246 Works

ISIMIP3b ocean input data

Matthias Büchner
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 ISIMIP3b part of the third simulation round is dedicated to a quantification of climate-related risks at different levels of global warming and socio-economic change. ISIMIP3b group I simulations are based on historical...

Data from: Population genetics and independently replicated evolution of predator-associated burst speed ecophenotypy in mosquitofish

Thomas J DeWitt, Nicholas J Troendle, Mariana Mateos & Rodney Mauricio
Many species show replicated ecophenotypy due to recurring patterns of natural selection. Based on the presence or absence of pursuit predators, at least 17 species of fish repeatedly differentiated in body shape in a manner that increases burst swimming speed and the likelihood of predator escape. The predator-associated burst speed (PABS) ecophenotype is characterized by a small head and trunk and enlarged caudal region. Mechanisms promoting replicated phenotype-environment association include selection (without evolution), a single...

Data from: Genetic isolation within the malaria mosquito Anopheles melas

Kevin C. Deitz, Giridhar Athrey, Michael R. Reddy, Hans J. Overgaard, Abrahan Matias, Jawara Musa, Alessandra Della Torre, Vincenzo Petrarca, Joao Pinto, Anthony E. Kiszewski, Pierre Kengne, Carlo Costantini, Adalgisa Caccone, Michel A. Slotman, Musa Jawara & Giri Athrey
Anopheles melas is a brackish water-breeding member of the An. gambiae complex that is distributed along the coast of West Africa and is a major malaria vector within its range. Because little is known about the population structure of this species, we analyzed 15 microsatellite markers and 1,161 bp of mtDNA in 11 An. melas populations collected throughout its range. Compared to its sibling species An. gambiae, An. melas populations have a high level of...

Data from: The lek mating system of the worm pipefish (Nerophis lumbriciformis): a molecular maternity analysis and test of the phenotype-linked fertility hypothesis

Nuno M. Monteiro, Diana Carneiro, Agostinho Antunes, Nuno Queiroz, Maria N. Vieira & Adam G. Jones
The origin and maintenance of mating preferences continues to be an important and controversial topic in sexual selection research. Leks and lek-like mating systems, where individuals gather in particular spots for the sole purpose of mate choice, are particularly puzzling, because the strong directional selection imposed by mate choice should erode genetic variation among competing individuals and negate any benefit for the choosing sex. Here, we take advantage of the lek-like mating system of the...

Data from: Necrobiome framework for bridging decomposition ecology of autotrophically and heterotrophically derived organic matter

Mark Eric Benbow, Philip S. Barton, Michael D. Ulyshen, James C. Beasley, Travis L. DeVault, Michael S. Strickland, Jeffery K. Tomberlin, Heather R. Jordan & Jennifer L. Pechal
Decomposition contributes to global ecosystem function by contributing to nutrient recycling, energy flow and limiting biomass accumulation. The decomposer organisms influencing this process form diverse, complex, and highly dynamic communities that often specialize on different plant or animal resources. Despite performing the same net role, there is a need to conceptually synthesize information on the structure and function of decomposer communities across the spectrum of dead plant and animal resources. A lack of synthesis has...

Data from: Maternal size and age shape offspring size in a live-bearing fish, Xiphophorus birchmanni

Holly K. Kindsvater, Gil G. Rosenthal & Suzanne H. Alonzo
Many studies of offspring size focus on differences in maternal investment that arise from ecological factors such as predation or competition. Classic theory predicts that these ecological factors will select for an optimal offspring size, and therefore that variation in a given environment will be minimized. Yet recent evidence suggests maternal traits such as size or age could also drive meaningful variation in offspring size. The generality of this pattern is unclear, as some studies...

Data from: Soil carbon response to woody plant encroachment: Importance of spatial heterogeneity and deep soil storage

Yong Zhou, Thomas W. Boutton & X. Ben Wu
1. Recent global trends of increasing woody plant abundance in grass-dominated ecosystems may substantially enhance soil organic carbon (SOC) storage and could represent a strong carbon (C) sink in the terrestrial environment. However, few studies have quantitatively addressed the influence of spatial heterogeneity of vegetation and soil properties on SOC storage at the landscape scale. In addition, most studies assessing SOC response to woody encroachment consider only surface soils, and have not explicitly assessed the...

