ficient samples such as blood or tissue. We overcome this problem by using genetic samples non-invasively collected from tiger scats to assess genetic variation, phylogeography and demographic history of tigers in the Indian subcontinent.
In this paper we investigate (1) the proportion of global tiger genetic variation harboured by tigers in the Indian subcontinent and (2) the demographic history of tigers in the Indian subcontinent, with a synthesis based on historical population sizes and recent human impacts. We address these questions using 1.26 kb of mitochondrial DNA and 10 microsatellite loci surveyed in 73 individual tigers from 28 different populations, and compare our results to published data from 68 tigers outside the Indian subcontinent.
Our sampling strategy concentrated on tiger populations living in varied habitats throughout the Indian subcontinent. Using 71 (Table S1) non-invasively collected fecal samples and two tissue samples from across the Indian subcontinent, we investigated genetic variability of Indian tigers using mtDNA and microsatellite loci. Our results reveal that Indian tigers have much higher genetic variation than wild tigers elsewhere. For mitochondrial DNA, 76% of all tiger genetic variability (32 out of 42 haplotypes) is found within the Indian subcontinent (Figure 1A). These results are robust to differences in sample size (67 within India versus 57 outside India). Re-sampling simulations reveal that if only 57 Indian tigers were sampled, we would expect between 18 and 25 haplotypes, much higher than the observed 10 haplotypes. Similarly, five microsatellite loci reveal higher average number of alleles (Table 1), allelic size range (Table 1) and heterozygosity (Table 1) in Indian subcontinent tigers compared to tigers from the rest of the world. Additionally, the program STRUCTURE  (based on five loci) illustrates that Indian tigers retain high allelic richness and varied ancestry (Figure 1B). Thus both markers and several analyses suggest higher genetic variability within the Indian subcontinent compared to any other subspecies, as well as all compared to all tiger subspecies outside the Indian subcontinent (Figure 1, Table 1).
(A) A haplotype network based on 1,263 bp of mitochondrial DNA reveals that 76% of global tiger genetic variation (32 haplotypes out of 42) is retained within the Indian subcontinent. Locations of each haplotype within India correspond only approximately to the site of sample collection. 71 samples are included from Myanmar, Nepal, and India. All samples from outside India are from Luo et al., 2004 . (B) The partitioning of microsatellite genetic variation based on 5 common microsatellite loci between different sub-species of tigers, with program STRUCTURE (k = 5). Individuals within the Indian subcontinent are the most variable, indicated by the fact that all 5 colours are present, compared to other subspecies, which retain only one colour (e.g. Siberian tigers). All samples from outside India are from Luo et al., 2004 .
Viewed alone, this higher genetic variability observed within the Indian subcontinent is concordant with India being the geographic source for tigers. However, fossil evidence suggests that the tiger evolved in southern China . Phylogenetic and phylogeographic data  suggest the genetic antiquity of the Indochinese tigers (very limited samples from South China tigers), and that Indian tigers are of relatively recent origin. Coalescent-based two population models (LAMARC ; Indian subcontinent tigers versus Indochinese tigers) based on both mitochondrial DNA and microsatellite data (based on five loci) estimate significantly higher immigration into the Indian subcontinent [MLEmtDNA (maximum likelihood estimate) = 185.8 (44.72, 486.63); MLEmicrosats = 36.82 (31.17, 40.40)] compared to emigration [MLEmtDNA = 0.19 (0.000001, 59.84); MLEmicrosats = 13.77 (11.31, 15.32)] out of the subcontinent. Although not conclusive, these independent lines of evidence suggest that Indian tigers are not ancestral to the species.
The higher genetic diversity of In