One evening in 2010, ecologist SP Vijayakumar and his two field assistants stood in a faint drizzle, listening carefully to the evening’s orchestra. It was August, and they were in a forest patch hemmed in by tea bushes in Upper Manalar, an estate in the Meghamalai Hills on the Kerala-Tamil Nadu border. In a symphony dominated by cooing wild pigeons and buzzing cicadas, Vijay was focused on one series of notes: the calls of bush frogs. He was studying these nocturnal creatures as part of his doctoral research at Bengaluru’s Indian Institute of Science. 
“Soon, we were engulfed in frog calls,” Vijay recalled.  “It was a cacophony.” He could hear the voices of the Bedomme’s and the green-eyed, two species of bush frogs. Notes from a popular Tamil song emanated from a distant loudspeaker. Through all this, one unfamiliar sound kept breaking through: repeated metallic clinks. Vijay was flummoxed when he spotted the source on a slim branch nearby. He’d never seen a frog exactly like it before: brilliant apple-green coat, “bright and burning” black eyes striped with an egg-yolk yellow, and crucially, a white lichen-like pattern on its back.
The green coat and the black eyes were familiar, he felt. They reminded him of the white-spotted bush frog, Raorchestes chalazodes. But that lichen-like pattern was baffling. Chalazodes had nothing so strange on its back. In any case, white-spotted bush frogs were only found in the Agastya Hills, which are about 100km away—as the crow flies—from Meghamalai. There are dense forests, small towns, paddy fields and a 7km break in the mountains known as the Shencottah Gap between them. The white-spotted bush frogs have been isolated for thousands of years. There wasn’t much chance of them breeding successfully with individuals from a different population.
Only after thinking through various possibilities did Vijay begin to entertain the most thrilling one. Could the creature in his palm be hitherto unknown to science?
ndia is one of 17 “megadiverse” nations.  The main criterion to make the list is a high degree of endemism. That means megadiverse countries have the highest number of species that are not found anywhere else in the world. Within countries, endemic species can be spread over territory (like the kangaroo in Australia) or restricted to a specific geography (the Komodo dragon, which inhabits just five islands in Indonesia).
In India, discovering new species is now a common thing. It excites people in the evolutionary biology and conservation communities but remains otherwise undissected in the popular imagination. Discoveries are regularly reported in mainstream media, but it’s mostly for their surprise value. Look, a lizard under windmills in Maharashtra! An eel buried under the earth in Meghalaya! A four-foot-long walking fish in Bengal!
There’s a larger phenomenon at work. In the last few years, an increase in the number of explorations and game changing developments in scientific technique have helped us make better sense of what these discoveries mean. Some are clues to the past: what was the earth like millions of years ago, before mountains were born and rivers flowed? Others piece together the puzzle of the present: how and why did we get here? Still others provide warnings about the future: what would the world possibly look like if we don’t amend the way we live?
Not quite apart from these big questions, the lab work potentially has a make-or-break fallout. Billions of dollars tied to institutional conservation programmes are funnelled towards quantifiable and easily observable metrics. In that sense, “species” is a convenient category. But it comes with its own politics. The mills of evolution grind finely but slowly. So from the myopic view of several million generations, the scientific baptism of the Meghamalai frog marks neither the end nor the beginning of its evolutionary story. It captures only a snapshot.
Back at the Indian Institute of Science, Vijay set about confirming his hunch in the lab of his mentor, evolutionary ecologist Kartik Shanker. In addition to recording the calls of the lichen-backed frog and taking its photographs, he had euthanised a couple of individuals.  Studying their genetic material, or DNA, would tell him what he needed to know. Preparing DNA samples for analysis is delicate lab work. Vijay  started by placing pieces of the frog’s thigh muscles in a sterilised plastic tube smaller than the size of a little finger. But muscle cells also contain other components, such as proteins, which come in the way of isolating DNA. A cocktail of chemicals is used to break open the muscle cells, dissolve the proteins and separate the DNA for purification.
Another chemical dunk helped isolate the three specific genes Vijay was after. His team made millions of copies of the gene fragments. A few drops of clear liquid—all there was to show after this intricate work—were then sent to a gene lab for sequencing.
There are presently more than 30 approaches to define a species, variously based in ancestry, ecology, appearances, even sound.