Data from: The curious case of Hermodice carunculata (Annelida: Amphinomidae): evidence for genetic homogeneity throughout the Atlantic Ocean and adjacent basins

Joseph B. Ahrens, Elizabeth Borda, Rômulo Barroso, Paulo C. Paiva, Alexandra M. Campbell, Alexander Wolf, Maggy M. Nugues, Greg W. Rouse & Anja Schulze
Over the last few decades, advances in molecular techniques have led to the detection of strong geographic population structure and cryptic speciation in many benthic marine taxa, even those with long-lived pelagic larval stages. Polychaete annelids, in particular, generally show a high degree of population divergence, especially in mitochondrial genes. Rarely have molecular studies confirmed the presence of ‘cosmopolitan’ species. The amphinomid polychaete Hermodice carunculata was long considered the sole species within its genus, with...

Data from: Natural selection interacts with recombination to shape the evolution of hybrid genomes

Molly Schumer, Chenling Xu, Daniel L Powell, Arun Durvasula, Laurits Skov, Chris Holland, John C Blazier, Sriram Sankararaman, Peter Andolfatto, Gil G Rosenthal & Molly Przeworski
To investigate the consequences of hybridization between species, we studied three replicate hybrid populations that formed naturally between two swordtail fish species, estimating their fine-scale genetic map and inferring ancestry along the genomes of 690 individuals. In all three populations, ancestry from the “minor” parental species is more common in regions of high recombination and where there is linkage to fewer putative targets of selection. The same patterns are apparent in a reanalysis of human...

Data from: Effects of mating order and male size on embryo survival in a pipefish

Ines Braga Goncalves, Kenyon B. Mobley, Ingrid Ahnesjö, Gry Sagebakken, Adam G. Jones & Charlotta Kvarnemo
In species that provide parental care, individuals should invest adaptively in their offspring in relation to the pre- and post-zygotic care provided by their partners. In the broad-nosed pipefish, Syngnathus typhle L., females transfer large, nutrient-rich eggs into the male brood pouch during mating. The male broods and nourishes the embryos for several weeks before independent juveniles emerge at parturition. Given a choice, females clearly prefer large partners. Yet, females provide protein-richer eggs when the...

Data from: Genome-wide selection components analysis in a fish with male pregnancy

Sarah P. Flanagan & Adam G. Jones
A major goal of evolutionary biology is to identify the genome-level targets of natural and sexual selection. With the advent of next-generation sequencing, whole-genome selection components analysis provides a promising avenue in the search for loci affected by selection in nature. Here, we implement a genome-wide selection components analysis in the sex-role-reversed Gulf pipefish, Syngnathus scovelli. Our approach involves a double-digest restriction-site associated DNA sequencing (ddRAD-seq) technique, applied to adult females, non-pregnant males, pregnant males...

Conflicting signal in transcriptomic markers leads to a poorly resolved backbone phylogeny of Chalcidoid wasps

Junxia Zhang, Amelia R.I. Lindsey, Ralph S. Peters, John M. Heraty, Keith R. Hopper, John H. Werren, Ellen O. Martinson, James B. Woolley, Matt J. Yoder & Lars Krogmann
Chalcidoidea (Hymenoptera) are a megadiverse superfamily of wasps with astounding variation in both morphology and biology. Most species are parasitoids and important natural enemies of insects in terrestrial ecosystems. In this study, we explored a transcriptome-based phylogeny of Chalcidoidea and found that poorly resolved relationships could only be marginally improved by adding more genes (a total of 5,591) and taxa (a total of 65), proof-checking for errors of homology and contamination, and decreasing missing data....

Adaptive associations among life history, reproductive traits, environment, and origin in the Wisconsin angiosperm flora

Ricardo Kriebel, Thomas Givnish, John Zaborsky, Jeffrey Rose, Daniel Spalink, Donald Waller, Kenneth Cameron & Kenneth Sytsma
PREMISE OF THE STUDY: We tested 25 classic and novel hypotheses regarding trait-origin, trait-trait, and trait-environment relationships to account for flora-wide variation in life history, habit, and especially reproductive traits using a plastid DNA phylogeny of most native (96.6%, or 1494/1547 species) and introduced (87.5%, or 690/789 species) angiosperms in Wisconsin, USA. METHODS: We assembled data on life history, habit, flowering, dispersal, mating system, and occurrence across open/closed/mixed habitats across species in the state phylogeny....

