52 Works

Assessing the effects of elephant foraging on the structure and diversity of an Afrotropical forest

Cooper Rosin, Kendall Beals, Michael Belovitch, Ruby Harrison, Megan Pendred, Megan Sullivan, Nicolas Yao & John Poulsen
African forest elephants (Loxodonta cyclotis) are ecosystem engineers that browse and damage large quantities of vegetation during their foraging and movement. Though elephant trail networks and clearings are conspicuous features of many African forests, the consequences of elephant foraging for forest structure and diversity are poorly documented. In this study in northeastern Gabon, we compare stem size, stem density, proportional damage, species diversity, and species relative abundance of seedlings and saplings in the vicinity of...

Divergent evolution of mutation rates and biases in the long-term evolution experiment with Escherichia coli

Rohan Maddamsetti & Nkrumah A. Grant
Abstract All organisms encode enzymes that replicate, maintain, pack, recombine, and repair their genetic material. For this reason, mutation rates and biases also evolve by mutation, variation, and natural selection. By examining metagenomic time series of the Lenski long-term evolution experiment (LTEE) with Escherichia coli (Good, et al. 2017), we find that local mutation rate variation has evolved during the LTEE. Each LTEE population has evolved idiosyncratic differences in their rates of point mutations, indels,...

Identifying the fitness consequences of sex in complex natural environments

Catherine Rushworth, Yaniv Brandvain & Thomas Mitchell-Olds
In the natural world, sex prevails, despite its costs. While much effort has been dedicated to identifying the intrinsic costs of sex (e.g. the cost of males), few studies have identified the ecological fitness consequences of sex. Furthermore, correlated biological traits that differ between sexuals and asexuals may alter these costs, or even render the typical costs of sex irrelevant. We conducted a large-scale multi-site reciprocal transplant using multiple sexual and asexual genotypes of a...

Harnessing environmental Ca2+ for extracellular protein thermostabilization

Homme Hellinga & Malin Allert
Ca2+ is the third-most prevalent metal ion in the environment. EF hands are common Ca2+-binding motifs found in both extracellular and intracellular proteins of eukaryotes and prokaryotes. Cytoplasmic EF hand proteins often mediate allosteric control of signal transduction pathway components in response to intracellular Ca2+ concentration fluctuations by coupling Ca2+ binding to changes in protein structure. We show that an extracellular structural Ca2+-binding site mediates protein thermostabilization by such conformational coupling as well. Binding Ca2+...

Winner effects and switching assessment strategies facilitate fast and frugal decisions in territorial contests

Jason Dinh, Joshua Azza & S.N. Patek
Animals compete in contests over limited resources, and contestants with greater fighting ability, or resource holding potential (RHP), typically win contests. Contest strategies have evolved to balance contest costs with the benefit of winning resources. Sometimes, contestants decide to leave by estimating their opponent’s relative RHP . This strategy (mutual assessment) is cost-effective because it allows weaker opponents to leave contests against formidable opponents before accruing higher costs. However, acquiring reliable information can be costly....

Ancestral reconstruction of sunflower karyotypes reveals non-random chromosomal evolution

Kate Ostevik, Kieran Samuk & Loren Rieseberg
Mapping the chromosomal rearrangements between species can inform our understanding of genome evolution, reproductive isolation, and speciation. Here we present a novel algorithm for identifying regions of synteny in pairs of genetic maps, which is implemented in the accompanying R package, syntR. The syntR algorithm performs as well as previous methods while being systematic and repeatable and can be used to map chromosomal rearrangements in any group of species. In addition, we present a systematic...

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...

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...

Impacts of female body size on cannibalism and juvenile abundance in a dominant arctic spider

Amanda Koltz & Justin Wright
1. Body size influences an individual’s physiology and the nature of its intra- and interspecific interactions. Changes in this key functional trait can therefore have important implications for populations as well. For example, among invertebrates, there is typically a positive correlation between female body size and reproductive output. Increasing body size can consequently trigger changes in population density, population structure (e.g., adult to juvenile ratio), and the strength of intraspecific competition. 2. Body size changes...