Scientists read genetic data as a long string of four letters—A (for adenine), T (for thymine), G (for guanine) and C (for cytosine). These ATGC molecules are the building blocks of DNA.  The order in which these letters are arranged in a gene sequence reveal who you are: a human, lion, house cat or frog. Comparing sequences, particularly since some combinations of letters remain similar across different groups, unravels further information about immediate ancestors and closest relatives. Think of it as tracing a family tree in which each branch stands for a single species. Its length can denote the time that has passed since its ancestors inhabited the earth. 
It took Vijay, Shanker and their team two years to build the gene trees for the bush frogs of the Western Ghats. These included the sequences of well-known species, as well as of the more obscure ones Vijay had collected on his field expeditions. His excitement rose as a pattern finally emerged: the money moment in this line of work. “I knew we had hit treasure,” he recalled. The research concluded that the genetic make-up of the mystery frog warranted the “new species” tag. It turned out that the white-spotted bush frog was its “sister” species: they shared a common ancestor that no other species did.
The lichen-backed frog finally had a name: Raorchestes flaviocularis, the yellow-eyed bush frog, after its “bright, burning eyes.”
o what is a species? In the seventeenth century, European thinkers proposed that a group of organisms that could breed with each other could be called a species. A century on, Carl Linnaeus, the pioneering Swedish naturalist, popularised the use of combining two Latin terms: first the name of the genus,  then that of the species. The yellow-eyed bush frog has the name Raorchestes because it signifies the genus Raorchestes, which encompasses almost 65 species of bush frogs mostly from South Asia; flaviocularis is its species.
For all this time, scientists have been having furious arguments about the best way to classify species. There are presently more than 30 approaches to define a species, variously based in ancestry, ecology, appearances, even sound. The general consensus these days is to take an “integrative” approach. So Vijay started off with flaviocularis’s distinct looks––its morphology––and then worked on tracing its family tree in the DNA lab. The distinctiveness of its metallic calls, as well as its geographical distribution, helped along the hypothesis that flaviocularis was a species that hadn’t been described previously.
“Documenting the existence of a species is the first step to understanding our biodiversity,” Shanker said. It’s an exciting field because there is so much we don’t know. Ecologists have terms of art associated with these knowledge gaps. The Linnean Shortfall refers to the problem of undescribed lineages. A Wallacean Shortfall  refers to the lack of information about a species’ geographical distribution. “These shortfalls are the starting point for our exploration of ecology and evolution. There are lots of questions that can be answered once both these knowledge gaps are addressed,” said Shanker.
One set of questions is evolutionary in nature: Where did a species originate? If it started from Africa, how did it find its way into Asia and diversify? That’s how we got Asian elephants for instance: fossil remains indicate that the first elephant ancestors originated in Africa during the geological epoch known as the Early Pliocene.  Recent genetic and fossil studies now confirm that their descendants moved into Asia 2-4 million years ago, and gave rise to the modern Asian elephant just 2.5 lakh years ago.
Geographic barriers such as deep gorges and wide rivers also affect dispersal, and can isolate populations. The gaps and valleys of the Western Ghats explain why there are so many different kinds of bush frogs. A species’ own ability to move around determines the kind of places it eventually gets to: birds are likelier than frogs to move from one mountain to another, for example.
Then they could ask after ecological factors such as rainfall, temperature and altitude, gradients along which species can adapt and evolve into different groups.
Finally, there are questions related to conservation. Research may focus on the availability of a type of plant if it appears that a species relies on it for survival. This data is analysed to help us approach answers to speculative questions like: what could happen to the species a hundred years from now; how would they adapt to climate change?
One of the things that is clear after a couple of centuries of study is that the species richness of a region increases as you move from the poles to the tropics. Within the tropics, you get “biodiversity hotspots.”  These are sites that represent only 2.4% of the earth’s land surface, support more than 40% of endemic fauna, and are threatened by human habitation.
The Himalayas, with an estimated 10,000 species of plants including more than 3,100 endemics, is one of them. The states of north-eastern India that form part of the larger Indo-Burma hotspot are another. But easily the most well-studied hotspot in India is the Western Ghats.
he Western Ghats stretch almost parallel to India’s west coast. They variously constitute about 1600kms of sparse and dense forests, blue mountains, steep cliffs, thorny bushes, flat plateaus, leech-ridden swamps and windy grasslands. At one end, they start as shrub-bearing hillocks about 10km north of India’s southernmost tip. Then, they become the Ashambu Hills, mighty granite mountains forming a natural border between Tamil Nadu and Kerala, and in the shadow of which lie spice gardens and homesteads.
