Research Publication and Spreadsheet Resource Center

[Kapisa]

Ancient Migrations - The first complete genome assembly, annotation and variants of the Zoroastrian-Parsi community of India
Naseer Pasha, Kashyap Krishnasamy, Naveenkumar Nagarajan, Seshank Mutya, Bhavika Mam, Kouser Sonnekhan, Chellappa Gopalakrishnan, Renuka Jain, Villoo Morawala-Patell
Abstract
With the advent of Next Generation Sequencing, many population specific whole genome sequences published thus far, predominantly represent individuals of European ancestry. While sequencing efforts of underrepresented communities in genomes datasets, like the Yoruba West-African, Han Chinese, Tibetan, South Korean, Egyptian and Japanese have recently added to the public genomic repositories, a comprehensive understanding of human genomic diversity and discovery of trait-associated variants necessitates the need for additional population specific analysis. In this context, the genomics of the population from the Indian sub-continent, given its genetic heterogeneity needs further elucidation.

In this context, the endogamous Zoroastrian-Parsi community of India, offer an exceptional insight into a homogenous population that has culturally, socially, and genetically remained intact, for 13 centuries amidst the genomic, social and cultural Indian landscape, consequent to their migration from the ancient Persian plateau.

Notwithstanding longevity as a trait, this endangered community is highly susceptible to cancers, rare genetic disorders, and display a documented high incidence of neurodegenerative and autoimmune conditions. The community as a matter of cultural practice abstains from smoking.

Here, we describe the assembly and annotation of the genome of an adult female, Zoroastrian-Parsi individual sequenced at a high depth of 173X using a combination of short Illumina reads (160X) and long nanopore reads (13X). Using a combination of hybrid assemblers, we created a new, population-specific human reference genome, The Zoroastrian-Parsi Genome Reference Female, AGENOME-ZPGRF, contains 2,778,216,114 nucleotides as compared to 3,096,649,726 in GRCh38 constituting 93.235% of the total genomic fraction. Annotation identified 20833 genomic features, of which 14996 are almost identical to their counterparts on GRCh38 while 5837 genomic features were covered in partial. AGENOME-ZPGRF contained 5,426,310 variants of which the majority were SNP’s (4,291,601) and 960,867 SNPs were AGENOME-ZPGRF specific personal variants not listed in dbSNP.

We present, AGENOME-ZPGRF as a whole reference for any genetic studies involving Zoroastrian-Parsi individuals extending their application to identify disease relevant prognostic biomarkers and variants in global population genomics studies.
https://www.biorxiv.org/content/10.1...02.17.431362v1

Note: Reviving thread only to post research publications relevant to South and Central Asia.

[Kapisa]

Integrating linguistics, social structure, and geography to model genetic diversity within India
Aritra Bose, Daniel E. Platt, Laxmi Parida, Petros Drineas, Peristera Paschou
doi: https://doi.org/10.1101/164640
Abstract
India represents an intricate tapestry of population substructure shaped by geography, language, culture and social stratification. While 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 COGG (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 highlighted by COGG. Integrating data from India with a data set of additional 1,323 individuals from 50 populations we find that Europeans show shared genetic drift with the Indo-European and Dravidian speakers of India, whereas the East Asians have the maximum shared genetic drift with Tibeto-Burman speaking tribal groups.

Note: Interesting approach but unfortunately like previous papers IE populations from Pakistan parts of North India were not included which is bound to effect the analysis.
IMO there should be atleast two clusters among IE speakers.

[Ryukendo]

A paper on the Gandhara grave culture of Swat, i.e. where the Swat_IA samples came from:

https://www.researchgate.net/publica...stern_Pakistan

Abstract

This chapter describes the manner in which the archaeological record of northwest Pakistan was initially interpreted and new insights from more recent work on the Gandharan Grave Culture. The analysis of the grave goods within the protohistoric cemeteries reveals that the majority of the graves contained fewer than five artifacts. Pottery was the most common variety of grave good and was present in almost all the analyzed graves within the protohistoric cemeteries. The prevalent understandings of the protohistoric cemeteries within Pakistan archaeology are shaped by two contemporary archaeological models, developed by teams of archaeologists from Istituto Italiano per il Medio ed Estremo Oriente (IsMEO) and University of Peshawar (UoP). These models are mainly concerned with the ethnic identification of the people buried within graves and both models associated the protohistoric cemeteries with groups of people discernible in Rg Vedic and classical literary sources.

