26 Works

Data from: Data reuse and the open data citation advantage

Heather A. Piwowar & Todd J. Vision
Background: Attribution to the original contributor upon reuse of published data is important both as a reward for data creators and to document the provenance of research findings. Previous studies have found that papers with publicly available datasets receive a higher number of citations than similar studies without available data. However, few previous analyses have had the statistical power to control for the many variables known to predict citation rate, which has led to uncertain...

Data from: Postcranial morphology and the locomotor habits of living and extinct carnivorans

Joshua X. Samuels, Julie A. Meachen & Stacey A. Sakai
Members of the order Carnivora display a broad range of locomotor habits, including cursorial, scansorial, arboreal, semiaquatic, aquatic, and semifossorial species from multiple families. Ecomorphological analyses from osteological measurements have been used successfully in prior studies of carnivorans and rodents to accurately infer the locomotor habits of extinct species. This study uses 20 postcranial measurements that have been shown to be effective indicators of locomotor habits in rodents and incorporates an extensive sample of over...

Data from: Global biogeography of scaly tree ferns (Cyatheaceae): evidence for Gondwanan vicariance and limited transoceanic dispersal

Petra Korall & Kathleen M. Pryer
Aim: Scaly tree ferns, Cyatheaceae, are a well-supported group of mostly tree-forming ferns found throughout the tropics, the subtropics and the south-temperate zone. Fossil evidence shows that the lineage originated in the Late Jurassic period. We reconstructed large-scale historical biogeographical patterns of Cyatheaceae and tested the hypothesis that some of the observed distribution patterns are in fact compatible, in time and space, with a vicariance scenario related to the break-up of Gondwana. Location: Tropics, subtropics...

Data from: How hot are Drosophila hotspots? Examining recombination rate variation and associations with nucleotide diversity, divergence, and maternal age in Drosophila pseudoobscura

Brenda Manzano-Winkler, Suzanne E. McGaugh & Mohamed A. F. Noor
Fine scale meiotic recombination maps have uncovered a large amount of variation in crossover rate across the genomes of many species, and such variation in mammalian and yeast genomes is concentrated to <5 kb regions of highly elevated recombination rates (10–100x the background rate) called “hotspots.” Drosophila exhibit substantial recombination rate heterogeneity across their genome, but evidence for these highly-localized hotspots is lacking. We assayed recombination across a 40 Kb region of Drosophila pseudoobscura chromosome...

Data from: Stasis and convergence characterize morphological evolution in eupolypod II ferns

Michael A. Sundue & Carl J. Rothfels
Background and Aims: Patterns of morphological evolution at levels above family rank remain underexplored in the ferns. The present study seeks to address this gap through analysis of 79 morphological characters for 81 taxa, including representatives of all ten families of eupolypod II ferns. Recent molecular phylogenetic studies demonstrate that the evolution of the large eupolypod II clade (which includes nearly one-third of extant fern species) features unexpected patterns. The traditional ‘athyrioid’ ferns are scattered...

Data from: Integrative taxonomy resolves the cryptic and pseudo-cryptic Radula buccinifera complex (Porellales: Jungermanniopsida), including two reinstated and five new species

Matt A. M. Renner, Nicolas Devos, Jairo Patiño, Elizabeth A. Brown, Andrew Orme, Michael Elgy, Trevor Wilson, Lindsey J. Gray, Matt J. Von Konrat, Lindsey Gray, Matt Renner, Elizabeth Brown & Matt Von Konrat
Molecular data from three chloroplast markers resolve individuals attributable to Radula buccinifera in six lineages belonging to two subgenera, indicating the species is polyphyletic as currently circumscribed. All lineages are morphologically diagnosable, but one pair exhibits such morphological overlap that they can be considered cryptic. Molecular and morphological data justify the re-instatement of a broadly circumscribed ecologically variable R. strangulata, of R. mittenii, and the description of five new species. Two species Radula mittenii Steph....

Data from: Strong selection genome-wide enhances fitness trade-offs across environments and episodes of selection

Jill Theresa Anderson, Cheng-Ruei Lee & Thomas Mitchell-Olds
Fitness trade-offs across episodes of selection and environments influence life-history evolution and adaptive population divergence. Documenting these trade-offs remains challenging as selection can vary in magnitude and direction through time and space. Here, we evaluate fitness trade-offs at the levels of the whole organism and the quantitative trait locus (QTL) in a multiyear field study of Boechera stricta (Brassicaceae), a genetically tractable mustard native to the Rocky Mountains. Reciprocal local adaptation was pronounced for viability,...

