87 Works

Data from: Double-digest RAD sequencing outperforms microsatellite loci at assigning paternity and estimating relatedness: a proof of concept in a highly promiscuous bird

Derrick J. Thrasher, Bronwyn G. Butcher, Leonardo Campagna, Michael S. Webster & Irby J. Lovette
Information on genetic relationships among individuals is essential to many studies of the behavior and ecology of wild organisms. Parentage and relatedness assays based on large numbers of SNP loci hold substantial advantages over the microsatellite markers traditionally used for these purposes. We present a double-digest restriction site-associated DNA sequencing (ddRAD-seq) analysis pipeline that, as such, simultaneously achieves the SNP discovery and genotyping steps and which is optimized to return a statistically powerful set of...

Data from: Agricultural pastures challenge the attractiveness of natural saltmarsh for a migratory goose

Adriaan M. Dokter, Wimke Fokkema, Barwolt S. Ebbinge, Han Olff, Henk P. Van Der Jeugd & Bart A. Nolet
1. Broad-scale land conversions and fertilizer use have dramatically altered the available staging area for herbivorous long-distance migrants. Instead of natural land, these birds rely increasingly on pastures for migratory fuelling and stopover, often conflicting with farming practices. To be able to predict and manage birds’ future habitat use, the relative advantages and disadvantages of natural (e.g. saltmarsh, intertidal) versus anthropogenic staging sites for foraging need to be understood. 2. We compared the migratory staging...

Data from: Genomewide genotyping of a novel Mexican Chile Pepper collection illuminates the history of landrace differentiation after Capsicum annuum L. domestication

Nathan Taitano, Vivian Bernau, Lev Jardón-Barbolla, Brian Leckie, Michael Mazourek, Kristin Mercer, Leah McHale, Andrew Michel, David Baumler, Michael Kantar, Esther Van Der Knapp & Esther Van Der Knaap
Studies of genetic diversity among phenotypically distinct crop landraces improve our understanding of fruit evolution and genome structure under domestication. Chile peppers (Capsicum spp. L.) are economically valuable and culturally important species, and extensive phenotypic variation among landraces exists in southern Mexico, a center of C. annuum diversity. We collected 103 chile pepper seed accessions from 22 named landraces across 27 locations in southern Mexico. We genotyped these accessions with genotyping-by-sequencing (GBS), yielding 32,623 filtered...

Data from: What doesn’t kill you makes you stronger: the burdens and benefits of toxin sequestration in a milkweed aphid

Tobias Züst, Sophie Mou & Anurag A. Agrawal
1. Specialized insect herbivores commonly co-opt plant defences for protection against predators, but the costs, benefits, and mechanisms of sequestration are poorly understood. 2. We quantified sequestration of toxic cardenolides by the specialist aphid Aphis nerii when reared on four closely related milkweed (Asclepias) species with >20-fold variation in cardenolide content, and in the presence or absence of ladybug predators. 3. Increasing concentrations of apolar plant cardenolides increased sequestered amounts in aphids. High concentrations in...

Data from: The low but uncertain measured benefits of U.S. water quality policy

David A. Keiser, Catherine L. Kling & Joseph S. Shapiro
US investment to decrease pollution in rivers, lakes, and other surface waters has exceeded $1.9 trillion since 1960, and has also exceeded the cost of most other US environmental initiatives. These investments come both from the 1972 Clean Water Act and the largely voluntary efforts to control pollution from agriculture and urban runoff. This paper reviews the methods and conclusions of about 20 recent evaluations of these policies. Surprisingly, most analyses estimate that these policies’...

Data from: Causes of seasonal decline in reproduction of the cooperatively-breeding acorn woodpecker

Walter D. Koenig & Eric L. Walters
Clutch size and reproductive success decline seasonally in a wide range of temperate avian taxa. Two competing hypotheses have been proposed to explain such declines: the “timing” hypothesis, which states that conditions affecting reproduction decline intrinsically with date, and the “quality” hypothesis, which proposes that high-quality individuals or individuals in high-quality situations breed earlier. We contrasted the relative importance of these two hypotheses using a long-term dataset of the cooperatively-breeding acorn woodpecker (Melanerpes formicivorus) in...

Data from: Prevalence and diversity of haemosporidian parasites in the yellow-rumped warbler hybrid zone

Camille-Sophie Cozzarolo, Tania Jenkins, David P.L. Toews, Alan Brelsford, Philippe Christe & David P. L. Toews
Parasites can play a role in speciation, by exerting different selection pressures on different host lineages, leading to reproductive barriers in regions of possible interbreeding. Hybrid zones therefore offer an ideal system to study the effect of parasites on speciation. Here we study a hybrid zone in the foothills of the Rocky Mountains where two yellow-rumped warbler subspecies, Setophaga coronata coronata and S. c. auduboni, interbreed. There is partial reproductive isolation between them, but no...

