A genetic chronology for the Indian Subcontinent points to heavily sex-biased dispersals

The maternal genetic history of tribal populations of Chhattisgarh, India

The central region of India boasts a rich tribal heritage and the highest number of tribal populations in the country. Analysing the genetic history of this population can offer valuable insights into various demographic processes that shaped the gene pool of present-day settlers of this region. In this study, we utilize a recently validated Next-generation sequencing (NGS) technique to sequence 24 tribal mitogenomes from the Chhattisgarh population for genetic ancestry and forensic analysis. The identified ancient haplogroups in this population can be traced back to the pre-Last Glacial Maximum (LGM) period. Our Bayesian analysis provides evidence for maternal ancestral expansion following the earliest Out-of-Africa migration, followed by a prolonged steady phase. We identified three basal founding haplogroups, M2, R5, and U2 in the Chhattisgarh region that diversified during the Neolithic period. Indistinct distribution pattern of these haplogroups among tribes and castes suggests that the maternal ancestry of Chhattisgarh population predates any kind of social stratification that exists today in the Indian subcontinent. Furthermore, our analysis suggests that this region remained unaffected by the Last Glacial Maximum. The forensic analysis of the mitogenomes demonstrates a high power of discrimination (0.9256) within the Chhattisgarh population, thus supporting the applicability of mitogenome NGS technology in forensic contexts.

Human Y chromosome haplogroup L1-M22 traces Neolithic expansion in West Asia and supports the Elamite and Dravidian connection

West and South Asian populations profoundly influenced Eurasian genetic and cultural diversity. We investigate the genetic history of the Y chromosome haplogroup L1-M22, which, while prevalent in these regions, lacks in-depth study. Robust Bayesian analyses of 165 high-coverage Y chromosomes favor a West Asian origin for L1-M22 ∼20.6 thousand years ago (kya). Moreover, this haplogroup parallels the genome-wide genetic ancestry of hunter-gatherers from the Iranian Plateau and the Caucasus. We characterized two L1-M22 harboring population groups during the Early Holocene. One expanded with the West Asian Neolithic transition. The other moved to South Asia ∼8-6 kya but showed no expansion. This group likely participated in the spread of Dravidian languages. These South Asian L1-M22 lineages expanded ∼4-3 kya, coinciding with the Steppe ancestry introduction. Our findings advance the current understanding of Eurasian historical dynamics, emphasizing L1-M22's West Asian origin, associated population movements, and possible linguistic impacts.

The maternal U1 haplogroup in the Koraga tribe as a correlate of their North Dravidian linguistic affinity

Introduction: The Koraga tribe are an isolated endogamous tribal group found in the southwest coastal region of India. The Koraga language shares inherited grammatical features with North Dravidian languages. To seek a possible genetic basis for this exceptionality and understand the maternal lineage pattern, we have aimed to reconstruct the inter-population and intra-population relationships of the Koraga tribal population by using mtDNA markers for the hypervariable regions along with a partial coding region sequence analysis. Methods and Results: Amongst the 96 individuals studied, we observe 11 haplogroups, of which a few are shared and others are unique to the clans Soppu, Oṇṭi and Kuṇṭu. In addition to several deep rooted Indian-specific lineages of macrohaplogroups M and U, we observe a high frequency of the U1 lineage (∼38%), unique to the Koraga. A Bayesian analysis of the U1 clade shows that the Koraga tribe share their maternal lineage with ancestral populations of the Caucasus at the cusp of the Last Glacial Maximum. Discussion: Our study suggests that the U1 lineage found in the Indian subcontinent represents a remnant of a post-glacial dispersal. The presence of West Asian U1 when viewed along with historical linguistics leads us to hypothesise that Koraga represents a mother tongue retained by a vanquished population group that fled southward at the demise of the Indus civilisation as opposed to a father tongue, associated with a particular paternal lineage.

Mitogenome analysis reveals predominantly ancient Yellow River origin of population inhabiting Datong agro-pastoral ecotone along Great Wall

The Datong Basin was an important arena for population movement and admixture between the Yellow River Valley and Eastern Steppe. In historical materials, the region was often the setting for a tug-of-war between Han farmers and non-Han nomads. The genetic makeup and population history of this Datong population has, however, remained uncertain. In this study, we analysed 289 mitogenomes from Datong individuals. Our primary findings were: (1) population summary statistics analysis revealed a high level of genetic diversity and strong signals of population expansion in the Datong population; (2) inter-population comparisons (PCA and Fst heatmap) exhibited a close clustering between the Datong population and Northern Han, especially northern frontier groups, such as the Inner Mongolia Han, Heilongjiang Han, Liaoning Han and Tianjin Han; (3) phylogeographic analysis of complete mitogenomes revealed the presence of different components in the maternal gene pools of Datong population-the northern East Asian component was dominant (66.44%), whereas the southern East Asians were the second largest component with 31.49%. We also observed a much reduced west Eurasian (2.07%) component; (4) direct comparisons with ancient groups showed closer relationship between Datong and Yellow River farmers than Eastern Steppe nomads. Despite, therefore, centuries of Eastern Steppe nomadic control over the Datong area, Yellow River farmers had a much more significant impact on the Datong population.

The maternal ancestry of the Kavaratti islanders and the last glacial maximum aftermath

The prehistoric human settlement of the Lakshadweep islands remains a mystery for various reasons. Uncertainty about the existence of indigenous tribes in these islands and the lack of folklore records present major obstacles to the reconstruction of Lakshadweep ancestry. However, with extant population data, we seek to understand the maternal ancestry of the Kavaratti islanders. Mitochondrial control region variation analysis of 80 individuals from this island shows maternal links with the populations in the northwestern region of the South Asian mainland. The founder clade R30b2, observed in the Kavaratti islanders, is so far present only in the Scheduled Castes from the Punjab region, Jat Sikhs and Nairs. All other mainland populations carry basal R30 or R30a subclades. The presence of a specific Uralic U4 lineage in our samples, in addition to the Indo-European affinity observed in the phylogeny tree, substantiates a northwestern maternal ancestry of the Kavaratti islanders and implies an ancestral admixture with early humans in the Near East at the time of the last glacial maximum (LGM). Based on our Bayesian analysis, we furthermore propose that a group bearing mostly R30b2 during the LGM recovery, moved eastward and southward, where they received Indian-specific M haplogroups. Hence, the maternal ancestry of the Kavaratti islanders is evidently a consequence of the demographic changes in the northwestern region of the Indian subcontinent caused by the Last Glacial Maximum. The haplogroup distribution pattern and nucleotide sequence data produced in this study will enrich the forensic database of the Lakshadweep islands.

