33 Works

Data from: Range-wide multilocus phylogeography of the red fox reveals ancient continental divergence, minimal genomic exchange, and distinct demographic histories

Mark J. Statham, Zhenghuan Wang, Carl D. Soulsbury, Jan Janecka, Benjamin N. Sacks, Keith B. Aubry, Oliver Berry, Ceiridwen J. Edwards & James Murdoch
Widely distributed taxa provide an opportunity to compare biogeographic responses to climatic fluctuations on multiple continents and to investigate speciation. We conducted the most geographically and genomically comprehensive study to date of the red fox (Vulpes vulpes), the world's most widely distributed wild terrestrial carnivore. Analyses of 697 bp of mitochondrial sequence in ~1000 individuals suggested an ancient Middle Eastern origin for all extant red foxes and a 400 kya (SD = 139 kya) origin...

Data from: Context-dependent effects of large wildlife declines on small mammal communities in central Kenya

Hillary S. Young, Douglas J. McCauley, Rodolfo Dirzo, Jacob R. Goheen, Bernard Agwanda, Cara Brook, Erik O. Castillo, Adam W. Ferguson, Stephen N. Kinyua, Molly M. McDonough, Todd M. Palmer, Robert M. Pringle, Truman P. Young & Kristofer M. Helgen
Many species of large wildlife have declined drastically worldwide. These reductions often lead to profound shifts in the ecology of entire communities and ecosystems. However, the effects of these large wildlife declines on other taxa likely hinge upon both underlying abiotic properties of these systems and on the types of secondary anthropogenic changes associated with wildlife loss, making impacts difficult to predict. To better understand how these important contextual factors determine the consequences of large-wildlife...

Data from: Pathogen burden, co-infection and major histocompatibility complex variability in the European badger (Meles meles)

Yung Wa Sin, Geetha Annavi, Hannah L. Dugdale, Chris Newman, Terry Burke & David W. Macdonald
Pathogen-mediated selection is thought to maintain the extreme diversity in the major histocompatibility complex (MHC) genes, operating through the heterozygote advantage, rare-allele advantage and fluctuating selection mechanisms. Heterozygote advantage (i.e., recognizing and binding a wider range of antigens than homozygotes) is expected to be more detectable when multiple pathogens are considered simultaneously. Here, we test if MHC diversity in a wild population of European badgers (Meles meles) is driven by pathogen-mediated selection. We examined individual...

Data from: A Palaeozoic stem-group to mite harvestmen revealed through integration of phylogenetics and development

Russell J. Garwood, Prashant P. Sharma, Jason A. Dunlop & Gonzalo Giribet
Successfully placing fossils in phylogenies is integral to understanding the tree of life. Crown-group Paleozoic members of the arachnid order Opiliones are indicative of ancient origins and one of the earliest arthropod terrestrialization events. Opiliones epitomize morphological stasis, and all known fossils have been placed within the four extant suborders. Here we report a Carboniferous harvestman species, Hastocularis argusgen. nov., sp. nov., reconstructed with microtomography (microCT). Phylogenetic analysis recovers this species, and the Devonian Eophalangium...

Data from: Metabolic erosion primarily through mutation accumulation, and not tradeoffs, drives limited evolution of substrate specificity in Escherichia coli

Nicholas Leiby & Christopher J. Marx
Evolutionary adaptation to a constant environment is often accompanied by specialization and a reduction of fitness in other environments. We assayed the ability of the Lenski Escherichia coli populations to grow on a range of carbon sources after 50,000 generations of adaptation on glucose. Using direct measurements of growth rates, we demonstrated that declines in performance were much less widespread than suggested by previous results from Biolog assays of cellular respiration. Surprisingly, there were many...

Data from: Neighbouring-group composition and within-group relatedness drive extra-group paternity rate in the European badger (Meles meles)

Geetha Annavi, Chris Newman, Hannah L. Dugdale, Christina C. Buesching, Yung W. Sin, Terry Burke & David W. Macdonald
Extra-group paternity (EGP) occurs commonly among group-living mammals and plays an important role in mating systems and the dynamics of sexual selection; however, socio-ecological and genetic correlates of EGP have been underexplored. We use 23 years of demographic and genetic data from a high-density European badger (Meles meles) population, to investigate the relationship between the rate of EGP in litters and mate availability, mate incompatibility and mate quality (heterozygosity). Relatedness between within-group assigned mothers and...

