27 Works

Data from: A phylogenomic analysis of turtles

Nicholas G. Crawford, James F. Parham, Anna B. Sellas, Brant C. Faircloth, Travis C. Glenn, Theodore J. Papefuss, James B. Henderson, Madison H. Hansen, W. Brian Simison & Theodore J. Papenfuss
Molecular analyses of turtle relationships have overturned prevailing morphological hypotheses and prompted the development of a new taxonomy. Here we provide the first genome-scale analysis of turtle phylogeny. We sequenced 2,381 ultraconserved element (UCE) loci representing a total of 1,718,154 bp of aligned sequence. Our sampling includes 32 turtle taxa representing all 14 recognized turtle families and an additional six outgroups. Maximum likelihood, Bayesian, and species tree methods produce a single resolved phylogeny. This robust...

Data from: The relationship between risk of bias criteria, research outcomes, and study sponsorship in a cohort of preclinical thiazolidinedione animal studies: a meta-analysis

Maher Abdel-Sattar, David Krauth, Andrew Anglemyer & Lisa Bero
Introduction: There is little evidence regarding the influence of conflicts of interest on preclinical research. This study examines whether industry sponsorship is associated with increased risks of bias and/or effect sizes of outcomes in published preclinical thiazolidinedione (TZD) studies. Methods: We identified preclinical TZD studies published between January 1, 1965, and November 14, 2012. Coders independently extracted information on study design criteria aimed at reducing bias, results for all relevant outcomes, sponsorship source and investigator...

Data from: Context-dependent reproductive isolation mediated by floral scent and color

Mascha Bischoff, Robert A. Raguso, Andreas Jürgens & Diane R. Campbell
Reproductive isolation due to pollinator behavior is considered a key mode of speciation in flowering plants. Although floral scent is thought to mediate pollinator behavior, little is known about its effects on pollinator attraction and floral visitation in the wild. We used field experiments with wild hawkmoths and laboratory experiments with naïve hawkmoths to investigate attraction to and probing of flowers in response to indole, a volatile emitted by Ipomopsis tenuituba but not its close...

Data from: Warning signals are seductive: relative contributions of color and pattern to predator avoidance and mate attraction in Heliconius butterflies

Susan D. Finkbeiner, Adriana D. Briscoe & Robert D. Reed
Visual signaling in animals can serve many uses, including predator deterrence and mate attraction. In many cases, signals used to advertise unprofitability to predators are also used for intraspecific communication. Although aposematism and mate choice are significant forces driving the evolution of many animal phenotypes, the interplay between relevant visual signals remains little explored. Here, we address this question in the aposematic passion-vine butterfly Heliconius erato by using color- and pattern-manipulated models to test the...

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

S. N. Patek & 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: 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: Maximally informative foraging by Caenorhabditis elegans

Adam J. Calhoun, Sreekanth H. Chalasani & Tatyana O. Sharpee
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: 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: Speciation, population structure, and demographic history of the Mojave Fringe-toed Lizard (Uma scoparia), a species of conservation concern

Andrew D. Gottscho, Sharyn B. Marks & William Bryan Jennings
The North America deserts were impacted by both Neogene plate tectonics and Quaternary climatic fluctuations, yet it remains unclear how these events influenced speciation in this region. We tested published hypotheses regarding the timing and mode of speciation, population structure, and demographic history of the Mojave Fringe-toed Lizard (Uma scoparia), a sand dune specialist endemic to the Mojave Desert of California and Arizona. We sampled 109 individual lizards representing 22 insular dune localities, obtained DNA...

Data from: The emotion system promotes diversity and evolvability

Jarl Giske, Sigrunn Eliassen, Øyvind Fiksen, Per J. Jakobsen, Dag L. Aksnes, Marc Mangel, Christian Jørgensen & O. Fiksen
Studies on the relationship between the optimal phenotype and its environment have had limited focus on genotype-to-phenotype pathways and their evolutionary consequences. Here, we study how multi-layered trait architecture and its associated constraints prescribe diversity. Using an idealized model of the emotion system in fish, we find that trait architecture yields genetic and phenotypic diversity even in absence of frequency-dependent selection or environmental variation. That is, for a given environment, phenotype frequency distributions are predictable...

Data from: Mapping migration in a songbird using high-resolution genetic markers

Kristen Ruegg, Eric C. Anderson, Kristina L. Paxton, Vanessa Apkenas, Sirena Lao, Rodney B. Siegel, David F. DeSante, Frank Moore, Thomas B. Smith & Kristen C. Ruegg
Neotropical migratory birds are declining across the Western Hemisphere, but conservation efforts have been hampered by the inability to assess where migrants are most limited – the breeding grounds, migratory stopover sites, or wintering areas. A major challenge has been the lack of an efficient, reliable, and broadly applicable method for measuring the strength of migratory connections between populations across the annual cycle. Here we show how high-resolution genetic markers can be used to identify...

Data from: Shifting habitats, morphology and selective pressures: developmental polyphenism in an adaptive radiation of Hawaiian spiders

Michael S. Brewer, Rebecca Alice Carter, Peter J. P. Croucher & Rosemary G. Gillespie
Particularly intriguing examples of adaptive radiation are those in which lineages show parallel or convergent evolution, suggesting utilization of similar genetic or developmental pathways. The current study focuses on an adaptive radiation of Hawaiian “spiny-leg” spiders in which diversification is associated with repeated convergent evolution leading to similar sets of ecomorphs on each island. However, two species on the oldest islands in the archipelago exhibit variability, occurring as two different ecomorphs. More derived species on...

