63 Works

Data from: Convergent evolution of alternative developmental trajectories associated with diapause in African and South American killifish

Andrew I. Furness, David N. Reznick, Mark S. Springer, Robert W. Meredith, A. I. Furness, D. N. Reznick, M. S. Springer & R. W. Meredith
Annual killifish adapted to life in seasonally ephemeral water-bodies exhibit desiccation resistant eggs that can undergo diapause, a period of developmental arrest, enabling them to traverse the otherwise inhospitable dry season. Environmental cues that potentially indicate the season can govern whether eggs enter a stage of diapause mid-way through development or skip this diapause and instead undergo direct development. We report, based on construction of a supermatrix phylogenetic tree of the order Cyprinodontiformes and a...

Data from: Maximally informative foraging by Caenorhabditis elegans

Adam J. Calhoun, Sreekanth H. Chalasani, Tatyana O. Sharpee, Adam J Calhoun, Tatyana O Sharpee & Sreekanth H Chalasani
Animals have evolved intricate search strategies to find new sources of food. Here, we analyze a complex food seeking behavior in the nematode Caenorhabditis elegans (C. elegans) to derive a general theory describing different searches. We show that C. elegans, like many other animals, uses a multi-stage search for food, where they initially explore a small area intensively (‘local search’) before switching to explore a much larger area (‘global search’). We demonstrate that these search...

Data from: Passively stuck: death does not affect gecko adhesion strength

William J. Stewart, Timothy E. Higham, T. E. Higham & W. J. Stewart
Many geckos use adhesive toe pads on the bottom of their digits to attach to surfaces with remarkable strength. Although gecko adhesion has been studied for hundreds of years, gaps exist in our understanding at the whole-animal level. It remains unclear whether the strength and maintenance of adhesion are determined by the animal or are passively intrinsic to the system. Here we show, for the first time, that strong adhesion is produced passively at the...

Data from: Gene flow between nascent species: geographic, genotypic and phenotypic differentiation within and between Aquilegia formosa and A. pubescens.

Christos Noutsos, Justin O. Borevitz, Scott A. Hodges, J. O. Borevitz, C. Noutsos & S. A. Hodges
Speciation can be described as a reduction, and the eventual cessation, in the ability to interbreed. Thus, determining how gene flow differs within and between nascent species can illuminate the relative stage the taxa have attained in the speciation process. Aquilegia formosa and A. pubescens are fully intercompatible yet occur in different habitats and have flowers specialized for pollination by hummingbirds and hawkmoths respectively. Using 79 SNP loci we genotyped nearly 1,000 individuals from populations...

Data from: Geckos significantly alter foot orientation to facilitate adhesion during downhill locomotion

Aleksandra V. Birn-Jeffery, Timothy E. Higham & A. V. Birn-Jeffery
Geckos employ their adhesive system when moving up an incline, but the directionality of the system may limit function on downhill surfaces. Here, we use a generalist gecko to test whether limb modulation occurs on downhill slopes to allow geckos to take advantage of their adhesive system. We examined three-dimensional limb kinematics for geckos moving up and down a 45° slope. Remarkably, the hind limbs were rotated posteriorly on declines, resulting in digit III of...

Data from: Assembly of root-associated bacteria communities: interactions between abiotic and biotic factors

Sarah L. Dean, Emily C. Farrer, Andrea Porras-Alfaro, Katharine N. Suding, Robert L. Sinsabaugh, Sarah L Dean, Robert L Sinsabaugh, Emily C Farrer & Katharine N Suding
Nitrogen (N) deposition in many areas of the world is over an order of magnitude greater than it would be in absence of human activity. We ask how abiotic (N) and biotic (plant host and neighborhood) effects interact to influence root-associated bacterial (RAB) community assembly. Using 454 pyrosequencing, we examined RAB communities from two dominant alpine tundra plants, Geum rossii and Deschampsia cespitosa, under control, N addition and D. cespitosa removal treatments, implemented in a...

Data from: Species delimitation in the ground beetle subgenus Liocosmius (Coleoptera: Carabidae: Bembidion), including standard and next-generation sequencing of museum specimens

David R. Maddison & Kenneth W. Cooper
The species of subgenus Liocosmius Casey of genus Bembidion Latreille are delimited and documented using DNA sequences from eight genes, morphological data, and geography. The subgenus consists of six known species, three of which are described as new: Bembidion orion Cooper and Maddison (California), B. darlingtonielum Cooper and Maddison (California), and B. cooperi Maddison (New Mexico and Arizona). The group ranges from British Columbia south to Baja California, and east to Colorado and New Mexico,...

