Electronic Data Supplement: Male Orang-Utan Bimaturism and Reproductive Success at Camp

Electronic data supplement: Male orang-utan bimaturism and reproductive success at
Camp Leakey in Tanjung Puting National Park, Indonesia
(Behavioral Ecology and Sociobiology)

Authors

Graham L Banes123, Biruté M F Galdikas4 and Linda Vigilant3

Author affiliations

1School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, AB24 2TZ, United Kingdom.

2Division of Biological Anthropology, Department of Archaeology and Anthropology, University of Cambridge, Pembroke Street, Cambridge, CB2 3QY, United Kingdom.

3Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.

4Department of Archaeology, Simon Fraser University, 8888 University Drive, Burnaby, B.C., V5A 1S6, Canada.

Corresponding author

Dr Graham L Banes, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany. .

Table S1 Autosomal microsatellite and sex-linked loci co-amplified in the multiplex stage. Multiple PCR products were then ‘singleplexed’ using a fluorescently-labelled forward primer at a locus-specific annealing temperature (Ta), prior to DNA size fragment analysis. ‘-‘ indicates loci that were not singleplexed for this study. References refer to the first known instance where these loci were used in orang-utans.

locus / label / forward primer sequence (5’ – 3’) / reverse primer sequence (5’ – 3’) / Ta (oC) / reference
D1S550 / FAM / CCTGTTGCCACCTACAAAAG / TAAGTTAGTTCAAATTCATCAGTGC / 59 / Zhang et al. (2001)
D2S1326 / FAM / AGACAGTCAAGAATAACTGCCC / CTGTGGCTCAAAAGCTGAAT / 57 / Zhang et al. (2001)
D3S2459 / HEX / CTGGTTTGGGTCTGTTATGG / AGGGACTTAGAAAGATAGCAGG / 57 / Zhang et al. (2001)
D4S1627 / NED / AGCATTAGCATTTGTCCTGG / GACTAACCTGACTCCCCCTC / 57 / Zhang et al. (2001)
D4S2408 / FAM / AATAAACTTCAACTTCAATTCATCC / AGGTAAAGGCTCTTCTTGGC / 57 / Zhang et al. (2001)
D5S1457 / FAM / TAGGTTCTGGGCATGTCTGT / TGCTTGGCACACTTCAGG / 57 / Kanthaswamy & Smith (2002)
D5S1470 / HEX / CATGCACAGTGTGTTTACTGG / TAGGATTTTACTATATTCCCCAGG / 59 / Kanthaswamy & Smith (2002)
D5S1505 / FAM / TAAGTGCCAGAGTCTCCCAC / TAAGGCATGTCTCGGAGCTA / 59 / Zhang et al. (2001)
D6S501 / NED / GCTGGAAACTGATAAGGGCT / GCCACCCTGGCTAAGTTACT / 59 / Zhang et al. (2001)
D12S375 / HEX / TTGTTGAGGGTCTTTCTCCA / TCTTCTTATTTGGAAAAGTAACCC / 59 / Utami et al. (2002)
D13S765 / HEX / TGTAACTTACTTCAAATGGCTCA / TTGAAACTTACAGACAGCTTGC / 59 / Zhang et al. (2001)
O4_A5 / - / ATGGGCCCAGAAAACAACTCAGT / AGATAAAGGAATGGATAGATGGACAGA / - / Nietlisbach et al. (2010)
O4_B6 / NED / TGGAGCCTGAATATGTGACTGAAT / AATGCCAGGATTTCCTTCTTTTT / 59 / Nietlisbach et al. (2010)
O4_B17 / - / GTACCGACGGTGCACGAACAATGTA / AGCCTGGCTGAAAAGTGGAACTGAG / - / Nietlisbach et al. (2010)
SRY / HEX / AGTGAAGCGACCCATGAACG / TGTGCCTCCTGGAAGAATGG / 58 / Di Fiore (2005)
AMEL / FAM / ACCACCAGCTTCCCAGTTTA / GCTGGGWTAGAACCAAGCTG / 58 / Di Fiore (2005)

Statistics for microsatellite loci

The mean proportion of individuals typed was 0.9556 across 11 loci, of which the mean number of alleles per locus was 5.64. The mean expected heterozygosity over all loci was 0.6785, ranging from 0.4222 to 0.8572 per locus, and the mean observed heterozygosity was 0.7035, ranging from 0.3636 to 0.9111 per locus(Kalinowski et al., 2007). Further statistics are detailed in Table S2.

TableS2Summary statistics for the 11 microsatellite loci used in paternity analyses. ‘He’ and ‘Ho’ are the mean expected and observed heterozygosity values, respectively. ‘HWE-p’ indicates the p values for the significance of deviation from Hardy-Weinberg equilibrium, none of which were significant after Bonferroni correction.

Locus / No. of alleles / N / Heterozygotes / Homozygotes / He / Ho / HWE-p
D5S1457 / 7 / 45 / 41 / 4 / 0.7833 / 0.9111 / 0.1175
D4S2408 / 6 / 42 / 30 / 12 / 0.7401 / 0.7143 / 0.1802
D3S2459 / 7 / 44 / 35 / 9 / 0.7939 / 0.7955 / 0.3584
D6S501 / 6 / 45 / 39 / 6 / 0.6969 / 0.8667 / 0.0437
D5S1470 / 4 / 43 / 29 / 14 / 0.6268 / 0.6744 / 0.9538
D2S1326 / 3 / 44 / 16 / 28 / 0.4222 / 0.3636 / 0.2713
D12S375 / 4 / 41 / 25 / 16 / 0.5297 / 0.6098 / 0.1538
O4_B6 / 9 / 43 / 34 / 9 / 0.8572 / 0.7907 / 0.2843
D5S1505 / 7 / 40 / 33 / 7 / 0.7301 / 0.8250 / 0.8181
D13S765 / 5 / 45 / 26 / 19 / 0.6255 / 0.5778 / 0.7552
D4S1627 / 4 / 41 / 25 / 16 / 0.6573 / 0.6098 / 0.2862