Some interesting quotes:

The human remains were either inhumed or cremated within these protohistoric
cemeteries. There was a lot of variation within the different inhumation styles (flexed and
disarticulated) and cremation practices within each of the cemeteries and no two cemeteries
were the same in terms of the burial practices. Both the flexed and disarticulated human
remains were carefully manipulated within the graves to reflect on the concepts or ideologies
of devotion to the deceased and regeneration of the survivors. The cremated remains
were mostly placed within urns, some of which were decorated with the human face, and
were probably linked with the concepts of regeneration and ancestor veneration or cult.
The analysis of the sex‐ and age‐based groups suggests that both males and females, and
children (with few exceptions at Timargarha 1) and adults, were buried in similar fashion,
in similar graves, and with the same repertoire of grave goods. There were no specific sex‐
or age‐based differentiations that were systematically maintained within all cemeteries. The
double (and multiple) burials involving both sexes were probably part of a tradition of
family or lineage burials. Children were included in the inhumations and the cremation
burials, buried individually or with other adults.

Dani believed that the Gandhara Grave Culture represented Aryans, who were the people
named in the Rg Veda (Dani, 1968a: 23, 55). However, Gupta (1972: 168) considered
Dani’s (1968a: 23–24) association of different chronological periods with events from
Indian mythology and history (e.g., Mahabharata or Achaemenid’s invasion) as “premature.” There is no reference in Rg Veda to elaborate grave constructions (e.g., stone‐lined
lower grave chambers, upper stone circles) and rectangular shapes (Gupta, 1972: 165).
Neither the complete inhumations of period I nor the flexed inhumations are mentioned in
Rg Veda (Gupta, 1972: 167). In Rg Veda, too, there is no report of erecting a grave or
monument over urn burials and there is no mention of multiple cremation (of sex‐ and
age‐based groups). Burials in urns actually run against the teaching of the Rg Veda (Gupta,
1972: 166–167). Dani’s category of “mixed burials” (containing inhumations and cremation burials)
has no parallels within the Rg Vedic literature or with burial practices in South
Asia generally (Gupta, 1972: 168). There is no reference to large‐scale cemeteries—such as
Timargarha 1—in Rg Veda either (Gupta, 1972: 167).

The more I read about this, the more I think some sort of endogamy/barriers to marriage in certain directions may have dated back even to the initial impulse of Steppe_MLBA populations into India, and the SWAT_IA samples may have come from non-Aryans.

[parasar]

A paper on the Gandhara grave culture of Swat, i.e. where the Swat_IA samples came from:

https://www.researchgate.net/publica...stern_Pakistan

Abstract


Some interesting quotes:





The more I read about this, the more I think some sort of endogamy/barriers to marriage in certain directions may have dated back even to the initial impulse of Steppe_MLBA populations into India, and the SWAT_IA samples may have come from non-Aryans.

The Italian group's finding are also similar to Zahir's.

"Archaeologists have caught another glimpse of Swat’s glorious past — revealing secrets of a civilisation that have been buried in the earth for over 3,000 years.
The Italian Archaeological Mission on Wednesday discovered an ancient cemetery dating back thousands of years at Odigram, Swat — a site experts believe was built between 1500 BC to 500 BC...
... It clearly indicates that Swat Valley was thickly populated at that time ... What we can understand from the graves is that they were a very powerful civilisation. They were socially well organised and apparently very peaceful because no weapons were found from the site, unlike most civilisations ..." https://tribune.com.pk/story/466048/...overed-in-swat

"a female-centred pattern: women were buried in megalithic graves, thereby alluding to their leading role in the household, while the remains of a male relative played an important but secondary
role as an ‘accessory’"
"the primary burial was a mature adult female, resting directly on the floor of the grave, followed by a secondary burial of a male"
"burials of males often followed the primary interment of an adult female"
https://www.researchgate.net/publica...78ea5/download

[Kapisa]

Differences in the Patterns of Kidarite and Alkhon Coin Distribution at Begram

Elizabeth Errington
2010, Coins, Art amd Chronology II. The First Millennium C.E. in the Indo-Iranian Borderlands.
https://www.academia.edu/3687672/Dif...ard=view-paper

[Kapisa]

Buddhism in North-western India and Eastern Afghanistan, Sixth to Ninth Century AD
Giovanni VERARDI
2012
https://core.ac.uk/download/pdf/39283136.pdf

[Kapisa]

Lost and Found - Prehistoric Pottery Treasures from Baluchistan

Page Numbers: 400
Publication Date: 2015
Publication Name: U. Franke, E. Cortesi (eds.), Lost and Found Prehistoric Pottery Treasures from Baluchistan
The outstanding collection of several hundred vessels confiscated by the Pakistani customs in the port of Karachi and presented here provides a glimpse into this amazing past and rich cultural heritage of Baluchistan. The sheer amount of objects on the art market is a sad message about the loss of this legacy and underlines the need to protect its treasures from being lost. This book puts them into a cultural and chronological perspective from the Neaolithic through the Indus Period and gives an account of the archaeological research carried out by the German-Pakistan Archaeological Mission to Kalat and the French Archaeological Mission to Pakistan, with a contribution by Aurore Didier and Benjamin Mutin.

