68 Works

Data from: Genome-environment associations in sorghum landraces predict adaptive traits

Jesse R. Lasky, Hari D. Upadhyaya, Punna Ramu, Santosh Deshpande, C. Tom Hash, Jason Bonnette, Thomas E. Juenger, Katie Hyma, Charlotte Acharya, Sharon E. Mitchell, Edward S. Buckler, Zachary Brenton, Stephen Kresovich & Geoffrey P. Morris
Improving environmental adaptation in crops is essential for food security under global change, but phenotyping adaptive traits remains a major bottleneck. If associations between single-nucleotide polymorphism (SNP) alleles and environment of origin in crop landraces reflect adaptation, then these could be used to predict phenotypic variation for adaptive traits. We tested this proposition in the global food crop Sorghum bicolor, characterizing 1943 georeferenced landraces at 404,627 SNPs and quantifying allelic associations with bioclimatic and soil...

Data from: Environmental drivers of mast-seeding in Mediterranean oak species: does leaf habit matter?

Ignacio M. Pérez-Ramos, Carmen M. Padilla-Díaz, Walter D. Koenig & Teodoro Marañón
Understanding the proximate factors that govern the widespread mast-seeding process is a question of considerable interest that remains poorly understood. The identity and effect of these factors may vary among coexisting species that differ in leaf habit, potentially resulting in temporally asynchronous patterns of seed production. In this study we aim to identify the proximate causes of mast-seeding using two oak species with contrasting leaf habit that coexist in southern Spain, the deciduous Quercus canariensis...

Data from: Perinatal and juvenile social environments interact to shape cognitive behaviour and neural phenotype in prairie voles

George S. Prounis, Lauren Foley, Asad Rehman & Alexander G. Ophir
Social environments experienced at different developmental stages profoundly shape adult behavioural and neural phenotypes, and may have important interactive effects. We asked if social experience before and after weaning influenced adult social cognition in male prairie voles. Animals were raised either with or without fathers and then either housed singly or in sibling pairs. Males that were socially deprived before (fatherless) and after (singly housed) weaning did not demonstrate social recognition or dissociate spatial from...

Data from: Queen killing is linked to high worker-worker relatedness in a social wasp

Kevin J. Loope
Social insect colonies are pinnacles of evolved altruism, but also contain dramatic conflict among relatives [1, 2]. In many species, a colony’s workers compete with the queen and each other over the production of males. Interspecific comparisons demonstrate the importance of within-colony relatedness in determining the outcome of this conflict [3, 4], but facultative responses to within-colony relatedness are rarely reported [5-7]. Here, I report facultative matricide (worker killing of a colony’s queen) in the...

Data from: Chronic household air pollution exposure is associated with impaired alveolar macrophage function in Malawian non-smokers

Jamie Rylance, Chikondi Chimpini, Sean Semple, David G. Russell, Malcolm J. Jackson, Robert S. Heyderman & Stephen B. Gordon
Background: Household air pollution in low income countries is an important cause of mortality from respiratory infection. We hypothesised that chronic smoke exposure is detrimental to alveolar macrophage function, causing failure of innate immunity. We report the relationship between macrophage function and prior smoke exposure in healthy Malawians. Methods: Healthy subjects exposed daily to cooking smoke at home volunteered for bronchoalveolar lavage. Alveolar macrophage particulate content was measured as a known correlate of smoke exposure....

Data from: The importance of terrestrial subsidies in stream food webs varies along a stream size gradient

Sarah M. Collins, Tyler J. Kohler, Steven A. Thomas, William W. Fetzer & Alexander S. Flecker
Cross system subsidies of energy and materials can be a substantial fraction of food web fluxes in ecosystems, especially when autochthonous production is strongly limited by light or nutrients. We explored whether assimilation of terrestrial energy varied in specific consumer taxa collected from streams of different sizes and resource availabilities. Since headwater streams are often unproductive, we expected that inputs from surrounding terrestrial systems (i.e. leaf litter, terrestrial invertebrates) would be a more important food...

Data from: A voyage to Terra Australis: human-mediated dispersal of cats

Katrin Koch, Dave Algar, Jeremy B. Searle, Markus Pfenninger & Klaus Schwenk
Background. Cats have been transported as human commensals worldwide giving rise to many feral populations. In Australia, feral cats have caused decline and extinction of native mammals, but their time of introduction and origin is unclear. Here, we investigate hypotheses of cat arrival pre- or post-European settlement, and the potential for admixture between cats of different invasion events. We analyse the genetic structure and diversity of feral cats from six locations on mainland Australia, seven...

