Decoding the Genetic Identities of the Kumhar and Kurcha Populations from the Indian Subcontinent Ranajit Das1* , Vladimir A
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Das et al. BMC Genetics 2020, 21(Suppl 1):117 https://doi.org/10.1186/s12863-020-00919-2 RESEARCH Open Access The story of the lost twins: decoding the genetic identities of the Kumhar and Kurcha populations from the Indian subcontinent Ranajit Das1* , Vladimir A. Ivanisenko2,3, Anastasia A. Anashkina4,5 and Priyanka Upadhyai6 From 11th International Young Scientists School “Systems Biology and Bioinformatics”–SBB-2019 Novosibirsk, Russia. 24-28 June 2019 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: Kumhar, Kurchas, Indus Valley civilization, South Asian population history * Correspondence: [email protected] 1Yenepoya Research Centre (YRC), Yenepoya (Deemed to be University), Mangalore, Karnataka, India Full list of author information is available at the end of the article © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Das et al. BMC Genetics 2020, 21(Suppl 1):117 Page 2 of 11 Background are significantly higher than that of the Ashkenazi Jews The Indian subcontinent and adjoining regions in South and the Finns [23]. Kumhars are found throughout large Asia have been a cradle for several waves of human mi- parts of northern, western, and eastern India, as well as gration during Paleolithic, Neolithic Periods, Bronze and in Pakistan. The name ‘Kumhar’ is derived from the San- Iron Age [1–6]. The genetic and ethnolinguistic land- skrit term ‘Kumbhakar’, which literally means earthen- scape of the Indian subcontinent is remarkably heteroge- pot makers alluding to their ancestral way of earning a neous and sculpted by the confluence of the indigenous living [24]. Interestingly, the potters from Amritsar, Pun- people with immigrants that arrived into India following jab in north India are also known as Kulal or Kalal,a diverse routes [7–13]. The extant Indian gene pool is term phonetically similar to Kulala, a group of people composed of largely four ancestral genetic components, from Kasaragod district of the southern Indian state of namely Ancestral North Indian (ANI), Ancestral South Kerala, whose traditional occupation is also pottery. The Indian (ASI), Ancestral Tibeto-Burman (ATB), and An- phonetic similarity between the two terms is potentially cestral Austro-Asiatic (AAA) [14–16]. Recent studies due to their common origin from the Yajurveda, an an- dissecting the complex genetic history of South Asia cient Vedic Sanskrit text where potters were termed as suggested that a South Asia Hunter Gatherer lineage ‘Kulals’ [25]. In this study we aimed to delineate the with close proximity to the present day Andamanese population history of Kumhars and examined their gen- (AASI) admixed with individuals related to Iranian agri- omic similarity with other populations from the Indian culturalists from Zagros mountains, Iran and West_Si- subcontinent. To this end we assessed 27 previously berian_HG (West Siberian Hunter Gatherers) forming published Kumhar samples, which were sampled from the Indus_Periphery gene pool, in the larger Indus valley the north Indian state of Uttar Pradesh and compared to area during the 3rd millennium BCE, and may be a vital 2013 modern day South Asian populations [16, 23]. ancestral source for the subsequent peopling of South Asia [17]. Consistent with previous evidences [11, 18] Results the autochthonous Indian ancestral lineages prior to Clustering of Kumhars in the context of other south Asian their admixture with West Eurasians, likely split during populations eastward migration of the anatomically modern humans, Principal component analysis (PCA) of South Asian out of Africa, later giving rise to AASI groups [17]. The samples exhibited previously described [14, 26] ANI – ANI and ASI gene pools arose subsequently around ~ ASI -AAA cline along the horizontal principal compo- the 2nd millennium BCE, concurrent with the decline of nent (PC1) with Ashkenazi Jews, Kalash and other Paki- the Indus Valley civilization (IVC) [19] that propelled a stani populations, and Shia Iranians from Hyderabad massive upheaval in human settlements across northern clustering at one extreme of the cline, and Juang and parts of the Indian subcontinent. The southward disper- other AAA populations congregating at the other ex- sal of Steppe_MLBA (later Middle to late Bronze Age treme (Fig. 1 and Additional file 1 Fig. S2). Concurrent Steppe) populations occurred around this time into with our previous study [26], ASI-AAA-Ancestral South Asia [20–22]; it is envisioned that the Indus_Per- Tibeto-Burman (ATB) contrast was observed along the iphery related groups admixed with the Steppe_MLBA vertical principal component (PC2) with Juangs cluster- immigrants to form the ANI, while additional Indus_ ing at one end, while Nyshi and other ATB populations Periphery people migrated further south and eastward clustered at the other end. Out of 27 Kumhar samples within peninsular India to mingle with AASI and formed employed in this study, barring three (stockplate_14_C2, the ASI [17]. The distinctive population structure of the stockplate_14_C4, stockplate_14_C6), the remaining Indian subcontinent is a unique amalgamation resulting clustered with ASI and AAA samples, largely overlap- from the extensive and intricate percolation of people ping with tribal populations from Kerala such as the across it for long periods together with the rigorous en- Kurchas. According to PCA, the only North Indian forcement of sociocultural practices, such as endogamy population that revealed genomic proximity to Kumhars, in many groups. Interrogation of population structure, were the Syons from Uttarakhand. Further we note that relatedness and ancestry of Indian populations provide the three above-mentioned outlier Kumhar samples valuable insight to not only reconstruct their evolution- overlapped with a population cluster that largely com- ary past but may also have important implications in prised of various non-Brahmin backward castes from medical genetics and understanding relevant disease Uttar Pradesh. biology. Weighted pairwise FST between Kumhars and 63 se- Here we have investigated the population history of lected populations across India using Weir and Cocker- the Kumhars, a north Indian population that has likely ham approach [27] implemented in PLINK v1.9 revealed been practicing endogamy over long periods of time, as the Kumhars to be genetically almost identical to evidenced by their Identical by descent (IBD) scores that Kurchas from Kerala in southern India (weighted FST = Das et al. BMC Genetics 2020, 21(Suppl 1):117 Page 3 of 11 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