Geographic Population Structure (GPS) - The new tool

[djoser-xyyman]

Geographic Population Structure (GPS) - The new tool


Geographic Population Structure (GPS) - The new tool

Any one has access or know how to use this tool?

IIRC this tool pinpoint the Makrani and Siddhi as originating from Botswana. Remember Botswana carry unusual population structure at K6?

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Pitfalls of the Geographic Population Structure (GPS) Approach Applied to Human Genetic History: A Case Study of Ashkenazi Jews.
Flegontov P1,

Abstract
In a recent interdisciplinary study, Das et al. have attempted to trace the homeland of Ashkenazi Jews and of their historical language, Yiddish (Das et al. 2016 Localizing Ashkenazic Jews to Primeval Villages in the Ancient Iranian Lands of Ashkenaz. Genome Biol Evol. 8:1132-1149). Das et al. applied the geographic population structure (GPS) method to autosomal genotyping data and inferred geographic coordinates of populations supposedly ancestral to Ashkenazi Jews, placing them in Eastern Turkey. They argued that this unexpected genetic result goes against the widely accepted notion of Ashkenazi origin in the Levant, and speculated that Yiddish was originally a Slavic language strongly influenced by Iranian and Turkic languages and later remodeled completely under Germanic influence. In our view, there are major conceptual problems with both the genetic and linguistic parts of the work. We argue that GPS is a provenancing tool suited to inferring the geographic region where a modern and recently unadmixed genome is most likely to arise, but is hardly suitable for admixed populations and for tracing ancestry up to 1,000 years before present, as its authors have previously claimed. Moreover, all methods of historical linguistics concur that Yiddish is a Germanic language, with no reliable evidence for Slavic, Iranian, or Turkic substrata.

[djoser-xyyman]

homedna.com/product/gps-origins

[djoser-xyyman]

1 May 2014
The DNA sat nav: find your ancestor's home from 1,000 years ago

•Geographic Population Structure can locate the village your ancestors lived 1,000 years ago.
•Breakthrough has massive implications for life-saving personalised treatment.
•Previous tools were only accurate to within 700km.

Tracing where your DNA was formed over 1,000 years ago is now possible due to a revolutionary technique developed by a team of international scientists led by experts from the University of Sheffield.

The groundbreaking Geographic Population Structure (GPS) tool, created by Dr Eran Elhaik from the University of Sheffield's Department of Animal and Plant Sciences and Dr Tatiana Tatarinova from the University of Southern California, works similarly to a satellite navigation system as it helps you to find your way home, but not the one you currently live in – but rather your actual ancestor's home from 1,000 years ago.


DNA
DNA
Previously, scientists have only been able to locate where your DNA was formed to within 700km, which in Europe could be two countries away; however this pioneering technique has been 98 per cent successful in locating worldwide populations to their right geographic regions, and down to their village and island of origin.

The breakthrough of knowing where the gene pools that created your DNA were last mixed has massive implications for life-saving personalised medicine, advancing forensic science and for the study of populations whose ancestral origins are under debate, such as African Americans, Roma gypsies and European Jews.

Genetic admixture occurs when individuals from two or more previously separated populations begin interbreeding. This results in the creation of new gene pools representing a mixture of the founder gene pool.

Such processes are extremely common in history during migrations and invasions, for example, when the Vikings invaded Britain and Europe in the 11th Century and settled with locals some of them formed a new Viking-Anglo-Saxon gene pool, but some married other Vikings and maintained their original gene pool, allowing GPS to trace their Scandinavian origins.

Dr Eran Elhaik said: "If we think of our world as being made up of different colours of soup – representing different populations - it is easy to visualise how genetic admixture occurs. If a population from the blue soup region mixes with a population from the red soup region their offspring would appear as a purple soup.

"The more genetic admixture that takes place, the more different colours of soup are introduced which makes it increasingly difficult to locate your DNA's ancestry using traditional tools like Spatial Ancestry analysis (SPA) which has an accuracy level of less than two per cent."





He added: "What we have discovered is a way to find not where you were born – as you have that information on your passport – but where your DNA was formed up to 1,000 years ago by modelling these admixture processes.

"What is remarkable is that, we can do this so accurately that we can locate the village where your ancestors lived hundreds and hundreds of years ago – until now this has never been possible."

To demonstrate how accurate GPS predictions are, Dr Elhaik and his colleagues analysed data from 10 villages in Sardinia and over 20 islands in Oceania.

The research published today in the journal Nature Communications shows that Dr Elhaik and his team were able to place a quarter of the residents in Sardinia directly to their home village and most of the remaining residents within 50km of their village.

The results for Oceania were no less impressive with almost 90 per cent success of tracing islanders exactly to their island.

"This is a significant improvement compared to the alternative SPA tool that placed Oceanians in India," said Elhaik.

