@ARTICLE{TreeBASE2Ref16538, author = {Paul S. Manos and Pamela S. Soltis and Douglas E. Soltis and S. R. Manchester and S. H. Oh and Charles D. Bell and David L. Dilcher and Donald E. Stone}, title = {Phylogeny of Extant and Fossil Juglandaceae Inferred from the Integration of Molecular and Morphological Data Sets.}, year = {2006}, keywords = {}, doi = {10.1080/10635150701408523}, url = {}, pmid = {}, journal = {Systematic Biology}, volume = {56}, number = {3}, pages = {412--430}, abstract = {It is widely acknowledged that integrating fossils into data sets of extant taxa is imperative for proper placement of fossils, resolution of relationships, and a better understanding of character evolution. The importance of this process has been further magnified because of the crucial role of fossils in dating divergence times. Outstanding issues remain, including appropriate methods to place fossils in phylogenetic trees, the importance of molecules vs. morphology in these analyses, as well as the impact of potentially large amounts of missing data for fossil taxa. In this study we used the angiosperm clade Juglandaceae as a model for investigating methods of integrating fossils into a phylogenetic framework of extant taxa. The clade has a rich fossil record relative to low extant diversity, as well as a robust molecular phylogeny and morphological database for extant taxa. After combining fossil organ genera into composite, terminal taxa our objectives were to: 1) compare multiple methods for the integration of the fossils and extant taxa (including total evidence, molecular scaffolds, and molecular matrix representation with parsimony: MRP); 2) explore the impact of missing data (incomplete taxa and characters) and the weight of evidence for placing fossils on the topology; 3) simulate the phylogenetic effect of missing data using our molecular data sets; and 4) place fossils and compare the impact of single and multiple fossil constraints in estimating the age of clades. Despite large and variable amounts of missing data, each of the methods provided reasonable placement of both fossils and simulated ?artificial fossils? in the phylogeny previously inferred only from extant taxa. Three fossil taxa (Cruciptera simsonii, Paleoplatycarya wingii, and Platycarya americana) were placed in crown clades containing living taxa for which morphological affinities had previously been suggested based on descriptive morphology, whereas Polyptera manningii was placed as sister to two well established subclades. The position of Paleooreomunnea stoneana was ambiguous with total evidence, but conclusive with DNA scaffolds and MRP. There was less disturbance of relationships among extant taxa using a total evidence approach, and the DNA scaffold approach did not provide improved resolution or internal support for clades compared to total evidence, whereas weighted MRP retained comparable levels of support, but lost crown clade resolution. Multiple calibration points generally provided reasonable age estimates, but the use of single constraints provided by extinct genera tended to underestimate clade ages.} }

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