103 Works

Data from: Correlated divergence of female and male genitalia in replicated lineages with ongoing ecological speciation

Ryan Greenway, Rachel McNemee, Alexander Okamoto, Martin Plath, Lenin Arias‐Rodriguez, Michael Tobler & Lenin Arias-Rodriguez
Divergence of genital traits among lineages has the potential to serve as a reproductive isolating barrier when copulation, insemination, or fertilization are inhibited by incompatibilities between female and male genitalia. Despite widespread evidence for genital trait diversity among closely related lineages and coevolution of female and male genitalia within lineages, few studies have investigated genital evolution during the early stages of speciation. We quantified genital variation in replicated population pairs of Poecilia mexicana with ongoing...

Genotyping-by-sequencing data for a Haitian sorghum breeding program

Geoffrey Morris, Terry Felderhoff, Noah Winans, Rachel Walstead, Jean Rigaud Charles, Gael Pressoir & Kebede Muleta
Rapid environmental change can lead to extinction of populations or evolutionary rescue via genetic adaptation. In the past several years, smallholder and commercial cultivation of sorghum (Sorghum bicolor), a global cereal and forage crop, has been threatened by a global outbreak of an aggressive new biotype of sugarcane aphid (SCA; Melanaphis sacchari). Here we characterized genomic signatures of adaptation in a Haitian sorghum breeding population, which had been recently founded from admixed global germplasm, extensively...

ISIMIP3a reservoirs & dams input data

María del Rocío Rivas López, Jida Wang & Fangfang Yao
The Inter-Sectoral Impact Model Intercomparison Project (ISIMIP) provides a framework for the collation of a consistent set of climate impact data across sectors and scales. It also provides a unique opportunity for considering interactions between climate change impacts across sectors through consistent scenarios.
The ISIMIP3a part of the third simulation round is dedicated to i) impact model evaluation and improvement and ii) detection and attribution of observed impacts according to the framework of IPCC AR5 Working...

Data from: Climatic warming and the future of bison as grazers

Joseph M. Craine, E. Gene Towne, Mary Miller & Noah Fierer
Climatic warming is likely to exacerbate nutritional stress and reduce weight gain in large mammalian herbivores by reducing plant nutritional quality. Yet accurate predictions of the effects of climatic warming on herbivores are limited by a poor understanding of how herbivore diet varies along climate gradients. We utilized DNA metabarcoding to reconstruct seasonal variation in the diet of North American bison (Bison bison) in two grasslands that differ in mean annual temperature by 6 °C....

Data from: Prevalence of transcription factors in ascomycete and basidiomycete fungi

Richard B. Todd, Miaomiao Zhou, Robin A. Ohm, Melissa A. C. F. Leeggangers, Loek Visser & Ronald P. De Vries
Background: Gene regulation underlies fungal physiology and therefore is a major factor in fungal biodiversity. Analysis of genome sequences has revealed a large number of putative transcription factors in most fungal genomes. The presence of fungal orthologs for individual regulators has been analysed and appears to be highly variable with some regulators widely conserved and others showing narrow distribution. Although genome-scale transcription factor surveys have been performed before, no global study into the prevalence of...

Data from: Population genomics of pearl millet (Pennisetum glaucum (L.) R. Br.): comparative analysis of global accessions and Senegalese landraces

Zhenbin Hu, Bassirou Mbacké, Ramasamy Perumal, Mame Codou Guèye, Ousmane Sy, Sophie Bouchet, P. V. Vara Prasad & Geoffrey P. Morris
Background: Pearl millet is a staple food for people in arid and semi-arid regions of Africa and South Asia due to its high drought tolerance and nutritional qualities. A better understanding of the genomic diversity and population structure of pearl millet germplasm is needed to support germplasm conservation and genetic improvement of this crop. Here we characterized two pearl millet diversity panels, (i) a set of global accessions from Africa, Asia, and the America, and...

Data from: Population genomics of sorghum (Sorghum bicolor) across diverse agroclimatic zones of Niger

Fanna Maina, Sophie Bouchet, Sandeep R. Marla, Zhenbin Hu, Jianan Wang, Aissata Mamadou, Magagi Abdou, Abdoul-Aziz Saïdou & Geoffrey Preston Morris
Improving adaptation of staple crops in developing countries is important to ensure food security. In the West African country of Niger, the staple crop sorghum (Sorghum bicolor) is cultivated across diverse agroclimatic zones, but the genetic basis of local adaptation has not been described. The objectives of this study were to characterize the genomic diversity of sorghum from Niger and to identify genomic regions conferring local adaptation to agroclimatic zones and farmer preferences. We analyzed...

