39 Works

Data from: De novo assembly and characterization of the transcriptome of the parasitic weed Cuscuta pentagona identifies genes associated with plant parasitism

Aashish Ranjan, Yasunori Ichihashi, Moran Farhi, Kristina Zumstein, Brad Townsley, Rakefet David-Schwartz, Neelima R. Sinha, A. Ranjan, Y. Ichihashi, M. Farhi, K. Zumstein, B. Townsley, R. David-Schwartz & N. R. Sinha
Parasitic flowering plants are one of the most destructive agricultural pests and have major impact on crop yields throughout the world. Being dependent on finding a host plant for growth, parasitic plants penetrate their host using specialized organs called haustoria. Haustoria establish vascular connections with the host, which enable the parasite to steal nutrients and water. The underlying molecular and developmental basis of parasitism by plants is largely unknown. In order to investigate the process...

Data from: The rise of army ants and their relatives: diversification of specialized predatory doryline ants

Sean G. Brady, Brian L. Fisher, Ted R. Schultz & Philip S. Ward
Background Army ants are dominant invertebrate predators in tropical and subtropical terrestrial ecosystems. Their close relatives within the dorylomorph group of ants are also highly specialized predators, although much less is known about their biology. We analyzed molecular data generated from 11 nuclear genes to infer a phylogeny for the major dorylomorph lineages, and incorporated fossil evidence to infer divergence times under a relaxed molecular clock. Results Because our results indicate that one subfamily and...

Data from: Why is Madagascar special? The extraordinarily slow evolution of pelican spiders (Araneae, Archaeidae)

Hannah Marie Wood, Rosemary G. Gillespie, Charles E. Griswold, Peter C. Wainwright & Hannah M. Wood
Although Madagascar is an ancient fragment of Gondwana, the majority of taxa studied thus far appear to have reached the island through dispersal from Cenozoic times. Ancient lineages may have experienced a different history compared to more recent Cenozoic arrivals, as such lineages would have encountered geoclimatic shifts over an extended time period. The motivation for this study was to unravel the signature of diversification in an ancient lineage by comparing an area known for...

Data from: Sex ratio effects on reproductive strategies in humans

Ryan Schacht, Monique Borgerhoff Mulder, M. Borgerhoff Mulder & R. Schacht
Characterizations of coy females and ardent males are rooted in models of sexual selection that are increasingly outdated. Evolutionary feedbacks can strongly influence the sex roles and subsequent patterns of sex differentiated investment in mating effort, with a key component being the adult sex ratio (ASR). Using data from eight Makushi communities of southern Guyana, characterized by varying ASRs contingent on migration, we show that even within a single ethnic group, male mating effort varies...

Data from: Aquatic polymers can drive pathogen transmission in coastal ecosystems

Karen Shapiro, Colin Krusor, Fernanda F. M. Mazzillo, Patricia A. Conrad, John L. Largier, Jonna A. K. Mazet, Mary W. Silver, J. A. K. Mazet & M. W. Silver
Gelatinous polymers including extracellular polymeric substances (EPSs) are fundamental to biophysical processes in aquatic habitats, including mediating aggregation processes and functioning as the matrix of biofilms. Yet insight into the impact of these sticky molecules on the environmental transmission of pathogens in the ocean is limited. We used the zoonotic parasite Toxoplasma gondii as a model to evaluate polymer-mediated mechanisms that promote transmission of terrestrially derived pathogens to marine fauna and humans. We show that...

Data from: Persistence of an extinction-prone predator-prey interaction through metapopulation dynamics

Marcel Holyoak & Sharon P. Lawler
In theory, predator-prey pairs with extinction-prone local populations can persist through metapopulation dynamics, wherein local populations fluctuate asynchronously, occasionally providing dispersers that prevent permanent extinction in all patches. A few studies have shown that spatial structure can extend predator-prey persistence. However, no studies have unequivocally demonstrated the asynchrony among patches, low dispersal rates, and rescue effects that prove metapopulation dynamics extend persistence. We used a protist predator-prey pair to show that spatial subdivision lengthens persistence...

