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-- last updated August 2005 --

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Floral diversity in Amorpheae:

    The legume clade Amorpheae has about 240 described species, distributed throughout arid and semi-arid regions of the New World.  In this relatively small clade, the standard papilionoid floral form has been lost several times.  The result of these evolutionary modifications are:  flowers without petals (Errazurizia rotundata and Parryella filifolia), flowers with one petal (all ~15 spp. of Amorpha), flowers with undifferentiated wing and keel petals (all ~12 Eysenhardtia spp., 3 Errazurizia spp., Apoplanesia paniculata, several Dalea spp., and a few Marina spp.), and flowers with a highly unusual structure which I have been calling a "stemonozone" (Dalea, Marina, and some Psorothamnus), which is formed by zonal growth below the stamens and petals.  This diversity stands out among papilionoid legumes.  My previous research has included inferring phylogenetic relationships within the group and attempting to place the group among papilionoids (pub), and studying the developmental morphology of most of the major floral forms (pub1, pub2). 
    The next set of goals for this system include:
• Phylogenetic relationships and taxonomic revision of the species currently placed in paraphyletic genera.
• Biogeographic studies of North America/South America disjunctions and/or invasions. 

    A preliminary photo gallery of Amorpheae will soon be available.

Evolutionary simplification in papilionoid flowers:

     Evolutionary simplification, like the evolution of complexity, is a framework for comparing patterns of change across different groups and different character sets.  The papilionoid flower is well conserved among the c. 12000 papilionoid legumes, but there are several apparently independent examples of floral simplification.  The papilionoids therefore are a good candidate system for studying what may be a trend towards simplification.  Looking for a macroevolutionary pattern of simplification requires a precise definition of simplification, an accurate assessment of morphology, and a good phylogeny; none of these are yet in hand.
    Inferring the processes that may be involved in such a macroevolutionary pattern requires even more than establishing the patterns.  Discovering correlates of morphological simplifications and understanding functional effects of morphological changes may provide hypotheses for these processes.  For example, it has been suggested that the papilionoid flower functions best with bee pollinators.  Therefore, perhaps there have been shifts away from bee pollination in the cases of floral simplification. 
    To approach these issues, the following questions will be addressed:
• What is common and what is unique, morphologically, about each of the cases of floral simplification in the papilionoid legumes?
• What other characters correlate with the floral simplifications (e.g., pollinators, fruit morphology, inflorescence structure, ...)?


Elusive nodes near the base of the papilionoid phylogeny:

    To study evolution of floral form in the papilionoids requires a well resolved phylogeny.  Tremendous advances in the understanding of the entire tree of papilionoids have been made recently (citations coming), but a few nodes of particular interest to the study of floral simplifications, including where exactly the Amorpheae are placed, have not yet been resolved with strong support.  This project takes advantage of techniques recently developed in the lab of M. J. Sanderson that produce large data sets from public databases (pub). 
    The goals of this project include:
• To assess the current state of knowledge regarding these nodes of interest, drawing data from all available molecular sources.
•To extend the techniques (developed for the characterization of phylogenetic content in databases) to the problem of developing a strategy for solving particular relationships.


Bias-variance tradeoffs in phylogenetic inference:

Abstract from the 2004 Evolution meetings:
    A key question in model-based phylogenetics is the impact of model misspecification.  We challenged a simple model-based inference method and a simple non-model-based inference method with data generated by a complex model of evolution.  Sequences were simulated under highly heterogeneous mixtures of substitution models.  Accuracy was assessed by decomposing error into bias and variance components.  Under simulation conditions that produced moderately well supported trees, both parsimony and likelihood were nearly unbiased but likelihood had significantly lower variance and overall error.
    Ongoing work on this project includes:
• Comparing bias and variance among likelihood models of inference
• Adding complexity to the likelihood models of inference
• Studying the role of phenomena such as long branch attraction and long branch repulsion in the distribution of bias and variance



Current collaborations:

Following are brief descriptions of several collaborative projects with which I am (or have been recently) involved.

Covarion evolution: 

   Together with Gordon Burleigh, Mike Sanderson and Cécile Ané (University of Wisconsin), we investigated a new statitsical test for distinguishing covarion evolution. 


PhyLoTA:  A phylogenomic toolbox for assembling the Tree of Life

    Together with Amy Driskell, Gordon Burleigh, Brian O'Meara, Cécile Ané, and Mike Sanderson as project leader, we are developing tools for the automated investigation of public databases and for assessing and assembling large phylogenetic data matrices.

Efficiency of phylogenetic methods:

    Together with Gordon Burleigh and Brian O'Meara, we are comparing methods for efficiently inferring an optimal tree. 

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