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{{Short description|Genetic diversity in human populations}}
==Origins of modern humans==
{{Redirect|Human biodiversity|the far-right movement promoting scientific racism|Human Biodiversity Institute}}
Any biological model for race must account for the development of racial differences during human evolution. For much of the 20th century, however, anthropologists relied on an incomplete ] record for reconstructing human evolution. Their models seldom provided a firm basis for drawing inferences about the origin of races. Modern research in ], however, has provided evolutionary scientists with a whole new kind of data, which adds considerably to the knowledge of our past.
{{Use dmy dates|date=August 2021}}
]]]
]


'''Human genetic variation''' is the genetic differences in and among ]s. There may be multiple variants of any given gene in the human population (]s), a situation called ].
There has been considerable debate among anthropologists as to the origins of ''Homo sapiens''. About a million years ago ] migrated out of Africa and into Europe and Asia. The debate hinges on whether ''Homo erectus'' evolved into ''Homo sapiens'' more or less simultaneously in Africa, Europe, and Asia, or whether ''Homo sapiens'' evolved only in Africa, and eventually supplanted ''Homo erectus'' in Europe and Asia. Each model suggests different possible scenarios for the evolution of distinct races.


No two humans are genetically identical. Even ] (who develop from one zygote) have infrequent genetic differences due to mutations occurring during development and gene ].<ref>{{cite journal |vauthors = Bruder CE, Piotrowski A, Gijsbers AA, Andersson R, Erickson S, Diaz de Ståhl T, Menzel U, Sandgren J, von Tell D, Poplawski A, Crowley M, Crasto C, Partridge EC, Tiwari H, Allison DB, Komorowski J, van Ommen GJ, Boomsma DI, Pedersen NL, den Dunnen JT, Wirdefeldt K, Dumanski JP |display-authors = 6 |title = Phenotypically concordant and discordant monozygotic twins display different DNA copy-number-variation profiles |journal = American Journal of Human Genetics |volume = 82 |issue = 3 |pages = 763–71 |date = March 2008 |pmid = 18304490 |pmc = 2427204 |doi = 10.1016/j.ajhg.2007.12.011 }}</ref> Differences between individuals, even closely related individuals, are the key to techniques such as ].
===Multiregional hypothesis===
{{main|multiregional hypothesis}}
Advocates of the multiregional continuity evolution model (see Frayer ''et al.'' 1993) cite as evidence ] continuity in the fossil record in South Central Europe (Smith 1982), East Asia and Australia (Wolpoff 1993) (anatomical affinity is taken to suggest genetic affinity). They argue that very strong genetic similarities among all humans do not prove recent common ancestry, but rather reflect the interconnectedness of human populations around the world, resulting in relatively constant gene flow (Thorne and Wolpoff 1992). They further argue that this model is consistent with clinal patterns (Wolpoff 1993).


The human genome has a total length of approximately 3.2 billion ]s (bp) in 46 chromosomes of DNA as well as slightly under 17,000 bp DNA in cellular ]. In 2015, the typical difference between an individual's genome and the reference genome was estimated at 20 million base pairs (or 0.6% of the total).<ref name="kGP15" /> As of 2017, there were a total of 324 million known variants from sequenced ]s.<ref name=RefSNP/>
The most important element of this model for theories of race is that it allows a million years for the evolution of ''Homo sapiens'' around the world; this is more than enough time for the evolution of different races. Leiberman and Jackson (1995), however, have noted that this model depends on several findings relevant to race: (1) that marked ] contrasts exist between individuals found at the center and at the perimeter of ] range of the genus ''Homo''; (2) that many features can be shown to emerge at the edge of that range before they develop at the center; and (3) that these features exhibit great tenacity through time. Regional variations in these features can thus be taken as evidence for long term differences among genus Homo individuals that prefigure different races among present-day Homo sapiens individuals.


Comparatively speaking, humans are a genetically homogeneous species. Although a small number of genetic variants are found more frequently in certain geographic regions or in people with ancestry from those regions, this variation accounts for a small portion (~15%) of human genome variability. The majority of variation exists within the members of each human population. For comparison, ]s exhibit 2.5-fold greater DNA sequence diversity compared to humans.<ref>{{Cite journal |last1=Xue |first1=Cheng |last2=Raveendran |first2=Muthuswamy |last3=Harris |first3=R. Alan |last4=Fawcett |first4=Gloria L. |last5=Liu |first5=Xiaoming |last6=White |first6=Simon |last7=Dahdouli |first7=Mahmoud |last8=Deiros |first8=David Rio |last9=Below |first9=Jennifer E. |last10=Salerno |first10=William |last11=Cox |first11=Laura |date=2016-12-01 |title=The population genomics of rhesus macaques (Macaca mulatta) based on whole-genome sequences |url=https://genome.cshlp.org/content/26/12/1651 |journal=Genome Research |language=en |volume=26 |issue=12 |pages=1651–1662 |doi=10.1101/gr.204255.116 |issn=1088-9051 |pmid=27934697 |pmc=5131817 }}</ref> These rates differ depending on what macromolecules are being analyzed. Chimpanzees have more genetic variance than humans when examining nuclear DNA, but humans have more genetic variance when examining at the level of proteins.<ref>{{cite journal |last1=Curnoe |first1=Darren |title=Number of ancestral human species: a molecular perspective |journal=HOMO |date=2003 |volume=53 |issue=3 |pages=208–209 |doi=10.1078/0018-442x-00051 |pmid=12733395}}</ref>
===Out of Africa===
{{main|recent single-origin hypothesis}}
] ] (numbers are ] before present).]]


The lack of discontinuities in genetic distances between human populations, absence of discrete branches in the human species, and striking homogeneity of human beings globally, imply that there is no scientific basis for inferring races or subspecies in humans, and for most ], there is much more variation ''within'' populations than between them.<ref>{{Cite news |last=Reich |first=David |date=2018-03-23 |title=Opinion {{!}} How Genetics Is Changing Our Understanding of 'Race' |language=en-US |work=The New York Times |url=https://www.nytimes.com/2018/03/23/opinion/sunday/genetics-race.html |access-date=2022-08-15 |issn=0362-4331}}</ref><ref>{{Cite journal |last=Williams |first=David R. |date=1997-07-01 |title=Race and health: Basic questions, emerging directions |url=https://www.sciencedirect.com/science/article/pii/S1047279797000513 |journal=Annals of Epidemiology |series=Special Issue: Interface Between Molecular and Behavioral Epidemiology |language=en |volume=7 |issue=5 |pages=322–333 |doi=10.1016/S1047-2797(97)00051-3 |pmid=9250627 |issn=1047-2797}}</ref><ref>{{Cite book |url=https://www.worldcat.org/oclc/42389561 |title=Race and racism in theory and practice |date=2000 |publisher=Rowman & Littlefield |others=] |isbn=0-8476-9692-8 |location=Lanham, Md. |oclc=42389561|chapter=1}}</ref><ref>{{Cite journal |last1=Lee |first1=Jun-Ki |last2=Aini |first2=Rahmi Qurota |last3=Sya’bandari |first3=Yustika |last4=Rusmana |first4=Ai Nurlaelasari |last5=Ha |first5=Minsu |last6=Shin |first6=Sein |date=2021-04-01 |title=Biological Conceptualization of Race |journal=Science & Education |language=en |volume=30 |issue=2 |pages=293–316 |doi=10.1007/s11191-020-00178-8 |bibcode=2021Sc&Ed..30..293L |s2cid=231598896 |issn=1573-1901|doi-access=free }}</ref><ref>{{Cite web |first=Elizabeth |last=Kolbert |date=2018-04-04 |title=There's No Scientific Basis for Race—It's a Made-Up Label |url=https://www.nationalgeographic.co.uk/people-and-culture/2018/04/theres-no-scientific-basis-for-race-its-a-made-up-label |access-date=2022-08-15 |website=National Geographic |language=en-gb}}</ref><ref>{{Cite book |last=Templeton |first=Alan Robert |url=https://www.worldcat.org/oclc/1062418886 |title=Human Population Genetics and Genomics |date=2018 |isbn=978-0-12-386026-2 |location=London |pages=445–446 |oclc=1062418886}}</ref><ref name = Reich2018/><ref>{{Cite journal |last1=Witherspoon |first1=D. J. |last2=Wooding |first2=S. |last3=Rogers |first3=A. R. |last4=Marchani |first4=E. E. |last5=Watkins |first5=W. S. |last6=Batzer |first6=M. A. |last7=Jorde |first7=L. B. |title=Genetic Similarities Within and Between Human Populations |journal=Genetics |year=2007 |volume=176 |issue=1 |pages=351–359 |doi=10.1534/genetics.106.067355 |issn=0016-6731 |pmc=1893020 |pmid=17339205}}</ref>
Information about the history of our species comes from two main sources: the paleoanthropological record and historical inferences based on current genetic differences observed in humans. Although both sources of information are fragmentary, they have been converging in recent years on the same general story.
Despite this, modern genetic studies have found substantial average genetic differences across human populations in traits such as skin colour, bodily dimensions, lactose and starch digestion, high altitude adaptions, drug response, taste receptors, and predisposition to developing particular diseases.<ref>{{cite journal |last1=Campbell |first1=Michael |title=African Genetic Diversity: Implications for Human Demographic History, Modern Human Origins, and Complex Disease Mapping |journal=Annual Review of Genomics and Human Genetics |date=2008 |volume=9 |pages=403–433 |doi=10.1146/annurev.genom.9.081307.164258 |pmid=18593304 |pmc=2953791 }}</ref><ref name = Reich2018>{{Cite book |last=Reich |first=David |url=https://www.worldcat.org/oclc/1006478846 |title=Who we are and how we got here: ancient DNA and the new science of the human past |date=2018 |isbn=978-0-19-882125-0 |edition=First |location=Oxford, United Kingdom |oclc=1006478846 |page=255}}</ref> The greatest diversity is found within and among populations in ],<ref name="ReferenceB">{{Cite journal |last1=Campbell |first1=Michael C. |last2=Tishkoff |first2=Sarah A. |date=2008 |title=AFRICAN GENETIC DIVERSITY: Implications for Human Demographic History, Modern Human Origins, and Complex Disease Mapping |journal=Annual Review of Genomics and Human Genetics |volume=9 |pages=403–433 |doi=10.1146/annurev.genom.9.081307.164258 |issn=1527-8204 |pmc=2953791 |pmid=18593304}}</ref> and gradually declines with increasing distance from the African continent, consistent with the ] theory of human origins.<ref name="ReferenceB"/>


