A multiplex-system to target 16 male-specific and 15 autosomal genetic markers for orang-utans (genus: Pongo)
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Genetic studies of dispersal on local spatial and short temporal scales require a large number of autosomal microsatellites. However, the study of dispersal over large spatial scales and the resolution of deep evolutionary histories require marker systems that are preferentially inherited through the male or female line. Addressing such questions in endangered orang-utans (genus: Pongo) bears significant relevance to species conservation, as habitat destruction and fragmentation pose a significant threat to the whole genus. Here, we report 16 male-specific markers (nine human-derived microsatellites, six single nucleotide and one insertion-deletion polymorphisms), and 15 novel Pongo-derived autosomal microsatellite loci. All 31 markers can be amplified in four multiplex polymerase chain reactions even in DNA derived from faecal material. The markers can be applied to studying a wide range of important questions in this genus, such as conservation genetics, social structure, phylogeny and phylogeography.
KeywordsPongo spp. Single nucleotide polymorphisms Microsatellites Y chromosome SNP typing Non-invasive samples
We thank C. van Schaik, M. van Noordwijk, J. Pamungkas, and D. Perwitasari-Farajallah. We are also indebted to all individuals who helped collecting samples in the field. This study was funded by the Swiss National Science Foundation (31003A-116848 to MK), Messerli Foundation, A.H.-Schultz Stiftung, and Claraz Schenkung. We thank the Indonesian Institute of Sciences (LIPI), the Indonesian State Ministry for Research and Technology (RISTEK), and the Sabah Wildlife Department for granting permission to undertake this research. All sampling and transportation of samples was conducted in accordance with Indonesian, Malaysian and international regulations (CITES).
- Goossens B, Chikhi L, Jalil MF, Ancrenaz M, Lackman-Ancrenaz I, Mohamed M, Andau P, Bruford MW (2005) Patterns of genetic diversity and migration in increasingly fragmented and declining orang-utan (Pongo pygmaeus) populations from Sabah, Malaysia. Mol Ecol 14(2):441–456. doi:10.1111/j.1365-294X.02421.x CrossRefPubMedGoogle Scholar
- Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New YorkGoogle Scholar
- Nietlisbach P (2009) Male-specific markers in orang-utans (Pongo spp.)—Dispersal and phylogeny. MSc thesis. University of ZurichGoogle Scholar
- Park SDE (2001) Trypanotolerance in West African cattle and the population genetic effects of selection. University of Dublin, Dublin, IrelandGoogle Scholar
- Warren KS, Verschoor EJ, Langenhuijzen S, Heriyanto, Swan RA, Vigilant L, Heeney JL (2001) Speciation and intrasubspecific variation of Bornean orang-utans, Pongo pygmaeus pygmaeus. Mol Biol Evol 18 (4):472-480Google Scholar
- Wich SA, Meijaard E, Marshall AJ, Husson S, Ancrenaz M, Lacy RC, van Schaik CP, Sugardjito J, Simorangkir T, Traylor-Holzer K, Doughty M, Supriatna J, Dennis R, Gumal M, Knott CD, Singleton I (2008) Distribution and conservation status of the orang-utan (Pongo spp.) on Borneo and Sumatra: how many remain? Oryx 42(3):329–339. doi:10.1017/s003060530800197x CrossRefGoogle Scholar