Data from: Generalized selection to overcome innate immunity selects for host breadth in an RNA virus

Brian R. Wasik, Andrés R. Muñoz-Rojas, Kenichi W. Okamoto, Kathryn Miller-Jensen & Paul E. Turner
Virus-host co-evolution has selected for generalized host defense against viruses, exemplified by interferon production/signaling and other innate immune function in eukaryotes such as humans. Although cell-surface binding primarily limits virus infection success, generalized adaptation to counteract innate immunity across disparate hosts may contribute to RNA virus emergence potential. We examined this idea using vesicular stomatitis virus (VSV) populations prevoously evolved on strictly immune deficient (HeLa) cells, strictly immune competent (MDCK) cells, or on alternating deficient/competent...

Data from: Differentially expressed genes match bill morphology and plumage despite largely homogenous genomes in a Holarctic songbird

Nicholas A. Mason & Scott A. Taylor
Understanding the patterns and processes that contribute to phenotypic diversity and speciation is a central goal of evolutionary biology. Recently, high-throughput sequencing has provided unprecedented phylogenetic resolution in many lineages that have experienced rapid diversification. The Holarctic redpoll finches (Genus: Acanthis) provide an intriguing example of a recent, phenotypically diverse lineage; traditional sequencing and genotyping methods have failed to detect any genetic differences between currently recognized species, despite marked variation in plumage and morphology within...

Data from: Evaluating the performance of selection scans to detect selective sweeps in domestic dogs

Florencia Schlamp, Julian Van Der Made, Rebecca Stambler, Lewis Chesebrough, Adam R. Boyko & Philipp W. Messer
Selective breeding of dogs has resulted in repeated artificial selection on breed-specific morphological phenotypes. A number of quantitative trait loci associated with these phenotypes have been identified in genetic mapping studies. We analyzed the population genomic signatures observed around the causal mutations for 12 of these loci in 25 dog breeds, for which we genotyped 25 individuals in each breed. By measuring the population frequencies of the causal mutations in each breed, we identified those...

Data from: High opportunity for postcopulatory sexual selection under field conditions

Biz R. Turnell & Kerry L. Shaw
In polygamous systems, male fitness is determined not only by mating success but also by fertilization success. Despite the growing interest over the past several decades in postcopulatory sexual selection, its relative importance compared to precopulatory sexual selection remains a subject of debate. Here, we use extensive behavioral observations of a semi-natural population of Hawaiian swordtail crickets, Laupala cerasina, and molecular paternity assignment to measure the opportunities for pre- and postcopulatory selection. Because postcopulatory selection...

Data from: Long-term avian community response to housing development at the boundary of U.S. protected areas: effect size increases with time

Eric M. Wood, Anna M. Pidgeon, Volker C. Radeloff, David P. Helmers, Patrick D. Culbert, Nicholas S. Keuler & Curtis H. Flather
1. Biodiversity conservation is a primary function of protected areas. However, protected areas also attract people, and therefore, land use has intensified at the boundaries of these lands globally. In the USA, since the 1970s, housing growth at the boundaries (<1 km) of protected areas has increased at a rate far higher than on more distant private lands. Here, we designed our analyses to address our central hypothesis that increasing housing density in and near...

Data from: Nest suitability, fine-scale population structure and male-mediated dispersal of a solitary ground nesting bee in an urban landscape

Margarita M. López-Uribe, Stephen J. Morreale, Christine K. Santiago & Bryan N. Danforth
Bees are the primary pollinators of flowering plants in almost all ecosystems. Worldwide declines in bee populations have raised awareness about the importance of their ecological role in maintaining ecosystem functioning. The naturally strong philopatric behavior that some bee species show can be detrimental to population viability through increased probability of inbreeding. Furthermore, bee populations found in human-altered landscapes, such as urban areas, can experience lower levels of gene flow and effective population sizes, increasing...

