9 Works

Data from: Dietary hardness, loading behavior, and the evolution of skull form in bats

Sharlene E. Santana, Ian R. Grosse & Elizabeth R. Dumont
The morphology and biomechanics of the vertebrate skull reflect the physical properties of diet and behaviors used in food acquisition and processing. We use phyllostomid bats, the most diverse mammalian dietary radiation, to investigate if and how changes in dietary hardness and loading behaviors during feeding shaped the evolution of skull morphology and biomechanics. When selective regimes of food hardness are modeled, we found that species consuming harder foods have evolved skull shapes that allow...

Data from: A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing

John E. McCormack, Michael G. Harvey, Brant C. Faircloth, Nicholas G. Crawford, Travis C. Glenn & Robb T. Brumfield
Evolutionary relationships among birds in Neoaves, the clade comprising the vast majority of avian diversity, have vexed systematists due to the ancient, rapid radiation of numerous lineages. We applied a new phylogenomic approach to resolve relationships in Neoaves using target enrichment (sequence capture) and high-throughput sequencing of ultraconserved elements (UCEs) in avian genomes. We collected sequence data from UCE loci for 32 members of Neoaves and one outgroup (chicken) and analyzed data sets that differed...

Data from: Influence of environmental heterogeneity on genetic diversity and structure in an endemic southern Californian oak

Joaquín Ortego, Erin C. Riordan, Paul F. Gugger & Victoria L. Sork
Understanding how specific environmental factors shape gene flow while disentangling their importance relative to the effects of geographical isolation is a major question in evolutionary biology and a specific goal of landscape genetics. Here, we combine information from nuclear microsatellite markers and ecological niche modelling to study the association between climate and spatial genetic structure and variability in Engelmann oak (Quercus engelmannii), a wind-pollinated species with high potential for gene flow. We first test whether...

Data from: Systems and trans-system level analysis identifies conserved iron deficiency responses in the plant lineage

Eugen I. Urzica, David Casero, Hiroaki Yamasaki, Scott I. Hsieh, Lital N. Adler, Steven J. Karpowicz, Crysten E. Blaby-Haas, Steven G. Clarke, Joseph A. Loo, Matteo Pellegrini & Sabeeha S. Merchant
We surveyed the iron nutrition-responsive transcriptome of Chlamydomonas reinhardtii using RNA-Seq methodology. Presumed primary targets were identified in comparisons between visually asymptomatic iron-deficient versus iron-replete cells. This includes the known components of high-affinity iron uptake as well as candidates for distributive iron transport in C. reinhardtii. Comparison of growth-inhibited iron-limited versus iron-replete cells revealed changes in the expression of genes in chloroplastic oxidative stress response pathways, among hundreds of other genes. The output from the...

Data from: Iterative ecological radiation and convergence during the evolutionary history of damselfishes (Pomacentridae)

Bruno Frédérich, Laurie Sorenson, Francesco Santini, Graham J. Slater & Michael E. Alfaro
Coral reef fishes represent one of the most spectacularly diverse assemblages of vertebrates on the planet, but our understanding of their mode of diversification remains limited. Here we test whether the diversity of the damselfishes (Pomacentridae), one of the most species-rich families of reef-associated fishes, was produced by a single or multiple adaptive radiation(s) during their evolutionary history. Tests of the tempo of lineage diversification using a time-calibrated phylogeny including 208 species revealed that crown...

Data from: More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs

Nicholas G. Crawford, Brant C. Faircloth, John E. McCormack, Robb T. Brumfield, Kevin Winker & Travis C. Glenn
We present the first genomic-scale analysis addressing the phylogenetic position of turtles, using over 1,000 loci from representatives of all major reptile lineages including tuatara. Previously, studies of morphological traits positioned turtles either at the base of the reptile tree or with lizards, snakes, and tuatara (lepidosaurs), whereas molecular analyses typically allied turtles with crocodiles and birds (archosaurs). A recent analysis of shared microRNA families found that turtles are more closely related to lepidosaurs. To...

Data from: Not all sequence tags are created equal: designing and validating sequence identification tags robust to indels

Brant C. Faircloth & Travis C. Glenn
Ligating adapters with unique synthetic oligonucleotide sequences (sequence tags) onto individual DNA samples before massively parallel sequencing is a popular and efficient way to obtain sequence data from many individual samples. Tag sequences should be numerous and sufficiently different to ensure sequencing, replication, and oligonucleotide synthesis errors do not cause tags to be unrecoverable or confused. However, many design approaches only protect against substitution errors during sequencing and extant tag sets contain too few tag...

Data from: The genomic consequences of adaptive divergence and reproductive isolation between species of manakins

Thomas L. Parchman, Zachariah Gompert, Michael J. Braun, Robb T. Brumfield, D. B. McDonald, J. Albert C. Uy, G. Zhang, Erich D. Jarvis, B. A. Schlinger & C. A. Buerkle
The processes of adaptation and speciation are expected to shape genomic variation within and between diverging species. Here we analyze genomic heterogeneity of genetic differentiation and introgression in a hybrid zone between two bird species (Manacus candei and M. vitellinus) using 59 100 SNPs, a whole genome assembly, and Bayesian models. Measures of genetic differentiation (inline image) and introgression (genomic cline center [α] and rate [β]) were highly heterogeneous among loci. We identified thousands of...

Data from: Use of alpha, beta, and gamma diversity measures to characterize seed dispersal by animals

Douglas G. Scofield, Peter E. Smouse, Jordan Karubian & Victoria L. Sork
Seed dispersal shapes ecological and evolutionary dynamics of plant populations. Here, we extend classical diversity measures to study the impact of disperser behavior on seed dispersal. We begin by extending our previous diversity structure approach, which partitioned seed source diversity within and among dispersal sites, into the more general framework of traditional diversity measures. This statistical approach allows an assessment of the extent to which foraging behavior shapes α and γ diversity, as well as...

Registration Year

  • 2012

Resource Types

  • Dataset


  • University of California Los Angeles
  • University of Georgia
  • Louisiana State University of Alexandria
  • Boston University
  • University of Massachusetts Amherst
  • University of Liège
  • Duke University
  • University of Wyoming
  • Smithsonian Institution
  • University of Miami