Data from: Reproductive aging patterns in primates reveal that humans are distinct

Susan C. Alberts, Jeanne Altmann, Diane K. Brockman, Marina Cords, Linda M. Fedigan, Anne Pusey, Tara S. Stoinski, Karen B. Strier, William F. Morris & Anne M. Bronikowski
Women rarely give birth after approximately 45 years of age, and they experience the cessation of reproductive cycles – menopause – at approximately 50 years of age, after a fertility decline lasting almost two decades. Such reproductive senescence in mid-lifespan is an evolutionary puzzle of enduring interest because it should be inherently disadvantageous. Further, comparative data on reproductive senescence from other primates, or indeed other mammals, remains relatively rare. Here we carried out the first...

Data from: Complex trait divergence contributes to environmental niche differentiation in ecological speciation of Boechera stricta

Cheng-Ruei Lee & Thomas Mitchell-Olds
Ecological factors may contribute to reproductive isolation if differential local adaptation causes immigrant or hybrid fitness reduction. Because local adaptation results from the interaction between natural selection and adaptive traits, it is crucial to investigate both to understand ecological speciation. Previously, we used niche modelling to identify local water availability as an environmental correlate of incipient ecological speciation between two subspecies in Boechera stricta, a close relative of Arabidopsis. Here, we performed several large-scale glasshouse...

Data from: Evolution of resistance to a multiple-herbavore community: genetic correlations, diffuse coevolution, and constraints on the plant's response to selection

Michael J. Wise & Mark D. Rausher
Although plants are generally attacked by a community of several species of herbivores, relatively little is known about the strength of natural selection for resistance in multiple-herbivore communities—particularly how the strength of selection differs among herbivores that feed on different plant organs or how strongly genetic correlations in resistance affect the evolutionary responses of the plant. Here, we report on a field study measuring natural selection for resistance in a diverse community of herbivores of...

Data from: Obtaining mtDNA genomes from next-generation transcriptome sequencing: a case study on the basal Passerida (Aves: Passeriformes) phylogeny.

Benoit Nabholz, Erich D. Jarvis & Hans Ellegren
Classically, the mitochondrial genome is sequenced by a series of amplicons using conserved PCR primers. Here we show how shot-gun transcriptome sequencing can be used to obtain the complete set of protein-coding genes from the mtDNA of four passerine bird species. With these sequences, we address the still unresolved basal Passerida relationships (Aves: Passeriformes). Our analysis suggests a new hypothesis for the basal relationships of Passerida, namely a clade grouping Sylvioidea and Passeroidea, with Paridae...

Data from: Social environment influences the relationship between genotype and gene expression in wild baboons

Daniel E. Runcie, Ralph T. Wiedmann, Elizabeth A. Archie, Jeanne Altmann, Gregory A. Wray, Susan C. Alberts & Jenny Tung
Variation in the social environment can have profound effects on survival and reproduction in wild social mammals. However, we know little about the degree to which these effects are influenced by genetic differences among individuals, and conversely, the degree to which social environmental variation mediates genetic reaction norms. To better understand these relationships, we investigated the potential for dominance rank, social connectedness and group size to modify the effects of genetic variation on gene expression...

Data from: Latitude drives diversification in Madagascar’s endemic dry forest rodent, Eliurus myoxinus (sub-family Nesomyinae)

Jeff J. Shi, Lauren M. Chan, Zafimahery Rakotomalala, Amy M. Heilman, Steven M. Goodman & Anne D. Yoder
Numerous hypotheses have been proposed for the historical processes governing the rich endemism of Madagascar's biodiversity. The ‘watershed model’ suggests that drier climates in the recent geological past have resulted in the contraction of forests around major watersheds, thereby defining areas of endemism. We test whether this hypothesis explains phylogeographical patterns in a dry forest-dependent rodent, Eliurus myoxinus, an endemic species widely distributed through western Madagascar. We sequenced the mitochondrial cytochrome b locus and nuclear...

