Abstract
Bornean orang-utans experienced a major demographic decline and local extirpations during the Pleistocene and Holocene due to climate change, the arrival of modern humans, of farmers and recent commercially-driven habitat loss and fragmentation. The recent loss of habitat and its dramatic fragmentation has affected the patterns of genetic variability and differentiation among the remaining populations and increased the extinction risk of the most isolated ones. However, the contribution of recent demographic events to such genetic patterns is still not fully clear. Indeed, it can be difficult to separate the effects of recent anthropogenic fragmentation from the genetic signature of prehistoric demographic events. Here, we investigated the genetic structure and population size dynamics of orang-utans from different sites. Altogether 126 individuals were analyzed and a full-likelihood Bayesian approach was applied. All sites exhibited clear signals of population decline. Population structure is known to generate spurious bottleneck signals and we found that it does indeed contribute to the signals observed. However, population structure alone does not easily explain the observed patterns. The dating of the population decline varied across sites but was always within the 200–2000 years period. This suggests that in some sites at least, orang-utan populations were affected by demographic events that started before the recent anthropogenic effects that occurred in Borneo. These results do not mean that the recent forest exploitation did not leave its genetic mark on orang-utans but suggests that the genetic pool of orang-utans is also impacted by more ancient events. While we cannot identify the main cause for this decline, our results suggests that the decline may be related to the arrival of the first farmers or climatic events, and that more theoretical work is needed to understand how multiple demographic events impact the genome of species and how we can assess their relative contributions.
Highlights
Genetic data are increasingly used to infer the demographic history of natural populations, such as population size changes, gene flow/connectivity between populations and other processes that influenced species over millennia [1,2,3]
We have shown that Bornean orang-utans underwent at least one population collapse, and that this is not due to confounding effect of population structure
We cannot exclude the possibility that other events have generated this genetic signature
Summary
Genetic data are increasingly used to infer the demographic history of natural populations, such as population size changes, gene flow/connectivity between populations and other processes that influenced species over millennia [1,2,3]. The last couple of decades have seen an increase in the use of full likelihood-based methods and software to estimate important demographic parameters [2,3,8,9,10,11,12,13] Even though these methods provide important insights into the demographic history of the species studied, their power to infer demographic processes in natural populations are still being explored and under much debate, when trying to understand the combined or confounding effect of population size change, structure and fragmentation [14,15,16,17,18]. Reports from early explorers and naturalists in the 19th century suggest that wild orang-utans in these islands were historically encountered at high densities across their distribution range [20]
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