90 Works

Data from: Simultaneous delimitation of species and quantification of interspecific hybridization in Amazonian peacock cichlids (genus Cichla) using multi-locus data

Stuart C. Willis, Jason Macrander, Izeni P. Farias & Guillermo Orti
BACKGROUND: Introgression likely plays a significant role in evolution, but understanding the extent and consequences of this process requires a clear identification of species boundaries in each focal group. The delimitation of species, however, is a contentious endeavor. This is true not only because of the inadequacy of current tools to identify species lineages, but also because of the inherent ambiguity between natural populations and species paradigms. The result has been a debate about the...

Data from: Phylogenomic analyses reveal convergent patterns of adaptive evolution in elephant and human ancestries

Morris Goodman, Kirstin N. Sterner, M. Munirul Islam, Monica Uddin, Chet C. Sherwood, Patrick R. Hof, Zhuo-Cheng Hou, Leonard Lipovich, Hui Jia, Lawrence I. Grossman, Derek E. Wildman, M. Islam & Z. C. Hou
Specific sets of brain-expressed genes, such as aerobic energy metabolism genes, evolved adaptively in the ancestry of humans and may have evolved adaptively in the ancestry of other large-brained mammals. The recent addition of genomes from two afrotherians (elephant and tenrec) to the expanding set of publically available sequenced mammalian genomes provided an opportunity to test this hypothesis. Elephants resemble humans by having large brains and long life spans; tenrecs, in contrast, have small brains...

Data from: Multi-locus phylogenetic analysis reveals the pattern and tempo of bony fish evolution

Richard E. Broughton, Ricardo Betancur-R., Chenhong Li, Gloria Arratia & Guillermo Orti
Over half of all vertebrates are “fishes”, which exhibit enormous diversity in morphology, physiology, behavior, reproductive biology, and ecology. Investigation of fundamental areas of vertebrate biology depend critically on a robust phylogeny of fishes, yet evolutionary relationships among the major actinopterygian and sarcopterygian lineages have not been conclusively resolved. Although a consensus phylogeny of teleosts has been emerging recently, it has been based on analyses of various subsets of actinopterygian taxa, but not on a...

Data from: Sapwood capacitance is greater in evergreen sclerophyll species growing in high compared to low rainfall environments

Anna E. Richards, Ian J. Wright, Tanja I. Lenz & Amy E. Zanne
1. The capacitative release of water from sapwood allows photosynthesis to continue for longer into dry periods, both diurnally and seasonally. However, costs of high capacitance include increased vulnerability to xylem cavitation. The degree of reliance on stored water is predicted to differ among environments as a result of this trade off 2. Xylem water potential and sapwood capacitance were measured on 32 evergreen sclerophyll shrub and tree species in eastern Australia, sampled from four...

Data from: Systematics of the blindsnakes (Serpentes: Scolecophidia: Typhlopoidea) based on molecular and morphological evidence

Robert Alexander Pyron & Van Wallach
The blindsnake superfamily Typhlopoidea (Gerrhopilidae, Typhlopidae, and Xenotyphlopidae) is a diverse, widespread part of the global snake fauna. A recent systematic revision based on molecular phylogenetic analyses and some morphological evidence presented a preliminary solution to the non-monophyly of many previously recognized genera, but additional clarification is needed regarding the recognition of some species and genera. We rectify these problems here with a new molecular phylogenetic analysis including 95 of the 275 currently recognized, extant...

Data from: Effectiveness of phylogenomic data and coalescent species-tree methods for resolving difficult nodes in the phylogeny of advanced snakes (Serpentes: Caenophidia)

R. Alexander Pyron, Catriona R. Hendry, Vincent M. Chou, Emily M. Lemmon, Alan R. Lemmon & Frank T. Burbrink
Next-generation genomic sequencing promises to quickly and cheaply resolve remaining contentious nodes in the Tree of Life, and facilitates species-tree estimation while taking into account stochastic genealogical discordance among loci. Recent methods for estimating species trees bypass full likelihood-based estimates of the multi-species coalescent, and approximate the true species-tree using simpler summary metrics. These methods converge on the true species-tree with sufficient genomic sampling, even in the anomaly zone. However, no studies have yet evaluated...

