David Reich (geneticist)

Last updated
David Reich
Born
David Emil Reich

(1974-07-14) July 14, 1974 (age 49)
Washington, D.C., United States
Alma mater Harvard University
St Catherine's College, Oxford
Awards
Scientific career
Thesis Genetic analysis of human evolutionary history with implications for gene mapping  (1999)
Doctoral advisor David Goldstein [3]

David Emil Reich [4] (born July 14, 1974) is an American geneticist known for his research into the population genetics of ancient humans, including their migrations and the mixing of populations, discovered by analysis of genome-wide patterns of mutations. He is professor in the department of genetics at the Harvard Medical School, and an associate of the Broad Institute. Reich was highlighted as one of Nature's 10 for his contributions to science in 2015. [5] He received the Dan David Prize in 2017, the NAS Award in Molecular Biology, the Wiley Prize, and the Darwin–Wallace Medal in 2019. In 2021 he was awarded the Massry Prize. [6]

Contents

Early life

Reich grew up as part of a Jewish family in Washington, D.C. His parents are novelist Tova Reich (sister of Rabbi Avi Weiss) and Walter Reich, a professor at George Washington University, who served as the first director of the United States Holocaust Memorial Museum. [7] [8] David Reich started out as a sociology major as an undergraduate at Harvard College, but later turned his attention to physics and medicine. After graduation, he attended the University of Oxford, originally with the intent of preparing for medical school. [7] He was awarded a PhD in zoology in 1999 for research supervised by David Goldstein. His thesis was titled "Genetic analysis of human evolutionary history with implications for gene mapping". [3]

Academic career

Reich received a BA in physics from Harvard University and a PhD in zoology from St. Catherine's College in the University of Oxford. [9] He joined Harvard Medical School in 2003. [7] Reich is currently a geneticist and professor in the department of genetics at Harvard Medical School, and an associate of the Broad Institute, whose research studies compare the modern human genome with those of chimpanzees, Neanderthals, and Denisovans.

Reich's genetics research focuses primarily on finding complex genetic patterns that cause susceptibility to common diseases among large populations, rather than looking for specific genetic markers associated with relatively rare illnesses.

Genetic research

Split of chimpanzees and humans (2006)

Reich's research team at Harvard University has produced evidence that, over a span of at least four million years, various parts of the human genome diverged gradually from those of chimpanzees. [10] The split between the human and chimpanzee lineages may have occurred millions of years later than fossilized bones suggest, and the break may not have been as clean as previously thought. The genetic evidence developed by Reich's team suggests that after the two species initially separated, they may have continued interbreeding for several million years. A final genetic split transpired between 6.3 million and 5.4 million years ago. [11]

Indian population (2009)

Reich's 2009 paper Reconstructing Indian population history [12] was a landmark study in the research on India's genepool and the origins of its population. Reich et al. (2009), in a collaborative effort between the Harvard Medical School and the Indian Centre for Cellular and Molecular Biology (CCMB), examined the entire genomes worth 560,000 single-nucleotide polymorphisms (SNPs), as compared to 420 SNPs in prior work. They also cross-compared them with the genomes of other regions available in the global genome database. [13] Through this study, they were able to discern two genetic groups in the majority of populations in India, which they called "Ancestral North Indians" (ANI) and "Ancestral South Indians" (ASI). [note 1] They found that the ANI genes are close to those of Middle Easterners, Central Asians and Europeans whereas the ASI genes are dissimilar to all other known populations outside India. [note 2] [note 3] These two distinct groups, which had split ca. 50,000 years ago, formed the basis for the present population of India. [14]

A follow-up study by Moorjani et al. (2013) revealed that the two groups mixed between 1,900 and 4,200 years ago (2200 BCE–100 CE), after which a shift to endogamy took place and admixture became rare. [note 4] Speaking to Fountain Ink, David Reich stated, "Prior to 4,200 years ago, there were unmixed groups in India. Sometime between 1,900 to 4,200 years ago, profound, pervasive convulsive mixture occurred, affecting every Indo-European and Dravidian group in India without exception." Reich pointed out that their work does not show that a substantial migration occurred during this time. [15]

