32 Works

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: 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: 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: 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: What can interaction webs tell us about species roles?

J. Timothy Wootton, Elizabeth L. Sander & Stefano Allesina
The group model is a useful tool to understand broad-scale patterns of interaction in a network, but it has previously been limited in use to food webs, which contain only predator-prey interactions. Natural populations interact with each other in a variety of ways and, although most published ecological networks only include information about a single interaction type (e.g., feeding, pollination), ecologists are beginning to consider networks which combine multiple interaction types. Here we extend the...

Data from: Rearing temperature influences adult response to changes in mating status

Erica L. Westerman, Antónia Monteiro & Erica Westerman
Rearing environment can have an impact on adult behavior, but it is less clear how rearing environment influences adult behavior plasticity. Here we explore the effect of rearing temperature on adult mating behavior plasticity in the butterfly Bicyclus anynana, a species that has evolved two seasonal forms in response to seasonal changes in temperature. These seasonal forms differ in both morphology and behavior. Females are the choosy sex in cohorts reared at warm temperatures (WS...

Data from: Stable recombination hotspots in birds

Sonal Singhal, Ellen M. Leffler, Keerthi Sannareddy, Isaac Turner, Oliver Venn, Daniel M. Hooper, Alva I. Strand, Qiye Li, Brian Raney, Christopher N. Balakrishnan, Simon C. Griffith, Gil McVean & Molly Przeworski
The DNA-binding protein PRDM9 has a critical role in specifying meiotic recombination hotspots in mice and apes, but it appears to be absent from other vertebrate species, including birds. To study the evolution and determinants of recombination in species lacking the gene that encodes PRDM9, we inferred fine-scale genetic maps from population resequencing data for two bird species: the zebra finch, Taeniopygia guttata, and the long-tailed finch, Poephila acuticauda. We found that both species have...

Data from: Endoskeletal structure in Cheirolepis (Osteichthyes, Actinopterygii), an early ray-finned fish

Sam Giles, Michael I. Coates, Russell J. Garwood, Martin D. Brazeau, Robert Atwood, Zerina Johanson & Matt Friedman
As the sister lineage of all other actinopterygians, the Middle to Late Devonian (Eifelian–Frasnian) Cheirolepis occupies a pivotal position in vertebrate phylogeny. Although the dermal skeleton of this taxon has been exhaustively described, very little of its endoskeleton is known, leaving questions of neurocranial and fin evolution in early ray-finned fishes unresolved. The model for early actinopterygian anatomy has instead been based largely on the Late Devonian (Frasnian) Mimipiscis, preserved in stunning detail from the...

Data from: The genomes of two key bumblebee species with primitive eusocial organisation

Ben M. Sadd, Seth M. Barribeau, Guy Bloch, Dirk C. De Graaf, Peter Dearden, Christine Elsik, Jurgen Gadau, Cornelius Grimmelikhuijzen, Martin Hasselmann, Jeffrey Lozier, Hugh Robertson, Guy Smagghe, Eckart Stolle, Matthias Van Vaerenbergh, Robert Waterhouse, Erich Bornberg-Bauer, Steffan Klasberg, Anna Bennett, Francisco Camara, Roderic Guigo, Katharina Hoff, Marco Mariotti, Monica Munos-Torres, Terence Murphy, Didac Santesmasses … & Kim C. Worley
Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome...

Data from: Evolutionary patterns of shape and functional diversification in the skull and jaw musculature of triggerfishes (Teleostei: Balistidae)

Charlene McCord, Mark W. Westneat & Charlene L. McCord
The robust skull and highly subdivided adductor mandibulae muscles of triggerfishes provide an excellent system within which to analyze the evolutionary processes underlying phenotypic diversification. We surveyed the anatomical diversity of balistid jaws using Procrustes-based geometric morphometric analyses and a phylomorphospace approach to quantifying morphological transformation through evolution. We hypothesized that metrics of interspecific cranial shape would reveal patterns of phylogenetic diversification that are congruent with functional and ecological transformation. Morphological landmarks outlining skull and...

Data from: Inferring skeletal production from time-averaged assemblages: skeletal loss pulls the timing of production pulses towards the modern period

Adam Tomašových, Susan M. Kidwell & Rina Foygel Barber
Age-frequency distributions of dead skeletal material on the landscape or seabed—information on the time that has elapsed since the death of individuals—provide decadal- to millennial-scale perspectives both on the history of production and on the processes that lead to skeletal disintegration and burial. So far, however, models quantifying the dynamics of skeletal loss have assumed that skeletal production is constant during time-averaged accumulation. Here, to improve inferences in conservation paleobiology and historical ecology, we evaluate...