The study of human genetic variation has evolutionary significance and medical applications. It can help scientists reconstruct and understand patterns of past human migration. In medicine, study of human genetic variation may be important because some disease-causing alleles occur more often in certain population groups. For instance, the mutation for ] is more often found in people with ancestry from certain sub-Saharan African, south European, Arabian, and Indian populations, due to the evolutionary pressure from mosquitos carrying malaria in these regions.
Since the 1990s, it has become common to use ] genotypes to distinguish different human groups and to allocate individuals to groups (Bamshad ''et al.'' 2004). These data have led to an examination of the biological validity of races as ] and the description of races in ] terms. The technique of multilocus genotyping has been used to determine patterns of ]. Thus, the concept of "race" afforded by these techniques is synonymous with ], broadly understood.


New findings show that each human has on average 60 new mutations compared to their parents.<ref>
Studies of human genetic variation imply that ] was the ancestral source of all modern humans, and that ''Homo sapiens'' migrated out of Africa and displaced ''Homo erectus'' starting 50,000 years ago . ] are believed to be an early out-group that remained isolated. Most other groups, including ], Eurasians , and ], were found to be a single related (]) group resulting from a later out-migration from Africa, and could reasonably be divided into West and East Eurasian subgroups.
{{cite web |title=We are all mutants: First direct whole-genome measure of human mutation predicts 60 new mutations in each of us
|url=https://www.sciencedaily.com/releases/2011/06/110613012758.htm |publisher=]
|date=13 June 2011
|access-date=2011-09-05
}}</ref><ref>{{cite journal |vauthors = Conrad DF, Keebler JE, DePristo MA, Lindsay SJ, Zhang Y, Casals F, Idaghdour Y, Hartl CL, Torroja C, Garimella KV, Zilversmit M, Cartwright R, Rouleau GA, Daly M, Stone EA, Hurles ME, Awadalla P |display-authors = 6 |title = Variation in genome-wide mutation rates within and between human families |journal = Nature Genetics |volume = 43 |issue = 7 |pages = 712–4 |date = June 2011 |pmid = 21666693 |pmc = 3322360 |doi = 10.1038/ng.862 }}</ref>


== Causes of variation ==
The existing fossil evidence suggests that anatomically modern humans evolved in Africa, within the last ∼200,000 years, from a pre-existing population of humans (Klein 1999). Although it is not easy to define "anatomically modern" in a way that encompasses all living humans and excludes all archaic humans (Lieberman ''et al.'' 2002), the generally agreed-upon physical characteristics of anatomical modernity include a high rounded skull, facial retraction, and a light and gracile, as opposed to heavy and robust, skeleton (Lahr 1996). Early fossils with these characteristics have been found in eastern Africa and have been dated to ∼160,000–200,000 years ago (White ''et al.'' 2003; McDougall ''et al.'' 2005). At that time, the population of anatomically modern humans appears to have been small and localized (Harpending ''et al.'' 1998). Much larger populations of archaic humans lived elsewhere in the Old World, including the Neandertals in Europe and an earlier species of humans, Homo erectus, in Asia (Swisher ''et al.'' 1994).
{{further|Recent human evolution}}
Causes of differences between individuals include ], the ] during reproduction (through ]) and various ]al events.


There are at least three reasons why genetic variation exists between populations. ] may confer an adaptive advantage to individuals in a specific environment if an allele provides a competitive advantage. Alleles under selection are likely to occur only in those geographic regions where they confer an advantage. A second important process is ], which is the effect of random changes in the gene pool, under conditions where ] (that is, they do not appear to have any positive or negative selective effect on the organism). Finally, small migrant populations have statistical differences – called the ] – from the overall populations where they originated; when these migrants settle new areas, their descendant population typically differs from their population of origin: different genes predominate and it is less genetically diverse.
Fossils of the earliest anatomically modern humans found outside Africa are from two sites in the Middle East and date to a period of relative global warmth, ∼100,000 years ago, though this region was reinhabited by Neandertals in later millennia as the climate in the northern hemisphere again cooled (Lahr and Foley 1998). Groups of anatomically modern humans appear to have moved outside Africa permanently sometime >60,000 years ago. One of the earliest modern skeletons found outside Africa is ], from Australia, and has been dated to ∼42,000 years ago (Bowler ''et al.'' 2003), although studies of environmental changes in Australia argue for the presence of modern humans in Australia >55,000 years ago (Miller ''et al.'' 1999). To date, the earliest anatomically modern skeleton discovered from Europe comes from the Carpathian Mountains of Romania and is dated to 34,000–36,000 years ago (Trinkaus ''et al.'' 2003).


In humans, the main cause is ].<ref>{{Cite journal |last1=Ackermann |first1=R. R. |last2=Cheverud |first2=J. M. |date=2004-12-16 |title=Detecting genetic drift versus selection in human evolution |journal=Proceedings of the National Academy of Sciences |volume=101 |issue=52 |pages=17946–17951 |doi=10.1073/pnas.0405919102 |issn=0027-8424 |pmc=539739 |pmid=15604148|bibcode=2004PNAS..10117946A |doi-access=free }}</ref> Serial ]s and past small population size (increasing the likelihood of genetic drift) may have had an important influence in neutral differences between populations. {{citation needed|date=February 2015}} The second main cause of genetic variation is due to the high degree of ]. A small, but significant number of genes appear to have undergone recent natural selection, and these selective pressures are sometimes specific to one region.<ref>{{cite journal | vauthors = Guo J, Wu Y, Zhu Z, Zheng Z, Trzaskowski M, Zeng J, Robinson MR, Visscher PM, Yang J | title = Global genetic differentiation of complex traits shaped by natural selection in humans | journal = Nature Communications | volume = 9 | issue = 1 | pages = 1865 | date = May 2018 | pmid = 29760457 | pmc = 5951811 | doi = 10.1038/s41467-018-04191-y | bibcode = 2018NatCo...9.1865G }}</ref><ref>{{cite journal | vauthors = Wang ET, Kodama G, Baldi P, Moyzis RK | title = Global landscape of recent inferred Darwinian selection for Homo sapiens | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 103 | issue = 1 | pages = 135–40 | date = January 2006 | pmid = 16371466 | pmc = 1317879 | doi = 10.1073/pnas.0509691102 | quote = By these criteria, 1.6% of Perlegen SNPs were found to exhibit the genetic architecture of selection. | bibcode = 2006PNAS..103..135W | doi-access = free }}</ref>
Existing data on human genetic variation support and extend conclusions based on the fossil evidence. African populations exhibit greater genetic diversity than do populations in the rest of the world, implying that humans appeared first in Africa and later colonized Eurasia and the Americas (Tishkoff and Williams 2002; Yu ''et al.'' 2002; Tishkoff and Verrelli 2003). The genetic variation seen outside Africa is generally a subset of the variation within Africa, a pattern that would be produced if the migrants from Africa were limited in number and carried just part of African genetic variability with them (Cavalli-Sforza and Feldman 2003). Patterns of genetic variation suggest an earlier population expansion in Africa followed by a subsequent expansion in non-African populations, and the dates calculated for the expansions generally coincide with the archaeological record (Jorde ''et al.'' 1998).


