Table 2.
Testing for Gene Conversion in CERs.
| CER ID | La | Observed C-Sites | Expected C-Sites | P | Proportion of C-Sites (PC) | Tree Shapeb | Evidence for Conversionc |
Evidence for Conversion by SD Analysisd | |
|---|---|---|---|---|---|---|---|---|---|
| Hsa | Ptr | ||||||||
| CER1 | 601 | 4 | 0.43 | 1 × 10−3 | 1 | ((((Xp,Yp),Yh),Xh),Xo) | No | Yes | Yes |
| CER2 | 931 | 11 | 0.28 | <10−12 | 1 | ((Xp,Yp),(Yh,Xh),Xo) | Yes | Yes | Yes |
| CER3 | 776 | 9 | 0.59 | 1.5 × 10−8 | 0.53 | ((Xp,Yp),(Yh,Xh),Xo) | Yes | Yes | Yes |
| CER4 | 1,458 | 7 | 0.54 | 1.6 × 10−6 | 0.58 | ((((Xp,Yp),Xh),Yh),Xo) | No | Yes | Yes |
| CER5 | 351 | 4 | 0.27 | 1.8 × 10−4 | 1 | (((Xp,Yp),Xh,Yh),Xo) | No | Yes | No |
| CER6 | 493 | 5 | 0.29 | 1.3 × 10−5 | 0.83 | ((((Xh,Yh),Yp),Xp),Xo) | Yes | No | Yes |
| CER7 | 1,283 | 8 | 0.48 | 4.7 × 10−8 | 0.61 | ((((Xp,Yp),Yh),Xh),Xg) | No | Yes | Yes |
| CER8 | 402 | 4 | 0.08 | 1.79 × 10−6 | 1 | ((((Xp,Yp),Xh),Yh),Xo) | No | Yes | Yes |
| CER9 | 489 | 4 | 0.15 | 2 × 10−5 | 1 | ((Xp,Yp),(Yh,Xh),Xg) | Yes | Yes | Yes |
| CER10 | 1,321 | 8 | 0.41 | 1.46 × 10−8 | 0.35 | ((((Yp,Yh),Xh),Xp),Xg) | No | No | Yes |
| CER11 | 441 | 4 | 0.59 | 3.3 × 10−3 | 1 | ((((Yp,Xp),Yh),Xh),Xo) | No | Yes | Yes |
| CER12 | 429 | 8 | 0.32 | 1.8 × 10−9 | 1 | ((Xp,Yp),(Xh,Yh),Xo) | Yes | Yes | Yes |
| CER13 | 884 | 10 | 0.42 | 3.2 × 10−11 | 0.14 | ((Yh,Yp),(Xh,Xp),Xo) | No | No | Yes |
| CER14 | 757 | 6 | 1.25 | 1.8 × 10−3 | 1 | ((((Xp,Yp),Yh),Xh),Xg) | No | Yes | No |
| CER15 | 73 | 4 | 0.451 | 1.2 × 10−3 | 0.8 | ((Xp,Yp),(Xh,Yh),Xo) | Yes | Yes | Yes |
| CER16 | 627 | 8 | 0.88 | 4.13 × 10−6 | 0.8 | ((((Xp,Yp),Yh),Xh),Xo) | No | Yes | Yes |
| CER17 | 884 | 12 | 0.5 | <10−12 | 1 | ((((Xp,Yp),Yh),Xh),Xo) | No | Yes | Yes |
| CER18 | 655 | 4 | 0.16 | 2.7 × 10−5 | 0.15 | ((((Yp,Yh),Xh),Xp),Xg) | No | No | Yes |
| CER19 | 535 | 6 | 0.59 | 3.4 × 10−5 | 1 | ((Xp,Yp),(Xh,Yh),Xo) | Yes | Yes | Yes |
| Stratum 5e | 7,498 | 2 | 0.51 | 9.3 × 10−2 | 3 × 10−2 | ((Yh,Yp),(Xh,Xp),Xg) | No | No | No |
aLength (bp) of the four-way alignment.
bShape of the NJ tree in newick format. Xp and Yp are X and Y chromosomes of Pan troglodytes, respectively; Xh and Yh are X and Y chromosomes of Homo sapiens, respectively; Xo and Xg indicate the X chromosome of Pongo pygmaeus and Gorilla gorilla, respectively.
cEvidence for gene conversion based on the tree shape analysis. Yes or no means the presence or absence of gene conversion in NJ-phylogenetic analyses, respectively.
dEvidence for gene conversion based on the Split Decomposition (SD) analysis. Yes or no means the presence or absence of a reticulation, respectively.
eNon-CER portion of the four-way alignment representative of the stratum 5.