Genographic Project

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Genographic Project

The Genographic Project, launched on 13 April 2005 by the National Geographic Society and IBM, was a genetic anthropological study (sales discontinued on 31 May 2019) that aimed to map historical human migrations patterns by collecting and analyzing DNA samples. [1] The final phase of the project was Geno 2.0 Next Generation. [2] Upon retirement of the site, 1,006,542 participants in over 140 countries had joined the project.[ citation needed ]

Contents

Project history

Beginnings

Created and led by project director Spencer Wells in 2005, the Genographic Project was a privately funded, not-for-profit collaboration between the National Geographic Society, IBM and the Waitt Foundation. [3] Field researchers at eleven regional centers around the world began by collecting DNA samples from indigenous populations. Since the fall of 2015, the Project was led by Miguel Vilar. [4]

In fall 2012, the Genographic Project announced the completion of a new genotyping array, dedicated to genetic anthropology, called GenoChip. GenoChip is specifically designed for anthropological testing and includes SNPs from autosomal DNA, X-chromosome DNA, Y-chromosome DNA and mitochondrial DNA (mtDNA). The design of the new chip was a collaborative effort between Wells of National Geographic, Eran Elhaik of Johns Hopkins, Family Tree DNA, and Illumina. [5]

In the fall of 2015, a new chip was designed as a joint effort between Vilar, Genographic Lead Scientist, and Family Tree DNA.[ citation needed ]

In the spring of 2019, it was announced that the Geno project had ended but results would remain available online until 2020. In July 2020 the site was retired.

Geno 2.0

Phylogeny of mitochondrial DNA haplogroups Phylogeny of mtDNA Haplogroups.png
Phylogeny of mitochondrial DNA haplogroups

The autosomal admixture analysis developed by Wells and Elhaik classifies individuals by assessing their proportions of genomic ancestry related to nine ancestral regions: East Asian, Mediterranean, Southern African, Southwest Asian, Oceanian, Southeast Asian, Northern European, Sub-Saharan African and Native American. [6]

Population Mediterranean Northern European Southwest Asian Sub-Saharan African Southern African East Asian Southeast Asian Native American Oceanian Total
Altaian 2172253498
Amerindian (Mexico) 45348399
Bermudian 1520748374100
British 335017100
Bulgarian 4731202100
Chinese 7228100
Danish 30531699
Dominican 2911147111495
Eastern Indian 224350299
Egyptian 65181497
Finnish 175717798
Georgian 6173199
German 36461799
Greek 54281799
Iberian 48371398
Iranian 42842597
Japanese 7525100
Khoisan 475299
Kinh 5743100
Kuwaiti 574278298
Lebanese 66526299
Luhya 289899
Malagasy 2574152098
Mexican 28208423698
Mongolian 612679498
Northern Caucasian 461633499
Northern Indian 6534262798
Oceanian 1288100
Papuan 5491100
Highland Peruvian 229599
Peruvians 1510326898
Puerto Rican 312192521199
Romanian 4336192100
Russians 255118498
Sardinian 6724899
Southern Indian 42583599
Tajikistan 2222441098
Tatar 2140211698
Tunisian 6261019299
Tuscan 54281799
Vanuatu 4157897
Western Indian 96582699
Yoruba people 973100

Geno 2.0 Next Generation

In 2016, the project began utilizing cutting-edge [2] Helix DNA sequencing for Geno 2.0 Next Generation, [2] [7] the current phase of the Genographic Project. As compared to earlier phases which used nine regional affiliations, Geno 2.0 Next Generation analyzes modern-day indigenous populations around the world using either 18 or 22 regional affiliations. [8] Utilizing a DNA-collection kit, Helix acquires a saliva sample from a participant, which is then analyzed for genomic identifiers that offer unprecedented [2] insight into the person's genetic origins. [2] The data is then uploaded to the Genographic Project DNA database. [2]