Maternal Ancestry of First Parsi Settlers of India Using Ancient Mitogenome

The rich cultural and genetic diversity of South Asia emerged from multiple migrations and cultural assimilation of multiple waves of migrants. The Parsi community of North-western India were one of those who migrated from West Eurasia in the aftermath of 7^th century CE and assimilated into the local cultural framework. Earlier genetic studies further strengthened this notion with the finding that they harbour both Middle Eastern and South Asian genetic components. Although these studies covered both autosomal and uniparental markers, still maternal ancestry was not covered in depth and with good resolution of mitochondrial markers. Hence in our current study, we have first time generated a complete mitogenome of 19 ancient samples of the first Parsi settlers excavated from the archaeological site of Sanjan and performed detailed phylogenetic analysis to infer their maternal genetic affinity. In our analysis, we found that the Parsi mitogenome with mtDNA haplogroup M3a1+204 shares clade with both Middle Eastern and South Asian modern individuals in both the Maximum Likelihood tree and Bayesian phylogenetic tree. This haplogroup was also prevalent among the medieval Swat valley population of present-day Northern Pakistan and was also observed in two Roopkund A individuals. In the phylogenetic network this sample share haplotype with both South Asian and Middle Eastern samples. So conclusively, the first Parsi settlers' maternal ancestry encompasses both South Asian and Middle Eastern genetic composition.

A Population Genetic Perspective on Subsistence Systems in the Sahel/Savannah Belt of Africa and the Historical Role of Pastoralism

This review focuses on the Sahel/Savannah belt, a large region of Africa where two alternative subsistence systems (pastoralism and agriculture), nowadays, interact. It is a long-standing question whether the pastoralists became isolated here from other populations after cattle began to spread into Africa (~8 thousand years ago, kya) or, rather, began to merge with other populations, such as agropastoralists, after the domestication of sorghum and pearl millet (~5 kya) and with the subsequent spread of agriculture. If we look at lactase persistence, a trait closely associated with pastoral lifestyle, we see that its variants in current pastoralists distinguish them from their farmer neighbours. Most other (mostly neutral) genetic polymorphisms do not, however, indicate such clear differentiation between these groups; they suggest a common origin and/or an extensive gene flow. Genetic affinity and ecological symbiosis between the two subsistence systems can help us better understand the population history of this African region. In this review, we show that genomic datasets of modern Sahel/Savannah belt populations properly collected in local populations can complement the still insufficient archaeological research of this region, especially when dealing with the prehistory of mobile populations with perishable material culture and therefore precarious archaeological visibility.

The mitochondrial genomes of two Pre-historic Hunter Gatherers in Sri Lanka

Sri Lanka is an island in the Indian Ocean connected by the sea routes of the Western and Eastern worlds. Although settlements of anatomically modern humans date back to 48,000 years, to date there is no genetic information on pre-historic individuals in Sri Lanka. We report here the first complete mitochondrial sequences for Mesolithic hunter-gatherers from two cave sites. The mitochondrial haplogroups of pre-historic individuals were M18a and M35a. Pre-historic mitochondrial lineage M18a was found at a low prevalence among Sinhalese, Sri Lankan Tamils, and Sri Lankan Indian Tamil in the Sri Lankan population, whereas M35a lineage was observed across all Sri Lankan populations with a comparatively higher frequency among the Sinhalese. Both haplogroups are Indian derived and observed in the South Asian region and rarely outside the region.

The matrilineal ancestry of Nepali populations

The Tibetan plateau and high mountain ranges of Nepal are one of the challenging geographical regions inhabited by modern humans. While much of the ethnographic and population-based genetic studies were carried out to investigate the Tibetan and Sherpa highlanders, little is known about the demographic processes that enabled the colonization of the hilly areas of Nepal. Thus, the present study aimed to investigate the past demographic events that shaped the extant Nepalese genetic diversity using mitochondrial DNA (mtDNA) variations from ethnic Nepalese groups. We have analyzed mtDNA sequences of 999 Nepalese and compared data with 38,622 published mtDNA sequences from rest of the world. Our analysis revealed that the genomic landscapes of prehistoric Himalayan settlers of Nepal were similar to that of the low-altitude extant Nepalese (LAN), especially Newar and Magar population groups, but differ from contemporary high-altitude Sherpas. LAN might have derived their East Eurasian ancestry mainly from low-altitude Tibeto-Burmans, who likely have migrated from East Asia and assimilated across the Eastern Himalayas extended from the Eastern Nepal to the North-East of India, Bhutan, Tibet and Northern Myanmar. We also identified a clear genetic sub-structure across different ethnic groups of Nepal based on mtDNA haplogroups and ectodysplasin-A receptor (EDAR) gene polymorphism. Our comprehensive high-resolution mtDNA-based genetic study of Tibeto-Burman communities reconstructs the maternal origins of prehistoric Himalayan populations and sheds light on migration events that have brought most of the East Eurasian ancestry to the present-day Nepalese population.

Sequence analyses of Malaysian Indigenous communities reveal historical admixture between Hoabinhian hunter-gatherers and Neolithic farmers

Southeast Asia comprises 11 countries that span mainland Asia across to numerous islands that stretch from the Andaman Sea to the South China Sea and Indian Ocean. This region harbors an impressive diversity of history, culture, religion and biology. Indigenous people of Malaysia display substantial phenotypic, linguistic, and anthropological diversity. Despite this remarkable diversity which has been documented for centuries, the genetic history and structure of indigenous Malaysians remain under-studied. To have a better understanding about the genetic history of these people, especially Malaysian Negritos, we sequenced whole genomes of 15 individuals belonging to five indigenous groups from Peninsular Malaysia and one from North Borneo to high coverage (30X). Our results demonstrate that indigenous populations of Malaysia are genetically close to East Asian populations. We show that present-day Malaysian Negritos can be modeled as an admixture of ancient Hoabinhian hunter-gatherers and Neolithic farmers. We observe gene flow from South Asian populations into the Malaysian indigenous groups, but not into Dusun of North Borneo. Our study proposes that Malaysian indigenous people originated from at least three distinct ancestral populations related to the Hoabinhian hunter-gatherers, Neolithic farmers and Austronesian speakers.

