Combining phylogenomics and fossils in higher-level squamate reptile phylogeny: Molecular data change the placement of fossil taxa

John J Wiens, Caitlin A. Kuczynski, Ted Townsend, Tod W. Reeder, Daniel G. Mulcahy, Jack W. Sites

Research output: Contribution to journalArticle

141 Citations (Scopus)

Abstract

Molecular data offer great potential to resolve the phylogeny of living taxa but can molecular data improve our understanding of relationships of fossil taxa? Simulations suggest that this is possible, but few empirical examples have demonstrated the ability of molecular data to change the placement of fossil taxa. We offer such an example here. We analyze the placement of snakes among squamate reptiles, combining published morphological data (363 characters) and new DNA sequence data (15,794 characters, 22 nuclear loci) for 45 living and 19 fossil taxa. We find several intriguing results. First, some fossil taxa undergo major changes in their phylogenetic position when molecular data are added. Second, most fossil taxa are placed with strong support in the expected clades by the combined data Bayesian analyses, despite each having >98% missing cells and despite recent suggestions that extensive missing data are problematic for Bayesian phylogenetics. Third, morphological data can change the placement of living taxa in combined analyses, even when there is an overwhelming majority of molecular characters. Finally, we find strong but apparently misleading signal in the morphological data, seemingly associated with a burrowing lifestyle in snakes, amphisbaenians, and dibamids. Overall, our results suggest promise for an integrated and comprehensive Tree of Life by combining molecular and morphological data for living and fossil taxa.

Original languageEnglish (US)
Pages (from-to)674-688
Number of pages15
JournalSystematic Biology
Volume59
Issue number6
DOIs
StatePublished - Dec 2010
Externally publishedYes

Fingerprint

Reptiles
Snakes
Squamata
Phylogeny
reptile
reptiles
phylogeny
fossils
fossil
Aptitude
Bayes Theorem
Life Style
snakes
snake
burrowing
lifestyle
phylogenetics
nucleotide sequences
loci

Keywords

  • Combined analysis
  • Fossils
  • Lizards
  • Morphology
  • Phylogeny
  • Snakes
  • Squamates

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

Cite this

Combining phylogenomics and fossils in higher-level squamate reptile phylogeny : Molecular data change the placement of fossil taxa. / Wiens, John J; Kuczynski, Caitlin A.; Townsend, Ted; Reeder, Tod W.; Mulcahy, Daniel G.; Sites, Jack W.

In: Systematic Biology, Vol. 59, No. 6, 12.2010, p. 674-688.

Research output: Contribution to journalArticle

Wiens, John J ; Kuczynski, Caitlin A. ; Townsend, Ted ; Reeder, Tod W. ; Mulcahy, Daniel G. ; Sites, Jack W. / Combining phylogenomics and fossils in higher-level squamate reptile phylogeny : Molecular data change the placement of fossil taxa. In: Systematic Biology. 2010 ; Vol. 59, No. 6. pp. 674-688.
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