"In his third book, children's author L. Frank Baum revealed that Oz resided around Australia. It always troubled me that if I ever met anyone claiming to be from the wonderful world of Oz, I would like to be able to verify their origins and now we can!

"This technique also means that we can no longer easily classify people's ethnic identities with one single label. It is impossible for any of us to tick one box on a form such as White British or African as we are much complex models with our own unique identities. The notion of races is simply not plausible."

Tracing our ancestry is now a major social trend and genealogy is the number one hobby in America. An estimated one million people in the USA have already had their DNA genotyped. People can explore their DNA by simply taking a swab from inside their mouth and sending it to a company such as 23andme or ancestry.com for costs ranging from $99-$200.

Dr Elhaik's co-author, Dr Tatiana Tatarinova, developed a website making GPS accessible to the public.

"To help people find their roots, I developed a website that allows anyone who has had their DNA genotyped to upload their results and use GPS to find their ancestral home," said Dr Tatarinova, who is also an Associate Professor of Research Paediatrics at the Keck School of Medicine of the University of Southern California.

"We were surprised by the simplicity and precision of this method. People in a given geographical area are more likely to have similar genetics. When they also have genetic traits typically found in other, distant regions, the geographical origin of those traits is generally the closest location where those traits can be found."

According to the researchers, in ethnically-diverse regions like the UK or US, where many people know only a few generations of their descendants, this kind of screening has huge, important medical implications.

Discovery of a certain genotype might indicate the potential for a genetic disease and suggest that diagnostic testing be done. Also, as scientists learn more about personalized medicine, there is evidence that specific genotypes respond differently to medications – making this information potentially useful when selecting the most effective therapy and appropriate dosage.

The investigators are currently designing a study to correlate pharmacokinetics - the time course of drug metabolism - with genotype.


The Geographic Population Structure (GPS) tool on BBC News:


www.sheffield.ac.uk/news/nr/dna-sat-nav-gps-tool-find-your-ancestors-home-1.370846

[djoser-xyyman]

cruwys.blogspot.com/2016/11/a-review-of-gps-origins-test-four.html

[djoser-xyyman]

www.timesofisrael.com/new-dna-tech-pinpoints-yiddish-origins-to-north-turkey/


www.legalgenealogist.com/2017/04/25/dna-tests-not-to-bother-with/

[kel]

Ashkenazi Jews arent Hebrews of the Bible

[djoser-xyyman]

Unraveling the Population History of Indian Siddis
Ranajit Das

The Siddis are a unique Indian tribe of African, South Asian, and European ancestry. While previous investigations have traced their ancestral origins to the Bantu populations from subSaharan Africa, the geographic localization of their ancestry has remained elusive. Here, we performed biogeographical analysis to delineate the ancestral origin of the Siddis employing an admixture based algorithm, Geographical Population Structure (GPS) . We evaluated the Siddi genomes in reference to five African populations from the 1000 Genomes project, two Bantu groups from the Human Genome Diversity Panel (HGDP) and five South Indian populations. The Geographic Population Structure analysis localized the ancestral Siddis to Botsawana and its present-day northeastern border with Zimbabwe, overlapping with one of the principal areas of secondary Bantu settlement in southeast Africa. Our results further indicated that while the Siddi genomes are ****significantly ****diverged from that of the Bantus, they manifested the highest genomic proximity to the North-East Bantus and the Luhyas from Kenya. Our findings resonate with evidences supporting secondary Bantu dispersal routes that progressed southward from the east African Bantu center, in the interlacustrine region and likely brought the ancestral Siddis to settlement sites in south and southeastern Africa from where they were disseminated to India, by the Portuguese. We evaluated our results in the light of existing historical, linguistic and genetic evidences, to glean an improved resolution into the reconstruction of the distinctive population history of the Siddis, and advance our knowledge of the demographic factors that likely contributed to the contemporary Siddi genomes.

Siddi, geo-location, GPS, admixture, Portuguese

[djoser-xyyman]

homedna.com/

[djoser-xyyman]

Pinpoint your DNA!

How does this test differ from other DNA tests for ancestry?
Other DNA tests for ancestry provide a limited ethnic composition at a regional or country level. For example, they might indicate 33% East Asian, 40% sub-Saharan African and 27% European.

GPS Origins goes beyond these broad ethnic classifications to identify your ancestral origins to a precise geographic location using an unprecedented number of gene pools and reference populations.

Can I use an existing DNA test for ancestry? Do I need to take another one?
It depends on the test you have already taken. You can upload results from 23andMe, Ancestry.com, National Geographic Geno 2.0, or the Family Tree DNA Family Finder; we can analyze them with our GPS Origins tool to provide the full report of where your DNA began. If your previous DNA test was a Y-chromosome test or Mitochondrial DNA (mtDNA) test, it is not compatible, and you will need to purchase the GPS Origins DNA test.