Reference Populations Next-Gen based on Biogeographical Ancestry [9]
PopulationArabiaAsia MinorCentral AsiaEastern AfricaEastern EuropeGreat Britain & IrelandJewish DiasporaNorthern AfricaSouthern AfricaSouthern AsiaSouthwest Asia & Persian GulfSouthern EuropeWestern & Central Africa
African-American (Southwestern USA)2%4%9%3%81%
Egyptian 3%3%4%68%17%3%
Ethiopian 11%64%5%7%8%5%
Greek 9%7%2%2%79%
Iranian 56%6%4%4%2%24%2%
Kuwaiti 7%3%4%84%
Luhya (Kenyan)81%4%4%4%2%5%
Tunisian 88%4%5%2%
Yoruban (West African)2%3%6%89%

Volunteer participation

Genographic Project public participation

From 2005 to 2019 Genographic engaged volunteers (in fieldwork and providing DNA samples) and citizen science projects. During this time the National Geographic Society sold non-profit self-testing kits to members of the general public who wished to participate in the project as "citizen scientists". Such outreach for public participation in research has been encouraged by organizations such as International Society of Genetic Genealogy (ISOGG), which is seeking to promote benefits from scientific research. [10] [11] [12] This includes supporting, organization and dissemination of personal DNA (genetic) testing.

The ISOGG supports citizen participation in genetic research, [13] and believes such volunteers have provided valuable information and research to the professional scientific community. [14]

In a 2013 speech to the Southern California Genealogical Society, Spencer Wells discussed its encouragement of citizen scientists. He said:

Since 2005, the Genographic Project has used the latest genetic technology to expand our knowledge of the human story, and its pioneering use of DNA testing to engage and involve the public in the research effort has helped to create a new breed of "citizen scientist." Geno 2.0 expands the scope for citizen science, harnessing the power of the crowd to discover new details of human population history. [15]

Criticism

Shortly after the announcement of the project in April 2005, the Indigenous Peoples Council on Biocolonialism (IPCB) noted its connections to controversial issues (such as concern among some tribes that the results of genetic human migration studies might indicate that Native Americans are not indigenous to North America). The IPCB recommended against indigenous people participating. [16]

The founder of IPCB, Debra Harry, offered a rationale for why Indigenous people were discouraged to participate in the Genographic Project. According to Harry, a Northern Paiute Native American and Associate Professor in Indigenous Studies at Nevada University, the Genographic Project resulted in a human genetic testing practice that appeared to mask an ulterior motive rather than mere scientific research. Particularly, the great concern about the possible political interest behind the Genographic Project, motivated the IPCB to preemptively alert the global indigenous community on the “not so altruistic motivations” [17] of the project. Additionally, IPCB argues that the Genographic project not only provides no direct benefit to Indigenous peoples but instead raises considerable risks. Such risks, raised by Harry in an interview released in December 2005, [18] were used to advocate against the indigenous participation in the project. Another comment made by IPCB founder Debra Harry was that the Genographic Project served as a method to discredit kin relations through the possibility that ancestral identities may be invalidated and to deny Indigenous peoples’ access and authority over the resource-rich territories that they had for long inhabited. [18] The IPCB also identified another attempt at biocolonialism in the Genographic Project. The latter involved the high probability of genetic testing results producing errors such as false negatives and positives that lead to the misidentification of Native people as non-Native and vice versa. [19] Another negative consequence expressed by TallBear is the risk that an individual's cultural identity can be conclusively established through biocolonialist projects such as the Genographic Project. [19] Ultimately, TallBear's argument is in close agreement with Harry's concerns regarding the Genographic Project and serves as a significant force motivating IPCB to advocate against Biocolonialism.