Data from: Associations between changes in city and address specific temperature and QT interval - the VA Normative Aging Study

Amar J. Mehta, Itai Kloog, Antonella Zanobetti, Brent A. Coull, David Sparrow, Pantel Vokonas & Joel Schwartz
Background: The underlying mechanisms of the association between ambient temperature and cardiovascular morbidity and mortality are not well understood, particularly for daily temperature variability. We evaluated if daily mean temperature and standard deviation of temperature was associated with heart rate-corrected QT interval (QTc) duration, a marker of ventricular repolarization in a prospective cohort of older men. Methods: This longitudinal analysis included 487 older men participating in the VA Normative Aging Study with up to three...

Data from: Positive selection drives faster-Z evolution in silkmoths

Timothy B. Sackton, Russell B. Corbett-Detig, Javaregowda Nagaraju, R. Lakshmi Vaishna, Kallare P. Arunkumar & Daniel L. Hartl
Genes linked to X or Z chromosomes, which are hemizygous in the heterogametic sex, are predicted to evolve at different rates than those on autosomes. This “faster-X effect” can arise either as a consequence of hemizygosity, which leads to more efficient selection for recessive beneficial mutations in the heterogametic sex, or as a consequence of reduced effective population size of the hemizygous chromosome, which leads to increased fixation of weakly deleterious mutations due to genetic...

Data from: Basal metabolism in tropical birds: latitude, altitude, and the “pace of life”

Gustavo A. Londoño, Mark A. Chappell, María Del Rosario Castañeda, Jill E. Jankowski & Scott K. Robinson
1. Life history varies across latitudes, with the ‘pace of life’ being ‘slower’ in tropical regions. Because life history is coupled to energy metabolism via allocation tradeoffs and links between performance capacity and energy use, low metabolic intensity is expected in tropical animals. Low metabolism has been reported for lowland tropical birds, but it is unclear if this is due to ‘slow’ life history or to a warm, stable environment. 2. We measured Basal Metabolic...

Data from: Delayed transmission selects for increased survival of vesicular stomatitis virus

Brian R. Wasik, Ambika Bhushan, C. Brandon Ogbunugafor & Paul E. Turner
Life-history theory predicts that traits for survival and reproduction cannot be simultaneous maximized in evolving populations. For this reason, in obligate parasites such as infectious viruses, selection for improved between-host survival during transmission may lead to evolution of decreased within-host reproduction. We tested this idea using experimental evolution of RNA virus populations, passaged under differing transmission times in the laboratory. A single ancestral genotype of Vesicular Stomatitis Virus (VSV), a negative-sense RNA Rhabdovirus, was used...

Data from: Mapping the fitness landscape of gene expression uncovers the cause of antagonism and sign epistasis between adaptive mutations

Hsin-Hung Chou, Nigel F. Delaney, Jeremy A. Draghi & Christopher J. Marx
How do adapting populations navigate the tensions between the costs of gene expression and the benefits of gene products to optimize the levels of many genes at once? Here we combined independently-arising beneficial mutations that altered enzyme levels in the central metabolism of Methylobacterium extorquens to uncover the fitness landscape defined by gene expression levels. We found strong antagonism and sign epistasis between these beneficial mutations. Mutations with the largest individual benefit interacted the most...

Data from: Sexual selection targets cetacean pelvic bones

James P. Dines, Erik Otárola-Castillo, Peter Ralph, Jesse Alas, Timothy Daley, Andrew D. Smith & Matthew D. Dean
Male genitalia evolve rapidly, probably as a result of sexual selection. Whether this pattern extends to the internal infrastructure that influences genital movements remains unknown. Cetaceans (whales and dolphins) offer a unique opportunity to test this hypothesis: since evolving from land-dwelling ancestors, they lost external hind limbs and evolved a highly reduced pelvis which seems to serve no other function except to anchor muscles that maneuver the penis. Here we create a novel morphometric pipeline...