Data from: Unexpected positive and negative effects of continuing inbreeding in one of the world’s most inbred wild animals

Emily L. Weiser, Catherine E. Grueber, Euan S. Kennedy & Ian G. Jamieson
Inbreeding depression, the reduced fitness of offspring of related individuals, is a central theme in evolutionary biology. Inbreeding effects are influenced by the genetic makeup of a population, which is driven by any history of genetic bottlenecks and genetic drift. The Chatham Island black robin represents a case of extreme inbreeding following two severe population bottlenecks. We tested whether inbreeding measured by a 20-year pedigree predicted variation in fitness among individuals, despite the high mean...

Data from: Intraspecific cytotypic variation and complicated genetic structure in the Phlox amabilis-P. woodhousei (Polemoniaceae) complex

Shannon D. Fehlberg & Carolyn J. Ferguson
PREMISE OF THE STUDY: Polyploidy is widely recognized as an important process in the evolution of plants, but less attention has been paid to the study of intraspecific polyploidy, including its prevalence, formation, taxonomic implications, and effect on genetic diversity, structure, and gene flow within and among individuals and populations. Here we studied intraspecific ploidy level variation in the Phlox amabilis-P. woodhousei complex in order to determine the amount and distribution of cytotypic and genetic...

Data from: Drivers of nocturnal water flux in a tallgrass prairie

Kimberly O'Keefe & Jesse B. Nippert
1. Nocturnal transpiration can impact water balance from the local community to earth-atmosphere fluxes. However, the dynamics and drivers of nocturnal transpiration among coexisting plant functional groups in herbaceous ecosystems are unknown. 2. Here, we addressed the following questions: (1) How do nocturnal (Enight) and diurnal (Eday) transpiration vary among coexisting grasses, forbs, and shrubs in a tallgrass prairie? (2) What environmental variables drive Enight and do these differ from the drivers of Eday? (3)...

Data from: Intraspecific variation of a dominant grass and local adaptation in reciprocal garden communities along a US Great Plains’ precipitation gradient: implications for grassland restoration with climate change

Loretta Johnson, Jacob T. Olsen, Hannah Tetreault, Nora M. Bello, Angel DeLaCruz, Johnny Bryant, Theodore J. Morgan, Mary Knapp, Sara G. Baer, Brian R. Maricle & Loretta C. Johnson
Identifying suitable genetic stock for restoration often employs a ‘best guess’ approach. Without adaptive variation studies, restoration may be misguided. We test the extent to which climate in central US grasslands exerts selection pressure on a foundation grass big bluestem (Andropogon gerardii), widely used in restorations, and resulting in local adaptation. We seeded three regional ecotypes of A. gerardii in reciprocal transplant garden communities across 1150 km precipitation gradient. We measured ecological responses over several...

Data from: Paths to selection on life history loci in different natural environments across the native range of Arabidopsis thaliana

Alexandre Fournier-Level, Amity M. Wilczek, Martha D. Cooper, Judith L. Roe, Jillian Anderson, Deren Eaton, Brook T. Moyers, Renee H. Petipas, Robert N. Schaeffer, Bjorn Pieper, Matthieu Reymond, Maarten Koornneef, Stephen M. Welch, David L. Remington & Johanna Schmitt
Selection on quantitative trait loci (QTL) may vary among natural environments due to differences in the genetic architecture of traits, environment-specific allelic effects or changes in the direction and magnitude of selection on specific traits. To dissect the environmental differences in selection on life history QTL across climatic regions, we grew a panel of interconnected recombinant inbred lines (RILs) of Arabidopsis thaliana in four field sites across its native European range. For each environment, we...

Data from: Comparative riverscape genetics reveals reservoirs of genetic diversity for conservation and restoration of Great Plains fishes.

Megan J. Osborne, Joshuah S. Perkin, Keith B. Gido, Tom F. Turner & Thomas F. Turner
We used comparative landscape genetics to examine the relative roles of historical events, intrinsic traits, and landscape factors in determining the distribution of genetic diversity of river fishes across the North American Great Plains. Spatial patterns of diversity were overlaid on a patch-based graphical model, and then compared within and among three species that co-occurred across five Great Plains watersheds. Species differing in reproductive strategy (benthic vs. pelagic spawning) were hypothesized to have different patterns...

