RT Journal
A1 Hardison, Ross C.
A1 Roskin, Krishna M.
A1 Yang, Shan
A1 Diekhans, Mark
A1 Kent, W. James
A1 Weber, Ryan
A1 Elnitski, Laura
A1 Li, Jia
A1 O'Connor, Michael
A1 Kolbe, Diana
A1 Schwartz, Scott
A1 Furey, Terrence S.
A1 Whelan, Simon
A1 Goldman, Nick
A1 Smit, Arian
A1 Miller, Webb
A1 Chiaromonte, Francesca
A1 Haussler, David
T1 Covariation in Frequencies of Substitution, Deletion, Transposition, and Recombination During Eutherian Evolution
JF Genome Research 
JO Genome Research 
YR 2003 
FD January 01 
VO 13 
IS 1 
SP 13 
OP 26 
DO 10.1101/gr.844103 
UL http://genome.cshlp.org/content/13/1/13.abstract 
AB Six measures of evolutionary change in the human genome were studied, three derived from the aligned human and mouse genomes in conjunction with the Mouse Genome Sequencing Consortium, consisting of (1) nucleotide substitution per fourfold degenerate site in coding regions, (2) nucleotide substitution per site in relics of transposable elements active only before the human–mouse speciation, and (3) the nonaligning fraction of human DNA that is nonrepetitive or in ancestral repeats; and three derived from human genome data alone, consisting of (4) SNP density, (5) frequency of insertion of transposable elements, and (6) rate of recombination. Features 1 and 2 are measures of nucleotide substitutions at two classes of “neutral” sites, whereas 4 is a measure of recent mutations. Feature 3 is a measure dominated by deletions in mouse, whereas 5 represents insertions in human. It was found that all six vary significantly in megabase-sized regions genome-wide, and many vary together. This indicates that some regions of a genome change slowly by all processes that alter DNA, and others change faster. Regional variation in all processes is correlated with, but not completely accounted for, by GC content in human and the difference between GC content in human and mouse. [Supplemental material is available online atwww.genome.org andhttp://www.soe.ucsc.edu/research/compbio/covariation/.]