Then comes the Shencottah Gap. After those 7km, the Ghats rise again to form the Meghamalai Hills, home of flaviocularis, the yellow-eyed bush frog. These are followed by a small plateau which leads to the hills of Palani and Anamalai. Cardamom, coffee and tea plantations blanket the slopes here. Look up, and mist permitting, you can see some of the tallest peaks in the south—“sky islands,” hosting ecosystems wildly different from those of the surrounding lowlands. In the shallow valleys of these highlands, naturally stunted forests known as the “sholas” occur alongside open grassland patches.
North of the Anamalais come the Nilgiris. But first, there’s a deep valley. At 32km wide, 100m above sea level, the Palghat Gap is the widest and lowest pass in the Ghats. A dusty national highway cuts right through it, connecting Coimbatore in Tamil Nadu and Palakkad in Kerala.
Beyond, the Ghats stretch into north Kerala and Karnataka, its high peaks separated occasionally by shallow valleys. They almost kiss the Arabian Sea before swerving east into Goa. By the time they taper off amidst the sugarcane fields of Maharashtra, they are less imposing and more climbable, now ambling along until they reach their other end in the deciduous forest tracts of south Gujarat.
The remarkable contiguity broken by wide gaps and valleys, the sheer range of landscapes, the distance covered: all this should indicate why the Ghats are a species discovery hotspot. They comprise less than 6% of India’s land area but are home to more than 30% of all plant, fish, amphibian, reptile, bird and mammal species found in the country. Of the 406 known frog and toad species in India, more than 200 are endemic to the Ghats. Over a hundred of these endemics have been discovered only in the last 20 years.
ijay and Shanker’s research in the Western Ghats has revealed several interesting patterns. Barring a few, most of the 60-odd bush frog lineages that Vijay collected from across the Ghats originated from a common ancestor. Then, they neatly separated into two groups: those born north of the Palghat Gap, and others that originated in its south. It appears that the geographic barrier, which caused two “sister” radiations, had a role to play in frog diversity.
After studying 15 mountaintops across the Ghats, the team noticed variations even on the same side of the gap. Vijay told me that all the bush frogs they studied had sisters on adjacent mountaintops. These sisters split from each other around one to 10 million years ago. Vijay attributed these splits to the formation of valleys of varying depths—possibly by erosion—that isolated frog populations.
Amazingly, there’s variation even within a single mountaintop ecosystem. Every sky island displays two distinct features: the dense shola forests that drape the valleys, and the open grasslands that are found on the slopes. Vijay found that the Theuerkauf's bush frog inhabits the shola forests of the Anamalais while the Bedomme’s, its sister species, lives in the grasslands nearby. This split occurred around 4-5 million years ago, during intermittent periods of glacial cold weather which are thought to have locked some of the bush frogs up in the sky islands.
he Palghat Gap could be limiting the movement of other, more mobile vertebrates as well. In the summer of 2001, researcher VV Robin was walking in a shola forest of the Nilgiris in search of the white-bellied shortwing, a famously elusive robin-like bird dressed in a coat of blue and white. It’d been spotted only a handful of times in the 120-odd years since it was first described. Biologists who were familiar with the area warned VV Robin that he would never see one.
He persevered, hauling along a cumbersome megaphone to play recordings of shortwing calls, hoping that this aural approach would cause the territorial birds to emerge from their hideout. At the very least, they would call back to him. Robin had already used this method with some success in the shola forests of the Anamalais. In the Nilgiris on the other side of the Gap, he drew blanks. Images of the shortwings found in these parts suggested they were slightly different than those found in the Anamalais. More white on the bellies, pale orange undersides. Could the Nilgiris shortwing be a different species altogether, then?
Robin’s colleague CK Vishnudas had a similar hunch about Anamalai-Nilgiris species differentiation in the Kerala laughingthrush. The Kerala laughingthrush’s call sounds like “cackling laughter,” Robin explained, very similar to the laughingthrushes up north, in the Himalayas. “I can imagine a bunch of Brits who surveyed the Northeast and the Himalayas in the 1800s, finding species with similar calls in the Western Ghats and thinking they must be laughingthrushes too.”
The Satpura corridor disappeared because of dry weather conditions. The birds were locked up for good in the high-elevation forests of the Ghats.