Data from: Cold adaptation increases rates of nutrient flow and metabolic plasticity during cold exposure in Drosophila melanogaster

Caroline M. Williams, Marshall D. McCue, Nishanth E. Sunny, Andre Szejner-Sigal, Theodore J. Morgan, David B. Allison & Daniel A. Hahn
Metabolic flexibility is an important component of adaptation to stressful environments, including thermal stress and latitudinal adaptation. A long history of population genetic studies suggest that selection on core metabolic enzymes may shape life histories by altering metabolic flux. However, the direct relationship between selection on thermal stress hardiness and metabolic flux has not previously been tested. We investigated flexibility of nutrient catabolism during cold stress in Drosophila melanogaster artificially selected for fast or slow...

Data from: Fifty thousand years of arctic vegetation and megafaunal diet

Eske Willerslev, John Davison, Mari Moora, Martin Zobel, Eric Coissac, Mary E. Edwards, Eline D. Lorenzen, Mette Vestergård, Galina Gussarova, James Haile, Joseph Craine, Gaddy Bergmann, Ludovic Gielly, Sanne Boessenkool, Laura S. Epp, Peter B. Pearman, Rachid Cheddadi, David Murray, Karri Anne Bråthen, Nigel Yoccoz, Heather Binney, Corinne Cruaud, Patrick Wincker, Tomasz Goslar, Inger Greve Alsos … & Pierre Taberlet
Although it is generally agreed that the arctic flora is among the youngest and least diverse on Earth, the processes that shaped it are poorly understood. Here we present 50 thousand years (kyr) of arctic vegetation history, derived from the first large-scale ancient DNA metabarcoding study of circumpolar plant diversity. For this interval we additionally explore nematode diversity as a proxy for modelling vegetation cover and soil quality, and diets of herbivorous megafaunal mammals, many...

Data from: Prophylactic digoxin treatment reduces IL-17 production in vivo in the neonatal calf and moderates RSV-associated disease

Jodi L. McGill, Mariana Guerra-Maupome & Sarah Schneider
Respiratory syncytial virus (RSV) is a leading cause of morbidity and mortality in human infants. Bovine RSV infection of neonatal calves is pathologically and immunologically similar to RSV infection in infants, and is therefore a useful preclinical model for testing novel therapeutics. Treatment of severe RSV bronchiolitis relies on supportive care and may include use of bronchodilators and inhaled or systemic corticosteroids. Interleukin-17A (IL-17) is an inflammatory cytokine that plays an important role in neutrophil...

Data from: Investigating behavioral drivers of seasonal Shiga-Toxigenic Escherichia Coli (STEC) patterns in grazing cattle using an agent-based model

Daniel E. Dawson, Jocelyn H. Keung, Monica G. Napoles, Michael R. Vella, Shi Chen, Mike Sanderson, Cristina Lanzas & Michael W. Sanderson
The causes of seasonal variability in pathogen transmission are not well understood, and have not been comprehensively investigated. In an example for enteric pathogens, incidence of Escherichia coli O157 (STEC) colonization in cattle is consistently higher during warmer months compared to cooler months in various cattle production systems. However, actual mechanisms for this seasonality remain elusive. In addition, the influence of host (cattle) behavior on this pattern has not been thoroughly considered. To that end,...

Data from: Ongoing changes in the avifauna of La Selva Biological Station, Costa Rica: twenty-three years of Christmas Bird Counts

W. Alice Boyle & Bryan J. Sigel
Tropical forest fragmentation influences community composition via differential species-level effects. Avian responses to fragmentation at La Selva Biological Station are, in part, responsible for the particular concern over the fate of understory insectivorous species. However, since the 1990s, much previously deforested land within and surrounding La Selva has reverted to forest, providing an opportunity to test hypotheses explaining ongoing avifaunal change. Analyses of 23 years (1989–2011) of Christmas Bird Counts reveal that 63 of 202...

Data from: Ecotypes of an ecologically dominant prairie grass (Andropogon gerardii) exhibit genetic divergence across the U.S. Midwest grasslands environmental gradient

Miranda M. Gray, Paul St. Amand, Nora M. Bello, Mary Knapp, Karen A. Garrett, Theodore J. Morgan, Sara G. Baer, Brian R. Maricle, Eduard D. Akhunov, Loretta C. Johnson & Matthew B. Galliart
Big bluestem (Andropogon gerardii) is an ecologically dominant grass with wide distribution across the environmental gradient of U.S. Midwest grasslands. This system offers an ideal natural laboratory to study the nature of population divergence and adaptation in spatially varying climates. Objectives were to: (i) characterize neutral genetic diversity and structure within and among three regional ecotypes derived from 11 prairies across the U.S. Midwest environmental gradient, (ii) distinguish between the relative roles of isolation-by-distance (IBD)...

