3,841 Works

Data from: Effects of deer density and land use on white-tailed deer

Trevor Hefley, Scott Hygnstrom, Jason Gilsdorf, Gregory Clements Clements, Myndi Clements, Andrew J. Tyre, David Baasch & Kurt VerCauteren
Local and regional land use changes, such as the expansion of cellulosic biofuels, and population density of deer can affect the health and body mass of white-tailed deer (Odocoileus virginianus). We collected hunter-harvest data for 1,731 white-tailed deer from DeSoto National Wildlife Refuge (DNWR) in eastern Nebraska and western Iowa, USA from 2003-2010. We used linear mixed-effects models and information theoretic methods to estimate effects of density of deer and proportion of total landcover area...

Data from: Eukaryotic metatranscriptomes of alpine soils and their links to the functioning of ecosystems

Mustafa Tarfa, Philippe Choler, Armelle Monier, Eric Coissac, Zinger Lucie, Roberto A. Geremia & Jean-Marc Bonneville
Above-below ground interactions are crucial to the functioning of terrestrial ecosystems. However, little is known about the functional links between plants and soil eukaryotic microorganisms. Exploring the genes expressed by soil micro-eukaryotes through metatranscriptomics may contribute to filling this knowledge gap. We applied this method to study two contrasting alpine soils in which plant growth rates differ, owing to different snow-cover durations. Soil polyA+ RNAs from Late Snow Melt site (LSM) and Early Snow Melt...

Data from: Lessons learned from microsatellite development for non-model organisms using 454 pyrosequencing

Corine Schoebel, Sabine Brodbeck, Dominique Buehler, Carolina Cornejo, Jyoti Gajurel, Hanna Hartikainen, Daniela Keller, Marie Leys, Štěpánka Říčanová, Gernot Segelbacher, Silke Werth, Daniela Csencsics, C. N. Schoebel, S. Brodbeck, D. Buehler, C. Cornejo, D. Keller, D. Csencsics, M. Leys, Š. Říčanová & G. Segelbacher
Microsatellites, also known as simple sequence repeats (SSRs), are among the most commonly used marker types in evolutionary and ecological studies. Next Generation Sequencing techniques such as 454 pyrosequencing allow the rapid development of microsatellite markers in nonmodel organisms. 454 pyrosequencing is a straightforward approach to develop a high number of microsatellite markers. Therefore, developing microsatellites using 454 pyrosequencing has become the method of choice for marker development. Here, we describe a user friendly way...

Data from: Genomic and morphological evidence converge to resolve the enigma of Strepsiptera

Oliver Niehuis, Gerrit Hartig, Sonja Grath, Hans Pohl, Jörg Lehmann, Hakim Tafer, Alexander Donath, Veiko Krauss, Carina Eisenhardt, Jana Hertel, Malte Petersen, Christoph Mayer, Karen Meusemann, Ralph S. Peters, Peter F. Stadler, Rolf G. Beutel, Erich Bornberg-Bauer, Duane D. McKenna & Bernhard Misof
The phylogeny of insects, one of the most spectacular radiations of life on earth, has received considerable attention. However, the evolutionary roots of one intriguing group of insects, the twisted-wing parasites (Strepsiptera), remain unclear despite centuries of study and debate. Strepsiptera exhibit exceptional larval developmental features, consistent with a predicted step from direct (hemimetabolous) larval development to complete metamorphosis that could have set the stage for the spectacular radiation of metamorphic (holometabolous) insects. Here we...

Data from: SNP-array reveals genome wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon (Salmo salar)

Vincent Bourret, Matthew P. Kent, Craig R. Primmer, Anti Vasemägi, Sten Karlsson, Kjetil Hindar, Philip McGinnity, Eric Verspoor, Louis Bernatchez & Sigbjørn Lien
Atlantic salmon (Salmo salar) is one of the most extensively studied fish species in the world due to its significance in aquaculture, fisheries and ongoing conservation efforts to protect declining populations. Yet, limited genomic resources have hampered our understanding of genetic architecture in the species and the genetic basis of adaptation to the wide range of natural and artificial environments it occupies. In this paper, we describe the development of a medium density Atlantic salmon...

