Ancient DNA (Anthropology)

The history of human populations in Africa is complex and includes various demographic events that influenced patterns of genetic variation across the continent. Through genetic studies of modern-day, and most recently, ancient African genetic variation, it became evident that deep African history is captured by the relationships among hunter-gatherers. Furthermore, it was shown that agriculture had a large influence on the distribution of current-day Africans. These later population movements changed the demographic face of the continent and descendants of farming groups today form the majority populations across Africa. Ancient DNA methods are continually evolving, and we see evidence of this in how research has advanced in the last decade. With the increased availability of full genomic data from diverse sets of modern-day and prehistoric Africans we now have more power to infer human demography. Future ancient DNA research promises to reveal more detailed stories of human prehistory in Africa.

The effects of European colonization on the genomes of Native Americans may have produced excesses of potentially deleterious features, mainly due to the severe reductions in population size and corresponding losses of genetic diversity. This assumption, however, neither considers actual genomic patterns that existed before colonization nor does it adequately capture the effects of admixture. In this study, we analyze the whole-exome sequences of modern and ancient individuals from a Northwest Coast First Nation, with a demographic history similar to other indigenous populations from the Americas. We show that in approximately ten generations from initial European contact, the modern individuals exhibit reduced levels of novel and low-frequency variants, a lower proportion of potentially deleterious alleles, and decreased heterozygosity when compared to their ancestors. This pattern can be explained by a dramatic population decline, resulting in the loss of potentially damaging low-frequency variants, and subsequent admixture. We also find evidence that the indigenous population was on a steady decline in effective population size for several thousand years before contact, which emphasizes regional demography over the common conception of a uniform expansion after entry into the Americas. This study examines the genomic consequences of colonialism on an indigenous group and describes the continuing role of gene flow among modern populations.

This is a brief introduction to my recently published book ‘Prachin Bharatiya Samskruti: Mooladharanchya Shodhat’ (In Search of  the Roots of Ancient Indian culture)—Gopal Chippalkatti

References to the West Asian and European contacts galore in the in the wake of Indo-European language and Aryan race studies in the histories books on ancient India. The East and China are seldom mentioned. Rare references to
contacts-relations-influences  between pre- Buddhist Magadh in Eastern India and Sichuan and Yunnan, the western provinces of China are somewhere mentioned in margins. However, in the eyes of this author these links point towards possibilities and for altering altogether our understanding of ancient Indian history, culture, religion, language and race. Connecting these links and destroying the myth of singular culture presuppositions of the ancient India it attempts to draw an altogether new picture. A new fountainhead of our cultural past emerges. It postulates an entirely new way of thinking and a new direction.

Zhang Quian, who  reached from China to Bactria via the trans Himalayan Silk Road  in 2nd century BCE, mentioned that  Sichuan cloth and Quian staves were transported directly to Magadh in Eastern India on ardourous routes for centuries together.  The book lists such references and expects thorough investigation using such scarce references,  both in Chinese and Indian sources, for detailed studies with all the concomitant cultural linkages. Though on a smaller scale and with limited resources, it begins to and expands the probing horizons into religion, language, philosophy and other spheres of culture.

Contents of the book are spread over eight chapters. In the first two chapters It lays threadbare the  linkages of varied relations between North East India, Bengal and Magadh with Sichuan and Yunnan with references to paths, trading commodities etc. in ancient and medieval times. It contains references from the  Indian scholars like Harprasad Ray, P.C. Bagchi, Sharat and Supriti Phukan, Arvind Jamkhedkar, Amalendu Guha,  Shridhar Vyankatesh Ketkar, Sunitikumar Chatterjee. It quotes from western  and Chinese scholars like Joseph Needham and Bin Yang. Giving a brief history of China it juxtaposes varied cultural contexts. It discusses the walls of China, Southwestern independent cultures in Sichuan and Yunnan,  use of bronze couldrauns and weapons, horses and chariots and things like bamboo, silk, rice and cowrees to weave a tapestry of an alternate coexistence of Eastern neighborhood cultures equally thick when compared with the western Aryans. It compares the philosophies, religions, social formations of the two landscapes of Eastern India and western China.