Identifying signatures of natural selection in Indian populations

In this study, we present the results of a genome-wide scan for signatures of positive selection using data from four tribal groups (Kokana, Warli, Bhil, and Pawara) and two caste groups (Deshastha Brahmin and Kunbi Maratha) from West of the Maharashtra State In India, as well as two samples of South Asian ancestry from the 1KG project (Gujarati Indian from Houston, Texas and Indian Telugu from UK). We used an outlier approach based on different statistics, including PBS, xpEHH, iHS, CLR, Tajima's D, as well as two recently developed methods: Graph-aware Retrieval of Selective Sweeps (GRoSS) and Ascertained Sequentially Markovian Coalescent (ASMC). In order to minimize the risk of false positives, we selected regions that are outliers in all the samples included in the study using more than one method. We identified putative selection signals in 107 regions encompassing 434 genes. Many of the regions overlap with only one gene. The signals observed using microarray-based data are very consistent with our analyses using high-coverage sequencing data, as well as those identified with a novel coalescence-based method (ASMC). Importantly, at least 24 of these genomic regions have been identified in previous selection scans in South Asian populations or in other population groups. Our study highlights genomic regions that may have played a role in the adaptation of anatomically modern humans to novel environmental conditions after the out of Africa migration.

Ancient DNA at the edge of the world: Continental immigration and the persistence of Neolithic male lineages in Bronze Age Orkney

The Orcadian Neolithic has been intensively studied and celebrated as a major center of cultural innovation, whereas the Bronze Age is less well known and often regarded as a time of stagnation and insularity. Here, we analyze ancient genomes from the Orcadian Bronze Age in the context of the variation in Neolithic Orkney and Bronze Age Europe. We find clear evidence for Early Bronze Age immigration into Orkney, but with an extraordinary pattern: continuity from the Neolithic on the male line of descent but immigration from continental Europe on the female side, echoed in the genome-wide picture. This suggests that despite substantial immigration, indigenous male lineages persisted for at least a thousand years after the end of the Neolithic.

Orkney was a major cultural center during the Neolithic, 3800 to 2500 BC. Farming flourished, permanent stone settlements and chambered tombs were constructed, and long-range contacts were sustained. From ∼3200 BC, the number, density, and extravagance of settlements increased, and new ceremonial monuments and ceramic styles, possibly originating in Orkney, spread across Britain and Ireland. By ∼2800 BC, this phenomenon was waning, although Neolithic traditions persisted to at least 2500 BC. Unlike elsewhere in Britain, there is little material evidence to suggest a Beaker presence, suggesting that Orkney may have developed along an insular trajectory during the second millennium BC. We tested this by comparing new genomic evidence from 22 Bronze Age and 3 Iron Age burials in northwest Orkney with Neolithic burials from across the archipelago. We identified signals of inward migration on a scale unsuspected from the archaeological record: As elsewhere in Bronze Age Britain, much of the population displayed significant genome-wide ancestry deriving ultimately from the Pontic-Caspian Steppe. However, uniquely in northern and central Europe, most of the male lineages were inherited from the local Neolithic. This suggests that some male descendants of Neolithic Orkney may have remained distinct well into the Bronze Age, although there are signs that this had dwindled by the Iron Age. Furthermore, although the majority of mitochondrial DNA lineages evidently arrived afresh with the Bronze Age, we also find evidence for continuity in the female line of descent from Mesolithic Britain into the Bronze Age and even to the present day.

Contrasting maternal and paternal genetic histories among five ethnic groups from Khyber Pakhtunkhwa, Pakistan

Northwest Pakistan has served as a point of entry to South Asia for different populations since ancient times. However, relatively little is known about the population genetic history of the people residing within this region. To better understand human dispersal in the region within the broader history of the subcontinent, we analyzed mtDNA diversity in 659 and Y-chromosome diversity in 678 individuals, respectively, from five ethnic groups (Gujars, Jadoons, Syeds, Tanolis and Yousafzais), from Swabi and Buner Districts, Khyber Pakhtunkhwa Province, Pakistan. The mtDNAs of all individuals were subject to control region sequencing and SNP genotyping, while Y-chromosomes were analyzed using 54 SNPs and 19 STR loci. The majority of the mtDNAs belonged to West Eurasian haplogroups, with the rest belonging to either South or East Asian lineages. Four of the five Pakistani populations (Gujars, Jadoons, Syeds, Yousafzais) possessed strong maternal genetic affinities with other Pakistani and Central Asian populations, whereas one (Tanolis) did not. Four haplogroups (R1a, R1b, O3, L) among the 11 Y-chromosome lineages observed among these five ethnic groups contributed substantially to their paternal genetic makeup. Gujars, Syeds and Yousafzais showed strong paternal genetic affinities with other Pakistani and Central Asian populations, whereas Jadoons and Tanolis had close affinities with Turkmen populations from Central Asia and ethnic groups from northeast India. We evaluate these genetic data in the context of historical and archeological evidence to test different hypotheses concerning their origins and biological relationships.

Is History the Same as Evolution? No. Is it Independent of Evolution? Certainly Not

History is full of violence and oppression within and between groups, and although group conflicts enhance within-group cooperation (mediated by oxytocin, which promotes parochial altruism) the hierarchy within groups ensures that spoils accrue very unevenly. Darwin suggested, and we now know, that sexual selection is as powerful as selection by mortality, and the main purpose of survival is reproduction. Male reproductive skew is greater than that among females in all societies, but the difference became much greater after the hunting-gathering era, and the rise of so-called "civilization" was everywhere a process of predatory expansion, producing kingdoms and empires where top males achieved astounding heights of reproductive success. This was shown by historical and ethnographic data now strongly confirmed by genomic science. Psychological research confirms that group identity, out-group stigmatization, leadership characterized by charisma, the will to power, narcissism, sociopathy, and cruelty, and followership characterized by hypnotic obedience, loss of individuality, and cruelty are integral parts of human nature. We can thank at least ten or twelve millennia of microevolutionary processes such as those described above, all more prominent in males than females. Followers in wars have faced a difficult risk-benefit analysis, but if they survived and won they too could increase their reproductive success through the rape and other sexual exploitation that have accompanied almost all wars. For modern leaders, social monogamy and contraception have separated autocracy from reproductive success, but only partly, and current worldwide autocratic trends still depend on the evolved will to power, obedience, and cruelty.

Mitogenomics of modern Mongolic-speaking populations

Here, we present a comprehensive data set of 489 complete mitogenomes (211 of which are new) from four Mongolic-speaking populations (Mongols, Barghuts, Khamnigans, and Buryats) to investigate their matrilineal genetic structure, ancestry and relationship with other ethnic groups. We show that along with very high levels of genetic diversity and lack of genetic differentiation, Mongolic-speaking populations exhibit strong genetic resemblance to East Asian populations of Chinese, Japanese, and Uyghurs. Phylogeographic analysis of complete mitogenomes reveals the presence of different components in the gene pools of modern Mongolic-speaking populations-the main East Eurasian component is represented by mtDNA lineages of East Asian, Siberian and autochthonous (the Baikal region/Mongolian) ancestry, whereas the less pronounced West Eurasian component can be ascribed to Europe and West Asia/Caucasus. We also observed that up to one third of the mtDNA subhaplogroups identified in Mongolic-speaking populations can be considered as Mongolic-specific with the coalescence age of most of them not exceeding 1.7 kya. This coincides well with the population size growth which started around 1.1 kya and is detectable only in the Bayesian Skyline Plot constructed based on Mongolic-specific mitogenomes. Our data suggest that the genetic structure established during the Mongol empire is still retained in present-day Mongolic-speaking populations.