But Robin and his colleagues discovered that the two birds couldn’t be lumped into the existing classifications of shortwings and laughingthrushes. They were born into their own genera, as different species. The researchers decided to call these species sholakilis (literally “bird of the sholas”) and chilappans. Today, you can spot different sholakili species in the Anamalais, Nilgiris and Ashambu Hills. Similarly, what was previously thought of as the black-chinned laughingthrush has been established as four different species of chilappans.
To figure all this out, Robin and his team analysed birdsong, morphology (including body lengths and colour patterns) and gene sequences. They used available records to estimate the ages of the sholakili and chilappan lineages, and find out where they had originated. Reconstructing the birds’ past revealed that their closest relatives had lived in the Himalayas and Southeast Asia. The ancestors of both birds split from their relatives at around the same time—11 million years ago.
From other studies, we already know that this was a time when the dense, wet forests that swathed the Satpura hills of central India served as a corridor for wildlife from the north to reach the Ghats.
This is probably when the birds’ ancestors made the journey. Perhaps they simply weren’t able to return. In the years that followed, the Satpura corridor disappeared because of dry weather conditions. The birds were locked up for good in the high-elevation forests of the Ghats. Robin and his colleagues’ data show that this was precisely the time that the birds began evolving into the sholakilis and chilappans of today.
“This study reveals how much there is to be discovered,” Robin told me. “Birds are perhaps the best-studied taxonomic group, and the Western Ghats are perhaps among the best-studied landscapes. And yet evolutionary patterns are hidden in plain sight.”
Often, these patterns challenge established knowledge. New research suggests that a climatic barrier could be a far bigger driver of bird diversity than the Palghat Gap. In a recent study, Robin and his colleagues found that the distinctly wetter weather south of the Goa Gap—separating the Maharashtra and Karnataka portions of the Ghats—could be the reason for the higher diversity among the birds of peninsular India.
NA-based techniques have transformed new species research across the world. Uma Ramakrishnan, a conservation geneticist and professor at Bengaluru’s National Centre for Biological Sciences who led the genetic component of the research on sholakilis and chilappans, told me that India was still heavily reliant on morphological methods and distribution information till about a decade ago. Now there’s a whole suite of new technologies, including better computational and simulation programmes, that have popularised the use of genetic techniques to answer ecological questions. These technologies both advance and confirm the educated hunches researchers develop as they work.
There’s a flip side to this, too: taxonomic inflation, the over-categorisation of newly sighted animals. Some experts feel that researchers have begun claiming the tag of “new species” in cases where it is clearly unwarranted. Robin Kurian Abraham, a researcher at the University of Kansas, told me that the “overinflation” problem afflicts some Indian frog lineages too. Often, “new species” might just be sub-species, or different populations of the same species. “Why is it that we rarely hear of sub-species in frogs? There are even five extant sub-species of tigers across the world,” Abraham asked me.
The ‘species versus sub-species’ debate has been raging for years. Take the world of wolf taxonomy as an example. The grey wolf (Canis lupus) is found in most parts of the world. In 2018, a paper published in Global Ecology and Conservation by a team of researchers led by Geraldine Werhahn created a splash. DNA analysis using scat and hair samples of the Himalayan wolf had revealed a genetic adaptation to cope with the lower oxygen levels of high altitudes.
It provided a massive shot in the arm to the theory that the Himalayan wolf is evolutionarily distinct: its lineage diverged before the radiation of the modern grey wolf. But the journey to species-hood is long and arduous. In February last year, Werhahn told The Guardian that researchers needed to obtain one final piece of higher-quality genomic data for the separate species case to succeed with the International Union for Conservation of Nature or IUCN, the global organisation which evaluates and assesses conservation status. That quest is still on.
n IUCN classification can be make-or-break for a species because it is inextricably linked to conservation funding. It can be the basis on which even ecosystem-focused institutional programmes like the Critical Ecosystem Partnership Fund (CEPF) make decisions about allocation. The equation is straightforward: the more endemic species there are in a particular region, the more funds will be made available for their research and conservation. For biodiversity hotspots, the stakes are even higher. The CEPF, for instance, funds research only in hotspots.
“The extinction crisis is vast, and conservation funds are limited, so focus is a critical element of CEPF’s approach,” their website says. So it’s not surprising when scientists tend to overinflate species lists. “But, at the end of the day, this need to label or classify species is a human construct,” Abraham pointed out. “It is a work in progress.”
