Digging Deep: What new research shows about the genetic diversity of India’s Gibbons

A recent study from CSIR-Centre for Cellular and Molecular Biology, Hyderabad, sheds light on the population structure of western hoolock gibbons (Hoolock hoolock) in the North-Eastern region of India. The species occupies a region marked with large rivers that flow throughout the year and pose a significant geographical barrier to populations on either side from mixing. Durbances in the landscape caused humans have made the problem even more acute, giving rise to more isolated subpopulations that are part of a wider ‘metapopulation’.
In order to map the genetic diversity of western hoolock gibbons, scholars collected faecal samples from across their geographical range. In order to obtain these samples, western hoolock gibbon individuals were followed closely over a few days in order to ensure a robust sampling strategy.

Faecal remains are useful as they cons not only of epithelial cells from the intestine, but also of undigested food remains. In an email conversation with , Dr Govindhaswamy Umapathy, the corresponding author of the study, explained that ‘when we extract DNA from faecal samples, we find all kinds of DNA, including from the food, but we only amplify further using primate specific markers for further analysis where in other species’ DNA will be left behind.’
Faecal DNA has been used extensively in the past to understand the occupancy, population size as well as diet of a wide range of species. Further, ‘barcoding undigested and digested food materials can be done using barcode markers to identify food species,’ adds Dr Umapathy.  Finally, faecal samples were supplemented blood samples from gibbons kept in captivity in zoos in Assam and Manipur.
The study taps into the mitochondrial DNA (mtDNA) of the remains, which, unlike nuclear DNA (nrDNA), is monoploid. In other words, mtDNA does not ex as a pair of chromosomes and instead exs as a small circular chromosome. Since it does not undergo recombination the way nrDNA does, it is inherited ‘as-is’ from mother to progeny, making it quite susceptible to demographic bottlenecks like disease outbreaks. These characterics make mitochondrial DNA a very useful molecular marker in ecological studies.
Ultimately, genetic diversity within and between populations needs to be quantified. Since mtDNA is inherited uniparentally as a single set of traits (aka haplotype), a good metric is that of ‘haplotype diversity’. In other words, haplotype diversity describes the number and diversity of different mitochondrial haplotypes. Another metric used Trivedi et al. (2022) was nucleotide diversity (), which quantifies how different genetic sequences are on average (one strand of DNA is nothing but nucleotides stitched together).
Finally, the study calculated fixation statics (FST) that measures allele frequencies between two or more populations. An allele is essentially one type of a particular gene, for eg for a gene that determines flower colour, one allele will code for yellow, another allele for pink and so on. Put simply, the higher the FST, the higher the genetic difference between two populations and vice versa.
For the metapopulation of western hoolock gibbons, the authors found a high haplotype diversity and low nucleotide diversity. These values are, nonetheless, higher than that of most primates, which ‘suggests a complex evolutionary hory… with multiple cases of bottlenecks and diversification… the rivers and other geographic barriers in this region might have influenced in high haplotype and low nucleotide diversities in western hoolock gibbons.’

The study identifies three subpopulations with 27 haplotypes. The ‘south’ subpopulation apparently has a genetic continuum with their counterparts in Bangladesh. The ‘north’ subpopulation conss of those from parts of Meghalaya, Assam (Tinsukia and Hollongapar) and Arunachal Pradesh (Roing). The samples collected from Wakro, Arunachal Pradesh, form a third, dinct, subpopulation.
The FST calculations show a fairly high value among all the populations (ie North-South, South-Wakro, North-Wakro), implying a high level of genetic differentiation and limited gene flow between all of them. The authors theorise that this is likely due to the riverine system dividing the region and preventing western hoolock gibbon populations from mixing with each other.
The study, however, notes that these populations are stable and resilient to habitat fragmentation and that their work will allow more targeted intervention in conservation efforts.
The author is a research fellow at the Indian Institute of Science (IISc), Bengaluru, and a freelance science communicator. He tweets at @critvik.