A basic ddRADseq two-enzyme protocol performs well in herbarium and silica-dried tissues across four genera

Ingrid Jordon-Thaden, James Beck, Catherine Rushworth, Michael Windham, Nicolas Diaz, Jason Cantley, Chris Martine & Carl Rothfels
Premise of the study: The ability to sequence genome-scale data from herbarium specimens would allow for the economical development of broad datasets with taxonomic and geographic sampling not otherwise possible. Here we evaluate the utility of a basic restriction site-associated DNA (ddRADseq) protocol with DNAs from four genera extracted from both silica-dried and herbarium tissue. Methods: DNAs from Draba, Boechera, Solidago, and Ilex were processed with a double-digest restriction-site associated DNA sequencing (ddRADseq) protocol. The...

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...

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...

Primer catálogo de los árboles de la amazonía de Mardre De Dios, Perú

Abel Monteagudo Mendoza, Rodolfo Vásquez Martínez, Oliver L. Phillips, Timothy R. Baker, Hugo Dueñas Linares, Georgia C. Pickavance, Percy Núñez Vargas, Fernando Cornejo Valverde, John P. Janovec, John W. Terborgh, Miles R. Silman, Luis Valenzuela Gamarra, Robin B. Foster, Nadir Carolina Pallqui Camacho, William Farfán Ríos, Víctor Chama Moscoso, Sufer Báez Quispe, Isau Huamantupa Chuquimaco, Patricia Álvarez Loayza, Nigel Pitman & Lucero Alfaro Curitumay
La Amazonía abarca un área de aproximada de 6.8 millones km² situada en la parte norte de América del Sur (Eva et al., 2005). Los bosques húmedos cubren casi el 80% de la Amazonía (5.5 millones de km²) y el restante 20%, está cubierto por bosques secos (1%), bosques inundados (3%), herbazales y matorrales (5%), vegetación escasa (1%), así como por agricultura y áreas urbanas (10%). La región Madre de Dios, ha revelado altos niveles...

Reactionary Populism and the Historical Erosion of Democracy in America

Nancy Maclean, Aimee Imlay & Matthew Wentz
Nancy MacLean is the William H. Chafe Professor of History and Public Policy at Duke University, and the award-winning author of several books, including Behind the Mask of Chivalry: The Making of the Second Ku Klux Klan; Freedom is Not Enough: The Opening of the American Workplace; The American Women’s Movement, 1945-2000: A Brief History with Documents; and Debating the American Conservative Movement: 1945 to the Present. She also served the editor of Scalawag: A...

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...

Data from: Higher dominance rank is associated with lower glucocorticoids in wild female baboons: A rank metric comparison

Emily Levy, Laurence Gesquiere, Emily McLean, Mathias Franz, J Kinyua Warutere, Serah Sayialel, Raphael Mututua, Tim Wango, Vivian Oudu, Jeanne Altmann, Elizabeth Archie & Susan Alberts
In vertebrates, glucocorticoid secretion occurs in response to energetic and psychosocial stressors that trigger the hypothalamic-pituitary-adrenal (HPA) axis. Measuring glucocorticoid concentrations can therefore shed light on the stressors associated with different social and environmental variables, including dominance rank. Using 14,172 fecal samples from 237 wild female baboons, we test the hypothesis that high-ranking females experience fewer psychosocial and/or energetic stressors than lower-ranking females. We predicted that high-ranking females would have lower fecal glucocorticoid (fGC) concentrations...

Genomic and phenotypic evolution of Escherichia coli in a novel citrate-only resource environment

Zachary Blount, Rohan Maddamsetti, Nkrumah Grant, Sumaya Ahmed, Tanush Jagdish, Brooke Sommerfeld, Alice Tillman, Jeremy Moore, Jessica Baxter, Joan L Slonczewski, Jeffrey E Barrick & Richard E Lenski
Evolutionary innovations allow populations to colonize new ecological niches. We previously reported that aerobic growth on citrate (Cit+) evolved in an Escherichia coli population during adaptation to a minimal glucose medium containing citrate (DM25). Cit+ variants can also grow in citrate-only medium (DM0), a novel environment for E. coli. To study adaptation to this niche, we founded two sets of Cit+ populations and evolved them for 2500 generations in DM0 or DM25. The evolved lineages...

Data from: Genotypic variation in the induction and persistence of transgenerational responses to seasonal cues

Mariano Alvarez, Andrew Bleich & Kathleen Donohue
Phenotypes respond to environments experienced directly by an individual, via phenotypic plasticity, or to the environment experienced by ancestors, via transgenerational environmental effects. The adaptive value of environmental effects depends not only on the strength and direction of the induced response, but also on how long the response persists within and across generations, and how stably it is expressed across environments that are encountered subsequently. Little is known about the genetic basis of those distinct...