Genetic diversity of 'Very Important Pharmacogenes' in two South-Asian populations

OBJECTIVES

Reliable identification of population-specific variants is important for building the single nucleotide polymorphism (SNP) profile. In this study, genomic variation using allele frequency differences of pharmacologically important genes for Gujarati Indians in Houston (GIH) and Indian Telugu in the U.K. (ITU) from the 1000 Genomes Project vis-à-vis global population data was studied to understand its role in drug response.

METHODS

Joint genotyping approach was used to derive variants of GIH and ITU independently. SNPs of both these populations with significant allele frequency variation (minor allele frequency ≥ 0.05) with super-populations from the 1000 Genomes Project and gnomAD based on Chi-square distribution with p-value of ≤ 0.05 and Bonferroni's multiple adjustment tests were identified. Population stratification and fixation index analysis was carried out to understand genetic differentiation. Functional annotation of variants was carried out using SnpEff, VEP and CADD score.

RESULTS

Population stratification of VIP genes revealed four clusters viz., single cluster of GIH and ITU, one cluster each of East Asian, European, African populations and Admixed American was found to be admixed. A total of 13 SNPs belonging to ten pharmacogenes were identified to have significant allele frequency variation in both GIH and ITU populations as compared to one or more super-populations. These SNPs belong to VKORC1 (rs17708472, rs2359612, rs8050894) involved in Vitamin K cycle, cytochrome P450 isoforms CYP2C9 (rs1057910), CYP2B6 (rs3211371), CYP2A2 (rs4646425) and CYP2A4 (rs4646440); ATP-binding cassette (ABC) transporter ABCB1 (rs12720067), DPYD1 (rs12119882, rs56160474) involved in pyrimidine metabolism, methyltransferase COMT (rs9332377) and transcriptional factor NR1I2 (rs6785049). SNPs rs1544410 (VDR), rs2725264 (ABCG2), rs5215 and rs5219 (KCNJ11) share high fixation index (≥ 0.5) with either EAS/AFR populations. Missense variants rs1057910 (CYP2C9), rs1801028 (DRD2) and rs1138272 (GSTP1), rs116855232 (NUDT15); intronic variants rs1131341 (NQO1) and rs115349832 (DPYD) are identified to be 'deleterious'.

CONCLUSIONS

Analysis of SNPs pertaining to pharmacogenes in GIH and ITU populations using population structure, fixation index and allele frequency variation provides a premise for understanding the role of genetic diversity in drug response in Asian Indians.

Fitness and Power: The Contribution of Genetics to the History of Differential Reproduction

Textual evidence from pre-modern societies supports the prediction that status differences among men translate to variance in reproductive success. In recent years, analysis of genetic data has opened up new ways of studying this relationship. By investigating cases that range over several millennia, these analyses repeatedly document the replacement of local men by newcomers and reveal instances of exceptional reproductive success of specific male lineages. These findings suggest that violent population transfers and conquests could generate considerable reproductive advantages for male dominants. At the same time, this does not always seem to have been the case. Moreover, it is difficult to link such outcomes to particular historical characters or events, or to identify status-biased reproductive inequalities within dominant groups. The proximate factors that mediated implied imbalances in reproductive success often remain unclear. A better understanding of the complex interplay between social power and genetic fitness will only arise from sustained transdisciplinary engagement.

Molecular genetic landscape of hereditary hearing loss in Pakistan

Approximately 14.5 million Pakistani individuals have a hearing loss and half of these cases may be due to genetic causes. Though significant progress has been made in uncovering genetic variants for recessively inherited nonsyndromic deafness, Pendred syndrome, and Usher syndromes, the same is not true for dominantly inherited hearing loss, most syndromic cases and deafness with complex inheritance patterns. Variants of 57 genes have been reported to cause nonsyndromic recessive deafness in Pakistan, though most are rare. Variants of just five genes GJB2, HGF, MYO7A, SLC26A4, and TMC1 together explain 57% of profound deafness while those of GJB2, MYO15A, OTOF, SLC26A4, TMC1, and TMPRSS3 account for 47% of moderate to severe hearing loss. In contrast, although variants of at least 39 genes have been implicated in different deafness syndromes, their prevalence in the population and the spectrum of mutations have not been explored. Furthermore, research on genetics of deafness has mostly focused on individuals from the Punjab province and needs to be extended to other regions of Pakistan. Identifying the genes and their variants causing deafness in all ethnic groups is important as it will pinpoint rare as well as recurrent mutations. This information may ultimately help in offering genetic counseling and future treatments.

Exchanging fluids The sociocultural implications of microbial, cultural, and ethnic admixture in Latin America

Knowledge of evolutionary influences on patterns of human mating, social interactions, and differential health is increasing, yet these insights have rarely been applied to historical analyses of human population dynamics. The genetic and evolutionary forces behind biases in interethnic mating and in the health of individuals of different ethnic groups in Latin America and the Caribbean since the European colonization of America are still largely ignored. We discuss how historical and contemporary sociocultural interactions and practices are strongly influenced by population-level evolutionary forces. Specifically, we discuss the historical implications of functional (de facto) polygyny, sex-biased admixture, and assortative mating in Latin America. We propose that these three evolutionary mechanisms influenced mating patterns, shaping the genetic and cultural landscape across Latin America and the Caribbean. Further, we discuss how genetic differences between the original populations that migrated at different times into Latin America contributed to their accommodation to and survival in the different local ecologies and interethnic interactions. Relevant medical and social implications follow from the genetic and cultural changes reviewed.

Integrating Linguistics, Social Structure, and Geography to Model Genetic Diversity within India

India represents an intricate tapestry of population substructure shaped by geography, language, culture, and social stratification. Although geography closely correlates with genetic structure in other parts of the world, the strict endogamy imposed by the Indian caste system and the large number of spoken languages add further levels of complexity to understand Indian population structure. To date, no study has attempted to model and evaluate how these factors have interacted to shape the patterns of genetic diversity within India. We merged all publicly available data from the Indian subcontinent into a data set of 891 individuals from 90 well-defined groups. Bringing together geography, genetics, and demographic factors, we developed Correlation Optimization of Genetics and Geodemographics to build a model that explains the observed population genetic substructure. We show that shared language along with social structure have been the most powerful forces in creating paths of gene flow in the subcontinent. Furthermore, we discover the ethnic groups that best capture the diverse genetic substructure using a ridge leverage score statistic. Integrating data from India with a data set of additional 1,323 individuals from 50 Eurasian populations, we find that Indo-European and Dravidian speakers of India show shared genetic drift with Europeans, whereas the Tibeto-Burman speaking tribal groups have maximum shared genetic drift with East Asians.