Exhibition catalogue presenting 820 objects dating from the 4th millennium BC to the 4th/3rd century BC, confiscated by Pakistani customs in Karachi.
Printed in Karachi 2015, 400 pages, c. 1800 illustrations and images.

https://www.academia.edu/42141893/Lo...ork_card=title

[Kapisa]

Craniofacial reconstruction of the Indus Valley Civilization individuals found at 4500-year-old Rakhigarhi cemetery

Won Joon Lee 1 , Vasant Shinde 2 , Yong Jun Kim 3 , Eun Jin Woo 4 , Nilesh Jadhav 5 , Pranjali Waghmare 5 , Yogesh Yadav 5 , Avradeep Munshi 5 , Amrithavalli Panyam 5 , Malavika Chatterjee 5 , Chang Seok Oh 3 , Jong Ha Hong 3 , Caroline M Wilkinson 6 , Christopher Rynn 7 , Dong Hoon Shin 8

Abstract

Despite academic efforts to study the Indus Valley Civilization (IVC), there have as yet been no successful attempts to unveil the IVC people's craniofacial appearance. We investigated the IVC cemetery area of Rakhigarhi site, which was estimated to be of 2273 ± 38 and 2616 ± 73 years BCE. By craniofacial reconstruction (CFR) procedure using computed tomography (CT) data of two Rakhigarhi skulls (A1 BR02 and A2 BR36), we successfully reconstructed the faces of the IVC individuals who were buried about 4500 years ago. This is the first attempt to unveil scientifically accurate representations of IVC people's actual facial morphology.

https://pubmed.ncbi.nlm.nih.gov/31578677/
Anat Sci Int
. 2020 Mar;95(2):286-292. doi: 10.1007/s12565-019-00504-3. Epub 2019 Oct 1.
Attachment 45292

[Kapisa]

Trace metals as markers for historical anthropogenic contamination: Evidence from the Peshawar Basin, Pakistan
Mehwish Bibi, Michael Wagreich, Shahid Iqbal
Department of Geodynamics and Sedimentology, University of Vienna, Austria
Department of Earth Sciences, Quaid-i-Azam University, Islamabad, Pakistan
Science of the Total Environment 703 (2020) 134926

Abstract
Trace element concentrations in the youngest Holocene sedimentary archives, historical mining, and archaeological sites are reliable indicators for historical anthropogenic contamination. The Pleistocene- Holocene strata and the overlying archaeological sites of the Peshawar Basin, NW Pakistan provide sed- imentary archives to explore historical anthropogenic controls on the distributions of trace elements. The basin with 2500 y of human civilization was sampled using archaeological trenches at Gor Khuttree and Hund, and six sections of youngest Pleistocene-Holocene strata along river banks. Geochemical analysis of high-resolution samples were conducted for both the lacustrine-floodplain sediments and archaeolog- ical sites. Results from various horizons of the archaeological sites provide signals for anthropogenic con- trol on the distribution of As, Zn, Cu, Mo, Pb, Hg, Ag, and Au during the Meghalayan Stage of Holocene that gain progressive strength since the 18th century. The geochemical proxies negate direct mining of Cu-Pb and Zn in the area. The consistent, anthropogenic Ag and Au contribution to the system throughout the basin’s archaeological history is a significant finding. When correlated against the anthropogenic mercury contamination, it appears that Hund was a major silver-gold panning site throughout its known history whereas Gor Khuttree was the major silver-gold processing center. The Peshawar Basin anthropogenic signals contribute to widespread European early Anthropocene signals at around 2000 BP related to the Greek and Roman mining. Signals during the Hindu Shahi period correlate well with the Medieval period mining and smelting peak signals observed in Europe and China. Hg, Ag, and Au concentrations in the area since the start of the 19th century CE correlates to the start of industrialisation. During the mid-20th century, these geochemical signals from the Gor Khuttree reflect anthropogenic contributions to the local system and correlate to the suggested base of a formalised Anthropocene.

https://anthropocene-vienna.univie.a....2019.SoTE.pdf

[Kapisa]

Analysis and contextualization of potential protohistoric petroglyphs at the Kalasha valley of Birir in Chitral
Muhammad Zahir, Ph.D.
Associate Professor, Department of Archaeology, Hazara University, Mansehra, Pakistan
&
Affiliate Researcher, Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
Zahir, M. (2020). JHSS. XXVIII No. (2)
https://www.researchgate.net/publica...rir_in_Chitral
Abstract
Petroglyphs were discovered in the Birir valley of district Chitral, Khyber Pakhtunkhwa province, Pakistan, on an ancient route connecting the Kalasha valleys with Nuristan, lower Chitral and Central Asia. The petroglyphs were engraved on a solitary schist stone. The rock, with associated structures, occupies a strategic location in the landscape, possibly representing a hunting outpost. The petroglyphs consist of 29 figures, including human, animal, geometric and indistinct figures. These figures seem to have been created through the use of a metal stylus/burin. The figures were produced through the percussion method, utilizing a stippling technique. The depiction of a dog, a goat and stylized human figures suggest a possible link to the subsistence and hunting strategies of the protohistoric people in the region. Based upon the limited archaeological knowledge of the region, the present petroglyph site may tentatively be dated to the 1st millennium BCE.

