Recently integrated Alu insertions in the squirrel monkey (Saimiri) lineage and application for population analyses

Baker, Jasmine N.; Walker, Jerilyn A.; Denham, Michael W.; Loupe, Charles D.; Batzer, Mark A.

doi:10.1186/s13100-018-0114-7

Mobile DNA

Table 4 Allele frequency data for Alu insertions with species informative distributions

From: Recently integrated Alu insertions in the squirrel monkey (Saimiri) lineage and application for population analyses

		a. N = 12	b. N = 14	c. N = 10
	Alu Locus Name	Saimiri sciureus	Saimiri boliviensis	Saimiri sciureus
1	L-20858-sf38	0.000	0.893	0.000
2	L-40335-subfam32	0.000	0.893	0.000
3	L-21370-subfam26	0.083	1.000	0.000
4	L-26673-subfam29	0.167	0.857	0.000
5	L-16089-Subfam26	0.167	1.000	0.050
6	L-27488-subfam4	0.167	1.000	0.000
7	L-27102-subfam5	0.083	0.929	0.000
8	L-29927-Subfam4	0.150	0.964	0.056
9	L-22568-sf37	0.167	0.929	0.000
10	L-18103-subfam11	0.125	0.964	0.050
11	L-11426-sf51	0.182	1.000	0.000
12	L-14471-sf63	0.083	0.964	0.000
13	L-19033-sf66	0.000	0.833	0.000
14	L-12684-sf63	0.000	0.786	0.000
15	L-1748-subfam0	0.167	1.000	0.000
16	L-13945-sf46	0.042	1.000	0.000
17	L-20802-sf62	0.167	1.000	0.000
18	L-17843-sf62	0.167	0.913	0.000
19	L-6918-subfam43	0.208	0.964	0.050
20	L-31469-subfam29	0.042	0.929	0.000
21	L-24998-subfam36	0.000	1.000	0.000
22	L-40504-sf42	0.167	1.000	0.000
23	L-26020-sf85	0.167	1.000	0.000
24	L-33213-sf86	0.167	1.000	0.000
25	L-2485-sf82	0.042	1.000	0.000
26	L-35028-sf63	0.125	1.000	0.000
27	L-18718-sf62	0.167	1.000	0.000
28	L-6892-sf71	0.167	1.000	0.000
29	L-7578-sf82	0.167	1.000	0.000
30	L-19942-sf73	0.167	1.000	0.000
31	L-20830-sf73	0.200	1.000	0.000
32	L-25034-subfam36	0.167	0.923	0.000
33	L-38119-subfam12	0.167	0.964	0.000
34	L-30099-sf52	0.167	1.000	0.000
35	L-36916-subfam12	0.208	1.000	0.050
36	L-8051-sf42	0.167	1.000	0.000
37	L-24655-s42	0.167	0.964	0.000
38	L-39021-sf51	0.167	1.000	0.000
39	L-16832-sf82	0.083	0.929	0.000
40	L-20778-sf73	0.167	1.000	0.000
41	L-37765-sf82	0.111	1.000	0.000
42	L-30633-sf86	0.125	1.000	0.000
43	L-431-sf66	0.125	1.000	0.000
44	L-20383-sf36	0.167	1.000	0.000
45	L-30828-subfam5	0.167	0.893	0.000
46	L-22291-sf46	0.125	0.893	0.000
47	L-25257-sf42	0.167	1.000	0.000
48	L-26813-sf42	0.125	1.000	0.000
49	L-28766-sf38	0.167	1.000	0.000
50	L-38773-sf44	0.167	1.000	0.000
51	L-10445-sf46	0.000	0.857	0.000

Allele frequency data for 51 polymorphic Alu insertions with species informative distribution between S. sciureus and S. boliviensis squirrel monkey species. Column C. with only ten S. sciureus samples has #75531 and #193661 omitted from the calculation because they clustered more closely with the Bolivian cluster (See Fig. 2). The 14 S. boliviensis group have an allele frequency of 80–100% whereas the 12 samples labeled S. sciureus have a group allele frequency of 0–20%. With #75531 and # 193661 omitted in column C, the group allele frequency in the S. sciureus group drops to near zero (0.5% on average). These 51 Alu insertion polymorphisms represent 26 different subfamilies: 10 Saimiri lineage specific Alu subfamilies reported in Baker et al. 2017 [48] and 16 NWM Alu subfamilies discovered in marmoset [49]

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ISSN: 1759-8753

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