Complete mitogenomes document substantial genetic contribution from the Eurasian Steppe into northern Pakistani Indo-Iranian speakers

To elucidate whether Bronze Age population dispersals from the Eurasian Steppe to South Asia contributed to the gene pool of Indo-Iranian-speaking groups, we analyzed 19,568 mitochondrial DNA (mtDNA) sequences from northern Pakistani and surrounding populations, including 213 newly generated mitochondrial genomes (mitogenomes) from Iranian and Dardic groups, both speakers from the ancient Indo-Iranian branch in northern Pakistan. Our results showed that 23% of mtDNA lineages with west Eurasian origin arose in situ in northern Pakistan since ~5000 years ago (kya), a time depth very close to the documented Indo-European dispersals into South Asia during the Bronze Age. Together with ancient mitogenomes from western Eurasia since the Neolithic, we identified five haplogroups (~8.4% of maternal gene pool) with roots in the Steppe region and subbranches arising (age ~5-2 kya old) in northern Pakistan as genetic legacies of Indo-Iranian speakers. Some of these haplogroups, such as W3a1b that have been found in the ancient samples from the late Bronze Age to the Iron Age period individuals of Swat Valley northern Pakistan, even have sub-lineages (age ~4 kya old) in the southern subcontinent, consistent with the southward spread of Indo-Iranian languages. By showing that substantial genetic components of Indo-Iranian speakers in northern Pakistan can be traced to Bronze Age in the Steppe region, our study suggests a demographic link with the spread of Indo-Iranian languages, and further highlights the corridor role of northern Pakistan in the southward dispersal of Indo-Iranian-speaking groups.

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

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.

Y-DNA genetic evidence reveals several different ancient origins in the Brahmin population

The ancient geographical origins of Brahmins-a prominent ethnic group in the Indian subcontinent-have remained controversial for a long time. This study employed the AMOVA (analysis of molecular variance) test to evaluate genetic affinities of this group with thirty populations of Central Asia and Europe. A domestic comparison was performed with fifty non-Brahmin groups in India. The results showed that Brahmins had genetic affinities with several foreign populations and also shared their genetic heritage with several domestic non-Brahmin groups. The study identified the deep ancient origins of Brahmins by tracing their Y-chromosome haplogroups and genetic markers on the Y-DNA phylogenetic tree. It was confirmed that the progenitors of this group emerged from at least 12 different geographic regions of the world. The study concluded that about 83% of the Brahmins in the dataset belonged to four major haplogroups, of which two emerged from Central Asia, one from the Fertile Crescent, and one was of an indigenous Indian origin.

Sex-biased patterns shaped the genetic history of Roma

The Roma population is a European ethnic minority characterized by recent and multiple dispersals and founder effects. After their origin in South Asia around 1,500 years ago, they migrated West. In Europe, they diverged into ethnolinguistically distinct migrant groups that spread across the continent. Previous genetic studies based on genome-wide data and uniparental markers detected Roma founder events and West-Eurasian gene flow. However, to the best of our knowledge, it has not been assessed whether these demographic processes have equally affected both sexes in the population. The present study uses the largest and most comprehensive dataset of complete mitochondrial and Y chromosome Roma sequences to unravel the sex-biased patterns that have shaped their genetic history. The results show that the Roma maternal genetic pool carries a higher lineage diversity from South Asia, as opposed to a single paternal South Asian lineage. Nonetheless, the European gene flow events mainly occurred through the maternal lineages; however, a signal of this gene flow is also traceable in the paternal lineages. We also detect a higher female migration rate among European Roma groups. Altogether, these results suggest that sociocultural factors influenced the emergence of sex-biased genetic patterns at global and local scales in the Roma population through time.

Mitochondrial DNA diversity in the Khattak and Kheshgi of the Peshawar Valley, Pakistan

The strategic location of Pakistan and its presence at the crossroads of Asia has resulted in it playing a central role in both prehistoric and historic human migratory events, thereby linking and facilitating contacts between the inhabitants of the Middle East, Central Asia, China and South Asia. Despite the importance of this region and its inhabitants for our understanding of modern human origins and population dispersals, the nature of mitochondrial DNA (mtDNA) variation among members of the myriad populations of this area has largely been unexplored. Here, we report mtDNA control region sequences in 58 individuals from the Khattak and the Kheshgi, two major Pakhtun tribes residing within the Peshawar Valley of northwestern Pakistan. The results reveal that these ethnic groups are genetically heterogeneous, having 55.7% West Eurasian, 33.9% South Asian and 10.2% East Asian haplogroups. The genetic diversity observed for the Kheshgi was somewhat higher than that of the Khattak. A multidimensional scaling plot based on haplogroup frequencies for the Khattak, Kheshgi and neighboring populations indicates that the Khattak have close affinities with Baluch, Uzbek and Kazak populations but are only distantly related to the Kheshgi and other Pakistani populations. By contrast, the Kheshgi cluster closely with other Pakhtun or Pathan populations of Pakistan, suggesting a possible common maternal gene pool shared amongst them. These mtDNA data allow us to begin reconstructing the origins of the Khattak and Kheshgi and describe their complex interactions with populations from the surrounding regions.

Novel insights on demographic history of tribal and caste groups from West Maharashtra (India) using genome-wide data

The South Asian subcontinent is characterized by a complex history of human migrations and population interactions. In this study, we used genome-wide data to provide novel insights on the demographic history and population relationships of six Indo-European populations from the Indian State of West Maharashtra. The samples correspond to two castes (Deshastha Brahmins and Kunbi Marathas) and four tribal groups (Kokana, Warli, Bhil and Pawara). We show that tribal groups have had much smaller effective population sizes than castes, and that genetic drift has had a higher impact in tribal populations. We also show clear affinities between the Bhil and Pawara tribes, and to a lesser extent, between the Warli and Kokana tribes. Our comparisons with available modern and ancient DNA datasets from South Asia indicate that the Brahmin caste has higher Ancient Iranian and Steppe pastoralist contributions than the Kunbi Marathas caste. Additionally, in contrast to the two castes, tribal groups have very high Ancient Ancestral South Indian (AASI) contributions. Indo-European tribal groups tend to have higher Steppe contributions than Dravidian tribal groups, providing further support for the hypothesis that Steppe pastoralists were the source of Indo-European languages in South Asia, as well as Europe.