Data from: Clonal relatedness between lobular carcinoma in situ and synchronous malignant lesions

Victor P. Andrade, Irina Ostrovnaya, Venkatraman E. Seshan, Mary Morrogh, Dilip Giri, Narciso Olvera, Marina De Brot, Monica Morrow, Colin B. Begg & Tari A. King
INTRODUCTION: Lobular carcinoma in situ (LCIS) has been accepted as a marker of risk for the development of invasive breast cancer, yet modern models of breast carcinogenesis include LCIS as a precursor of low-grade carcinomas. We provide evidence favoring a clonal origin for LCIS and synchronous estrogen receptor-positive malignant lesions of the ductal and lobular phenotype. METHODS: Patients with prior LCIS undergoing mastectomy were identified preoperatively from 2003-2008. Specimens were widely sampled, and frozen blocks...

Data from: CLIP test: a new fast, simple and powerful method to distinguish between linked or pleiotropic quantitative trait loci in linkage disequilibria analysis

Ingrid David, Jean-Michel Elsen & Didier Concordet
An important question arises when mapping quantitative trait loci (QTLs) for genetically correlated traits: is the correlation due to pleiotropy (a single QTL affecting more than one trait) and/or close linkage (different QTLs that are physically close to each other and influence the traits)? In this article, we propose the Close Linkage versus Pleiotropism (CLIP) test, a fast, simple and powerful method to distinguish between these two situations. The CLIP test is based on the...

Data from: Butterfly genome reveals promiscuous exchange of mimicry adaptations among species

The Heliconius Genome Consortium
The evolutionary importance of hybridization and introgression has long been debated. Hybrids are usually rare and unfit, but even infrequent hybridization can aid adaptation by transferring beneficial traits between species. Here we use genomic tools to investigate introgression in Heliconius, a rapidly radiating genus of neotropical butterflies widely used in studies of ecology, behaviour, mimicry and speciation. We sequenced the genome of Heliconius melpomene and compared it with other taxa to investigate chromosomal evolution in...

Data from: Latitudinal patterns in rodent metabolic flexibility

Daniel Ernesto Naya, Lucia Spangenberg, Hugo Naya & Francisco Bozinovic
Macrophysiology is defined as the study of variation in physiological traits--including physiological trait flexibility--over large geographical and temporal scales, and the ecological implications of this variation. A classic example of a macrophysiological trend is the one emerging from the climatic variability hypothesis (CVH), which states that as the range of climatic fluctuation experienced by terrestrial animals increases with latitude, individuals at higher latitudes should be more plastic than individuals inhabiting lower latitudes. In this context,...

Data from: Adaptive radiation driven by the interplay of eco-evolutionary and landscape dynamics

Robin Aguilée, David Claessen & Amaury Lambert
We investigate an individual-based model of adaptive radiation based on the biogeographical changes of the Great African Lakes where cichlid fishes radiated. In our model, the landscape consists of a mosaic of three habitat types which may or may not be separated by geographic barriers. We study the effect of the alternation between allopatry and sympatry called landscape dynamics. We show that landscape dynamics can generate a significantly higher diversity than allopatric or sympatric speciation...

Data from: Persistent genetic signatures of historic climatic events in an Antarctic octopus

Jan M. Strugnell, Phill C. Watts, Peter J. Smith & A. Louise Allcock
Repeated cycles of glaciation have had major impacts on the distribution of genetic diversity of the Antarctic marine fauna. During glacial periods, ice cover limited the amount of benthic habitat on the continental shelf. Conversely, more habitat and possibly altered seaways, were available during interglacials when the ice receded and the sea level was higher. We used microsatellites and partial sequences of the mitochondrial cytochrome oxidase c subunit 1 (MT-CO1) gene to examine genetic structure...

Data from: Use of alpha, beta, and gamma diversity measures to characterize seed dispersal by animals

Douglas G. Scofield, Peter E. Smouse, Jordan Karubian & Victoria L. Sork
Seed dispersal shapes ecological and evolutionary dynamics of plant populations. Here, we extend classical diversity measures to study the impact of disperser behavior on seed dispersal. We begin by extending our previous diversity structure approach, which partitioned seed source diversity within and among dispersal sites, into the more general framework of traditional diversity measures. This statistical approach allows an assessment of the extent to which foraging behavior shapes α and γ diversity, as well as...

