with the...

Variation in frequency of plastid RNA editing within Adiantum (Pteridaceae) implies rapid evolution in fern plastomes

Blake Fauskee, Erin Sigel, Kathleen Pryer & Amanda Grusz
Premise Recent advances in studies of plant RNA editing have demonstrated that the number of editing sites can vary widely among large taxonomic groups (orders, families). Yet, very little is known about intrageneric variation in frequency of plant RNA editing, and no study has been conducted in ferns. Methods We determined plastid RNA editing counts for two species of Adiantum (Pteridaceae), A. shastense and A. aleuticum, by implementing a pipeline that integrated read mapping and...

Ocean acidification induces distinct transcriptomic responses across life history stages of the sea urchin Heliocidaris erythrogramma

Hannah Devens, Phillip Davidson, Dione Deaker, Kathryn Smith, Maria Byrne & Gregory Wray
Ocean acidification (OA) from seawater uptake of rising carbon dioxide emissions impairs development in marine invertebrates, particularly in calcifying species. Plasticity in gene expression is thought to mediate many of these physiological effects, but how these responses change across life history stages remains unclear. The abbreviated lecithotrophic development of the sea urchin Heliocidaris erythrogramma provides a valuable opportunity to analyze gene expression responses across a wide range of life history stages, including the benthic, post-metamorphic...

Morning glory species co-occurrence is associated with asymmetrically decreased and cascading reproductive isolation

Kate Ostevik, Joanna Rifkin, Hanhan Xia & Mark Rausher
Hybridization between species can affect the strength of the reproductive barriers that separate those species. Two extensions of this effect are: (1) the expectation that asymmetric hybridization or gene flow will have asymmetric effects on reproductive barrier strength and (2) the expectation that local hybridization will affect only local reproductive barrier strength and could therefore alter within-species compatibility. We tested these hypotheses in a pair of morning glory species that exhibit asymmetric gene flow from...

Code for: Threshold assessment, categorical perception, and the evolution of reliable signaling

James Peniston, Patrick Green, Matthew Zipple & Stephen Nowicki
Animals often use assessment signals to communicate information about their quality to a variety of receivers, including potential mates, competitors, and predators. But what maintains reliable signaling and prevents signalers from signaling a better quality than they actually have? Previous work has shown that reliable signaling can be maintained if signalers pay fitness costs for signaling at different intensities and these costs are greater for lower quality individuals than higher quality ones. Models supporting this...

Social bonds fail to mediate the connection between early adversity and fecal glucocorticoids in wild baboons

Shuxi Zeng
Code scripts for "Social bonds fail to mediate the connection between early adversity and fecal glucocorticoids in wild baboons ".

Data from: Social bonds do not mediate the relationship between early adversity and adult glucocorticoids in wild baboons

Stacy Rosenbaum, Shuxi Zeng, Fernando Campos, Laurence Gesquiere, Jeanne Altmann, Susan Alberts, Fan Li & Elizabeth Archie
In humans and other animals, harsh conditions in early life can have profound effects on adult physiology, including the stress response. This relationship may be mediated by a lack of supportive relationships in adulthood. That is, early life adversity may inhibit the formation of supportive social ties, and weak social support is itself often linked to dysregulated stress responses. Here we use prospective, longitudinal data from wild baboons in Kenya to test the links between...

Data from: Longitudinal recordings of the vocalizations of immature Gombe chimpanzees for developmental studies

Frans X. Plooij, Hetty Van De Rijt-Plooij, Martha Fischer & Anne Pusey
Many researchers are interested in chimpanzee vocal communication, both as an important aspect of chimpanzee social behavior and as a source of insights into the evolution of human language. Nonetheless, very little is known about how chimpanzee vocal communication develops from infancy to adulthood. The largest dataset of audiorecordings from free-living immature chimpanzees was collected by the late Hetty van de Rijt-Plooij and Frans X. Plooij at Gombe National Park, Tanzania (1971–1973). These recordings have...

Data from: Canine length in wild male baboons: maturation, aging and social dominance rank

Jordi Galbany, Jenny Tung, Jeanne Altmann & Susan C. Alberts
Canines represent an essential component of the dentition for any heterodont mammal. In primates, like many other mammals, canines are frequently used as weapons. Hence, tooth size and wear may have significant implications for fighting ability, and consequently for social dominance rank, reproductive success, and fitness. We evaluated sources of variance in canine growth and length in a well-studied wild primate population because of the potential importance of canines for male reproductive success in many...

