Alu insertion polymorphisms shared by Papio baboons and Theropithecus gelada reveal an intertwined common ancestry

Table 1 Number of T. gelada Alu insertion polymorphisms shared in Papio individuals

A.	B.	Northern clade						Southern clade
		P. anubis		P. hamadryas		P. papio		P. cynocephalus		P. ursinus		P. kindae
		LIV5	L142	97124	97074	28547	30388	16066	16098	28697	28755	34449	34474
2	1139	112	122	192	179	136	146	127	140	155	111	486	372
3	989	174	169	210	205	166	184	227	231	249	185	537	430
4	944	296	248	268	261	206	259	282	297	343	247	567	502
5	839	294	290	248	280	241	294	342	375	413	310	574	534
6	938	396	396	360	381	370	396	491	497	531	421	727	662
7	851	495	466	448	456	395	430	497	480	505	428	702	655
8	991	626	638	631	645	546	617	623	663	677	584	849	929
9	1171	899	865	830	851	811	869	824	862	894	759	1040	1035
10	1881	1659	1635	1531	1522	1442	1516	1501	1563	1590	1405	1732	1714
11	3213	2980	2971	2890	2907	2966	3104	2811	2884	3025	2636	3079	3090
	12,956

The number of Alu insertion polymorphisms ascertained from T. gelada and not fixed in all 12 Papio individuals was calculated to be 12,956. The distribution of these when shared between any of 2 to 11 of the 12 Papio individuals (column A, 2 to 11) is shown in column B. The sum of the values in column B is 12,956. The ID for each Papio individual is shown at the top of the twelve adjacent columns, for each of the six Papio species, separated by northern and southern clades. The numbers in each column represent the number of times that the shared insertion with T. gelada was predicted in that individual. For example, when an Alu insertion was predicted to be shared in 4 of the 12 individuals and absent from the other 8, one of the four (column A, row 4) was P. anubis LIV5 296 times and one of the four was P. kindae 34474 (BZ11050) 502 times. All 12 Papio individuals share hundreds of Alu insertion polymorphisms with T. gelada in all categories. No Papio individuals are preferentially excluded from having shared insertions with T. gelada. ANOVA detected between-group differences in bins 2–10, but not bin 11. P. kindae has significantly more shared insertion events with T. gelada than all other five Papio species in bins 2 to 4 and 7 to 8, while significantly more in all except P. ursinus in the remaining bins 5, 6, 9 and 10. See Fig. 1

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