An archaeological and historical review of the Steppe Scythians- Shakas is attempted in Chapter III. It shows the advent of Scythian Northerners in early China and their possible connections with Shakys and Lichhavis of Magadh.
Chapter IV specifies the differences between Vedic and Shraman cultures and shows the eastern Shraman tradition as the foundation of earliest history and culture of India.  Chapter V brings forth Parshvanath as the founder of Shraman philosophy and shows Jain ethos in relief and it's connections with the aboriginals in central and eastern India. Buddhism- it's tradition, philosophy and religion- is portrayed in relation to the main thesis of the book and its spread across nations is shown in Chapter VI.  Languages in Assam Bengal and their connect with Sino-Tibetan-Burman languages is sketched in Chapter VII. A brief update on ancient Indian languages is attempted in Chapter VIII. The author has written a prologue to make his value premises clear. The book contains a considerably exhaustive bibliography.

As research into DNA and the ability to extract samples from increasingly older human remains grows and develops, so too have the legal and ethical quandaries of researching native and minority ethnic group’s ancestral remains.  In this paper, I explore these legal and ethical issues that have arisen, issues that may develop in the future, and potential solutions to these problems.

The reliquary of Jacques de Vitry, a prominent clergyman and theologian in the early 13th
century, has experienced several transfers over the last centuries, which seriously question
the attribution of the remains to the late Cardinal. Uncertainty about the year of his birth
poses an additional question regarding his age at death in 1240. The reliquary, located in
the Saint Marie d’Oigines church, Belgium, was reopened in 2015 for an interdisciplinary
study around his relics as well as the Treasure of Oignies, a remarkable cultural heritage
notably built from Jacques de Vitry’s donation. Anthropological, isotopic and genetic analyses
were performed independently on the remains found in the reliquary. Results of the
analyses provided evidence that the likelihood that these remains are those of Jacques de
Vitry is very high: the remains belong to the same human male individual and the historical
tradition about his age is confirmed. In addition, a separate relic (left tibia) was analysed and
found to match with the remains of the reliquary (right tibia). The unique Jacques de Vitry’s
mitre, made of parchment, was sampled non-destructively and the extracted parchment collagen
was analysed by a proteomic method in order to determine the animal species. The
results showed that, surprisingly, not all parts of the mitre were made from the same species.
All together, these findings are expected to fertilize knowledge carried by historical tradition
around the relics of Jacques de Vitry and his related cultural heritage.

Abstrak Penelitian migrasi dan penghunian manusia kuno di Indonesia masih memunculkan perdebatan sampai kini, baik dari perspektif antropologi biologis, genetika manusia atau arkeologis. Perdebatan itu selalu membuka ruang lagi untuk melakukan penelitian perihal itu. Kali ini kami berkonsentrasi dengan sampel Bali Kuno, yakni temuan sisa-sisa manusia dari Gilimanuk (Melaya, Jembrana) dan Semawang (Sanur, Denpasar). Bali merupakan pulau yang relatif terletak di tengah gugusan kepulauan Indonesia, di mana dapat mewakili jalur besar migrasi dan persebaran manusia seturut rute pulau-pulau busur luarnya. Penelitian ini bertujuan untuk mendeskripsikan variasi genetik manusia kuno dari dua situs arkeologis Bali itu. Berdasarkan lokus short tandem repeats (STR) combined DNA index system (CODIS), yakni CSF1PO, TH01 dan TP0X, penelitian ini mengambil sampel enam individu manusia Bali Kuno, yang meliputi masing-masing tiga individu Semawang dan Gilimanuk. Proses penelitian genetik itu telah dikerjakan di Laboratory of Human Genetics, Institute of Tropical Disease, Universitas Airlangga. Sampel Semawang dan Gilimanuk berasal dari populasi yang berbeda berdasarkan analisis visualisasi lokus CTT-nya. Hasil penelitian ini dengan merujuk semua kemungkinan aspek arkeologis dan antropologi biologisnya makin memperkaya khazanah pengetahuan tentang peristiwa migrasi manusia di Indonesia sekitar masa Neolitik, yang menjadi masa awal makin masifnya migrasi Mongoloid ke kawasan Nusantara. Hasil penelitian ini juga makin menguatkan hasil-hasil penelitian genetika populasi Bali sebelumnya bahwa populasi Bali dari sejak Neolitik sampai sekitar masa yang lebih resen diturunkan oleh banyak leluhur atau banyak sumber gen. Penduduk Bali telah mengalami percampuran genetik dari berbagai populasi pendatang sejak Neolitik atau awal Tarikh Masehi. Abstract The study of ancient human migration and peopling in Indonesia still raises debate until now, both from the perspective of biological anthropology, human genetics or archaeological. The debate was always open space again to do some research about that. We concentrated with samples of ancient Bali, the findings of human remains from Gilimanuk (Melaya, Jembrana) and Semawang (Sanur, Denpasar). Relatively, Bali is an island located in the centre of Indonesian Archipelago, which may represent a major pathway of human migration and distribution according to the outer arc islands. The research