Data from: Genome-wide evidence reveals that African and Eurasian Golden Jackals are distinct species

Klaus-Peter Koepfli, John Pollinger, Raquel Godinho, Jacqueline Robinson, Amanda Lea, Sarah Hendricks, Rena M. Schweizer, Olaf Thalmann, Pedro Silva, Zhenxin Fan, Andrey A. Yurchenko, Pavel Dobrynin, Alexey Makunin, James A. Cahill, Beth Shapiro, Francisco Álvares, José C. Brito, Eli Geffen, Jennifer A. Leonard, Kristofer M. Helgen, Warren E. Johnson, Stephen J. O'Brien, Blaire Van Valkenburgh & Robert K. Wayne
The golden jackal of Africa (Canis aureus) has long been considered a conspecific of jackals distributed throughout Eurasia, with the nearest source populations in the Middle East. However, two recent reports found that mitochondrial haplotypes of some African golden jackals aligned more closely to gray wolves (Canis lupus), which is surprising given the absence of gray wolves in Africa and the phenotypic divergence between the two species. Moreover, these results imply the existence of a...

Data from: Social and environmental impacts of forest management certification in Indonesia

Daniela A. Miteva, Colby J. Loucks & Subhrendu K. Pattanayak
In response to unsustainable timber production in tropical forest concessions, voluntary forest management certification programs such as the Forest Stewardship Council (FSC) have been introduced to improve environmental, social, and economic performance over existing management practices. However, despite the proliferation of forest certification over the past two decades, few studies have evaluated its effectiveness. Using temporally and spatially explicit village-level data on environmental and socio-economic indicators in Kalimantan (Indonesia), we evaluate the performance of the...

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: The origin and evolution of phototropins

Fay-Wei Li, Kathleen M. Pryer, Gane K.-S. Wong, Carl J. Rothfels, Michael Melkonian, Sarah Mathews, Juan C. Villarreal & Sean W. Graham
Plant phototropism, the ability to bend toward or away from light, is predominantly controlled by blue-light photoreceptors, the phototropins. Although phototropins have been well-characterized in Arabidopsis thaliana, their evolutionary history is largely unknown. In this study, we complete an in-depth survey of phototropin homologs across land plants and algae using newly available transcriptomic and genomic data. We show that phototropins originated in an ancestor of Viridiplantae (land plants + green algae). Phototropins repeatedly underwent independent...

Data from: A framework for detecting natural selection on traits above the species level

Kenneth B. Hoehn, Paul G. Harnik & V. Louise Roth
To what extent can natural selection act on groupings above the species level? Despite extensive theoretical discussion and growing practical concerns over increased rates of global ecological turnover, the question has largely evaded empirical resolution. A flexible and robust hypothesis-testing framework for detecting the phenomenon could facilitate significant progress in resolving this issue. We introduce a permutation-based approach, implemented in the R package perspectev, which provides an explicit test of whether empirical patterns of correlation...

Data from: Abortion legislation, maternal healthcare, fertility, female literacy, sanitation, violence against women, and maternal deaths: a natural experiment in 32 Mexican states

Elard Koch, Monique Chireau, Fernando Pliego, Joseph Stanford, Sebastián Haddad, Byron Calhoun, Paula Aracena, Miguel Bravo, Sebastián Gatica & John Thorp
Objective: To test whether there is an association between abortion legislation and maternal mortality outcomes after controlling for other factors thought to influence maternal health. Design: Population-based natural experiment. Setting and data sources: Official maternal mortality data from 32 federal states of Mexico between 2002 and 2011. Main outcomes: Maternal mortality ratio (MMR), MMR with any abortive outcome (MMRAO) and induced abortion mortality ratio (iAMR). Independent variables: Abortion legislation grouped as less (n=18) or more...

Data from: Exposure to mitochondrial genotoxins and dopaminergic neurodegeneration in Caenorhabditis elegans

Claudia P. Gonzalez-Hunt, Maxwell C. K. Leung, Rakesh K. Bodhicharla, Madeline G. McKeever, Andrew E. Arrant, Kathleen M. Margillo, Ian T. Ryde, Derek D. Cyr, Sara G. Kosmaczewski, Marc Hammarlund & Joel N. Meyer
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Data from: The extent and genetic basis of phenotypic divergence in life history traits in Mimulus guttatus

Jannice Friedman, Alex D. Twyford, John H. Willis & Benjamin K. Blackman
Differential natural selection acting on populations in contrasting environments often results in adaptive divergence in multivariate phenotypes. Multivariate trait divergence across populations could be caused by selection on pleiotropic alleles or through many independent loci with trait-specific effects. Here, we assess patterns of association between a suite of traits contributing to life history divergence in the common monkeyflower, Mimulus guttatus, and examine the genetic architecture underlying these correlations. A common garden survey of 74 populations...

