277 Works

Data from: Rates of karyotypic evolution in Estrildid finches differ between island and continental clades

Daniel M. Hooper & Trevor Douglas Price
Reasons why chromosomal rearrangements spread to fixation and frequently distinguish related taxa remain poorly understood. We used cytological descriptions of karyotype to identify large pericentric inversions between species of Estrildid finches (family Estrildidae) and a time-dated phylogeny to assess the genomic, geographic, and phylogenetic context of karyotype evolution in this group. Inversions between finch species fixed at an average rate of one every 2.26 My. Inversions were twice as likely to fix on the sex...

Data from: Acquisition of conditioning between methamphetamine and cues in healthy humans

Joel S. Cavallo, Leah M. Mayo & Harriet De Wit
Environmental stimuli repeatedly paired with drugs of abuse can elicit conditioned responses that are thought to promote future drug seeking. We recently showed that healthy volunteers acquired conditioned responses to auditory and visual stimuli after just two pairings with methamphetamine (MA, 20 mg, oral). This study extended these findings by systematically varying the number of drug-stimuli pairings. We expected that more pairings would result in stronger conditioning. Three groups of healthy adults were randomly assigned...

Data from: Shared extremes by ectotherms and endotherms: body elongation in mustelids is associated with small size and reduced limbs

Chris J. Law, Graham J. Slater & Rita S. Mehta
An elongate body with reduced or absent limbs has evolved independently in many ectothermic vertebrate lineages. While much effort has been spent examining the morphological pathways to elongation in these clades, quantitative investigations into the evolution of elongation in endothermic clades are lacking. We quantified body shape in 61 musteloid mammals (red panda, skunks, raccoons, and weasels) using the head-body elongation ratio. We also examined the morphological changes that may underlie the evolution towards more...

Effects of taphonomic deformation on geometric morphometric analysis of fossils: a case study using the dicynodont Diictodon feliceps (Therapsida, Anomodontia)

Christian Kammerer, Michol Deutsch, Jacqueline Lungmus & Kenneth Angielczyk
Taphonomic deformation, the distortion of fossils as a result of geological processes, poses problems for the use of geometric morphometrics in addressing paleobiological questions. Signal from biological variation, such as ontogenetic trends and sexual dimorphism, may be lost if variation from deformation is too high. Here, we investigate the effects of taphonomic deformation on geometric morphometric analyses of the abundant, well known Permian therapsid Diictodon feliceps. Distorted Diictodon crania can be categorized into seven typical...

Implementation of a learning healthcare system for Sickle Cell disease: List of smart data elements contained in the Epic Smartform and their SmartData types

Robin Miller, Erin Coyne, Erin Crowgey, Dan Eckrich, Jeffrey Myers, Raymond Villanueva, Jean Wadman, Sidnie Jacobs-Allen, Renee Gresh, Samuel Volchenboum & E Anders Kolb
Objective: Using Sickle Cell Disease (SCD) as a model, the objective of this study was to create a comprehensive learning healthcare system to support disease management and research. A multidisciplinary team developed a SCD clinical data dictionary to standardize bedside data entry and inform a scalable environment capable of converting complex electronic healthcare records (EHR) into knowledge accessible in real-time. Materials and Methods: Clinicians expert in SCD care developed a data dictionary to describe important...

Data from: Integration of genomics and transcriptomics predicts diabetic retinopathy susceptibility genes

Andrew Skol, Segun Jung, Ana Marija Sokovic, Siquan Chen, Sarah Fazal, Olukayode Sosina, Poulami Borkar, Amy Lin, Maria Sverdlov, Dingcai Cao, Anand Swaroop, Ionut Bebu, Barbara Stranger & Michael Grassi
We determined differential gene expression in response to high glucose in lymphoblastoid cell lines derived from matched individuals with type 1 diabetes with and without retinopathy. Those genes exhibiting the largest difference in glucose response were assessed for association to diabetic retinopathy in a genome-wide association study meta-analysis. Expression Quantitative Trait Loci (eQTLs) of the glucose response genes were tested for association with diabetic retinopathy. We detected an enrichment of the eQTLs from the glucose...

