Neolithic Mitochondrial Haplogroup H Genomes and the Genetic Origins of Europeans

Haplogroup H dominates present-day Western European mitochondrial DNA variability (\u3e40%), yet was less common (~19%) among Early Neolithic farmers (~5450 BC) and virtually absent in Mesolithic hunter-gatherers. Here we investigate this major component of the maternal population history of modern Europeans and sequence 39 complete haplogroup H mitochondrial genomes from ancient human remains. We then compare this ‘real-time’ genetic data with cultural changes taking place between the Early Neolithic (~5450 BC) and Bronze Age (~2200 BC) in Central Europe. Our results reveal that the current diversity and distribution of haplogroup H were largely established by the Mid Neolithic (~4000 BC), but with substantial genetic contributions from subsequent pan-European cultures such as the Bell Beakers expanding out of Iberia in the Late Neolithic (~2800 BC). Dated haplogroup H genomes allow us to reconstruct the recent evolutionary history of haplogroup H and reveal a mutation rate 45% higher than current estimates for human mitochondria

Population differentiation of Southern Indian male lineages correlates with agricultural expansions predating the caste system

Christina J. Adler, Alan Cooper, Clio S.I. Der Sarkissian and Wolfgang Haak are contributors to the Genographic ConsortiumPrevious studies that pooled Indian populations from a wide variety of geographical locations, have obtained contradictory conclusions about the processes of the establishment of the Varna caste system and its genetic impact on the origins and demographic histories of Indian populations. To further investigate these questions we took advantage that both Y chromosome and caste designation are paternally inherited, and genotyped 1,680 Y chromosomes representing 12 tribal and 19 non-tribal (caste) endogamous populations from the predominantly Dravidian-speaking Tamil Nadu state in the southernmost part of India. Tribes and castes were both characterized by an overwhelming proportion of putatively Indian autochthonous Y-chromosomal haplogroups (H-M69, F-M89, R1a1-M17, L1-M27, R2-M124, and C5-M356; 81% combined) with a shared genetic heritage dating back to the late Pleistocene (10–30 Kya), suggesting that more recent Holocene migrations from western Eurasia contributed, <20% of the male lineages. We found strong evidence for genetic structure, associated primarily with the current mode of subsistence. Coalescence analysis suggested that the social stratification was established 4–6 Kya and there was little admixture during the last 3 Kya, implying a minimal genetic impact of the Varna(caste) system from the historically-documented Brahmin migrations into the area. In contrast, the overall Y-chromosomal patterns, the time depth of population diversifications and the period of differentiation were best explained by the emergence of agricultural technology in South Asia. These results highlight the utility of detailed local genetic studies within India, without prior assumptions about the importance of Varna rank status for population grouping, to obtain new insights into the relative influences of past demographic events for the population structure of the whole of modern India.GaneshPrasad ArunKumar, David F. Soria-Hernanz, Valampuri John Kavitha, Varatharajan Santhakumari Arun, Adhikarla Syama, Kumaran Samy Ashokan, Kavandanpatti Thangaraj Gandhirajan, Koothapuli Vijayakumar, Muthuswamy Narayanan, Mariakuttikan Jayalakshmi, Janet S. Ziegle, Ajay K. Royyuru, Laxmi Parida, R. Spencer Wells, Colin Renfrew, Theodore G. Schurr, Chris Tyler Smith, Daniel E. Platt, Ramasamy Pitchappan, The Genographic Consortiu

Genome-wide signatures of male-mediated migration shaping the Indian gene pool

Multiple questions relating to contributions of cultural and demographical factors in the process of human geographical dispersal remain largely unanswered. India, a land of early human settlement and the resulting diversity is a good place to look for some of the answers. In this study, we explored the genetic structure of India using a diverse panel of 78 males genotyped using the GenoChip. Their genome-wide single-nucleotide polymorphism (SNP) diversity was examined in the context of various covariates that influence Indian gene pool. Admixture analysis of genome-wide SNP data showed high proportion of the Southwest Asian component in all of the Indian samples. Hierarchical clustering based on admixture proportions revealed seven distinct clusters correlating to geographical and linguistic affiliations. Convex hull overlay of Y-chromosomal haplogroups on the genome-wide SNP principal component analysis brought out distinct non-overlapping polygons of F*-M89, H*-M69, L1-M27, O2a-M95 and O3a3c1-M117, suggesting a male-mediated migration and expansion of the Indian gene pool. Lack of similar correlation with mitochondrial DNA clades indicated a shared genetic ancestry of females. We suggest that ancient male-mediated migratory events and settlement in various regional niches led to the present day scenario and peopling of India

