Phylogeny and Genomic Inference for Quantitative Traits It is proposed to develop statistical methods for analyzing data on phenotypic traits within populations, between populations, and between species, in an integrated way. Computer programs will be written and distributed to allow us to compare inferences at these levels and test whether divergence of characters among species shows different patterns of divergence when compared to the same characters observed between populations. Discrete 0/1 traits will be handled as well as quantitatively measurable traits. For the discrete traits, the threshold model of quantitative genetics will be used. Simple models of change of measurable environmental variables will be incorporated as well to allow testing of effects of these environments. These methods will be extended to also be able to handle neutral markers such as SNPs from genomic sequences. The pattern of variation within and between species of these SNPs creates opportunities to test for natural selection, by looking for combinations of characters that have evolved with a noticeably different pattern of covariation than the markers. In this way the testing framework will begin to unify population biology inferences with genomic methods, as genomic methods are increasingly applied to the biology of natural populations.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM071639-02
Application #
7030292
Study Section
Special Emphasis Panel (ZRG1-GVE (01))
Program Officer
Eckstrand, Irene A
Project Start
2005-04-01
Project End
2009-03-31
Budget Start
2006-04-01
Budget End
2007-03-31
Support Year
2
Fiscal Year
2006
Total Cost
$229,297
Indirect Cost
Name
University of Washington
Department
Genetics
Type
Schools of Medicine
DUNS #
605799469
City
Seattle
State
WA
Country
United States
Zip Code
98195
Felsenstein, Joseph (2014) Covariation of gene frequencies in a stepping-stone lattice of populations. Theor Popul Biol 100C:88-97
Bryant, David; Bouckaert, Remco; Felsenstein, Joseph et al. (2012) Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis. Mol Biol Evol 29:1917-32
RoyChoudhury, Arindam; Thompson, Elizabeth A (2012) Ascertainment correction for a population tree via a pruning algorithm for likelihood computation. Theor Popul Biol 82:59-65
Stone, Graham N; Nee, Sean; Felsenstein, Joseph (2011) Controlling for non-independence in comparative analysis of patterns across populations within species. Philos Trans R Soc Lond B Biol Sci 366:1410-24
RoyChoudhury, Arindam; Felsenstein, Joseph; Thompson, Elizabeth A (2008) A two-stage pruning algorithm for likelihood computation for a population tree. Genetics 180:1095-105
Felsenstein, Joseph (2008) Comparative methods with sampling error and within-species variation: contrasts revisited and revised. Am Nat 171:713-25
Felsenstein, Joseph (2006) Accuracy of coalescent likelihood estimates: do we need more sites, more sequences, or more loci? Mol Biol Evol 23:691-700