It is assumed that Mongoloid's migration came from western and northern part of Indonesia in various waves of migration. The migrant population then mixed with initial inhabitants, which are Australomelanesoid. The wave of migration moved further to the eastern Indonesia and mixed with migrant that entered from east (Papua). Some researches show that the concentration of mixture (hybridization) of migration was around Wallace's line. Gilimanuk is one of prehistoric site that yields Neolithic human remains. It is assumed that Gilimanuk can give worthy information about human variation at that time. The aim of the research is to describe the human genetic variation at site of Gilimanuk. The material is DNA (deoxyribonucleic acid) has been extracted from many piece of bone of Gilimanuk's human remains. We used STR (short tandem repeat) two loci (THO1 and TPOX) to gain human genetic variation. The result show all of sample yields band with different allele. This evidence confirms that they have a genetic affinity is not the same, or their genes from several population. ABSTRAK Migrasi Mongoloid diduga berasal dari wilayah barat dan utara Indonesia yang datang dalam berbagai gelombang. Kelompok migran ini bercampur dengan penduduk setempat yang berafiliasi Australomelanesoid. Migrasi ini bergerak ke arah timur Indonesia dan bercampur dengan migran yang masuk dari wilayah timur (Papua). Beberapa penelitian menunjukkan bahwa konsentrasi percampuran (hibridisasi) ada di sekitar wilayah Garis Wallace sampai ke timur. Gilimanuk adalah salah satu situs prasejarah yang kaya akan temuan sisa-sisa manusia Neolitik. Diasumsikan bahwa Gilimanuk ini dapat memberi petunjuk variasi manusia di wilayah ini. Tujuan dari penelitian ini adalah untuk mendeskripsikan variasi genetik populasi Gilimanuk. Bahan penelitian adalah DNA (deoxyribonucleic acid) yang diambil dari sisa-sisa rangka individu-individu Gilimanuk. Metode yang digunakan adalah STR (short tandem repeat) dengan menggunakan dua loci (THO1 dan TPOX). Sampel menunjukkan band/pita dengan allele yang berbeda-beda. Bukti ini menegaskan bahwa mereka mempunyai afinitas atau kekerabatan genetik yang tidak sama, atau gen mereka berasal dari beberapa populasi.

Farming was first introduced to southeastern Europe in the mid-7th millennium BCE - brought by migrants from Anatolia who settled in the region before spreading throughout Europe. To clarify the dynamics of the interaction between the first farmers and indigenous hunter-gatherers where they first met, we analyze genome-wide ancient DNA data from 223 individuals who lived in southeastern Europe and surrounding regions between 12,000 and 500 BCE. We document previously uncharacterized genetic structure, showing a West-East cline of ancestry in hunter-gatherers, and show that some Aegean farmers had ancestry from a different lineage than the northwestern Anatolian lineage that formed the overwhelming ancestry of other European farmers. We show that the first farmers of northern and western Europe passed through southeastern Europe with limited admixture with local hunter-gatherers, but that some groups mixed extensively, with relatively sex-balanced admixture compared to the male-biase...