Data from: Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement

Shan Wu, Kin H. Lau, Qinghe Cao, John P. Hamilton, Honghe Sun, Chenxi Zhou, Lauren Eserman, Dorcus Gemenet, Bode Olukolu, Haiyan Wang, Emily Crisovan, Grant T. Godden, Chen Jiao, Xin Wang, Mercy Kitavi, Norma Manrique-Carpintero, Brieanne Vaillancourt, Krystle Wiegert-Rininger, Xinsun Yang, Kan Bao, Yi Zheng, Jennifer Schaff, Jan Kreuze, Wolfgang Gruneberg, Awais Khan … & Zhangjun Fei
I_triloba_NSP323_stress_FPKM_expression_matrix_v3_anno.xlsxFPKM values of v3 high confidence gene models for 15 I. triloba abiotic and biotic stress RNA-seq libraries. The libraries are described in the 'Library Key' worksheet.I_triloba_NSP323_FPKM_expression_matrix_v3_anno.xlsxFPKM values of v3 high confidence gene models for 6 I. triloba RNA-seq libraries (flower, flowerbud, leaf, root1, root2, stem).NSP323_triloba_v3.hc.func_anno.txtPutative functional annotation of high confidence gene models.NSP323_triloba_v3.hc.gene_models.cdna.faNucleotide sequences of the high confidence gene model transcript sequences (cDNA).NSP323_triloba_v3.hc.gene_models.cds.faNucleotide sequences of the high confidence gene model coding sequences (CDS).NSP323_triloba_v3.hc.gene_models.gff3High confidence gene...

Data from: Risk taking of educated nematodes

Denis S. Willett, Hans T. Alborn, Lukasz L. Stelinski & David I. Shapiro-Ilan
Nematode parasites rely on successful host infection to perpetuate their species. Infection by individual nematode parasites can be risky, however; any one individual could be killed by the host's immune response. Here we use a model system to show that environmental cues and parasite past experience can be used by entomopathogenic nematodes to reduce individual risk of infection. Past parasite experience can more than double the infective virulence (number of host invaders) of a given...

Data from: The impact of bacteriophages on phyllosphere bacterial abundance and composition

Norma M. Morella, Annika L. Gomez, Grant Wang, Michelle S. Leung & Britt Koskella
Interactions between bacteria and bacteriophage viruses (phages) are known to influence pathogen growth and virulence, microbial diversity, and even biogeochemical cycling. Lytic phages in particular infect and lyse their host cells, and can therefore have significant effects on cell densities as well as competitive dynamics within microbial communities. Despite the known impacts of lytic phages on the ecology and evolution of bacteria in free-living communities, little is known about the role of lytic phages in...

Data from: Synchronous diversification of Sulawesi's iconic artiodactyls driven by recent geological events

Laurent A. F. Frantz, Anna Rudzinski, Abang Mansyursyah Surya Nugraha, Allowen Evin, James Burton, Ardern Hulme-Beaman, Anna Linderholm, Ross Barnett, Rodrigo Vega, Evan K. Irving-Pease, James Haile, Richard Allen, Kristin Leus, Jill Shephard, Mia Hillyer, Sarah Gillemot, Jeroen Van Den Hurk, Sharron Ogle, Cristina Atofanei, Mark G. Thomas, Friederike Johansson, Abdul Haris Mustari, John Williams, Kusdiantoro Mohamad, Chandramaya Siska Damayanti … & Greger Larson
The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back 40 Myr ago. Recent studies, however, suggest that much of Sulawesi’s fauna assembled over the last 15 Myr. Here, we test the hypothesis that more recent uplift of previously submerged portions of land on Sulawesi promoted diversification, and that much of its faunal assemblage is much younger than the island itself. To do so, we combined palaeogeographical reconstructions...

Data from: A flicker of hope: genomic data distinguish Northern Flicker taxa despite low levels of divergence

Stepfanie M. Aguillon, Leonardo Campagna, Richard G. Harrison & Irby J. Lovette
Next-generation sequencing technologies are increasingly being employed to explore patterns of genomic variation in avian taxa previously characterized using morphology and/or traditional genetic markers. The hybridization dynamics of the Northern Flicker complex have received considerable attention, primarily due to the conspicuous plumage differences among these birds and the geographically extensive hybrid zone between the Red-shafted (Colaptes auratus cafer) and Yellow-shafted (Colaptes auratus auratus) flickers in the Great Plains region of North America. However, no traditional...

