33 Works

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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: Scaling of phloem structure and optimality of photoassimilate transport in conifer needles

Henrik Ronellenfitsch, Johannes Liesche, Kaare H. Jensen, Noel Michele Holbrook, Alexander Schulz & Eleni Katifori
The phloem vascular system facilitates transport of energy-rich sugar and signalling molecules in plants, thus permitting long-range communication within the organism and growth of non-photosynthesizing organs such as roots and fruits. The flow is driven by osmotic pressure, generated by differences in sugar concentration between distal parts of the plant. The phloem is an intricate distribution system, and many questions about its regulation and structural diversity remain unanswered. Here, we investigate the phloem structure in...

Data from: Children reject inequity out of spite

Katherine McAuliffe, Peter R. Blake & Felix Warneken
When confronted with inequality, human children and adults sacrifice personal gain to reduce the pay-offs of other individuals, exhibiting apparently spiteful motivations. By contrast, sacrifice of personal gain by non-human animals is often interpreted as frustration. Spite may thus be a uniquely human motivator. However, to date, no empirical study has demonstrated that psychological spite actually drives human behaviour, leaving the motivation for inequity aversion unclear. Here, we ask whether 4- to 9-year-old children and...

Data from: Epistasis and allele specificity in the emergence of a stable polymorphism in Escherichia coli

Jessica Plucain, Thomas Hindré, Mickaël Le Gac, Olivier Tenaillon, Stéphane Cruveiller, Claudine Médigue, Nicholas Leiby, William R. Harcombe, Christopher J. Marx, Richard E. Lenski & Dominique Schneider
Ecological opportunities promote population divergence into coexisting lineages. However, the genetic mechanisms that enable new lineages to exploit these opportunities are poorly understood except in cases of single mutations. We examined how two Escherichia coli lineages diverged from their common ancestor at the outset of a long-term coexistence. By sequencing genomes and reconstructing the genetic history of one lineage, we showed that three mutations together were sufficient to produce the frequency-dependent fitness effects that allowed...

Data from: Evolution of sweet taste perception in hummingbirds by transformation of the ancestral umami receptor

Maude W. Baldwin, Yasuka Toda, Tomoya Nakagita, Mary J. O'Connell, Kirk C. Klasing, Takumi Misaka, Scott V. Edwards & Stephen D. Liberles
Sensory systems define an animal's capacity for perception and can evolve to promote survival in new environmental niches. We have uncovered a noncanonical mechanism for sweet taste perception that evolved in hummingbirds since their divergence from insectivorous swifts, their closest relatives. We observed the widespread absence in birds of an essential subunit (T1R2) of the only known vertebrate sweet receptor, raising questions about how specialized nectar feeders such as hummingbirds sense sugars. Receptor expression studies...

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...

Data from: Hybridization occurs between Drosophila simulans and D. sechellia in the Seychelles archipelago

Daniel R. Matute & Julien F. Ayroles
Drosophila simulans and D. sechellia are sister species that serve as a model to study the evolution of reproductive isolation. While D. simulans is a human commensal that has spread all over the world, D. sechellia is restricted to the Seychelles archipelago and is found to breed exclusively on the toxic fruit of Morinda citrifolia. We surveyed the relative frequency of males from these two species in a variety of substrates found on five islands...

Data from: Cryptic ecology among host generalist Campylobacter jejuni in domestic animals

Samuel K. Sheppard, Lu Cheng, Guillaume Méric, Caroline P. A. De Haan, Ann-Katrin Llarena, Pekka Marttinen, Ana Vidal, Anne Ridley, Felicity Clifton-Hadley, Thomas R. Connor, Norval J. C. Strachan, Ken Forbes, Frances M. Colles, Keith A. Jolley, Stephen D. Bentley, Martin C. J. Maiden, Marja-Liisa Hänninen, Julian Parkhill, William P. Hanage & Jukka Corander
Homologous recombination between bacterial strains is theoretically capable of preventing the separation of daughter clusters, and producing cohesive clouds of genotypes in sequence space. However, numerous barriers to recombination are known. Barriers may be essential such as adaptive incompatibility, or ecological, which is associated with the opportunities for recombination in the natural habitat. Campylobacter jejuni is a gut colonizer of numerous animal species and a major human enteric pathogen. We demonstrate that the two major...

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