Detecting substitution-rate heterogeneity among regions of a nucleotide sequence.
Likelihood-ratio statistics are proposed to test for heterogeneity in nucleotide substitution rate among regions of a DNA sequence. The tests examine three-sequence phylogenies, and two specific tests are proposed: a test to detect rate heterogeneity among genic regions within a sequence, over all evolutionary lineages; and a test to detect rate heterogeneity among regions in a specific evolutionary lineage. Simulations examine the ability of tests to detect a single region that varies in nucleotide substitution rate relative to the remainder of the sequence. A 50-bp region with a fivefold substitution-rate increase can be detected > or = 90% of the time when it is found in all three lineages of the phylogeny, and a 50-bp region of fivefold rate increase can be detected with approximately 70% power when it is found in only one evolutionary lineage. Simulation also examines the effect of transition- and transversion-rate differences. The tests are applied to published DNA sequences. While the tests are powerful, significant results can be difficult to interpret biologically.
Gaut
B S
BS
Department of Statistics, North Carolina State University, Raleigh 27695-8203.
Weir
B S
BS
D000818:Animals; D003198:Computer Simulation; D004251:DNA Transposable Elements; D017344:Genes, Insect; D014644:Genetic Variation; D007313:Insecta / Q000145:classification / Q000235:genetics; D016013:Likelihood Functions; D008957:Models, Genetic; D009154:Mutation; D010802:Phylogeny; D011544:Pseudogenes
D004251:DNA Transposable Elements