Data from: Fully-sampled phylogenies of squamates reveal evolutionary patterns in threat status

João Filipe Riva Tonini, Karen H. Beard, Rodrigo Barbosa Ferreira, Walter Jetz & R. Alexander Pyron
Macroevolutionary rates of diversification and anthropogenic extinction risk differ vastly throughout the Tree of Life. This results in a highly heterogeneous distribution of Evolutionary distinctiveness (ED) and threat status among species. We examine the phylogenetic distribution of ED and threat status for squamates (amphisbaenians, lizards, and snakes) using fully-sampled phylogenies containing 9574 species and expert-based estimates of threat status for ~ 4000 species. We ask whether threatened species are more closely related than would be...

Data from: Does increased heat resistance result in higher susceptibility to predation? A test using (Drosophila melanogaster) selection and hardening

Sandra Hangartner, Ian Dworkin, Michael DeNieu & Ary A. Hoffmann
Heat resistance of ectotherms can be increased both by plasticity and evolution, but these effects may have trade-offs resulting from biotic interactions. Here we test for predation costs in Drosophila melanogaster populations with altered heat resistance produced by adult hardening and directional selection for increased heat resistance. In addition, we also tested for genetic trade-offs by testing heat resistance in lines that have evolved under increased predation risk. We show that while 35/37°C hardening increases...

Data from: Ecological fidelity of functional traits based on species presence-absence in a modern mammalian bone assemblage (Amboseli, Kenya)

Joshua H. Miller, Anna Kay Behrensmeyer, Andrew Du, S. Kathleen Lyons, David Patterson, Anikó Tóth, Amelia Villaseñor, Erustus Kanga & Denné Reed
Comparisons between modern death assemblages and their source communities have demonstrated fidelity to species diversity across a variety of environments and taxonomic groups. However, differential species preservation and collection (including body-size bias) in both modern and fossil death assemblages may still skew the representation of other important ecological characteristics. Here, we move beyond live-dead taxonomic fidelity and focus on the recovery of functional ecology (how species interact with their ecosystem) at the community level for...

Data from: A quantitative method for inferring locomotory shifts in amniotes during ontogeny, its application to dinosaurs, and its bearing on the evolution of posture

Kimberley E. J. Chapelle, Roger B. J. Benson, Josef Stiegler, Alejandro Otero, Qi Zhao & Jonah N. Choiniere
Evolutionary transitions between quadrupedal and bipedal postures are pivotal to the diversification of amniotes on land, including in our own lineage (Hominini). Heterochrony is suggested as a macroevolutionary mechanism for postural transitions, but understanding postural evolution in deep time is hindered by a lack of methods for inferring posture in extinct species. Dinosaurs are an excellent natural laboratory for understanding postural transitions, because their lineage contains at least four instances of quadrupedality evolving from bipedality,...

Habitat transitions alter the adaptive landscape and shape phenotypic evolution in needlefishes (Belonidae)

Matthew Kolmann, Michael D. Burns, Justin Y. K. Ng, Nathan R. Lovjoy & Devin D. Bloom
Habitat occupancy can have a profound influence on macroevolutionary dynamics, and a switch in major habitat type may alter the evolutionary trajectory of a lineage. In this study we investigate how evolutionary transitions between marine and freshwater habitats affect macroevolutionary adaptive landscapes, using needlefishes (Belonidae) as a model system. We examined the evolution of body shape and size in marine and freshwater needlefishes and tested for phenotypic change in response to transitions between habitats. Using...

Data from: Assessment of disease progression in dysferlinopathy – a one year cohort study

Volker Straub, Ursula Moore, Marni Jacobs, Meredith K. James, Anna G. Mayhew, Roberto Fernandez-Torron, Jia Feng, Avital Cnaan, Michelle Eagle, Karen Bettinson, Laura E. Rufibach & Robert Muni Lofra
Objective: To assess the ability of functional measures to detect disease progression in dysferlinopathy over 6 months and 1 year. Methods: 193 patients with dysferlinopathy were recruited to the Jain Foundation’s International Clinical Outcome Study for Dysferlinopathy. Baseline, 6 months and 1 year assessments included: adapted North Star Assessment (a-NSAA), Motor Function Measure (MFM-20), timed function tests, 6 minute walk test (6MWT), Brooke Scale, Jebsen Test, manual muscle testing (MMT) and hand-held dynamometry (HHD). Patients...