Get details here: GPS Origins Algorithm - Upload Your Results

What does the GPS Origins report include?
Your report presents mixture proportions from 36 possible gene pools that cover the whole world as well as the history of the primary gene pools. Your report also shows the geographical origins of your DNA, which could be a country or as close to the nearest town. Your DNA signature was created when two different population groups mixed and created a new genetic signature—the one that you ultimately inherited.

You also see two migration routes for your DNA—one for each side of your family—back to where it came from, which may originate up to 10,000 years ago. Finally, GPS Origins dates the age of your DNA signature corresponding to when it last underwent a substantial change at the population level.

GPS Origins is a great tool to help you research your family tree!


What is a Reference Population?
Also referred to as a Study Base, a reference population is a defined, representative sample of individuals during a specific time range used to establish norms for reference ranges. GPS Origins uses 862 reference populations in its database when calculating your results. This large number of reference populations, obtained from publicly referenced datasets, along with the 36 gene pools helps deliver the accuracy in your GPS Origins results.

View Reference Populations






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Your GPS Origins kit contains easy-to-follow instructions, cheek swabs for collecting your DNA samples, and a postage-paid envelope for returning your samples to our lab (U.S. customers only). Using a DNA sample you provide through a simple cheek swab, our qualified laboratory tests more than 800,000 unique genetic markers. Cross-checking that information across dozens of gene pools and more than 800 reference populations, we use your DNA to create a detailed report about where your family originated and how it migrated around the world to where you are today. This can help you answer questions about your family’s history, shed light on the origins of certain family traits, and help you better understand exactly who you are.


This advanced autosomal test is so targeted, it may even indicate the town or village where groups of your ancestors from different cultures met—building a vibrant picture of the migration journeys that formed your deep genealogical heritage.

New ancestral tracking technique pinpoints your genetic genealogy
800,000 autosomal genetic markers tested, 862 reference populations and 36 gene pools analyzed
Simple and painless cheek swab to collect your DNA sample
Highly accredited lab with privacy-protected service and expert staff; your DNA is not sent to a third-party lab
Kit Contents:

Easy-to-follow instructions
Cheek swabs for DNA collection
Postage-paid envelope for returning samples to the lab (U.S. customers only)
Results Back:

Within 2-3 weeks

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Learning about your origins through DNA testing can reveal a lot you may not have known about your deepest roots. The story of your family is contained in your unique genetic code, just waiting for you to discover it. Although your family history may already contain a lot of information about your origins, some information can become lost over generations. With ancestry testing you can bridge the gaps in your family’s records and make connections you never knew were possible. Our advanced autosomal test is so targeted, it may even indicate the town or village where groups of your ancestors from different cultures met, building a vibrant picture of the migration journeys that formed your deep genealogical heritage.

Benefits of GPS Origins™:

The only DNA test with bio-geographical targeting capability to the town or village level
Identifies when and where your DNA formed by matching the populations that came together to create a genetic line leading to you
Traces the migration route of both your maternal and paternal lineages back to their origins and dates the age of your DNA signature
Provides detailed stories helping to explain DNA mixture events such as wars, famines, and migrations
Developed by a leading population geneticist from the University of Sheffield in England
Test Results Include:

Dynamic online experience featuring an interactive map, allowing you to zoom into your GPS pinpoints—revealing towns and cities
Downloadable PDF report that can be shared with family and friends
Your online and printable results feature:
Maps of your top three ancestral origins (the gene pools or ancestral communities that contributed to significant portions of your genetic makeup) along with the percentages of DNA you inherited from each
A comprehensive gene pool profile with DNA percentages that goes well beyond basic ethnicity tests
A detailed map illustrating your maternal and paternal migration journeys with descriptions on how your ancestors' circumstances changed as they crossed territories and continents to find better lives

[djoser-xyyman]

www.omim.org/

[zarahan]

Jan 19, 2018 16:01:47 GMT -5 djoser-xyyman said:

Geographic Population Structure (GPS) - The new tool


Geographic Population Structure (GPS) - The new tool

Any one has access or know how to use this tool?

IIRC this tool pinpoint the Makrani and Siddhi as originating from Botswana. Remember Botswana carry unusual population structure at K6?

