Homoplasy Increases Phylogenetic Structure

  title={Homoplasy Increases Phylogenetic Structure},
  author={Mari K{\"a}lersj{\"o} and Victor A. Albert and James S Farris},
According to currently accepted theories, rapidly evolving nucleotide sites are phylogenetically less informative than more slowly evolving ones, especially for recognizing more ancient groupings. For this reason third codon positions are often regarded as less reliable than first and second positions as indicators of phylogeny. Analysis of the largest nucleotide matrix treated to date—2538 rbc L sequences covering all major lineages of green plants—shows the opposite: although rapidly evolving… 
Conserved sequences identify the closest living relatives of primates
The phylogeny showed Cercopithecinae to have low levels of nucleotide divergence, especially for Papionini, and gibbons to have a high rate of divergence, and the MCMCtree comprehensively updated divergence dates of early evolution of Primatomorpha and Primates.
Weighting against homoplasy improves phylogenetic analysis of morphological data sets
The problem of character weighting in cladistic analysis is revisited. The finding that, in large molecular data sets, removal of third positions (with more homoplasy) decreases the number of well
Conflict between Amino Acid and Nucleotide Characters
It is shown that silent substitutions may be more phylogenetically informative than replacement substitutions and that artifacts caused by composite characters and/or convergence cause clades on amino acid trees to conflict with nucleotide trees and independent evidence.
How can third codon positions outperform first and second codon positions in phylogenetic inference? An empirical example from the seed plants.
Differential frequencies of observed character states and differential substitution probabilities among states were found to be the most limiting of the factors simulated for all three codon positions, and the amount of possible synapomorphy was predictive of the overall success of resolution.
Homoplasy as an Auxiliary Criterion for Species Delimitation
The absence of large changes of the HI within the species, and its increase when new species are added by HomoDist, suggest that homoplasy variation can be used as an auxiliary test in distance-based species delimitation with any type of marker.
Dental characters used in phylogenetic analyses of mammals show higher rates of evolution, but not reduced independence
Results indicate that the phylogenetic signal of discrete characters correlate most strongly with rates of evolution, with increased rates driving increased homoplasy and the dominance of dental characters in analyses of mammals could be leading to inaccurate phylogenies.
Inferring phylogeny at low taxonomic levels: utility of rapidly evolving cpDNA and nuclear ITS loci.
Results indicated that in preliminary studies, sampling strategy should include at least four exemplar taxa, and no single locus emerged as the best in all lineages for any of these measures of utility.
Quantification of homoplasy for nucleotide transitions and transversions and a reexamination of assumptions in weighted phylogenetic analysis.
Although homoplastic and consistent transition and transversion changes in mitochondrial protein coding genes were determined from character-state reconstructions on a highly corroborated phylogeny of mammals, it was found that although homoplasy was related to evolutionary rates and was greater for transitions, the absolute number of consistent transitions greatly exceeded thenumber of consistent transversions.