293 Works

Data from: The sampling and estimation of marine paleodiversity patterns: implications of a Pliocene model

James W. Valentine, David Jablonski, Andrew Z. Krug & Sarah K. Berke
Data that accurately capture the spatial structure of biodiversity are required for many paleobiological questions, from assessments of changing provinciality and the role of geographic ranges in extinction and originations, to estimates of global taxonomic or morphological diversity through time. Studies of temporal changes in diversity and global biogeographic patterns have attempted to overcome fossil sampling biases through sampling standardization protocols, but such approaches must ultimately be limited by available literature and museum collections. One...

Data from: Genome-level homology and phylogeny of Vibrionaceae (Gammaproteobacteria: Vibrionales) with three new complete genome sequences

Rebecca B. Dikow & William Leo Smith
Background: Phylogenetic hypotheses based on complete genome data are presented for the Gammaproteobacteria family Vibrionaceae. Two taxon samplings are presented: one including all those taxa for which the genome sequences are complete in terms of arrangement (chromosomal location of fragments; 19 taxa) and one for which the genome sequences contain multiple contigs (44 taxa). Analyses are presented under the Maximum Parsimony and Maximum Likelihood optimality criteria for total evidence datasets, the two chromosomes separately, and...

Data from: Impacts of bioturbation on temporal variation in bacterial and archaeal nitrogen-cycling gene abundance in coastal sediments

Bonnie Laverock, Karen Tait, Jack A. Gilbert, A. Mark Osborn & Steve Widdicombe
In marine environments, macrofauna living in or on the sediment surface may alter the structure, diversity and function of benthic microbial communities. In particular, microbial nitrogen (N)-cycling processes may be enhanced by the activity of large bioturbating organisms. Here, we study the effect of the burrowing mud shrimp Upogebia deltaura upon temporal variation in the abundance of genes representing key N-cycling functional guilds. The abundance of bacterial genes representing different N-cycling guilds displayed different temporal...

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: How little data is enough? Phase-diagram analysis of sparsity-regularized X-ray computed tomography

Jakob S. Jørgensen, Emil Y. Sidky & J. S. Jorgensen
We introduce phase-diagram analysis, a standard tool in compressed sensing (CS), to the X-ray computed tomography (CT) community as a systematic method for determining how few projections suffice for accurate sparsity-regularized reconstruction. In CS, a phase diagram is a convenient way to study and express certain theoretical relations between sparsity and sufficient sampling. We adapt phase-diagram analysis for empirical use in X-ray CT for which the same theoretical results do not hold. We demonstrate in...

Data from: Prevalence and beta diversity in avian malaria communities: host species is a better predictor than geography

Elizabeth S. C. Scordato & Melissa R. Kardish
1. Patterns of diversity and turnover in macroorganism communities can often be predicted from differences in habitat, phylogenetic relationships among species, and the geographic scale of comparisons. In this study, we asked if these factors also predict diversity and turnover in parasite communities. 2. We studied communities of avian malaria in two sympatric, ecologically similar, congeneric host species at three different sites. We asked if parasite prevalence and community structure varied with host population, host...

Data from: Geographic ranges of genera and their constituent species: structure, evolutionary dynamics, and extinction resistance

Michael Foote, Kathleen A. Ritterbush & Arnold I. Miller
We explore the relationships among the geographic ranges of genera, the ranges and positions of their constituent species, and the number of species they contain, considering variation among coeval genera and changes within genera over time. Measuring range size as the maximal distance, or extent, between occurrences within a taxon, we find that the range of the most widespread species is a good predictor of the range of the genus, and that the number of...

Data from: Phylogenetic relationships and the evolution of BMP4 in triggerfishes and filefishes (Balistoidea)

Charlene L. McCord & Mark W. Westneat
The triggerfishes (family Balistidae) and filefishes (family Monacanthidae) comprise a charismatic superfamily (Balistoidea) within the diverse order Tetraodontiformes. This group of largely marine fishes occupies an impressive ecological range across the world’s oceans, and is well known for its locomotor and feeding diversity, unusual body shapes, small genome size, and ecological and economic importance. In order to investigate the evolutionary history of these important fish families, we used multiple phylogenetic methods to analyze molecular data...

Data from: Exceptional avian herbivores: multiple transitions toward herbivory in the bird order Anseriformes and its correlation with body mass

Aaron M. Olsen
Herbivory is rare among birds and is usually thought to have evolved predominately among large, flightless birds due to energetic constraints or an association with increased body mass. Nearly all members of the bird order Anseriformes, which includes ducks, geese, and swans, are flighted and many are predominately herbivorous. However, it is unknown whether herbivory represents a derived state for the order and how many times a predominately herbivorous diet may have evolved. Compiling data...

