Abstract Detail

Empirical Approaches to Phylogenetic Comparative Methods in Plant Science

Yang, Ya [1], Moore, Michael J. [2], Brockington, Samuel F. [3], Smith, Stephen A. [4].

Using transcriptome for functional phylogenomic studies: an example from the Caryophyllales.

The Caryophyllales is a hyperdiverse and globally distributed group ranging from arid-adapted succulent cacti and halophytes to rainforest trees and carnivorous plants. We assembled a data set including 69 Caryophyllales transcriptomes plus 27 eudicot genomes as outgroups. Using a novel tree based orthology inference method we recovered 17,273 orthologs that each had at least 10 ingroup taxa. From there we constructed a robust phylogeny using a 1,122-gene matrix that had a 92% gene occupancy. We evaluated conflict among loci with a serial jackknife-by-loci strategy. By mapping gene duplications onto the species tree, we discovered three genome duplication events in Caryophyllales. Both the peptide and DNA data sets show faster substitution rates in herbaceous compared to woody relatives. This rate shift is up to three folds and is genome wide. Overall dN/dS ratios are high among genes involved in regulatory functions, while genes involved in housekeeping functions have relatively low dN/dS ratios. We further correlate the rate heterogeneity and gene family expansion to ecological and morphological traits in selected clades within the Caryophyllales.     Despite of the rich content of transcriptomes, availability of these data sets is contingent upon obtaining high quality RNA materials. In addition, transcriptome data sets are inherently incomplete and include errors. Tools for detecting natural selection, such as PAML and HYPHY were designed for model organisms and their behavior is yet unexplored when handling incomplete and noisy data. Those tools are also aimed at testing specific hypotheses, and are unsuited for exploring large and complex data sets. Future development will focus on scalable tools for detecting both the phylogenetic and functional location of phylogenetic conflict, rate shift and selection regime.

1 - University Of Michigan, Ann Arbor, Ecology And Evolutionary Biology, 2071 Kraus Natural Science Building, 830 North University Ave., Ann Arbor, MI, 48109, USA
2 - Oberlin College, Department of Biology, 119 Woodland St., Oberlin, OH, 44074, USA
3 - Department Of Plant Science, Downing Site, Cambridge, N/A, CB23AE, United Kingdom
4 - University of Michigan, Ecology and Evolutionary Biology, 2071A Kraus Natural Science Building, Ann Arbor, MI, 48109, USA

Keywords:
1KP
phylogenomics
polyploidy
molecular rates
Caryophyllales.

Presentation Type: Symposium or Colloquium Presentation
Session: C1
Location: Summit/Boise Centre
Date: Monday, July 28th, 2014
Time: 4:00 PM
Number: C1010
Abstract ID:386
Candidate for Awards:None