In May 2006, the project came to the attention of the United Nations Permanent Forum on Indigenous Issues (UNPFII). UNPFII conducted investigations into the objectives of the Genographic Project, and recommended that National Geographic and other sponsors suspend the project. [20] Concerns were that the knowledge gleaned from the research could clash with long-held beliefs of indigenous peoples and threaten their cultures. There were also concerns that indigenous claims to land rights and other resources could be threatened. [21]

As of December 2006, some federally recognized tribes in the United States declined to take part in the study including Maurice Foxx, chairman of the Massachusetts Commission on Indian Affairs and a member of the Mashpee Wampanoag. [20]

Not all Indigenous peoples agree with his position; as of December 2012, more than 70,000 indigenous participants from the Americas, Africa, Asia, Europe, and Oceania had joined the project. [8]

See also

Related Research Articles

Genetic genealogy is the use of genealogical DNA tests, i.e., DNA profiling and DNA testing, in combination with traditional genealogical methods, to infer genetic relationships between individuals. This application of genetics came to be used by family historians in the 21st century, as DNA tests became affordable. The tests have been promoted by amateur groups, such as surname study groups or regional genealogical groups, as well as research projects such as the Genographic Project.

<span class="mw-page-title-main">Spencer Wells</span> American author and geneticist

Spencer Wells is an American geneticist, anthropologist, author and entrepreneur. He co-hosts The Insight podcast with Razib Khan. Wells led The Genographic Project from 2005 to 2015, as an Explorer-in-Residence at the National Geographic Society, and is the founder and executive director of personal genomics nonprofit The Insitome Institute.

A genealogical DNA test is a DNA-based genetic test used in genetic genealogy that looks at specific locations of a person's genome in order to find or verify ancestral genealogical relationships, or to estimate the ethnic mixture of an individual. Since different testing companies use different ethnic reference groups and different matching algorithms, ethnicity estimates for an individual vary between tests, sometimes dramatically.

<span class="mw-page-title-main">Haplogroup</span> Group of similar haplotypes

A haplotype is a group of alleles in an organism that are inherited together from a single parent, and a haplogroup is a group of similar haplotypes that share a common ancestor with a single-nucleotide polymorphism mutation. More specifically, a haplotype is a combination of alleles at different chromosomal regions that are closely linked and that tend to be inherited together. As a haplogroup consists of similar haplotypes, it is usually possible to predict a haplogroup from haplotypes. Haplogroups pertain to a single line of descent. As such, membership of a haplogroup, by any individual, relies on a relatively small proportion of the genetic material possessed by that individual.

<span class="mw-page-title-main">Haplogroup J (Y-DNA)</span> Human Y-chromosome DNA haplogroup

Haplogroup J-M304, also known as J, is a human Y-chromosome DNA haplogroup. It is believed to have evolved in Western Asia. The clade spread from there during the Neolithic, primarily into North Africa, the Horn of Africa, the Socotra Archipelago, the Caucasus, Europe, Anatolia, Central Asia, South Asia, and Southeast Asia.

<span class="mw-page-title-main">Haplogroup F-M89</span> Human Y chromosome DNA grouping indicating common ancestry

Haplogroup F, also known as F-M89 and previously as Haplogroup FT, is a very common Y-chromosome haplogroup. The clade and its subclades constitute over 90% of paternal lineages outside of Africa.

Haplogroup K or K-M9 is a genetic lineage within human Y-chromosome DNA haplogroup. A sublineage of haplogroup IJK, K-M9, and its descendant clades represent a geographically widespread and diverse haplogroup. The lineages have long been found among males on every continent except Antarctica.

<span class="mw-page-title-main">Haplogroup M-P256</span> Human Y chromosome DNA grouping common in New Guinea

Haplogroup M, also known as M-P256 and Haplogroup K2b1b is a Y-chromosome DNA haplogroup. M-P256 is a descendant haplogroup of Haplogroup K2b1, and is believed to have first appeared between 32,000 and 47,000 years ago.

<span class="mw-page-title-main">Human Y-chromosome DNA haplogroup</span> Human DNA groupings

In human genetics, a human Y-chromosome DNA haplogroup is a haplogroup defined by mutations in the non-recombining portions of DNA from the male-specific Y chromosome. Many people within a haplogroup share similar numbers of short tandem repeats (STRs) and types of mutations called single-nucleotide polymorphisms (SNPs).