Data from: Genome-wide association study of Arabidopsis thaliana leaf microbial community

Matthew W. Horton, Natacha Bodenhausen, Kathleen Beilsmith, Dazhe Meng, Brian D. Muegge, Sathish Subramanian, M. Madlen Vetter, Bjarni J. Vilhjálmsson, Magnus Nordborg, Jeffrey I. Gordon & Joy Bergelson
Identifying the factors that influence the outcome of host–microbial interactions is critical to protecting biodiversity, minimizing agricultural losses and improving human health. A few genes that determine symbiosis or resistance to infectious disease have been identified in model species, but a comprehensive examination of how a host genotype influences the structure of its microbial community is lacking. Here we report the results of a field experiment with the model plant Arabidopsis thaliana to identify the...

Data from: Nonlinear thermal gradients shape broad-scale patterns in geographic range size and can reverse Rapoport’s rule

Adam Tomasovych, David Jablonski, Sarah K. Berke, Andrew Z. Krug & James W. Valentine
Aim: Species living at latitudes that have greater annual temperature variations are expected to achieve broader geographic ranges than species living at latitudes that have smaller annual temperature variations, generating a positive relationship between range size and latitude (Rapoport's rule). However, this prediction fails to take into account the greater latitudinal extent of tropical temperatures relative to those at higher latitudes. Here we model the contributions of the broader latitudinal extent of equal-temperature habitats at...

Data from: Adaptive, convergent origins of the pygmy phenotype in African rainforest hunter-gatherers

George H. Perry, Matthieu Foll, Jean-Christophe Grenier, Etienne Patin, Yohann Nédélec, Alain Pacis, Maxime Barakatt, Simon Gravel, Xiang Zhou, Sam L. Nsobya, Laurent Excoffier, Lluis Quintana-Murci, Nathaniel J. Dominy & Luis B. Barreiro
The evolutionary history of the human pygmy phenotype (small body size), a characteristic of African and Southeast Asian rainforest hunter-gatherers, is largely unknown. Here we use a genome-wide admixture mapping analysis to identify 16 genomic regions that are significantly associated with the pygmy phenotype in the Batwa, a rainforest hunter-gatherer population from Uganda (east central Africa). The identified genomic regions have multiple attributes that provide supporting evidence of genuine association with the pygmy phenotype, including...

Data from: Historical baselines and the future of shell calcification for a foundation species in a changing ocean

Catherine A. Pfister, Kaustuv Roy, J. Timothy Wootton, Sophie J. McCoy, Robert T. Paine, Thomas H. Suchanek & Eric Sanford
Seawater pH and the availability of carbonate ions is decreasing due to anthropogenic carbon dioxide emissions, posing challenges for calcifying marine species. Marine mussels are of particular concern given their role as foundation species worldwide. Here, we document shell growth and calcification patterns in Mytilus californianus, the California mussel, over millennial and decadal scales. By comparing shell thickness across the largest modern shells, the largest mussels collected in the 1960s-1970s and shells from two Native...

Data from: Genotype-by-genotype interactions between an insect and its pathogen

Asher I. Hudson, Arietta E. Fleming-Davies, David J. Paez & Greg Dwyer
Genotype-by-genotype (G×G) interactions are an essential requirement for the coevolution of hosts and parasites, but have only been documented in a small number of animal model systems. G×G effects arise from interactions between host and pathogen genotypes, such that some pathogen strains are more infectious in certain hosts and some hosts are more susceptible to certain pathogen strains. We tested for G×G interactions in the gypsy moth (Lymantria dispar) and its baculovirus. We infected 21...

Data from: Mechanosensation is evolutionarily tuned to locomotor mechanics

Brett R. Aiello, Mark W. Westneat & Melina E. Hale
The biomechanics of animal limbs has evolved to meet the functional demands for movement associated with different behaviors and environments. Effective movement relies not only on limb mechanics but also on appropriate mechanosensory feedback. By comparing sensory ability and mechanics within a phylogenetic framework, we show that peripheral mechanosensation has evolved with limb biomechanics, evolutionarily tuning the neuromechanical system to its functional demands. We examined sensory physiology and mechanics of the pectoral fins, forelimb homologs,...

Data from: Feeding ecology is the primary driver of beak shape diversification in waterfowl

Aaron M. Olsen
The diversity of beak shapes among birds is often assumed to be largely the result of adaptations to different feeding behaviors and diets. However, this assumption has only been tested for a small subset of avian diversity, primarily within the order Passeriformes. Moreover, given the role of the beak in behaviors other than feeding and given that most previously identified beak-feeding associations concern beak size rather than shape, it remains unclear how much of beak...

Data from: The evolutionary origin of variation in song length and frequency in the avian family Cettiidae

Chentao Wei, Trevor D. Price, Jiayu Liu, Per Alström & Yanyun Zhang
Aspects of bird song have been shown to correlate with morphological and ecological features, including beak and body size, and habitat. Here we study evolution of song length and song frequency among 30 species belonging to the Cettiidae. Frequency is negatively correlated with body size, and song length increases with latitude. Although migration distance correlates with latitude, the association of song length with latitude is only present within the non-migratory species, implying the association is...

