Supplementary information reports data on (i) population genetics of the orangutan chromosome 9polymorphism and on the Saimiri genus taxonomy.
The ENC polymorphism in orangutan chromosome 9 (human 12)
Supplementary Tables 1, 2, and 3 report in detail the unpublished data, from the laboratory of Freiburg,on Sumatran orangutan (Table 1), Bornean orangutan (Table 2), and hybrid Sumatra-Borneo orangutan, for a total of 59 individuals.
Table 1: Sumatran orang-utan (Pongo abelii) specimens – ENC polymorphism Chromosome 9
Name / Sex / Stud # / Birth Date / Chromosome 9 status1 / Asia / f / 2771 / 13.06.1996 / homozygous normal
2 / Bata / f / 1161 / 13.07.1971 / homozygous normal
3 / Batak / m / 1572 / 08.04.1977 / homozygous normal
4 / Benjamin / m / 1516 / 25.05.1976 / homozygous normal
5 / Buschi / m / 498 / wb ~1959 / heterozygous
6 / Charly / m / 497 / wb ~1957 / homozygous normal
7 / Conny / f / 2260 / 08.04.1989 / homozygous normal
8 / Dumai / m / 2273 / 07.09.1989 / heterozygous
9 / Dunja / f / 1302 / 19.04.1973 / homozygous normal
10 / Elsi / f / 446 / wb ~1958 / homozygous derived
11 / Hummel / m / 411 / wb ~1957 / homozygous normal
12 / Jolo / m / 1254 / 02.10.1972 / homozygous normal
13 / Kayan / m / 2368 / 28.07.1990 / homozygous normal
14 / Karolinch / f / 1349 / 08.12.1973 / heterozygous
15 / Kiki / f / 499 / wb ~1959 / homozygous normal
16 / Kwesida / f / 1555 / 15.01.1977 / homozygous normal
17 / Masala / m / 2404 / 21.01.1991 / homozygous normal
18 / Matra / f / 1465 / 19.11.1975 / heterozygous
19 / Moni / f / 1609 / 07.12.1977 / homozygous normal
20 / Pandai / m / 3368 / 13.09.2009 / homozygous normal
21 / Pini / f / 2184 / 30.06.1988 / homozygous normal
22 / Pongo / m / 787 / wb ~1961 / heterozygous
23 / Schubbi / m / 1237 / 28.05.1972 / homozygous normal
24 / Sirih / f / 2520 / 07.12.1992 / homozygous derived
25 / Sinjo / m / 1007 / 16.03.1969 / heterozygous
26 / Sitti / f / 2281 / 20.11.1989 / heterozygous
27 / Suma / f / 500 / wb ~1960 / homozygous normal
28 / Tuan/Tao / m / 2865 / 23.05.1998 / homozygous normal
29 / Ujian / m / 2664 / 25.06.1994 / heterozygous
30 / Vicky / f / 407 / wb ~1957 / heterozygous
2002 International studbook of the orang-utan (Pongo pygmaeus, Pongo abelii); Lori Perkins, studbook keeper, Lincoln Park Zoo, 2001 North Clark Street, Chicago, IL 60614, USA.
Orang-Utan Europäisches Erhaltungszuchtprogramm, Zuchtbuch für Europa XXVII/2009; Clemens Becker, Zuchtbuchführer und EEP-Koordinator, Zoo Karlsruhe, Ettlinger Strasse 6, D-76137 Karlsruhe.
wb: wild-born
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Table 2: Bornean orang-utan (Pongo pygmaeus) specimens – ENC polymorphism Chromosome 9
Name / Sex / Stud # / Birth Date / Chromosome 9 status1 / Amatis / f / 2263 / 29.04.1989 / homozygous derived
2 / Benjamin / m / 1601 / 06.11.1977 / heterozygous
3 / Gusti / f / 1665 / 28.08.1978 / homozygous normal
4 / Jonny / m / 1236 / 21.05.1972 / homozygous normal
5 / Kajan / m / 1610 / wb ~1969 / homozygous derived
6 / Lea / f / 2611 / 01.05.1993 / homozygous normal
7 / Lotti / f / 1125 / 29.01.1971 / homozygous derived
8 / Maias / m / 1052 / wb ~1967 / heterozygous
9 / Miri / f / 2406 / 14.02.1991 / heterozygous
10 / Napoleon / m / 898 / wb ~1965 / homozygous normal
11 / Rawit / f / 1778 / 02.07.1980 / heterozygous
12 / Sandai / m / 2617 / 20.08.1993 / heterozygous
13 / Sari / f / 1097 / 26.07.1970 / homozygous normal
14 / Susi / f / 794 / wb ~1960 / heterozygous
15 / Temmy / f / 1852 / 07.12.1981 / heterozygous
16 / Thai / m / 2861 / 25.04.1998 / heterozygous
17 / Thilda / f / 1452 / wb ~1967 / homozygous normal
18 / Tjantike / f / 1012 / wb ~1967 / homozygous normal
19 / Tuan / m / 1685 / 18.09.1978 / homozygous normal
20 / Wattana / f / 2721 / 17.11.1995 / homozygous normal
21 / Yogi/Joki / m / 828 / wb ~1964 / homozygous normal
2002 International studbook of the orang-utan (Pongo pygmaeus, Pongo abelii); Lori Perkins, studbook keeper, Lincoln Park Zoo, 2001 North Clark Street, Chicago, IL 60614, USA.
