Ancient Dna (Biology)

This groundbreaking study established that modern domesticated horses (the clade DOM2)  evolved in the Pontic-Caspian steppes. However, it also made claims that are in my estimation unsupported. “Our results reject the commonly held association between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000BC driving the spread of Indo-European languages,” argued Librado et al. Their results, while very important, did not support this rejection. No horse gene is known to enable riding, and the archaeological evidence for horseback riding was not examined. To connect the invention of horseback riding with the spread of Indo-European languages one must advance bridging arguments that were not articulated so were neither rejected nor supported. The genetic mutations manifested in DOM2 horses did not enable horseback riding or milking. Archaeological evidence indicates that both behaviors were conducted with horses in the late 4th millennium BCE and perhaps earlier in the Volga steppes and at Botai.

"It is unknown as to the extent that the arrival of modern humans into Europe (~ 40-30 kyr BP), or the unstable climate throughout Marine Isotope Stage 3 leading up to the Last Glacial Maximum led to Neanderthal extinction at ~30 kyr BP. However it is possible to determine this by reconstructing a model of evolution for the Neanderthals thus illustrating how their demography changes alongside a chronology.
Deducing this model of evolution can be achieved by inputting genetic data into the Bayesian programme BEAST (Bayesian Evolutionary Analysis of Sampling Trees), which has been previously used on North American bison. However it is necessary to input a sufficient amount of genetic data into the programme. For the Neanderthals though, the genetic data is limited quantitatively and qualitatively. The aim of this study is thus to assess the feasibility for obtaining a Neanderthal model of evolution.
In order to do this, the minimum quantitative requirements needed to yield a valid model of evolution were determined through analysis of the bison genetic data. In addition to this, Devensian spotted hyaena genetic data was added to the European hyaena genetic dataset. Being used as a proxy for the Neanderthals (due to possible shared sympatry), reconstruction of the hyaena evolutionary model could reveal similar trends between hyaenas and Neanderthals, thus providing insight into Neanderthal demographic changes. Additionally two hypothetical Neanderthal genetic datasets were simulated under two different demographic models. Portions of this data were analysed to determine if the demographic models could be recovered thus assessing if it is feasible to recover a Neanderthal demographic model given the current limitations of the genetic data.
The results here highlighted four key areas central to the feasibility of obtaining evolutionary models; archaeological considerations, importance of sampling, Bayesian considerations and the use of animal proxies. These key areas were then applied to the Neanderthals thus providing an assessment for the feasibility of obtaining a Neanderthal model of evolution."

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.

Update on ancient DNA: paleontoLogicMind coscious evolutionary consciousness become geopolitical as danisovian - Neandertal’s and Sapiens’ missing link - are occupying the Eurasian continental center as a nodding link with multi regional quarrelsome ethnicity of today. What it seems very relevant to me us that- apart from so called “junk” DNA (just another topical dooming hubris of inCoScientists)  it is chest that some chromosomic feature can lay inactive for millennia to activate when needed as the vitamin D factor intertwined with skin colors and the others adaptive immune system evolutionary malfunctioning, as for cancer and degenerative sicknesses:

https://youtu.be/OivG32DVArY
 
The problem is that all technology does not help to overcome the evolutionary problem of "consciousness" if it happens unconsciously ... it is useless and it is like a great global decay that occurs on the entire Neanderthal culture.
The evolutionary overlap and therefore at least my recovery is this conscious indecision to be managed lucidly by Fitzgerald, that is when the answer is in the question and it is in the answer that you find the question ... to posterity ...

Aggiornamento sul DNA antico: la coscienza evolutiva consapevole della PaleontoLogicMind diventa geopolitica mentre i danisoviani - l'anello mancante di Neandertal e Sapiens - stanno occupando il centro continentale eurasiatico come un nesso con l'etnia litigioso multiregionale di oggi.  Quello che mi sembra molto rilevante per noi è che, a parte il cosiddetto DNA "spazzatura" (solo un'altra arroganza topica di inCoScientists) è il torace che alcune caratteristiche cromosomiche possono rimanere inattive per millenni per attivarsi quando necessario poiché il fattore di vitamina D si intreccia con  colori della pelle e gli altri malfunzionamenti evolutivi del sistema immunitario adattativo, come per cancro e malattie degenerative:

https://youtu.be/OivG32DVArY

La sovrapposizione evolutiva e quindi almeno il mio recupero è questa indecisione cosciente da gestire lucidamente da Fitzgerald, cioè quando la risposta è nella domanda ed è nella risposta che trovate la domanda ... ai posteri ...

This review revealed a new mechanism for gene regulation through
“gene silencing” at the transcriptional level (TGS) or at the post -transcriptional level (PTGS), which play a key role in many essential
cellular processes. Today dsRNA is used as a powerful tool to
experimentally elucidate the function of essentially any gene in a
cell. The immense impact of the discovery of RNA interference
(RNAi) on biomedical research and its novel medical applications in
the future are reviewed in this article, with particular stress on
therapeutic applications of radio -labeled antisense oligonucleotides
(RASONs) for diagnosis and treatment of various  cancers and
neurodegenerative diseases by “gene silencing”. Antisense
oligonucleotides (ASONs) can also modulate alternative splicing
which 74% of all human genes undergo.  Epigenetic changes affect
chromatin structure and thus regulate processes such as transcription,
X-chromosome inactivation, allele-specific expression of imprinted
genes, and inactivation of tumor suppressor genes. Treatment with
inhibitors of DNA methylation and histone deacetylation can
reactivate epigenetically silenced genes and has been shown to
restore normal gene function. In cancer cells, this results in
expression of tumor suppressor genes and other regulatory functions,
inducing growth arrest and apoptosis.