Differentiation of Asian population samples using the Illumina ForenSeq kit

The Kidd set of ancestry informative SNPs are included in Illumina's ForenSeq DNA Signature Kit. We had previously reported on the capability of these SNPs together with some phenotypic SNPs with ancestry informative properties in differentiating individuals from the Chinese, Malay and Indian populations in Singapore. The Singapore population is primarily made up of Chinese, Malays and Indians, with individuals from other Asian countries making up the rest. In this study, we evaluated the ancestry prediction capabilities of the ForenSeq kit in 484 unrelated individuals of self-declared Bangladeshi, Burmese, Filipino, Indonesian and Vietnamese origin. 750 Chinese, Malay and Indian individuals previously reported were included in this study. 48 ancestry SNPs and 12 phenotypic SNPs with ancestry informative properties were selected for analyses. Ancestry modelling in STRUCTURE showed that the eight tested populations could be better classified as five. Principal component analysis also showed that the eight populations clustered in five groups based on general geographic location within Asia; with Chinese clustering with Vietnamese, Malays clustering with Indonesians, Indians clustering with Bangladeshi, and the Burmese and Filipino populations clustering in-between and overlapping with the Chinese and Malay populations. The 60 SNPs analysed could account for only 23 % of the variation between the populations. The lack of distinction between the populations resulted in poor (43 % correct self-classification) cross-validation using Snipper. While this was improved by merging the co-clustering populations into five groups (East, South-East, South Asian, Burmese & Filipino), successful self-classification was still relatively low (69 %). While the 60 tested ancestry informative markers were able to differentiate between individuals of East, South-East and South Asian origin, they are not sufficiently informative to effectively discriminate between Chinese, Malays and Indians, and Bangladeshi, Burmese, Filipino, Indonesian and Filipino populations in the country.

Munda languages are father tongues, but Japanese and Korean are not

Over two decades ago, it was observed that the linguistic affinity of the language spoken by a particular population tended to correlate with the predominant paternal, i.e. Y-chromosomal, lineage found in that population. Such correlations were found to be ubiquitous but not universal, and the striking exceptions to such conspicuous patterns of correlation between linguistic and genetic phylogeography elicit particular interest and beg for clarification. Within the Austroasiatic language family, the Munda languages are a clear-cut case of father tongues, whereas Japanese and Korean are manifestly not. In this study, the cases of Munda and Japanese are juxtaposed. A holistic understanding of these contrasting cases of ethnolinguistic prehistory with respect to the father tongue correlation will first necessitate a brief exposition of the phylogeography of the Y chromosomal lineage O. Then triangulation discloses some contours and particulars of both long lost episodes of ethnolinguistic prehistory.

The formation of human populations in South and Central Asia

By sequencing 523 ancient humans, we show that the primary source of ancestry in modern South Asians is a prehistoric genetic gradient between people related to early hunter-gatherers of Iran and Southeast Asia. After the Indus Valley Civilization's decline, its people mixed with individuals in the southeast to form one of the two main ancestral populations of South Asia, whose direct descendants live in southern India. Simultaneously, they mixed with descendants of Steppe pastoralists who, starting around 4000 years ago, spread via Central Asia to form the other main ancestral population. The Steppe ancestry in South Asia has the same profile as that in Bronze Age Eastern Europe, tracking a movement of people that affected both regions and that likely spread the distinctive features shared between Indo-Iranian and Balto-Slavic languages.

Sources of the mitochondrial gene pool of Russians by the results of analysis of modern and paleogenomic data

Paleogenomic studies of recent years have shown that the Bronze Age migrations of populations of the PontoCaspian steppes from the east to the west of Europe had a great influence on the formation of the genetic makeup of modern Europeans. The results of studies of the variability of mitochondrial genomes in the modern Russian populations of Eastern Europe also made it possible to identify an increase in the effective population size during the Bronze Age, which, apparently, could be related to the migration processes of this time. This paper presents the results of analysis of data on the variability of entire mitochondrial genomes in the modern Russian populations in comparison with the distribution of mtDNA haplogroups in the ancient populations of Europe and the Caucasus of the Neolithic and Bronze Age. It was shown that the formation of the modern appearance of the Russian mitochondrial gene pool began approximately 4 thousand years B.C. due to the influx of mtDNA haplotypes characteristic of the population of Central and Western Europe to the east of Europe. It is assumed that the migrations of the ancient populations of the Ponto-Caspian steppes in the western direction led to the formation of mixed populations in Central Europe, bearing mitochondrial haplogroups H, J, T, K, W characteristic of Western and Central Europeans. Further expansion of these populations to the east of Europe and further to Asia explains the emergence of new features of the mitochondrial gene pool in Eastern Europeans. The results of a phylogeographic analysis are also presented, showing that the features of the geographical distribution of the subgroups of the mitochondrial haplogroup R1a in Europe are a reflection of the “Caucasian” component that appeared in the gene pools of various groups of Europeans during the migration of the Bronze Age. The results of phylogeographic analysis of mitochondrial haplogroups U2e2a1d, U4d2, N1a1a1a1, H2b, and H8b1 testify to the migrations of ancient Eastern Europeans to Asia – the south of Siberia and the Indian subcontinent.

Untangling Neolithic and Bronze Age mitochondrial lineages in South Asia

Two key moments shaped the extant South Asian gene pool within the last 10 thousand years (ka): the Neolithic period, with the advent of agriculture and the rise of the Harappan/Indus Valley Civilisation; and Late Bronze Age events that witnessed the abrupt fall of the Harappan Civilisation and the arrival of Indo-European speakers. This study focuses on the phylogeographic patterns of mitochondrial haplogroups H2 and H13 in the Indian Subcontinent and incorporates evidence from recently released ancient genomes from Central and South Asia. It found signals of Neolithic arrivals from Iran and later movements in the Bronze Age from Central Asia that derived ultimately from the Steppe. This study shows how a detailed mtDNA phylogeographic approach, combining both modern and ancient variation, can provide evidence of population movements, even in a scenario of strong male bias such as in the case of the Bronze Age Steppe dispersals.

Ancient Indian history: What do we know and how?

When and where was the Rigveda (Rv) composed? How are the Vedic people related to the vast Harappan archaeological tradition? These quintessential questions have no direct answers. At our current level of understanding, archaeology and sacred texts constitute two distinct streams which do not intersect. We must therefore collate evidence from different sources and try to produce a synthesis. It is particularly important to take note of archaeological evidence from Central Asia, because it has not received the attention it deserves. What is well known in science must be kept in mind in the case of history also. A theory to be valid must explain each and every fact (known at present or to be known in future) in a selfconsistent manner. Conversely, even if there is one piece of evidence that a theory is unable to explain, it should be put on hold, modified or even rejected.