“The process of speciation is a continuum. It’s not something discrete: like today you’re a species, and yesterday you were not.”
Uma Ramakrishnan told me something similar. “It’s convenient to put organisms in bins,” she explained. “But overall, the process of speciation is a continuum. It’s not something discrete: like today you’re a species, and yesterday you were not.”
And you can’t talk of conserving a “continuum” of lizards or frogs, she added. Actionable units are needed to design conservation strategies. “So to me, the biggest justification of defining a species is for conservation, and we can only do that if we call them something,” she said. “What’s important is that in the race to name species, we don’t forget the habitats they live in.”
Species lists have proved especially handy for habitat prioritisation. Imagine having to choose between conserving two different patches: one that has three closely-related frogs and another that has the purple frog and two other distinct frogs. “You should vote for the second patch because that has more evolutionary diversity,” Ramakrishnan said.
The purple frog was described as a new species after scientist SD Biju first stumbled on it in a Kerala forest in 2000. Dating the frog’s lineage using an ancient fossil, Biju concluded that its closest relative lives an ocean apart, in the Seychelles islands. The purple frog’s uniqueness has been recognised by the influential EDGE of Existence programme, an initiative of the Zoological Society of London. (EDGE stands for Evolutionarily Distinct and Globally Endangered.) The programme is targeted at species that have few close relatives on the tree of life.
In the case of the purple frog and many others, international collaborations are crucial for countries to access data and advanced techniques from each other. Increased opportunities for this sort of teamwork is one of the reasons we’re seeing more species discoveries in India.
here have been relentless anthropogenic pressures on biodiversity hotspots even as attention to the lives they host has increased. The bleak future of newly-discovered species is illustrated in the tale of the snake-eyed lizards of Central India. Their story is connected to the climatic event that changed the evolutionary trajectory of the sholakilis and chilappans: the drying out of the Satpura forest corridor.
In 2017, Ramakrishnan and herpetologist Ishan Agarwal studied the genes of Ophisops, the snake-eyed lizards. They found that the lizards had adapted to the transformation of the dense, wet forests of ancient peninsular India into open, dry habitats by diversifying into different species. In areas that received regular rainfall, they remained as they were.
Crucially, Ramakrishnan and Agarwal’s findings reconfirmed that some peninsular and central Indian grasslands are ancient systems that have been around for at least five to 11 million years. There is an erroneous but influential view among some environmental policymakers that all grasslands are degraded forests, formed after humans burnt down the original vegetation and encouraged livestock grazing on the land. The fresh findings confirm that this is inaccurate, considering there is general agreement that the subcontinent was populated only about 65,000 to 80,000 years ago.
One fallout of these attitudes is that India has no policy to protect these savannah-grasslands. They are disappearing as industries and, ironically, afforestation programmes eat into the area. That is not good news for the snake-eyed lizard.
The fan-throated lizard might also suffer because of the lack of a grassland policy. Sarada superba, the “superb” fan-throated lizard, was only described in 2016, after it was found living under wind turbines on the Chalkewadi plateau in Maharashtra. Two years afterwards, scientists found that the wind farms had led to a drastic decrease in birds of prey in the area. Fewer raptors meant that the population of the fan-throated lizards increased three-fold. The population explosion had an adverse impact: competing for food made the lizards thinner and weaker. 
Even when it comes to frogs, the worry of extinction looms large. The white-spotted bush frog is listed as “Critically Endangered” in the IUCN's Red List of Threatened Species. Vijay told me that some frogs may have already become locally extinct because of their inability to disperse out of habitats that face anthropogenic pressures. The yellow-eyed bush frog is unlikely to have a smooth ride—it lives in fragmented forest patches that are disturbed by human activities such as firewood extraction.
We don’t know very much about the impact of climate change in the Ghats. We can’t say for certain that the frogs of the sky islands will have nowhere to go if their worlds become warmer. Given the patterns of their evolutionary past, there is a chance that they might adapt to warmer temperatures. Vijay stressed that the gaps in our knowledge are still dizzyingly large.
“I envision species discoveries as stop-over points on a treasure map,” he told me. “Like a giant jigsaw. There are several bits and pieces to a large puzzle. Any small idea will improve the clarity of the bigger picture.”
Aathira Perinchery is a Kochi-based independent journalist. A wildlife biologist by training, she writes mostly about the environment, wildlife and conservation in India.