Data from: Consequences of divergence and introgression for speciation in Andean cloud forest birds

Benjamin M. Winger
Divergence with gene flow is well documented and reveals the influence of ecological adaptation on speciation. Yet it remains intuitive that gene exchange inhibits speciation in many scenarios, particularly among ecologically similar populations. The influence of gene flow on the divergence of populations facing similar selection pressures has received less empirical attention than scenarios where differentiation is coupled with local environmental adaptation. I used a paired study design to test the influence of genomic divergence...

Data from: Nineteenth-century collapse of a benthic marine ecosystem on the open continental shelf

Adam Tomašových & Susan M. Kidwell
The soft-sediment seafloor of the open continental shelf is among the least-known biomes on Earth, despite its high diversity and importance to fisheries and biogeochemical cycling. Abundant dead shells of epifaunal suspension-feeding terebratulid brachiopods (Laqueus) and scallops on the now-muddy mainland continental shelf of southern California reveal the recent, previously unsuspected extirpation of an extensive offshore shell-gravel ecosystem, evidently driven by anthropogenic siltation. Living populations of attached epifauna, which formerly existed in a middle- and...

Data from: Diversity-dependent evolutionary rates in early Paleozoic zooplankton

Michael Foote, Roger A. Cooper, James S. Crampton & Peter M. Sadler
The extent to which biological diversity affects rates of diversification is central to understanding macroevolutionary dynamics, yet no consensus has emerged on the importance of diversity-dependence of evolutionary rates. Here we analyse the species-level fossil record of early Paleozoic graptoloids, documented with high temporal resolution, to test directly whether rates of diversification were influenced by levels of standing diversity within this major clade of marine zooplankton. To circumvent the statistical regression-to-the-mean artefact, whereby higher- and...

Data from: Comparative transcriptomics provides insights into reticulate and adaptive evolution of a butterfly radiation

Wei Zhang, Brian X. Leon-Ricardo, Bas Van Schooten, Steven Van Belleghem, Brian Counterman, W. Owen McMillan, Marcus R. Kronforst & Riccardo Papa
Butterfly eyes are complex organs that are composed of a diversity of proteins and they play a central role in visual signaling and ultimately, speciation and adaptation. Here, we utilized the whole eye transcriptome to obtain a more holistic view of the evolution of the butterfly eye while accounting for speciation events that co-occur with ancient hybridization. We sequenced and assembled transcriptomes from adult female eyes of eight species representing all major clades of the...

Clinical and Molecular Analysis in Two Families with Novel Compound Heterozygous SBP2 (SECISBP2) Mutations

Alexandra Dumitrescu
Context: Selenocysteine insertion sequence binding protein 2 (SECISBP2, SBP2) is an essential factor for selenoprotein synthesis. Individuals with SBP2 defects have characteristic thyroid function tests (TFT) abnormalities due to deficiencies in the selenoenzymes deiodinases. Eight families with recessive SBP2 gene mutations have been reported to date. We report two families with inherited defect in thyroid hormone metabolism caused by four novel compound heterozygous mutations in the SBP2 gene. Case Descriptions: Proband 1 and 2 presented...

Coping with impostor feelings: evidence-based recommendations from a mixed methods study

Jill Barr-Walker, Debra A. Werner, Liz Kellermeyer & Michelle B. Bass
The negative effects of impostor phenomenon, also called impostor syndrome, include burnout and decreased job satisfaction and have led to an increased interest in addressing this issue in libraries in recent years. While previous research has shown that many librarians experience impostor phenomenon, the experience of coping with these feelings has not been widely studied. Our study’s aim was to understand how health sciences librarians cope with impostor phenomenon in the workplace, using a quantitative...

Data from: Palaeoproteomics resolves sloth phylogeny

Samantha Presslee, Graham J. Slater, Francois Pujos, Analia M. Forasiepi, Roman Fischer, Kelly Molloy, Meaghan Mackie, Jesper V. Olsen, Alejandro Kramarz, Matias Taglioretti, Fernando Scaglia, Maximiliano Lezcano, José Luis Lanata, John Southon, Robert Feranec, Jonathan Bloch, Adam Hajduk, Fabiana M. Martin, Rodolfo Salas Gismondi, Marcelo Reguero, Christian De Muizon, Alex Greenwood, Brian T. Chait, Kirsty Penkman, Matthew Collins … & Ross D. E. MacPhee
The living tree sloths Choloepus and Bradypus are the only remaining members of Folivora, a major xenarthran radiation that occupied a wide range of habitats in many parts of the western hemisphere during the Cenozoic, including both continents and the West Indies. Ancient DNA evidence has played only a minor role in folivoran systematics, as most sloths lived in places not conducive to genomic preservation. Here we utilize collagen sequence information, both separately and in...

Data from: The social cost of lobbying over climate policy

Kyle C. Meng & Ashwin Rode
Domestic political processes shape climate policy. In particular, there is increasing concern regarding the role of political lobbying over climate policy. This paper examines how lobbying spending on the Waxman-Markey bill, the most prominent and promising U.S. climate regulation to date, altered its likelihood of being implemented. We combine data from comprehensive U.S. lobbying records together with an empirical method for forecasting the policy’s effect on the value of publicly-listed firms. Our statistical analysis suggests...

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