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: Community assembly and functional diversity along succession post-management

Radika Bhaskar, Todd E. Dawson & Patricia Balvanera
1. Despite extensive development of successional theory, few empirical studies have evaluated whether existing models are applicable to human-modified landscapes. Seasonally dry tropical forests are experiencing widespread transformation, and represent a critical system to assess in a successional framework to infer the mechanisms that shape assembly of secondary forests post-management. 2. We used a functional trait-based approach to assess changes in community assembly mechanisms along succession in secondary dry forests of varying stages following abandonment...

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...

Data from: Oxidative stress is a potential cost of breeding in male and female northern elephant seals.

Jeffrey T. Sharick, Jose P. Vazquez-Medina, Rudy M. Ortiz & Daniel E. Crocker
1.The trade-off between current reproductive effort and survival is a key concept of life history theory. A variety of studies support the existence of this trade-off but the underlying physiological mechanisms are not well-understood. Oxidative stress has been proposed as a potential mechanism underlying the observed inverse relationship between reproductive investment and lifespan. Prolonged fasting is associated with oxidative stress including increases in the production of reactive oxygen species, oxidative damage and inflammation. 2.Northern elephant...

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
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: A role for migration-linked genes and genomic islands in divergence of a songbird

Kristen Ruegg, Eric C. Anderson, Jason Boone, Jazz Pouls & Thomas B. Smith
Next-generation sequencing has made it possible to begin asking questions about the process of divergence at the level of the genome. For example, recently there has been a debate around the role of “genomic islands of divergence” (i.e. blocks of outlier loci) in facilitating the process of speciation-with-gene-flow. The Swainson’s thrush, Catharus ustulatus, is a migratory songbird with two genetically-distinct subspecies that differ in a number of traits known to be involved in reproductive isolation...

Data from: Investigating processes of neotropical rain forest tree diversification by examining the evolution and historical biogeography of the Protieae (Burseraceae)

Paul Van Antwerp Fine, Felipe Zapata & Douglas C. Daly
Andean uplift and the collision of North and South America are thought to have major implications for the diversification of the Neotropical biota. However, few studies have investigated how these geological events may have influenced diversification. We present a multilocus phylogeny of 102 Protieae taxa (73% of published species), sampled pantropically, to test hypotheses about the relative importance of dispersal, vicariance, habitat specialization, and biotic factors in the diversification of this ecologically dominant tribe of...

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: 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: Sequence Capture using PCR-generated Probes (SCPP): a cost-effective method of targeted high-throughput sequencing for non-model organisms

Joshua V. Peñalba, Lydia L. Smith, Maria A. Tonione, Chodon Sass, Sarah M. Hykin, Phillip L. Skipwith, James A. McGuire, Rauri C. K. Bowie, Craig Moritz & Jimmy A. McGuire
Recent advances in high-throughput sequencing library preparation and subgenomic enrichment methods have opened new avenues for population genetics and phylogenetics of non-model organisms. To multiplex large numbers of indexed samples while sequencing predominantly orthologous, targeted regions of the genome, we propose modifications to an existing, in-solution capture that utilizes PCR products as target probes to enrich library pools for the genomic subset of interest. The sequence capture using PCR-generated probes (SCPP) protocol requires no specialized...

Data from: Delimiting species in the genus Otospermophilus (Rodentia: Sciuridae) using genetics, ecology, and morphology

Mark A. Phuong, Marisa C. W. Lim, Daniel R. Wait, Kevin C. Rowe & Craig Moritz
We apply an integrative taxonomy approach to delimit species of ground squirrels in the genus Otospermophilus because the diverse evolutionary histories of organisms shape the existence of taxonomic characters. Previous studies of mitochondrial DNA from this group recovered three divergent lineages within Otospermophilus beecheyi separated into northern, central, and southern geographical populations, with Otospermophilus atricapillus nested within the southern lineage of O. beecheyi. To further evaluate species boundaries within this complex, we collected additional genetic...

Data from: Across-year social stability shapes network structure in wintering migrant sparrows

Daizaburo Shizuka, Alexis S. Chaine, Jennifer Anderson, Oscar Johnson, Inger Marie Laursen & Bruce E. Lyon
Migratory birds often form flocks on their wintering grounds, but important details of social structure such as the patterns of association between individuals are virtually unknown. We analysed networks of co-membership in short-term flocks for wintering golden-crowned sparrows (Zonotrichia atricapilla) across three years and discovered social complexity unsuspected for migratory songbirds. The population was consistently clustered into distinct social communities within a relatively small area (~ 7 ha). Birds returned to the same community across...

Data from: Shape-shift: semicircular canal morphology responds to selective breeding for increased locomotor activity

Heidi Schutz, Heather A. Jamniczky, Benedikt Hallgrímsson, & Theodore Garland
Variation in semicircular canal morphology correlates with locomotor agility among species of mammals. An experimental evolutionary mouse model was used to test the hypotheses that semicircular canal morphology (1) evolves in response to selective breeding for increased locomotor activity, (2) exhibits phenotypic plasticity in response to early-onset chronic exercise, and (3) is unique in individuals possessing the minimuscle phenotype. We examined responses in canal morphology to prolonged wheel access and selection in laboratory mice from...

Registration Year

  • 2014

Resource Types

  • Dataset


  • University of California System
  • University of California, Berkeley
  • Australian National University
  • Southwest Fisheries Science Center
  • University of California Los Angeles
  • Sonoma State University
  • Cornell University
  • University of Pennsylvania
  • University of Washington
  • University of Georgia