- Molecular studies have confirmed that there are at least four tiger subspecies that are genetically distinct and that each may require unique conservation strategies.
- Though Indian tigers have the most genetic diversity, they also show population sub-structuring and signs of recent inbreeding.
- In Simlipal, Odisha, a unique genetic mutation affecting the patterns on tiger coats, giving rise to the ‘black tiger’, has been found to occur at a high frequency in this region’s small and isolated tiger population.
- Overall, these data indicate that genomic perspectives are necessary for managerial decisions regarding tiger conservation efforts.
Tigers once roamed the lands from Turkey in the west to the Amur river basin in the east, across south and southeast Asia all the way to the island of Bali in Indonesia. Exploding human populations nearly wiped out tigers in the 20th century. Today, the world has lost more than 90% of the tiger population, with fewer than 3900 wild tigers surviving in just 4% of their historical range. Global tiger conservation efforts, however, have hit many roadblocks. One of the most serious is a lack of clarity on the tigers’ evolutionary and genetic histories. Unpacking these can strengthen conservation efforts. However, much of the knowledge of the evolutionary histories and genomic variation in tigers, especially Indian tigers, is only now being generated.
In an example of the efforts underway to unravel these sets of information, Indian scientists have zeroed in on the gene mutation that makes a small isolated population of tigers in Similipal forests in India unique: the ‘black tigers’ with broader and darker stripes that appear to be leaking into the tawny background of their coats.
Experts say genetic data can inform genetic rescue efforts which involves reviving the genetic diversity of a small, isolated, and often inbred population by introducing individuals from other populations.
How many tiger subspecies are there in the world?
Tigers are divided into six living subspecies based on molecular genetic evidence. They are Panthera tigris tigris (Bengal tigers), P. t. altaica (Amur tigers), P.t. amoyensis (South China tigers), P.t. sumatrae (Sumatran tigers), P.t. corbetti (Indochinese tigers), and P.t. jacksoni (Malayan tigers).
In 2015, however, according to purely physical characteristics and ecological analyses, a reclassification of tigers into two subspecies, P.t. tigris in continental Asia and P.t. sondaica in the Sunda Islands, was proposed. Such conflicting information can have huge effects on strategic conservation planning and management actions.
However, this controversy has been resolved in the light of two (somewhat) recent molecular studies that investigated the evolutionary histories of tigers. Both studies — one by a Chinese group in 2018 and the other by an international consortium of researchers in 2020 — have confirmed more than two living tiger subspecies.
Both studies further conclude that several factors have divided tigers into discrete subspecies. These factors are likely to be bottleneck events (natural or man-made disasters that drastically reduce population sizes of organisms), geographic isolation, and natural selection (a process by which organisms that are better adapted to an environment, survive, and pass on the genes that aided survival)
Ongoing natural selection in tigers
Further analysis of genetic data in each subspecies indicates that the Amur and Sumatran tigers are subject to natural selection.
In the Amur tigers’ genomes, many genes related to fat metabolism and energy generation show signs of being under active selection, suggesting that Amur tigers may be evolving specific adaptations to colder environments. Analyses of the Sumatran tiger genomes indicate that genes related to anatomical and morphological development are under selection, which means that selection for small body size and darker coloration may occur in these tigers. Since Sumatran tigers typically live in darker forested habitats with smaller prey species, they seem to be undergoing local adaptation to their island habitats.
It is therefore vital to consider how the local environment has affected the genetics of a population because of natural selection before relying on conservation strategies that include genetic rescue.
Population genetics
Population genetic analyses indicate that the Bengal tigers of India have the highest genomic diversity, which is perhaps unsurprising as India is home to nearly 70% of the current tiger population. Malayan tigers have the next highest genomic diversities, followed by the Amur and Sumatran tigers, respectively. The low genomic diversities of these two subspecies are probably due to their small population sizes.
There are, however, some interesting patterns in the population genetic structures of the Amur and Bengal tigers. Even with its much lower genomic diversity, the Amur tiger population shows little to no genetic structuring according to geographic location.
In India, however, this is not the case. As a stark contrast to the Amur tigers, Bengal tigers show strong population genetic structuring into four distinct subpopulations according to their geographic locations – south India, north and central India, northeast India, and northwest India. In addition, some small tiger populations in India, such as those in Ranthambore, have become isolated and show high levels of recent inbreeding.
A comparison of the landscapes and habitats of the Amur and Indian tigers reveals why this difference in population genetics exists between the two subspecies.
In India, tigers live in very variable habitats that are often nested within areas of extremely high human population densities. Landscape genetics studies of tigers suggest that high human presence can be a major barrier to their movements and gene flow between populations. This is why in India, despite high tiger numbers and densities, the tigers are isolated, and their populations are fragmented. Amur tigers live in landscapes that have relatively very low human densities. This means that despite their low numbers and densities, the Amur tigers are not isolated, and the population is panmictic (one where all individuals are potential partners).