Metspalu et al. (2011), representing a collaboration between the Estonian Biocenter and CCMB, confirmed that the Indian populations are characterized by two major ancestry components. One of them is spread at comparable frequency and haplotype diversity in populations of South and West Asia and the Caucasus. The second component is more restricted to South Asia and accounts for more than 50% of the ancestry in Indian populations. Haplotype diversity associated with these South Asian ancestry components is significantly higher than that of the components dominating the West Eurasian ancestry palette. [16]

Human genetic map (2011)

Reich was a co-leader, along with statistician Simon Myers, of a team of genetics researchers from Harvard University and the University of Oxford that made the most complete human genetic map then known in July 2011. [17]

Interbreeding of Neanderthals and humans (2010–2012)

Reich's research team significantly contributed to the discovery that Neanderthals and Denisovans interbred with modern human populations as they dispersed from Africa into Eurasia 70,000–30,000 years ago. [18]

Genetic markers for prostate cancer

Reich's lab received media attention following its discovery of a genetic marker which is linked to an increased likelihood of developing prostate cancer. [19] Reich has also argued that the higher incidence of prostate cancer among African Americans, compared to European Americans, appears to be largely genetic in origin. [20]

Indo-European origins

Reich has suggested that the Indo-European languages may have originated south of the Caucausus, in present day Iran or Armenia:

"Ancient DNA available from this time in Anatolia shows no evidence of steppe ancestry similar to that in the Yamnaya (although the evidence here is circumstantial as no ancient DNA from the Hittites themselves has yet been published). This suggests to me that the most likely location of the population that first spoke an Indo-European language was south of the Caucasus Mountains, perhaps in present-day Iran or Armenia, because ancient DNA from people who lived there matches what we would expect for a source population both for the Yamnaya and for ancient Anatolians. If this scenario is right the population sent one branch up into the steppe – mixing with steppe hunter-gatherers in a one-to-one ratio to become the Yamnaya as described earlier – and another to Anatolia to found the ancestors of people there who spoke languages such as Hittite." [20]

Software tools

Reich has developed ADMIXTOOLS 2, an R software package primarily used for analyzing admixture, in collaboration with Nick Patterson. [21]

Books

Notes

  1. ↑ Reich (2009) excluded the Austro-Asiatic and Tibeto-Burman speakers from their analysis in order to avoid interference.
  2. ↑ Reich (2009): "We analyze 25 diverse groups to provide strong evidence for two ancient populations, genetically divergent, that are ancestral to most Indians today. One, the "Ancestral North Indians" (ANI), is genetically close to Middle Easterners, Central Asians, and Europeans, while the other, the "Ancestral South Indians" (ASI), is as distinct from ANI and East Asians as they are from each other."
  3. ↑ Moorjani et al. (2013): "Most Indian groups descend from a mixture of two genetically divergent populations: Ancestral North Indians (ANI) related to Central Asians, Middle Easterners, Caucasians, and Europeans; and Ancestral South Indians (ASI) not closely related to groups outside the subcontinent."
  4. ↑ Moorjani et al. (2013): "We report genome-wide data from 73 groups from the Indian subcontinent and analyze linkage disequilibrium to estimate ANI-ASI mixture dates ranging from about 1,900 to 4,200 years ago. In a subset of groups, 100% of the mixture is consistent with having occurred during this period. These results show that India experienced a demographic transformation several thousand years ago, from a region in which major population mixture was common to one in which mixture even between closely related groups became rare because of a shift to endogamy."

Related Research Articles

<span class="mw-page-title-main">Human genome</span> Complete set of nucleic acid sequences for humans

The human genome is a complete set of nucleic acid sequences for humans, encoded as DNA within the 23 chromosome pairs in cell nuclei and in a small DNA molecule found within individual mitochondria. These are usually treated separately as the nuclear genome and the mitochondrial genome. Human genomes include both protein-coding DNA sequences and various types of DNA that does not encode proteins. The latter is a diverse category that includes DNA coding for non-translated RNA, such as that for ribosomal RNA, transfer RNA, ribozymes, small nuclear RNAs, and several types of regulatory RNAs. It also includes promoters and their associated gene-regulatory elements, DNA playing structural and replicatory roles, such as scaffolding regions, telomeres, centromeres, and origins of replication, plus large numbers of transposable elements, inserted viral DNA, non-functional pseudogenes and simple, highly repetitive sequences. Introns make up a large percentage of non-coding DNA. Some of this non-coding DNA is non-functional junk DNA, such as pseudogenes, but there is no firm consensus on the total amount of junk DNA.

