Any Wonder That the King-Sized Tiger Genome Still Has Its Secrets?

A new study has found that India’s tigers aren’t all the same. Instead, their genes suggest they form three distinct clusters.

A tiger in Ranthambore, Rajasthan. Credit: Christopher Kray/Flickr, CC BY 2.0

A tiger in Ranthambore, Rajasthan. Credit: Christopher Kray/Flickr, CC BY 2.0

Janaki Lenin is the author of My Husband and Other Animals. She lives in a forest with snake-man Rom Whitaker and tweets at @janakilenin.

India offers sanctuary to 60% of the world’s population of tigers. Even as they vanished from several countries, here in India, they’ve ceded as much as 89% of their original territory. Today, they are marooned in a few forested islands in a sea of agriculture and human settlements. About 2,500 live in woodlands that often average less than 300 sq. km in area. When populations are separated from one other, the succeeding generations could become inbred and unfit for survival.

Such a fate befell the Florida panther. When it began to show signs of inbreeding – crooked tails and a strange circular pattern of fur on the back – wildlife managers infused the population with animals from Texas.

Before resorting to such measures, scientists need to know how tigers naturalised in different landscapes. The cats cope with the heat of Rajasthan, the wetness of the Western Ghats and northeastern India, the open terrain of the Terai and tidal mangroves of the Sundarbans. When many generations live in specific terrains, natural selection could force them to evolve unique adaptations. For instance, a tiger living in Sundarbans may have special genes to deal with life in the swamp. In wildlife management, such populations are considered management units and conserved accordingly. Tigers from one unit, say Sundarbans, should not be introduced into another management unit, such as Ranthambore. So knowing the genetic underpinnings of local adaptations has implications for how tigers are to be managed and conserved.

An earlier study, using historical and modern mitochondrial and nuclear DNA, clubbed all tigers from peninsular India in one group. It said populations became distinct only in the modern era as they became more isolated from each other. The impacts of man were already beginning to tell. Many living tigers lacked most of the variations found in genetic material extracted from museum specimens.

With improved techniques, researchers from four Indian institutions examined the genes of Indian tigers to understand if they had distinct genetic differences by region and if they had any specialised adaptations. They collected tissue samples from dead or captured wild tigers across 21 locations.

The researchers obtained 54 samples for the study from 21 locations. The sample size from each location is denoted by ‘N’. Of these samples, they used 38 in the final analyses.

The researchers obtained 54 samples for the study from 21 locations. The sample size from each location is denoted by ‘N’. Of these samples, they used 38 in the final analyses.

“This is the first study that targets genome-wide data for a species of conservation concern in India,” Uma Ramakrishnan, corresponding author and assistant professor at the National Centre for Biological Sciences, Bengaluru, told The Wire.

The research team used the faster, cheaper and more accurate method of next-generation sequencing for the study. The DNA contained in our body’s cells is made up of two strands. Each strand is a long chain of four smaller molecules called nucleotides. When cells multiply, errors creep into the nucleotide sequence. An individual shares these errors, called single nucleotide polymorphisms (SNPs), with its family. By comparing them throughout a genome, geneticists can track them across time, and tell if these change the function or expression of genes.

In the earlier method, researchers looked for specific segments of DNA with repetitions of nucleotides called microsatellites. These were in the few tens compared to SNPs that are typed in the thousands, a quantity of data that makes geneticists’ conclusions much more certain.

“Acquiring tissue samples from tigers was logistically challenging,” say the authors in a press release. “For the first time, all tiger genetics labs, including the Wildlife Institute of India, Centre for Cellular and Molecular Biology, Kerala Veterinary and Agricultural Sciences University and Aaranyak, from across India came together to share their samples.” However, they still couldn’t access many populations. While researchers pick out microsatellites from DNA in faecal samples, so far they haven’t been able to do draw SNPs from them. So they’ve had to use tissue samples by necessity, which means they cannot cover as much area as they could with the more easily available poop samples.

“The tiger genome is about 2.4 gigabases – that is about 2.4 billion base pairs of DNA,” says Ramakrishnan. In this study, she and her colleagues investigated more than 10,000 SNPs from 38 tigers, compared to about 10 in previous studies. That’s like figuring out a gigantic 2.4-billion-piece puzzle with just 10,000 pieces, she says.

Unlike that earlier study that found no differences, Ramakrishnan and her team discovered the genetic diversity of Indian tigers formed three clusters.

The northwest

Ranthambore in Rajasthan provided all the samples from the northwest. Since genetic variation in these tigers was the least of all the clusters, the authors concluded the tigers’ chances of extinction were high.