==Measures of variation==
Aspects of the relationship between anatomically modern and archaic humans remain contentious. Studies of mtDNA (Ingman ''et al.'' 2000), the Y chromosome (Underhill ''et al.'' 2000), portions of the X chromosome (Kaessmann ''et al.'' 1999), and many (though not all) autosomal regions (Harpending and Rogers 2000) support the "Out of Africa" account of human history, in which anatomically modern humans appeared first in eastern Africa and then migrated throughout Africa and into the rest of the world, with little or no interbreeding between modern humans and the archaic populations they gradually replaced (Tishkoff ''et al.'' 2000; Stringer 2002). However, several groups of researchers cite fossil and genetic evidence to argue for a more complex account. They contend that humans bearing modern traits emerged several times from Africa, over an extended period, and mixed with archaic humans in various parts of the world (Hawks ''et al.'' 2000; Eswaran 2002; Templeton 2002; Ziętkiewicz ''et al.'' 2003). As a result, they say, autosomal DNA from archaic human populations living outside Africa persists in modern populations, and modern populations in various parts of the world still bear some physical resemblance to the archaic populations that inhabited those regions (Wolpoff ''et al.'' 2001).
Genetic variation among humans occurs on many scales, from gross alterations in the human ] to single ] changes.<ref>
{{cite journal | vauthors = Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, Graves T, Hansen N, Teague B, Alkan C, Antonacci F, Haugen E, Zerr T, Yamada NA, Tsang P, Newman TL, Tüzün E, Cheng Z, Ebling HM, Tusneem N, David R, Gillett W, Phelps KA, Weaver M, Saranga D, Brand A, Tao W, Gustafson E, McKernan K, Chen L, Malig M, Smith JD, Korn JM, McCarroll SA, Altshuler DA, Peiffer DA, Dorschner M, Stamatoyannopoulos J, Schwartz D, Nickerson DA, Mullikin JC, Wilson RK, Bruhn L, Olson MV, Kaul R, Smith DR, Eichler EE | display-authors = 6 | title = Mapping and sequencing of structural variation from eight human genomes | journal = Nature | volume = 453 | issue = 7191 | pages = 56–64 | date = May 2008 | pmid = 18451855 | pmc = 2424287 | doi = 10.1038/nature06862 | bibcode = 2008Natur.453...56K }}</ref> ] are detected in 1 of 160 live human births. Apart from ], most cases of aneuploidy result in death of the developing fetus (]); the most common extra ] chromosomes among live births are ], ] and ].<ref>{{cite journal | vauthors = Driscoll DA, Gross S | title = Clinical practice. Prenatal screening for aneuploidy | journal = The New England Journal of Medicine | volume = 360 | issue = 24 | pages = 2556–62 | date = June 2009 | pmid = 19516035 | doi = 10.1056/NEJMcp0900134 }}</ref>


] is the average proportion of nucleotides that differ between two individuals. As of 2004, the human nucleotide diversity was estimated to be 0.1%<ref name=Jorde04>{{cite journal | vauthors = Jorde LB, Wooding SP | title = Genetic variation, classification and 'race' | journal = Nature Genetics | volume = 36 | issue = 11 Suppl | pages = S28–33 | date = November 2004 | pmid = 15508000 | doi = 10.1038/ng1435 | doi-access = free }}</ref> to 0.4% of ]s.<ref name=Tishkoff04>{{cite journal | vauthors = Tishkoff SA, Kidd KK | title = Implications of biogeography of human populations for 'race' and medicine | journal = Nature Genetics | volume = 36 | issue = 11 Suppl | pages = S21–7 | date = November 2004 | pmid = 15507999 | doi = 10.1038/ng1438 | doi-access = free }}</ref> In 2015, the ], which sequenced one thousand individuals from 26 human populations, found that "a typical genome differs from the reference human genome at 4.1 million to 5.0 million sites … affecting 20 million bases of sequence"; the latter figure corresponds to 0.6% of total number of base pairs.<ref name="kGP15">{{cite journal | vauthors = Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR | display-authors = 6 | title = A global reference for human genetic variation | journal = Nature | volume = 526 | issue = 7571 | pages = 68–74 | date = October 2015 | pmid = 26432245 | pmc = 4750478 | doi = 10.1038/nature15393 | bibcode = 2015Natur.526...68T }}</ref> Nearly all (>99.9%) of these sites are small differences, either single nucleotide polymorphisms or brief insertions or deletions (]s) in the genetic sequence, but structural variations account for a greater number of base-pairs than the SNPs and indels.<ref name="kGP15" /><ref>{{cite journal | vauthors = Mullaney JM, Mills RE, Pittard WS, Devine SE | title = Small insertions and deletions (INDELs) in human genomes | journal = Human Molecular Genetics | volume = 19 | issue = R2 | pages = R131–6 | date = October 2010 | pmid = 20858594 | pmc = 2953750 | doi = 10.1093/hmg/ddq400 }}</ref>
However, distinguishing possible contributions to the gene pool of modern humans from archaic humans outside Africa is difficult, especially since many autosomal loci coalesce at times preceding the separation of archaic human populations (Pääbo 2003). In addition, studies of mtDNA from archaic and modern humans and extant Y chromosomes suggest that any surviving genetic contributions of archaic humans outside Africa must be small, if they exist at all (Krings ''et al.'' 1997; Nordborg 1998; Takahata ''et al.'' 2001; Serre ''et al.'' 2004). The observation that most genes studied to date coalesce in African populations points toward the importance of Africa as the source of most modern genetic variation, perhaps with some subdivision in the ancestral African population (Satta and Takahata 2002). Sequence data for hundreds of loci from widely distributed worldwide populations eventually may clarify the population processes associated with the appearance of anatomically modern humans (Wall 2000), as well as the amount of gene flow among modern humans since then.


{{As of|2017}}, the Single Nucleotide Polymorphism Database (]), which lists SNP and other variants, listed 324 million variants found in sequenced human genomes.<ref name=RefSNP>{{Cite web|url=https://ncbiinsights.ncbi.nlm.nih.gov/2017/05/08/dbsnps-human-build-150-has-doubled-the-amount-of-refsnp-records/|title=dbSNP's human build 150 has doubled the amount of RefSNP records!|author=NCBI |date=2017-05-08|website=NCBI Insights|access-date=2017-05-16}}</ref>
===Cladistics===
]


=== Single nucleotide polymorphisms ===
A ] like the one shown above is usually derived from ] or ] ] from populations. Often ] or ] sequences are used to study ancient human demographics. These single-] sources of DNA do not ] and are almost always inherited from a single parent, with only one known exception in mtDNA (Schwartz and Vissing 2002). Individuals from the various continental groups tend to be more similar to one another than to people from other continents. The tree is rooted in the common ancestor of ]s and humans, which is believed to have originated in ]. Horizontal distance corresponds to two things:
]
{{Main|Single nucleotide polymorphism}}
A ] (SNP) is a difference in a single nucleotide between members of one species that occurs in at least 1% of the population. The 2,504 individuals characterized by the ] had 84.7 million SNPs among them.<ref name="kGP15" /> SNPs are the most common type of sequence variation, estimated in 1998 to account for 90% of all sequence variants.<ref name="Collins_1998">{{cite journal | vauthors = Collins FS, Brooks LD, Chakravarti A | title = A DNA polymorphism discovery resource for research on human genetic variation | journal = Genome Research | volume = 8 | issue = 12 | pages = 1229–31 | date = December 1998 | pmid = 9872978 | doi = 10.1101/gr.8.12.1229 | doi-access = free }}</ref> Other sequence variations are single base exchanges, deletions and insertions.<ref name="Thomas_2011">{{cite journal | vauthors = Thomas PE, Klinger R, Furlong LI, Hofmann-Apitius M, Friedrich CM | title = Challenges in the association of human single nucleotide polymorphism mentions with unique database identifiers | journal = BMC Bioinformatics | volume = 12 | pages = S4 | year = 2011 | issue = Suppl 4 | pmid = 21992066 | pmc = 3194196 | doi = 10.1186/1471-2105-12-S4-S4 | doi-access = free }}</ref> SNPs occur on average about every 100 to 300 bases<ref name="pmid_18197193">{{cite journal | vauthors = Ke X, Taylor MS, Cardon LR | title = Singleton SNPs in the human genome and implications for genome-wide association studies | journal = European Journal of Human Genetics | volume = 16 | issue = 4 | pages = 506–15 | date = April 2008 | pmid = 18197193 | doi = 10.1038/sj.ejhg.5201987 | doi-access = free }}</ref> and so are the major source of heterogeneity.