Differential impacts of alternate primary producers on carbon cycling

Khashiff Miranda, Brooke Weigel, Sophie McCoy & Catherine Pfister
Disturbance impacts the spatial distribution of primary producers, which can have cascading effects on ecosystem function. The lower-intertidal zone on the rocky shores of the Pacific Northwest is one such place where wave energy creates a mosaic-like distribution between two assemblages: surfgrass (Phyllospadix scouleri) meadows and macroalgal forests dominated by kelp. We simulated wave disturbance by experimentally removing patches of surfgrass monocultures, resulting in a macroalgal assemblage with increased diversity, biomass, and net primary productivity...

Divergence, gene flow and the origin of leapfrog geographic distributions: the history of color pattern variation in Phyllobates poison-dart frogs

Roberto Márquez, Tyler Linderoth, Daniel Mejía-Vargas, Rasmus Nielsen, Adolfo Amézquita & Marcus Kronforst
The geographic distribution of phenotypic variation among closely related populations is a valuable source of information about the evolutionary processes that generate and maintain biodiversity. Leapfrog distributions, in which phenotypically similar populations are disjunctly distributed and separated by one or more phenotypically distinct populations, represent geographic replicates for the existence of a phenotype, and are therefore especially informative. Phyllobates poison frogs. We found evidence for high levels of gene flow between neighboring populations but not...

Supplemental figures from: Role of the thyroid gland in expression of the thyroid phenotype of SBP2 deficient mice

Alexandra Dumitrescu
Selenocysteine insertion sequence binding protein 2, SBP2 (SECISBP2), is required for selenoprotein synthesis. Partial SBP2 deficiency syndrome manifests characteristic thyroid function tests. The Sbp2 deficiency mouse model, Sbp2 iCKO, replicates this thyroid phenotype and was used for pathophysiologic investigations. As selenoproteins have antioxidative role in thyroid gland function, their deficiencies have potential to affect thyroid hormone (TH) synthesis. Sbp2 iCKO mice had larger thyroids relative to body weight and increased thyroidal T4 and T3 content...

Ecological limits as the driver of bird species richness patterns along the east Himalayan elevational gradient

Trevor Price, Matthew Schumm, Alex White & K Supriya
Variation in species richness across environmental gradients results from a combination of historical non-equilibrium processes (time, speciation, extinction) and present-day differences in environmental carrying capacities (i.e., ecological limits, affected by species interactions and the abundance and diversity of resources). In a study of bird richness along the sub-tropical east Himalayan elevational gradient, we test the prediction that species richness patterns are consistent with ecological limits using data on morphology, phylogeny, elevational distribution, and arthropod resources....

Origin of complexity in hemoglobin evolution

Arvind Pillai
Most proteins associate into multimeric complexes with specific architectures, which often have functional properties like cooperative ligand binding, allosteric regulation, or the capacity to perform mechanical work. We have no detailed knowledge of how any multimer and its functions arose during historical evolution. Here we use ancestral protein reconstruction and biophysical assays to dissect the evolutionary origins of vertebrate hemoglobin (Hb), a heterotetramer of paralogous α and β subunits, which mediates oxygen transport and exchange...

The impact of indoor residual spraying on Plasmodium falciparum microsatellite variation in an area of high seasonal malaria transmission in Ghana, West Africa

Dionne Argyropoulos, Shazia Ruybal‐Pesántez, Samantha L. Deed, Abraham R. Oduro, Samuel K. Dadzie, Maxwell A. Appawu, Victor Asoala, Mercedes Pascual, Kwadwo A. Koram, Karen P. Day, Maxwell A. Appawu, Kathryn E. Tiedje, Victor Asoala, Mercedes Pascual, Kwadwo A. Koram, Karen P. Day & Kathryn E. Tiedje
Here, we report the first population genetic study to examine the impact of indoor residual spraying (IRS) on Plasmodium falciparum in humans. This study was conducted in an area of high seasonal malaria transmission in Bongo District, Ghana. IRS was implemented during the dry season (November-May) in three consecutive years between 2013 and 2015 to reduce transmission and attempt to bottleneck the parasite population in humans towards lower diversity with greater linkage disequilibrium. The study...