Data from: Genetic subdivision and candidate genes under selection in North American gray wolves

Rena M. Schweizer, Bridgett M. VonHoldt, Ryan Harrigan, James C. Knowles, Marco Musiani, David Coltman, John Novembre & Robert K. Wayne
Previous genetic studies of the highly mobile gray wolf (Canis lupus) found population structure that coincides with habitat and phenotype differences. We hypothesized that these ecologically distinct populations (ecotypes) should exhibit signatures of selection in genes related to morphology, coat color, and metabolism. To test these predictions, we quantified population structure related to habitat using a genotyping array to assess variation in 42,036 SNPs in 111 North American gray wolves. Using these SNP data and...

Data from: Energetic benefits and adaptations in mammalian limbs: scale effects and selective pressures

Brandon M. Kilbourne & Louwrens C. Hoffman
Differences in limb size and shape are fundamental to mammalian morphological diversity; however, their relevance to locomotor costs has long been subject to debate. In particular, it remains unknown if scale effects in whole limb morphology could partially underlie decreasing mass-specific locomotor costs with increasing limb length. Whole fore- and hindlimb inertial properties reflecting limb size and shape – moment of inertia (MOI), mass, mass distribution, and natural frequency – were regressed against limb length...

Data from: Cascading effects of induced terrestrial plant defenses on aquatic and terrestrial ecosystem function

Sara L. Jackrel & J. Timothy Wootton
Herbivores induce plants to undergo diverse processes that minimize costs to the plant, such as producing defences to deter herbivory or reallocating limited resources to inaccessible portions of the plant. Yet most plant tissue is consumed by decomposers, not herbivores, and these defensive processes aimed to deter herbivores may alter plant tissue even after detachment from the plant. All consumers value nutrients, but plants also require these nutrients for primary functions and defensive processes. We...

Data from: The tempo of trait divergence in geographic isolation: avian speciation across the Marañon valley of Peru

Benjamin M. Winger & John M. Bates
Geographic isolation is considered essential to most speciation events, but our understanding of what controls the pace and degree of phenotypic divergence among allopatric populations remains poor. Why do some taxa exhibit phenotypic differentiation across barriers to dispersal, whereas others do not? To test factors controlling phenotypic divergence in allopatry, we employed a comparative phylogeographic approach consisting of replicates of ecologically similar Andean bird species isolated across a major biogeographic barrier, the Marañon valley of...

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: Accounting for experimental noise reveals that mRNA levels, amplified by post-transcriptional processes, largely determine steady-state protein levels in yeast

Gábor Csárdi, Alexander Franks, David S. Choi, Edoardo M. Airoldi & David Allan Drummond
Cells respond to their environment by modulating protein levels through mRNA transcription and post-transcriptional control. Modest observed correlations between global steady-state mRNA and protein measurements have been interpreted as evidence that mRNA levels determine roughly 40% of the variation in protein levels, indicating dominant post-transcriptional effects. However, the techniques underlying these conclusions, such as correlation and regression, yield biased results when data are noisy, missing systematically, and collinear---properties of mRNA and protein measurements---which motivated us...

Data from: Fungal specificity and selectivity for algae play a major role in determining lichen partnerships across diverse ecogeographic regions in the lichen-forming family Parmeliaceae

Steven D. Leavitt, Ekaphan Kraichak, Matthew P. Nelsen, Susanne Altermann, Pradeep K. Divakar, David Alors, Theodore L. Esslinger, Ana Crespo, H. Thorsten Lumbsch & Thorsten Lumbsch
Microbial symbionts are instrumental to the ecological and long-term evolutionary success of their hosts, and the central role of symbiotic interactions is increasingly recognized across the vast majority of life. Lichens provide an iconic group for investigating patterns in species interactions; however, relationships among lichen symbionts are often masked by uncertain species boundaries or an inability to reliably identify symbionts. The species-rich lichen-forming fungal family Parmeliaceae provides a diverse group for assessing patterns of interactions...

Data from: Reversible, specific, active aggregates of endogenous proteins assemble upon heat stress

Edward W. J. Wallace, Jamie L. Kear-Scott, Evgeny V. Pilipenko, Michael H. Schwartz, Pawel R. Laskowski, Alexandra E. Rojek, Christopher D. Katanski, Joshua A. Riback, Michael F. Dion, Alexander M. Franks, Edoardo M. Airoldi, Tao Pan, Bogdan A. Budnik & D. Allan Drummond
Heat causes protein misfolding and aggregation and in eukaryotic cells triggers aggregation of proteins and RNA into stress granules. We have carried out extensive proteomic studies to quantify heat-triggered aggregation and subsequent disaggregation in budding yeast, identifying >170 endogenous proteins aggregating within minutes of heat shock in multiple subcellular compartments. We demonstrate that these aggregated proteins are not misfolded and destined for degradation. Stable-isotope labeling reveals that even severely aggregated endogenous proteins are disaggregated without...

