Monday, 26 April 2021

Roopkund Lake's mysterious skeletons: mystery partially but not completely solved

Roopkund Lake’s mysterious skeletons: mystery partially but not completely solved by geneticists


Located at 5029 metres above sea level in the Himalayas, Roopkund Lake is a high altitude glacial lake situated in the Indian state of Uttarakhand. The lake is frozen in winter but when the snow melts, hundreds of skeletons of unknown origin are visible at the bottom of the lake and many artifacts have been found in the area.

A popular trekking, pilgrimage and tourist destination, visitors have removed many of the artifacts as souvenirs and conservationists fear that the precious remains that are shrouded in mystery will soon disappear. Details can be found in Wikipedia:  https://en.wikipedia.org/wiki/Roopkund


“Local legend says that the King of Kanauj, Raja Jasdhaval, with his pregnant wife, Rani Balampa, their servants, a dance troupe and others went on a pilgrimage to Nanda Devi shrine, and the group faced a storm with large hailstones, from which the entire party perished near Roopkund Lake” (cf. Wikipedia). Nanda Devi did not approve of their inappropriate celebratory behaviour and therefore punished them with death.


A team of geneticists led by David Reich, Kumarasamy Thangaraj and Niraj Rai have studied the DNA of several skeletons to try to understand their origin and the circumstances that led to their demise at Roopkund. They also carried out table isotope measurements, radiocarbon dating and oeteological analysis on the remains of the individuals.(https://www.academia.edu/40159432Ancient_DNA_from_the_skeletons_of_Roopkund_Lake_reveals_Mediterranean_migrants_in_India?email_work_card=title)

The team found that the skeletons did not result from a single event as would be expected from the local legend. They belonged to three different ancestries deposited there at different times approximately 1000 years apart:


  • present-day South Asians dated to around 800 CE 7th -10th century (India, Pakistan, Nepal, Bhutan, Bangladesh)
  • Eastern Mediterranean dated to around 1800 CE 17th-20th century (Primarily Crete, Mainland Greece)
  • Southeast Asian dated also to around 1800 CE 17th -20th century (Primarily Malaysia, Vietnam)


The study says that the individuals were “broadly healthy” but 3 of them had unhealed compression fractures compatible with the violent hailstorms for which the region is known. The stature (height and robustness or gracile) of the analysed individuals is equally compatible with the ancestries identified from their DNA.  They included both males and females in similar proportions, thus excluding the possibility that the groups may have belonged to a military expedition: when discovered in 1942, the British feared that the skeletons belonged to a hidden Japanese invasion force.


The researchers also discovered that they belonged to a diverse group and not members of a single family.


The two main groups showed different dietary patterns, the South Asians exhibiting a more varied diet than the Eastern Mediterraneans.


Roopkund Lake lies on the Nanda Devi Raj Jat pilgrimage route. The pilgrimage today occurs every 12 years and date back to the 8th and 10th centuries as suggested by inscriptions in nearby temples. The authors therefore theorise that the skeletons of the South Asians dating back to the 7th-10th century belong to pilgrims caught in violent hailstorms. They suggest that the South East Asian skeletons also belong to this category.


The source of the skeletons belonging to Crete/Greece ancestry is a mystery. The authors propose that they “were born during the period of Ottoman political control. As suggested by their predominantly terrestrial, rather than marine-based diet, they may have lived in an inland location, eventually travelling to and dying in the Himalayas”. 




ARTICLE 

https://doi.org/10.1038/s41467-019-11357-9 OPEN 

Ancient DNA from the skeletons of Roopkund Lake reveals Mediterranean migrants in India 

Éadaoin Harney1,2,3, Ayushi Nayak4,17, Nick Patterson5,6, Pramod Joglekar7, Veena Mushrif-Tripathy 7, Swapan Mallick3,5,8, Nadin Rohland3, Jakob Sedig 3, Nicole Adamski3,8, Rebecca Bernardos3,
Nasreen Broomandkhoshbacht 3,8, Brendan J. Culleton9,10, Matthew Ferry3,8, Thomas K. Harper10, Megan Michel3,8,11, Jonas Oppenheimer3,8, Kristin Stewardson3,8, Zhao Zhang3, Harashawaradhana12, Maanwendra Singh Bartwal12, Sachin Kumar13,14, Subhash Chandra Diyundi 15, Patrick Roberts 4, Nicole Boivin4, Douglas J. Kennett16,17, Kumarasamy Thangaraj13,17, David Reich2,3,5,8,17 & Niraj Rai13,14,17 