The atomic-level physiochemical determinants of T cell receptor dissociation kinetics

Zachary Rollins, Roland Faller, Ilias Tagkopolous, Jun Huang & Steven George
The force-dependent bond lifetime of a T Cell Receptors (TCR) to 17 peptide-Major Histocompatibility Complexes (pMHCs) was simulated using Steered Molecular Dynamics. Physiochemical descriptors of the TCR-pMHC interaction during simulation were then filtered and selected to understand the best feature sets that predict bond lifetime. This methodology sets precedence on the rational design of TCRs via force-dependent bond lifetime enhancement.

The functional diversity of marsupial limbs is influenced by both ecology and developmental constraint

Spencer Pevsner, David Grossnickle & Zhe-Xi Luo
Extant marsupials are less ecologically diverse than placentals, and this is reflected by placentals exhibiting a greater diversity of locomotor modes, including powered flight and fully aquatic swimming. One proposed explanation for this discrepancy is that the development of more disparate marsupial forelimbs is prevented by the neonate’s crawl to the pouch, which requires precocious forelimb development for climbing adaptations. To test predictions of this Developmental Constraint Hypothesis, we pursue a comparative morphometric study on...

The causes and ecological context of rapid morphological evolution in birds

Nicholas Crouch & Joseph Tobias
Episodic pulses in morphological diversification are a prominent feature of evolutionary history, driven by factors that remain widely disputed. Resolving this question has proved challenging because comprehensive species-level data are generally unavailable at sufficient scale. Combining global phylogenetic and morphological data for birds, we show that pulses of diversification in lineages and traits tend to occur independently and in different contexts. Speciation pulses are preceded by greater differentiation in overall morphology and habitat niche, then...

Data from: Mosaic heterochrony and evolutionary modularity: the trilobite genus Zacanthopsis as a case study

Sylvain Gerber & Melanie J. Hopkins
Logical connections exist between evolutionary modularity and heterochrony, two unifying and structuring themes in the expanding field of evolutionary developmental biology. The former sees complex phenotypes as being made up of semi-independent units of evolutionary transformation; the latter requires such a modular organization of phenotypes to occur in a localized or mosaic fashion. This conceptual relationship is illustrated here by analyzing the evolutionary changes in the cranidial ontogeny of two related species of Cambrian trilobites....

Data from: Testing for unequal rates of morphological diversification in the absence of a detailed phylogeny: case study from characiform fishes

Brian Sidlauskas
This study develops the random phylogenies rate test (RAPRATE), a likelihood method that simulates morphological evolution along randomly generated phylogenies, and uses it to determine whether a considerable difference in morphological diversity between two sister clades of South American fishes should be taken as evidence of differing rates of morphological change or lineage turnover. Despite identical ages of origin, similar species richness, and sympatric geographic distributions, the morphological and ecological diversity of the superfamily Anostomoidea...

Data from: Testing for differences in rates of speciation, extinction, and morphological evolution in four tribes of cichlids endemic to Lake Tanganyika, East Africa

Marie E. Hoerner
Patterns of morphological disparity yield important insight into the causes of diversification and adaptive radiation in East African cichlids. However, comparisons of cichlid disparity have often failed to consider the effects that differing clade ages or stochasticity may have on disparity before making interpretations. Here, a model of branching morphological evolution allows assessment of the relative contributions of differing turnover and morphological change rates, clade ages, and stochastic variation to the observed patterns of disparity...

Data from: Accounting for the effects of biological variability and temporal autocorrelation in assessing the preservation of species abundance

Adam Tomašových & Susan M. Kidwell
Quantifying the effects of taphonomic processes on species abundances in time-averaged death assemblages (DAs) is pivotal for paleoecological inference. However, fidelity estimates based on conventional “live-dead” comparisons are fundamentally ambiguous: (1) data on living assemblages (LAs) are based on a very short period of sampling and thus do not account for natural variability in the LA, (2) LAs are sampled at the same time as the DA and thus do not necessarily reflect past LAs...