Data from: Using filter-based community assembly models to improve restoration outcomes

Kristin B. Hulvey & Paul A. Aigner
1. Ecological filter models derived from community assembly theory can inform restoration planning by highlighting management actions most likely to affect community composition. Despite growing interest in these models, many restoration studies solely manipulate a single filter—the biotic filter by altering interspecific competition in studies—while ignoring abiotic and dispersal filters that may also influence restoration success. 2. To examine how manipulating all three filters (biotic, abiotic, dispersal) affected restoration in an annual-type grassland, we seeded...

Data from: Gene co-expression modules underlying polymorphic and monomorphic zooids in the colonial hydrozoan, Hydractinia symbiolongicarpus

M. Sabrina Pankey, Brian R. Johnson, Eric J. Ronne, Artyom Kopp, Richard K. Grosberg & David C. Plachetzki
Advances in sequencing technology have forced a quantitative revolution in Evolutionary Biology. One important feature of this renaissance is that comprehensive genomic resources can be obtained quickly for almost any taxon, thus speeding the development of new model organisms. Here, we analyze 20 RNA-seq libraries from morphologically, sexually, and genetically distinct polyp types from the gonochoristic colonial hydrozoan, Hydractinia symbiolongicarpus (Cnidaria). Analyses of these data using weighted gene co-expression networks highlight deeply conserved genetic elements...

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: Wolbachia do not live by reproductive manipulation alone: infection polymorphism in Drosophila suzukii and D. subpulchrella

Christopher A. Hamm, David J. Begun, Alexandre Vo, Chris C. R. Smith, Perot Saelao, Amanda O. Shaver, John Jaenike & Michael Turelli
Drosophila suzukii recently invaded North America and Europe. Populations in Hawaii, California, New York and Nova Scotia are polymorphic for Wolbachia, typically with <20% infection frequency. The Wolbachia in D. suzukii, denoted wSuz, is closely related to wRi, the variant prevalent in continental populations of D. simulans. wSuz is also nearly identical to Wolbachia found in D. subpulchrella, plausibly D. suzukii's sister species. This suggests vertical Wolbachia transmission through cladogenesis (“cladogenic transmission”). The widespread occurrence...

Data from: Context-dependent effects of large wildlife declines on small mammal communities in central Kenya

Hillary S. Young, Douglas J. McCauley, Rodolfo Dirzo, Jacob R. Goheen, Bernard Agwanda, Cara Brook, Erik O. Castillo, Adam W. Ferguson, Stephen N. Kinyua, Molly M. McDonough, Todd M. Palmer, Robert M. Pringle, Truman P. Young & Kristofer M. Helgen
Many species of large wildlife have declined drastically worldwide. These reductions often lead to profound shifts in the ecology of entire communities and ecosystems. However, the effects of these large wildlife declines on other taxa likely hinge upon both underlying abiotic properties of these systems and on the types of secondary anthropogenic changes associated with wildlife loss, making impacts difficult to predict. To better understand how these important contextual factors determine the consequences of large-wildlife...

Data from: Landscape structure and the genetic effects of a population collapse

Serena A. Caplins, Kimberly J. Gilbert, Claudia Ciotir, Jens Roland, Stephen F. Matter, Nusha Keyghobadi, J. Roland, S. F. Matter, C. Ciotir, N. Keyghobadi & S. A. Caplins
Both landscape structure and population size fluctuations influence population genetics. While independent effects of these factors on genetic patterns and processes are well studied, a key challenge is to understand their interaction, as populations are simultaneously exposed to habitat fragmentation and climatic changes that increase variability in population size. In a population network of an alpine butterfly, abundance declined 60–100% in 2003 because of low over-winter survival. Across the network, mean microsatellite genetic diversity did...