A functional, or non-synonymous, SNP is one that affects some factor such as ] or ], and so causes a ] difference between members of the species. About 3% to 5% of human SNPs are functional (see ]). Neutral, or synonymous SNPs are still useful as genetic markers in ], because of their sheer number and the stable inheritance over generations.<ref name="Collins_1998" />
#'''Genetic distance'''. Given below the diagram, the genetic difference between humans and chimps is roughly 2%, or 20 times larger than the variation among modern humans.
#'''Temporal remoteness''' of the most recent common ancestor. Rough estimates are given above the diagram, in millions of years. The ] most recent common ancestor of modern humans lived roughly 200,000 years ago, latest common ancestors of humans and chimps between four and seven million years ago.


A coding SNP is one that occurs inside a gene. There are 105 Human Reference SNPs that result in premature ]s in 103 genes. This corresponds to 0.5% of coding SNPs. They occur due to segmental duplication in the genome. These SNPs result in loss of protein, yet all these SNP alleles are common and are not purified in ].<ref name="Genetic Variation in an individual human exome">{{cite journal | vauthors = Ng PC, Levy S, Huang J, Stockwell TB, Walenz BP, Li K, Axelrod N, Busam DA, Strausberg RL, Venter JC | display-authors = 6 | title = Genetic variation in an individual human exome | journal = PLOS Genetics | volume = 4 | issue = 8 | pages = e1000160 | date = August 2008 | pmid = 18704161 | pmc = 2493042 | doi = 10.1371/journal.pgen.1000160 | editor1-last = Schork | editor1-first = Nicholas J | doi-access = free }}</ref>
Chimpanzees and humans belong to different ], indicated in red. Formation of ] and ] is also indicated, and the formation of "races" is indicated in the green rectangle to the right (note that only a very rough representation of human ] is given). Note that vertical distances are not meaningful in this representation.


==Distribution of variation== === Structural variation ===
{{Main|Structural variation}}
A thorough description of the differences in patterns of genetic variation between humans and other species awaits additional genetic studies of human populations and nonhuman species. But the data gathered to date suggest that human variation exhibits several distinctive characteristics. First, compared with many other mammalian species, humans are genetically less diverse—a counterintuitive finding, given our large population and worldwide distribution (Li and Sadler 1991; Kaessmann ''et al.'' 2001). For example, the chimpanzee subspecies living just in central and western Africa have higher levels of diversity than do humans (Ebersberger ''et al.'' 2002; Yu ''et al.'' 2003; Fischer ''et al.'' 2004).
] is the variation in structure of an organism's ]. Structural variations, such as copy-number variation and ], ], ] and ], account for much more human genetic variation than single nucleotide diversity. This was concluded in 2007 from analysis of the ] ] of the genomes of two humans: ] and ]. This added to the two ] sequences which were amalgamations of sequences from many individuals, published by the ] and ] respectively.<ref>{{cite journal | vauthors = Gross L | title = A new human genome sequence paves the way for individualized genomics | journal = PLOS Biology | volume = 5 | issue = 10 | pages = e266 | date = October 2007 | pmid = 20076646 | pmc = 1964778 | doi = 10.1371/journal.pbio.0050266 | doi-access = free }}</ref>


According to the 1000 Genomes Project, a typical human has 2,100 to 2,500 structural variations, which include approximately 1,000 large deletions, 160 copy-number variants, 915 ] insertions, 128 ] insertions, 51 SVA insertions, 4 ], and 10 inversions.<ref name="kGP15" />
Two random humans are expected to differ at approximately 1 in 1000 ]s, whereas two random chimpanzees differ at 1 in 500 nucleotide pairs. However, with a genome of approximate 3 billion nucleotides, on average two humans differ at approximately 3 million nucleotides. Most of these ] (SNPs) are ], but some are functional and influence the phenotypic differences between humans. It is estimated that about 10 million SNPs exist in human populations, where the rarer SNP allele has a frequency of at least 1% (see ]).


==== Copy number variation ====
The distribution of variants within and among human populations also differs from that of many other species. The details of this distribution are impossible to describe succinctly because of the difficulty of defining a "population," the clinal nature of variation, and heterogeneity across the genome (Long and Kittles 2003). In general, however, 5%–15% of genetic variation occurs between large groups living on different continents, with the remaining majority of the variation occurring within such groups (Lewontin 1972; Jorde ''et al.'' 2000a; Hinds ''et al.'' 2005). This distribution of genetic variation differs from the pattern seen in many other mammalian species, for which existing data suggest greater differentiation between groups (Templeton 1998; Kittles and Weiss 2003).
{{Main|Copy number variation}}
A copy-number variation (CNV) is a difference in the genome due to deleting or duplicating large regions of DNA on some chromosome. It is estimated that 0.4% of the genomes of unrelated humans differ with respect to copy number. When copy number variation is included, human-to-human genetic variation is estimated to be at least 0.5% (99.5% similarity).<ref>{{cite web
|date=3 September 2007
|title=First Individual Diploid Human Genome Published By Researchers at J. Craig Venter Institute
|url=http://www.jcvi.org/cms/press/press-releases/full-text/article/first-individual-diploid-human-genome-published-by-researchers-at-j-craig-venter-institute/
|publisher=]
|access-date=2011-09-05
|archive-url=https://web.archive.org/web/20110716022944/http://www.jcvi.org/cms/press/press-releases/full-text/article/first-individual-diploid-human-genome-published-by-researchers-at-j-craig-venter-institute/
|archive-date=16 July 2011
|url-status=dead
}}</ref><ref>
{{cite journal | vauthors = Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, Walenz BP, Axelrod N, Huang J, Kirkness EF, Denisov G, Lin Y, MacDonald JR, Pang AW, Shago M, Stockwell TB, Tsiamouri A, Bafna V, Bansal V, Kravitz SA, Busam DA, Beeson KY, McIntosh TC, Remington KA, Abril JF, Gill J, Borman J, Rogers YH, Frazier ME, Scherer SW, Strausberg RL, Venter JC | display-authors = 6 | title = The diploid genome sequence of an individual human | journal = PLOS Biology | volume = 5 | issue = 10 | pages = e254 | date = September 2007 | pmid = 17803354 | pmc = 1964779 | doi = 10.1371/journal.pbio.0050254 | doi-access = free }}</ref><ref>{{cite web
|date=24 January 2008
|title=Understanding Genetics: Human Health and the Genome
|url=http://www.thetech.org/genetics/news.php?id=74
|publisher=]
|access-date=2011-09-05
|archive-date=29 April 2012
|archive-url=https://web.archive.org/web/20120429102022/http://www.thetech.org/genetics/news.php?id=74
|url-status=dead
}}</ref><ref>
{{cite web
|url=https://www.sciencedaily.com/releases/2007/09/070904072204.htm
|title=First Diploid Human Genome Sequence Shows We're Surprisingly Different
|publisher=]
|date=4 September 2007
|access-date=2011-09-05
}}</ref> Copy number variations are inherited but can also arise during development.<ref>
{{cite web
|url=http://www.eurekalert.org/pub_releases/2007-12/bcom-cnv122607.php
|title=Copy number variation may stem from replication misstep
|publisher=]
|date=27 December 2007
|access-date=2011-09-05
}}</ref><ref>
{{cite journal | vauthors = Lee JA, Carvalho CM, Lupski JR | title = A DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders | journal = Cell | volume = 131 | issue = 7 | pages = 1235–47 | date = December 2007 | pmid = 18160035 | doi = 10.1016/j.cell.2007.11.037 | s2cid = 9263608 | doi-access = free }}</ref><ref>
{{cite journal | vauthors = Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W, Cho EK, Dallaire S, Freeman JL, González JR, Gratacòs M, Huang J, Kalaitzopoulos D, Komura D, MacDonald JR, Marshall CR, Mei R, Montgomery L, Nishimura K, Okamura K, Shen F, Somerville MJ, Tchinda J, Valsesia A, Woodwark C, Yang F, Zhang J, Zerjal T, Zhang J, Armengol L, Conrad DF, Estivill X, Tyler-Smith C, Carter NP, Aburatani H, Lee C, Jones KW, Scherer SW, Hurles ME | display-authors = 6 | title = Global variation in copy number in the human genome | journal = Nature | volume = 444 | issue = 7118 | pages = 444–54 | date = November 2006 | pmid = 17122850 | pmc = 2669898 | doi = 10.1038/nature05329 | bibcode = 2006Natur.444..444R }}</ref><ref>
{{cite journal | vauthors = Dumas L, Kim YH, Karimpour-Fard A, Cox M, Hopkins J, Pollack JR, Sikela JM | display-authors = 6 | title = Gene copy number variation spanning 60 million years of human and primate evolution | journal = Genome Research | volume = 17 | issue = 9 | pages = 1266–77 | date = September 2007 | pmid = 17666543 | pmc = 1950895 | doi = 10.1101/gr.6557307 }}</ref>
A visual map with the regions with high genomic variation of the modern-human reference assembly relatively to a
Neanderthal of 50k<ref name="Prufer2014">{{cite journal | vauthors = Prüfer K, Racimo F, Patterson N, Jay F, Sankararaman S, Sawyer S, Heinze A, Renaud G, Sudmant PH, de Filippo C, Li H, Mallick S, Dannemann M, Fu Q, Kircher M, Kuhlwilm M, Lachmann M, Meyer M, Ongyerth M, Siebauer M, Theunert C, Tandon A, Moorjani P, Pickrell J, Mullikin JC, Vohr SH, Green RE, Hellmann I, Johnson PL, Blanche H, Cann H, Kitzman JO, Shendure J, Eichler EE, Lein ES, Bakken TE, Golovanova LV, Doronichev VB, Shunkov MV, Derevianko AP, Viola B, Slatkin M, Reich D, Kelso J, Pääbo S | display-authors = 6 | title = The complete genome sequence of a Neanderthal from the Altai Mountains | journal = Nature | volume = 505 | issue = 7481 | pages = 43–9 | date = January 2014 | pmid = 24352235 | pmc = 4031459 | doi = 10.1038/nature12886 | bibcode = 2014Natur.505...43P }}</ref> has been built by Pratas et al.<ref name="sing">{{cite book| vauthors = Pratas D, Hosseini M, Silva R, Pinho A, Ferreira P |title=Pattern Recognition and Image Analysis|chapter=Visualization of Distinct DNA Regions of the Modern Human Relatively to a Neanderthal Genome|volume=10255|pages=235–242|date=20–23 June 2017|doi=10.1007/978-3-319-58838-4_26|series=Lecture Notes in Computer Science|isbn=978-3-319-58837-7}}</ref>


