49 Works

Data from: The effects of age, sex, and habitat on body size and shape of the blackstripe topminnow, Fundulus notatus

Daniel P. Welsh, Muchu Zhou, Steven M. Mussmann, Lauren G. Fields, Claire L. Thomas, Simon P. Pearish, Stephanie L. Kilburn, Jerrod L. Parker, Laura R. Stein, Jennifer A. Bartlett, Christopher R. Bertram, Thomas J. Bland, Kate L. Laskowski, Brett C. Mommer, Xuan Zhuang & Rebecca C. Fuller
Lake and stream habitats pose a variety of challenges to fishes due to differences in variables such as water velocity, habitat structure, prey community, and predator community. These differences can cause divergent selection on body size and/or shape. Here, we measured sex, age, length, and eight different morphological traits of the blackstripe topminnow, Fundulus notatus, from 19 lake and stream populations across four river drainages in central Illinois. Our goal was to determine whether size...

Data from: Genome-wide tests for introgression between cactophilic Drosophila implicate a role of inversions during speciation

Konrad Lohse, Magnus Clarke, Michael G. Ritchie & William J. Etges
Models of speciation-with-gene-flow have shown that the reduction in recombination between alternative chromosome arrangements can facilitate the fixation of locally adaptive genes in the face of gene flow and contribute to speciation. However, it has proven frustratingly difficult to show empirically that inversions have reduced gene flow and arose during or shortly after the onset of species divergence rather than represent ancestral polymorphisms. Here we present an analysis of whole genome data from a pair...

Data from: Validation of grain yield QTL from soft winter wheat using a CIMMYT spring wheat panel

Dennis N. Lozada, R. Esten Mason, Sivakumar Sukumaran & Susanne Dreisigacker
Validation of quantitative trait loci (QTLs) is an essential step in marker-assisted breeding. The objectives of this study were to validate grain yield (GY) QTLs previously identified in soft red winter wheat (Triticum aestivum L.) through biparental and association mapping using the spring wheat association mapping initiative (WAMI) panel from CIMMYT, Mexico, and to identify allele combinations of the validated QTLs that resulted to the highest GY. Linked single-nucleotide polymorphisms for IWA3560 (3A), IWA1818 (4B),...

Data from: Free‐moving artificial eggs containing temperature loggers reveal remarkable within‐clutch variance in incubation temperature

Sydney F. Hope, Sarah E. DuRant, John J. Hallagan, Michelle L. Beck, Robert A. Kennamer & William A. Hopkins
Incubation is a crucial aspect of avian parental care and measuring incubation temperature in the wild can improve our understanding of life history tradeoffs and inform conservation efforts. However, there are challenges associated with measuring the temperature of eggs in natural nests. Most studies to date have measured incubation temperature by using a single, stationary logger in each nest. However, real eggs are rotated and moved throughout the nest by the parent during the incubation...

Data from: Long-term stoichiometry and fates highlight animal egestion as nutrient repackaging, not recycling, in aquatic ecosystems

Halvor M. Halvorson, Delaney J. Hall & Michelle A. Evans-White
1. Animal defecation, or egestion, is a pronounced transformation of organic matter in many ecosystems. However, because egesta have been presumed recalcitrant and low-nutrient, their significance and variability as an animal nutrient flux in aquatic settings - especially relative to mineralization via excretion - are poorly known. 2. We compared carbon (C), nitrogen (N), and phosphorus (P) dynamics over short- to long-term (up to 107 days) microbial decomposition of egesta from the aquatic shredders Allocapnia...

Data from: Precipitation drives global variation in natural selection

Adam Siepielski, Michael B. Morrissey, Mathieu Buoro, Stephanie M. Carlson, Christina M. Caruso, Sonya M. Clegg, Tim Coulson, Joseph DiBattista, Kiyoko M. Gotanda, Clinton D. Francis, Joe Hereford, Joel G. Kingsolver, Kate E. Augustine, Loeske E. B. Kruuk, Ryan A. Martin, Ben C. Sheldon, Nina Sletvold, Erik I. Svensson, Michael J. Wade & Andrew D. C. MacColl
Climate change has the potential to affect the ecology and evolution of every species on Earth. Although the ecological consequences of climate change are increasingly well documented, the effects of climate on the key evolutionary process driving adaptation—natural selection—are largely unknown. We report that aspects of precipitation and potential evapotranspiration, along with the North Atlantic Oscillation, predicted variation in selection across plant and animal populations throughout many terrestrial biomes, whereas temperature explained little variation. By...

