y the British and first written history of tiger hunting by Mughals respectively. (D) The joint posterior distribution of ancestral and present effective population size based on Indian tiger data. The 90%, 50%, and 10% highest probability density (HPD) limits are plotted for the joint distribution of ancestral and current population size on a logarithmic scale. The diagonal line corresponds to stable population size.
We investigated the sensitivity of our results on demographic history to the number of genetic loci. Coalescent simulations that included 5 wild caught tigers (data from 13) genotyped at 30 microsatellite loci also revealed a very similar extent and timing of demographic decline (Figure S3). Further, using genetic data from tigers across the Indian subcontinent resulted in similar extent of population decline (Figure S2). Our sensitivity analyses re-iterate that the extent of demographic decline and its timing are robust to population structure as well as increased genetic data.
An assessment of genetic variation for tigers reveals tigers in the Indian subcontinent retain more than 60% of the genetic variability of the species. In this study, we have taken extreme care to sample Indian tigers in a spatially exhaustive way. However, our results are also conditional on adequate sampling of tiger variation outside the India. Future studies might also include additional sampling of wild tigers outside the Indian subcontinent. Additionally, data from captive tigers of known origin could also be used to investigate discrepancies in genetic variation.
Indian subcontinent tigers could retain higher genetic variation not only because they had high historical population size but also because other tiger subspecies declined more severely in the recent past. Single population models in LAMARC for Indochinese tigers using the microsatellite data also exhibit a signature of recent population decline (MLE of g = −0.881825 (−1.29, −0.560142)), although lower than the estimated decline for Indian tigers. We also quantified the timing and extent of demographic decline, and simulations revealed a relatively recent decline (158 years ago, Figure S6, Figure S7, and Figure S8) of about the same magnitude (90%) as for Central and South Indian tigers. However, the median ancestral effective size for Indochinese tigers was much lower than that of the Indian tigers in central and south India (23,280). The higher ancestral effective size explains the higher genetic variation among extant Indian tigers inspite of recent, human induced decline.
Data from mitochondrial DNA potentially reveal a signal of demographic expansion, while microsatellite data reveal a signal of a recent population decline. The strong population differentiation for mitochondrial DNA (Table 2) could also result in the observed, expansion-like pattern  and the resultant high mitochondrial genetic diversity in this part of the species' range.
Our genetic data in combination with a series of simulation models suggests that prior to historical human impacts, the genetic effective population size for tigers from peninsular India was between 2,964 and 151,008, with a median value of 23,280. Converting this effective population size into a population size suggests that between 7,412 and 377,520, with a median of 58,202 (using Ne/N = 0.4 , where Ne is the effective population size and N is the census size) adult wild tigers inhabited peninsular India prior to these human impacts. Given the recent census estimate of around 1,000 adult tigers in peninsular India , this corresponds to a median decline of approximately 98% over the last 200 years. Major demographic declines are evidenced by historical hunting records (based on bounty killings) during the Colonial rule, which suggest that over 80,000 tigers were hunted for bounties between 1875 and 1925  across the Indian subcontinent. These data potentially indicate an even higher historical population size for tigers than do our results. However, the demographic decline we detect is in the face of high potential annual grow