The geometry of resource constraint: an empirical study of the golden snub-nosed monkey

Rong Hou, Colin Chapman, Jessica Rothman, He Zhang, Kang Huang, Songtao Guo, Baoguo Li & David Raubenheimer
1. Apposite conceptualization and measurement of resource variation is critical for understanding many issues in ecology, including ecological niches, persistence and distribution of populations, the structure of communities, and population resilience to perturbations. 2. We apply the nutritional geometry framework to conceptualise and quantify the responses of a temperate-living primate, the golden snub-nosed monkey (Rhinopithecus roxellana) to variation in resource quality and quantity and in nutrient requirements associated with seasonal environments. 3. We present a...

Shame and Trauma Go to Class

Abby Wilkerson
To be a member of an oppressed social group is to face differential risk of trauma. Using Sandra Lee Bartky’s recognition of certain emotional states as “primordial disclosure,” I explore socially occasioned trauma, shame, and depression as gendered and racialized phenomena in higher education—a crucial site for exploring the processes that situate some bodyminds as normative, deserving, and competent, while others are situated as less able or deserving, or as intruders. Given systemic inequality, mental...

Data from: The tree of life and a new classification of bony fishes

Ricardo Betancur-R., Adela Roa-Varon, Nancy I. Holcroft, W. Calvin Borden, Terry Grande, Kent Carpenter, Millicent Sanciangco, Chenhong Li, Dahiana Arcila, Jesus A Ballesteros, Guillermo Ortí, J. Andrés López, Matthew A. Campbell, Edward O. Wiley, Gloria Arratia, Guoqing Lu, Stuart Willis, Richard E. Broughton, , Feifei Zhang & Daniel J. Hough
The tree of life of fishes is in a state of flux because we still lack a comprehensive phylogeny that includes all major groups. The situation is most critical for a large clade of spiny-finned fishes, traditionally referred to as percomorphs, whose uncertain relationships have plagued ichthyologists for over a century. Most of what we know about the higher-level relationships among fish lineages has been based on morphology, but rapid influx of molecular studies is...

Data from: Addressing gene tree discordance and non-stationarity to resolve a multi-locus phylogeny of the flatfishes (Teleostei: Pleuronectiformes)

Ricardo Betancur-R., Chenhong Li, Thomas A. Munroe, Jesus A. Ballesteros & Guillermo Ortí
Non-homogeneous processes and, in particular, base compositional non-stationarity have long been recognized as a critical source of systematic error. But only a small fraction of current molecular systematic studies methodically examine and effectively account for the potentially confounding effect of non-stationarity. The problem is especially overlooked in multi-locus or phylogenomic scale analyses, in part because no efficient tools exist to accommodate base composition heterogeneity in large data sets. We present a detailed analysis of a...

Data From: TERRA-REF, An open reference data set from high resolution genomics, phenomics, and imaging sensors

David LeBauer, Burnette Maxwell, Jeffrey Demieville, Noah Fahlgren, Andrew French, Roman Garnett, Zhenbin Hu, Kimberly Huynh, Rob Kooper, Zongyang Li, Maitiniyazi Maimaitijiang, Jerome Mao, Todd Mockler, Geoffrey Morris, Maria Newcomb, Michael Ottman, Philip Ozersky, Sidike Paheding, Duke Pauli, Robert Pless, Wei Qin, Kristina Riemer, Gareth Rohde, William Rooney, Vasit Sagan … & Charles Zender
The ARPA-E funded TERRA-REF project is generating open-access reference datasets for the study of plant sensing, genomics, and phenomics. Sensor data were generated by a field scanner sensing platform that captures color, thermal, hyperspectral, and active flourescence imagery as well as three dimensional structure and associated environmental measurements. This dataset is provided alongside data collected using traditional field methods in order to support calibration and validation of algorithms used to extract plot level phenotypes from...

Genetic algorithm-based personalized models of human cardiac action potential

Roman Syunyaev, Igor Efimov, Kedar Aras, Anna Gams, Aaron Koppel, Oleg Gusev, Andrey Pikunov & Ruslan Deviatiiarov
We present a novel modification of genetic algorithm (GA) which determines personalized parameters of cardiomyocyte electrophysiology model based on set of experimental human action potential (AP) recorded at different heart rates. In order to find the steady state solution, the optimized algorithm performs simultaneous search in the parametric and slow variables spaces. We demonstrate that several GA modifications are required for effective convergence. Firstly, we used a mutation operator, based on Cauchy amplitude distribution along...