Data from: Genetic structure, admixture, and invasion success in a Holarctic defoliator, the gypsy moth (Lymantria dispar, Lepidoptera: Erebidae)

Yunke Wu, John J. Molongoski, Deborah F. Winograd, Steven M. Bogdanowicz, Artemis S. Louyakis, David R. Lance, Victor C. Mastro & Richard G. Harrison
Characterizing the current population structure of potentially invasive species provides a critical context for identifying source populations and for understanding why invasions are successful. Non-native populations inevitably lose genetic diversity during initial colonization events, but subsequent admixture among independently introduced lineages may increase both genetic variation and adaptive potential. Here we characterize the population structure of the gypsy moth (Lymantria dispar Linnaeus), one of the world's most destructive forest pests. Native to Eurasia and recently...

Data from: Sensory-based niche partitioning in a multiple predator-multiple prey community

Jay J. Falk, Hannah M. Ter Hofstede, Patricia L. Jones, Marjorie M. Dixon, Paul A. Faure, Elisabeth K. V. Kalko & Rachel A. Page
Many predators and parasites eavesdrop on the communication signals of their prey. Eavesdropping is typically studied as dyadic predator–prey species interactions; yet in nature, most predators target multiple prey species and most prey must evade multiple predator species. The impact of predator communities on prey signal evolution is not well understood. Predators could converge in their preferences for conspicuous signal properties, generating competition among predators and natural selection on particular prey signal features. Alternatively, predator...

Data from: Resolving relationships within the palm subfamily Arecoideae (Arecaceae) using next-gen derived plastid sequences

Jason R. Comer, Wendy B. Zomlefer, Craig F. Barrett, Jerrold I. Davis, Dennis W. Stevenson, Karolina Heyduk & James H. Leebens-Mack
Premise of the study: Several studies have incorporated molecular and morphological data to study the phylogeny of the palms (Arecaceae), but some relationships within the family remain ambiguous—particularly those within Arecoideae, the most diverse subfamily including coconut and oil palm. Here, two next-generation, targeted plastid-enrichment methods were compared and used to elucidate Arecoideae phylogeny. Methods: Next-generation sequencing techniques were used to generate a plastid genome data set. Long range PCR and hybrid gene capture were...

Data from: Identification and distribution of the NBS-LRR gene family in the Cassava genome

Roberto Lozano, Martha T. Hamblin, Simon Prochnik & Jean-Luc Jannink
Background: Plant resistance genes (R genes) exist in large families and usually contain both a nucleotide-binding site domain and a leucine-rich repeat domain, denoted NBS-LRR. The genome sequence of cassava (Manihot esculenta) is a valuable resource for analysing the genomic organization of resistance genes in this crop. Results: With searches for Pfam domains and manual curation of the cassava gene annotations, we identified 228 NBS-LRR type genes and 99 partial NBS genes. These represent almost...

Data from: Kinship, inbreeding, and fine-scale spatial structure influence gut microbiota in a hindgut-fermenting tortoise

Michael L. Yuan, Samantha H. Dean, Ana V. Longo Berrios, Betsie B. Rothermel, Tracey D. Tuberville, Kelly R. Zamudio & Ana V. Longo
Herbivorous vertebrates rely on complex communities of mutualistic gut bacteria to facilitate the digestion of celluloses and hemicelluloses. Gut microbes are often convergent based on diet and gut morphology across a phylogenetically diverse group of mammals. However, little is known about microbial communities of herbivorous hindgut-fermenting reptiles. Here, we investigate how factors at the individual level might constrain the composition of gut microbes in an obligate herbivorous reptile. Using multiplexed 16S rRNA gene sequencing, we...

Data from: Vicariance and marine migration in continental island populations of a frog endemic to the Atlantic Coastal forest

M. Catherine Duryea, Kelly R. Zamudio & Cinthia A. Brasileiro
The theory of island biogeography is most often studied in the context of oceanic islands where all island inhabitants are descendants from founding events involving migration from mainland source populations. Far fewer studies have considered predictions of island biogeography in the case of continental islands, where island formation typically splits continuous populations and thus vicariance also contributes to the diversity of island populations. We examined one such case on continental islands in southeastern Brazil, to...

Data from: The distribution of fitness effects in an uncertain world

Tim Connallon & Andrew G. Clark
The distribution of fitness effects (DFE) among new mutations plays a critical role in adaptive evolution and the maintenance of genetic variation. While fitness landscape models predict several key features of the DFE, most theory to date focuses on predictable environmental conditions, while ignoring stochastic environmental fluctuations that feature prominently in the ecology of many organisms. Here, we derive an extension of Fisher's geometric model that incorporates two common effects of environmental variation: (1) non-adaptive...

