TY  - JOUR
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
Y1  - 2003/01/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 13 
EP  - 26 
DO  - 10.1101/gr.844103 
VL  - 13 
IS  - 1 
UR  - http://genome.cshlp.org/content/13/1/13.abstract 
N2  - 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/.] 
ER  -