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Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards.
A criterion, based on the Bayes factor, for selecting among competing partitioning strategies is proposed and tested and it is demonstrated that how one partitions the data is shown to be a greater concern than simply the overall number of partitions.
WHY DOES A TRAIT EVOLVE MULTIPLE TIMES WITHIN A CLADE? REPEATED EVOLUTION OF SNAKELIKE BODY FORM IN SQUAMATE REPTILES
- J. Wiens, M. Brandley, T. Reeder
- Biology, Environmental ScienceEvolution; international journal of organic…
The repeated origins of snakelike squamates appear to be associated with the in situ evolution of these two ecomorphs on different continental regions, with very little dispersal of most limb-reduced lineages between continental regions.
Rates and Patterns in the Evolution of Snake-Like Body Form in Squamate Reptiles: Evidence for Repeated Re-Evolution of Lost Digits and Long-Term Persistence of Intermediate Body Forms
- M. Brandley, J. Huelsenbeck, J. Wiens
- BiologyEvolution; international journal of organic…
- 1 August 2008
Using morphometric data for 258 species and a time-calibrated phylogeny to explore rates and patterns of body-form evolution across squamates, it is found that the transition from lizard-like to snake-like body form involves concerted evolution of limb reduction, digit loss, and body elongation.
Accommodating heterogenous rates of evolution in molecular divergence dating methods: an example using intercontinental dispersal of Plestiodon (Eumeces) lizards.
It is found that extreme saturation has obscured the underlying rate of evolution in the mitochondrial DNA, resulting in severe underestimation of the rate in this locus, indicating an inadequacy of current models to capture the complex nature of mtDNA evolution in over large time scales.
Seven new dolphin mitochondrial genomes and a time-calibrated phylogeny of whales
- Y. Xiong, M. Brandley, Shixia Xu, K. Zhou, Guang Yang
- BiologyBMC Evolutionary Biology
- 25 January 2009
By collecting and analyzing seven new mitochondrial genomes, this work provides strong evidence that the delphinid genera Tursiops and Stenella are not monophyletic, and the current taxonomy masks potentially interesting patterns of morphological, physiological, behavioral, and ecological evolution.
Relaxed clocks and inferences of heterogeneous patterns of nucleotide substitution and divergence time estimates across whales and dolphins (Mammalia: Cetacea).
Simulations demonstrate how increasing prior age uncertainty can bias rate and age estimates, even while the 95% highest posterior density around age estimates decreases, and interpret the use of external calibrations in divergence time studies in light of these results.
The phylogenetic systematics of blue-tailed skinks (Plestiodon) and the family Scincidae
A comprehensive molecular phylogeny of Plestiodon is constructed using Bayesian phylogenetic analyses of a nine-locus data set comprising 8308 base pairs of DNA, sampled from 38 of the 43 species in the genus and replaces the existing supraspecific taxonomy with one congruent with the phylogenetic results.
Evidence for determinism in species diversification and contingency in phenotypic evolution during adaptive radiation
- F. Burbrink, Xin Chen, E. A. Myers, M. Brandley, R. A. Pyron
- Environmental Science, BiologyProceedings of the Royal Society B: Biological…
- 7 December 2012
The test of well-sampled phylogenies of four squamate groups that colonized the New World in the Late Oligocene suggests that the processes that drive diversification and disparification are not mechanistically linked, even among similar groups of taxa experiencing the same sources of EO.
Which came first: The lizard or the egg? Robustness in phylogenetic reconstruction of ancestral states.
- A. Wright, K. Lyons, M. Brandley, D. Hillis
- BiologyJournal of experimental zoology. Part B…
- 1 September 2015
The results emphasize that because the conclusions of ancestral state reconstruction studies are often highly sensitive to the methods and assumptions of analysis, researchers should carefully consider this sensitivity when evaluating alternative hypotheses of character-state evolution.