Comparison of environmental inference approaches for ecometric analyses: Using hypsodonty to estimate precipitation

Rachel A. Short, Katherine Pinson & A. Michelle Lawing
Ecometrics is the study of community-level functional trait-environment relationships. We use ecometric analyses to estimate paleoenvironment and to investigate community-level functional changes through time. We evaluate four methods that have been used or have the potential to be used in ecometric analyses for estimating paleoenvironment to determine whether there have been systematic differences in paleoenvironmental estimation due to choice of the estimation method. Specifically, we evaluated linear regression, polynomial regression, nearest neighbor, and maximum likelihood...

Data from: Co-occurrence of bobcats, coyotes, and ocelots in Texas

Jason Lombardi, Darryl MacKenzie, Michael Tewes, Humberto Perotto, Jose Mata & Tyler Campbell
Interspecific competition among carnivores has been linked to differences in behavior, morphology, and resource use. Insights into these interactions can enhance understanding of local ecological processes that can have impacts on the recovery of endangered species, such as the ocelot (Leopardus pardalis). Ocelots, bobcats (Lynx rufus), and coyotes (Canis latrans) share a small geographic range overlap from South Texas to south-central Mexico but relationships among the three are poorly understood. From May 2011 to March...

Lineage-specific patterns of chromosome evolution are the rule not the exception in Polyneoptera insects

Terrence Sylvester, Carl Hjelmen, Shawn Hanrahan, Paul Lenhart, Spencer Johnston & Heath Blackmon
The structure of a genome can be described at its simplest by the number of chromosomes and the sex chromosome system it contains. Despite over a century of study, the evolution of genome structure on this scale remains recalcitrant to broad generalisations that can be applied across clades. To address this issue, we have assembled a dataset of 823 karyotypes from the insect group Polyneoptera. This group contains orders with a range of variations in...

Data from: Decadal heat and drought drive body size of North American bison (Bison bison) along the Great Plains

Jeff Martin & Perry S. Barboza
Large grazers are visible and valuable indicators of the effects of projected changes in temperature and drought on grasslands. The grasslands of the Great Plains has supported the greatest number of bison (Bison bison; Linnaeus, 1758) since prehistoric times. We tested the hypothesis that body mass (BM; kg) and asymptotic body mass (ABM; kg) of Bison decline with rising temperature and increasing drought over both temporal and spatial scales along the Great Plains. Temporally, we...

Season of prescribed fire determines grassland restoration outcomes after fire exclusion and overgrazing

Erin N. Novak, Michelle Bertelsen, Dick Davis, Devin M. Grobert, Kelly G. Lyons, Jason P. Martina, W. Matt McCaw, Matthew O'Toole & Joseph W. Veldman
Fire exclusion and mismanaged grazing are globally important drivers of environmental change in mesic C4 grasslands and savannas. Although interest is growing in prescribed fire for grassland restoration, we have little long-term experimental evidence of the influence of burn season on the recovery of herbaceous plant communities, encroachment by trees and shrubs, and invasion by exotic grasses. We conducted a prescribed fire experiment (seven burns between 2001 and 2019) in historically fire-excluded and overgrazed grasslands...

A comparative analysis of analytical techniques for rapid oil spill identification

Alina T. Roman‐Hubers, Thomas J. McDonald, Erin S. Baker, Ivan Rusyn & Weihsueh Chiu
The complex chemical composition of crude oils presents many challenges for rapid chemical characterization in the case of a spill. A number of approaches are currently used to “fingerprint” petroleum‐derived samples. Gas chromatography coupled with mass spectrometry (GC‐MS) is the most common, albeit not very rapid, technique; however, with GC‐MS alone, it is difficult to resolve the complex substances in crude oils. This study examined the potential application of ion mobility spectrometry–mass spectrometry (IMS‐MS), coupled...

