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Abstract Detail



Phylogenomics

DAVIS , JERROLD I [1], Barrett, Craig [2].

The Stratified Jackknife, a method for the analysis of phylogenetic support in multi-partition data matrices.

Phylogenetic data matrices frequently include multiple character partitions, including sequences of several genes, and other kinds of of character sets, such as morphology.  All or most of the terminal taxa often lack data for one or more of the partitions, and in many cases several data partitions are scored for only a minority of the taxa.  Data sets with these qualities are sometimes called "supermatrices".  The distribution of empty cells in such matrices can be extremely nonrandom if genomic data (i.e., sequences for numerous genes) are present for a subset of the taxa.  An important element of data analysis is the apportionment of support for particular clades among the various data partitions.  One common approach to this is to conduct a series of analyses that include different character partitions (i.e., single genes, or genes from a particular genome) but when some or all of the genes are not scored comprehensively across all taxa, each single-partition analysis excludes some taxa, and in consequence, the clades that are resolved by each partition are not strictly comparable.  An alternative approach is Partitioned Bremer Support (PBS) analysis, but the computational demands of such analyses are great if support values are desired for all clades.  Also, clade support in parsimony and maximum likelihood analyses is usually assessed by resampling methods (i.e., the bootstrap and jackknife), and the support values derived from PBS analysis are not comparable to those derived from resampling analyses.  The Stratified Jackknife (SJ) is a resampling method that provides a measure of the contribution of each data partition to overall support for each clade in the form of a percentage score, just as the standard jackknife does.  SJ analysis is conducted with the entire data matrix, thereby avoiding the use of different gene/taxon subsets for evaluating the contribution of each data partition to overall support.  Also, unlike PBS analysis, SJ analysis does not require a separate tree search for each clade of interest.


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1 - CORNELL UNIVERSITY, PLANT BIOLOGY AND L.H. BAILEY HORTORIUM, 412 MANN LIBRARY BUILDING, ITHACA, NY, 14853-4301, USA
2 - California State University Los Angeles, Department of Biological Sciences, 5151 State University Drive, Los Angeles, CA, 90032, USA

Keywords:
jackknife
phylogenetics
supermatrix
support.

Presentation Type: Oral Paper:Papers for Topics
Session: 43
Location: Evergreen/Grove
Date: Wednesday, July 30th, 2014
Time: 2:00 PM
Number: 43003
Abstract ID:593
Candidate for Awards:None


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