TableS3Known, identifiable orang-utans that were sampled and genotyped for this study. ‘Mother' indicates that an individual's mother, and her genotype, are known. 'Status' denotes age and reproductive state; ‘-‘ is used when the individual was unborn. Young, dependent orang-utans are described as either infant (0-4 years) or juvenile (4-8 years). To avoid ambiguity, older males are described as 'unflanged' and older females as 'nulliparous'.* identifies orang-utans whose genotypes were used to test for linkage disequilibrium.‘X’ indicates that an individual was included as a candidate in parentage analyses.

Status / Included as candidate
Orang-utan / Sex / Mother / 1995 / 2003 / 2006 / Mother / Father / Offspring
OU1* / F / Multiparous / Multiparous / Multiparous / X
OU2* / F / Nulliparous / Primiparous / Multiparous / X / X
OU3 / F / OU1 / - / Juvenile / Nulliparous / X
OU4 / F / OU2 / - / Infant / Juvenile / X
OU5* / F / Primiparous / Multiparous / Multiparous / X
OU6 / F / OU5 / - / Juvenile / Nulliparous / X / X
OU7 / M / OU8 / - / Infant / Infant / X / X
OU8* / F / Multiparous / Multiparous / Multiparous / X
OU9 / F / OU8 / Primiparous / Primiparous / Multiparous / X / X
OU10 / F / OU9 / - / - / Infant / X
Kusasi* / M / Flanged / Flanged / Flanged / X
OU11* / F / Nulliparous / Multiparous / Multiparous / X
OU12 / M / OU13 / - / - / Infant / X
OU13* / F / Multiparous / Multiparous / Multiparous / X
OU14 / M / OU13 / Infant / Juvenile / Unflanged / X / X
OU15 / M / OU18 / Infant / Unflanged / Unflanged / X / X
OU16 / M / OU18 / - / Infant / Juvenile / X / X
OU17 / F / OU18 / Juvenile / Primiparous / Multiparous / X
Ponorogo* / M / Unknown / Flanged / Flanged / X / X
OU18* / F / Multiparous / Multiparous / Multiparous / X
OU19 / F / OU18 / - / - / - / X
OU20 / F / OU24 / - / Juvenile / Nulliparous / X / X
OU21* / F / Multiparous / Multiparous / Multiparous / X
OU22 / M / OU21 / - / Infant / Juvenile / X / X
OU23 / M / OU21 / - / - / Infant / X

Table S3Continued

Status / Included as candidate
Orang-utan / Sex / Mother / 1995 / 2003 / 2006 / Mother / Father / Offspring
OU24 / F / OU21 / Adolescent / Multiparous / Multiparous / X / X
OU25 / M / OU24 / - / Infant / Juvenile / X / X
Sampson / M / OU26 / Infant / Unflanged / Unflanged / X / X
OU26* / F / Multiparous / Multiparous / Multiparous / X
OU27* / F / Juvenile / Primiparous / Multiparous / X
OU28 / M / OU33 / - / Infant / Juvenile / X / X
OU29 / M / OU33 / - / - / - / X
OU30 / M / OU33 / - / - / Infant / X
OU31 / M / OU33 / Unflanged / Flanged / Flanged / X / X
OU32 / F / OU27 / - / - / Infant / X
OU33* / F / Multiparous / Multiparous / Multiparous / X
OU34 / F / OU35 / - / Juvenile / Nulliparous / X
OU35* / F / Multiparous / Multiparous / Multiparous / X
OU36 / M / OU35 / Unflanged / Unflanged / Flanged / X / X

TableS4Unknown, unidentifiable orang-utans that were sampled and genotyped for this study. 'Status' denotes age and reproductive state at the time of sample collection, either in the field season conducted from 2008-2009 or that in 2010-2011. ‘X’ indicates that an individual was included as a candidate in parentage analyses. The genotypes of all these orang-utans were used in the test for linkage disequilibrium.

Status / Included as candidate
Orang-utan / Sex / 2008 / 2011 / Father / Offspring
UK1 / M / Unknown / Transitioning / X / X
UK2 / M / Unknown / Unflanged / X / X
UK3 / M / Unknown / Unflanged / X / X
UK4 / M / Unknown / Juvenile/Unflanged / X
UK5 / M / Flanged / Flanged / X / X
UK6 / M / Unknown / Flanged / X / X

References

Di Fiore A(2005) A rapid genetic method for sex assignment in non-human primates.Conserv Genet6:1053-1058.

Kalinowski ST, Taper, ML,Marshall TC(2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. MolEcol16:1099–106.

Kanthaswamy S, Smith DG(2002) Population subdivision and gene flow amongwild orangutans. Primates43:315–27.

Nietlisbach P, Nater A, Greminger MP, Arora N,Krützen, M(2010) Amultiplex-system to target 16 male-specific and 15 autosomal genetic markers for orangutans (genus: Pongo). Conserv Genet Res 2:153-158.

Utami SS, Goossens B, Bruford MW, de Ruiter JR, van Hooff JARAM(2002) Male bimaturism and reproductive success in Sumatran orang-utans. BehavEcol 13:643–652.

Zhang Y, Morin PA, Ryder OA, Zhang Y(2001) A set of human tri-and tetra nucleotide microsatellite loci useful for population analyses in gorillas (Gorilla gorilla gorilla) and orangutans (Pongo pygmaeus). Conserv Genet 2:391-395.