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Whole-genome analyses resolve early branches in the tree of life of modern birds
A genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves recovered a highly resolved tree that confirms previously controversial sister or close relationships and identifies the first divergence in Neoaves, two groups the authors named Passerea and Columbea.
Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales.
- B. Faircloth, J. McCormack, Nicholas G. Crawford, Michael G. Harvey, R. T. Brumfield, T. Glenn
- BiologySystematic biology
- 1 October 2012
A new class of molecular marker, anchored by ultraconserved genomic elements (UCEs), that universally enable target enrichment and sequencing of thousands of orthologous loci across species separated by hundreds of millions of years of evolution is introduced.
Applications of next-generation sequencing to phylogeography and phylogenetics.
The utility of single nucleotide polymorphisms in inferences of population history
Estimating Species Trees Using Multiple-Allele DNA Sequence Data
- Liang Liu, D. Pearl, R. T. Brumfield, S. Edwards
- BiologyEvolution; international journal of organic…
- 1 August 2008
The Bayesian approach described here provides a powerful framework for statistical testing and integration of population genetics and phylogenetics, and provides credible regions for the species tree.
LINEAGE DIVERSIFICATION AND MORPHOLOGICAL EVOLUTION IN A LARGE‐SCALE CONTINENTAL RADIATION: THE NEOTROPICAL OVENBIRDS AND WOODCREEPERS (AVES: FURNARIIDAE)
- E. Derryberry, S. Claramunt, R. T. Brumfield
- Biology, Environmental ScienceEvolution; international journal of organic…
- 1 October 2011
It is found that the Furnariidae exhibit nearly constant rates of lineage accumulation but show evidence of constrained morphological evolution, suggesting that lineage accumulation in tropical continental radiations may not be as limited by ecological opportunities as in temperate or island radiations.
hzar: hybrid zone analysis using an R software package
- E. Derryberry, G. Derryberry, James M. Maley, R. T. Brumfield
- BiologyMolecular ecology resources
- 1 May 2014
We present a new software package (hzar) that provides functions for fitting molecular genetic and morphological data from hybrid zones to classic equilibrium cline models using the…
The drivers of tropical speciation
It is shown that spatial and temporal patterns of genetic differentiation in Neotropical birds are highly discordant across lineages and are not reconcilable with a model linking speciation solely to landscape change, and the strongest predictors of speciation are the amount of time a lineage has persisted in the landscape and the ability of birds to move through the landscape matrix.
Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis.
- J. McCormack, B. Faircloth, Nicholas G. Crawford, P. Gowaty, R. T. Brumfield, T. Glenn
- BiologyGenome research
- 1 April 2012
This study outlines a phylogenomic approach using a novel class of phylogenetic markers derived from ultraconserved elements and flanking DNA, and shows that this class of marker is useful for recovering deep-level phylogeny in placental mammals.
EVOLUTION INTO AND OUT OF THE ANDES: A BAYESIAN ANALYSIS OF HISTORICAL DIVERSIFICATION IN THAMNOPHILUS ANTSHRIKES
- R. T. Brumfield, S. Edwards
- Environmental Science, BiologyEvolution; international journal of organic…
- 1 February 2007
A molecular phylogeny of Thamnophlius antshrikes, a clade of 30 species whose collective distribution spans nearly the entirety of lowland habitats in tropical South America, the eastern slope foothills of the Andes, and the tepuis, finds the highest transition rates were between highland-restricted and lowland-to-highland distributions, with extremely low rates into and out of low land-restricted distributions.