Ethnogenetic analysis reveals that Kohistanis of Pakistan were genetically linked to west Eurasians by a probable ancestral genepool from Eurasian steppe in the bronze age

Despite the unique geographic, ethnic, social and cultural features of Kohistan in Pakistan, the origin and descent of Kohistanis remain still obscure. In an effort to address questions concerning the genetic structure, origin and genetic affinities of Kohistanis, we herein applied an ethnogenetic approach consisting on mitochondrial DNA (mtDNA) analysis and dental morphology analysis. We sequenced HVS1 of mtDNA, observed 14 haplotypes and assigned a total of 9 haplogroups belonging to macrolineages M (17%) and N (83%). Genetic diversity estimates in Kohistanis (Hd = 0.910 ± 0.014; Pi = 0.019 ± 0.001; θw = 0.019 ± 0.006) were similar to that of previous studies in other Pakistani populations. Overall, the analyses of dental morphology and mtDNA profile of Kohistanis resulted in similar findings. All the analyses indicate that Kohistanis share affinities to populations from Europe, Near East, Central Asia and South Asia. The Kohistani HVS1 haplotype 2 shares 100% identity to HVS1 haplotypes across the Europe. These results in light of recent insights into ancient genomics lead us to conclude that ancestry from Eurasian Steppe genetically linked Kohistanis to all these populations in the Bronze Age. This is consistent with linguistic evidence and also with the Indo-Aryan migration model for the peopling of South Asia.

A dispersal of Homo sapiens from southern to eastern Africa immediately preceded the out-of-Africa migration

Africa was the birth-place of Homo sapiens and has the earliest evidence for symbolic behaviour and complex technologies. The best-attested early flowering of these distinctive features was in a glacial refuge zone on the southern coast 100–70 ka, with fewer indications in eastern Africa until after 70 ka. Yet it was eastern Africa, not the south, that witnessed the first major demographic expansion, ~70–60 ka, which led to the peopling of the rest of the world. One possible explanation is that important cultural traits were transmitted from south to east at this time. Here we identify a mitochondrial signal of such a dispersal soon after ~70 ka – the only time in the last 200,000 years that humid climate conditions encompassed southern and tropical Africa. This dispersal immediately preceded the out-of-Africa expansions, potentially providing the trigger for these expansions by transmitting significant cultural elements from the southern African refuge.

The genetic legacy of continental scale admixture in Indian Austroasiatic speakers

Surrounded by speakers of Indo-European, Dravidian and Tibeto-Burman languages, around 11 million Munda (a branch of Austroasiatic language family) speakers live in the densely populated and genetically diverse South Asia. Their genetic makeup holds components characteristic of South Asians as well as Southeast Asians. The admixture time between these components has been previously estimated on the basis of archaeology, linguistics and uniparental markers. Using genome-wide genotype data of 102 Munda speakers and contextual data from South and Southeast Asia, we retrieved admixture dates between 2000–3800 years ago for different populations of Munda. The best modern proxies for the source populations for the admixture with proportions 0.29/0.71 are Lao people from Laos and Dravidian speakers from Kerala in India. The South Asian population(s), with whom the incoming Southeast Asians intermixed, had a smaller proportion of West Eurasian genetic component than contemporary proxies. Somewhat surprisingly Malaysian Peninsular tribes rather than the geographically closer Austroasiatic languages speakers like Vietnamese and Cambodians show highest sharing of IBD segments with the Munda. In addition, we affirmed that the grouping of the Munda speakers into North and South Munda based on linguistics is in concordance with genome-wide data.

Rectifying long-standing misconceptions about the ρ statistic for molecular dating

When divided by a given mutation rate, the ρ (rho) statistic provides a simple estimator of the age of a clade within a phylogenetic tree by averaging the number of mutations from each sample in the clade to its root. However, a long-standing critique of the use of ρ in genetic dating has been quite often cited. Here we show that the critique is unfounded. We demonstrate by a formal mathematical argument and illustrate with a simulation study that ρ estimates are unbiased and also that ρ and maximum likelihood estimates do not differ in any systematic fashion. We also demonstrate that the claim that the associated confidence intervals commonly estimate the uncertainty inappropriately is flawed since it relies on a means of calculating standard errors that is not used by any other researchers, whereas an established expression for the standard error is largely unproblematic. We conclude that ρ dating, alongside approaches such as maximum likelihood (ML) and Bayesian inference, remains a useful tool for genetic dating.

The genetic legacy of the Yaghnobis: A witness of an ancient Eurasian ancestry in the historically reshuffled central Asian gene pool

OBJECTIVES

The Yaghnobis are an ethno-linguistic minority historically settled along the Yaghnob River in the Upper-Zarafshan Valley in Tajikistan. They speak a language of Old Sogdian origin, which is the only present-day witness of the Lingua Franca used along the Silk Road in Late Antiquity. The aim of this study was to reconstruct the genetic history of this community in order to shed light on its isolation and genetic ancestry within the Euro-Asiatic context.

MATERIALS AND METHODS

A total of 100 DNA samples were collected in the Yaghnob and Matcha Valleys during several expeditions and their mitochondrial, Y-chromosome and autosomal genome-wide variation were compared with that from a large set of modern and ancient Euro-Asiatic samples.

RESULTS

Findings from uniparental markers highlighted the long-term isolation of the Yaghnobis. Mitochondrial DNA ancestry traced an ancient link with Middle Eastern populations, whereas Y-chromosome legacy showed more tight relationships with Central Asians. Admixture, outgroup-f3, and D-statistics computed on autosomal variation corroborated Y-chromosome evidence, pointing respectively to low Anatolian Neolithic and high Steppe ancestry proportions in Yaghnobis, and to their closer affinity with Tajiks than to Iranians.

DISCUSSION

Although the Yaghnobis do not show evident signs of recent admixture, they could be considered a modern proxy for the source of gene flow for many Central Asian and Middle Eastern groups. Accordingly, they seem to retain a peculiar genomic ancestry probably ascribable to an ancient gene pool originally wide spread across a vast area and subsequently reshuffled by distinct demographic events occurred in Middle East and Central Asia.