Data from: Mapping of craniofacial traits in outbred mice identifies major developmental genes involved in shape determination

Luisa F. Pallares, Peter Carbonetto, Shyam Gopalakrishnan, Clarissa C. Parker, Cheryl L. Ackert-Bicknell, Abraham A. Palmer & Diethard Tautz
The vertebrate cranium is a prime example of the high evolvability of complex traits. While evidence of genes and developmental pathways underlying craniofacial shape determination is accumulating, we are still far from understanding how such variation at the genetic level is translated into craniofacial shape variation. Here we used 3D geometric morphometrics to map genes involved in shape determination in a population of outbred mice (Carworth Farms White, or CFW). We defined shape traits via...

Data from: Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in gray wolves

Rena M. Schweizer, Jacqueline Robinson, Ryan Harrigan, Pedro Silva, Marco Galaverni, Marco Musiani, Richard E. Green, John Novembre & Robert K. Wayne
In an era of ever-increasing amounts of whole genome sequence data for individuals and populations, the utility of traditional single nucleotide polymorphisms (SNPs) array-based genome scans is uncertain. We previously performed a SNP array-based genome scan to identify candidate genes under selection in six distinct gray wolf (Canis lupus) ecotypes. Using this information, we designed a targeted capture array for 1040 genes, including all exons and flanking regions, as well as 5000 1 kb non-genic...

Data from: Inferring speciation history in the Andes with reduced-representation sequence data: an example in the bay-backed antpittas (Aves; Grallariidae; Grallaria hypoleuca s. l.)

Benjamin M. Winger, Peter A. Hosner, Gustavo A. Bravo, Andrés M. Cuervo, Natalia Aristizábal, Luis E. Cueto & John M. Bates
In the Andes, humid-forest organisms frequently exhibit pronounced genetic structure and geographic variation in phenotype, often coincident with physical barriers to dispersal. However, phylogenetic relationships of clades have often been difficult to resolve due to short internodes. Consequently, even in taxa with well-defined genetic structure, the temporal and geographic sequences of dispersal and vicariance events that led to this differentiation have remained opaque, hindering efforts to test the association between diversification and earth history and...

Data from: Newspaper coverage of maternal health in Bangladesh, Rwanda, and South Africa: a quantitative and qualitative content analysis

Frey Gugsa, Ellora Karmarkar, Andrew Cheyne & Gavin Yamey
Objective: To examine newspaper coverage of maternal health in three countries that have made varying progress towards Millennium Development Goal 5 (MDG 5): Bangladesh (on track), Rwanda (making progress, but not on track) and South Africa (no progress). Design: We analysed each country's leading national English-language newspaper: Bangladesh's The Daily Star, Rwanda's The New Times/The Sunday Times, and South Africa's Sunday Times/The Times. We quantified the number of maternal health articles published from 1 January...

Data from: Revisiting Fisher: range size drives the correlation between variability and abundance of British bird eggs

Oriol Lapiedra & Trevor D. Price
We evaluate the correlation between intraspecific variation in egg size and population size in breeding British birds. Using information on abundance, range occupancy, migration status and phylogenetic relationships among species, we show that a wider geographical distribution rather than larger population size per se best predicts egg size variability. A similar result applies to wing length variability. Results from a phylogenetic path analysis suggest that geographical variation is the most parsimonious causal explanation for high...

Data from: Infant feeding and risk of developing celiac disease: a systematic review

Marco Silano, Carlo Agostoni, Yolanda Sanz & Stefano Guandalini
Objective: To review the evidence for the association of breast feeding, breastfeeding duration or the timing of gluten introduction and the later development of celiac disease (CD). Design: Systematic review. Methods: We searched MEDLINE, via PubMed, EMBASE and Web of Science, for studies published up to 31 August 2015 investigating the association of breastfeeding duration, breast feeding at the moment of gluten introduction or the timing of gluten introduction and the later development of CD....

Registration Year

  • 2015
    32

Resource Types

  • Dataset
    32

Affiliations

  • University of Chicago
    32
  • Field Museum of Natural History
    5
  • Harvard University
    2
  • University of Calgary
    2
  • University of California Los Angeles
    2
  • University of Kansas
    1
  • Federal Institute of São Paulo
    1
  • Sao Paulo State University
    1
  • London School of Hygiene & Tropical Medicine
    1
  • University of Hohenheim
    1