=== Epigenetics ===
] claimed in 2003 that ''such conclusions are unwarranted because the argument ignores the fact that most of the information that distinguishes populations is hidden in the correlation structure of the data and not simply in the variation of the individual factors.''<ref>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12879450&dopt=Abstract</ref> While it makes Lewontin's argument unwarranted, Edward's paper does not address the existence or absence of human race, see ].
] variation is variation in the chemical tags that attach to ] and affect how genes get read. The tags, "called epigenetic markings, act as switches that control how genes can be read."<ref>{{cite web
|date=19 August 2011
|title=Human Genetic Variation Fact Sheet
|url=http://www.nigms.nih.gov/Publications/Factsheet_GeneticVariation.htm
|publisher=]
|access-date=2011-09-05
|archive-date=16 September 2008
|archive-url=https://web.archive.org/web/20080916091604/http://www.nigms.nih.gov/Publications/Factsheet_GeneticVariation.htm
|url-status=dead
}}</ref> At some alleles, the epigenetic state of the DNA, and associated phenotype, can be ].<ref>
{{cite journal | vauthors = Rakyan V, Whitelaw E | title = Transgenerational epigenetic inheritance | journal = Current Biology | volume = 13 | issue = 1 | pages = R6 | date = January 2003 | pmid = 12526754 | doi = 10.1016/S0960-9822(02)01377-5 | doi-access = free | bibcode = 2003CBio...13...R6R }}</ref>


=== Genetic variability ===
Also, it has been argued that the calculation of within group and between group diversity has violated certain assumptions regarding human genetic variation. Calculation of this variation is known as F<sub>ST</sub> and Long and Kittles (2003) have questioned the validity of this reproducible statistic. The first problem is that effective population size is assumed to be equal in the calculation of F<sub>ST</sub>, if population sizes vary, then allele relatedness among alleles will also vary. The second problem is that F<sub>ST</sub> calculation has assumed that each population is evolutionarily independent. Calculation of F<sub>ST</sub> can therefore only be made for the set of populations being observed, and generalisations from specific data sets cannot be applied to the species as a whole.<ref name="long">Keita, S. O. Y., Kittles, R. A., Royal, C. D. M., Bonney, G. E., Furbert-Harris, P., Dunston, D. M., and Rotimi, C. M. (2004). ''Conceptualizing human variation'': '''Nature Genetics''' 36, S17 - S20 (2004) {{doi|10.1038/ng1455}}</ref>
{{Main|Genetic variability}}
Genetic variability is a measure of the tendency of individual ]s in a population to vary (become different) from one another. Variability is different from ], which is the amount of variation seen in a particular population. The variability of a trait is how much that trait tends to vary in response to environmental and ] influences.


=== Clines ===
Long and Kittles tested four models for determining F<sub>ST</sub> and concluded that the model used most often for estimating this statistic is the simplest and worst fitting. Their best fit model was still a poor fit for the observed genetic variation, and calculation of F<sub>ST</sub> for this model can only be made on a population by population basis. They conclude that African populations have the highest level of genetic diversity, with diversity much reduced in populations outside of Africa. They postulate that if an extra-terrestrial alien life form killed the entire human species, but kept a single population which it preserved, the choice of population to keep would greatly effect the level of diversity represented. If an African population were selected then no diversity would be lost, whereas nearly a third of genetic diversity would be lost if a Papuan New Guinea population were chosen. Indeed within population genetic diversity in African populations has been shown to be greater than between population genetic diversity for Asians and Europeans. They conclude that their findings are consistent with the ] 1996 statement on race <blockquote>that all human populations derive from a common ancestral group, that there is great genetic diversity within all human populations, and that the geographic pattern of variation is complex and presents no major discontinuity.</blockquote> They also state that none of the race concepts they discuss are compatible with their results.<ref name="long"/>
{{Main|Cline (biology)}}
In ], a cline is a continuum of ], populations, varieties, or forms of organisms that exhibit gradual phenotypic and/or genetic differences over a geographical area, typically as a result of environmental heterogeneity.<ref>
{{cite encyclopedia
|year=2009
|title=Cline
|encyclopedia=]
}}</ref><ref>
{{cite book
| vauthors = King RC, Stansfield WD, Mulligan PK
|chapter=Cline
|title=A dictionary of genetics
| url = https://archive.org/details/dictionaryofplan0000unse_a2q0
| url-access = registration
|edition=7th
|year=2006
|publisher=]
|isbn=978-0195307610
}}</ref><ref>
{{cite book
| vauthors = Begon M, Townsend CR, Harper JL
|year=2006
|title=Ecology: From individuals to ecosystems
|edition=4th |page=10
|publisher=]
|isbn=978-1405111171
}}</ref> In the scientific study of human genetic variation, a gene cline can be rigorously defined and subjected to quantitative metrics.


=== Haplogroups ===
Our history as a species also has left genetic signals in regional populations. For example, in addition to having higher levels of genetic diversity, populations in Africa tend to have lower amounts of ] than do populations outside Africa, partly because of the larger size of human populations in Africa over the course of human history and partly because the number of modern humans who left Africa to colonize the rest of the world appears to have been relatively low (Gabriel ''et al.'' 2002). In contrast, populations that have undergone dramatic size reductions or rapid expansions in the past and populations formed by the mixture of previously separate ancestral groups can have unusually high levels of linkage disequilibrium (Nordborg and Tavare 2002).
{{Main|Haplogroup}}
In the study of ], a haplogroup is a group of similar ]s that share a ] with a ] (SNP) mutation. The study of haplogroups provides information about ancestral origins dating back thousands of years.<ref>{{cite web |title=Haplogroup |url=https://isogg.org/Haplogroup |publisher=] |work=DNA-Newbie Glossary |access-date=2012-09-05}}</ref>


The most commonly studied human haplogroups are ] and ], both of which can be used to define genetic populations. Y-DNA is passed solely along the ] line, from father to son, while mtDNA is passed down the ] line, from mother to both daughter or son. The Y-DNA and mtDNA may change by chance mutation at each generation.
In the field of ], it is believed that the distribution of ]s among contemporary humans reflects human demographic history. It is believed that humans passed through a ] before a rapid expansion coinciding with migrations ] leading to an African-Eurasian divergence around 100,000 years ago (ca. 5,000 generations), followed by a European-Asian divergence about 40,000 years ago (ca. 2,000 generations). ], ] and ], among others, have postulated that modern humans did not leave Africa and successfully colonize the rest of the world until as recently as 50,000 years B.P., pushing back the dates for subsequent population splits as well.