Nova Science Publishers. https://www.novapublishers.com/catalog/product_info.php?products_id=65113
This monograph presents a new discipline—cultural genomics—as a complex approach for studying the interrelation between genomic data and culture and the impact of culture on genomic evolution in human history. It analyzes three basic components of cultural genomics—archaeology, genealogy, and genomics. The author explores the classifications of archaeology and genealogy as traditional disciplines and tests their peculiarities against the limitations and delimitations of genomics to resolve the problems of human origin and historical demography. The main thesis in the book is that cultural genomics as a complex discipline has been changing the dynamics of exploring the human cultural identity in revolutionary ways and the problems of personal origin and lineage. Additionally, this book analyzes the evolution of human civilization and its requirement for close integration of genomics, archaeology, genetic genealogy, traditional genealogy, and other related social and cultural disciplines.
Cultural identity is the basic constructor of the progress of human civilization. Cultural genomics allows researchers to personalize human history and embed new parameters of identity from the perspective of origin. However, the success of the scholarly results depends on how well genomics is blended with related branches of the science of humanity to produce quality results. Many topics of cultural identity still dwell only in the domain of traditional archaeology and genealogy, although genomics has expanded the opportunity to learn not only how cultural identity evolved, but also to create platforms of global networks of interrelatedness that have no analogies in the previous human scholarly experience.
The innovative scholarly problems that the author addresses and the general attempt to constitute cultural genomics as a leading complex discipline of human cultural identity in the 21st century connect the book to the interests of the global scholarly community and all who are interested in cultural identity, genomic archaeology, genetic genealogy, and human origin as well as the evolution of human civilization. The author of this study, Dr. Lolita Nikolova, is a globally renowned scientist who has conducted an in-depth and complex original research; she uniquely combines expertise in the fields of prehistoric archaeology, genealogy, and cultural genomics.

Authors: Rachel Summers-Wilson, Meradeth Snow,
Duane Moser and Joshua Sackett

With implications involving health, nutrition, and even behavior, research into the human microbiome is a burgeoning field within the biological sciences. Less well understood is whether humans, both modern and past, share(d) a recognizable core microbiome. Archaeological materials represent a window into microbiome structure and function of ancient peoples. Assuming microorganisms or their DNA persist for many years under optimal conditions, coprolites should represent time capsules into the distal gut microbiome of ancient people; potentially providing information concerning subsistence practices and health. A vital step towards understanding how such information presents in the archaeological record would be the capacity to recognize and differentiate ancient microbiome constituents against potential contaminants, especially from soil. To test this, we performed parallel microbial 16S rRNA gene surveys using DNA extracted from co-located cave soil and coprolite samples. To verify that microbial DNA is distinct between the two sample types, principal coordinate analysis was applied to rRNA gene libraries from both. Microbial genera associated with modern humans were also tracked. Differentiation of coprolite microbial communities from those of native soil will increase our confidence that detected microbial communities are indeed derived from ancient peoples; an approach that will be applicable to other locales. https://www.ncbi.nlm.nih.gov/ pmc/articles/PMC3426293/