Data from: Geographic variation and environmental correlates of apparent survival rates in adult tree swallows Tachycineta bicolor

Robert G. Clark, David W. Winkler, Russell D. Dawson, Dave Shutler, David J. T. Hussell, Michael P. Lombardo, Patrick A. Thorpe, Peter O. Dunn & Linda A. Whittingham
Determining demographic rates in wild animal populations and understanding why rates vary are important challenges in population ecology and conservation. Whereas reproductive success is reported frequently for many songbird species, there are relatively few corresponding estimates of annual survival for widespread populations of the same migratory species. We incorporated mark-recapture data into Cormack-Jolly-Seber models to estimate annual apparent survival and recapture rates of adult male and female tree swallows Tachycineta bicolor in eight local breeding...

Avifauna occurrence data from a longitudinal experiment in human-modified Amazonian forests affected by the 2015-16 El Niño drought and associated fires

A. Lees, N. Moura, F.M. Franca, J.N. Ferreira, T. Gardner, E. Berenguer, L. Chesini, C. Andertti & J. Barlow
This data set includes longitudinal occurrence of bird species at 36 forest plots – half of which burned during the 2015-16 El Niño drought – distributed across a gradient of prior human disturbance in the Brazilian Amazon. Data was collected in 2010 and 2016 (around 6 years before, and one year after the 2015-16 El Niño, respectively) as part of the projects ‘Assessing ENSO-induced Fire Impacts in tropical Rainforest Ecosystems’ (AFIRE) and ‘Biodiversity and Ecosystem...

Data from: Temperature drives Zika virus transmission: evidence from empirical and mathematical models

Blanka Tesla, Leah Demakovsky, Erin Mordecai, Sadie Ryan, Matthew Bonds, Calistus Ngonghala, Melinda Brindley & Courtney Murdock
Temperature is a strong driver of vector-borne disease transmission. Yet, for emerging arboviruses we lack fundamental knowledge on the relationship between transmission and temperature. Current models rely on the untested assumption that Zika virus responds similarly to dengue virus, potentially limiting our ability to accurately predict the spread of Zika. We conducted experiments to estimate the thermal performance of Zika virus (ZIKV) in field-derived Aedes aegypti across eight constant temperatures. We observed strong, unimodal effects...

Data from: Male body size predicts reproductive success but not within-clutch paternity patterns in gopher tortoises (Gopherus polyphemus)

K. Nicole White, Betsie B. Rothermel, Kelly R. Zamudio & Tracey D. Tuberville
In many vertebrates, body size is an important driver of variation in male reproductive success. Larger, more fit individuals are more likely to dominate mating opportunities, skewing siring success and resulting in lower effective population sizes and genetic diversity. The mating system of the gopher tortoise (Gopherus polyphemus) has been characterized as both female-defense and scramble-competition polygyny. Mating systems are typically not fixed and can be influenced by factors such as population density, demographic structure,...

Data from: Air pollution and visitation at national parks

David Keiser, Gabriel Lade & Ivan Rudik
Hundreds of millions of visitors travel to U.S. national parks every year to visit America’s iconic landscapes. Concerns about air quality in these areas have led to strict, yet controversial pollution control policies. We document pollution trends in U.S. national parks and estimate the relationship between pollution and park visitation. From 1990-2014, average ozone concentrations in national parks were statistically indistinguishable from the 20 largest U.S. metropolitan areas. Further, relative to U.S. cities, national parks...

Data from: Disease where you dine: plant species and floral traits associated with pathogen transmission in bumble bees

Lynn S. Adler, Kristen M. Michaud, Stephen P. Ellner, Scott H. McArt, Phillip C. Stevenson, Rebecca E. Irwin & Philip C. Stevenson
Hotspots of disease transmission can strongly influence pathogen spread. Bee pathogens may be transmitted via shared floral use, but the role of plant species and floral trait variation in shaping transmission dynamics is almost entirely unexplored. Given the importance of pathogens for the decline of several bee species, understanding whether and how plant species and floral traits affect transmission could give us important tools for predicting which plant species may be hotspots for disease spread....

Data from: Aquatic insects rich in omega-3 fatty acids drive breeding success in a widespread bird

Cornelia Wingfield Twining, Jeremy Ryan Shipley & David W. Winkler
Ecologists studying bird foraging ecology have generally focused on food quantity over quality. Emerging work suggests that food quality, in terms of highly unsaturated omega-3 fatty acids (HUFA), can have equally important effects on performance. HUFA, which are present in aquatic primary producers, are all but absent in vascular plants, and HUFA content is also correspondingly higher in aquatic insects. Here, we show that Tree Swallow (Tachycineta bicolor) chicks rapidly accumulate HUFA from food during...