=== Variable number tandem repeats ===
The rapid expansion of a previously ] has two important effects on the distribution of genetic variation. First, the so-called ] occurs when founder populations bring only a subset of the genetic variation from their ancestral population. Second, as founders become more geographically separated, the probability that two individuals from different founder populations will mate becomes smaller. The effect of this ] is to reduce gene flow between geographical groups, and to increase the genetic distance between groups. The expansion of humans from Africa affected the distribution of genetic variation in two other ways. First, smaller (founder) populations experience greater ] because of increased fluctuations in neutral polymorphisms. Second, new polymorphisms that arose in one group were less likely to be transmitted to other groups as gene flow was restricted.
{{Main|Variable number tandem repeat}}
A variable number tandem repeat (VNTR) is the variation of length of a ]. A tandem repeat is the adjacent repetition of a short ]. Tandem repeats exist on many ], and their length varies between individuals. Each variant acts as an ] ], so they are used for personal or parental identification. Their analysis is useful in genetics and biology research, ], and ].


Short tandem repeats (about 5 base pairs) are called ], while longer ones are called ]s.
Many other geographic, climatic, and historical factors have contributed to the patterns of human genetic variation seen in the world today. For example, population processes associated with colonization, periods of geographic isolation, socially reinforced endogamy, and natural selection all have affected allele frequencies in certain populations (Jorde ''et al.'' 2000b; Bamshad and Wooding 2003). In general, however, the recency of our common ancestry and continual gene flow among human groups have limited genetic differentiation in our species.


==History and geographic distribution==
==Substructure in the human population==
]. Colored rings indicate thousand years before present.]]
]
]
{{See also|Human evolutionary genetics#Modern humans|Recent human evolution}}


===Recent African origin of modern humans===
New data on human genetic variation has reignited the debate surrounding race. Most of the controversy surrounds the question of how to interpret these new data, and whether conclusions based on existing data are sound. A large majority of researchers endorse the view that continental groups do not constitute different subspecies. However, other researchers still debate whether evolutionary lineages should rightly be called "races". These questions are particularly pressing for ], where self-described race is often used as an indicator of ancestry (see ] below).
The ] paradigm assumes the ] of non-African populations of ] after 70,000 years ago. Dispersal within Africa occurred significantly earlier, at least 130,000 years ago. The "out of Africa" theory originates in the 19th century, as a tentative suggestion in Charles Darwin's '']'',<ref>{{cite web | url = http://darwin-online.org.uk/content/frameset?viewtype=text&itemID=F937.1&pageseq=212 | title = The descent of man Chapter 6 – On the Affinities and Genealogy of Man | publisher = Darwin-online.org.uk | access-date = 11 January 2011 | quote = In each great region of the world the living mammals are closely related to the extinct species of the same region. It is, therefore, probable that Africa was formerly inhabited by extinct apes closely allied to the gorilla and chimpanzee; and as these two species are now man's nearest allies, it is somewhat more probable that our early progenitors lived on the African continent than elsewhere. But it is useless to speculate on this subject, for an ape nearly as large as a man, namely the Dryopithecus of Lartet, which was closely allied to the anthropomorphous Hylobates, existed in Europe during the Upper Miocene period; and since so remote a period the earth has certainly undergone many great revolutions, and there has been ample time for migration on the largest scale. }}</ref> but remained speculative until the 1980s when it was supported by the study of present-day mitochondrial DNA, combined with evidence from ] of archaic ].


According to a 2000 study of Y-chromosome sequence variation,<ref name="Underhill_2000">{{cite journal | vauthors = Underhill PA, Shen P, Lin AA, Jin L, Passarino G, Yang WH, Kauffman E, Bonné-Tamir B, Bertranpetit J, Francalacci P, Ibrahim M, Jenkins T, Kidd JR, Mehdi SQ, Seielstad MT, Wells RS, Piazza A, Davis RW, Feldman MW, Cavalli-Sforza LL, Oefner PJ | display-authors = 6 | title = Y chromosome sequence variation and the history of human populations | journal = Nature Genetics | volume = 26 | issue = 3 | pages = 358–61 | date = November 2000 | pmid = 11062480 | doi = 10.1038/81685 | s2cid = 12893406 }}</ref> human Y-chromosomes trace ancestry to Africa, and the descendants of the derived lineage left Africa and eventually were replaced by archaic human Y-chromosomes in Eurasia. The study also shows that a minority of contemporary populations in East Africa and the ] are the descendants of the most ancestral patrilineages of anatomically modern humans that left Africa 35,000 to 89,000 years ago.<ref name="Underhill_2000" /> Other evidence supporting the theory is that variations in skull measurements decrease with distance from Africa at the same rate as the decrease in genetic diversity. Human genetic diversity decreases in native populations with migratory distance from Africa, and this is thought to be due to ] during human migration, which are events that temporarily reduce population size.<ref name="sciencedaily.com">{{cite web |date=19 July 2007 |title=New Research Proves Single Origin of Humans in Africa |url=https://www.sciencedaily.com/releases/2007/07/070718140829.htm |publisher=] |access-date=2011-09-05}}</ref><ref>{{cite journal | vauthors = Manica A, Amos W, Balloux F, Hanihara T|author-link3=Francois Balloux | title = The effect of ancient population bottlenecks on human phenotypic variation | journal = Nature | volume = 448 | issue = 7151 | pages = 346–8 | date = July 2007 | pmid = 17637668 | pmc = 1978547 | doi = 10.1038/nature05951 | bibcode = 2007Natur.448..346M }}</ref>
Although the genetic differences among human groups are relatively small, these differences in certain genes such as ], ], ], called ]s (AIMs) nevertheless can be used to reliably situate many individuals within broad, geographically based groupings or self-identified race. For example, computer analyses of hundreds of polymorphic loci sampled in globally distributed populations have revealed the existence of genetic clustering that roughly is associated with groups that historically have occupied large continental and subcontinental regions (Rosenberg ''et al.'' 2002; Bamshad ''et al.'' 2003).


A 2009 genetic clustering study, which genotyped 1327 polymorphic markers in various African populations, identified six ancestral clusters. The clustering corresponded closely with ethnicity, culture and language.<ref>{{cite journal | vauthors = Tishkoff SA, Reed FA, Friedlaender FR, Ehret C, Ranciaro A, Froment A, Hirbo JB, Awomoyi AA, Bodo JM, Doumbo O, Ibrahim M, Juma AT, Kotze MJ, Lema G, Moore JH, Mortensen H, Nyambo TB, Omar SA, Powell K, Pretorius GS, Smith MW, Thera MA, Wambebe C, Weber JL, Williams SM | display-authors = 6 | title = The genetic structure and history of Africans and African Americans | journal = Science | volume = 324 | issue = 5930 | pages = 1035–44 | date = May 2009 | pmid = 19407144 | pmc = 2947357 | doi = 10.1126/science.1172257 | url = http://faculty.washington.edu/wjs18/Pop_Structure/TishkoffAfrican.pdf | bibcode = 2009Sci...324.1035T | quote = We incorporated geographic data into a Bayesian clustering analysis, assuming no admixture (TESS software) (25) and distinguished six clusters within continental Africa (Fig. 5A). The most geographically widespread cluster (orange) extends from far Western Africa (the Mandinka) through central Africa to the Bantu speakers of South Africa (the Venda and Xhosa) and corresponds to the distribution of the Niger-Kordofanian language family, possibly reflecting the spread of Bantu-speaking populations from near the Nigerian/Cameroon highlands across eastern and southern Africa within the past 5000 to 3000 years (26,27). Another inferred cluster includes the Pygmy and SAK populations (green), with a noncontiguous geographic distribution in central and southeastern Africa, consistent with the STRUCTURE (Fig. 3) and phylogenetic analyses (Fig. 1). Another geographically contiguous cluster extends across northern Africa (blue) into Mali (the Dogon), Ethiopia, and northern Kenya. With the exception of the Dogon, these populations speak an Afroasiatic language. Chadic-speaking and Nilo-Saharan–speaking populations from Nigeria, Cameroon, and central Chad, as well as several Nilo-Saharan–speaking populations from southern Sudan, constitute another cluster (red). Nilo-Saharan and Cushitic speakers from the Sudan, Kenya, and Tanzania, as well as some of the Bantu speakers from Kenya, Tanzania, and Rwanda (Hutu/Tutsi), constitute another cluster (purple), reflecting linguistic evidence for gene flow among these populations over the past ~5000 years (28,29). Finally, the Hadza are the sole constituents of a sixth cluster (yellow), consistent with their distinctive genetic structure identified by PCA and STRUCTURE. }}</ref> A 2018 ] study of the world's populations observed similar clusters among the populations in Africa. At K=9, distinct ancestral components defined the ]-speaking populations inhabiting ] and ]; the ]-speaking populations in Northeast Africa and ]; the ] populations in Northeast Africa; the ]-speaking populations in West-Central Africa, ], East Africa and ]; the ] populations in ]; and the ] populations in Southern Africa.<ref>{{cite journal | vauthors = Schlebusch CM, Jakobsson M | title = Tales of Human Migration, Admixture, and Selection in Africa | journal = Annual Review of Genomics and Human Genetics | volume = 19 | pages = 405–428 | date = August 2018 | pmid = 29727585 | doi = 10.1146/annurev-genom-083117-021759 | s2cid = 19155657 | url = http://docdro.id/C0L2mMo | access-date = 28 May 2018 | doi-access = free }}</ref>
Some commentators have argued that these patterns of variation provide a biological justification for the use of traditional racial categories. They argue that the continental clusterings correspond roughly with the division of human beings into sub-Saharan Africans; Europeans, Western Asians, Southern Asians and Northern Africans + Eastern Asians, Southeast Asians, Polynesians and Native Americans; and other inhabitants of Oceania (Melanesians, Micronesians & Australian Aborigines) (Risch ''et al.'' 2002). Other observers disagree, saying that the same data undercut traditional notions of racial groups (King and Motulsky 2002; Calafell 2003; Tishkoff and Kidd 2004). They point out, for example, that major populations considered races or subgroups within races do not necessarily form their own clusters. Thus, samples taken from India and Pakistan affiliate with Europeans or eastern Asians rather than separating into a distinct cluster.