Data from: Genetic population structure of U.S. Atlantic coastal striped bass (Morone saxatilis)

David T. Gauthier, Corinne A. Audemard, Jeanette E. L. Carlsson, Tanya L. Darden, Michael R. Denson, Kimberly S. Reece & Jens Carlsson
Genetic population structure of anadromous striped bass along the US Atlantic coast was analyzed using 14 neutral nuclear DNA microsatellites. Young-of-the-year and adult striped bass (n = 1114) were sampled from Hudson River, Delaware River, Chesapeake Bay, North Carolina, and South Carolina. Analyses indicated clear population structure with significant genetic differentiation between all regions. Global multilocus F ST was estimated at 0.028 (P < 0.001). Population structure followed an isolation-by-distance model and temporal sampling indicated...

Data from: Female competition in chimpanzees

Anne E. Pusey & Kara Schroepfer-Walker
Female chimpanzees exhibit exceptionally slow rates of reproduction and raise their offspring without direct paternal care. Therefore, their reproductive success depends critically on long-term access to high-quality food resources over a long lifespan. Chimpanzee communities contain multiple adult males, multiple adult females and their offspring. Because males are philopatric and jointly defend the community range while most females transfer to new communities before breeding, adult females are typically surrounded by unrelated competitors. Communities are fission–fusion...

Data from: Predictability and irreversibility of genetic changes associated with flower color evolution in Penstemon barbatus

Carolyn A. Wessinger & Mark D. Rausher
Two outstanding questions in evolutionary biology are whether, and how often, the genetic basis of phenotypic evolution is predictable; and whether genetic change constrains evolutionary reversibility. We address these questions by studying the genetic basis of red flower color in Penstemon barbatus. The production of red flowers often involves the inactivation of one or both of two anthocyanin pathway genes, Flavonoid 3',5'-hydroxylase (F3'5'h) and Flavonoid 3'-hydroxylase (F3'h). We used gene expression and enzyme function assays...

Data from: Combining genetic and demographic information to prioritize conservation efforts for anadromous alewife and blueback herring

Eric P. Palkovacs, Daniel J. Hasselman, Emily E. Argo, Stephen R. Gephard, Karin E. Limburg, David M. Post, Thomas F. Schultz & Theodore V. Willis
A major challenge in conservation biology is the need to broadly prioritize conservation efforts when demographic data are limited. One method to address this challenge is to use population genetic data to define groups of populations linked by migration and then use demographic information from monitored populations to draw inferences about the status of unmonitored populations within those groups. We applied this method to anadromous alewife (Alosa pseudoharengus) and blueback herring (Alosa aestivalis), species for...

Data from: A total evidence approach to understanding phylogenetic relationships and ecological diversity in Selaginella subg. Tetragonostachys

Nils Arrigo, James Therrien, Cajsa Lisa Anderson, Michael D. Windham, Christopher H. Haufler & Michael S. Barker
Premise of the Study: Several members of Selaginella are renowned for their ability to survive extreme drought and “resurrect” when conditions improve. Many of these belong to subgenus Tetragonostachys, a group of ∼45 species primarily found in North and Central America, with substantial diversity in the Sonoran and Chihuahuan Deserts. We evaluated the monophyly and the age of subgenus Tetragonostachys and assess how drought tolerance contributed to the evolution of this clade. Methods: Our study...

Data from: When good neighbors don’t need fences: Temporal landscape partitioning among baboon social groups

A. Catherine Markham, Vishwesha Guttal, Susan C. Alberts & Jeanne Altmann
Intraspecific competition is a key factor shaping space-use strategies and movement decisions inmany species, yet how and when neighbors utilize shared areas while exhibiting active avoidance of one another is largely un- known. Here, we investigated temporal landscape partitioning in a population of wild baboons (Papio cynocephalus). We used global positioning system (GPS) collars to synchronously record the hourly locations of five baboon social groups for ∼900 days, and we used behavioral, demographic, and life...

Data from: Accelerated rate of molecular evolution for vittarioid ferns is strong and not due to selection

Carl J. Rothfels & Eric Schuettpelz
Molecular evolutionary rate heterogeneity—the violation of a molecular clock—is a prominent feature of many phylogenetic datasets. It has particular importance to systematists not only because of its biological implications, but also for its practical effects on our ability to infer and date evolutionary events. Here we show, using both maximum likelihood and Bayesian approaches, that a remarkably strong increase in substitution rate in the vittarioid ferns is consistent across the nuclear and plastid genomes. Contrary...