Data from: No support for the sexy‐sperm hypothesis in the seed beetle: sons of monandrous females fare better in post‐copulatory competition

Kristin A. Hook
The sexy-sperm hypothesis posits that polyandrous females derive an indirect fitness benefit from multi-male mating because they increase the probability their eggs are fertilized by males whose sperm have high fertilizing efficiency, which is assumed to be heritable and conferred on their sons. However, whether this process occurs is contentious because father-to-son heritability may be constrained by the genetic architecture underlying traits important in sperm competition within certain species. Previous empirical work has revealed such...

Data from: Elucidating biogeographical patterns in Australian native canids using genome wide SNPs

Kylie M. Cairns, Laura M. Shannon, Janice Koler-Matznick, J. William O. Ballard & Adam R. Boyko
Dingoes play a strong role in Australia’s ecological framework as the apex predator but are under threat from hybridization and agricultural control programs. Government legislation lists the conservation of the dingo as an important aim, yet little is known about the biogeography of this enigmatic canine, making conservation difficult. Mitochondrial and Y chromosome DNA studies show evidence of population structure within the dingo. Here, we present the data from Illumina HD canine chip genotyping for...

Data from: Bidirectional adaptive introgression between two ecologically divergent sparrow species

Jennifer Walsh, Adrienne I. Kovach, Brian Justin Olsen, W. Gregory Shriver & Irby J. Lovette
Natural hybrid zones can be used to dissect the mechanisms driving key evolutionary processes by allowing us to identify genomic regions important for establishing reproductive isolation and that allow for transfer of adaptive variation. We leverage whole-genome data in a system where two bird species, the saltmarsh (Ammospiza caudacutus) and Nelson’s (A. nelsoni) sparrow, hybridize despite their relatively high background genetic differentiation and past ecological divergence. Adaptive introgression is plausible in this system because Nelson’s...

Data from: A comparison of genomic islands of differentiation across three young avian species pairs

Darren E. Irwin, Borja Milá, David P. L. Toews, Alan Brelsford, Haley L. Kenyon, Alison N. Porter, Christine Grossen, Kira E. Delmore, Miguel Alcaide & Jessica H. Irwin
Detailed evaluations of genomic variation between sister species often reveal distinct chromosomal regions of high relative differentiation (i.e., “islands of differentiation” in FST), but there is much debate regarding the causes of this pattern. We briefly review the prominent models of genomic islands of differentiation and compare patterns of genomic differentiation in three closely related pairs of New World warblers with the goal of evaluating support for the four models. Each pair (MacGillivray's / mourning...

Data from: Guidelines and considerations for designing field experiments simulating precipitation extremes in forest ecosystems

Heidi Asbjornsen, John L. Campbell, Katie A. Jennings, Matthew A. Vadeboncoeur, Cameron McIntire, Pamela H. Templer, Richard P. Phillips, Taryn L. Bauerle, Michael C. Dietze, Serita D. Frey, Peter M. Groffman, Rosella Guerrieri, Paul J. Hanson, Eric P. Kelsey, Alan K. Knapp, Nathan G. McDowell, Patrick Meir, Kimberly A. Novick, Scott V. Ollinger, Will T. Pockman, Paul G. Schaberg, Stan D. Wullschleger, Melinda D. Smith & Lindsey E. Rustad
1. Context. Precipitation regimes are changing in response to climate change, yet understanding of how forest ecosystems respond to extreme droughts and pluvials remains incomplete. As future precipitation extremes will likely fall outside the range of historical variability, precipitation manipulation experiments (PMEs) are critical to advancing knowledge about potential ecosystem responses. However, few PMEs have been conducted in forests compared to short-statured ecosystems, and forest PMEs have unique design requirements and constraints. Moreover, past forest...

Data from: Phenotypic traits and resource quality as factors affecting male reproductive success in a toadfish

Aneesh P H Bose, Karen M Cogliati, Nick Luymes, Andrew H Bass, Margaret A Marchaterre, Joseph A Sisneros, Benjamin Bolker, Sigal Balshine & Benjamin M Bolker
A male’s reproductive success often depends on both his phenotypic quality and the quality of the resources he controls. An important and longstanding challenge for evolutionary biologists has been to disentangle these two often-correlated factors. Here, we present a large multi-year, multi-population field study along with complementary laboratory experiments aimed at disentangling the effects of male quality and nest quality in driving male reproductive success in the plainfin midshipman fish, Porichthys notatus. We investigate how...

Registration Year

  • 2018

Resource Types

  • Dataset


  • Cornell University
  • University of California, Berkeley
  • University of Georgia
  • Michigan State University
  • University of Adelaide
  • Stanford University
  • The Ohio State University
  • Lund University
  • University of Wisconsin-Madison
  • Agricultural Research Service