The genetic makings of South Asia

South Asia is home for more than a billion people culturally structured into innumerable groups practicing different levels of endogamy. Linguistically South Asia is broadly characterized by four major language families which has served as access way for disentangling the genetic makings of South Asia. In this review we shall give brief account on the recent developments in the field. Advances are made in two fronts simultaneously. Whole genome characterisation of many extant South Asians paint the picture of the genetic diversity and its implications to health-care. On the other hand ancient DNA studies, which are finally reaching South Asia, provide new incites to the demographic history of the subcontinent. Before the spread of agriculture, South Asia was likely inhabited by hunter-gatherer groups deriving much of their ancestry from a population that split from the rest of humanity soon after expanding from Africa. Early Iranian agriculturalists mixing with these local hunter-gatherers probably formed the population that flourished during the blossoming of the Indus Valley Civilisation. Further admixture with the still persisting HG groups and population(s) from the Eurasian Steppe, formed the two ancestral populations (ANI and ASI), the north-south mixing pattern of whom is known today as the 'Indian Cline'. Studies on natural selection in South Asia have so far revealed strong signals of sweeps that are shared with West Eurasians. Future studies will have to fully unlock the aDNA promise for South Asia.

Global demographic history of human populations inferred from whole mitochondrial genomes

The Neolithic transition has led to marked increases in census population sizes across the world, as recorded by a rich archaeological record. However, previous attempts to detect such changes using genetic markers, especially mitochondrial DNA (mtDNA), have mostly been unsuccessful. We use complete mtDNA genomes from over 1700 individuals, from the 1000 Genomes Project Phase 3, to explore changes in populations sizes in five populations for each of four major geographical regions, using a sophisticated coalescent-based Bayesian method (extended Bayesian skyline plots) and mutation rates calibrated with ancient DNA. Despite the power and sophistication of our analysis, we fail to find size changes that correspond to the Neolithic transitions of the study populations. However, we do detect a number of size changes, which tend to be replicated in most populations within each region. These changes are mostly much older than the Neolithic transition and could reflect either population expansion or changes in population structure. Given the amount of migration and population mixing that occurred after these ancient signals were generated, we caution that modern populations will often carry ghost signals of demographic events that occurred far away from their current location.

New insights from Thailand into the maternal genetic history of Mainland Southeast Asia

Tai-Kadai (TK) is one of the major language families in Mainland Southeast Asia (MSEA), with a concentration in the area of Thailand and Laos. Our previous study of 1234 mtDNA genome sequences supported a demic diffusion scenario in the spread of TK languages from southern China to Laos as well as northern and northeastern Thailand. Here we add an additional 560 mtDNA genomes from 22 groups, with a focus on the TK-speaking central Thai people and the Sino-Tibetan speaking Karen. We find extensive diversity, including 62 haplogroups not reported previously from this region. Demic diffusion is still a preferable scenario for central Thais, emphasizing the expansion of TK people through MSEA, although there is also some support for gene flow between central Thai and native Austroasiatic speaking Mon and Khmer. We also tested competing models concerning the genetic relationships of groups from the major MSEA languages, and found support for an ancestral relationship of TK and Austronesian-speaking groups.

Ancient Human Migrations to and through Jammu Kashmir- India were not of Males Exclusively

Jammu and Kashmir (J&K), the Northern most State of India, has been under-represented or altogether absent in most of the phylogenetic studies carried out in literature, despite its strategic location in the Himalayan region. Nonetheless, this region may have acted as a corridor to various migrations to and from mainland India, Eurasia or northeast Asia. The belief goes that most of the migrations post-late-Pleistocene were mainly male dominated, primarily associated with population invasions, where female migration may thus have been limited. To evaluate female-centered migration patterns in the region, we sequenced 83 complete mitochondrial genomes of unrelated individuals belonging to different ethnic groups from the state. We observed a high diversity in the studied maternal lineages, identifying 19 new maternal sub-haplogroups (HGs). High maternal diversity and our phylogenetic analyses suggest that the migrations post-Pleistocene were not strictly paternal, as described in the literature. These preliminary observations highlight the need to carry out an extensive study of the endogamous populations of the region to unravel many facts and find links in the peopling of India.

Application of geographic population structure (GPS) algorithm for biogeographical analyses of populations with complex ancestries: a case study of South Asians from 1000 genomes project

Background

The utilization of biological data to infer the geographic origins of human populations has been a long standing quest for biologists and anthropologists. Several biogeographical analysis tools have been developed to infer the geographical origins of human populations utilizing genetic data. However due to the inherent complexity of genetic information these approaches are prone to misinterpretations. The Geographic Population Structure (GPS) algorithm is an admixture based tool for biogeographical analyses and has been employed for the geo-localization of various populations worldwide. Here we sought to dissect its sensitivity and accuracy for localizing highly admixed groups. Given the complex history of population dispersal and gene flow in the Indian subcontinent, we have employed the GPS tool to localize five South Asian populations, Punjabi, Gujarati, Tamil, Telugu and Bengali from the 1000 Genomes project, some of whom were recent migrants to USA and UK, using populations from the Indian subcontinent available in Human Genome Diversity Panel (HGDP) and those previously described as reference.

Results

Our findings demonstrate reasonably high accuracy with regards to GPS assignment even for recent migrant populations sampled elsewhere, namely the Tamil, Telugu and Gujarati individuals, where 96%, 87% and 79% of the individuals, respectively, were positioned within 600 km of their native locations. While the absence of appropriate reference populations resulted in moderate-to-low levels of precision in positioning of Punjabi and Bengali genomes.

Conclusions

Our findings reflect that the GPS approach is useful but likely overtly dependent on the relative proportions of admixture in the reference populations for determination of the biogeographical origins of test individuals. We conclude that further modifications are desired to make this approach more suitable for highly admixed individuals.

Electronic supplementary material

The online version of this article (doi: 10.1186/s12863-017-0579-2) contains supplementary material, which is available to authorized users.

Population resequencing of European mitochondrial genomes highlights sex-bias in Bronze Age demographic expansions

Interpretations of genetic data concerning the prehistory of Europe have long been a subject of great debate, but increasing amounts of ancient and modern DNA data are now providing new and more informative evidence. Y-chromosome resequencing studies in Europe have highlighted the prevalence of recent expansions of male lineages, and focused interest on the Bronze Age as a period of cultural and demographic change. These findings contrast with phylogeographic studies based on mitochondrial DNA (mtDNA), which have been interpreted as supporting expansions from glacial refugia. Here we have undertaken a population-based resequencing of complete mitochondrial genomes in Europe and the Middle East, in 340 samples from 17 populations for which Y-chromosome sequence data are also available. Demographic reconstructions show no signal of Bronze Age expansion, but evidence of Paleolithic expansions in all populations except the Saami, and with an absence of detectable geographical pattern. In agreement with previous inference from modern and ancient DNA data, the unbiased comparison between the mtDNA and Y-chromosome population datasets emphasizes the sex-biased nature of recent demographic transitions in Europe.