Data from: Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data

Lily C. Hughes, Guillermo Ortí, Yu Huang, Ying Sun, Carole C. Baldwin, Andrew W. Thompson, Dahiana Arcila, Ricardo Betancur-R, Chenhong Li, Leandro Becker, Nicolás Bellora, Xiaomeng Zhao, Xiaofeng Li, Min Wang, Chao Fang, Bing Xie, Zhuocheng Zhou, Hai Huang, Songlin Chen, Byrappa Venkatesh & Qiong Shi
Our understanding of phylogenetic relationships among bony fishes has been transformed by analysis of a small number of genes, but uncertainty remains around critical nodes. Genome-scale inferences so far have sampled a limited number of taxa and genes. Here we leveraged 144 genomes and 159 transcriptomes to investigate fish evolution with an unparalleled scale of data: >0.5 Mb from 1,105 orthologous exon sequences from 303 species, representing 66 out of 72 ray-finned fish orders. We...

Allometric escape from acoustic constraints in frog calls is rare

Joao Filipe Tonini, Diogo Provete, Natan Maciel, Alessandro Morais, Sandra Goutte, Felipe Toledo & R. Alexander Pyron
Allometric constraint is a product of natural selection, particularly with respect to body size and traits constrained by physical properties thereof, such as metabolism, longevity, and vocal frequency. Parameters describing allometric relationships are conserved across most lineages, indicating that physical constraints dictate scaling patterns in deep time, despite substantial genetic and ecological divergence among organisms. Acoustic allometry (sound frequency ~ body size) is conserved across frogs, in defiance of massive variation in both body size...

Data from: Synthesis of phylogeny and taxonomy into a comprehensive tree of life

Cody E. Hinchliff, Stephen A. Smith, James F. Allman, J. Gordon Burleigh, Ruchi Chaudhary, Lyndon M. Coghill, Keith A. Crandall, Jiabin Deng, Bryan T. Drew, Romina Gazis, Karl Gude, David S. Hibbett, Laura A. Katz, , Emily Jane McTavish, Peter E. Midford, Christopher L. Owen, Richard H. Ree, Jonathan A. Rees, Douglas E. Soltis, Tiffani Williams & Karen Ann Cranston
Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips—the Open Tree of Life. Realization of this tree required the assembly...

Data from: Ecological divergence and sexual selection drive sexual size dimorphism in new world pitvipers (Serpentes: Viperidae)

Catriona R. Hendry, Timothy J. Guiher & Robert A. Pyron
Hypotheses for the origin and maintenance of sexual size dimorphism (SSD) fall into three primary categories: (i) sexual selection on male size, (ii) fecundity selection on female size and (iii) ecological selection for gender-specific niche divergence. We investigate the impact of these forces on SSD evolution in New World pitvipers (Crotalinae). We constructed a phylogeny from up to eight genes (seven mitochondrial, one nuclear) for 104 species of NW crotalines. We gathered morphological and ecological...

Data from: How much of the world is woody?

Richard G. FitzJohn, Matt W. Pennell, Amy E. Zanne, Peter F. Stevens, David C. Tank, William K. Cornwell & Matthew W. Pennell
1.The question posed by the title of this paper is a basic one, and it is surprising that the answer is not known. Recently assembled trait datasets provide an opportunity to address this, but scaling these datasets to the global scale is challenging because of sampling bias. Although we currently know the growth form of tens of thousands of species, these data are not a random sample of global diversity; some clades are exhaustively characterised,...

Data from: Predicting community structure in snakes on Eastern Nearctic islands using ecological neutral theory and phylogenetic methods

Frank T. Burbrink, Alexander D. McKelvy, R. Alexander Pyron & Edward A. Myers
Predicting species presence and richness on islands is important for understanding the origins of communities and how likely it is that species will disperse and resist extinction. The equilibrium theory of island biogeography (ETIB) and, as a simple model of sampling abundances, the unified neutral theory of biodiversity (UNTB), predict that in situations where mainland to island migration is high, species-abundance relationships explain the presence of taxa on islands. Thus, more abundant mainland species should...

Data from: The heritability of chimpanzee and human brain asymmetry

Aida Gómez-Robles, William D. Hopkins, Steven J. Schapiro & Chet C. Sherwood
Human brains are markedly asymmetric in structure and lateralized in function, which suggests a relationship between these two properties. The brains of other closely related primates, such as chimpanzees, show similar patterns of asymmetry, but to a lesser degree, indicating an increase in anatomical and functional asymmetry during hominin evolution. We analysed the heritability of cerebral asymmetry in chimpanzees and humans using classic morphometrics, geometric morphometrics, and quantitative genetic techniques. In our analyses, we separated...

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