Data from: Genomic-scale capture and sequencing of endogenous DNA from feces

George Perry, John Marioni, Pall Melsted & Yoav Gilad
Genomic-level analyses of DNA from non-invasive sources would facilitate powerful conservation and evolutionary studies in natural populations of endangered and otherwise elusive species. However, the typical low quantity and poor quality of DNA that is extracted from non-invasive samples have generally precluded such work. Here we apply a modified DNA capture protocol that, when used in combination with massively-parallel sequencing technology, facilitates efficient and highly-accurate resequencing of megabases of specified nuclear genomic regions from fecal...

Data from: Genetic structure in a dynamic baboon hybrid zone corroborates behavioral observations in a hybrid population

Marie J.E. Charpentier, Michael C. Fontaine, Julien P. Renoult, Thomas Jenkins, Erwan Cherel, Laure Benoit, Nicolas Barthès, Susan C. Alberts & Jenny Tung
Behavior and genetic structure are intimately related: mating patterns and patterns of movement between groups or populations influence the movement of genetic variation across the landscape and from one generation to the next. In hybrid zones, the behavior of the hybridizing taxa can also have an important impact on the incidence and outcome of hybridization events. Hybridization between yellow baboons and anubis baboons has been well-documented in the Amboseli basin of Kenya, where more anubis-like...

Data from: Comparing the differential filling of morphospace and allometric space through time: the morphological and developmental dynamics of early Jurassic ammonoids

Sylvain Gerber
The evolutionary history of shell geometry of Early Jurassic ammonoids during the Pliensbachian–Toarcian second-order mass extinction is explored at both adult and ontogenetic levels. The ontogenetic approach builds on the concept of allometric space to get insights into the developmental aspects of morphological evolution. Investigation of the deployment of taxa in adult morphospace and allometric space allows the appraisal of the temporal evolution of morphological and allometric disparities. Curves of taxonomic diversity, adult morphological disparity,...

Data from: Wing patterning gene redefines the mimetic history of Heliconius butterflies

Heather M. Hines, Brian A. Counterman, Riccardo Papa, Priscila Albuquerque De Moura, Marcio Z. Cardoso, Mauricio Linares, James Mallet, Robert D. Reed, Chris D. Jiggins, Marcus R. Kronforst, W. Owen McMillan, R. D. Reed, J. Mallet, W. O. McMillan, M. R. Kronforst, H. M. Hines, B. A. Counterman, M. Linares, M. Z. Cardoso & C. D. Jiggins
The mimetic butterflies Heliconius erato and H. melpomene have undergone parallel radiations to form a near-identical patchwork of over 20 different wing pattern races across the Neotropics. Previous molecular phylogenetic work on these radiations has suggested that similar but geographically disjunct color patterns arose multiple times independently in each species. The neutral markers used in these studies, however, can move freely across color pattern boundaries and therefore might not represent the history of the adaptive...

Data from: Predicting the effects of increasing temporal scale on species composition, diversity, and rank-abundance distributions

Adam Tomašových & Susan M. Kidwell
Paleoecological analyses that test for spatial or temporal variation in diversity must consider not only sampling and preservation bias, but also the effects of temporal scale (i.e., time averaging). The species-time relationship (STR) describes how species diversity increases with the elapsed time of observation, but its consequences for assessing the effects of time averaging on diversity of fossil assemblages remain poorly explored. Here, we use a neutral, dispersal-limited model of metacommunity dynamics, with parameters estimated...

Data from: Pathogen persistence in the environment and insect-baculovirus interactions: disease-density thresholds, epidemic burnout, and insect outbreaks

Emma Fuller, Bret D. Elderd & Greg Dwyer
Classical epidemic theory focuses on directly transmitted pathogens, but many pathogens are instead transmitted when hosts encounter infectious particles. Theory has shown that for such diseases pathogen persistence time in the environment can strongly affect disease dynamics, but estimates of persistence time, and consequently tests of the theory, are extremely rare. We consider the consequences of persistence time for the dynamics of the gypsy moth baculovirus, a pathogen transmitted when larvae consume foliage contaminated with...

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  • University of Chicago
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