In Arunachal Pradesh, conversations in mithun-rearing communities often find their way to the animal. For outsiders, one question almost inevitably follows: “How many mithuns do you own?”
When John Pei Cander was asked the same question, the enthusiasm with which he had been talking moments earlier suddenly faded. He paused before replying quietly, almost apologetically. “Now, I have just four,” he said. “During my father’s time, our family had around 30.”
John runs a successful business, owns agricultural land, and has built a concrete two-storied house, drives an SUV. His children are studying in private schools. Yet it was not these achievements that defined his pride. It was the shrinking number of mithuns his family owned. He is not alone.
Many with government jobs, thriving farms or successful businesses hesitate before revealing a single-digit number when asked about their mithuns. Their responses carried a sense of shame. Owning fewer mithuns, several people suggested, is not merely an economic reality; it was a loss of status and inheritance.
For generations, the mithun (Bos frontalis) has occupied a unique place amongst many Indigenous societies of northeast India. Neither fully domesticated nor truly wild, the semi-free-ranging bovine represents symbols of wealth, prestige and social standing, woven deeply into customary practices and family life.
According to the 20th Livestock Census published in 2019, India is home to nearly 384,000 individuals. Arunachal Pradesh supports close to 70% of the country’s mithun population, making the state’s breeding practices central to the species’ future. The remaining animals are distributed across Nagaland, Manipur and Mizoram.
Yet remarkably little has been known about the mithun’s genetic health. While earlier genetic studies have offered insights into the species’ ancestry and diversity, they examined only small portions of the genome, leaving scientists without a comprehensive understanding of how genetically healthy today’s mithun populations are or how they have changed over time.
Identifying the Siangmi breed
India’s first population-level whole-genome analysis of the Arunachali mithun, published earlier this year in the International Journal of Molecular Sciences, attempts to fill that gap. By analysing the complete genomes, the study provides the first comprehensive assessment of its genetic diversity, inbreeding and demographic history, establishing a genomic baseline that could guide future conservation and breeding efforts.
“Our mandate is the conservation and characterisation of different mithun germplasm. Last year, we registered the world’s first recognised mithun breed, the Nagami mithun,” said Girish Patil S, Director of the ICAR–National Research Centre on Mithun and a co-author of the genome analysis study. “Simultaneously, we are characterising other mithun populations because unless a population is recognised as a breed, farmers cannot effectively avail the benefits of many Central Sector schemes, like the National Livestock Mission and the Rashtriya Gokul Mission, that are specified only for recognised breeds,” added Patil, who leads Project Siangmi.
“There are about three to four distinct mithun populations in Arunachal Pradesh. We have successfully characterised one from the Siang region, covering Siang, East Siang, Lower Siang, Upper Siang, Lepa Rada and Shi Yomi districts. We found this to be a distinct population, which we now call the Siangmi,” he explained. Based on the 20th Livestock Census, they estimate over 20,000 individuals of this breed. “Although it is yet to be formally registered, it is expected to become the world’s second recognised mithun breed,” Patil added.
Harshit Kumar, a scientist (Animal Genetics and Breeding) at NCR-Mithun and another co-author, said that the whole-genome study was undertaken on this distinct breed to establish whether it constituted a genetically homogeneous population. As the population is yet to be officially recognised as a breed, the study does not refer to it as the Siangmi. Instead, it describes the sampled animals as the “Arunachali mithun population”.
The analyses found little evidence of genetic sub-structure, indicating that the sampled animals largely belong to a single, homogeneous population. Along with distinct phenotypic characteristics, including a convex forehead and shorter, smoother horns, he said these findings strengthen the case for recognising the Siangmi as a separate breed.
Tadang Tamut, chairman of the Jomlo Mongku Mithun Farmers’ Federation, Siang, told Mongabay-India, “We, the Adi and Galo tribes of the Siang region, have been rearing mithuns for generations. Yet we never knew that these were a different breed. According to the scientists, this is probably the oldest mithun breed in the world.”
What the mithun genome reveals
“Arunachali mithuns are reared under a unique semi-free-ranging system, where animals roam within village territories mating naturally, and there is limited exchange between herds. With the absence of pedigree records and the repeated use of a few breeding bulls, these husbandry practices can gradually increase mating between related animals without it being noticed. Over time, this can erode the population’s genetic diversity,” said Kumar.
“Genetic diversity forms the foundation of a population’s long-term survival. Populations with greater diversity are generally better equipped to adapt to changing environments, resist emerging diseases and avoid the harmful effects of inbreeding. Once diversity is lost, recovering it becomes increasingly difficult,” he explained.