<span class="mw-page-title-main">Indigenous Peoples Council on Biocolonialism</span>

The Indigenous Peoples Council on Biocolonialism (IPCB) is a non-profit organization based in Nixon, Nevada for the purpose of political activism against the emergent field of population genetics for human migration research. The term "biocolonialism" is a neologism —a portmanteau of "bio-" and "colonialism" —used by the IPCB to pejoratively characterize population genetics research as part of invasive and destructive assimilation against indigenous peoples.

In human genetics, Haplogroup O-M119 is a Y-chromosome DNA haplogroup. Haplogroup O-M119 is a descendant branch of haplogroup O-F265 also known as O1a, one of two extant primary subclades of Haplogroup O-M175. The same clade previously has been labeled as O-MSY2.2.

<span class="mw-page-title-main">Family Tree DNA</span> Commercial genetic testing company

FamilyTreeDNA is a division of Gene by Gene, a commercial genetic testing company based in Houston, Texas. FamilyTreeDNA offers analysis of autosomal DNA, Y-DNA, and mitochondrial DNA to individuals for genealogical purpose. With a database of more than two million records, it is the most popular company worldwide for Y-DNA and mitochondrial DNA, and the fourth most popular for autosomal DNA. In Europe, it is the most common also for autosomal DNA. FamilyTreeDNA as a division of Gene by Gene were acquired by MYDNA, Inc., an Australian company, in January 2021.

<span class="mw-page-title-main">Haplogroup S-M230</span> Human Y-chromosome DNA haplogroup

Haplogroup S-M230, also known as S1a1b, is a Y-chromosome DNA haplogroup. It is by far the most numerically significant subclade of Haplogroup S1a.

Haplogroup E-M132, formerly known as E-M33 (E1a), is a human Y-chromosome DNA haplogroup. Along with E-P177, it is one of the two main branches of the older E-P147 paternal clade. E-M132 is divided into two primary sub-branches, E-M44 and E-Z958, with many descendant subclades.

Haplogroup E-P177 is a human Y-chromosome DNA haplogroup. E-P177 has two known subclades, which are haplogroup E-P2 and haplogroup E-P75.

<span class="mw-page-title-main">International Society of Genetic Genealogy</span>

The International Society of Genetic Genealogy (ISOGG) is an independent non-commercial nonprofit organization of genetic genealogists run by volunteers. It was founded by a group of surname DNA project administrators in 2005 to promote DNA testing for genealogy. It advocates the use of genetics in genealogical research, provides educational resources for genealogists interested in DNA testing, and facilitates networking among genetic genealogists. As of June 2013, it comprises over 8,000 members in 70 countries. As of July 2013, regional meetings are coordinated by 20 volunteer regional coordinators located in the United States, Australia, Brazil, Canada, England, Egypt, Ireland and Russia.

Eran Elhaik is an Israeli-American geneticist and bioinformatician, an associate professor of bioinformatics at Lund University in Sweden and Chief of Science Officer at an ancestry testing company called Ancient DNA Origins owned by Enkigen Genetics Limited, registered in Ireland. His research uses computational, statistical, epidemiological and mathematical approaches to fields such as complex disorders, population genetics, personalised medicine, molecular evolution, genomics, paleogenomics and epigenetics.

Haplogroup P1, also known as P-M45 and K2b2a, is a Y-chromosome DNA haplogroup in human genetics. Defined by the SNPs M45 and PF5962, P1 is a primary branch (subclade) of P.

