284 Works

Choice of 3D morphometric method leads to diverging interpretations of form-function relationships in the carnivoran calcaneus

Alexa Wimberly, Rossy Natale, Robert Higgins & Graham Slater
Three dimensional morphometric methods are a powerful tool for comparative analysis of shape. However, morphological shape is often represented using landmarks selected by the user to describe features of perceived importance, and this may lead to over confident prediction of form-function relationships in subsequent analyses. We used Generalized Procrustes Analysis (GPA) of 13 homologous 3D landmarks and spherical harmonics (SPHARM) analysis, a homology-free method that describes the entire shape of a closed surface, to quantify...

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: 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: 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: 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: Population structure, genetic connectivity, and adaptation in the Olympia oyster (Ostrea lurida) along the west coast of North America

Katherine Silliman
Effective management of threatened and exploited species requires an understanding of both the genetic connectivity among populations and local adaptation. The Olympia oyster (Ostrea lurida), patchily distributed from Baja California to the central coast of Canada, has a long history of population declines due to anthropogenic stressors. For such coastal marine species, population structure could follow a continuous isolation-by-distance model, contain regional blocks of genetic similarity separated by barriers to gene flow, or be consistent...

Data from: Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours

John M. Jumper, Nabil F. Faruk, Karl F. Freed & Tobin R. Sosnick
An ongoing challenge in protein chemistry is to identify the underlying interaction energies that capture protein dynamics. The traditional trade-off in biomolecular simulation between accuracy and computational efficiency is predicated on the assumption that detailed force fields are typically well-parameterized, obtaining a significant fraction of possible accuracy. We re-examine this trade-off in the more realistic regime in which parameterization is a greater source of error than the level of detail in the force field. To...

Data from: Morphology of the petrosal and stapes of Borealestes (Mammaliaformes, Docodonta) from the Middle Jurassic of Skye, Scotland

Elsa Panciroli, Julia A. Schultz & Zhe-Xi Luo
\We describe, in unprecedented detail, the petrosals and stapes of the docodont Borealestes from the Middle Jurassic of Scotland, using high resolution μCT and phase‐contrast synchrotron imaging. We describe the inner ear endocast and the vascularized interior structure of the petrosal, and provide the first endocranial view of a docodontan petrosal. Our study confirms some similarities in petrosal and stapedial morphology with the better known Haldanodon of the Late Jurassic of Portugal, including: (1) the...

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: Detecting past and ongoing natural selection among ethnically Tibetan women at high altitude in Nepal

Choongwon Jeong, David B. Witonsky, Buddha Basnyat, Maniraj Neupane, Cynthia M. Beall, Geoff Childs, Sienna R. Craig, John Novembre & Anna Di Rienzo
Adaptive evolution in humans has rarely been characterized for its whole set of components, i.e. selective pressure, adaptive phenotype, beneficial alleles and realized fitness differential. We combined approaches for detecting selective sweeps and polygenic adaptations and for mapping the genetic bases of physiological and fertility phenotypes in approximately 1000 indigenous ethnically Tibetan women from Nepal, adapted to high altitude. We performed genome-wide association analysis and tests for polygenic adaptations which showed evidence of positive selection...

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: 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: Testing the adaptive hypothesis of Batesian mimicry among hybridizing North American admiral butterflies

Evan Breaux Kristiansen, Susan D. Finkbeiner, Ryan Isaac Hill, Louis Prusa & Sean Patrick Mullen
Batesian mimicry is characterized by phenotypic convergence between an unpalatable model and a palatable mimic. However, because convergent evolution may arise via alternative evolutionary mechanisms, putative examples of Batesian mimicry must be rigorously tested. Here we used artificial butterfly facsimiles (N=4000) to test the prediction that 1) palatable Limenitis lorquini butterflies should experience reduced predation when in sympatry with their putative model, Adelpha californica, 2) protection from predation on L. lorquini should erode outside of...

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: 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: Does batrachotoxin autoresistance co-evolve with toxicity in Phyllobates poison-dart frogs?

Roberto Márquez, Valeria Ramírez-Castañeda & Adolfo Amézquita
Toxicity is widespread among living organisms, and evolves as a multimodal phenotype. Part of this phenotype is the ability to avoid self-intoxication (autoresistance). Evolving toxin resistance can involve fitness tradeoffs, so autoresistance is often expected to evolve gradually and in tandem with toxicity, resulting in a correlation between the degrees of toxicity and autoresistance among toxic populations. We investigate this correlation in Phyllobates poison frogs, notorious for secreting batrachotoxin (BTX), a potent neurotoxin that targets...

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: 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: 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: 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: 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 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: 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: 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...

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