<span class="mw-page-title-main">Yamnaya culture</span> Archaeological culture from the Pontic steppe

The Yamnaya culture or the Yamna culture, also known as the Pit Grave culture or Ochre Grave culture, was a late Copper Age to early Bronze Age archaeological culture of the region between the Southern Bug, Dniester, and Ural rivers, dating to 3300–2600 BCE. It was discovered by Vasily Gorodtsov following his archaeological excavations near the Donets River in 1901–1903. Its name derives from its characteristic burial tradition: Я́мная is a Russian adjective that means 'related to pits ', as these people used to bury their dead in tumuli (kurgans) containing simple pit chambers.

<span class="mw-page-title-main">Indo-Aryan migrations</span> Migrations of Indo-Aryans into the Indian subcontinent

The Indo-Aryan migrations were the migrations into the Indian subcontinent of Indo-Aryan peoples, an ethnolinguistic group that spoke Indo-Aryan languages, the predominant languages of today's North India, Pakistan, Nepal, Bangladesh, Sri Lanka and the Maldives. Indo-Aryan population movements into the region from Central Asia are considered to have started after 2000 BCE, as a slow diffusion during the Late Harappan period, which led to a language shift in the northern Indian subcontinent. Several hundred years later, the Iranian languages were brought into the Iranian plateau by the Iranians, who were closely related to the Indo-Aryans.

<span class="mw-page-title-main">Chimpanzee genome project</span> Effort to determine the DNA sequence of the chimpanzee genome

The Chimpanzee Genome Project was an effort to determine the DNA sequence of the chimpanzee genome. Sequencing began in 2005 and by 2013 twenty-four individual chimpanzees had been sequenced. This project was folded into the Great Ape Genome Project.

Genetics and archaeogenetics of South Asia is the study of the genetics and archaeogenetics of the ethnic groups of South Asia. It aims at uncovering these groups' genetic histories. The geographic position of the Indian subcontinent makes its biodiversity important for the study of the early dispersal of anatomically modern humans across Asia.

<span class="mw-page-title-main">Human genetic variation</span> Genetic diversity in human populations

Human genetic variation is the genetic differences in and among populations. There may be multiple variants of any given gene in the human population (alleles), a situation called polymorphism.

Human evolutionary genetics studies how one human genome differs from another human genome, the evolutionary past that gave rise to the human genome, and its current effects. Differences between genomes have anthropological, medical, historical and forensic implications and applications. Genetic data can provide important insights into human evolution.

The Karitiana or Caritiana are an indigenous people of Brazil, whose reservation is located in the western Amazon. They count 320 members, and the leader of their tribal association is Renato Caritiana. They subsist by farming, fishing and hunting, and have almost no contact with the outside world. Their tongue, the Karitiâna language, is an Arikém language of Brazil.

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<span class="mw-page-title-main">Recent African origin of modern humans</span> "Out of Africa" theory of the early migration of humans

In paleoanthropology, the recent African origin of modern humans or the "Out of Africa" theory (OOA) is the most widely accepted model of the geographic origin and early migration of anatomically modern humans. It follows the early expansions of hominins out of Africa, accomplished by Homo erectus and then Homo neanderthalensis.

<span class="mw-page-title-main">Peopling of India</span> Immigration patterns of different races of people of India

The peopling of India refers to the migration of Homo sapiens into the Indian subcontinent. Anatomically modern humans settled India in multiple waves of early migrations, over tens of millennia. The first migrants came with the Coastal Migration/Southern Dispersal 65,000 years ago, whereafter complex migrations within south and southeast Asia took place. West-Asian (Iranian) hunter-gatherers migrated to South Asia after the Last Glacial Period but before the onset of farming. Together with ancient South Asian hunter-gatherers they formed the population of the Indus Valley civilisation (IVC).

<span class="mw-page-title-main">Interbreeding between archaic and modern humans</span> Evidence of human hybridization during the Paleolithic

Interbreeding between archaic and modern humans occurred during the Middle Paleolithic and early Upper Paleolithic. The interbreeding happened in several independent events that included Neanderthals and Denisovans, as well as several unidentified hominins.

