68 Works

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: 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: 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: Divergence in DNA photorepair efficiency among genotypes from contrasting UV radiation environments in nature

Brooks E. Miner, Paige M. Kulling, Karlyn D. Beer & Benjamin Kerr
Populations of organisms routinely face abiotic selection pressures, and a central goal of evolutionary biology is to understand the mechanistic underpinnings of adaptive phenotypes. Ultraviolet radiation (UVR) is one of earth’s most pervasive environmental stressors, potentially damaging DNA in any organism exposed to solar radiation. We explored mechanisms underlying differential survival following UVR exposure in genotypes of the water flea Daphnia melanica derived from natural ponds of differing in UVR intensity. The UVR tolerance of...

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: 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: 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: 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: 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: 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: 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...

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: Sons do not take advantage of a head start: parity in herring gull offspring sex ratios despite greater initial investment in males

David N. Bonter, Michelle C. Moglia & Luke E. DeFisher
Skewed adult sex ratios sometimes occur in populations of free-living animals yet the proximate mechanisms, timing of sex-biases, and the selective agents contributing to skew remain a source of debate with contradictory evidence from different systems. We investigated potential mechanisms contributing to sex biases in a population of herring gulls with an apparent female skew in the adult population. Theory predicts that skewed adult sex ratios will adaptively lead to skewed offspring sex ratios to...

Data from: Population growth and sequestration of plant toxins along a gradient of specialization in four aphid species on the common milkweed Asclepias syriaca

Tobias Züst & Anurag A. Agrawal
Dietary specialization in insect herbivores has long been hypothesized to predict tolerance of plant defences, with more specialized herbivores being highly tolerant of and sometimes sequestering plant secondary compounds. Plant variation in secondary compounds should thus play an important and predictable role in shaping the performance and distribution of insect communities. We compared the performance of four naturally co-occurring aphid species on twenty genotypes of the common milkweed Asclepias syriaca. Genotypes of milkweed consistently differed...

Data from: Experimental food supplementation reveals habitat-dependent male reproductive investment in a migratory bird

Sara A. Kaiser, T. Scott Sillett, Benjamin B. Risk & Michael S. Webster
Environmental factors can shape reproductive investment strategies and influence the variance in male mating success. Environmental effects on extrapair paternity have traditionally been ascribed to aspects of the social environment, such as breeding density and synchrony. However, social factors are often confounded with habitat quality and are challenging to disentangle. We used both natural variation in habitat quality and a food supplementation experiment to separate the effects of food availability—one key aspect of habitat quality—on...

Data from: Sexual fidelity trade-offs promote regulatory variation in the prairie vole brain

Mariam Okhovat, Alejandro Berrio, Gerard Wallace, Alexander G. Ophir & Steven M. Phelps
Individual variation in social behavior seems ubiquitous, but we know little about how it relates to brain diversity. Among monogamous prairie voles, levels of vasopressin receptor (encoded by the gene avpr1a) in brain regions related to spatial memory predict male space use and sexual fidelity in the field. We find that trade-offs between the benefits of male fidelity and infidelity are reflected in patterns of territorial intrusion, offspring paternity, avpr1a expression, and the evolutionary fitness...

Data from: Seasonal and ontogenetic variation of skin microbial communities and relationships to natural disease dynamics in declining amphibians

Ana V. Longo, Anna E. Savage, Ian Hewson & Kelly R. Zamudio
Recently, microbiologists have focused on characterizing the probiotic role of skin bacteria for amphibians threatened by the fungal disease chytridiomycosis. However, the specific characteristics of microbial diversity required to maintain health or trigger disease are still not well understood in natural populations. We hypothesized that seasonal and developmental transitions affecting susceptibility to chytridiomycosis could also alter the stability of microbial assemblages. To test our hypothesis, we examined patterns of skin bacterial diversity in two species...

Data from: The complex contributions of genetics and nutrition to immunity in Drosophila melanogaster

Robert L. Unckless, Susan M. Rottschaefer & Brian P. Lazzaro
Both malnutrition and undernutrition can lead to compromised immune defense in a diversity of animals, and “nutritional immunology” has been suggested as a means of understanding immunity and determining strategies for fighting infection. The genetic basis for the effects of diet on immunity, however, has been largely unknown. In the present study, we have conducted genome-wide association mapping in Drosophila melanogaster to identify the genetic basis for individual variation in resistance, and for variation in...

Data from: Genomic selection and association mapping in rice (Oryza sativa): effect of trait genetic architecture, training population composition, marker number and statistical model on accuracy of rice genomic selection in elite, tropical rice breeding lines

Jennifer Spindel, Hasina Begum, Deniz Akdemir, Parminder Virk, Bertrand Collard, Edilberto Redoña, Gary Atlin, Jean-Luc Jannink & Susan R. McCouch
Genomic Selection (GS) is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population. GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species, and here we evaluate for the first time its efficacy for breeding inbred lines of rice. We performed a genome-wide association study (GWAS) in conjunction with five-fold GS cross-validation on a population of 363...

Data from: Wolbachia infection in a natural parasitoid wasp population

Anne Duplouy, Christelle Couchoux, Ilkka Hanski & Saskya Van Nouhuys
The maternally transmitted bacterium Wolbachia pipientis is well known for spreading and persisting in insect populations through manipulation of the fitness of its host. Here, we identify three new Wolbachia pipientis strains, wHho, wHho2 and wHho3, infecting Hyposoter horticola, a specialist wasp parasitoid of the Glanville fritillary butterfly. The wHho strain (ST435) infects about 50% of the individuals in the Åland islands in Finland, with a different infection rate in the two mitochondrial (COI) haplotypes...

Data from: Plant resistance reduces the strength of consumptive and non-consumptive effects of predators on aphids

Monica F. Kersch-Becker & Jennifer S. Thaler
1. The impact of predators on prey has traditionally been attributed to the act of consumption. Prey responses to the presence of the predator (non-consumptive effects), however, can be as important as predation itself. While plant defences are known to influence predator–prey interactions, their relative effects on consumptive vs. non-consumptive effects are not well understood. 2. We evaluated the consequences of plant resistance and predators (Hippodamia convergens) on the mass, number of nymphs, population growth,...

Data from: Intermediate habitat associations by hybrids may facilitate genetic introgression in a songbird

Eric M. Wood, Sara E. Barker Swarthout, Wesley M. Hochachka, Jeffrey L. Larkin, Ronald W. Rohrbaugh, Kenneth V. Rosenberg, Amanda D. Rodewald & Jeffery L. Larkin
Hybridization or the interbreeding of genetically discrete populations or species can occur where ranges of genetically distinct units overlap. Golden-winged warblers Vermivora chrysoptera, a species that has been in steady decline for decades, highlight the potential population-level consequences of hybridization. A major factor implicated in their decline is hybridization with their sister species, the blue-winged warbler Vermivora cyanoptera, which has likely been exacerbated by historic and current land-use practices. We examined habitat associations of golden-winged...

Data from: Variation in thermal stress response in two populations of the brown seaweed, Fucus distichus, from the Arctic and subarctic intertidal

Irina Smolina, Spyros Kollias, Alexander Jueterbock, James A. Coyer & Galice Hoarau
It is unclear whether intertidal organisms are ‘preadapted’ to cope with the increase of temperature and temperature variability or if they are currently at their thermal tolerance limits. To address the dichotomy, we focused on an important ecosystem engineer of the Arctic intertidal rocky shores, the seaweed Fucus distichus and investigated thermal stress responses of two populations from different temperature regimes (Svalbard and Kirkenes, Norway). Thermal stress responses at 20°C, 24°C and 28°C were assessed...

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