Table 1.

Estimated Parameters for Each Chromosomal Alignment Set^a

Regionsb	Alignment Length (Mb)	τHC	τHCG	τHCGO	θHC	θHCG	θHCGO	Branch Lengthc	−ln L
Whole genomed	40.8	0.00330	0.00423	0.00819	0.00264	0.00229	0.00709	0.0352	−66,035,045
Autosomesd	38.7	0.00326	0.00423	0.00835	0.00286	0.00223	0.00659	0.0355	−62,585,914
Chr. 1	3.28	0.00313	0.00408	0.00778	0.00270	0.00216	0.00691	0.0335	−5,289,418
Chr. 2	3.49	0.00327	0.00426	0.00827	0.00284	0.00223	0.00671	0.0350	−5,650,076
Chr. 3	2.92	0.00324	0.00429	0.00837	0.00303	0.00225	0.00679	0.0352	−4,736,827
Chr. 4	2.79	0.00345	0.00434	0.00886	0.00288	0.00254	0.00676	0.0368	−4,545,603
Chr. 5	2.61	0.00327	0.00436	0.00855	0.00316	0.00221	0.00644	0.0354	−4,243,851
Chr. 6	2.43	0.00307	0.00423	0.00837	0.0036	0.00225	0.00629	0.0346	−3,934,109
Chr. 7	2.13	0.00345	0.00426	0.00826	0.00221	0.00227	0.00705	0.0352	−3,458,675
Chr. 8	2.09	0.00352	0.00453	0.00899	0.00311	0.00242	0.00650	0.0372	−3,419,007
Chr. 9	1.62	0.00332	0.00431	0.00786	0.00282	0.00215	0.00678	0.0340	−2,620,109
Chr. 10	1.86	0.00331	0.00422	0.00827	0.00263	0.00228	0.00723	0.0353	−3,027,929
Chr. 11	1.86	0.00324	0.00415	0.00827	0.00271	0.00233	0.00692	0.0348	−3,022,784
Chr. 12	1.93	0.00317	0.00408	0.00818	0.00264	0.00234	0.00671	0.0342	−3,127,323
Chr. 13	1.43	0.00321	0.00434	0.00878	0.00364	0.00239	0.00660	0.0361	−2,336,632
Chr. 14	1.29	0.00310	0.00413	0.00792	0.00296	0.00220	0.00721	0.0344	−2,093,555
Chr. 15	1.14	0.00317	0.00421	0.00786	0.00324	0.00216	0.00731	0.0343	−1,850,007
Chr. 16	1.07	0.00360	0.00459	0.00870	0.00277	0.00238	0.00730	0.0374	−1,755,416
Chr. 17	1.09	0.00294	0.00385	0.00726	0.00264	0.00195	0.00827	0.0330	−1,752,968
Chr. 18	1.11	0.00330	0.00433	0.00880	0.00342	0.00243	0.00616	0.0358	−1,801,757
Chr. 19	0.725	0.00315	0.00401	0.00751	0.00285	0.00237	0.00895	0.0350	−1,173,725
Chr. 20	0.878	0.00310	0.00415	0.00798	0.00325	0.00225	0.00706	0.0344	−1,418,404
Chr. 21	0.466	0.00337	0.00444	0.00910	0.00370	0.00278	0.00665	0.0376	−761,073
Chr. 22	0.454	0.00299	0.00401	0.00796	0.00328	0.00241	0.00744	0.0348	−733,646
Chr. Xe	2.07	0.00277	0.00371	0.00637	0.00153	0.00171	0.00627	0.0295	−3,286,104
Coding regionsd	2.37	0.00156	0.00249	0.00418	0.00367	0.00137	0.00552	0.0213	−3,632,995
FFD 3rd positionsd,f	0.351	0.00437	0.00548	0.0135	0.00401	0.00480	0.00708	0.05359	−598,524

^a95% CI of each estimated parameter and the estimates based on the sample 2 were shown in supplementary table S2, Supplementary Material online.

^bAnalyzed based on the method (2), assuming heterogeneity of mutation rates across the lineages (see Materials and Methods), except the regions with footnote d.

^cAverage of sum of the branch lengths in each locus.

^dAnalyzed based on the method (3), assuming heterogeneity of mutation rates across lineages and chromosomes (see Materials and Methods).

^eθ = 3μgN based on X chromosome.

^fFour-fold degenerate sites at third codon positions.