Data from: Gigantic lion, (Panthera leo), from the Pleistocene of Natodomeri, eastern Africa

Fredrick K. Manthi, Francis H. Brown, Michael J. Plavcan & Lars Werdelin
The partial skull of a lion from Natodomeri, northwest Kenya is described. The Natodomeri sites are correlated with Member I of the Kibish Formation, dated to between 195 ka and ∼205 ka. The skull is remarkable for its very great size, equivalent to the largest cave lions (Panthera spelaea) of Pleistocene Eurasia and much larger than any previously known lion from Africa, living or fossil. We hypothesize that this individual represents a previously unknown population...

Data from: Female mate preferences on high dimensional shape variation for male species recognition traits

Adam M. Siepielski, Sarah J. McPeek & Mark A. McPeek
Females in many animal species must discriminate between conspecific and heterospecific males when choosing mates. Such mating preferences that discriminate against heterospecifics may inadvertently also affect the mating success of conspecific males, particularly those with more extreme phenotypes. From this expectation, we hypothesized that female mate choice should cause Enallagma females (Odonata: Coenagrionidae) to discriminate against conspecific males with more extreme phenotypes of the claspers males use to grasp females while mating – the main...

Data from: Fine-scale spatial homogenization of microbial habitats: a multivariate index of headwater wetland complex condition

Jessica B. Moon, Denice H. Wardrop, Erica A.H. Smithwick, Kusum J. Naithani & Erica A. H. Smithwick
With growing public awareness that wetlands are important to society, there are intensifying efforts to understand the ecological condition of those wetlands that remain, and to develop indicators of wetland condition. Indicators based on soils are not well developed and are absent in some current assessment protocols; these could be advantageous, particularly for soils, which are complex habitats for plants, invertebrates, and microbial communities. In this study, we examine whether multivariate soil indicators, correlated with...

Data from: Endothermic mosasaurs? Possible thermoregulation of Late Cretaceous mosasaurs (Reptilia, Squamata) indicated by stable oxygen isotopes in fossil bioapatite in comparison with coeval marine fish and pelagic seabirds

, Alberto Pérez-Huerta & Celina A. Suarez
The thermoregulatory style of Late Cretaceous mosasaurs has become a highly controversial subject in vertebrate palaeontology. These extinct marine reptiles have previously been described as poikilothermic, endothermic or gigantothermic. Here we analyse three genera of mosasaurs from the Mooreville Chalk in Alabama (USA) of differing body mass, and compare their δ18OPO4 derived body temperatures (Tb) with those of coeval poikilothermic fish (Enchodus) and endothermic pelagic seabirds (Ichthyornis). Results show that all mosasaurs, Clidastes (Tb =...

Data from: Stream hierarchy defines riverscape genetics of a North American desert fish

Matthew W. Hopken, Marlis R. Douglas & Michael E. Douglas
Global climate change is apparent within the Arctic and the south-western deserts of North America, with record drought in the latter reflected within 640 000 km2 of the Colorado River Basin. To discern the manner by which natural and anthropogenic drivers have compressed Basin-wide fish biodiversity, and to establish a baseline for future climate effects, the Stream Hierarchy Model (SHM) was employed to juxtapose fluvial topography against molecular diversities of 1092 Bluehead Sucker (Catostomus discobolus)....

Data from: Preadult life history variation determines adult transcriptome expression

William J. Etges, Cassia De Oliveira, Subhash Rajpurohit & Allen G. Gibbs
Preadult determinants of adult fitness and behavior have been documented in a variety of organisms with complex life cycles, but little is known about expression patterns of genes underlying these adult traits. We explored the effects of differences in egg to adult development time on adult transcriptome and cuticular hydrocarbon variation in order to understand the nature of the genetic correlation between preadult development time and premating isolation between populations of Drosophila mojavensis reared in...

Data from: Genetic rescue, the greater prairie chicken and the problem of conservation reliance in the Anthropocene

Steven M. Mussmann, Marlis R. Douglas, Whitney J.B. Anthonysamy, Mark A. Davis, Scott A. Simpson, Wade Louis, Michael E. Douglas & W. J. B. Anthonysamy
A central question in conservation is how best to manage biodiversity, despite human domination of global processes (= Anthropocene). Common responses (i.e. translocations, genetic rescue) forestall potential extirpations, yet have an uncertain duration. A textbook example is the greater prairie chicken (GRPC: Tympanuchus cupido pinnatus), where translocations (1992–1998) seemingly rescued genetically depauperate Illinois populations. We re-evaluated this situation after two decades by genotyping 21 microsatellite loci from 1831 shed feathers across six leks in two...