In May 2023, scientists reported, based on genetic studies, a more complicated pathway of human evolution than previously understood. According to the studies, humans evolved from different places and times in Africa, instead of from a single location and period of time.<ref name="NYT-20230517">{{cite news |last=Zimmer |first=Carl |authorlink=Carl Zimmer |title=Study Offers New Twist in How the First Humans Evolved – A new genetic analysis of 290 people suggests that humans emerged at various times and places in Africa. |url=https://www.nytimes.com/2023/05/17/science/human-origins-africa.html |date=17 May 2023 |work=] |url-status=live |archiveurl=https://archive.today/20230517235653/https://www.nytimes.com/2023/05/17/science/human-origins-africa.html |archivedate=17 May 2023 |accessdate=18 May 2023 }}</ref><ref name="NAT-20230517">{{cite journal |author=Ragsdale, Aaron P. |display-authors=et al.|title=A weakly structured stem for human origins in Africa |date=17 May 2023 |journal=] |volume=167 |issue=7962 |pages=755–763 |doi=10.1038/s41586-023-06055-y |pmid=37198480 |pmc=10208968 |bibcode=2023Natur.617..755R }}</ref>

=== Population genetics ===
{{See also|Population genetics}}
Because of the common ancestry of all humans, only a small number of variants have large differences in frequency between populations. However, some rare variants in the world's human population are much more frequent in at least one population (more than 5%).<ref name="pmid26432245">{{cite journal | vauthors = Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR | display-authors = 6 | collaboration = 1000 Genomes Project Consortium | title = A global reference for human genetic variation | journal = Nature | volume = 526 | issue = 7571 | pages = 68–74 | date = October 2015 | pmid = 26432245 | pmc = 4750478 | doi = 10.1038/nature15393 | bibcode = 2015Natur.526...68T }}</ref>

]]

It is commonly assumed that early humans left Africa, and thus must have passed through a population bottleneck before their African-Eurasian divergence around 100,000 years ago (ca. 3,000 generations). The rapid expansion of a previously ] has two important effects on the distribution of genetic variation. First, the so-called ''']''' occurs when founder populations bring only a subset of the genetic variation from their ancestral population. Second, as founders become more geographically separated, the probability that two individuals from different founder populations will mate becomes smaller. The effect of this ] is to reduce gene flow between geographical groups and to increase the genetic distance between groups.{{Citation needed|date=December 2017}}

The expansion of humans from Africa affected the distribution of genetic variation in two other ways. First, smaller (founder) populations experience greater ] because of increased fluctuations in neutral polymorphisms. Second, new polymorphisms that arose in one group were less likely to be transmitted to other groups as gene flow was restricted.{{Citation needed|date=December 2017}}

Populations in Africa tend to have lower amounts of ] than do populations outside Africa, partly because of the larger size of human populations in Africa over the course of human history and partly because the number of modern humans who left Africa to colonize the rest of the world appears to have been relatively low.<ref name="ReferenceA">{{cite journal | vauthors = Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, Liu-Cordero SN, Rotimi C, Adeyemo A, Cooper R, Ward R, Lander ES, Daly MJ, Altshuler D | display-authors = 6 | title = The structure of haplotype blocks in the human genome | journal = Science | volume = 296 | issue = 5576 | pages = 2225–9 | date = June 2002 | pmid = 12029063 | doi = 10.1126/science.1069424 | bibcode = 2002Sci...296.2225G | s2cid = 10069634 | doi-access = free }}</ref> In contrast, populations that have undergone dramatic size reductions or rapid expansions in the past and populations formed by the mixture of previously separate ancestral groups can have unusually high levels of linkage disequilibrium<ref name="ReferenceA"/>

=== Distribution of variation ===
] loci taken from 1484 individuals in 78 human populations. The upper graph illustrates that as populations are further from East Africa, they have declining genetic diversity as measured in average number of microsatellite repeats at each of the loci. The bottom chart illustrates ]. Populations with a greater distance between them are more dissimilar (as measured by the Fst statistic) than those which are geographically close to one another. The horizontal axis of both charts is geographic distance as measured along likely routes of human migration. (Chart from Kanitz et al. 2018)]]

The distribution of genetic variants within and among human populations are impossible to describe succinctly because of the difficulty of defining a "population," the clinal nature of variation, and heterogeneity across the genome (Long and Kittles 2003). In general, however, an average of 85% of genetic variation exists within local populations, ~7% is between local populations within the same continent, and ~8% of variation occurs between large groups living on different continents.<ref name="lewontin" /><ref>{{cite journal | vauthors = Bamshad MJ, Wooding S, Watkins WS, Ostler CT, Batzer MA, Jorde LB | title = Human population genetic structure and inference of group membership | journal = American Journal of Human Genetics | volume = 72 | issue = 3 | pages = 578–89 | date = March 2003 | pmid = 12557124 | pmc = 1180234 | doi = 10.1086/368061 }}</ref> The ] theory for humans would predict that in Africa there exists a great deal more diversity than elsewhere and that diversity should decrease the further from Africa a population is sampled.

====Phenotypic variation====
{{Further|Phenotype#Phenotypic variation}}
<!-- {{see|skin color|hair color|eye color|body hair|Human height|Human weight|human intelligence}}
{{further|], ], ]}} -->

] has the most human genetic diversity and the same has been shown to hold true for phenotypic variation in skull form.<ref name="sciencedaily.com"/><ref>Manica, Andrea, William Amos, François Balloux, and Tsunehiko Hanihara. "The Effect of Ancient Population Bottlenecks on Human Phenotypic Variation". ''Nature'' 448, no. 7151 (July 2007): 346–48. {{doi|10.1038/nature05951}}.</ref> Phenotype is connected to genotype through ]. Genetic diversity decreases smoothly with migratory distance from that region, which many scientists believe to be the origin of modern humans, and that decrease is mirrored by a decrease in phenotypic variation. Skull measurements are an example of a physical attribute whose within-population variation decreases with distance from Africa.

The distribution of many physical traits resembles the distribution of genetic variation within and between human populations (] 1996; Keita and Kittles 1997). For example, ~90% of the variation in human head shapes occurs within continental groups, and ~10% separates groups, with a greater variability of head shape among individuals with recent African ancestors (Relethford 2002).

A prominent exception to the common distribution of physical characteristics within and among groups is ]. Approximately 10% of the variance in skin color occurs within groups, and ~90% occurs between groups (Relethford 2002). This distribution of skin color and its geographic patterning – with people whose ancestors lived predominantly near the equator having darker skin than those with ancestors who lived predominantly in higher latitudes – indicate that this attribute has been under strong ]. Darker skin appears to be strongly selected for in equatorial regions to prevent sunburn, skin cancer, the ] of ], and damage to sweat glands.<ref>{{cite book |last=Jablonski |first=Nina G. | name-list-style = vanc |title=Living Color: The Biological and Social Meaning of Skin Color |url=https://books.google.com/books?id=Jw7loAEACAAJ |date=10 January 2014 |publisher=University of California Press |isbn=978-0-520-28386-2 |jstor=10.1525/j.ctt1pn64b |chapter=The Biological and Social Meaning of Skin Color }}</ref>