7,000 years of turnover: historical contingency and human niche construction shape the Caribbean’s Anthropocene biota

Melissa Kemp, Alexis Mychajliw, Jenna Wadman & Amy Goldberg
The human-mediated movement of species across biogeographic boundaries—whether intentional or accidental—is dramatically reshaping the modern world. Conservation biologists are grappling with the present-day effects of these introductions, but humans have in fact been reshaping ecosystems and translocating species for millennia. Acknowledging the effects of human-mediated species introductions through time is important for understanding present-day biodiversity loss, ecosystem functioning, and management needs. Here, we present the first database of terrestrial vertebrate species introductions spanning the entire...

Heterogeneous timing of asexual cycles in Plasmodium falciparum quantified by extended time-lapse microscopy

Heungwon Park, Shuqiang Huang, Katelyn Walzer, Lingchong You, Jen-Tsan Chi & Nicolas Buchler
Malarial fever arises from the synchronous bursting of human red blood cells by the Plasmodium parasite. The released parasites re-infect neighboring red blood cells and undergo another asexual cycle of differentiation and proliferation for 48 hours, before again bursting synchronously. The synchrony of bursting is lost during in vitro culturing of the parasite outside the human body, presumably because the asexual cycle is no longer entrained by host-specific circadian cues. Therefore, most in vitro malaria...

Data from: Phylogenetic structure in the Sphagnum recurvum complex (Bryophyta: Sphagnaceae) relative to taxonomy and geography

Aaron Duffy, Blanka Aguero, Hans Stenoien, Kjell Ivar Flatberg, Michael S. Ignatov, Kristian Hassel & Jonathan Shaw
METHODS RADseq analyses were applied to a sample of 384 collections representing the European, North American, and (to a lesser extent) Asian ranges of the complex. The data were subjected to maximum likelihood phylogenetic analyses and analyses of genetic structure using the software, STRUCTURE, and multivariate ordination approaches. RESULTS Defined phylogenetically, the S. recurvum complex includes S. angustifolium , S. fallax , S. flexuosum , S. pacificum , and S. recurvum , as distinct clades...

Natural selection shapes variation in genome-wide recombination rate in Drosophila pseudoobscura

Kieran Samuk, Brenda Manzano-Winkler, Kathryn R. Ritz & Mohamed A.F. Noor
While recombination is widely recognized to be a key modulator of numerous evolutionary phenomena, we have a poor understanding of how recombination rate itself varies and evolves within a species. Here, we performed a comprehensive study of recombination rate (rate of meiotic crossing over) in two natural populations of Drosophila pseudoobscura from Utah and Arizona, USA. We used an amplicon sequencing approach to obtain high-quality genotypes in approximately 8000 individual backcrossed offspring (17 mapping populations...

The evolution of sex is tempered by costly hybridization in Boechera (rock cress)

Catherine Rushworth & Tom Mitchell-Olds
Despite decades of research, the evolution of sex remains an enigma in evolutionary biology. Typically, research addresses the costs of sex and asexuality to characterize the circumstances favoring one reproductive mode. Surprisingly few studies address the influence of common traits that are, in many organisms, obligately correlated with asexuality, including hybridization and polyploidy. These traits have substantial impacts on traits under selection. In particular, the fitness consequences of hybridization (that is, reduced fitness due to...

Data from: Cryptic patterns of speciation in cryptic primates: microendemic mouse lemurs and the multispecies coalescent

Jelmer Poelstra, Jordi Salmona, George Tiley, Dominik Schüßler, Marina Blanco, Jean Andriambeloson, Olivier Bouchez, C. Ryan Campbell, Paul Etter, Amaia Iribar-Pelozuelo, Paul Hohenlohe, Kelsie Hunnicutt, Eric Johnson, Peter Kappeler, Peter Larsen, Sophie Manzi, Jose Ralison, Blanchard Randrianambinina, Rodin Rasoloarison, David Rasolofoson, Amanda Stahlke, David Weisrock, Rachel Williams, Lounes Chikhi, Ed Louis … & Anne Yoder
Species delimitation is ever more critical for assessing biodiversity in threatened regions of the world, especially when undescribed lineages may be at risk from habitat loss. Mouse lemurs (Microcebus) are an example of a rapid radiation of morphologically cryptic species that are distributed throughout Madagascar in its rapidly vanishing forested habitats. Here, we focus on two pairs of sister lineages that occur in a region in northeastern Madagascar that shows high levels of microendemism. We...

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