Data from: Single nucleotide polymorphism (SNP) variation of wolves (Canis lupus) in Southeast Alaska and comparison with wolves, dogs, and coyotes in North America

Juan F. Medrano, Matthew A. Cronin, Angela Cánovas, Anita M. Oberbauer & Danika L. Bannasch
There is considerable interest in the genetics of wolves (Canis lupus) because of their close relationship to domestic dogs (C. familiaris) and the need for informed conservation and management. This includes wolf populations in Southeast Alaska for which we determined genotypes of 305 wolves at 173662 single nucleotide polymorphism (SNP) loci. After removal of invariant and linked SNP, 123801 SNP were used to quantify genetic differentiation of wolves in Southeast Alaska and wolves, coyotes (C....

Data from: Novel trophic niches drive variable progress toward ecological speciation within an adaptive radiation of pupfishes

Christopher H. Martin & Laura C. Feinstein
Adaptive radiation is recognized by a rapid burst of phenotypic, ecological, and species diversification. However, it is unknown whether different species within an adaptive radiation evolve reproductive isolation at different rates. We compared patterns of genetic differentiation among nascent species within an adaptive radiation of Cyprinodon pupfishes using genotyping by sequencing. Similar to classic adaptive radiations, this clade exhibits rapid morphological diversification rates and two species are novel trophic specialists, a scale-eater and hard-shelled prey...

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: Erosion of beta diversity under interacting global change impacts in a semiarid grassland

Anu Eskelinen & Susan Harrison
1. Human impacts are often thought of as homogenizing natural communities, but it is unclear how these impacts interact to alter the beta diversity (spatial variability) of plant communities. 2. In a grassland with high beta diversity along a soil fertility gradient, we asked which combinations of nutrient enrichment, precipitation enhancement, and disturbance would homogenize communities along the gradient by allowing dominant species from one part of the gradient to increase their abundances in other...

Data from: Bayesian species delimitation can be robust to guide tree inference errors

Chi Zhang, Bruce Rannala & Ziheng Yang
The Bayesian method of species delimitation (Yang and Rannala, 2010) uses a so-called guide tree to reduce the number of models to be evaluated in the reversible-jump Markov chain Monte Carlo (rjMCMC) algorithm (Green, 1995). It has been pointed out that the method tends to over-split if a random population tree is used as the guide tree (Fujita and Leaché, 2011). Here we conduct a simulation study to examine the performance of the method under...

Data from: Short-term priority over exotic annuals increases the initial density and longer-term cover of native perennial grasses

Kurt Vaughn, Truman Young, Kurt J. Vaughn & Truman P. Young
Temporal priority can affect individual performance and reproduction, as well as community assembly, but whether these effects persist over time remains unclear, and their demographic mechanisms have been little explored. The continued dominance of exotic annual grasses in California has been commonly attributed to their demonstrated early germination and rapid early growth relative to native perennial grasses. This advantage may play a crucial role in the structure of California exotic annual grasslands, as well as...

Data from: Multiple stressors and the cause of amphibian abnormalities

Mari K. Reeves, Margaret Perdue, Marcel Holyoak, Birgit Hagedorn, Daniel Rinella, Daniel Bogan, LeeAnn Munk, William Battaglin, Christine L. Dolph & Kimberly A. Trust
The repeated occurrence of abnormal amphibians in nature points to ecological imbalance, yet identifying causes of these abnormalities has proved complex. Multiple studies have linked amphibian abnormalities to chemically contaminated areas, but inference about causal mechanisms is lacking. Here we use a high incidence of abnormalities in Alaskan wood frogs to strengthen inference about the mechanism for these abnormalities. We suggest that limb abnormalities are caused by a combination of multiple stressors. Specifically, toxicants lead...

Data from: Phylogenetically driven sequencing of extremely halophilic archaea reveals strategies for static and dynamic osmo-response

Erin A. Becker, Phillip M. Seitzer, Andrew Tritt, David Larsen, Megan Krusor, Andrew I. Yao, Dongying Wu, Dominique Madern, Jonathan A. Eisen, Aaron E. Darling & Marc T. Facciotti
Organisms across the tree of life use a variety of mechanisms to respond to stress-inducing fluctuations in osmotic conditions. Cellular response mechanisms and phenotypes associated with osmoadaptation also play important roles in bacterial virulence, human health, agricultural production and many other biological systems. To improve understanding of osmoadaptive strategies, we have generated 59 high-quality draft genomes for the haloarchaea (a euryarchaeal clade whose members thrive in hypersaline environments and routinely experience drastic changes in environmental...