Since 1998, at least 11 tigers from this park settled down in other forests in Rajasthan and Madhya Pradesh. But no striped cats seem to have come in from elsewhere, leading to the park tigers’ genetic isolation. It wasn’t always like this. At one time, tigers from areas in present-day Pakistan would have swapped genes with the ones from Rajasthan. But not anymore since those western populations went extinct. Ranthambore has now become the westernmost limit of the tiger range.

Even if there are no populations in the west, tigers from the east could have ventured into Ranthambore. These large cats can cover marathon distances in a generation or two, but some combination of factors appears to curtail their movement. Poachers cleaned out Panna of its tigers, which otherwise would have been within striking distance of Ranthambore. But even when they had the chance, these tigers didn’t look westward, leading to the Ranthambore population becoming estranged.

If nothing is done about this isolated bunch of tigers, damaging mutations can tote up and they, like the Florida panther, could start showing strange features.

Central India

The central Indian cluster included not only the tigers of the deciduous forests of Madhya Pradesh and Maharashtra but also ones from Corbett in the north, Simlipal and Sundarbans in the east, and Arunachal Pradesh and Assam in the northeast. This massive cluster enjoys the highest genetic range.

Despite their tiny forested homes being fractured by fields, settlements and roads, tigers in the heartland of India dodge humans and duck the inbreeding bullet by trekking farther and finding unrelated mates. One study found migrants from 690 kilometres away. Most dispersing tigers seem to be going to or leaving Kanha, the reserve with the highest density of predator and prey.

Since the samples for the central Indian cluster came from a wide area, many variations are only to be expected. But even within individual parks, genetic diversity is high. The mosaic of central Indian forests are at the junction of the northwest, south and northeast, and may have acted as a node that swapped genes between all these different populations.

“The study’s findings emphasise connectivity among tiger habitat is key to maintaining viable populations and is a keystone to their conservation,” Anthony Caragiulo, assistant director of Genomic Operations, American Museum of Natural History, New York, told The Wire. “Genetic diversity is the key to persistence – it’s the toolbox through which species derive their ability to adapt to change. The lack of genetic diversity is akin to having only a hammer in your toolbox – your success, when faced with household repairs, is extremely limited.”

Any structures, like the NH7 that snips two corridors, will confine these central Indian tigers geographically and genetically, consigning them to a fate similar to that of the Ranthambore tigers.

The status of the northeastern tigers is unresolved. The earlier study that pegged all Indian tigers in one group concluded the northeastern ones shared similarities with ones from central India. A later report using many more genetic samples determined that the northeast was a unique cluster in its own right.

Ramakrishnan and her team had few samples to conclusively settle the question of how related these cats are to the mainland ones.

“One individual sampled from Arunachal Pradesh shows mixed ancestry,” says Ramakrishnan. “We speculate that potentially northeast tigers could derive ancestry from other regions in Southeast Asia as well. Understanding these patterns will require further study.”

The south

The research team sourced tissue samples from five forests in Kerala, Karnataka and Tamil Nadu that formed a distinct third cluster. Analysis of a sole tiger from the far off Nagarjunsagar-Srisailam Tiger Reserve, Telangana, was inconclusive. The little the researchers gleaned from that one cat showed similarities with others from the south and central India. The reserve perhaps serves as an important conduit for the flow of genes.

Contrary to the earlier study that found no major genetic differences between Indian tigers, Ramakrishnan and her colleagues identified three distinct clusters.

“Using higher information content in our analyses has helped us identify this finer scale population structure/differentiation,” she says.

Despite shrinking of their habitats, enforced isolation in tiny forested remains and a drastic reduction in numbers about 200 years ago, the shared genetic diversity of tigers was 62%.

Since they live in a broad range of ecosystems, one would expect they’d have some local adaptations. The big surprise is the researchers didn’t find any evidence. Ramakrishnan explains this is because one type of habitat melds into another. The lack of local adaptations isn’t surprising for another reason: the tigers’ prowess as cross-country walkers. It is still possible that they may be specifically adapted to local conditions that the current technique hasn’t identified.

“Examining many more SNPs or even the whole genome may be necessary to actually detect such signatures,” says Ramakrishnan.

The differences that separate the three clusters aren’t shaped by natural selection. Instead, they arose because of circumscribed habitats, low numbers and breeding within that population. However, since Indian tigers don’t show any variation that implies adaptation to local conditions, all three clusters should be treated as one, say Meghana Natesh, the lead author, and Ramakrishnan. In this prescription of what makes a management unit, they follow established scientific protocol.

This study offers a tantalising glimpse of what is to come in the field of tiger genetics, and more generally in conservation genetics. It was published in the journal Scientific Reports on August 29, 2017.