Data from: Iterative ecological radiation and convergence during the evolutionary history of damselfishes (Pomacentridae)

Bruno Frédérich, Laurie Sorenson, Francesco Santini, Graham J. Slater & Michael E. Alfaro
Coral reef fishes represent one of the most spectacularly diverse assemblages of vertebrates on the planet, but our understanding of their mode of diversification remains limited. Here we test whether the diversity of the damselfishes (Pomacentridae), one of the most species-rich families of reef-associated fishes, was produced by a single or multiple adaptive radiation(s) during their evolutionary history. Tests of the tempo of lineage diversification using a time-calibrated phylogeny including 208 species revealed that crown...

Data from: Divergent natural selection with gene flow along major environmental gradients in Amazonia: insights from genome scans, population genetics and phylogeography of the characin fish Triportheus albus

Georgina M. Cooke, Ning L. Chao & Luciano B. Beheregaray
The unparalleled diversity of tropical ecosystems like the Amazon Basin has been traditionally explained using spatial models within the context of climatic and geological history. Yet, it is adaptive genetic diversity that defines how species evolve and interact within an ecosystem. Here we combine genome scans, population genetics and sequenced-based phylogeographic analyses to examine spatial and ecological arrangements of selected and neutrally evolving regions of the genome of an Amazonian fish, Triportheus albus. Using a...

Data from: Deciphering the evolutionary history and developmental mechanisms of a complex sexual ornament: the abdominal appendages of Sepsidae (Diptera)

Julia H. Bowsher, Yuchen Ang, Tanner Ferderer & Rudolf Meier
Male abdomen appendages are a novel trait found within Sepsidae (Diptera). Here we demonstrate that they are likely to have evolved once, were lost three times, and then secondarily gained in one lineage. The developmental basis of these appendages was investigated by counting the number of histoblast cells in each abdominal segment in four species: two that represented the initial instance of appendage evolution, one that has secondarily gained appendages, and one species that did...

Data from: Opposing mechanisms drive richness patterns of core and transient bird species

Jessica R. Coyle, Allen H. Hurlbert & Ethan P. White
Studies of biodiversity typically assume that all species are equivalent. However, some species in a community maintain viable populations in the study area, while others occur only occasionally as transient individuals. Here we show that North American bird communities can reliably be divided into core and transient species groups, and that the richness of each group is driven by different processes. The richness of core species is influenced primarily by local environmental conditions, while the...

Data from: Historical and anthropogenic factors affecting the population genetic structure of Ontario’s inland lake populations of walleye (Sander vitreus)

Ryan P. Walter, Christopher J. Cena, George C. Morgan & Daniel D. Heath
Populations existing in formerly glaciated areas often display composite historical and contemporary patterns of genetic structure. For Canadian freshwater fishes, population genetic structure is largely reflective of dispersal from glacial refugia and isolation within drainage basins across a range of scales. Enhancement of sport fisheries via hatchery stocking programs and other means has the potential to alter signatures of natural evolutionary processes. Using 11 microsatellite loci genotyped from 2182 individuals, we analyzed the genetic structure...

Data from: The Teleost Anatomy Ontology: anatomical representation for the genomics age

Wasila M. Dahdul, John G. Lundberg, Peter E. Midford, James P. Balhoff, Hilmar Lapp, Todd J. Vision, Melissa A. Haendel, Monte Westerfield & Paula M. Mabee
The rich knowledge of morphological variation among organisms reported in the systematic literature has remained in free-text format, impractical for use in large-scale synthetic phylogenetic work. This noncomputable format has also precluded linkage to the large knowledgebase of genomic, genetic, developmental, and phenotype data in model organism databases. We have undertaken an effort to prototype a curated, ontology-based evolutionary morphology database that maps to these genetic databases (http://kb.phenoscape.org) to facilitate investigation into the mechanistic basis...

Data from: Novel forests maintain ecosystem processes after the decline of native tree species

Joseph Mascaro, R. Flint Hughes & Stefan A. Schnitzer
The positive relationship between species diversity (richness and evenness) and critical ecosystem functions, such as productivity, carbon storage, and nutrient cycling, is often used to predict the consequences of extinction. At regional scales, however, plant species richness is mostly increasing rather than decreasing because successful plant species introductions far outnumber extinctions. If these regional increases in richness lead to local increases in diversity, a reasonable prediction is that productivity, carbon storage, and nutrient cycling will...