--
Pitfalls of the Geographic Population Structure (GPS) Approach Applied to Human Genetic History: A Case Study of Ashkenazi Jews.
Flegontov P1,

Abstract
In a recent interdisciplinary study, Das et al. have attempted to trace the homeland of Ashkenazi Jews and of their historical language, Yiddish (Das et al. 2016 Localizing Ashkenazic Jews to Primeval Villages in the Ancient Iranian Lands of Ashkenaz. Genome Biol Evol. 8:1132-1149). Das et al. applied the geographic population structure (GPS) method to autosomal genotyping data and inferred geographic coordinates of populations supposedly ancestral to Ashkenazi Jews, placing them in Eastern Turkey. They argued that this unexpected genetic result goes against the widely accepted notion of Ashkenazi origin in the Levant, and speculated that Yiddish was originally a Slavic language strongly influenced by Iranian and Turkic languages and later remodeled completely under Germanic influence. In our view, there are major conceptual problems with both the genetic and linguistic parts of the work. We argue that GPS is a provenancing tool suited to inferring the geographic region where a modern and recently unadmixed genome is most likely to arise, but is hardly suitable for admixed populations and for tracing ancestry up to 1,000 years before present, as its authors have previously claimed. Moreover, all methods of historical linguistics concur that Yiddish is a Germanic language, with no reliable evidence for Slavic, Iranian, or Turkic substrata.

It would be interesting to see how the schools of thought hold up in ultra diverse Africa. There is a
language component in there as well to the debate, so the geonomic data might not yield the decisive word.
If Das et al are correct, their findings may find links with those who argue for the Khazar area in Turkey
re Ashkenazic origins. Further testing will shed light on if they are right.

[Ish Gebor]

So shall the king of Assyria lead the captivity of Egypt and the exile of Cush, youths and old men, naked and barefoot, with bare buttocks, the shame of Egypt.

www.chabad.org/library/bible_cdo/aid/15951/jewish/Chapter-20.htm

The earliest certain link with Egypt is 664 B.C., the date of the Assyrian sack of the Egyptian capital at Thebes. Although it is often possible to locate earlier events quite precisely relative to each other, neither surviving contemporary documents nor scientific dating methods such as carbon 14, dendrochronology, thermoluminescence, and archaeoastronomy are able to provide the required accuracy to fix these events  absolutely in time.[/qoute]

www.metmuseum.org/toah/ht/02/waa.html

The Lachish reliefs are a set of Assyrian palace reliefs narrating the story of the Assyrian victory over the kingdom of Judah during the siege of Lachish in 701 BCE. Carved between 700-681 BCE, as a decoration of the South-West Palace of Sennacherib in Nineveh (in modern Iraq) […]

The events surrounding the conquest of Lachish are recorded in an unparalleled number of sources for the 8th century BCE; in the Hebrew Bible, the Lachish reliefs, Assyrian cuneiform prisms and in the archeological excavations at Lachish.[7] Sennacherib's conquests of Judean cities, without the capital Jerusalem, are mentioned in the Bible, the book of Kings, Book of Chronicles and in the book of Isaiah.

"Later, when Sennacherib king of Assyria and all his forces were laying siege to Lachish, he sent his officers to Jerusalem with this message for Hezekiah king of Judah and for all the people of Judah who were there"-(II Chronicles 32:9)

"Now it came to pass in the fourteenth year of King Hezekiah that Sennacherib king of Assyria came up against all the fortified cities of Judah and took them." - (Isaiah 36:1-2)

en.wikipedia.org/wiki/Lachish_reliefs

The Ezra and Nehemiah traditions also show Jews who were given significant posts by Persian rulers. Yet Ezra states that the Jews of the province of Yehud are “slaves” in the Persian Empire (Ezra 9:7-9). Some of the hardships suffered by the people are outlined in Neh 5, though whether their lot was different then than it was in other periods is an open question (since crop failure, borrowing, and losing loan collateral were problems experienced throughout history). [...]

In other texts, individuals with Yahwistic names were small holders or lower-rank officials. We also have an archive of texts relating to the house of Murashu, a business and financial establishment of the Persian period that employed Jews as servants or agents. The Jews seem to have been well integrated into society. Apart from Antiochus IV, persecutions of Jewish communities seem to have been local rather than imperial actions, until the Roman Empire became Christianized.

www.bibleodyssey.org/en/people/related-articles/life-under-empire

The Murashu tablets provide a glimpse into what life was like for fifth-century Jewish descendants of the Babylonian Exile and captivity. After the Persian king Cyrus the Great captured Babylon in 539 BCE, he allowed and helped finance the return of Jews to Judea with the Edict of Cyrus in 538. The Murashu tablets are dated to this period after Jews were allowed to return to Judea. The fact that the banking house "Murashu & Sons" conducted business with Jews who decided to remain in Nippur rather than return to Judea suggests that life in Persian-controlled Nippur was at least somewhat tolerable for Jews.[20]

en.wikipedia.org/wiki/Murashu_family

This decorative frieze of polychrome glazed brick shows an army, the men carrying spears, bows and quivers. Are they the royal guards of Darius I (522–486 BC), whom Herodotus called “the Immortals,” or might they represent an idealized image of the Persian people?

www.louvre.fr/en/oeuvre-notices/frieze-archers