Orang-Utan Europäisches Erhaltungszuchtprogramm, Zuchtbuch für Europa XXVII/2009; Clemens Becker, Zuchtbuchführer und EEP-Koordinator, Zoo Karlsruhe, Ettlinger Strasse 6, D-76137 Karlsruhe.
wb: wild-born
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Table 3: Hybrid Sumatra/Bornean orang-utan specimens – ENC polymorphism Chromosome 9
Name / Sex / Stud # / Birth Date / Chromosome 9 status / Parents1 / Bassir II / m / 2423 / 21.09.1991 / homozygous normal
2 / Bulu / m / 1741 / 29.12.1979 / heterozygous / Dam Elsi
3 / Kasih / f / 485 / 19.03.1962 / homozygous normal
4 / Katai / m / 2039 / 07.02.1985 / homozygous normal
5 / Kupang / m / 2146 / 12.11.1987 / heterozygous / Dam Elsi
6 / Pendek / m / 1636 / 23.01.1978 / homozygous normal
7 / Shinta / f / 2603 / 01.02.1993 / heterozygous / Dam Sumbo
8 / Sumbo / m / 1942 / 13.10.1983 / heterozygous / Dam Elsi
2002 International studbook of the orang-utan (Pongo pygmaeus, Pongo abelii); Lori Perkins, studbook keeper, Lincoln Park Zoo, 2001 North Clark Street, Chicago, IL 60614, USA.
Orang-Utan Europäisches Erhaltungszuchtprogramm, Zuchtbuch für Europa XXVII/2009; Clemens Becker, Zuchtbuchführer und EEP-Koordinator, Zoo Karlsruhe, Ettlinger Strasse 6, D-76137 Karlsruhe.
wb: wild-born
Saimiri genus taxonomy
Combining the taxa distinguished by Groves (2001)(Groves, 2001) with the cytogenetic findings the taxonomy can be summarized as follows:
1. S. boliviensis
S.b. boliviensis (Bolivia, Brazil, Peru) with 6 acrocentric and 15 SM chromosomes
S.b. peruviensis (Peru, between rivers Huallanga and Tapiche) with 5 acrocentric (A) and 16 submetacentric (SM) chromosomes
2. S. oerstedii with 5 A 16 SM chromosomes
S.o. oerstedii(Panama, Costa Rica,
S.o. citrinellus (Rio Panita Basin in Costa Rica)
3. S. Sciureus
S.s. sciureus (northern Brazil, Guyana) with 7 A and 14 SM chromosomes
S.s. albigena (Columbia)
S.s. cassiquiarensis (Apopris and Jura River basins)
S.s. macrodon (Equador) with 6 A and 15 SM chromosomes
4. S. ustus (Brazil)
5. S. vanzolinii (Central Amazon) with 6 A and 15 SM chromosomes.
The various cytogenetic reports use a confusing array of numbering systems. For instance, the two chromosomes recognized as variable were inconsistently numbered. Jones and Ma (1975)(Jones and Ma, 1975) even refered to one variable pair as 10 when it was a submetacentric, 17 when it was an acrocentric while the other smaller chromosome was called 15 when it is a submetacentric and 18 when it was an acrocentric. Lau and Arrigni (1976)(Lau and Arrighi, 1976), Moore et al. (1990)(Moore et al., 1990), and Scammell et al. (2001)(Scammell et al., 2001) refered to them as 15 and 16. Camberfort and Moro (1978)(Cambefort and Moro, 1978) refered to them as chromosomes 14 and 15, Dutrillaux and Couturier (1981)(Dutrillaux and Couturier, 1981) as 15 and 17, Yanenaga-Yassuda and Chu (1985) (Yonenaga-Yassuda and Chu, 1985) and Minezawa et al. (1990)(Minezawa et al., 1990) as 10 and 16. Garcia et al. (1995) (Garcia et al., 1995) reverted to a double numbering system: B5, C1 and B10, C2. In these paper the chromosomes are numbered according to length and defined the Saimiri karyotype on the basis of chromosome painting and reciprocal chromosome painting respectively (Dumas et al., 2007; Stanyon et al., 2000). The chromosomes, which vary are chromosomes 5 and 15, homologous to human chromosomes 12 and 8q respectively.The finding of at least one wild caught squirrel monkey which was polymorphic for both inversions on chromosomes 5 and 15 raised the possibility that some taxa may be polymorphic for these pericentric inversions as well as the X-chromosome. In any case, given the current assessment of phylogenetic relationships with squirrel monkeys (Chiou et al., 2011; Lavergne et al., 2010; Perelman et al., 2011) it is almost certain that lineage sorting accounts for the present day distribution pattern (the inversion of chromosome 5 and 15 where likely polymorphic in the last common ancestor).
The Supplementary Figure 1 shows the Saimiri sciureus sciureus karyotype DAPI banded (below) and G-banded (above). The nomenclature is according to Stanyon et al. (2000) and Dumas et al. (2007). In parenthesis is reported, for the variant chromosomes only, the nomenclature used by Scammel et al. (2001). The ideograms on the right show the human synteny. The boxed chromosomes on the right are reported the variant chromosomes of Saimiri boliviensis boliviensis (SBOb) and S.b. peruviensis (SBOp).
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