"Six prehistoric sites, with stone tools, and some associated rock shelters, dateable from 8th to 3rd millennium BP, were discovered from the upper reaches of Yarkhun Valley in northern Chitral in the 1990s by a joint team of French and Pakistani researchers (Gaillard et al, 2002: 25). The possible persistence of stone tools by prehistoric communities until the first millennium BCE in Chitral is potentially significant to our broader understanding of the region‟s prehistory and needs to be further investigated in the future."

Discovery of recent lithic industries with archaic features in the Hindu Kush range (Chitral district, North Pakistan).
Claire Gaillard, Anne Dambricourt Malassé, J. Magraner, A. Maitrerobert, Taj Ali, Jean-Luc Voisin, Nasir Abdul...

https://halshs.archives-ouvertes.fr/halshs-00355935
Abstract : Survey in the upper reaches of the Yarkhun valley (Chitral district, northern Pakistan), on the southern slopes of the Hindu Kush range, led to the discovery of six sites yielding lithic industries at altitudes between 3000 and 4000 m. These lithic series bear common features. Technologically they appear archaic for they just consist of coarsely trimmed cobbles or chips collected from close surroundings. The collection, however, satisfies some selection criteria based on shape and raw material (quartz, quartzite, amphibolite, sometimes marble). There is no core reduction for producing flakes. Typologically most of the tools look like axes of various shapes, but with smooth rather than sharp edges; there are also choppers and some smaller tools like notches and end-scrapers with a very particular form of bipolar retouch.
According to their geomorphological situation and referring to the chronology established in the neighbouring range of Karakoram, these industries belong to a time period between 8000 and 3000 years BP. They are contemporary with the Neolithic and related to a tradition of pebble tools characteristic of the sub-Himalayan belt from the Lower Palaeolithic to the late Neolithic.
These new sites in the Hindu Kush, in association with those in the Pamir (Tajikistan), in the Siwaliks (Pakistan, India, Nepal) and maybe further east along the southern fringes of the Himalayas, raise the question of cultural isolation of the mountain populations away from the plain populations. At high altitudes, environmental or behavioural factors might have delayed the introduction of technological innovations as well as the neolithisation process.

Relations between climatic changes and prehistoric human migrations during Holocene between Gissar Range, Pamir, Hindu Kush and Kashmir: The archaeological and ecological data

January 2011Quaternary International 22(1-2):123-131
DOI:10.1016/j.quaint.2010.04.001
Project: Prehistory of Siwaliks

a b s t r a c t In the beginning of the Holocene, hunteregatherer populations settled in the Pamir plateau, especially in the tectonic depression of Markansu near the Kara Kul Lake (Osh Kona site, 4100 m, 9580 BP and 7145 BP). These populations were well adapted to high altitude life conditions in summer. They were using stone tools related to a cobble tool tradition that Ranov considered as the local continuation of an Asian Middle Palaeolithic (Ferghana, Darwaz or Punjab). However, they disappeared during the second half of the Holocene. As well, huntersegatherers characterised by a tradition close to Markansu Culture, namely Hissar Culture, appeared during the Holocene in the northern mountains of the TajikeAfghan depression (Amu Darya upper basin) occupying the middle altitude valleys (Gissar Range) when Neolithic pop-ulations began to develop at lower altitudes. For Ranov, origin and destiny of both Markansu and Hissar cultures were the most important questions to solve in this region. The Department of Prehistory, National Museum of Natural History (Paris) conducted field work in collaboration with the University of Peshawar between 1996 and 1998 in the northernmost valley of the Indus basin giving access to the Wakhan corridor. The upper Yarkhun valley (Chitral district, Pakistan), accessible only by foot, was surveyed from 2500 to 4000 m altitude. This allowed the discovery of 6 sites yielding lithic artefacts, among which half are cobble tools. They attest to human activity later than 5500 BP, suggesting pop-ulation movements between the Amu Darya and Indus basins. The consequences of the Quaternary climate oscillations between South Asian monsoon and Northern hemisphere influences on the one hand, and the impact on biotopes of the increasing pastoral activity on the other hand, are discussed as probable causes for the disappearance of the mountainous nomadic hunters of Central Asia.

https://www.researchgate.net/publica...cological_data