Short-term treatment of golden retriever muscular dystrophy (GRMD) dogs with rAAVrh74.MCK.GALGT2 induces muscle glycosylation and utrophin expression but has no significant effect on muscle strength

Paul Martin, Deborah Zygmunt, Anna Ashbrook, Sonia Hamilton, Davin Packer, Sharla Birch, Amanda Bettis, Cynthia Balog-Alvarez, Lee-Jae Guo, Peter Nghiem & Joe Kornegay
We have examined the effects of intravenous (IV) delivery of rAAVrh74.MHCK7.GALGT2 in the golden retriever muscular dystrophy (GRMD) model of Duchenne Muscular Dystrophy (DMD). After baseline testing, GRMD dogs were treated at 3 months of age and reassessed at 6 months. This 3-6 month age range is a period of rapid disease progression, thus offering a relatively short window to establish treatment efficacy. Measures analyzed included muscle AAV transduction, GALGT2 transgene expression, GALGT2-induced glycosylation, muscle...

Data from: Polyceraty (multi-horns) in Damara sheep maps to ovine chromosome 2

Ockert F. C. Greyvenstein, Coralie M. Reich, Este Van Marle-Koster, David G. Riley & Ben J. Hayes
Polyceraty (presence of multiple horns) is rare in modern day ungulates. Although not found in wild sheep, polyceraty does occur in a small number of domestic sheep breeds covering a wide geographical region. Damara are fat-tailed hair sheep, from the south-western region of Africa, which display polyceraty, with horn number ranging from zero to four. We conducted a genome-wide association study for horn number with 43 Damara genotyped with 606 006 SNP markers. The analysis...

Data from: Constraints on the FST–heterozygosity outlier approach

Sarah P. Flanagan & Adam G. Jones
The FST-heterozygosity outlier approach has been a popular method for identifying loci under balancing and positive selection since Beaumont and Nichols first proposed it in 1996 and recommended its use for studies sampling a large number of independent populations (at least 10). Since then, their program FDIST2 and a user-friendly program optimized for large datasets, LOSITAN, have been used widely in the population genetics literature, often without the requisite number of samples. We observed empirical...

Data from: Combined analyses of kinship and FST suggest potential drivers of chaotic genetic patchiness in high gene flow populations

Matthew Iacchei, Tal Ben-Horin, Kimberly A. Selkoe, Christopher E. Bird, Francisco J. Garcia-Rodriguez & Robert J. Toonen
We combine kinship estimates with traditional F-statistics to explain contemporary drivers of population genetic differentiation despite high gene flow. We investigate range-wide population genetic structure of the California spiny (or red rock) lobster (Panulirus interruptus) and find slight, but significant global population differentiation in mtDNA (ΦST = 0.006, P = 0.001; Dest_Chao = 0.025) and seven nuclear microsatellites (FST = 0.004, P < 0.001; Dest_Chao = 0.03), despite the species’ 240- to 330-day pelagic larval...

Data from: Evolution in extreme environments: replicated phenotypic differentiation in livebearing fish inhabiting sulfidic springs

Michael Tobler, Maura Palacios, Lauren J Chapman, Igor Mitrofanov, David Bierbach, Martin Plath, Lenin Arias-Rodriguez, Francisco J García De León & Mariana Mateos
We investigated replicated ecological speciation in the livebearing fishes Poecilia mexicana and P. sulphuraria (Poeciliidae), which inhabit freshwater habitats and have also colonized multiple sulfidic springs in southern Mexico. These springs exhibit extreme hypoxia and high concentrations of hydrogen sulfide, which is lethal to most metazoans. We used phylogenetic analyses to test whether springs were independently colonized, performed phenotypic assessments of body and gill morphology variation to identify convergent patterns of trait differentiation, and conducted...

Data from: Limitations of climate data for inferring species boundaries: insights from speckled rattlesnakes

Jesse M. Meik, Jeffrey W. Streicher, A. Michelle Lawing, Oscar Flores-Villela & Matthew K. Fujita
Phenotypes, DNA, and measures of ecological differences are widely used in species delimitation. Although rarely defined in such studies, ecological divergence is almost always approximated using multivariate climatic data associated with sets of specimens (i.e., the “climatic niche”); the justification for this approach is that species-specific climatic envelopes act as surrogates for physiological tolerances. Using identical statistical procedures, we evaluated the usefulness and validity of the climate-as-proxy assumption by comparing performance of genetic (nDNA SNPs...

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