Data from: Barcoding the kingdom Plantae: new PCR primers for ITS regions of plants with improved universality and specificity

Tao Cheng, Chao Xu, Li Lei, Changhao Li, Yu Zhang & Shiliang Zhou
The internal transcribed spacer (ITS) of nuclear ribosomal DNA is one of the most commonly used DNA markers in plant phylogenetic and DNA barcoding analyses, and it has been recommended as a core plant DNA barcode. Despite this popularity, the universality and specificity of PCR primers for the ITS region are not satisfactory, resulting in amplification and sequencing difficulties. By thoroughly surveying and analysing the 18S, 5.8S and 26S sequences of Plantae and Fungi from...

Data from: Divergence of the diapause transcriptome in apple maggot flies: winter regulation and post-winter transcriptional repression

Peter J. Meyers, Thomas H. Q. Powell, Kimberly K. O. Walden, Adam Shieferecke, Jeffrey L. Feder, Daniel A. Hahn, Hugh M. Robertson, Stewart H. Berlocher & Gregory J. Ragland
Duration of dormancy regulates seasonal timing in many organisms and may be modulated by day length and temperature. Though photoperiodic modulation has been well studied, temperature modulation of dormancy has received less attention. Here, we leverage genetic variation in diapause in the apple maggot fly, Rhagoletis pomonella, to test whether gene expression during winter or following spring warming regulates diapause duration. We used RNAseq to compare transcript abundance during and after simulated winter between an...

Data from: Phylogeography and species delimitation in convict cichlids (Cichlidae: Amatitlania): implications for taxonomy and Plio–Pleistocene evolutionary history in Central America

Justin C. Bagley, Wilfredo A. Matamoros, Caleb D. McMahan, Michael Tobler, Prosanta Chakrabarty & Jerald B. Johnson
We investigate phylogeographic patterns and delimit species boundaries within Amatitlania, a genus of Central American cichlid fishes. Phylogenetic analyses of mitochondrial DNA sequences from 318 individuals spanning the geographical ranges of all three currently recognized Amatitlania species strongly supported one major clade, with a relatively diverged subclade corresponding to A. kanna samples from eastern Costa Rica and Panama. Gene trees and networks revealed marked incongruences between phylogeographic structure and morpho-species taxonomy as a result of...

Mass ratio effects underlie ecosystem responses to environmental change

Melinda Smith, Sally Koerner, Alan Knapp, Meghan Avolio, Francis Chaves, Elsie Denton, John Dietrich, David Gibson, Jesse Gray, Ava Hoffman, David Hoover, Kimberly Komatsu, Andrea Silletti, Kevin Wilcox, Qiang Yu & John Blair
1. Random species loss has been shown experimentally to reduce ecosystem function, sometimes more than other anthropogenic environmental changes. Yet, controversy surrounds the importance of this finding for natural systems where species loss is non-random. 2. We compiled data from 16 multi-year experiments located at a single site in native tallgrass prairie. These experiments included responses to 11 anthropogenic environmental changes, as well as non-random biodiversity loss - either the removal of uncommon/rare plant species...

Frequent burning causes large losses of carbon from deep soil layers in a temperate savanna

Adam Francis Pellegrini, Kendra K. McLauchlan, Sarah E. Hobbie, Michelle C. Mack, Abbey L. Marcotte, David M. Nelson, Steven Perakis, Peter B. Reich & Kyle Whittinghill
1. Fire activity is changing dramatically across the globe, with uncertain effects on ecosystem processes, especially belowground. Fire‐driven losses of soil carbon (C) are often assumed to occur primarily in the upper soil layers because the repeated combustion of aboveground biomass limits organic matter inputs into surface soil. However, C losses from deeper soil may occur if frequent burning reduces root biomass inputs of C into deep soil layers or stimulates losses of C via...

Data from: Adaptive genetic potential and plasticity of trait variation in the foundation prairie grass Andropogon gerardii across the US Great Plains’ climate gradient: Implications for climate change and restoration

Loretta C. Johnson, Matthew Galliart, Sofia Sabates, Hannah Tetreault, Angel DeLaCruz, Johnny Bryant, Jacob Alsdurf, Mary Knapp, Nora Bello, Sara Baer, Brian Maricle, David Gibson, Jesse Poland, Paul St. Amand, Natalie Unruh, Olivia Parrish & Loretta Johnson
Plant response to climate depends on a species’ adaptive potential. To address this, we used reciprocal gardens to detect genetic and environmental plasticity effects on phenotypic variation and combined with genetic analyses. Four reciprocal garden sites were planted with three regional ecotypes of Andropogon gerardii, a dominant Great Plains prairie grass, using dry, mesic, wet ecotypes originating from western KS to Illinois that span 500 to 1,200 mm rainfall year-1. We aimed to answer: (1)...

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