Data from: Habitat collapse due to overgrazing threatens turtle conservation in marine protected areas

Marjolijn J. A. Christianen, Peter M. J. Herman, Tjeerd J. Bouma, Leon P. M. Lamers, Marieke M. Van Katwijk, Tjisse Van Der Heide, Peter J. Mumby, Brian R. Silliman, Sarah L. Engelhard, Madelon Van De Kerk, Wawan Kiswara & Johan Van De Koppel
Marine protected areas (MPAs) are key tools for combatting the global overexploitation of endangered species. The prevailing paradigm is that MPAs are beneficial in helping to restore ecosystems to more ‘natural’ conditions. However, MPAs may have unintended negative effects when increasing densities of protected species exert destructive effects on their habitat. Here, we report on severe seagrass degradation in a decade-old MPA where hyper-abundant green turtles adopted a previously undescribed below-ground foraging strategy. By digging...

Data from: First direct measurements of behavioural responses by Cuvier’s beaked whales to mid-frequency active sonar

Stacy L. DeRuiter, Brandon L. Southall, John Calambokidis, Walter M. X. Zimmer, Dinara Sadykova, Erin A. Falcone, Ari S. Friedlaender, John E. Joseph, David Moretti, Gregory S. Schorr, Len Thomas & Peter L. Tyack
Most marine mammal strandings coincident with naval sonar exercises have involved Cuvier’s beaked whales (Ziphius cavirostris). We recorded acoustic and animal movement data on two tagged Ziphius and obtained the first direct measurements of behavioural responses of this species to mid-frequency active (MFA) sonar signals. Each recording included a 30-minute playback (one 1.6-s simulated MFA sonar signal repeated every 25 s); one whale was also incidentally exposed to MFA sonar from distant naval exercises. Whales...

Data from: The impact of gene expression variation on robustness and evolvability of a developmental gene regulatory network

David A. Garfield, Daniel E. Runcie, Courtney C. Babbitt, Ralph Haygood, William J. Nielsen & Gregory A. Wray
Regulatory interactions buffer development against genetic and environmental perturbations, but adaptation requires phenotypes to change. We investigated the relationship between robustness and evolvability within the gene regulatory network underlying development of the larval skeleton in the sea urchin Strongylocentrotus purpuratus. We find extensive variation in gene expression in this network throughout development in a natural population, some of which has a heritable genetic basis. Switch-like regulatory interactions predominate during early development, buffer expression variation, and...

Data from: Comparative linkage maps suggest that fission, not polyploidy, underlies near-doubling of chromosome number within monkeyflowers (Mimulus; Phrymaceae)

Lila Fishman, John H. Willis, Carrie A. Wu & Young-Wha Lee
Changes in chromosome number and structure are important contributors to adaptation, speciation, and macroevolution. In flowering plants, polyploidy and subsequent reductions in chromosome number by fusion are major sources of chromosomal evolution, but chromosome number increase by fission has been relatively unexplored. Here, we use comparative linkage mapping with gene-based markers to reconstruct chromosomal synteny within the model flowering plant genus Mimulus (monkeyflowers). Two sections of the genus with haploid numbers {greater than or equal...

Data from: Genetic drift or natural selection? Hybridization and asymmetric mitochondrial introgression in two Caribbean lizards (Anolis pulchellus and Anolis krugi)

Tereza Jezkova, Manuel Leal & Javier A. Rodríguez-Robles
Hybridization and gene introgression can occur frequently between closely related taxa, but appear to be rare phenomena among members of the species-rich West Indian radiation of Anolis lizards. We investigated the pattern and possible mechanism of introgression between two sister species from Puerto Rico, Anolis pulchellus and Anolis krugi, using mitochondrial (ND2) and nuclear (DNAH3, NKTR) DNA sequences. Our findings demonstrated extensive introgression of A. krugi mtDNA (k-mtDNA) into the genome of A. pulchellus in...

Registration Year

  • 2013
    26

Resource Types

  • Dataset
    26

Affiliations

  • Duke University
    26
  • Princeton University
    2
  • University of North Carolina
    2
  • Uppsala University
    2
  • University of Kansas
    1
  • National Evolutionary Synthesis Center
    1
  • University of Montana
    1
  • University of Liège
    1
  • Columbia University
    1
  • Field Museum of Natural History
    1