With the advent of ancient DNA, as well as other methods such as isotope analysis, destructive sampling of archaeofaunal remains has increased much faster than the effort to collect and curate them. While there has been considerable discussion regarding the ethics of destructive sampling and analysis of human remains, this dialogue has not extended to archaeofaunal material. Here we address this gap and discuss the ethical challenges surrounding destructive sampling of materials from archaeofaunal collections. We suggest ways of mitigating the negative aspects of destructive sampling and present step-by-step guidelines aimed at relevant stakeholders, including scientists, holding institutions and scientific journals. Our suggestions are in most cases easily implemented without significant increases in project costs, but with clear long-term benefits in the preservation and use of zooarchaeological material.

Ancient DNA (aDNA) approaches have been successfully used to infer the long-term impacts of climate change, domestication, and human exploitation in a range of terrestrial species. Nonetheless, studies investigating such impacts using aDNA in marine species are rare. Atlantic cod ( Gadus morhua ), is an economically important species that has experienced dramatic census population declines during the last century. Here, we investigated 48 ancient mitogenomes from historical specimens obtained from a range of archeological excavations in northern Europe dated up to 6,500 BCE. We compare these mitogenomes to those of 496 modern conspecifics sampled across the North Atlantic Ocean and adjacent seas. Our results confirm earlier observations of high levels of mitogenomic variation and a lack of mutation-drift equilibrium—suggestive of population expansion. Furthermore, our temporal comparison yields no evidence of measurable mitogenomic changes through time. Instead, our results indicate that mitogenomic variation in Atlantic cod reflects past demographic processes driven by major historical events (such as oscillations in sea level) and subsequent gene flow rather than contemporary fluctuations in stock abundance. Our results indicate that historical and contemporaneous anthropogenic pressures such as commercial fisheries have had little impact on mitogenomic diversity in a wide-spread marine species with high gene flow such as Atlantic cod. These observations do not contradict evidence that overfishing has had negative consequences for the abundance of Atlantic cod and the importance of genetic variation in implementing conservation strategies. Instead, these observations imply that any measures toward the demographic recovery of Atlantic cod in the eastern Atlantic, will not be constrained by recent loss of historical mitogenomic variation.

For societies with writing systems, hereditary leadership is documented as one of the hallmarks of early political complexity and governance. In contrast, it is unknown whether hereditary succession played a role in the early formation of prehistoric complex societies that lacked writing. Here we use an archaeogenomic approach to identify an elite matriline that persisted between 800 and 1130 CE in Chaco Canyon, the centre of an expansive prehistoric complex society in the Southwestern United States. We show that nine individuals buried in an elite crypt at Pueblo Bonito, the largest structure in the canyon, have identical mitochondrial genomes. Analyses of nuclear genome data from six samples with the highest DNA preservation demonstrate mother-daughter and grandmother-grandson relationships, evidence for a multigenerational matrilineal descent group. Together, these results demonstrate the persistence of an elite matriline in Chaco for ∼330 years.

"The Neanderthal extinction approximately 30 ka BP has been a contentious issue in archaeology, where the role of the deteriorating climate and/or the arrival of modern humans (from 40 ka BP) could have played a part. By reconstructing the evolutionary and demographic model alongside a palaeo-climatic chronology, this can allow the changing demography over time to be observed, in order to view how the Neanderthals responded to their environment. Such changes in the demography can then be linked to either a significant change in the deterioration of the climate or the arrival of modern humans. This could then allow for the initial trigger behind the Neanderthal extinction to be identified.
One way to reconstruct the evolutionary/demographic model is through the use of a Bayesian based software programme known as BEAST (Bayesian Evolutionary Analysis of Sampling Trees). An evolutionary/demographic model has been reconstructed for North American bison (Bison cf. priscus) whereby their decline in population growth was associated with the climate instead of overhunting by modern humans.

The long term goal of this study is to reconstruct the Neanderthal evolutionary/demographic model in order to answer the question of the factors behind the Neanderthal extinction. However, as the Neanderthal genetic data is currently limited, the aim of this study is to identify the more practical issues behind the construction of an evolutionary model and then apply this to the Neanderthal dataset. This shall be done by analyses of a bison genetic dataset in BEAST. The results outline the practical issues affecting the potential reconstruction of the Neanderthal evolutionary/demographic model."

For societies with writing systems, hereditary leadership is documented as one of the hallmarks of early political complexity and governance. In contrast, it is unknown whether hereditary succession played a role in the early formation of prehistoric complex societies that lacked writing. Here we use an archaeogenomic approach to identify an elite matriline that persisted between 800 and 1130 CE in Chaco Canyon, the centre of an expansive prehistoric complex society in the Southwestern United States. We show that nine individuals buried in an elite crypt at Pueblo Bonito, the largest structure in the canyon, have identical mitochondrial genomes. Analyses of nuclear genome data from six samples with the highest DNA preservation demonstrate mother-daughter and grandmother-grandson relationships, evidence for a multigenerational matrilineal descent group. Together, these results demonstrate the persistence of an elite matriline in Chaco for ∼330 years.

For societies with writing systems, hereditary leadership is documented as one of the hallmarks of early political complexity and governance. In contrast, it is unknown whether hereditary succession played a role in the early formation of prehistoric complex societies that lacked writing. Here we use an archaeogenomic approach to identify an elite matriline that persisted between 800 and 1130 CE in Chaco Canyon, the centre of an expansive prehistoric complex society in the Southwestern United States. We show that nine individuals buried in an elite crypt at Pueblo Bonito, the largest structure in the canyon, have identical mitochondrial genomes. Analyses of nuclear genome data from six samples with the highest DNA preservation demonstrate mother–daughter and grandmother–grandson relationships, evidence for a multigenerational matrilineal descent group. Together, these results demonstrate the persistence of an elite matriline in Chaco for B330 years.