50 Works

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: 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: 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: 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: 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: 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: 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: 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...

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: 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...

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: 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: 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: Can we build it? Yes we can, but should we use it? Assessing the quality and value of a very large phylogeny of campanulid angiosperms

Jeremy M. Beaulieu & Brian C. O'Meara
The study of very large and very old clades holds the promise of greater insights into evolution across the tree of life. However, there has been a fair amount of criticism regarding the interpretations and quality of studies to date, with some suggesting that detailed studies carried out on smaller, tractable scales should be preferred over the increasingly grand syntheses of these data. Methods - We provided in detail our trials and tribulations of compiling...

Data from: Gene flow and species delimitation in fishes of Western North America: Flannelmouth (Catostomus latipinnis) and Bluehead sucker (C. Pantosteus discobolus)

Max Bangs, Marlis Douglas, Tyler Chafin & Michael Douglas
The delimitation of species-boundaries, particularly those obscured by reticulation, is a critical step in contemporary biodiversity assessment. It is especially relevant for conservation and management of indigenous fishes in western North America, represented herein by two species with dissimilar life-histories co-distributed in the highly modified Colorado River (i.e., Flannelmouth Sucker, Catostomus latipinnis; Bluehead Sucker, C. (Pantosteus) discobolus). To quantify phylogenomic patterns and examine proposed taxonomic revisions, we first employed double-digest restriction-site associated DNA sequencing (ddRAD),...

Data from: Detrital nutrient content and leaf species differentially affect growth and nutritional regulation of detritivores

Halvor M. Halvorson, Chris L. Fuller, Sally A. Entrekin, J. Thad Scott & Michelle A. Evans-White
Resource nutrient content and identity are common bottom-up controls on organismal growth and nutritional regulation. One framework to study these factors, ecological stoichiometry theory, predicts that elevated resource nitrogen (N) and phosphorus (P) contents enhance organism growth by alleviating constraints on N and P acquisition. However, the regulatory mechanisms underlying this response – including whether responses depend on resource identity – remain poorly understood. In this study, we tested roles of detrital N and P...

Data from: Indirect effects of invasive Burmese pythons on ecosystems in southern Florida

John D. Willson
Invasive predators can dramatically alter ecosystems through both direct predation and indirect effects such as tropic cascades. However, most examples of top-down effects of invasive predators in terrestrial systems stem from islands or similar low-diversity ecosystems. Snakes are an emerging guild of damaging invasive predators, but demonstration of ecosystem-level impacts of invasive snakes are limited to the single case of the brown treesnake on Guam. Invasive Burmese pythons are firmly established in southern Florida and...

Data from: Adaptive evolution to novel predators facilitates the evolution of damselfly species range shifts

Adam M. Siepielski & Jeremy M. Beaulieu
Most species have evolved adaptations to reduce the chances of predation. In many cases adaptations to coexist with one predator generate tradeoffs in the ability to live with other predators. Consequently, the ability to live with one predator may limit the geographic distributions of species, such that adaptive evolution to coexist with novel predators may facilitate range shifts. In a case study with Enallagma damselflies, we used a comparative phylogenetic approach to test the hypothesis...

Data from: Using citizen science monitoring data in species distribution models to inform isotopic assignment of migratory connectivity in wetland birds

Auriel M.V. Fournier, Kiel L. Drake, Douglas C. Tozer & Auriel M. V. Fournier
Stable isotopes have been used to estimate migratory connectivity in many species. Estimates are often greatly improved when coupled with species distribution models (SDMs), which temper estimates in relation to occurrence. SDMs can be constructed using from point locality data from a variety of sources including extensive monitoring data typically collected by citizen scientists. However, one potential issue with SDM is that these data oven have sampling bias. To avoid this potential bias, an approach...

Data from: Functional genomic and phenotypic responses to desiccation in natural populations of a desert drosophilid

Subhash Rajpurohit, Cassia C. Oliveira, William J. Etges & Allen G. Gibbs
We used whole transcriptome microarrays to assess changes in gene expression and monitored mortality rates and epicuticular hydrocarbons (CHCs) in response to desiccation stress in four natural populations of Drosophila mojavensis from Baja California and mainland Mexico. Desiccation had the greatest effect on gene expression, followed by biogeographical variation at regional and population levels. Genes involved in environmental sensing and cuticular structure were up-regulated in dry conditions, while genes involved in transcription itself were down-regulated....

Data from: Effects of conditionally expressed phenotypes and environment on amphibian dispersal in nature

Brittany H. Ousterhout & Raymond D. Semlitsch
Individuals vary greatly in the distance they disperse, and in doing so, strongly affect ecological and evolutionary processes. Dispersal, when viewed as a component of phenotype, can be affected independently or jointly by environment. However, among taxa with complex life cycles that occupy different habitats over ontogeny, the effects of environment on dispersal and the interaction between environment and phenotype remains poorly understood. Here, we conducted a field experiment to measure how dispersal distance was...

Six years of wild bee monitoring collections data using Blue Vane traps in Southern Pennsylvania, USA

Nash Turley, David Biddinger, Neelendra Joshi & Margarita López-Uribe
Turley NE, Biddinger DJ, Joshi NK, López-Uribe MM. 2022. Six years of wild bee monitoring shows changes in biodiversity within and across years and declines in abundance. Ecology and Evolution. Wild bees form diverse communities that pollinate plants in both native and agricultural ecosystems making them both ecologically and economically important. The growing evidence of bee declines has sparked increased interest in monitoring bee community and population dynamics using standardized methods. Here, we studied the...

Data from: Influence of drift and admixture on population structure of American black bears (Ursus americanus) in the Central Interior Highlands, U.S.A. 50 years after translocation

Emily E. Puckett, Thea V. Kristensen, Clay M. Wilton, Sara B. Lyda, Karen V. Noyce, Paula M. Holahan, , Jeff Beringer, Jerrold L. Belant, , Lori S. Eggert & David M. Leslie
Bottlenecks, founder events, and genetic drift often result in decreased genetic diversity and increased population differentiation. These events may follow abundance declines due to natural or anthropogenic perturbations, where translocations may be an effective conservation strategy to increase population size. American black bears (Ursus americanus) were nearly extirpated from the Central Interior Highlands, USA by 1920. In an effort to restore bears, 254 individuals were translocated from Minnesota, USA and Manitoba, Canada, into the Ouachita...

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: 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...

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