Data from: Data-driven discovery of the spatial scales of habitat choice by elephants

Andrew F. Mashintonio, Stuart L. Pimm, Grant M. Harris, Rudi J. Van Aarde & Gareth J. Russell
Setting conservation goals and management objectives relies on understanding animal habitat preferences. Models that predict preferences combine location data from tracked animals with environmental information, usually at a spatial resolution determined by the available data. This resolution may be biologically irrelevant for the species in question. Individuals likely integrate environmental characteristics over varying distances when evaluating their surroundings; we call this the scale of selection. Even a single characteristic might be viewed differently at different...

Data from: Paternity analyses in wild-caught and lab-reared Caribbean cricket females reveal the influence of mating environment on post-copulatory sexual selection

Elen Oneal & L. Lacey Knowles
Polyandry is ubiquitous in insects and provides the conditions necessary for male- and female-driven forms of post-copulatory sexual selection to arise. Populations of Amphiacusta sanctaecrucis exhibit significant divergence in portions of the male genitalia that are inserted directly into the female reproductive tract, suggesting that males may exercise some post-copulatory control over fertilization success. We examine the potential for male-male and male-female post-copulatory interactions to influence paternity in wild-caught females of A. sanctaecrucis and contrast...

Data from: Genetic diversity, sexual condition, and microhabitat preference determine mating patterns in Sphagnum (Sphagnaceae) peat-mosses.

Matthew G. Johnson & A. Jonathan Shaw
In bryophytes, the possibility of intragametophytic selfing creates complex mating patterns that are not possible in seed plants, although relatively little is known about patterns of inbreeding in natural populations. In the peat-moss genus Sphagnum, taxa are generally bisexual (gametophytes produce both sperm and egg) or unisexual (gametes produced by separate male and female plants). We sampled populations of 14 species, aiming to assess inbreeding variation and inbreeding depression in sporophytes, and to evaluate correlations...

Data from: The contrasting phylodynamics of human influenza B viruses

Dhanasekaran Vijaykrishna, Edward C. Holmes, Udayan Joseph, Mathieu Fourment, Yvonne C. F. Su, Rebecca Halpin, Raphael T. C. Lee, Yi-Mo Deng, Vithiagaran Gunalan, Xudong Lin, Tim Stockwell, Nadia B. Fedorova, Bin Zhou, Natalie Spirason, Denise K. Kühnert, Veronika Bošková, Tanja Stadler, Anna-Maria Costa, Dominic E. Dwyer, Q. Sue Huang, Lance C. Jennings, William Rawlinson, Sheena G. Sullivan, Aeron C. Hurt, Sebastian Maurer-Stroh … & Raphael TC Lee
A complex interplay of viral, host and ecological factors shape the spatio-temporal incidence and evolution of human influenza viruses. Although considerable attention has been paid to influenza A viruses, a lack of equivalent data means that an integrated evolutionary and epidemiological framework has until now not been available for influenza B viruses, despite their significant disease burden. Through the analysis of over 900 full genomes from an epidemiological collection of more than 26,000 strains from...

Data from: The emergent geography of biophysical dispersal barriers across the Indo-West Pacific

Eric A. Treml, Jason Roberts, Patrick N. Halpin, Hugh P. Possingham & Cynthia Riginos
Aim: To discover and evaluate potential dispersal barriers across the Indo-West Pacific Ocean and to develop spatially explicit hypotheses regarding the location of barriers and their capacity to filter taxa. Additionally, to compare model predictions with previously described barriers and build a more thorough understanding of the region's biogeographic patterns. Location: The reefs of the Indo-West Pacific Ocean, from 100 to 170°E and from 30°N to 30°S. Methods: A biophysical larval dispersal model was used...

Data from: Diversity and evolution of the primate skin microbiome

Sarah E. Council, Amy M. Savage, Julie M. Urban, Megan E. Ehlers, J. H. Pate Skene, Michael L. Platt, Robert R. Dunn & Julie E. Horvath
Skin microbes play a role in human body odour, health and disease. Compared to gut microbes we know comparatively little about the changes in the composition of skin microbes in response to evolutionary changes in hosts, or more recent behavioral and cultural changes in humans. No studies have used sequence-based approaches to consider the skin microbe communities of gorillas and chimpanzees, for example. Comparison of the microbial associates of non-human primates with those of humans...

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