Data from: Dissecting signal and noise in diatom chloroplast protein encoding genes with phylogenetic information profiling

Edward C. Theriot, Matthew P. Ashworth, Teofil Nakov, Elizabeth Ruck, Robert K. Jansen & Matt P. Ashworth
Previous analyses of single diatom chloroplast protein-encoded genes recovered results highly incongruent with both traditional phylogenies and phylogenies derived from the nuclear encoded small subunit (SSU) gene. Our analysis here of six individual chloroplast genes (atpB, psaA, psaB, psbA, psbC and rbcL) obtained similar anomalous results. However, phylogenetic noise in these genes did not appear to be correlated, and their concatenation appeared to effectively sum their collective signal. We empirically demonstrated the value of combining...

Data from: Spatial genetic structure in American black bears (Ursus americanus): female philopatry is variable and related to population history

Thea V. Kristensen, Emily E. Puckett, Erin L. Landguth, Jerrold L. Belant, John T. Hast, Colin Carpenter, Jaime L. Sajecki, Jeff Beringer, Myron Means, John J. Cox, Lori S. Eggert, & Kimberly G. Smith
Previously, American black bears (Ursus americanus) were thought to follow the pattern of female philopatry and male-biased dispersal. However, recent studies have identified deviations from this pattern. Such flexibility in dispersal patterns can allow individuals greater ability to acclimate to changing environments. We explored dispersal and spatial genetic relatedness patterns across ten black bear populations—including long established (historic), with known reproduction >50 years ago, and newly established (recent) populations, with reproduction recorded <50 years ago—in...

Data from: Selection on fruit traits is mediated by the interplay between frugivorous birds, fruit flies, parasitoid wasps, and seed-dispersing ants

Facundo Palacio, Adam Siepielski, Mariela Lacoretz & Mariano Ordano
Every organism on Earth must cope with a multitude of species interactions both directly and indirectly throughout its life cycle. However, how selection from multiple species occupying different trophic levels affects diffuse mutualisms has received little attention. As a result, how a given species amalgamates the combined effects of selection from multiple mutualists and antagonists to enhance its own fitness remains little understood. We investigated how multispecies interactions (frugivorous birds, ants, fruit flies, and parasitoid...

Data from: Unraveling historical introgression and resolving phylogenetic discord within Catostomus (Osteichthys: Catostomidae)

Max Russell Bangs, Marlis R Douglas, Steven M Mussmann & Michael E Douglas
Background: Porous species boundaries can be a source of conflicting hypotheses, particularly when coupled with variable data and/or methodological approaches. Their impacts can often be magnified when non-model organisms with complex histories of reticulation are investigated. One such example is the genus Catostomus (Osteichthys, Catostomidae), a freshwater fish clade with conflicting morphological and mitochondrial phylogenies. The former is hypothesized as reflecting the presence of admixed genotypes within morphologically distinct lineages, whereas the latter is interpreted...

Data from: Assessment of plasma proteomics biomarker’s ability to distinguish benign from malignant lung nodules

Gerard A. Silvestri, Nichole T. Tanner, Paul Kearney, Anil Vachani, Pierre P. Massion, Alexander Porter, Steven C. Springmeyer, Kenneth C. Fang, David Midthun, Peter J. Mazzone, D. Madtes, J. Landis, A. Levesque, K. Rothe, M. Balaan, B. Dimitt, B. Fortin, N. Ettinger, A. Pierre, L. Yarmus, K. Oakjones-Burgess, N. Desai, Z. Hammoud, A. Sorenson, R. Murali … & F. Allison
Background: Lung nodules are a diagnostic challenge, with an estimated yearly incidence of 1.6 million in the United States. This study evaluated the accuracy of an integrated proteomic classifier in identifying benign nodules in patients with a pretest probability of cancer (pCA) ≤ 50%. Methods: A prospective, multicenter observational trial of 685 patients with 8- to 30-mm lung nodules was conducted. Multiple reaction monitoring mass spectrometry was used to measure the relative abundance of two...

Genetic diversity and the origins of parthenogenesis in the teiid lizard Aspidoscelis laredoensis

Anthony Barley, James Cordes, James Walker & Robert Thomson
Unisexual vertebrates typically form through hybridization events between sexual species in which reproductive mode transitions occur in the hybrid offspring. This evolutionary history is thought to have important consequences for the ecology of unisexual lineages and their interactions with congeners in natural communities. However, these consequences have proven challenging to study owing to uncertainty about patterns of population genetic diversity in unisexual lineages. Of particular interest is resolving the contribution of historical hybridization events vs....