Situated at over 5,000 meters above sea level in the Himalayan Mountains, Roopkund Lake is home to the scattered skeletal remains of several hundred individuals of unknown origin. We report genome-wide ancient DNA for 38 skeletons from Roopkund Lake, and find that they cluster into three distinct groups. A group of 23 individuals have ancestry that falls within the range of variation of present-day South Asians. A further 14 have ancestry typical of the eastern Mediterranean. We also identify one individual with Southeast Asian-related ancestry. Radiocarbon dating indicates that these remains were not deposited simulta- neously. Instead, all of the individuals with South Asian-related ancestry date to ~800 CE (but with evidence of being deposited in more than one event), while all other individuals date to ~1800 CE. These differences are also reflected in stable isotope measurements, which reveal a distinct dietary profile for the two main groups. 


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NATURE COMMUNICATIONS | (2019)10:3670 | https://doi.org/10.1038/s41467-019-11357-9 | www.nature.com/naturecommunications 1

Nestled deep in the Himalayan mountains at 5029 m above sea level, Roopkund Lake is a small body of water (~40 m in diameter) that is colloquially referred to as Skeleton Lake due to the remains of several hundred ancient humans scattered around its shores (Fig. 1)1. Little is known about the origin of these skeletons, as they have never been subjected to systematic anthropological or archaeological scrutiny, in part due to the disturbed nature of the site, which is frequently affected by rockslides2, and which is often visited by local pilgrims and hikers who have manipulated the skeletons and removed many of the artifacts3. There have been multiple proposals to explain the origins of these skeletons. Local folklore describes a pilgrimage to the nearby shrine of the mountain goddess, Nanda Devi, undertaken by a king and queen and their many attendants, who —due to their inappropriate, celebratory behavior—were struck down by the wrath of Nanda Devi4. It has also been suggested that these are the remains of an army or group of merchants who were caught in a storm. Finally, it has been suggested that they were the victims of an epidemic5

To shed light on the origin of the skeletons of Roopkund, we analyzed their remains using a series of bioarcheological analyses, including ancient DNA, stable isotope dietary reconstruction, radiocarbon dating, and osteological analysis. We find that the Roopkund skeletons belong to three genetically distinct groups that were deposited during multiple events, separated in time by approximately 1000 years. These findings refute previous suggestions that the skeletons of Roopkund Lake were deposited in a single catastrophic event. 

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Thursday, 25 March 2021

ANCESTRAL NORTH INDIANS ANI: ORIGINS AND HISTORY OF Y DNA HAPLOGROUP R1a by Maciano Hays.

Based on brilliant genetics research, David Reich et al. discovered that migrants from the Steppes to the Indian sub-continent mixed with the population of the Indus Valley Civilisation (IVC) on the decline that they encountered to form the Ancient North Indian ANI population. The IVC population was itself a mixture of Iranians from the Zagros mountains and the local Onge-related people.

This paper by Maciano Hays describes succinctly the Indo-Iranian branch of the Y Haplogroup R1a to which the Steppe migrants to India belonged.

Please copy/paste the link below to your browser to open the file.

https://drive.google.com/file/d/1s_zuc6OHDUXy33XSQHY5R9LgRMAkv22g/view?usp=sharing


