642 Works

Data from: Advancing population ecology with integral projection models: a practical guide

Cory Merow, Johan P. Dalgren, C. Jessica E. Metcalf, Dylan Z. Childs, M. E. K. Evans, Eelke Jongejans, Sydne Record, Mark Rees, Roberto Salguero-Gómez, Sean M. McMahon, Margaret E.K. Evans & Johan P. Dahlgren
Integral Projection Models (IPMs) use information on how an individual's state influences its vital rates - survival, growth and reproduction - to make population projections. IPMs are constructed from regression models predicting vital rates from state variables (e.g., size or age) and covariates (e.g., environment). By combining regressions of vital rates, an IPM provides mechanistic insight into emergent ecological patterns such as population dynamics, species geographic distributions, or life history strategies. Here, we review important...

Data from: Divergence and reticulation among montane populations of a jumping spider (Habronattus pugillis Griswold)

Wayne Maddison & Michelle McMahon
Populations of the jumping spider Habronattus pugillis Griswold isolated on nearby mountain ranges in southern Arizona are differentiated in many features of the males (color, shape and orientation of setae on face, shape of carapace, markings of palpi and legs, motions during courtship behavior). These features are (mostly) consistent within a range and different between ranges. The concentration of differences to male courtship behavior and body parts exposed to the female during courtship and correlations...

Data from: Reinforcement selection acting on the European house mouse hybrid zone

Barbora Vošlajerová Bimová, Miloš Macholán, Stuart J E Baird, Pavel Munclinger, Petra Dufková, Christina M Laukaitis, Robert C Karn, Kenneth Luzynski, Priscilla K Tucker & Jaroslav Piálek
Behavioural isolation may lead to complete speciation when partial postzygotic isolation acts in the presence of divergent specific mate recognition systems. These conditions exist where Mus musculus musculus and M. m. domesticus come into contact and hybridize. We studied two mate recognition signal systems, based on urinary and salivary proteins, across a Central European portion of the mouse hybrid zone. Introgression of the genomic regions responsible for these signals: the major urinary proteins (MUPs) and...

Data from: Evolution of viviparity: a phylogenetic test of the cold-climate hypothesis in Phrynosomatid lizards

Shea M. Lambert & John J. Wiens
The evolution of viviparity is a key life-history transition in vertebrates, but the selective forces favoring its evolution are not fully understood. With >100 origins of viviparity, squamate reptiles (lizards and snakes) are ideal for addressing this issue. Some evidence from field and laboratory studies supports the “cold-climate” hypothesis, wherein viviparity provides an advantage in cold environments by allowing mothers to maintain higher temperatures for developing embryos. Surprisingly, the cold-climate hypothesis has not been tested...

Data from: Allelopathy as an emergent, exploitable public good in the bloom-forming microalga Prymnesium parvum

William Wallace Driscoll, Noelle Justine Espinosa, Omar Tonsi Eldakar & Jeremiah D. Hackett
Many microbes cooperatively secrete extracellular products that favorably modify their environment. Consistent with social evolution theory, structured habitats play a role in maintaining these traits in microbial model systems, by localizing the benefits and separating strains that invest in these products from ‘cheater’ strains that benefit without paying the cost. It is thus surprising that many unicellular, well-mixed microalgal populations invest in extracellular toxins that confer ecological benefits upon the entire population, for example, by...

Data from: Steep clines within a highly permeable genome across a hybrid zone between two subspecies of the European rabbit

Miguel Carneiro, Stuart J. E. Baird, Sandra Afonso, Esther Ramirez, Pedro Tarroso, Henrique Teotonio, Rafael Villafuerte, Michael W. Nachman & Nuno Ferrand
Maintenance of genetic distinction in the face of gene flow is an important aspect of the speciation process. Here, we provide a detailed spatial and genetic characterization of a hybrid zone between two subspecies of the European rabbit. We examined patterns of allele frequency change for 22 markers located on the autosomes, X-chromosome, Y-chromosome, and mtDNA in 1078 individuals sampled across the hybrid zone. While some loci revealed extremely wide clines (w>=300 km) relative to...

Data from: Integrated analyses resolve conflicts over squamate reptile phylogeny and reveal unexpected placements for fossil taxa

Tod W. Reeder, Ted M. Townsend, Daniel G. Mulcahy, Brice P. Noonan, Perry L. Wood, , John J. Wiens & Jack W. Sites
Squamate reptiles (lizards and snakes) are a pivotal group whose relationships have become increasingly controversial. Squamates include >9000 species, making them the second largest group of terrestrial vertebrates. They are important medicinally and as model systems for ecological and evolutionary research. However, studies of squamate biology are hindered by uncertainty over their relationships, and some consider squamate phylogeny unresolved, given recent conflicts between molecular and morphological results. To resolve these conflicts, we expand existing morphological...

