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 language | English (US) |
|---|---|
| Pages (from-to) | 674-688 |
| Number of pages | 15 |
| Journal | Systematic Biology |
| Volume | 59 |
| Issue number | 6 |
| DOIs | |
| State | Published - Dec 2010 |
| Externally published | Yes |
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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 journal › Article
}
TY - JOUR
T1 - Combining phylogenomics and fossils in higher-level squamate reptile phylogeny
T2 - Molecular data change the placement of fossil taxa
AU - Wiens, John J
AU - Kuczynski, Caitlin A.
AU - Townsend, Ted
AU - Reeder, Tod W.
AU - Mulcahy, Daniel G.
AU - Sites, Jack W.
PY - 2010/12
Y1 - 2010/12
N2 - 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.
AB - 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.
KW - Combined analysis
KW - Fossils
KW - Lizards
KW - Morphology
KW - Phylogeny
KW - Snakes
KW - Squamates
UR - http://www.scopus.com/inward/record.url?scp=78651454774&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=78651454774&partnerID=8YFLogxK
U2 - 10.1093/sysbio/syq048
DO - 10.1093/sysbio/syq048
M3 - Article
C2 - 20930035
AN - SCOPUS:78651454774
VL - 59
SP - 674
EP - 688
JO - Systematic Biology
JF - Systematic Biology
SN - 1063-5157
IS - 6
ER -