Life-history traits drive the evolutionary rates of mammalian coding and noncoding genomic elements
Nikolaev et al. 10.1073/pnas.0705658104.
Supporting Information
Files in this Data Supplement:
SI Figure 5SI Table 1
SI Table 2
SI Table 3
SI Figure 6
SI Dataset 1
Fig. 5. Maximum likelihood branch length estimates of the mammalian tree for three genomic metrics: yellow, synonymous (dS) substitutions; red, nonsynonymous (dN) substitutions; blue, conserved noncoding (CNCr) sequences rates. The imposed topology was taken from Nikolaev et al. [Nikolaev S, Montoya-Burgos JI, Margulies EH, Rougemont J, Nyffeler B, Antonarakis SE (2007) PLoS Genet 3:e2].
Table 1. Relative rate test: Comparisons of evolutionary changes among several mammalian lineages in three genomic categories (CNCr, dN, and dS)
|
Lineage 1 |
Lineage 2 |
Outgroup |
Cat. |
No. of sites |
K1 |
K2 |
dK |
sd_dK |
% |
P |
|
Human |
Chimpanzee |
Baboon |
CNC |
1545360 |
0,0239909 |
0,0249748 |
-0,000983908 |
6,74654E-05 |
-14,5839 |
0,0000001 |
|
|
|
|
dN |
126219 |
0,0184417 |
0,0192161 |
-0,000774386 |
0,000183478 |
-4,22059 |
2,60329E-05 |
|
|
|
|
dS |
61971,3 |
0,0753219 |
0,0770245 |
-0,00170259 |
0,000577833 |
-2,94652 |
0,00321881 |
|
Hominoids |
Cercopithecoids |
Marmoset |
CNC |
1294580 |
0,0401991 |
0,0424911 |
-0,002292 |
0,000132858 |
-17,2515 |
0,0000001 |
|
|
|
|
dN |
107221 |
0,0243503 |
0,0293531 |
-0,00500281 |
0,000399587 |
-12,5199 |
0,0000001 |
|
|
|
|
dS |
53063,1 |
0,107989 |
0,130779 |
-0,0227902 |
0,00149919 |
-15,2017 |
0,0000001 |
|
Primates |
Glires |
Laurasiatheria |
CNC |
419589 |
0,104642 |
0,160302 |
-0,0556602 |
0,000457282 |
-121,72 |
0,0000001 |
|
|
|
|
dN |
48059 |
0,0916464 |
0,110502 |
-0,0188552 |
0,000926279 |
-20,3559 |
0,0000001 |
|
|
|
|
dS |
23920 |
0,459009 |
0,628456 |
-0,169446 |
0,00509652 |
-33,2474 |
0,0000001 |
|
Primates |
Laurasiatheria |
Afrotheria |
CNC |
216912 |
0,135724 |
0,155664 |
-0,0199394 |
0,000498471 |
-40,0011 |
0,0000001 |
|
|
|
|
dN |
32720 |
0,0936488 |
0,133071 |
-0,0394222 |
0,00142992 |
-27,5695 |
0,0000001 |
|
|
|
|
dS |
16213 |
0,510833 |
0,675656 |
-0,164824 |
0,00637906 |
-25,8382 |
0,0000001 |
|
Primates |
Xenarthra |
Afrotheria |
CNC |
467352 |
0,132863 |
0,13861 |
-0,00574677 |
0,000473143 |
-12,146 |
0,0000001 |
|
|
|
|
dN |
57059,9 |
0,0966618 |
0,102095 |
-0,00543338 |
0,00113324 |
-4,79456 |
2,20259E-06 |
|
|
|
|
dS |
27906,1 |
0,475684 |
0,477754 |
-0,00206973 |
0,0052725 |
-0,392551 |
0,694654 |
|
Primates |
Afrotheria |
Monodelphis |
CNC |
445438 |
0,228994 |
0,257717 |
-0,0287229 |
0,000533178 |
-53,8711 |
0,0000001 |
|
|
|
|
dN |
56449,6 |
0,142899 |
0,156406 |
-0,0135075 |
0,00114096 |
-11,8387 |
0,0000001 |
|
|
|
|
dS |
28306,4 |
0,834135 |
0,905861 |
-0,0717261 |
0,00803028 |
-8,93196 |
0,0000001 |
|
Glires |
Laurasiatheria |
Afrotheria |
CNC |
267087 |
0,186884 |
0,144984 |
0,0418995 |
0,000607539 |
68,9659 |
0,0000001 |
|
|
|
|
dN |
42490,1 |
0,125862 |
0,139297 |
-0,0134357 |
0,00139721 |
-9,61611 |
0,0000001 |
|
|
|
|
dS |
20917,9 |
0,696532 |
0,646624 |
0,0499079 |
0,00730646 |
6,83066 |
0,0000001 |
Ki, number of substitutions per site that lineage i accumulated starting from the split with lineage j; dK, the difference between Ki and Kj numbers of substitutions; sd_dK, standard deviation for dK; P, significance value for differences in substitution rates between lineage 1 and lineage 2.