Data from: Size, shape, and systematics of the Silurian trilobite Aulacopleura koninckii

Paul S. Hong, Nigel C. Hughes & H. David Sheets
A new dataset of the highest quality specimens of fully articulated, juvenile and mature exoskeletons of the Czech middle Silurian trilobite Aulacopleura koninckii offers improved resolution of original morphology by all measures considered. The degree of variation in both size and shape among later meraspid instars was constant, and suggesting targeted growth in both attributes. Size-related changes in the shape of the dorsal exoskeleton and of the segment-invariant cephalon were detected in the meraspid stage,...

Data from: A hybrid phylogenetic–phylogenomic approach for species tree estimation in African Agama lizards with applications to biogeography, character evolution, and diversification

Adam D. Leaché, Philipp Wagner, Charles W. Linkem, Wolfgang Böhme, Theodore J. Papenfuss, Rebecca A. Chong, Brian R. Lavin, Aaron M. Bauer, Stuart V. Nielsen, Eli Greenbaum, Mark-Oliver Rödel, Andreas Schmitz, Matthew LeBreton, Ivan Ineich, Laurent Chirio, Caleb Ofori-Boateng, Edem A. Eniang, Sherif Baha El Din, Alan R. Lemmon & Frank T. Burbrink
Africa is renowned for its biodiversity and endemicity, yet little is known about the factors shaping them across the continent. African Agama lizards (45 species) have a pan-continental distribution, making them an ideal model for investigating biogeography. Many species have evolved conspicuous sexually dimorphic traits, including extravagant breeding coloration in adult males, large adult male body sizes, and variability in social systems among colorful versus drab species. We present a comprehensive time-calibrated species tree for...

Data from: Controlling meiotic recombinational repair: specifying the roles of ZMMs, Sgs1 and Mus81/Mms4 in crossover formation

Ashwini Oke, Carol M. Anderson, Phoebe Yam & Jennifer C. Fung
Crossovers (COs) play a critical role in ensuring proper alignment and segregation of homologous chromosomes during meiosis. How the cell balances recombination between CO vs. noncrossover (NCO) outcomes is not completely understood. Further lacking is what constrains the extent of DNA repair such that multiple events do not arise from a single double-strand break (DSB). Here, by interpreting signatures that result from recombination genome-wide, we find that synaptonemal complex proteins promote crossing over in distinct...

Data from: Range-wide multilocus phylogeography of the red fox reveals ancient continental divergence, minimal genomic exchange, and distinct demographic histories

Mark J. Statham, Zhenghuan Wang, Carl D. Soulsbury, Jan Janecka, Benjamin N. Sacks, Keith B. Aubry, Oliver Berry, Ceiridwen J. Edwards & James Murdoch
Widely distributed taxa provide an opportunity to compare biogeographic responses to climatic fluctuations on multiple continents and to investigate speciation. We conducted the most geographically and genomically comprehensive study to date of the red fox (Vulpes vulpes), the world's most widely distributed wild terrestrial carnivore. Analyses of 697 bp of mitochondrial sequence in ~1000 individuals suggested an ancient Middle Eastern origin for all extant red foxes and a 400 kya (SD = 139 kya) origin...

Data from: Species distribution models of an endangered rodent offer conflicting measures of habitat quality at multiple scales

William T. Bean, R. Stafford, H. Scott Butterfield, Laura R. Prugh, Michael Westphal & Justin S. Brashares
1. The high cost of directly measuring habitat quality has led ecologists to test alternate methods for estimating and predicting this critically important ecological variable. In particular, it is frequently assumed but rarely tested that models of habitat suitability (“species distribution models”, SDMs) may provide useful indices of habitat quality, either from an individual animal or manager’s perspective. Critically, SDMs are increasingly used to estimate species’ ranges, with an implicit assumption that areas of high...