Data from: A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes

R. Alexander Pyron, Frank T. Burbrink & John J. Wiens
Background: The extant squamates (>9400 known species of lizards and snakes) are one of the most diverse and conspicuous radiations of terrestrial vertebrates, but no studies have attempted to reconstruct a phylogeny for the group with large-scale taxon sampling. Such an estimate is invaluable for comparative evolutionary studies, and to clarify their taxonomy. Here, we present the first large-scale phylogenetic estimate for Squamata. Results: The estimated phylogeny contains 4161 species representing all currently recognized families...

Data from: Development of an ultra-dense genetic map of the sunflower genome

John E. Bowers, Savithri Nambeesan, Jonathan Corbi, John M. Burke, Michael S. Barker, Loren H. Rieseberg & Steven J. Knapp
The development of ultra-dense genetic maps has the potential to facilitate detailed comparative genomic analyses and whole genome sequence assemblies. Here we describe the use of a custom Affymetrix GeneChip containing nearly 2.4 million features (25 bp sequences) targeting 86,023 unigenes from sunflower (Helianthus annuus L.) and related species to test for single-feature polymorphisms (SFPs) in a recombinant inbred line (RIL) mapping population derived from a cross between confectionery and oilseed sunflower lines (RHA280 x...

fitdcemri: a Matlab function for the analysis of DCE MRI data

Joey DeGrandchamp & Julio Cárdenas-Rodríguez
Matlab Function for the analysis of DCE MRI data

Data from: “Darwin’s corollary” and cytoplasmic incompatibility induced by Cardinium may contribute to speciation in Encarsia wasps (Hymenoptera: Aphelinidae)

Marco Gebiola, Suzanne E. Kelly, Peter Hammerstein, Massimo Giorgini, Molly S. Hunter & Martha S. Hunter
The potential importance of cytoplasmic incompatibility (CI) – inducing bacterial symbionts in speciation of their arthropod hosts has been debated. Theoretical advances have led to a consensus that a role is plausible when CI is combined with other isolating barriers. However, the insect model systems Nasonia and Drosophila are the only two experimental examples documented. Here we analyzed the components of reproductive isolation between the parasitoid wasp Encarsia suzannae, which is infected by the CI-inducing...

Data from: The small nuclear genomes of Selaginella are associated with a low rate of genome size evolution

Anthony E. Baniaga, Nils Arrigo & Michael S. Barker
The haploid nuclear genome size (1C DNA) of vascular land plants varies over several orders of magnitude. Much of this observed diversity in genome size is due to the proliferation and deletion of transposable elements. To date, all vascular land plant lineages with extremely small nuclear genomes represent recently derived states, having ancestors with much larger genome sizes. The Selaginellaceae represent an ancient lineage with extremely small genomes. It is unclear how small nuclear genomes...

Data from: Population structure of a vector-borne plant parasite

Kelsey M. Yule, Jennifer A. H. Koop, Nicolas M. Alexandre, Lauren R. Johnston & Noah K. Whiteman
Parasites are among the most diverse groups of life on Earth, yet complex natural histories often preclude studies of their speciation processes. The biology of parasitic plants facilitates in situ collection of data on both genetic structure and the mechanisms responsible for that structure. Here, we studied the role of mating, dispersal and establishment in host race formation of a parasitic plant. We investigated the population genetics of a vector-borne desert mistletoe (Phoradendron californicum) across...

Data from: Viral dark matter and virus–host interactions resolved from publicly available microbial genomes

Simon Roux, Steven J. Hallam, Tanja Woyke & Matthew B. Sullivan
The ecological importance of viruses is now widely recognized, yet our limited knowledge of viral sequence space and virus-host interactions precludes accurate prediction of their roles and impacts. Here we mined publicly available bacterial and archaeal genomic datasets to identify 12,498 high‑confidence viral genomes linked to their microbial hosts. These data augment public datasets 10-fold, provide first viral sequences for 13 new bacterial phyla including ecologically abundant phyla, and help taxonomically identify 7-38% of 'unknown'...

Design and Optimization of Pulsed Chemical Exchange Saturation Transfer MRI Using a Multiobjective Genetic Algorithm: A Matlab Code

Julio Cárdenas-Rodríguez, Eriko Yoshimaru & Edward Randtke
This collection of matlab scripts and functions was used to design and optimize shaped pulses for CEST MRI

Data from: A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny

, Anne Bruneau, Nasim Azani, Marielle Babineau, Edeline Gagnon, Carole Sinou, Royce Steeves, Erin Zimmerman, C. Donovan Bailey, Lynsey Kovar, Madhugiri Nageswara-Rao, Hannah Banks, RuthP. Clark, Manuel De La Estrella, Peter Gasson, GeoffreyC. Kite, BenteB. Klitgaard, GwilymP. Lewis, Danilo Neves, Gerhard Prenner, María De Lourdes Rico-Arce, ArianeR. Barbosa, Maria Cristina López-Roberts, Luciano Paganucci De Queiroz, PétalaG. Ribeiro … & Tingshuang Yi
The classification of the legume family proposed here addresses the long-known non-monophyly of the traditionally recognised subfamily Caesalpinioideae, by recognising six robustly supported monophyletic subfamilies. This new classification uses as its framework the most comprehensive phylogenetic analyses of legumes to date, based on plastid matK gene sequences, and including near-complete sampling of genera (698 of the currently recognised 765 genera) and ca. 20% (3696) of known species. The matK gene region has been the most...

