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Methods and theory of phylogenetic inference

Soltis, Pamela S. [1], Manos, Paul S. [3], Manchester, Steven R. [1], Bell, Charles [1], Soltis, Douglas E. [2].

Dead Green: Conceptual and Empirical Perspectives on Integrating Fossils and Extant Taxa in Phylogenetic Analysis.

Integrating fossils into phylogenetic trees of living taxa is imperative for understanding both the origins of extant groups and the evolution of their characters. However, such synthetic analyses and collaboration between paleontologists and systematists have been infrequent. Analytical and methodological issues have hampered attempts to integrate fossil and living taxa. Foremost among these are the potential problems of missing data, concerns over the combinability of morphological and molecular data sets, and the question of how best to “insert” a fossil into an analysis. However, recent analyses of both real and simulated data suggest that issues of missing data may not be as severe as expected, and that inclusion of fossils is not only possible but may be necessary to achieve the correct phylogenetic solution. We provide examples from our own work to explore the effects of missing data on the placement of fossils in simulations and in the Juglandaceae. Our comparative analyses using total evidence and “molecular scaffold” approaches favor total evidence: inclusion of all characters, molecular and morphological, for all taxa, living and fossil, with question marks to denote missing data as necessary. We conclude that the amount of missing data per se will not necessarily lead to chaotic phylogenetic results and that a few key morphological features may be sufficient to place a fossil confidently within a clade of extant taxa. Furthermore, the confident placement of fossils paves the way for additional studies of character evolution and provides calibration points for estimation of divergence times and rates of molecular evolution. We conclude with a comparison of divergence time estimates for angiosperms obtained via different methods; in our analyses with combined data the use of nonparametric rate smoothing, penalized likelihood, and Bayesian methods have yielded similar results.

1 - University of Florida, Department of Natural History, Florida Museum of Natural History, P.O. Box 117800, Gainesville, Florida, 32611-7800, USA
2 - University of Florida, Department of Botany, 220 Bartram Hall, P.O. Box 118526, Gainesville, Florida, 32611-8526, USA
3 - Duke University, Department of Biology, 139 Biological Sciences Building, PO Box 90338, Durham, North Carolina, 27708-0338, USA

divergence time estimates
phylogeny reconstruction
missing data.

Presentation Type: Symposium
Session: 31-4
Location: Alpine A (Snowbird Center)
Date: Tuesday, August 3rd, 2004
Time: 10:00 AM
Abstract ID:437

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