If H2a1 Mitochondrial DNA (MtDNA) bearers suddenly appeared in Eastern Europe in late 6th millennium BC and were omnipresent during Eurasian Copper and Bronze Ages, their modern dispersion's pattern seems to indicate they consciously overlapped Palaeolithic sites we have linked to the practice of early medicine. However they brought new characteristics from a prior southeastern Anatolian (Taurus Mountains) and Levantine (Galilea) ethnogenesis based on the convergence of Pastoralism for Milk (PM), co-evolution between gene and food practice implying the development of Lactase Persistence (LP), the Early Seeds Processing and specific associated behaviours such as selected body parts or perforated teeth as beads in burials. A Levantine thaumaturgical and matriarchal organization based on military force seemed to have synthesized all these influences and has diffused a culture whose elements are all reunited in the grave of Individual from Hilazon Tachtit Stage D (12000 cal BP, Natufian Culture). The lineage seemed to have followed the Fertile Crescent corridor that leads to Lesser Caucasus and reconstituted in Karabakh, close to the Kalavan-1 site, most of the Natufian cultural context. During Pre-Pottery Neolithic B (PPNB), while H2a1 MtDNA bearers expanded in Western Asia by Levant to become one of the most frequent sub-haplogroup of H, the corridor that promoted exchanges between Armenian Obsidian sites and the later Halaf site of Domuztepe, close to the modern Cilician H2a1 MtDNA hotspot, imposed advanced agricultural technics on the Araxes and Vorotan rivers. Thanks to a solid transgenerational transmission of medicinal practices that allowed overpassing the simultaneous development of new diseases like Yersinia Pestis, the innovative woman's lineage became a key element in the new population's admixture from Araxes – Vorotan-Hakari Rivers, future pillar of the Kura-Araxes Culture. While the agricultural Halaf influence extended towards the Caspian maritime plain, Bolgarçay River (Azerbaijan) and Gilan, (Iran), medicinal exchanges with central Asia triggered a new military network specialized in the trade of Boric acid and projected H2a1 MtDNA bearers in Inner Asia. West, the Transcaucasian expansion of H2a1 MtDNA bearers put an end to the Shulaveri-Shomu Tepe culture and their penetration between Don and Volga broadcasted thaumaturgy and advanced agricultural technics until Rhine following Gravettian sites we have demonstrated to be dedicated to medical practices. A last wave of H2a1 MtDNA coincides with the expansion of the Kura Araxes Culture in all Fertile Crescent and reached Atlantic during late 3 rd and early 2 nd millennia BC, changing the whole agricultural landscape of Western Europe until the Roman Empire. This paper demonstrate that Epi Palaeolithic elites were personally engaged in the survival and well-being of their groups, the Neolithic increasing demography forcing them to find solutions (*həll (n.) modern Azeri) making the 'Hellenism' the common base of the Indo-European culture born in Fertile Crescent.

The colonization of the human environment by plants, and the consequent evolution of domesticated forms is increasingly being viewed as a co-evolutionary plant-human process that occurred over a long time period, with evidence for the co-evolutionary relationship between plants and humans reaching ever deeper into the hominin past. This developing view is characterized by a change in emphasis on the drivers of evolution in the case of plants. Rather than individual species being passive recipients of artificial selection pressures and ultimately becoming domesticates, entire plant communities adapted to the human environment. This evolutionary scenario leads to systems level genetic expectations from models that can be explored through ancient DNA and Next Generation Sequencing approaches. Emerging evidence suggests that domesticated genomes fit well with these expectations, with periods of stable complex evolution characterized by large amounts of change associated with relatively small selective value, punctuated by periods in which changes in one-half of the plant-hominin relationship cause rapid, low-complexity adaptation in the other. A corollary of a single plant-hominin co-evolutionary process is that clues about the initiation of the domestication process may well lie deep within the hominin lineage.

The colonization of the human environment by plants, and the consequent evolution of domesticated forms is increasingly being viewed as a co-evolutionary plant-human process that occurred over a long time period, with evidence for the co-evolutionary relationship between plants and humans reaching ever deeper into the hominin past. This developing view is characterized by a change in emphasis on the drivers of evolution in the case of plants. Rather than individual species being passive recipients of artificial selection pressures and ultimately becoming domesticates, entire plant communities adapted to the human environment. This evolutionary scenario leads to systems level genetic expectations from models that can be explored through ancient DNA and Next Generation Sequencing approaches. Emerging evidence suggests that domesticated genomes fit well with these expectations, with periods of stable complex evolution characterized by large amounts of change associated with relatively ...

Our understanding of the evolution of domestication has changed radically in the past 10 years, from a relatively simplistic rapid origin scenario to a protracted complex process in which plants adapted to the human environment. The adaptation of plants continued as the human environment changed with the expansion of agriculture from its centres of origin. Using archaeogenomics and computational models, we can observe genome evolution directly and understand how plants adapted to the human environment and the regional conditions to which agriculture expanded. We have applied various archaeogenomics approaches as exemplars to study local adaptation of barley to drought resistance at Qasr Ibrim, Egypt. We show the utility of DNA capture, ancient RNA, methylation patterns and DNA from charred remains of archaeobotanical samples from low latitudes where preservation conditions restrict ancient DNA research to within a Holocene timescale. The genomic level of analyses that is now possibl...