Sunday, 21 March 2021

THE DISCOVERY OF HOW AND WHY LYNETTE REIS AND I ARE RELATED

 The discovery of how and why Lynette Reis and I are related


It all started with an email from Lynette’s husband. He had discovered The Last Prabhu from the internet and ordered a copy. Gedmatch showed that his wife and I shared DNA segments and did I have an explanation for that? I consulted geni.com to find out if there was any connection but could find none.
   I next asked him to communicate to me Lynette’s mtDNA haplogroup, and if possible also her father’s or brothers’ Y DNA haplogroup. Fortunately he had both and they were completely different from mine. Clearly, therefore, we were not related directly through either of her parents, the relationship would have to be an indirect one. 
   Lynette’s maternal grandmother was her favourite and she knew that she was from Aldona and her maiden name was de Sousa. Was there perhaps a connection? I advised her husband upon his request to contact the Parish priest of Aldona for a baptismal certificate and a second option would be to apply for one from the archives at the Patriarchal House in Altinho, Panaji. Aldona’s Parish priest ignored his request - why am I not surprised? - but with some difficulty he managed to obtain a copy from the Panaji archives, a digitalised version of poor legibility but good enough for our purpose. We discovered that her maternal grandmother was from Dauzavaddo, a part of Aldona’s Quitula ward. So far so good.
   I had a hunch and to check this out, I would need the assistance of an expert  who was were familiar with the old records of Aldona’s Comunidade Fraternal. I turned to my good friend Hector Fernandes, the highly knowledgeable president of Aldona’s Comunidade Fraternal. He confirmed very rapidly that Dauzavaddo had about ten homes that belonged to a de Sousa/D’Souza/de Souza and all belonged to the comunidade’s fourth vangad, just as I do. One of those houses had been Lynette’s maternal grandmother’s home.
   Eureka! That was the explanation for why Lynette and I shared DNA segments and are genetic cousins. As I have explained in my book, genetics proves that all the members of a specific vangad are descendants of the founder of this vangad, in our case a Prabhu. Thus, all members of Aldona’s 4th vangad and their descendants share his DNA and that includes me. As the daughter of a 4th vangad gaunkar, Lynette’s maternal grandmother had inherited some of the 4th vangad founder’s DNA through her father, and Lynette's mother and through her, Lynette as well.

   Thus, a combination of approaches i.e. genetics, the family tree and old documents/records together enabled us to find an answer to how and why Lynette Reis and I are related.

Saturday, 30 January 2021

SIMPLY EXPLAINED: What is mRNA, what does it do, what is its role in a Covid-19 vaccine? How can we be sure that a mRNA-based Covid-19 vaccine is safe?

 (Source: Moderna, 

https://www.modernatx.com/mrna-technology/science-and-fundamentals-mrna-technology)


What does mRNA do? mRNA produces instructions to make proteins that may treat or prevent disease


mRNA medicines aren’t small molecules, like traditional pharmaceuticals. And they aren’t traditional biologics (recombinant proteins and monoclonal antibodies) – which were the genesis of the biotech industry. Instead, mRNA medicines are sets of instructions. And these instructions direct cells in the body to make proteins to prevent or fight disease.

It’s actually basic human biology. 

DNA (deoxyribonucleic acid) is a double-stranded molecule that stores the genetic instructions your body’s cells need to make proteins. Proteins, on the other hand, are the ‘workhorses’ of the body. Nearly every function in the human body – both normal and disease-related – is carried out by one or many proteins.

mRNA is just as critical as DNA.

Without mRNA, your genetic code would never get used by your body. Proteins would never get made. And your body wouldn’t – actually couldn’t – perform its functions. Messenger ribonucleuc acid, or mRNA for short, plays a vital role in human biology, specifically in a process known as protein synthesis. mRNA is a single-stranded molecule that carries genetic code from DNA in a cell’s nucleus to ribosomes, the cell’s protein-making machinery.

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mRNA’s role in protein synthesis

 

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  • Through a process known as transcription, an RNA copy of a DNA sequence for creating a given protein is made.
  • This copy – mRNA – travels from the nucleus of the cell to the part of the cell known as the cytoplasm, which houses ribosomes. Ribosomes are complex machinery in the cells that are responsible for making proteins.
  • Then, through another process known as translation, ribosomes ‘read’ the mRNA, and follow the instructions, creating the protein step by step. 
  • The cell then expresses the protein and it, in turn, carries out its designated function in the cell or the body. 


Using mRNA to develop a new category of medicines.


At Moderna, we are leveraging the fundamental role that mRNA plays in protein synthesis. We have developed proprietary technologies and methods to create mRNA sequences that cells recognize as if they were produced in the body. We focus on diseases where enabling targeted cells to produce – or turn ‘on’ – one or more given proteins will enable the body to fight or prevent a given disease.

  • We start with our desired sequence for a protein.
  • We design and synthesize the corresponding mRNA sequence – the code that will create that protein.
  • Before synthesis, we also engineer that mRNA sequence to optimize the mRNA’s physical properties, as well as those of the encoded protein.
  • We deliver the mRNA sequence to the cells responsible for making that protein via one of several modalities. Reaching different types of cells requires different delivery methods.
  • And, once the mRNA – the instructions – are in the cell … human biology takes over. Ribosomes read the code and build the protein, and the cells express the protein in the body.

