16,959 Works

Whale Sharks Control region raw 506 individuals

Thomas M. Vignaud, Mark G. Meekan, Ricardo Vázquez-Juárez, Dení Ramírez-Macías, Simon J. Pierce, David Rowat, Michael L. Berumen, Sandra Baksay & Serge Planes
This excel dataset can be saved in .fasta - Locations and year of collection are described when available. 'N' means unknown, while '-' indicates gap. Additional sequences can be found on genebank from Castro et al. 2007, but seems to be reversed. Analysis performed in Vignaud et al. 2014 used modified dataset to remove N and large gaps as described in the methods.


Tatiana A. Semenova, Luis N. Morgado, Jeffrey M. Welker, Marilyn D. Walker, Erik Smets & József Geml
ITS2 rDNA sequence data partitioned into individual soil samples based on tag identifiers.

Long-term flowering time at the plot level

Jill T. Anderson, David W. Inouye, Amy M. McKinney, Robert I. Colautti & Thomas Mitchell-Olds
These are data on flowering time (first flowering time and peak flowering time) for all plots from 1973-2011. Data were collected by David Inouye and collaborators. Temperature data are from the Crested Butte, CO NOAA station, and snowmelt data were collected by billy barr. The data file was created in Text Wrangler.

Data from: Target capture and massively parallel sequencing of ultraconserved elements for comparative studies at shallow evolutionary time scales

Brian Tilston Smith, Michael G. Harvey, Brant C. Faircloth, Travis C. Glenn & Robb T. Brumfield
Comparative genetic studies of non-model organisms are transforming rapidly due to major advances in sequencing technology. A limiting factor in these studies has been the identification and screening of orthologous loci across an evolutionarily distant set of taxa. Here, we evaluate the efficacy of genomic markers targeting ultraconserved DNA elements (UCEs) for analyses at shallow evolutionary timescales. Using sequence capture and massively parallel sequencing to generate UCE data for five co-distributed Neotropical rainforest bird species,...

Data from: Herbarium specimens reveal a historical shift in phylogeographic structure of common ragweed during native range disturbance

Michael D. Martin, Elizabeth A. Zimmer, Morten T. Olsen, Andrew D. Foote, M. Thomas P. Gilbert & Grace S. Brush
Invasive plants provide ample opportunity to study evolutionary shifts that occur after introduction to novel environments. However, although genetic characters pre-dating introduction can be important determinants of later success, large-scale investigations of historical genetic structure have not been feasible. Common ragweed (Ambrosia artemisiifolia L.) is an invasive weed native to North America that is known for its allergenic pollen. Palynological records from sediment cores indicate that this species was uncommon before European colonization of North...

Data from: Fire-regime complacency and sensitivity to centennial- through millennial-scale climate change in Rocky Mountain subalpine forests, Colorado, U.S.A.

Philip E. Higuera, Christy E. Briles & Cathy Whitlock
1. Key uncertainties in anticipating future fire regimes are their sensitivity to climate change, and the degree to which climate will impact fire regimes directly, through increasing the probability of fire, versus indirectly, through changes in vegetation and landscape flammability. 2. We studied the sensitivity of subalpine forest fire regimes (i.e., fire frequency, fire severity) to previously documented climate variability over the past 6000 years, utilizing pollen and macroscopic charcoal from high-resolution lake-sediment records in...

Data from: Hypoxia-inducible factor-1 mediates adaptive developmental plasticity of hypoxia tolerance in zebrafish, Danio rerio

Cayleih E. Robertson, Patricia A. Wright, Louise Köblitz, Nicholas J. Bernier, L. Koblitz, N. J. Bernier, C. E. Robertson & P. A. Wright
In recent years, natural and anthropogenic factors have increased aquatic hypoxia the world over. In most organisms, the cellular response to hypoxia is mediated by the master regulator hypoxia-inducible factor-1 (HIF-1). HIF-1 also plays a critical role in the normal development of the cardiovascular system of vertebrates. We tested the hypothesis that hypoxia exposures which resulted in HIF-1 induction during embryogenesis would be associated with enhanced hypoxia tolerance in subsequent developmental stages. We exposed zebrafish...

Data from: Chloroplast phylogenomic analyses resolve deep-level relationships of an intractable bamboo tribe Arundinarieae (Poaceae)

Peng-Fei Ma, Yu-Xiao Zhang, Chun-Xia Zeng, Zhen-Hua Guo & De-Zhu Li
The temperate woody bamboos constitute a distinct tribe Arundinarieae (Poaceae: Bambusoideae) with high species diversity. Estimating phylogenetic relationships among the 11 major lineages of Arundinarieae has been particularly difficult, owing to a possible rapid radiation and the extremely low rate of sequence divergence. Here we explore the use of chloroplast genome sequencing for phylogenetic inference. We sampled 25 species (22 temperate bamboos and 3 outgroups) for the complete genome representing 8 major lineages of Arundinarieae...

