Abstract Detail

Fossil plants at the intersection of evo-devo and phylogeny: celebrating the contributions of Gar W. Rothwell to biodiversity and evolution

Nixon, Kevin C [1].

Character Homology Estimation (CHE).

As more and more molecular sequence data are captured and used for reconstruction of phylogenetic trees, certain parts of the green plant phylogeny remain problematic. With the advent of model-based approaches (e.g., maximum likelihood [ML] and Bayesian analysis [BA]), efforts to improve phylogenetic estimation have focused on gathering more genomic data and improving models. Part of this expansion of phylogenetics has also propagated the mantra that model-based methods are not susceptible to long branch attraction (LBA) artifacts. Results that are problematic or conflict with previous results or the consensus view are often attributed to specific problems such as issues with GC content bias, third position homoplasy, or other model misspecification. Rarely if ever is LBA invoked by name in discussions of ML or BA results, although the end results of model misspecification (e.g., homogeneous models where heterogeneous models are appropriate, or GC content bias) are in fact examples of LBA artifacts. Unfortunately, the actual susceptibility of ML or BA to LBA cannot be addressed by testing different models or modifying such models until acceptable results are obtained. I here propose a new method that utilizes recoding of data that results in consistent results across both parsimony and ML (and by implication, BA). The new method (Character Homology Estimation, or CHE) treats molecular sequence data as similar to morphological data, under the assumption that confidence is highest in groupings that are supported by the most complex characters. A typical CHE analysis can be viewed as a relaxed heterogeneous model with highest likelihood of homology to be found in the most complex characters. Examples of CHE analyses from the whole chloroplast genome will be presented with special emphasis on the positions of gnetopsids, the monophyly or lack thereof of the bryophytes, the lycophyte clade, and the relationships among early angiosperm clades such as Ceratophyllum.

1 - Cornell University, Plant Biology, 405 Mann Library Building, Plant Biology Section, SIPS, Cornell University, Ithaca, NY, 14853, USA

Keywords:
phylogenetic analysis.

Presentation Type: Colloquium Presentations
Session: C11b, Fossil plants at the intersection of evo-devo and phylogeny: celebrating the contributions of Gar W. Rothwell to biodiverstiy and evolution Part 2
Location: 110/Mayo Civic Center
Date: Wednesday, July 25th, 2018
Time: 2:30 PM
Number: C11b003
Abstract ID:849
Candidate for Awards:None