Data from: Genetic structure in village dogs reveals a Central Asian domestication origin

Laura M. Shannon, Ryan H. Boyko, Marta Castelhano, Elizabeth Corey, Jessica J. Hayward, Corin McLean, Michelle E. White, Mounir Abi Said, Baddley A. Anita, Nono Bondjengo Ikombe, Jorge Calero, Ana Galov, Marius Hedimbi, Bulu Imam, Rajashree Khalap, Douglas Lally, Andrew Masta, Kyle C. Oliveira, Lucía Pérez, Julia Randall, Nguyen Minh Tam, Francisco J. Trujillo-Cornejo, Carlos Valeriano, Nathan B. Sutter, Rory J. Todhunter … & Adam R. Boyko
Dogs were the first domesticated species, originating at least 15,000 y ago from Eurasian gray wolves. Dogs today consist primarily of two specialized groups—a diverse set of nearly 400 pure breeds and a far more populous group of free-ranging animals adapted to a human commensal lifestyle (village dogs). Village dogs are more genetically diverse and geographically widespread than purebred dogs making them vital for unraveling dog population history. Using a semicustom 185,805-marker genotyping array, we...

Data from: The challenge of accurately documenting bee species richness in agroecosystems: bee diversity in eastern apple orchards

Laura A. Russo, Mia Park, Jason Gibbs, Bryan Danforth & Laura Russo
Bees are important pollinators of agricultural crops, and bee diversity has been shown to be closely associated with pollination, a valuable ecosystem service. Higher functional diversity and species richness of bees have been shown to lead to higher crop yield. Bees simultaneously represent a mega-diverse taxon that is extremely challenging to sample thoroughly and an important group to understand because of pollination services. We sampled bees visiting apple blossoms in 28 orchards over 6 years....

Data from: Distinguishing noise from signal in patterns of genomic divergence in a highly polymorphic avian radiation

Leonardo Campagna, Ilan Gronau, Luís Fábio Silveira, Adam Siepel & Irby J. Lovette
Recently diverged taxa provide the opportunity to search for the genetic basis of the phenotypes that distinguish them. Genomic scans aim to identify loci that are diverged with respect to an otherwise weakly differentiated genetic background. These loci are candidates for being past targets of selection because they behave differently from the rest of the genome that has either not yet differentiated or that may cross species barriers through introgressive hybridization. Here we use a...

Data from: Disentangling visual and olfactory signals in mushroom-mimicking Dracula orchids using realistic three-dimensional printed flowers

Tobias Policha, Aleah Davis, Melinda Barnadas, Bryn T. M. Dentinger, Robert A. Raguso & Bitty A. Roy
Flowers use olfactory and visual signals to communicate with pollinators. Disentangling the relative contributions and potential synergies between signals remains a challenge. Understanding the perceptual biases exploited by floral mimicry illuminates the evolution of these signals. Here, we disentangle the olfactory and visual components of Dracula lafleurii, which mimics mushrooms in size, shape, color and scent, and is pollinated by mushroom-associated flies. To decouple signals, we used three-dimensional printing to produce realistic artificial flower molds...

Data from: Seasonal changes in the altitudinal distribution of nocturnally migrating birds during autumn migration

Frank A. La Sorte, Wesley M. Hochachka, Andrew Farnsworth, Daniel Sheldon, Benjamin M. Van Doren, Daniel Fink & Steve Kelling
Wind plays a significant role in the flight altitudes selected by nocturnally migrating birds. At mid-latitudes in the Northern Hemisphere, atmospheric conditions are dictated by the polar-front jet stream, whose amplitude increases in the autumn. One consequence for migratory birds is that the region’s prevailing westerly winds become progressively stronger at higher migration altitudes. We expect this seasonality in wind speed to result in migrants occupying progressively lower flight altitudes, which we test using density...

Registration Year

  • 2015

Resource Types

  • Dataset


  • Cornell University
  • University of Massachusetts Amherst
  • The University of Texas at Austin
  • University of Georgia
  • University of California System
  • Oregon State University
  • United States Department of Agriculture
  • University of Florida
  • University of Utah
  • University of Nebraska - Lincoln