Data from: Patterns of selection on Plasmodium falciparum erythrocyte binding antigens after the colonisation of the New World

Erhan Yalcindag, Virginie Rougeron, Eric Elguero, Céline Arnathau, Patrick Durand, Sylvain Brisse, Laure Diancourt, Agnes Aubouy, Pierre Becquart, Umberto D'Alessandro, Didier Fontenille, Dionicia Gamboa, Amanda Maestre, Didier Ménard, Lise Musset, Oscar Noya, Vincent Veron, Albina Wide, Bernard Carme, Eric Legrand, Christine Chevillon, Francisco J. Ayala, François Renaud & Franck Prugnolle
Pathogens, which have recently colonized a new host species or new populations of the same host, are interesting models for understanding how populations may evolve in response to novel environments. During its colonization of South America from Africa Plasmodium falciparum, the main agent of malaria, has been exposed to new conditions in distinctive new human populations (Amerindian and populations of mixed origins), that likely exerted new selective pressures on the parasite's genome. Among the genes...

Data from: Muscle tradeoffs in a power-amplified prey capture system

S. N. Patek, M. Mendoza Blanco & M. Mendoza Blanco
Should animals operating at great speeds and accelerations use fast or slow muscles? The answer hinges on a fundamental tradeoff: muscles can be maximally fast or forceful, but not both. Direct lever systems offer a straightforward manifestation of this tradeoff, yet the fastest organisms use power amplification, not direct lever action. Power-amplified systems typically use slow, forceful muscles to pre-load springs which then rapidly release elastic potential energy to generate high speeds and accelerations. However,...

Data from: Niche and range size patterns suggest that speciation begins in small, ecologically diverged populations in North American monkeyflowers (Mimulus spp.)

Dena Louise Grossenbacher, Samuel D. Veloz, Jason P. Sexton & Dena L. Grossenbacher
Closely related species (e.g., sister taxa) often occupy very different ecological niches and can exhibit large differences in geographic distributions despite their shared evolutionary history. Budding speciation is one process that may partially explain how differences in niche and distribution characteristics may rapidly evolve. Budding speciation is the process through which new species form as initially small colonizing populations that acquire reproductive isolation. This mode of species formation predicts that, at the time of speciation,...

Data from: The splicing regulator PTBP2 controls a program of embryonic splicing required for neuronal maturation

Qin Li, Sika Zheng, Areum Han, Chia-Ho Lin, Peter Stoilov, Xiang-Dong Fu, Douglas L. Black & Douglas L Black
We show that the splicing regulator PTBP2 controls a genetic program essential for neuronal maturation. Depletion of PTBP2 in developing mouse cortex leads to degeneration of these tissues over the first three postnatal weeks, a time when the normal cortex expands and develops mature circuits. Cultured Ptbp2−/− neurons exhibit the same initial viability as wild type, with proper neurite outgrowth and marker expression. However, these mutant cells subsequently fail to mature and die after a...

Data from: Hybridization at an ecotone: ecological and genetic barriers between three Iberian vipers

Pedro Tarroso, Ricardo J. Pereira, Fernando Martínez-Freiría, Raquel Godinho & José Carlos Brito
The formation of stable genetic boundaries between emerging species is often diagnosed by reduced hybrid fitness relative to parental taxa. This reduced fitness can arise from endogenous and/or exogenous barriers to gene flow. Although detecting exogenous barriers in nature is difficult, we can estimate the role of ecological divergence in driving species boundaries by integrating molecular and ecological niche modelling tools. Here, we focus on a three-way secondary contact zone between three viper species (Vipera...

Data from: Chromatin signature of widespread monoallelic expression

Anwesha Nag, Virginia Savova, Ho-Lim Fung, Alexander Miron, Guo-Cheng Yuan, Kun Zhang, Alexander Gimelbrant & Alexander A Gimelbrant
In mammals, numerous autosomal genes are subject to mitotically stable monoallelic expression (MAE), including genes that play critical roles in a variety of human diseases. Due to challenges posed by the clonal nature of MAE, very little is known about its regulation; in particular, no molecular features have been specifically linked to MAE. Here we report an approach that distinguishes MAE genes in human cells with great accuracy: a chromatin signature consisting of chromatin marks...

Data from: Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera

Brant C. Faircloth, Michael G. Branstetter, Noor D. White & Séan G. Brady
Gaining a genomic perspective on phylogeny requires the collection of data from many putatively independent loci across the genome. Among insects, an increasingly common approach to collecting this class of data involves transcriptome sequencing, because few insects have high-quality genome sequences available; assembling new genomes remains a limiting factor; the transcribed portion of the genome is a reasonable, reduced subset of the genome to target; and the data collected from transcribed portions of the genome...