Data from: Standard sister clade comparison fails when testing derived character states

Jos Käfer & Sylvain Mousset
Comparing species richness in sister clades that differ in a character is one of the ways to study factors influencing diversification. While most of its applications focused on traits that increase diversification, some were used to study the association of a trait with less species richness, e.g. the occurrence of dioecy in flowering plants. We show here, using simulations and an analytical model, that the null expectation of equal species richness that is generally used...

Data from: A genomic perspective on a new bacterial genus and species from the Alcaligenaceae family, Basilea psittacipulmonis

Katrine L. Whiteson, David Hernandez, Vladimir Lazarevic, Nadia Gaia, Laurent Farinelli, Patrice François, Paola Pilo, Joachim Frey & Jacques Schrenzel
Background: A novel Gram-negative, non-haemolytic, non-motile, rod-shaped bacterium was discovered in the lungs of a dead parakeet (Melopsittacus undulatus) that was kept in captivity in a petshop in Basel, Switzerland. The organism is described with a chemotaxonomic profile and the nearly complete genome sequence obtained through the assembly of short sequence reads. Results: Genome sequence analysis and characterization of respiratory quinones, fatty acids, polar lipids, and biochemical phenotype is presented here. Comparison of gene sequences...

Data from: Plant-herbivore interactions: silicon concentration in tussock sedges and population dynamics of root voles

Monika Wieczorek, Karol Zub, Paulina A. Szafrańska, Aneta Książek & Marek Konarzewski
1. It has been hypothesized that the induction of silicon (Si)-based plant defence in response to herbivore damage may engender rodent population cycles. Many studies have also considered accumulation of Si as a process controlled by geo-hydrological factors. 2. To test these ideas, we investigated the relationship between concentration of Si in fibrous tussock sedge (Carex appropinquata) and the population density of a major sedge consumer, the root vole (Microtus oeconomus), in field enclosures in...

Data from: Comparative support for the expensive tissue hypothesis: big brains are correlated with smaller gut and greater parental investment in Lake Tanganyika cichlids

Masahito Tsuboi, Arild Husby, Alexander Kotrschal, Alexander Hayward, Séverine Denise Büchel, Josefina Zidar, Hanne Løvlie & Niclas Kolm
The brain is one of the most energetically expensive organs in the vertebrate body. Consequently, the energetic requirements of encephalization are suggested to impose considerable constraints on brain size evolution. Three main hypotheses concerning how energetic constraints might affect brain evolution predict covariation between brain investment and i) investment into other costly tissues, ii) overall metabolic rate, and iii) reproductive investment. To date, these hypotheses have mainly been tested in homeothermic animals and the existing...

Data from: Species identification and likely catch time period of whale bones from South Georgia

Angela L. Sremba, Anthony R. Martin, C. Scott Baker & C. Scott Baker
Skeletal remains of baleen whales killed during the onset of 20th century commercial whaling lie scattered across the shores and abandoned whaling stations of the subantarctic island of South Georgia. Here we report on genetic species identification of whale bones collected from South Georgia using standard historical DNA protocols. We amplified and sequenced short fragments of the mitochondrial DNA (mtDNA) control region from 281 available bone samples. Of these, 231 provided mtDNA sequences of sufficient...

Data from: How innovative are new drugs launched in the UK? A retrospective study of new drugs listed in the British National Formulary (BNF) 2001-2012

Derek J. Ward, Angharad Slade, Tracey Genus, Orsolina I. Martino & Andrew J. Stevens
Objectives: Innovative new drugs offer potential benefits to patients, healthcare systems, governments and the pharmaceutical industry. Recent data suggest annual numbers of new drugs launched in the UK have increased in recent years, and we sought to understand whether this represents increasing numbers of highly innovative drugs being made available or the introduction of increasing numbers of drugs with limited additional therapeutic value. Design and setting: Retrospective observational study of new drug entries in the...

Data from: Growth trajectory influences temperature preference in fish through an effect on metabolic rate

Shaun S. Killen
Most animals experience temperature variations as they move through the environment. For ectotherms in particular, temperature has a strong influence on habitat choice. While well-studied at the species level, less is known about factors affecting the preferred temperature of individuals. Especially lacking is information on how physiological traits are linked to thermal preference and whether such relationships are affected by factors such feeding history and growth trajectory. This study examined these issues in the common...

Data from: Probabilistic graphical model representation in phylogenetics

Sebastian Höhna, Tracy A. Heath, Bastien Boussau, Michael J. Landis, Fredrik Ronquist & John P. Huelsenbeck
Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation of the chosen model is crucial for: (1) reproducibility of an analysis, (2) model development and (3) software design. Moreover, a unified, clear and understandable framework for model representation lowers the barrier for beginners and non-specialists to grasp complex phylogenetic models, including their...

Data from: Is diagnosability an indicator of speciation? Response to ‘Why one century of phenetics is enough’

Rasmus Heller, Peter Frandsen, Eline Dierdre Lorenzen, Hans R. Siegismund & Eline Deirdre Lorenzen
Recently (Heller et al. 2013; H&A), we commented on a revision of the bovid taxonomy, which proposes a doubling in the number of recognized species (Groves and Grubb 2011; G&G). The subsequent response by Cotterill et al. (2014; C&A) contains a number of misunderstandings and leaves much of the critique voiced in our paper unanswered, focusing instead on species ontologies and taxonomic history. C&A argue strongly against phenetics, morphospecies and taxonomic conservatism, ascribing us views...

