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Probabilistic Phylogenetic Inference in the Fossil Record: Current and Future Applications

Published online by Cambridge University Press:  21 July 2017

Peter J. Wagner  and
Jonathan D. Marcot
Peter J. Wagner
Affiliation:
Department of Paleobiology, National Museum of Natural History, Smithsonian Institution [NHB, MRC 121], P.O. Box 37012, Washington DC 20013-7012
Jonathan D. Marcot
Affiliation:
Department of Animal Biology, University of Illinois, 515 Morrill Hall, 505 S. Goodwin Ave., Urbana, IL, 61801
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Abstract

Quantitative phylogenetic inference estimates the probability of observed character distributions given trees and rates. Most available programs for doing this assume (tacitly or explicitly) that the sampled taxa are contemporaneous. However, paleontologists usually sample taxa over a clade's history. Thus, we must estimate the probability of observed character-state distributions over time given trees and rates. When we include information about sampling intensity, then we really are estimating the probability of the observed record given trees and rates. Some additional problems that should be issues for neontologists, but which are much more obvious concerns for paleontologists include: 1) ancestor-descendant relationships; 2) punctuated versus continuous morphological change; and, 3) the effects of extinction and speciation rates on prior probabilities of trees. Future goals of paleosystematists include incorporating these and other “nuisance” parameters so that, ultimately, our tests of phylogeny are really tests of evolutionary histories.

Type
Morphological Data
Information
The Paleontological Society Papers , Volume 16: Quantitative Methods in Paleobiology , October 2010 , pp. 189 - 211
Copyright
Copyright © 2010 by the Paleontological Society 

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