To build the baseline, blood samples were collected from 11 unrelated mithuns maintained under semi-intensive production systems across five villages in East Siang and Lepa Rada districts. High-throughput whole-genome sequencing generated around 30 gigabases of DNA sequence from each animal. After quality filtering, the analysis identified nearly five million high-quality single nucleotide polymorphisms (SNPs)- small genetic variations that collectively provide a detailed picture of diversity across the genome.
Across four independent genomic analyses, the sampled mithuns consistently showed moderate levels of genomic inbreeding.
The researchers classified ROHs into four length categories, ranging from 100 kilobases to more than one megabase. More than 93% of the 24,937 ROHs identified across the sampled mithuns measured between 100 and 250 kilobases, while none exceeded one megabase. This pattern suggests that historical demographic events, rather than recent intensive inbreeding, have largely shaped the genomes of the sampled animals.
Further estimates of nucleotide diversity and heterozygosity indicated that the sampled mithuns continue to maintain moderate levels of genetic variation. The authors, however, cautioned that genetic diversity alone does not provide a complete picture of population health. While the sampled mithuns retained moderate genetic variation, other genomic indicators, including inbreeding and effective population size, point to aspects of the population’s genetic health that require continued monitoring.
The researchers then examined whether the sampled mithuns belonged to distinct genetic groups or a largely connected population. Using two complementary genomic analyses, they found little evidence of strong genetic subdivision, suggesting that the sampled herds continue to exchange genes and largely belong to a single, connected population.
According to Kumar, the absence of strong genetic substructure suggests that the population remains genetically well connected. This gives the population considerable potential to improve further, not only in numbers, but also in traits such as body weight, fertility and overall viability.
“Although the sampled mithuns appeared genetically well connected overall, we also found that closely related animals can occur within village herds,” he added. “This highlights the importance of understanding relatedness when making future breeding decisions so that mating between close relatives can be avoided.”
A shrinking breeding population
The study reconstructed the demographic history of the sampled population and estimated its recent effective population size (Ne). Unlike the census population, effective population size is a genetic measure of the number of individuals effectively contributing genes to the next generation. In most species, this number is considerably smaller than the total population because not every individual contributes equally to breeding.
They found evidence of a long-term decline, with the recent effective breeding population estimated at around 160 individuals. “Considering the estimated Siangmi population of around 20,000 animals, this Ne size suggests the population has not yet reached a stage of irreversible genetic erosion, but it is at a point where timely interventions are needed to maintain its genetic diversity and prevent further decline,” Kumar said.
“From a conservation perspective, Ne is one of the strongest indicators of a population’s long-term evolutionary potential. As fewer animals contribute genetically over successive generations, rare genetic variants are gradually lost, reducing the population’s ability to respond to future environmental or disease-related challenges,” he added.
Though the estimate itself should be interpreted cautiously. “Effective population size is influenced by sample size, and our analysis is based on genomes from only 11 animals. While the results clearly indicate a declining trend, broader sampling across the mithun’s distribution will be necessary to refine these estimates and determine whether similar patterns occur in other populations.”
Towards evidence-based mithun conservation
The findings suggest that conserving mithuns must move beyond population counts and observational management towards evidence-based genetic management. Importantly, the researchers do not advocate replacing the traditional free-ranging husbandry systems.
Three major gaps have been identified in the current management of Arunachali mithuns. First, village herds lack a system of individual animal identification, making it difficult to track animals over time or across herds, with the authors proposing ear-tagging or biometric identification as a prerequisite for any structured breeding programme.
Second, as parentage verification remains largely absent, genomic tools developed from the present study could cost-effectively confirm parentage and identify closely related animals before they are bred, reducing the risk of inadvertent inbreeding.
Third, systematic performance records are lacking, with information on traits such as body weight, growth rate and disease resistance not linked to individual animals. The authors suggest combining such phenotypic records with genomic data would allow future studies to identify the genetic basis of economically important traits and support breeding programmes that improve productivity while conserving genetic diversity.
Tamut said the federation had signed a memorandum of understanding (MoU) with NRC-Mithun. “Over the past two years, we have ear-tagged and vaccinated more than 16,000 Siangmis, and we are working to document every single animal.”
He added they have been conducting awareness programmes about the breed. “Our goal is to reach every farmer and ensure that the benefits reach even the remotest villages. Once the breed is officially recognised, we can also apply for a GI tag”. The mithun breeders hope that with the GI tag, they can preserve the uniqueness of the Siangmi breed and save it from crossbreeding.
This article is republished from Mongabay under a Creative Commons license. Read the original article here.