Sequence differences at orthologous microsatellites inflate estimates of human-chimpanzee differentiation

BMC Genomics

Table 2 Comparison of measures of variation across individuals at orthologous microsatellites

Variable	1 STR region				2 STR regions
	Tri		Tetra		Tetra
	n = 31		n = 79		n = 21
	ARD (SD)	P	ARD (SD)	P	ARD (SD)	P
Number of distinct alleles	0.949 (0.366)	0.264	1.257 (0.448)	3.73 × 10 ^-6	1.508 (0.477)	1.97 × 10 ^-4
Variance in the number of repeats	1.025 (1.030)	0.120	1.813 (1.623)	8.08 × 10 ^-4	2.413 (2.401)	0.065
Range of the number of repeats	0.915 (0.336)	0.157	1.167 (0.336)	5.65 × 10 ^-5	1.302 (0.354)	0.011
Mean PCR fragment length	0.962 (0.045)	3.18 × 10 ^-5	0.965 (0.056)	7.12 × 10 ^-7	0.951 (0.064)	0.003
Mean number of repeats	0.793 (0.220)	1.05 × 10 ^-5	0.875 (0.230)	4.07 × 10 ^-7	0.861 (0.189)	0.001
Maximum number of repeats	0.830 (0.178)	2.99 × 10 ^-6	0.967 (0.197)	0.022	0.959 (0.170)	0.495
Minimum number of repeats	0.794 (0.210)	5.08 × 10 ^-5	0.887 (0.639)	6.44 × 10 ^-7	0.734 (0.263)	5.25 × 10 ^-5

Wilcoxon signed-rank tests are shown for comparisons of measures of variation across individuals calculated separately among chimpanzees and humans. Microsatellites were grouped by their number of separate STR regions and repeat unit size. No comparisons were performed for microsatellites with one dinucleotide STR region, two trinucleotide STR regions, or three or four tetranucleotide STR regions because of small sample sizes (1, 1, 4, and 1, respectively). Average relative difference (ARD) was calculated by taking the average across microsatellites of the division of the value in chimpanzees by the value in humans. The standard deviation (SD) in relative difference across microsatellites is provided in parentheses. P < 0.05 are shown in bold.

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