Data from: An experimental test of the testosterone mediated oxidation handicap hypothesis in a wild bird

Conor C. J. Taff, Corey R. Freeman-Gallant & Conor C. Taff
The oxidation handicap hypothesis (OHH) proposed that honesty in sexual signals is maintained when testosterone simultaneously promotes the development of elaborate signals and imposes an oxidative cost. Although there is evidence that testosterone enhances display traits in some cases, relatively few studies have tested the prediction that testosterone generates oxidative costs. We tested this prediction experimentally by administering testosterone (n = 14) and control (n = 14) implants to free-living common yellowthroat warblers (Geothlypis trichas)...

Data from: New host and lineage diversity of avian haemosporidia in the Northern Andes

Ryan J. Harrigan, Raul Sedano, Anthony C. Chasar, Jaime A. Chaves, Jennifer T. Nguyen, Alexis Whitaker & Thomas B. Smith
The northern Andes, with their steep elevational and climate gradients, are home to an exceptional diversity of flora and fauna, particularly rich in avian species that have adapted to divergent ecological conditions. With this diversity comes the opportunity for parasites to exploit a wide breadth of avian hosts. However, little research has focused on examining the patterns of prevalence and lineage diversity of avian parasites in the Andes. Here, we screened a total of 428...

Data from: Shotgun microbial profiling of fossil remains

Clio Der Sarkissian, Luca Ermini, Hákon Jónsson, Anatoly N. Alekseev, Éric Crubézy, Beth Shapiro & Ludovic Orlando
Millions to billions of DNA sequences can now be generated from ancient skeletal remains thanks to the massive throughput of next-generation sequencing platforms. Except in cases of exceptional endogenous DNA preservation, most of the sequences isolated from fossil material do not originate from the specimen of interest, but instead reflect environmental organisms that colonized the specimen after death. Here, we characterize the microbial diversity recovered from seven ca. 200-13,000 year old horse bones collected from...

Data from: Rapid diversification of sexual signals in Hawaiian Nesosydne planthoppers (Hemiptera: Delphacidae): the relative role of neutral and selective forces

Kari Roesch Goodman, J. Patrick Kelley, Stephen Welter, George K. Roderick, Damian O. Elias, S. C. Welter, J. P. Kelley, K. R. Goodman, G. K. Roderick & D. O. Elias
Changes in sexual signals have the potential to promote rapid divergence and reproductive isolation among populations of animals. Thus, identifying processes contributing to variation in signals is key to understanding the drivers of speciation. However, it is difficult to identify the processes initiating changes in signals in empirical systems because (1) the demographic history of populations under study is usually unclear, and (2) there is no unified hypothesis-testing framework for evaluating the simultaneous contribution of...

Data from: Cold adaptation shapes the robustness of metabolic networks in Drosophila melanogaster.

Caroline Margaret Williams, Miki Watanabe, Mario R. Guarracino, Maria Brigida Ferraro, Arthur S. Edison, Theodore J. Morgan, Arezue F. B. Boroujerdi, Dan A. Hahn, Caroline M. Williams, Maria B. Ferraro & Daniel A. Hahn
When ectotherms are exposed to low temperatures, they enter a cold-induced coma (chill coma) that prevents resource acquisition, mating, oviposition, and escape from predation. There is substantial variation in time taken to recover from chill coma both within and among species, and this variation is correlated with habitat temperatures such that insects from cold environments recover more quickly. This suggests an adaptive response, but the mechanisms underlying variation in recovery times are unknown, making it...

Data from: Human-induced biotic invasions and changes in plankton interaction networks

Pavel Kratina, Ralph Mac Nally, James R. Thomson, Wim J. Kimmerer & Monika Winder
1.Pervasive and accelerating changes to ecosystems due to human activities remain major sources of uncertainty in predicting the structure and dynamics of ecological communities. Understanding which biotic interactions within natural multitrophic communities are threatened or augmented by invasions of non-native species in the context of other environmental pressures is needed for effective management. 2.We used multivariate autoregressive models with detailed time-series data from largely freshwater and brackish regions of the upper San Francisco Estuary to...

Registration Year

  • 2014

Resource Types

  • Dataset


  • University of California System
  • University of Western Australia
  • Australian National University
  • University of British Columbia
  • University of California, Los Angeles
  • Cornell University
  • Duke University
  • University of Georgia
  • University of Minnesota
  • Southwest Fisheries Science Center
  • French National Centre for Scientific Research
  • Humboldt State University
  • Paul Sabatier University
  • University of Florida
  • University of Calgary