Data from: Coalescent versus concatenation methods and the placement of Amborella as sister to water lilies

Zhenxiang Xi, Liang Liu, Joshua S. Rest & Charles C. Davis
The molecular era has fundamentally reshaped our knowledge of the evolution and diversification of angiosperms. One outstanding question is the phylogenetic placement of Amborella trichopoda Baill., commonly thought to represent the first lineage of extant angiosperms. Here, we leverage publicly available data and provide a broad coalescent-based species tree estimation of 45 seed plants. By incorporating 310 nuclear genes, our coalescent analyses strongly support a clade containing Amborella plus water lilies (i.e., Nymphaeales) that is...

Data from: Rapid evolution of a native species following invasion by a congener

Yoel E. Stuart, Todd S. Campbell, Paul A. Hohenlohe, Robert G. Reynolds, Liam J. Revell & Jonathan B. Losos
In recent years, biologists have increasingly recognized that evolutionary change can occur rapidly when natural selection is strong; thus, real-time studies of evolution can be used to test classic evolutionary hypotheses directly. One such hypothesis is that negative interactions between closely related species can drive phenotypic divergence. Such divergence is thought to be ubiquitous, though well-documented cases are surprisingly rare. On small islands in Florida, we found that the lizard Anolis carolinensis moved to higher...

Data from: Evolutionary bursts in Euphorbia (Euphorbiaceae) are linked with photosynthetic pathway

James W. Horn, Zhenxiang Xi, Ricarda Riina, Jess A. Peirson, Ya Yang, Brian L. Dorsey, Paul E. Berry, Charles C. Davis & Kenneth J. Wurdack
The mid-Cenozoic decline of atmospheric CO2 levels that promoted global climate change was critical to shaping contemporary arid ecosystems. Within angiosperms, two CO2-concentrating mechanisms (CCMs)—CAM and C4—evolved from the C3 photosynthetic pathway, enabling more efficient whole-plant function in such environments. Many angiosperm clades with CCMs are thought to have diversified rapidly due to Miocene aridification, but links between this climate change, CCM evolution, and increased net diversification rates (r) remain to be further understood. Euphorbia...

Data from: Non-nest mate discrimination and clonal colony structure in the parthenogenetic ant Cerapachys biroi

Daniel J. C. Kronauer, Kazuki Tsuji, Naomi E. Pierce & Laurent Keller
Understanding the interplay between cooperation and conflict in social groups is a major goal of biology. One important factor is genetic relatedness, and animal societies are usually composed of related but genetically different individuals, setting the stage for conflicts over reproductive allocation. Recently, however, it has been found that several ant species reproduce predominantly asexually. Although this can potentially give rise to clonal societies, in the few well-studied cases, colonies are often chimeric assemblies of...

Data from: A new earthworm species within a controversial genus: Eiseniona gerardoi sp. n. (Annelida, Lumbricidae) - description based on morphological and molecular data.

Marta Novo, Rosa Fernández, Mónica Gutiérrez, Dario J. Díaz Cosín, Daniel Fernández Marchán & Dario Diaz Cosin
The morphological and anatomical simplicity of soil dwelling animals, such as earthworms, has limited the establishment of a robust taxonomy making it sometimes subjective to authors’ criteria. Within this context, integrative approaches including molecular information are becoming more popular to solve the phylogenetic positioning of conflictive taxa. Here we present the description of a new lumbricid species from the region of Extremadura (Spain), Eiseniona gerardoi sp. n. The assignment to this genus is based on...

Data from: Reading the leaves: a comparison of leaf rank and automated areole measurement for quantifying aspects of leaf venation

Walton A. Green, Stefan A. Little, Charles A. Price, Scott L. Wing, Selena Y. Smith, Benjamin Kotrc & Gabriela Doria
The reticulate venation that is characteristic of a dicot leaf has excited interest from systematists for more than a century, and from physiological and developmental botanists for decades. The tools of digital image acquisition and computer image analysis, however, are only now approaching the sophistication needed to quantify aspects of the venation network found in real leaves quickly, easily, accurately, and reliably enough to produce biologically meaningful data. In this paper, we examine 120 leaves...

Data from: Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model

Liang Liu, Scott V. Edwards & Shaoyuan Wu
The reconstruction of the Tree of Life has relied almost entirely on concatenation methods, which do not accommodate gene tree heterogeneity, a property that simulations and theory have identified as a likely cause of incongruent phylogenies. However, this incongruence has not yet been demonstrated in empirical studies. Several key relationships among eutherian mammals remain controversial and conflicting among previous studies, including the root of eutherian tree and the relationships within Euarchontoglires and Laurasiatheria. Both Bayesian...