A late neolithic expansion of Y chromosomal haplogroup O2a1-M95 from east to west

The origin and dispersal of Y-Chromosomal haplogroup O2a1-M95, distributed across the Austro Asiatic speaking belt of East and South Asia, are yet to be fully understood. Various studies have suggested either an East Indian or Southeast Asian origin of O2a1-M95. We addressed the issue of antiquity and dispersal of O2a1-M95 by sampling 8748 men from India, Laos, and China and compared them to 3307 samples from other intervening regions taken from the literature. Analyses of haplogroup frequency and Y-STR data on a total 2413 O2a1-M95 chromosomes revealed that the Laos samples possessed the highest frequencies of O2a1-M95 (74% with &gt;0.5) and its ancestral haplogroups (O2*-P31, O*-M175) as well as a higher proportion of samples with 14STR-median haplotype (17 samples in 14 populations), deep coalescence time (5.7 ± 0.3 Kya) and consorted O2a1-M95 expansion evidenced from STR evolution. All these suggested Laos to carry a deep antiquity of O2a1-M95 among the study regions. A serial decrease in expansion time from east to west: 5.7 ± 0.3 Kya in Laos, 5.2 ± 0.6 in Northeast India, and 4.3 ± 0.2 in East India, suggested a late Neolithic east to west spread of the lineage O2a1-M95 from Laos

Modal tree obtained by BATWING indicating the coalescence time divergence estimates (in years) among Major Populations Groups (MPG) after using 17 STRs from all haplogroups.

<p>BATWING estimates suggest that all populations groups started to diverge 7.1 Kya (95% CI: 5.5–9.2 Kya), with limited admixture among them for the last 3.0 Kya (2.3–4.3 Kya), the youngest diverge time estimate. The modal tree shows two differentiated nodes with clear overlapping estimates of the splits: a first node including one of the tribal groups (HTC) together with all the non-tribal MPGs (castes) with a divergence time of 6.2 Kya (4.7–8.0 Kya), while the second node embraces the HTF and HTK tribal groups with an estimated divergence between then of 4.9 Kya (3.6–7.1 Kya).</p

Reduced median network of 17 microsatellite haplotypes within haplogroup F-M89.

<p>The network depicts clear isolated evolution among HTF populations with a few shared haplotypes between Kurumba (HTK) and Irula (HTF) populations. Circles are colored based on the 7 Major Population Groups as shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0050269#pone-0050269-g001" target="_blank">Figure 1</a>, and the area is proportional to the frequency of the sampled haplotypes. Branch lengths between circles are proportional to the number of mutations separating haplotypes.</p

Y chromosome haplogroup frequencies (%) in the 31 populations from Tamil Nadu.

<p>SD (Standard Deviation).</p

Analysis of molecular variance (AMOVA).

a<p> <i>P</i><0.00001.</p>b<p> <i>P</i><0.001.</p>c<p> <i>P</i><0.01.</p>d<p> No Significant, <i>P</i><0.2.</p><p>TR (Tribes), HTF (Hill Tribe Foragers), BRH (Brahmins), HTK (Hill Tribe Kannada speakers), SC (Schedule Castes), DLF (Dry Land Farmers), AW (Artisan & Warriors).</p><p>HG, MID, LOW – High, Middle and Low caste-rank hierarchy as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0050269#pone-0050269-t001" target="_blank">Table 1</a>.</p><p>Endogamous populations were grouped based on geography, tribe-caste dichotomy, caste-rank hierarchy, and socio-cultural features mainly reflecting subsistence (7 Major Population Groups, MPG). The maximal genetic variation among groups (<i>F_CT</i>) and the minimal variation among populations within groups (<i>F_SC</i>) was observed when populations were grouped based on the 7 MPG classification.</p