Incomplete lineage sorting, also termed hemiplasy, deep coalescence, retention of ancestral polymorphism, or trans-species polymorphism, describes a phenomenon in population genetics when ancestral gene copies fail to coalesce into a common ancestral copy until deeper than previous speciation events. It is caused by lineage sorting of genetic polymorphisms that were retained across successive nodes in the species tree. In other words, the tree produced by a single gene differs from the population or species level tree, producing a discordant tree. Whatever the mechanism, the result is that a generated species level tree may differ depending on the selected genes used for assessment. This is in contrast to complete lineage sorting, where the tree produced by the gene is the same as the population or species level tree. Both are common results in phylogenetic analysis, although it depends on the gene, organism, and sampling technique.

<span class="mw-page-title-main">Ust'-Ishim man</span> Hominin fossil found in Siberia

The study of the genetics and archaeogenetics of the Gujarati people of India aims at uncovering these people's genetic history. According to the 1000 Genomes Project, "Gujarati" is a general term used to describe people who trace their ancestry to the region of Gujarat, located in the northwestern part of the Indian subcontinent, and who speak the Gujarati language, an Indo-European language. They have some genetic commonalities as well as differences with other ethnic groups of India.

<span class="mw-page-title-main">Ancient North Eurasian</span> Archaeogenetic name for an ancestral genetic component

In archaeogenetics, the term Ancient North Eurasian (ANE) is the name given to an ancestral component that represents the lineage of the people of the Mal'ta–Buret' culture (c. 24,000 BP) and populations closely related to them, such as the Upper Paleolithic individuals from Afontova Gora in Siberia. Genetic studies indicate that the ANE are closely related to the Ancient North Siberians (ANS) represented by two ancient specimens from the preceding Yana Culture (c. 32,000 BP). The ANE can either be considered to descend from the earlier ANS population, or that both ANE and ANS are closely related, albeit differentiated, sister lineages, with both having originated from an 'Early West Eurasian' hunter-gatherer lineage (represented by Kostenki-14, c. 40,000 BP), which absorbed an 'Early East Eurasian' population (represented by the Tianyuan man, c. 40,000 BP). The ANS and ANE each derive between 18% to one third of their ancestry from an Early East Eurasian lineage and between two thirds to 82% from an Early West Eurasian lineage.

Genetic studies on Neanderthal ancient DNA became possible in the late 1990s. The Neanderthal genome project, established in 2006, presented the first fully sequenced Neanderthal genome in 2013.

<i>Who We Are and How We Got Here</i> Book by David Reich

Who We Are and How We Got Here is a 2018 book on the contribution of genome-wide ancient DNA research to human population genetics by the geneticist David Reich. He describes discoveries made by his group and others, based on analysis and comparison of ancient and modern DNA from human populations around the world. Central to these is the finding that almost all human populations are mixtures resulting from multiple population migrations and gene flow.

<span class="mw-page-title-main">Western Hunter-Gatherer</span> Archaeogenetic name for an ancestral genetic component

In archaeogenetics, the term Western Hunter-Gatherer (WHG), West European Hunter-Gatherer, Western European Hunter-Gatherer, Villabruna cluster, or Oberkassel cluster names a distinct ancestral component of modern Europeans, representing descent from a population of Mesolithic hunter-gatherers who scattered over Western, Southern and Central Europe, from the British Isles in the west to the Carpathians in the east, following the retreat of the ice sheet of the Last Glacial Maximum.

Caucasus hunter-gatherer (CHG), also called Satsurblia cluster, is an anatomically modern human genetic lineage, first identified in a 2015 study, based on the population genetics of several modern Western Eurasian populations.