——————————————————————————————————


(Source: CDC Centers for disease control and prevention

https://www.cdc.gov/coronavirus/2019-ncov/vaccines/different-vaccines/mrna.html)


Vaccines Are New, But Not Unknown


Researchers have been studying and working with mRNA vaccines for decades. Interest has grown in these vaccines because they can be developed in a laboratory using readily available materials. This means the process can be standardized and scaled up, making vaccine development faster than traditional methods of making vaccines.

mRNA vaccines have been studied before for flu, Zika, rabies, and cytomegalovirus (CMV). As soon as the necessary information about the virus that causes COVID-19 was available, scientists began designing the mRNA instructions for cells to build the unique spike protein into an mRNA vaccine.

Future mRNA vaccine technology may allow for one vaccine to provide protection for multiple diseases, thus decreasing the number of shots needed for protection against common vaccine-preventable diseases.

Beyond vaccines, cancer research has used mRNA to trigger the immune system to target specific cancer cells.


A Closer Look at How COVID-19 mRNA Vaccines Work


COVID-19 mRNA vaccines give instructions for our cells to make a harmless piece of what is called the “spike protein.” The spike protein is found on the surface of the virus that causes COVID-19.

COVID-19 mRNA vaccines are given in the upper arm muscle. Once the instructions (mRNA) are inside the immune cells, the cells use them to make the protein piece. After the protein piece is made, the cell breaks down the instructions and gets rid of them.

Next, the cell displays the protein piece on its surface. Our immune systems recognize that the protein doesn’t belong there and begin building an immune response and making antibodies, like what happens in natural infection against COVID-19.

At the end of the process, our bodies have learned how to protect against future infection. The benefit of mRNA vaccines, like all vaccines, is those vaccinated gain this protection without ever having to risk the serious consequences of getting sick with COVID-19.

COVID-19 mRNA Vaccines cannot give someone COVID-19.

  • mRNA vaccines do not use the live virus that causes COVID-19.

They do not affect or interact with our DNA in any way.

  • mRNA never enters the nucleus of the cell, which is where our DNA (genetic material) is kept.
  • The cell breaks down and gets rid of the mRNA soon after it is finished using the instructions.

Thursday, 17 December 2020

Origins and history of Y DNA Haplogroup J2

This short paper by Maciano Hay provides a good insight into the origin and distribution of this Y DNA Haplogroup to which I belong.

https://www.academia.edu/6089464/Origins_and_history_of_Haplogroup_J2_Y_DNA_?auto=download&email_work_card=download-paper

Wednesday, 9 December 2020

Sanauli's Mysterious Warriors by Disha Ahluwalia: a symbiosys of IVC and Steppe warriors?


 The Sanaulians coexisted with the late Harappan (Indus Valley Civilisation IVC) and I am of the opinion that this society was a symbiosys of IVC and the warriors from the Steppes.

Tuesday, 17 November 2020

Recommended literature on DNA and genetic genealogy, some free, other available on Amazon as well as to understand the mRNA-based COVID-19 vaccines

1. Family Tree DNA Learning Center, Glossaryhttps://learn.familytreedna.com/glossary/

2. International Society of Genetic Genealogy Glossaryhttps://isogg.org/wiki/Genetics_Glossary

3. Emily D. Aulicino, Genetic Genealogy: The Basics and Beyond 

4. Calladine, Horace R. Drew, “Understanding DNA, The molecule and how it works” 

5. Y-DNA Haplogroup Tree: International Society of Genetic Genealogy ISOGG, Y- DNA Haplogroup 

6. mtDNA Haplogroup Tree, PhyloTree mt, van Oven M, Kayser M. 2009. Updated comprehensive 
   phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat 30(2):E386-E394. 
   http://www.phylotree.org. doi:10.1002/humu.20921

7. David Reich, “Who We Are and How We Got Here. Ancient DNA and the new science of the human 
    past”

8. Narasimhan et al. “The formation of human populations in South and Central Asia”,  

9.  Messenger RNAhttps://www.sciencedirect.com/topics/pharmacology-toxicology-and- 
     pharmaceutical-science/messenger-rna

10. CRISPR: Jennifer Doudna, Samuel H. Sternberg: “A Crack in Creation: Gene Editing and the 
      Unthinkable Power to Control Evolution”. 
      Jennifer Doudna was awarded the 2020 Nobel prize in chemistry

The last two on mRNA (9) and CRISPR-CAS9 (10) are very helpful to better understand the development of the BioNTech/Pfizer and MODERNA/AstraZeneca COVID-19 vaccines.