Data from: Seasonality of precipitation interacts with exotic species to alter composition and phenology of a semi-arid grassland

Janet S. Prevéy & Timothy R. Seastedt
While modeling efforts suggest that invasive species will track climate changes, empirical studies are few. A relevant and largely unaddressed research question is: how will the presence of exotic species interact with precipitation change to alter ecosystem structure and function? We studied the effects of changes in seasonal timing of precipitation on species composition and resource availability in a grassland community in Colorado, USA. We examined how seasonal precipitation patterns affect the abundance of historically...

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: Women are underrepresented on the editorial boards of journals in environmental biology and natural resource management

Alyssa H. Cho, Shelley A. Johnson, Carrie E. Schuman, Jennifer M. Adler, Oscar Gonzalez, Sarah J. Graves, Jana R. Huebner, D. Blaine Marchant, Sami W. Rifai, Irina Skinner, Emilio M. Bruna & Shelly A. Johnson
Despite women earning similar numbers of graduate degrees as men in STEM disciplines, they are underrepresented in upper level positions in both academia and industry. Editorial board memberships are an important example of such positions; membership is both a professional honor in recognition of achievement and an opportunity for professional advancement. We surveyed 10 highly regarded journals in environmental biology, natural resource management, and plant sciences to quantify the number of women on their editorial...

Data from: Sediment and turbidity associated with offshore dredging increase coral disease prevalence on nearby reefs

F. Joseph Pollock, Joleah B. Lamb, Stuart N. Field, Scott F. Heron, Britta Schaffelke, George Shedrawi, David G. Bourne, Bette L Willis & Bette L. Willis
In recent decades, coral reef ecosystems have declined to the extent that reefs are now threatened globally. While many water quality parameters have been proposed to contribute to reef declines, little evidence exists conclusively linking specific water quality parameters with increased disease prevalence in situ. Here we report evidence from in situ coral health surveys confirming that chronic exposure to dredging-associated sediment plumes significantly increase the prevalence of white syndromes, a devastating group of globally...

Data from: Site-specific group selection drives locally adapted group compositions

Jonathan N. Pruitt & Charles J. Goodnight
Group selection may be defined as selection caused by the differential extinction or proliferation of groups. The socially polymorphic spider Anelosimus studiosus exhibits a behavioral polymorphism where females exhibit either a “docile” or “aggressive” behavioral phenotype. Natural colonies are composed of a mixture of related docile and aggressive individuals, and populations differ in colonies’ characteristic docile:aggressive ratios. Using experimentally-constructed colonies of known composition, we demonstrate that population-level divergence in docile:aggressive ratios is driven by site-specific...

Data from: Fisher's geometric model with a moving optimum

Sebastian Matuszewski, Joachim Hermisson & Michael Kopp
Fisher's geometric model has been widely used to study the effects of pleiotropy and organismic complexity on phenotypic adaptation. Here, we study a version of Fisher's model in which a population adapts to a gradually moving optimum. Key parameters are the rate of environmental change, the dimensionality of phenotype space, and the patterns of mutational and selectional correlations. We focus on the distribution of adaptive substitutions, that is, the multivariate distribution of the phenotypic effects...

Data from: Measuring fecal testosterone in females and fecal estrogens in males: comparison of RIA and LC/MS/MS methods for wild baboons (Papio cynocephalus).

Laurence R. Gesquiere, Toni E. Ziegler, Patricia A. Chen, Katherine A. Epstein, Susan C. Alberts & Jeanne Altmann
The development of non-invasive methods, particularly fecal determination, has made possible the assessment of hormone concentrations in wild animal populations. However, measuring fecal metabolites needs careful validation for each species and for each sex. We investigated whether radioimmunoassays (RIAs) previously used to measure fecal testosterone (fT) in male baboons and fecal estrogens (fE) in female baboons were well suited to measure these hormones in the opposite sex. We compared fE and fT concentrations determined by...

Data from: Relationships in the Lupinus albifrons species complex (Fabaceae) based on two highly variable chloroplast regions

Daisie I. Huang & Elizabeth A. Friar
The perennial lupines of western North America, previously suggested to be monophyletic, comprise an apparently rapid and recent species radiation concentrated in the California Floristic Province. The Lupinus albifrons species complex consists of a number of closely related yet morphologically variable taxa within the larger group of perennial lupines. We used sequence data from two rapidly evolving noncoding chloroplast regions to analyze relationships in the perennial lupines, with special emphasis on the Lupinus albifrons species...

Registration Year

  • 2014

Resource Types

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  • University of California System
  • University of British Columbia
  • University of Oxford
  • French National Centre for Scientific Research
  • University of Western Australia
  • Uppsala University
  • Duke University
  • Michigan State University
  • University of Florida
  • University of Toronto
  • University of Lausanne
  • French National Institute for Agricultural Research
  • University of Michigan–Ann Arbor
  • University of Zurich
  • University of Exeter