The story of the lost twins: decoding the genetic identities of the Kumhar and Kurcha populations from the Indian subcontinent

Abstract

Background: The population structure of the Indian subcontinent is a tapestry of extraordinary diversity characterized by the amalgamation of autochthonous and immigrant ancestries and rigid enforcement of sociocultural stratification. Here we investigated the genetic origin and population history of the Kumhars, a group of people who inhabit large parts of northern India. We compared 27 previously published Kumhar SNP genotype data sampled from Uttar Pradesh in north India to various modern day and ancient populations.

Results: Various approaches such as Principal Component Analysis (PCA), Admixture, TreeMix concurred that Kumhars have high ASI ancestry, minimal Steppe component and high genomic proximity to the Kurchas, a small and relatively little-known population found ~ 2500 km away in Kerala, south India. Given the same, biogeographical mapping using Geographic Population Structure (GPS) assigned most Kumhar samples in areas neighboring to those where Kurchas are found in south India.

Conclusions: We hypothesize that the significant genomic similarity between two apparently distinct modern-day Indian populations that inhabit well separated geographical areas with no known overlapping history or links, likely alludes to their common origin during or post the decline of the Indus Valley Civilization (estimated by ALDER). Thereafter, while they dispersed towards opposite ends of the Indian subcontinent, their genomic integrity and likeness remained preserved due to endogamous social practices. Our findings illuminate the genomic history of two Indian populations, allowing a glimpse into one or few of numerous of human migrations that likely occurred across the Indian subcontinent and contributed to shape its varied and vibrant evolutionary past.

Keywords: Indus Valley civilization; Kumhar; Kurchas; South Asian population history.

Fig. 1

Principal Component Analysis (PCA) of South Asians. PCA plot showing genetic differentiation among South Asians. The X-axis (PC1) explained 18.3% variance while the Y-axis (PC2) explained 16% variance of the data. Notable populations are marked with circles. A more detailed population classification is shown in Additional file 1 Fig. S2. PCA was performed in PLINK v1.9 and the top four principal components (PCs) were extracted. Top two PCs (PC1 and PC2), explaining the highest variance of the data were plotted in R v3.5.1

Fig. 2

Admixture analysis of South Asians. Admixture plot showing the ancestry components of South Asian samples employed in the study. Admixture proportions were generated through an unsupervised admixture analysis at K = 11 using ADMIXTURE v1.3 and plotted in R v3.5.1. Each individual is represented by a vertical line partitioned into colored segments whose lengths are proportional to the contributions of the ancestral components to the genome of the individual

Fig. 3

Comparison of Bronze Age Steppe Ancestry proportion among populations from Uttar Pradesh (UP) and Uttarakhand (UK). The ancestry proportions were obtained using ADMIXTURE v1.3. Multiple comparisons were performed using Tukey’s post hoc analysis implemented in GraphPad Prism v7. While Brahmin and Bhumihars contained the highest fraction of the Steppe Ancestry component (k3) Kumhars contained the least (Tukey’s post hoc analysis, p-value < 0.0001)

Fig. 4

A maximum likelihood (ML) tree examining the genetic relatedness between Kumhars and selected South Asian populations. The ML tree was constructed using TreeMix v1.13. The tree was rooted using Onge, a non-African Andamanese population. Some populations are grouped together for aesthetic reason. The horizontal axis depicts the drift parameter. The scale bar shows ten times the average standard error of the entries in the sample covariance matrix. The tree confirmed the high genetic relatedness between Kumhars and Kurchas, and their genetic similarities with several South Indian populations such as Kurumba, Kuruman and Sugali

Fig. 5

Maps depicting the GPS predicted locations of the Kumhar samples. GPS predicted coordinates were plotted in Google Maps (Google LLC) as well as using ‘rworldmap’ package implemented in R v3.5.1. The black triangle represents the original sampling location of Kumhars and the red triangles represent GPS predicted locations of Kumhars. To note, GPS localized 23 out of 27 Kumhar samples to south-western Karnataka across Western Ghats in southern India with 16 being localized at the Karnataka-Kerala border