Data from: Biting disrupts integration to spur skull evolution in eels

David C. Collar, Peter C. Wainwright, Michael E. Alfaro, Liam J. Revell & Rita S. Mehta
The demand that anatomical structures work together to perform biological functions is thought to impose strong limits on morphological evolution. Breakthroughs in diversification can occur, however, when functional integration among structures is relaxed. Although such transitions are expected to generate variation in morphological diversification across the tree of life, empirical tests of this hypothesis are rare. Here we show that transitions between suction-based and biting modes of prey capture, which require different degrees of coordination...

Data from: Three-dimensional morphological variability of recent rhynchonellide brachiopod crura

Holly A. Schreiber, Peter D. Roopnarine & Sandra J. Carlson
Crura, the calcareous support structures of the lophophore in rhynchonellide brachiopods, have historically been used to justify higher-level rhynchonellide classification and reveal major evolutionary lineages within rhynchonellides. Seventeen crural types have been described and categorized into four groups based on variation in overall structure and cross-sectional shape, but not evaluated in a quantitative or comprehensive manner. Heterochrony has been hypothesized to play a role in the evolutionary transitions among some types, but the structural, developmental,...

Data from: Reading the leaves: a comparison of leaf rank and automated areole measurement for quantifying aspects of leaf venation

Walton A. Green, Stefan A. Little, Charles A. Price, Scott L. Wing, Selena Y. Smith, Benjamin Kotrc & Gabriela Doria
The reticulate venation that is characteristic of a dicot leaf has excited interest from systematists for more than a century, and from physiological and developmental botanists for decades. The tools of digital image acquisition and computer image analysis, however, are only now approaching the sophistication needed to quantify aspects of the venation network found in real leaves quickly, easily, accurately, and reliably enough to produce biologically meaningful data. In this paper, we examine 120 leaves...

Data from: Fluctuations in neighbourhood fertility generate variable signaling effort

Conor C. Taff, Gail L. Patricelli, Corey R. Freeman-Gallant, G. L. Patricelli & C. R. Freeman-Gallant
Studies of sexual signalling generally focus on interactions between dyadic pairs, yet communication in natural populations often occurs in the context of complex social networks. The ability to survey social environments and adjust signal production appropriately should be a critical component of success in these systems, but has rarely been documented empirically. Here, we used autonomous recording devices to identify 118 472 songs produced by 26 male common yellowthroats (Geothlypis trichas) over two breeding seasons,...

Data from: Fatal attraction: vegetation responses to nutrient inputs attract herbivores to infectious anthrax carcass sites

Wendy C. Turner, Kyrre L. Kausrud, Yathin S. Krishnappa, Joris P. G. M. Cromsigt, Holly H. Ganz, Isaac Mapaure, Claudine C. Cloete, Zepee Havarua, Martina Küsters, Wayne M. Getz, Nils Chr. Stenseth, K. L. Kausrud, Y. S. Krishnappa, W. C. Turner, J. P. G. M. Cromsigt, H. H. Ganz, W. M. Getz, C. C. Cloete, Z. Havarua & I. Mapaure
Parasites can shape the foraging behaviour of their hosts through cues indicating risk of infection. When cues for risk co-occur with desired traits such as forage quality, individuals face a trade-off between nutrient acquisition and parasite exposure. We evaluated how this trade-off may influence disease transmission in a 3-year experimental study of anthrax in a guild of mammalian herbivores in Etosha National Park, Namibia. At plains zebra (Equus quagga) carcass sites we assessed (i) carcass...

Registration Year

  • 2014

Resource Types

  • Dataset


  • University of California, Davis
  • Harvard University
  • University of Georgia
  • University of California, Berkeley
  • California Academy of Sciences
  • University of Western Australia
  • Stanford University
  • University of Minnesota
  • Smithsonian Institution
  • University of California, Santa Barbara