References

  1. "Council for Responsible Genetics". Archived from the original on 16 May 2008. Retrieved 16 May 2015.
  2. 1 2 3 4 5 6 "Geno 2.0 Next Generation". National Geographic. 28 June 2018. Archived from the original on 22 January 2013. Retrieved 28 June 2018.
  3. "Ocean Protection Funding". Waitt Foundation. La Jolla, California. Retrieved 25 January 2022.
  4. "Dr. Miguel Vilar is the 29th Speaker in UOG Presidential Lecture Series". University of Guam. Retrieved 10 May 2022.
  5. Elhaik, Eran; Greenspan, Elliott; Staats, Sean; Krahn, Thomas; Tyler-Smith, Chris; Xue, Yali; Tofanelli, Sergio; Francalacci, Paolo; Cucca, Francesco; Pagani, Luca; Jin, Li; Li, Hui; Schurr, Theodore G.; Greenspan, Bennett; Spencer Wells, R. (9 May 2013). "The GenoChip: A New Tool for Genetic Anthropology". Genome Biology and Evolution . 5 (5): 1021–1031. doi: 10.1093/gbe/evt066 . PMC   3673633 . PMID   23666864 . Retrieved 28 June 2018.
  6. "Who Am I: Regions Overview". Archived from the original on 30 October 2014. Retrieved 30 November 2022.
  7. Helix DNA Sequencing and Geno 2.0 Archived 21 October 2023 at the Wayback Machine Helix. 26 January 2018. Retrieved 28 June 2018.
  8. 1 2 "Next Generation Reference Populations". National Geographic. 23 February 2018. Archived from the original on 7 April 2016. Retrieved 28 June 2018.
  9. National Geographic Geno 2.0 Project, archived from the original on 7 February 2017, retrieved 22 October 2018
  10. Bonney, R.; LaBranche, M. (2004). "Citizen Science: Involving the Public in Research". ASTC Dimensions (May/June 2004): 13.
  11. Baretto, C.; Fastovsky, D.; Sheehan, P. (2003). "A Model for Integrating the Public into Scientific Research". Journal of Geoscience Education. 50 (1): 71–75. Bibcode:2003JGeEd..51...71B. doi:10.5408/1089-9995-51.1.71. S2CID   67761505.
  12. McCaffrey, R. E. (2005). "Using Citizen Science in Urban Bird Studies". Urban Habitats. 3 (1): 70–86.
  13. King, Turi E.; Jobling, Mark A. (2009). "What's in a name? Y chromosomes, surnames and the genetic genealogy revolution". Trends in Genetics. 25 (8): 351–60. doi:10.1016/j.tig.2009.06.003. hdl: 2381/8106 . PMID   19665817. The International Society of Genetic Genealogy (www.isogg.org) advocates the use of genetics as a tool for genealogical research, and provides a support network for genetic genealogists. It hosts the ISOGG Y-haplogroup tree, which has the virtue of being regularly updated.
  14. Mendex, etc. al., Fernando (28 February 2013). "An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree". The American Society of Human Genetics. pp. 454–459. Retrieved 10 July 2013.
  15. Wells, Spencer (2013). "The Genographic Project and the Rise of Citizen Science". Southern California Genealogical Society (SCGS). Archived from the original on 10 July 2013. Retrieved 10 July 2013.
  16. Harry, Debra and Le'a Malia Kanehe. "Genetic Research: Collecting Blood to Preserve Culture?" Cultural Survival, 29.4 (Winter 2005). Accessed 4 February 2014.
  17. "Indigenous Peoples Council on Biocolonialism". ipcb.org. Retrieved 9 November 2022.
  18. 1 2 "Interview with Debra Harry and the Indigenous Peoples Council on Biocolonialism". New Internationalist. 1 December 2005. Archived from the original on 24 October 2022. Retrieved 9 November 2022.
  19. 1 2 Ellen, Samuels (2014). Fantasies of identification : disability, gender, race. New York University Press. ISBN   978-1-4798-1298-1. OCLC   900357752.
  20. 1 2 Harmon, Amy (10 December 2006). "DNA Gatherers Hit Snag: Tribes Don't Trust Them". The New York Times .
  21. "United Nations Recommends Halt to Genographic Project". ipcb.

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