Data from: Interaction rewiring and the rapid turnover of plant-pollinator networks

Paul J. CaraDonna, William K. Petry, Ross M. Brennan, James L. Cunningham, Judith L. Bronstein, Nickolas M. Waser & Nathan J. Sanders
Whether species interactions are static or change over time has wide-reaching ecological and evolutionary consequences. However, species interaction networks are typically constructed from temporally aggregated interaction data, thereby implicitly assuming that interactions are fixed. This approach has advanced our understanding of communities, but it obscures the timescale at which interactions form (or dissolve) and the drivers and consequences of such dynamics. We address this knowledge gap by quantifying the within-season turnover of plant–pollinator interactions from...

Data from: Less favorable climates constrain demographic strategies in plants

Anna M. Csergo, Roberto Salguero-Gómez, Olivier Broennimann, Shaun R. Coutts, Antoine Guisan, Amy L. Angert, Erik Welk, Iain Stott, Brian J. Enquist, Brian McGill, Jens-Christian Svenning, Cyrille Violle & Yvonne M. Buckley
Correlative species distribution models are based on the observed relationship between species’ occurrence and macroclimate or other environmental variables. In climates predicted less favourable populations are expected to decline, and in favourable climates they are expected to persist. However, little comparative empirical support exists for a relationship between predicted climate suitability and population performance. We found that the performance of 93 populations of 34 plant species worldwide – as measured by in situ population growth...

Data from: Resistance to Bacillus thuringiensis toxin Cry2Ab and survival on single-toxin and pyramided cotton in cotton bollworm from China

Laipan Liu, Meijing Gao, Song Yang, Shaoyan Liu, Yidong Wu, Yves Carrière & Yihua Yang
Evolution of Helicoverpa armigera resistance to Bacillus thuringiensis (Bt) cotton producing Cry1Ac is progressing in northern China and replacement of Cry1Ac cotton by pyramided Bt cotton has been considered to counter such resistance. Here, we investigated four of the eight conditions underlying success of the refuge strategy for delaying resistance to Cry1Ac+Cry2Ab cotton, a pyramid that has been used extensively against H. armigera outside China. Laboratory bioassays of a Cry2Ab-selected strain (An2Ab) and a related...

Data from: Task-switching is associated with temporal delays in Temnothorax rugatulus ants

Gavin M. Leighton, Daniel Charbonneau & Anna Dornhaus
The major evolutionary transitions often result in reorganization of biological systems, and a component of such reorganization is that individuals within the system specialize on performing certain tasks, resulting in a division of labor. Although the traditional benefit of division of labor is thought to be a gain in work efficiency, one alternative benefit of specialization is avoiding temporal delays associated with switching tasks. While models have demonstrated that costs of task switching can drive...

Central Coordinating Committee

Jessica Meyerson, Zach Vowell, Megan Potterbusch & Lauren Work

Curation-Ready Software

Fernando Rios, Bridget Almas, Nicole Contaxis, Alexandra Chassanoff, Paula Jabloner, Heidi Kelly, Megan Potterbusch & Lauren Work
The curation-ready working group aims to develop principles, guidelines, resources to guide curators and data managers to help make software in archives more useful for its intended purpose at the time of archiving

Report 1: Exploring Curation-ready Software: Use Cases

Fernando Rios, Bridget Almas, Nicole Contaxis, Paula Jabloner, Heidi Kelly, Alexandra Chassanoff, Megan Potterbusch & Lauren Work
This is the first progress report of the Software Preservation Network Curation-ready Software Working Group. Also available here http://www.softwarepreservationnetwork.org/exploring-curation-ready-software-use-cases/

Data from: Adaptive diversification of growth allometry in the plant Arabidopsis thaliana

François Vasseur, Moises Exposito-Alonso, Oscar J. Ayala-Garay, George Wang, Brian J. Enquist, Denis Vile, Cyrille Violle & Detlef Weigel
Seed plants vary tremendously in size and morphology. However, variation and covariation between plant traits may at least in part be governed by universal biophysical laws and biological constants. Metabolic Scaling Theory (MST) posits that whole-organismal metabolism and growth rate are under stabilizing selection that minimizes the scaling of hydrodynamic resistance and maximizes the scaling of resource uptake. This constrains variation in physiological traits and in the rate of biomass accumulation, so that they can...

Data from: Bison body size and climate change

Jeff M. Martin, Jim I. Mead & Perry S. Barboza
The relationship between body size and temperature of mammals is poorly resolved, especially for large keystone species such as bison (Bison bison). Bison are well-represented in the fossil record across North America, which provides an opportunity to relate body size to climate within a species. We measured the length of a leg bone (calcaneal tuber, DstL) in 849 specimens from 60 localities that were dated by stratigraphy and 14C decay. We estimated body mass (M)...

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