References

  1. ↑ "365 days: Nature's 10". Nature. 528 (7583): 459–467. 2015. Bibcode:2015Natur.528..459.. doi: 10.1038/528459a . ISSN   0028-0836. PMID   26701036.
  2. ↑ https://www.york.ac.uk/archaeology/news-and-events/news/external/news2022/antiquity-prize-win/
  3. 1 2 Reich, David Emile (1999). Genetic analysis of human evolutionary history with implications for gene mapping. ox.ac.uk (DPhil thesis). University of Oxford. OCLC   863264589. EThOS   uk.bl.ethos.580823. Lock-green.svg
  4. ↑ "David Reich | Genetics". genetics.hms.harvard.edu. Retrieved 2018-01-08.
  5. ↑ "Nature's 10". Nature. 528 (7583): 459–467. December 2015. Bibcode:2015Natur.528..459.. doi: 10.1038/528459a . PMID   26701036. S2CID   4450003.
  6. ↑ Massry Prize 2021
  7. 1 2 3 Zimmer, Carl (2018-03-20). "David Reich Unearths Human History Etched in Bone". The New York Times. Retrieved 2018-03-20.
  8. ↑ Rincon, Paul (11 April 2018). "How ancient DNA is transforming our view of the past". BBC. Retrieved 11 April 2018.
  9. ↑ Emile., Reich, David (1999). Genetic analysis of human evolutionary history with implications for gene mapping (Thesis). University of Oxford.{{cite thesis}}: CS1 maint: multiple names: authors list (link)
  10. ↑ ScienceNews.org – 'Hybrid-Driven Evolution: Genomes show complexity of human-chimp split: Not only did the evolutionary parting of human from chimpanzee ancestors occur more recently than had been indicated by previous data, but it also played out over an extended period during which forerunners of people and chimps interbred', Bruce Bower, Science News (May 20, 2006)
  11. ↑ Patterson, N.; Richter, D. J.; Gnerre, S.; Lander, E. S.; Reich, D. (2006). "Genetic evidence for complex speciation of humans and chimpanzees". Nature. 441 (7097): 1103–1108. Bibcode:2006Natur.441.1103P. doi:10.1038/nature04789. PMID   16710306. S2CID   2325560.
  12. ↑ Reich 2009.
  13. ↑ Chakravarti, Aravinda (24 September 2009). "Tracing India's invisible lthreads" (PDF). Nature (News & Views). Archived from the original (PDF) on 3 September 2015. Retrieved 16 March 2016.
  14. ↑ Dolgin, Elie (September 23, 2009). "Indian ancestry revealed". Nature. doi:10.1038/news.2009.935 – via www.nature.com.
  15. ↑ Srinath Perur, The origins of Indians. What our genes are telling us., Fountain Ink
  16. ↑ Metspalu et al. 2011.
  17. ↑ David Cameron (July 20, 2011). "Detail distinguishes map of African-American genomics". Harvard Gazette. Retrieved July 22, 2011.
  18. ↑ Reich, D.; Green, R.E.; Kircher, M.; Krause, J.; Patterson, N.; Durand, E.Y.; et al. (2010). "Genetic history of an archaic hominin group from Denisova Cave in Siberia". Nature. 468 (7327): 1053–1060. Bibcode:2010Natur.468.1053R. doi:10.1038/nature09710. PMC   4306417 . PMID   21179161.Reich, D.; Patterson, N.; Kircher, M.; Delfin, F.; Nandineni, M.R.; Pugach, I.; et al. (2011). "Denisova Admixture and the First Modern Human Dispersals into Southeast Asia and Oceania". The American Journal of Human Genetics. 89 (4): 516–528. doi:10.1016/j.ajhg.2011.09.005. PMC   3188841 . PMID   21944045.Sankararaman, S.; Patterson, N.; Li, H.; Pääbo, S.; Reich, D; Akey, J.M. (2012). "The Date of Interbreeding between Neandertals and Modern Humans". PLOS Genetics. 8 (10): e1002947. arXiv: 1208.2238 . doi: 10.1371/journal.pgen.1002947 . PMC   3464203 . PMID   23055938. Carl Zimmer, "Interbreeding with Neanderthals", Discover , March 2013, pp. 38–44.
  19. ↑ https://reich.hms.harvard.edu/sites/reich.hms.harvard.edu/files/inline-files/2007_NG_Haiman_colorectal_and_prostate.pdf [ bare URL PDF ]
  20. 1 2 Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past. By David Reich. New York: Pantheon, 2018.
  21. ↑ "Inferring demographic history from genetic data". uqrmaie1.github.io. Retrieved 2022-05-18.

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