8 Works

Data from: Ecological opportunity and diversification in a continental radiation of birds: climbing adaptations and cladogenesis in the Furnariidae

Santiago Claramunt, Elizabeth P. Derryberry, Robb T. Brumfield, & J. V. Remsen
Ecological theories of adaptive radiation predict that ecological opportunity stimulates cladogenesis through its effects on competitive release and niche expansion. Given that key innovations may confer ecological opportunity, we investigate the effect of the acquisition of climbing adaptations on rates of cladogenesis in a major avian radiation, the Neotropical bird family Furnariidae, using a species-level phylogeny. Morphological specializations for vertical climbing originated in the woodcreepers ca. 23 Mya, well before that adaptation occurred in woodpeckers...

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: No gene flow across the Eastern Pacific Barrier in the reef-building coral Porites lobata

Iliana B. Baums, Jennifer N. Boulay, Nicholas R. Polato & Michael E. Hellberg
The expanse of deep water between the Central Pacific islands and the continental shelf of the Eastern Tropical Pacific is regarded as the world’s most potent marine biogeographic barrier. During recurrent climatic fluctuations (ENSO - El Niño Southern Oscillation), however, changes in water temperature and the speed and direction of currents become favorable for trans-oceanic dispersal of larvae from central Pacific to marginal Eastern Pacific reefs. Here we investigate the population connectivity of the reef...

Data from: The first record of a trans-oceanic sister-group relationship between obligate vertebrate troglobites

Prosanta Chakrabarty, Matthew P. Davis & John S. Sparks
We show using the most complete phylogeny of one of the most species-rich orders of vertebrates (Gobiiformes), and calibrations from the rich fossil record of teleost fishes, that the genus Typhleotris, endemic to subterranean karst habitats in southwestern Madagascar, is the sister group to Milyeringa, endemic to similar subterranean systems in northwestern Australia. Both groups are eyeless, and our phylogenetic and biogeographic results show that these obligate cave fishes now found on opposite ends of...

Data from: Identifying biases at different spatial and temporal scales of diversification: a case study in the Neotropical parrotlet genus Forpus

Brian Tilston Smith, Camila C. Ribas, Bret M. Whitney, Blanca E. Hernández-Baños & John Klicka
The temporal origins of the extraordinary biodiversity of the Neotropical region are highly debated. Recent empirical work has found support for alternative models on the tempo of speciation in Neotropical species further fuelling the debate. However, relationships within many Neotropical lineages are poorly understood and it is unclear how this uncertainty impacts inferences on the evolution of taxa in the region. We examined the robustness of diversification patterns in the avian genus Forpus by testing...

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: Deep phylogeographic structure and environmental differentiation in the carnivorous plant Sarracenia alata

Amanda J. Zellmer, Margaret M. Hanes, Sarah M. Hird & Bryan C. Carstens
We collected ~29kb of sequence data using Roche 454 pyrosequencing in order to estimate the timing and pattern of diversification in the carnivorous pitcher plant Sarracenia alata. Utilizing modified protocols for reduced representation library construction, we generated sequence data from 86 individuals across 10 populations from throughout the range of the species. We identified 76 high quality and high coverage loci (containing over 500 SNPs) using the bioinformatics pipeline PRGmatic. Results from a Bayesian clustering...

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...

Registration Year

  • 2012

Resource Types

  • Dataset


  • Louisiana State University of Alexandria
  • University of California Los Angeles
  • University of Georgia
  • Boston University
  • Field Museum of Natural History
  • Duke University
  • University of Wyoming
  • University of Nevada Reno
  • Smithsonian Institution
  • National Autonomous University of Mexico