The scene in India
In India, conservationists and tiger experts are becoming increasingly concerned about the fragmentation of tiger habitats.
In 2019, a study from the Wildlife Institute of India (WII) highlighted the need to strengthen tiger genetic diversity through habitat restoration and management rather than indiscriminately doubling tiger numbers.
New research shows that although India’s two large, well-connected tiger populations (in south India and central India) are genetically quite robust, tigers in the northwest (from Ranthambore and Sariska) are showing high levels of inbreeding. These tigers’ parents were not only related to each other but were most likely close relatives. Such a genetic history has caused the northwest tiger populations to bear large mutation loads, which puts them at a high risk of inbreeding depression.
“Though Bengal tigers have high genetic variation and are known to be the largest population, they are not necessarily safe from the impacts of inbreeding. We find that Bengal tigers have some of the most inbred individuals, and this could be due to habitat fragmentation,” says Anubhab Khan, a researcher from Uma Ramakrishnan’s group at the National Centre for Biological Sciences (NCBS), Bangalore.
“Previous research using simulations predicted that small isolated populations could have lower numbers of harmful mutations. We find this to be true empirically in some tiger populations in India. But, we also show that the few harmful mutations that remain have a high potential of being expressed and causing disease. This means that even if small isolated populations have fewer harmful mutations, whatever remains, poses a serious threat to the population’s survival.”
Like the 2019 WII work, another recent study highlights the importance of the northeast tiger populations, specifically in Similipal, a unique tiger population. Similipal is home to the rare ‘black’ tiger, a pseudomelanistic (pseudo = false; melanistic = dark/black coloured) tiger variant that was once thought to be a myth.
These animals develop broader than average black stripes that look like they have spread or leaked onto the surrounding tawny background. All the black tigers of Similipal carry a single mutation in the gene Transmembrane Aminopeptidase Q (Taqpep) which seems to be the cause of this odd patterning.
Mutations in this gene are known to cause changes in coat patterning in several other species of cats, including king cheetahs (where it is responsible for blotchy and striped patterning) and splotchy markings in feral tabby cats in California.
The Similipal mutation is either very rare or absent in any other captive or wild Indian tiger population. The only other black tigers outside of Similipal in India (from Nandankanan zoo at Bhubaneswar and Arignar Anna Zoological Park at Chennai), which are captive-born, share a common ancestor with Similipal tigers. As of now, only 3 black tigers of the 12 tigers identified in Similipal have been seen through photo trapping.
Due to its geographic isolation (the nearest tiger population is roughly 800 km away), the Similipal tiger population likely arose from a small founding group of tigers. This isolation combined with inbreeding and genetic drift were probably the driving forces behind the unique black tiger population of Similipal.
“We began to understand the role of genetic drift and inbreeding in Similipal tigers and gained two main insights—one, the appearance of peculiar physical traits in some populations may indicate unique evolutionary trajectories, and two, such populations must be studied from a genomic perspective to make managerial decisions important for their survival,” adds Vinay Sagar, who also works with Ramakrishnan at NCBS.
Implications for conservation
Lessons learned from cheetahs, gophers, lions, and even sparrows and whales echo the same message: current population genetics and genetic histories of endangered species are indispensable for meaningful conservation efforts. Over the last two decades, it has become increasingly clear that ignoring genetics can lead to disasters such as the tragic ‘genetic rescue’ of the Alpine ibex.
“The genetic work on tigers from India, especially from Uma Ramakrishnan’s group is one of the best examples of applying genomics to a conservation problem with a large mammal,” says biologist Fred Allendorf, who works on conservation genetics.
Allendorf, the Regents Professor of Biology Emeritus at the University of Montana, U.S.A., explains that genomic studies provide key information on whether different populations can be managed as one or need to be managed as different isolated populations. “This is necessary for genetic rescue efforts in conservation. Previously, the genetic rescue was being done blindly, without really understanding how it would affect populations. But now, with genomic data, we can identify good candidates for genetic rescue efforts—which populations are in genetic trouble and which ones are good source populations. For example, we now know that due to local adaptation, placing Siberian tigers in India will not work out,” he adds.
Allendorf further explains that these animals are exceptional for many reasons, but conservation problems are largely centered on their populations being small, fragmented, and often isolated. When this happens, chance and inbreeding overwhelm natural selection, and harmful genes often reach high frequencies. “The work on the melanistic tiger population shows this very clearly; it is an excellent example of genetically identifying small isolated populations and trying to deal with them through conservation efforts.”
Banner image: All ‘black tigers’ of Similipal carry a single mutation in the gene Transmembrane Aminopeptidase Q (Taqpep) which seems to be the cause of their broader than usual black stripes. Photo by Rajesh Kumar Mohapatra/Nandankanan Biological Park.