Statistical phylogenetic tree analysis using differences of means.
We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by two input alignments, instead of comparing point estimations of trees. This statistical approach can be applied to gene tree analysis for example, detecting unusual events in genome evolution such as horizontal gene transfer and reshuffling. Our method uses difference of means to compare two distributions of trees, after mapping trees into a vector space. Bootstrapping alignment columns can then be applied to obtain p-values. To compute distances between means, we employ a "kernel method" which speeds up distance calculations when trees are mapped in a high-dimensional feature space, e.g., splits or quartets feature space. In this pilot study, first we test our statistical method on data sets simulated under a coalescence model, to test whether two alignments are generated by congruent gene trees. We follow our simulation results with applications to data sets of gophers and lice, grasses and their endophytes, and different fungal genes from the same genome. A companion toolkit, Phylotree, is provided to facilitate computational experiments.
Arnaoudova
Elissaveta
E
Department of Computer Science, University of Kentucky Lexington, KY, USA.
Haws
David C
DC
Huggins
Peter
P
Jaromczyk
Jerzy W
JW
Moore
Neil
N
Schardl
Christopher L
CL
Yoshida
Ruriko
R
Fungal Genet Biol. 2002 Aug;36(3):242-54
12135580
Syst Biol. 2003 Feb;52(1):15-22
12554436
J Mol Evol. 1989 Aug;29(2):170-9
2509717
Proc Natl Acad Sci U S A. 2007 Apr 3;104(14):5936-41
17392434
Mol Phylogenet Evol. 2005 Aug;36(2):249-60
15955508
Syst Biol. 2011 Jul;60(4):528-40
21471560
Syst Biol. 2007 Jun;56(3):504-14
17562474
Syst Biol. 2003 Oct;52(5):696-704
14530136
Bioinformatics. 2006 Nov 1;22(21):2688-90
16928733
Syst Biol. 2006 Feb;55(1):21-30
16507521
Mol Biol Evol. 2007 Feb;24(2):412-26
17095535
J Clin Microbiol. 1999 Dec;37(12):3957-64
10565914
Fungal Genet Biol. 2000 Aug;30(3):167-71
11035938
J Mol Evol. 1981;17(6):368-76
7288891
Mol Biol Evol. 1987 Jul;4(4):406-25
3447015
Bioinformatics. 2001 Aug;17(8):754-5
11524383
Proc Natl Acad Sci U S A. 1999 Dec 7;96(25):14400-5
10588717
Mol Biol Evol. 1997 Jul;14(7):717-24
9214744
Syst Biol. 2008 Jun;57(3):483-98
18570040
Evolution. 2008 Aug;62(8):2080-91
18462214