Data from: Comparison and optimization of hiPSC forebrain cortical differentiation protocols

Christina R. Muratore, Priya Srikanth, Dana G. Callahan & Tracy L. Young-Pearse
Several protocols have been developed for human induced pluripotent stem cell neuronal differentiation. We compare several methods for forebrain cortical neuronal differentiation by assessing cell morphology, immunostaining and gene expression. We evaluate embryoid aggregate vs. monolayer with dual SMAD inhibition differentiation protocols, manual vs. AggreWell aggregate formation, plating substrates, neural progenitor cell (NPC) isolation methods, NPC maintenance and expansion, and astrocyte co-culture. The embryoid aggregate protocol, using a Matrigel substrate, consistently generates a high yield...

Data from: An integrated approach reveals regulatory controls on bacterial translation elongation

Arvind R. Subramaniam, Brian M. Zid & Erin K. O'Shea
Ribosomes elongate at a nonuniform rate during translation. Theoretical models and experiments disagree on the in vivo determinants of elongation rate and the mechanism by which elongation rate affects protein levels. To resolve this conflict, we measured transcriptome-wide ribosome occupancy under multiple conditions and used it to formulate a whole-cell model of translation in E. coli. Our model predicts that elongation rates at most codons during nutrient-rich growth are not limited by the intracellular concentrations...

Data from: The generification of the fossil record

Jonathan R. Hendricks, Erin E. Saupe, Corinne E. Myers, Elizabeth J. Hermsen & Warren D. Allmon
Many modern paleobiological analyses are conducted at the generic level, a practice predicated on the validity of genera as meaningful proxies for species. Uncritical application of genera in such analyses, however, has led, perhaps inadvertently, to the unjustified reification of genera in an evolutionary context. While the utility of genera as proxies for species in evolutionary studies should be evaluated as an empirical issue, in practice it is increasingly assumed (rather than demonstrated) that genera...

Data from: CRISPR-induced distributed immunity in microbial populations

Lauren M. Childs, Whitney E. England, Mark J. Young, Joshua S. Weitz & Rachel J. Whitaker
In bacteria and archaea, viruses are the primary infectious agents, acting as virulent, often deadly pathogens. A form of adaptive immune defense known as CRISPR-Cas enables microbial cells to acquire immunity to viral pathogens by recognizing specific sequences encoded in viral genomes. The unique biology of this system results in evolutionary dynamics of host and viral diversity that cannot be fully explained by the traditional models used to describe microbe-virus coevolutionary dynamics. Here, we show...

Data from: Sequence co-evolution gives 3D contacts and structures of protein complexes

Thomas A. Hopf, Charlotta P. I. Schärfe, João P. G. L. M. Rodrigues, Anna G. Green, Chris Sander, Alexandre M. J. J. Bonvin, Debora S. Marks & Oliver Kohlbacher
Protein-protein interactions are fundamental to many biological processes. Experimental screens have identified tens of thousands of interactions and structural biology has provided detailed functional insight for select 3D protein complexes. An alternative rich source of information about protein interactions is the evolutionary sequence record. Building on earlier work, we show that analysis of correlated evolutionary sequence changes across proteins identifies residues that are close in space with sufficient accuracy to determine the three-dimensional structure of...

Data from: Inclusive taxon sampling suggests a single, stepwise origin of ectolecithality in Platyhelminthes

Christopher E. Laumer & Gonzalo Giribet
Ectolecithality is a form of oogenesis unique within Metazoa but common in Platyhelminthes, in which nearly-yolkless oocytes and tightly associated yolk cells are deposited together in egg capsules. Despite profound impacts on the embryogenesis and morphology of its beneficiaries, the origins of this developmental phenomenon remain obscure. Traditionally, all ectolecithal flatworms were grouped in a clade called Neoophora. However, there are also morphological arguments for multiple origins of ectolecithality, and Neoophora has to date seen...

Registration Year

  • 2014

Resource Types

  • Dataset


  • Harvard University
  • University of Oxford
  • Cornell University
  • University of California, Davis
  • University of Michigan-Ann Arbor
  • University of Groningen
  • Smithsonian Institution
  • University of Florida
  • Cardiff University
  • University of British Columbia