Data from: Molecular phylogenetics of Braconidae (Hymenoptera: Ichneumonoidea) based on multiple nuclear genes and implications for classification

Barbara J. Sharanowski, Ashley P.G. Dowling & Michael J. Sharkey
This study examined subfamilial relationships within Braconidae, using 4kb of sequence data for 139 taxa. Genetic sampling included previously used markers for phylogenetic studies of Braconidae (28S and 18S rDNA) as well as new nuclear protein-coding genes (CAD and ACC). Maximum likelihood and Bayesian inference of the concatenated dataset recovered a robust phylogeny, particularly for early divergences within the family. This study focused primarily on non-cyclostome subfamilies, but the monophyly of the cyclostome complex was...

Data from: Genetics of incipient speciation in Drosophila mojavensis. III. Life history divergence in allopatry and reproductive isolation

William J. Etges, Cássia Cardoso De Oliveira, Mohamed A. F. Noor & Michael G. Ritchie
We carried out a three-tiered genetic analysis of egg-to-adult development time and viability in ancestral and derived populations of cactophilic D. mojavensis to test the hypothesis that evolution of these life history characters has shaped premating reproductive isolation in this species. First, a common garden experiment with 11 populations from Baja California and mainland Mexico and Arizona reared on two host cacti revealed significant host plant X region and population interactions for viability and development...

Data from: Predator olfactory cues generate a foraging-predation tradeoff through prey apprehension

Adam M. Siepielski, Eric Fallon & Kate Boersma
Most animals are faced with the challenge of securing food under the risk of predation. This frequently generates a trade-off whereby animals respond to predator cues with reduced movement to avoid predation at the direct cost of reduced foraging success. However, predators may also cause prey to be apprehensive in their foraging activities, which would generate an indirect ‘apprehension cost’. Apprehension arises when a forager redirects attention from foraging tasks to predator detection and incurs...

Data from: Organelles that illuminate the origins of Trichomonas hydrogenosomes and Giardia mitosomes

Michelle M. Leger, Martin Kolisko, Ryoma Kamikawa, Courtney W. Stairs, Keitaro Kume, Ivan Čepička, Jeffrey D. Silberman, Jan O. Andersson, Feifei Xu, Akinori Yabuki, Laura Eme, Qianqian Zhang, Kiyotaka Takishita, Yuji Inagaki, Alastair G. B. Simpson, Tetsuo Hashimoto & Andrew J. Roger
Many anaerobic microbial parasites possess highly modified mitochondria known as mitochondrion-related organelles (MROs). The best-studied of these are the hydrogenosomes of Trichomonas vaginalis and Spironucleus salmonicida, which produce ATP anaerobically through substrate-level phosphorylation with concomitant hydrogen production; and the mitosomes of Giardia intestinalis, which are functionally reduced and lack any role in ATP production. However, to understand the metabolic specializations that these MROs underwent in adaptation to parasitism, data from their free-living relatives are needed....

Data from: Flow-ecology relationships are spatially structured and differ among flow regimes

Lindsey A. Bruckerhoff, Douglas R. Leasure & Daniel D. Magoulick
1. In streams, hydrology is a predominant driver of ecological structure and function. Providing adequate flows to support aquatic life, or environmental flows, is therefore a top management priority in stream systems. 2. Flow regime classification is a widely accepted approach for establishing environmental flow guidelines. However, it is surprisingly difficult to quantify relationships between hydrology and ecology (flow-ecology relationships) while describing how these relationships vary across classified flow regimes. Developing such relationships is complicated...

Data from: SNF1-related protein kinase 1: the many-faced signaling hub regulating developmental plasticity in plants

Muhammed Jamsheer K, Manoj Kumar & Vibha Srivastava
The Snf1-Related Protein Kinase 1 (SnRK1) is the plant homolog of the heterotrimeric AMP-activated Protein Kinase/ Sucrose Non-Fermenting 1 (AMPK/Snf1), which works as a major regulator of growth under nutrient-limiting conditions in eukaryotes. Along with its conserved role as a master regulator of sugar starvation responses, SnRK1 is involved in controlling the developmental plasticity and resilience under diverse environmental conditions in plants. In this review, through mining and analyzing the interactome and phosphoproteome data of...

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