Data from: Supportive breeding boosts natural population abundance with minimal negative impacts on fitness of a wild population of Chinook salmon

Maureen A. Hess, Craig D. Rabe, Jason L. Vogel, Jeff J. Stephenson, Doug D. Nelson & Shawn R. Narum
While supportive breeding programs strive to minimize negative genetic impacts to populations, case studies have found evidence for reduced fitness of artificially produced individuals when they reproduce in the wild. Pedigrees of two complete generations were tracked with molecular markers to investigate differences in reproductive success (RS) of wild and hatchery-reared Chinook salmon spawning in the natural environment to address questions regarding the demographic and genetic impacts of supplementation to a natural population. Results show...

Data from: De novo sequencing and assembly of Azadirachta indica fruit transcriptome

Neeraja M. Krishnan, Swetansu Pattnaik, S. A. Deepak, Arun K. Hariharan, Prakhar Gaur, Rakshit Chaudhary, Prachi Jain, Srividya Vaidyanathan, P. G. Bharath Krishna & Binay Panda
Azadirachta indica (neem) is a unique, versatile and important tree species. Many parts of the plant are traditionally used as pesticide, insecticide, fungicide and for other medicinal purposes. Azadirachta fruits and seeds, a good source of oil, are widely used for agriculturally important pest management. Neem oil and its derivatives also support multiple cottage industries in India. Past efforts have been mostly concentrated towards identifying, characterizing and synthesizing one of its principal components, i.e. azadirachtin...

Data from: Altitudinal clinal variation in wing form in African Drosophila melanogaster: one cline or many?

William R. Pitchers, John E. Pool & Ian Dworkin
Geographical patterns of morphological variation have been useful in addressing hypotheses about environmental adaptation. In particular, latitudinal clines in phenotypes have been studied in a number of Drosophila species. Some environmental conditions along latitudinal clines—for example, temperature—also vary along altitudinal clines, but these have been studied infrequently and it remains unclear whether these environmental factors are similar enough for convergence or parallel evolution. Most clinal studies in Drosophila have dealt exclusively with univariate phenotypes, allowing...

Data from: Treating fossils as terminal taxa in divergence time estimation reveals ancient vicariance patterns in the palpimanoid spiders

Hannah Marie Wood, Nicholas J. Matzke, Rosemary G. Gillespie & Charles E. Griswold
Incorporation of fossils into biogeographic studies can have a profound effect on the conclusions that result, particularly when fossil ranges are nonoverlapping with extant ranges. This is the case in archaeid spiders, where there are known fossils from the Northern Hemisphere, yet all living members are restricted to the Southern Hemisphere. To better understand the biogeographic patterns of archaeid spiders and their palpimanoid relatives, we estimate a dated phylogeny using a relaxed clock on a...

Data from: Phylogenomic insights into the cambrian explosion, the colonization of land and the evolution of flight in arthropoda

Christopher W. Wheat & Niklas Wahlberg
The timing of the origin of arthropods in relation to the Cambrian explosion is still controversial, as are the timing of other arthropod macroevolutionary events such as the colonization of land and the evolution of flight. Here we assess the power of a phylogenomic approach to shed light on these major events in the evolutionary history of life on earth. Analyzing a large phylogenomic dataset (122 taxa, 62 genes) with a Bayesian-relaxed molecular clock, we...

Data from: Early evolutionary trends in ammonoid embryonic development

Kenneth De Baets, Christian Klug, Dieter Korn & Neil H. Landman
During the Devonian Nekton Revolution, ammonoids show a progressive coiling of their shell just like many other pelagic mollusk groups. These now extinct, externally shelled cephalopods derived from bactritoid cephalopods with a straight shell in the Early Devonian. During the Devonian, evolutionary trends toward tighter coiling and a size reduction occurred in ammonoid embryonic shells. In at least three lineages, descendants with a closed umbilicus evolved convergently from forms with an opening in the first...

Registration Year

  • 2012

Resource Types

  • Dataset


  • University of British Columbia
  • Duke University
  • University of Exeter
  • University of California System
  • French National Centre for Scientific Research
  • French National Institute for Agricultural Research
  • University of Florida
  • Université Laval
  • University of Cambridge
  • University of Georgia
  • University of Lausanne
  • Cornell University
  • University of Washington
  • Australian National University
  • Stanford University