Mar 23, 2012

The pipid root

Systematic Biology
Adam J BewickBen J Evans

Abstract

The estimation of phylogenetic relationships is an essential component of understanding evolution. Accurate phylogenetic estimation is difficult, however, when internodes are short and old, when genealogical discordance is common due to large ancestral effective population sizes or ancestral population structure, and when homoplasy is prevalent. Inference of divergence times is also hampered by unknown and uneven rates of evolution, the incomplete fossil record, uncertainty in relationships between fossil and extant lineages, and uncertainty in the age of fossils. Ideally, these challenges can be overcome by developing large "phylogenomic" data sets and by analyzing them with methods that accommodate features of the evolutionary process, such as genealogical discordance, recurrent substitution, recombination, ancestral population structure, gene flow after speciation among sampled and unsampled taxa, and variation in evolutionary rates. In some phylogenetic problems, it is possible to use information that is independent of fossils, such as the geological record, to identify putative triggers for diversification whose associated estimated divergence times can then be compared a posteriori with estimated relationships and ages of...Continue Reading

  • References42
  • Citations25

References

Mentioned in this Paper

Genus Pipa
Salientia
Recombination, Genetic
Phylogeny
Sorting - Cell Movement
Sequencing
Burrowing toad
Sequence Determinations, DNA
Open Reading Frames
Silurana

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