|
Clade1/Clade2 |
|
dS1/dS2 without CpG prone |
dN1/dN2 |
CNCr1/CNCr2 |
GT1/GT2 |
|
Human/chimpanzee |
0.77 |
- |
0.63 |
0.63 |
1.33 |
|
Baboon/macaque |
0.52 |
0.66 |
0.48 |
0.39 |
1.20 |
|
Hominoids/cercopithecoids |
0.55 |
0.46 |
0.59 |
0.60 |
3.18 |
|
Catarrhini/marmoset |
0.43 |
0.40 |
0.47 |
0.37 |
5.75 |
|
Euprimates/galago |
0.67 |
0.71 |
0.85 |
0.76 |
9.60 |
|
Mouse/rat |
0.83 |
0.81 |
0.80 |
0.91 |
1.00 |
|
Rabbit/rodents |
0.68 |
0.65 |
0.71 |
0.61 |
5.00 |
|
Dog/cow |
0.79 |
0.98 |
0.68 |
0.92 |
1.50 |
|
Bat/cow-dog |
0.84 |
0.76 |
0.93 |
1.03 |
0.40 |
|
Cow-dog-bat/shrew |
0.49 |
0.41 |
0.63 |
0.55 |
20.00 |
|
Elephant/tenrec |
0.36 |
0.38 |
0.50 |
0.36 |
24.00 |
The average branch lengths and generation times (GT) were calculated for each clade.
Table 3. dN, dS, and CNCr branch lengths of original alignments and alignments without CpG prone sites, species generation time and body mass
|
|
CDS |
CDS without CpG prone sites |
CNCr |
CNCr prone |
Generation time |
Body mass, g |
||||||
|
Lineage name |
dN |
N |
dS |
S |
dN |
N |
dS |
S |
||||
|
Human |
0.00175 |
138,557 |
0.00614 |
57,433 |
0.0007 |
20,313 |
0.00275 |
13,386 |
0.00261 |
0.00249 |
20 |
70,000 |
|
Hominoids |
0.00483 |
146,072 |
0.02053 |
58,714 |
0.00192 |
21,837 |
0.00876 |
11,745 |
0.00871 |
0.00797 |
|
|
|
Chimpanzee |
0.00279 |
141,499 |
0.00794 |
54,491 |
0.00137 |
21,304 |
0.00176 |
12,395 |
0.00413 |
0.00333 |
15 |
45,000 |
|
Baboon |
0.00253 |
127,386 |
0.00875 |
48,489 |
0.00102 |
21,459 |
0.00475 |
9,180 |
0.00313 |
0.00226 |
6 |
21,400 |
|
Catarrhini |
0.00381 |
134,740 |
0.01782 |
57,428 |
0.00207 |
18,657 |
0.0068 |
12,633 |
0.00541 |
0.00448 |
|
|
|
Cercopithecoids |
0.01076 |
147,409 |
0.04253 |
57,377 |
0.00438 |
21,350 |
0.0174 |
12,233 |
0.01277 |
0.01143 |
|
|
|
Euprimates |
0.0123 |
132,359 |
0.06186 |
50,719 |
0.00664 |
16,941 |
0.02975 |
10,158 |
0.01773 |
0.01455 |
|
|
|
Macaque |
0.00522 |
128,170 |
0.01688 |
47,706 |
0.0012 |
21,341 |
0.00724 |
9,298 |
0.00812 |
0.00633 |
5 |
3,700 |
|
Primates |
0.00373 |
147,985 |
0.01726 |
56,801 |
0.00206 |
21,444 |
0.00819 |
12,609 |
0.0047 |
0.00416 |
|
|
|
Marmoset |
0.01453 |
138,008 |
0.06416 |
54,160 |
0.00726 |
19,692 |
0.02766 |
11,598 |
0.02707 |
0.02386 |
2 |
300 |
|
Galago |
0.02697 |
131,607 |
0.16045 |
51,471 |
0.01431 |
17,061 |
0.0693 |
10,038 |
0.04755 |
0.03887 |
1 |
|