Population genetics and structure of the Sumatran tiger

The two key determinants of population persistence in fragmented landscapes are population size and connectivity. Populations with high levels of genetic variation and large population size are expected to have a lower risk of extinction. Similarly, populations with high rates of connectivity are expected to persist long-term. For many elusive landscape species it is difficult to obtain direct estimates of these parameters, but genetic sampling can offer powerful indirect assessments. Whilst these techniques have been applied to the study of many wide-ranging carnivores, this study represents the first example in the Sumatran tiger (Panthera tigris sumatrae). Extensive field surveys were conducted to collect faecal samples from several Tiger Conservation Landscapes and protected areas on Sumatra. Samples were then processed according to optimised protocols to obtain reliable results. In order to quantify extinction risk I first estimated genetic variation and effective population size using microsatellite loci. I also determined relative levels of connectivity using estimates of differentiation (FST), gene flow and genetic clustering. Results indicate that Sumatran tigers have high levels of genetic variation and that their effective population size is within the expected range. There is very little population structure and there is no obvious evidence for barriers to dispersal. The Batang Hari/Kerinci Seblat ecosystem emerged as a potential source population and in contrast there was some evidence of isolation affecting the population of Way Kambas NP in the extreme south of the island. Overall, despite high levels of human land cover conversion over the past 20-30 years, few genetic changes have been expressed in the Sumatran tiger. The immediate threat to tigers is not the loss of genetic diversity, but the rapidly declining area of suitable habitat in which they can survive

Emerging patterns of genetic diversity in the critically endangered Malayan tiger (Panthera tigris jacksoni)

Southeast Asia experiences some of the highest deforestation in the world. Loss of tropical forest typically leads to widespread habitat fragmentation, with detrimental effects on dispersal ability and gene flow—particularly for large carnivores. We conducted mtDNA and microsatellite analysis to assess—for the first time—contemporary patterns of genetic diversity in the Malayan tiger. We collected 295 suspected carnivore samples in Peninsular Malaysia, from which we identified 26 as originating from tiger using 16 polymorphic microsatellite loci, comprising 22 individual tigers. Despite limitations of the study, our findings suggest tiger subpopulations in the north of the peninsula maintain some genetic connectivity and migration between two putative geographic subpopulations in the Main Range and Greater Taman Negara, with negligible population segregation due to dispersal barriers such as road infrastructure. We identified consistently lower levels of genetic diversity in tigers in the Greater Taman Negara region compared to tigers in the Main Range and small but emerging differences in nuclear and mitochondrial genetic diversity. Our mtDNA haplotype and nuclear DNA analyses suggest the levels of genetic diversity in Malayan tigers may be amongst some of the lowest of the surviving tiger subspecies, though the study is limited both in scale and genomic loci. Our findings are consistent with an expected lag between the rapid decline of tigers in Peninsular Malaysia by over 95% in the last 70 years and observed differences in their levels of genetic diversity

Evaluating the effect of forest loss and agricultural expansion on Sumatran tigers from scat surveys

Sumatran tigers (Panthera tigris sumatrae) are a critically endangered carnivore restricted to the island of Sumatra, and like many other large mammals on the Indonesian archipelago, they are threatened by high levels of poaching and widespread habitat degradation. Here, we conduct the first range-wide assessment of Sumatran tiger genetics using scat surveys and show that the wild population retains levels of genetic heterozygosity comparable to mainland tigers. However, the population also exhibits signs of subdivision due to the unprecedented rates of deforestation and land conversion in the last 30–40 years. The fact that this subspecies retains such levels of heterozygosity despite high rates of habitat loss and increasing isolation suggests a form of genetic extinction debt with an elevated risk of extinction if no action is taken within the next 30–100 years (see Kenney et al., 2014). However, the inherent time delay in extinction debt provides opportunities for conservation if habitat quality can be improved and connections between existing population fragments can be made. Our study highlights the importance of genetic studies for providing baseline information to improve the population management of highly threatened carnivore species. Mitigating further habitat degradation and expansion of oil palm and other cash crops in this region would improve the viability not only of Sumatran tiger populations, but of other threatened large mammal species as well