Molecular Ecology (2005) 14, 441–456 doi: 10.1111/j.1365-294X.2004.02421.x © 2005 Blackwell Publishing Ltd Blackwell Publishing, Ltd. Patterns of genetic diversity and migration in increasingly fragmented and declining orang-utan (Pongo pygmaeus) populations from Sabah, Malaysia B. GOOSSENS,*†‡§ L. CHIKHI,§ M. F. JALIL,*‡ M. ANCRENAZ,† I. LACKMAN-ANCRENAZ,† M. MOHAMED, ‡ P. ANDAU ¶ and M. W. BRUFORD * * Biodiversity and Ecological Processes Group, Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3TL, UK, † Kinabatangan Orang-utan Conservation Project, PO Box 3109, 90734 Sandakan, Sabah, Malaysia, ‡ Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah, Locked Bag 2073, 88999 Kota Kinabalu, Sabah, Malaysia, § UMR 5174 Evolution et Diversité Biologique, Bâtiment 4R3b2, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse cédex 4, France, ¶ Sabah Wildlife Department, Muis Complex, 88100 Kota Kinabalu, Sabah, Malaysia Abstract We investigated the genetic structure within and among Bornean orang-utans (Pongo pyg- maeus) in forest fragments of the Lower Kinabatangan flood plain in Sabah, Malaysia. DNA was extracted from hair and faecal samples for 200 wild individuals collected during boat surveys on the Kinabatangan River. Fourteen microsatellite loci were used to charac- terize patterns of genetic diversity. We found that genetic diversity was high in the set of samples (mean H E = 0.74) and that genetic differentiation was significant between the sam- ples (average F ST = 0.04, P < 0.001) with F ST values ranging from low (0.01) to moderately large (0.12) values. Pairwise F ST values were significantly higher across the Kinabatangan River than between samples from the same river side, thereby confirming the role of the river as a natural barrier to gene flow. The correlation between genetic and geographical distance was tested by means of a series of Mantel tests based on different measures of geo- graphical distance. We used a Bayesian method to estimate immigration rates. The results indicate that migration is unlikely across the river but cannot be completely ruled out because of the limited F ST values. Assignment tests confirm the overall picture that gene flow is limited across the river. We found that migration between samples from the same side of the river had a high probability indicating that orang-utans used to move relatively freely between neighbouring areas. This strongly suggests that there is a need to maintain migration between isolated forest fragments. This could be done by restoring forest corri- dors alongside the river banks and between patches. Keywords: genetic diversity, immigration, microsatellites, noninvasive sampling, Pongo pygmaeus, population fragmentation Received 3 August 2004; revision received 19 October 2004; accepted 22 October 2004 Introduction Current trends in great ape populations indicate a dramatic ongoing decline, which is predicted to result in the extin- ction of ape species in the wild for entire regions in the near future. Recent findings have particularly focused on African apes, and have implicated multiple factors, such as deforestation, hunting and disease (Walsh et al . 2003; Leendertz et al . 2004; Leroy et al . 2004). Less well pub- licised, but equally dramatic, has been the decline in Asia’s only great ape, the orang-utan species of Sumatra and Borneo ( Pongo abelii and Pongo pygmaeus ). Current trends suggest that extinction is potentially imminent for the Sumatran species in the wild and although anthropogenic pressures are equally severe in parts of the orang-utan’s range in Borneo, some potentially viable populations remain. On both islands, orang-utans exist now mainly in frag- mented and isolated populations, the sizes of which are Correspondence: Benoît Goossens, Fax: + 33 5 61 55 73 27; E-mail: goossensbr@cardiff.ac.uk