38 Works

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: 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: 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: 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: 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: Contrasting patterns of selection on the size and coloration of a female plumage ornament in common yellowthroats

Corey R. Freeman-Gallant, Rebecca L. Schneider, Conor C. Taff, Peter O. Dunn & Linda A. Whittingham
Females often possess ornaments that appear smaller and duller than homologous traits in males. These ornaments may arise as nonfunctional by-products of sexual selection in males and cause negative viability or fecundity selection in females in proportion to the cost of their production and maintenance. Alternatively, female ornaments may function as signals of quality that are maintained by sexual or social selection. In a 4-year study of 83 female common yellowthroats (Geothlypis trichas) and their...

Data from: Genetic architecture of a hormonal response to gene knockdown in honey bees

Kate E. Ihle, Olav Rueppell, Ying Wang, M. Kim Fondrk, , Gro V. Amdam & Zachary Y. Huang
Variation in endocrine signaling is proposed to underlie the evolution and regulation of social life histories, but the genetic architecture of endocrine signaling is still poorly understood. An excellent example of a hormonally influenced set of social traits is found in the honey bee (Apis mellifera): a dynamic and mutually suppressive relationship between juvenile hormone (JH) and the yolk precursor protein vitellogenin (Vg) regulates behavioral maturation and foraging of workers. Several other traits cosegregate with...

Data from: A target enrichment method for gathering phylogenetic information from hundreds of loci: an example from the Compositae

Jennifer R. Mandel, Rebecca B. Dikow, Vicki A. Funk, Rishi R. Masalia, S. Evan Staton, Alex Kozik, Richard W. Michelmore, Loren H. Rieseberg & John M. Burke
Premise of the study: The Compositae (Asteraceae) are a large and diverse family of plants, and the most comprehensive phylogeny to date is a meta-tree based on 10 chloroplast loci that has several major unresolved nodes. We describe the development of an approach that enables the rapid sequencing of large numbers of orthologous nuclear loci to facilitate efficient phylogenomic analyses. Methods and Results: We designed a set of sequence capture probes that target conserved orthologous...

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
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
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...

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
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: 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
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: 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: 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: 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: Sex ratio effects on reproductive strategies in humans

Ryan Schacht & Monique Borgerhoff Mulder
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: 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
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: Evolution of sweet taste perception in hummingbirds by transformation of the ancestral umami receptor

Maude W. Baldwin, Yasuka Toda, Tomoya Nakagita, Mary J. O'Connell, Kirk C. Klasing, Takumi Misaka, Scott V. Edwards & Stephen D. Liberles
Sensory systems define an animal's capacity for perception and can evolve to promote survival in new environmental niches. We have uncovered a noncanonical mechanism for sweet taste perception that evolved in hummingbirds since their divergence from insectivorous swifts, their closest relatives. We observed the widespread absence in birds of an essential subunit (T1R2) of the only known vertebrate sweet receptor, raising questions about how specialized nectar feeders such as hummingbirds sense sugars. Receptor expression studies...

Data from: Phylogenetic signal in extinction selectivity in Devonian terebratulide brachiopods

Paul G. Harnik, Paul C. Fitzgerald, Jonathan L. Payne & Sandra J. Carlson
Determining which biological traits affect taxonomic durations is critical for explaining macroevolutionary patterns. Two approaches are commonly used to investigate the associations between traits and durations and/or extinction and origination rates: analyses of taxonomic occurrence patterns in the fossil record and comparative phylogenetic analyses, predominantly of extant taxa. By capitalizing upon the empirical record of past extinctions, paleontological data avoid some of the limitations of existing methods for inferring extinction and origination rates from molecular...

Data from: Fractured genetic connectivity threatens a southern California puma (Puma concolor) population

Holly B. Ernest, T. Winston Vickers, Scott A. Morrison, Michael R. Buchalski & Walter M. Boyce
Pumas (Puma concolor; also known as mountain lions and cougars) in southern California live among a burgeoning human population of roughly 20 million people. Yet little is known of the consequences of attendant habitat loss and fragmentation, and human-caused puma mortality to puma population viability and genetic diversity. We examined genetic status of pumas in coastal mountains within the Peninsular Ranges south of Los Angeles, in San Diego, Riverside, and Orange counties. The Santa Ana...

Data from: Resolving distinct genetic regulators of tomato leaf shape within a heteroblastic and ontogenetic context

Daniel H. Chitwood, Aashish Ranjan, Ravi Kumar, Yasunori Ichihashi, Kristina Zumstein, Lauren R. Headland, Enrique Ostria-Gallardo, José A. Aguilar-Martínez, Susan Bush, Leonela Carriedo, Daniel Fulop, Ciera C. Martinez, Jie Peng, Julin N. Maloof & Neelima R. Sinha
Leaf shape is mutable, changing in ways modulated by both development and environment within genotypes. A complete model of leaf phenotype would incorporate the changes in leaf shape during juvenile-to-adult phase transitions and the ontogeny of each leaf. Here, we provide a morphometric description of >33,000 leaflets from a set of tomato (Solanum spp) introgression lines grown under controlled environment conditions. We first compare the shape of these leaves, arising during vegetative development, with >11,000...

Data from: Genetic analysis of safflower domestication

Stephanie A. Pearl, John E. Bowers, Sebastian Reyes-Chin-Wo, Richard W. Michelmore & John M. Burke
Background: Safflower (Carthamus tinctorius L.) is an oilseed crop in the Compositae (a.k.a. Asteraceae) that is valued for its oils rich in unsaturated fatty acids. Here, we present an analysis of the genetic architecture of safflower domestication and compare our findings to those from sunflower (Helianthus annuus L.), an independently domesticated oilseed crop within the same family. We mapped quantitative trait loci (QTL) underlying 24 domestication-related traits in progeny from a cross between safflower and...

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