Understanding how genetic diversity in the human population impacts various levels of gene expression is an active area of research. While earlier studies focused on the relationship between DNA variation and RNA expression, more recent efforts are characterizing the genetic control of various aspects of gene expression including chromatin states,<ref>{{cite journal | vauthors = Grubert F, Zaugg JB, Kasowski M, Ursu O, Spacek DV, Martin AR, Greenside P, Srivas R, Phanstiel DH, Pekowska A, Heidari N, Euskirchen G, Huber W, Pritchard JK, Bustamante CD, Steinmetz LM, Kundaje A, Snyder M | display-authors = 6 | title = Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions | journal = Cell | volume = 162 | issue = 5 | pages = 1051–65 | date = August 2015 | pmid = 26300125 | pmc = 4556133 | doi = 10.1016/j.cell.2015.07.048 }}</ref> translation,<ref>
{{cite journal | vauthors = Cenik C, Cenik ES, Byeon GW, Grubert F, Candille SI, Spacek D, Alsallakh B, Tilgner H, Araya CL, Tang H, Ricci E, Snyder MP | display-authors = 6 | title = Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans | journal = Genome Research | volume = 25 | issue = 11 | pages = 1610–21 | date = November 2015 | pmid = 26297486 | pmc = 4617958 | doi = 10.1101/gr.193342.115 }}</ref> and protein levels.<ref>{{cite journal | vauthors = Wu L, Candille SI, Choi Y, Xie D, Jiang L, Li-Pook-Than J, Tang H, Snyder M | title = Variation and genetic control of protein abundance in humans | journal = Nature | volume = 499 | issue = 7456 | pages = 79–82 | date = July 2013 | pmid = 23676674 | pmc = 3789121 | doi = 10.1038/nature12223 | bibcode = 2013Natur.499...79W }}</ref> A study published in 2007 found that 25% of genes showed different levels of gene expression between populations of European and Asian descent.<ref>{{cite web
|vauthors=Phillips ML
|date=9 January 2007
|title=Ethnicity tied to gene expression
|url=http://classic.the-scientist.com/?articles.view/articleNo/24657/
|archive-url=https://archive.today/20150508183458/http://classic.the-scientist.com/?articles.view/articleNo/24657/
|url-status=dead
|archive-date=8 May 2015
|work=]
|access-date=2011-09-05
}}</ref><ref>
{{cite journal | vauthors = Spielman RS, Bastone LA, Burdick JT, Morley M, Ewens WJ, Cheung VG | title = Common genetic variants account for differences in gene expression among ethnic groups | journal = Nature Genetics | volume = 39 | issue = 2 | pages = 226–31 | date = February 2007 | pmid = 17206142 | pmc = 3005333 | doi = 10.1038/ng1955 }}</ref><ref>
{{cite web
|vauthors = Swaminathan N
|date=9 January 2007
|url=http://www.scientificamerican.com/article.cfm?id=ethnic-differences-traced
|title=Ethnic Differences Traced to Variable Gene Expression
|work=]
|access-date=2011-09-05
}}</ref><ref>
{{cite journal
| vauthors = Check E
|year=2007
|title=Genetic expression speaks as loudly as gene type
|journal=]
|doi=10.1038/news070101-8
|s2cid=84380725
}}</ref><ref>{{cite web
|vauthors=Bell L
|date=15 January 2007
|url=http://www.bionews.org.uk/page_12961.asp
|title=Variable gene expression seen in different ethnic groups
|work=BioNews.org
|access-date=2011-09-05
|archive-date=26 March 2016
|archive-url=https://web.archive.org/web/20160326105441/http://www.bionews.org.uk/page_12961.asp
|url-status=dead
}}</ref> The primary cause of this difference in gene expression was thought to be SNPs in gene regulatory regions of DNA. Another study published in 2007 found that approximately 83% of genes were expressed at different levels among individuals and about 17% between populations of European and African descent.<ref>{{cite web
|vauthors=Kamrani K
|date=28 February 2008
|url=http://anthropology.net/2008/02/29/differences-of-gene-expression-between-human-populations/
|title=Differences of gene expression between human populations
|publisher=Anthropology.net
|access-date=2011-09-05
|archive-date=30 September 2011
|archive-url=https://web.archive.org/web/20110930163052/http://anthropology.net/2008/02/29/differences-of-gene-expression-between-human-populations/
|url-status=dead
}}</ref><ref>
{{cite journal | vauthors = Storey JD, Madeoy J, Strout JL, Wurfel M, Ronald J, Akey JM | title = Gene-expression variation within and among human populations | journal = American Journal of Human Genetics | volume = 80 | issue = 3 | pages = 502–9 | date = March 2007 | pmid = 17273971 | pmc = 1821107 | doi = 10.1086/512017 }}</ref>

===== Wright's fixation index as measure of variation =====
The population geneticist ] developed the ] (often abbreviated to ''F''<sub>ST</sub>) as a way of measuring genetic differences between populations. This statistic is often used in taxonomy to compare differences between any two given populations by measuring the genetic differences among and between populations for individual genes, or for many genes simultaneously.<ref name="Graves 2006">{{cite web |url=http://raceandgenomics.ssrc.org/Graves/ |title=What We Know and What We Don't Know: Human Genetic Variation and the Social Construction of Race |work=Is Race "Real"? |access-date=2011-01-22 |last=Graves |first=Joseph L. |name-list-style=vanc |date=2006 |publisher=Social Science Research Council |archive-date=3 June 2019 |archive-url=https://web.archive.org/web/20190603030227/http://raceandgenomics.ssrc.org/Graves/ |url-status=dead }}<!--This site describes itself as "A Web Forum organized by the Social Science Research Council". This does not mean a "web forum" in the usual sense of "Internet chatroom"; it means a "forum" in the formal sense, a symposium, that in this case is online.--></ref> It is often stated that the fixation index for humans is about 0.15. This translates to an estimated 85% of the variation measured in the overall human population is found within individuals of the same population, and about 15% of the variation occurs between populations. These estimates imply that any two individuals from different populations may be more similar to each other than either is to a member of their own group.<ref name="Keita2004">{{cite journal | vauthors = Keita SO, Kittles RA, Royal CD, Bonney GE, Furbert-Harris P, Dunston GM, Rotimi CN | title = Conceptualizing human variation | journal = Nature Genetics | volume = 36 | issue = 11 Suppl | pages = S17–20 | date = November 2004 | pmid = 15507998 | doi = 10.1038/ng1455 | doi-access = free }}</ref><ref name="Hawks 2013 p. 438">{{cite book |last=Hawks |first=John | name-list-style = vanc |date=2013 |title=Significance of Neandertal and Denisovan Genomes in Human Evolution |journal=Annual Review of Anthropology |publisher=Annual Reviews |volume=42 |issue=1 |pages=433–49 |isbn=978-0-8243-1942-7 |doi=10.1146/annurev-anthro-092412-155548 }}</ref>
"The shared evolutionary history of living humans has resulted in a high relatedness among all living people, as indicated for example by the very low fixation index (F<sub>ST</sub>) among living human populations." ], who affirmed these ratios, thus concluded neither "race" nor "subspecies" were appropriate or useful ways to describe human populations.<ref name="lewontin">{{cite book |last1=Lewontin |first1=Richard C. | name-list-style = vanc |date=1972 |chapter=The Apportionment of Human Diversity |editor=Theodosius Dobzhansky |editor2=Max K. Hecht |editor3=William C. Steere |title=Evolutionary Biology |volume=6 |pages=381–97 |doi=10.1007/978-1-4684-9063-3_14|isbn=978-1-4684-9065-7 |location=New York |publisher=Appleton–Century–Crofts|s2cid=21095796 }}</ref>

Wright himself believed that values >0.25 represent very great genetic variation and that an ''F''<sub>ST</sub> of 0.15–0.25 represented great variation. However, about 5% of human variation occurs between populations within continents, therefore ''F''<sub>ST</sub> values between continental groups of humans (or races) of as low as 0.1 (or possibly lower) have been found in some studies, suggesting more moderate levels of genetic variation.<!--there's an argument here maybe but I don't get it. Is the allusion to >0.25 a strawman or red herring? Where come these justifications for downward adjustments from 15%?--><ref name="Graves 2006" /> Graves (1996) has countered that ''F''<sub>ST</sub> should not be used as a marker of subspecies status, as the statistic is used to measure the degree of differentiation between populations,<ref name="Graves 2006" /> although see also Wright (1978).<ref name="Wright 1978">* {{cite book |last=Wright |first=Sewall | name-list-style = vanc |date=1978 |title=Evolution and the Genetics of Populations |volume=4, Variability Within and Among Natural Populations |publisher=Univ. Chicago Press |location=Chicago, Illinois |page=438 }}
</ref>

Jeffrey Long and Rick Kittles give a long critique of the application of ''F''<sub>ST</sub> to human populations in their 2003 paper "Human Genetic Diversity and the Nonexistence of Biological Races". They find that the figure of 85% is misleading because it implies that all human populations contain on average 85% of all genetic diversity. They argue the underlying statistical model incorrectly assumes equal and independent histories of variation for each large human population. A more realistic approach is to understand that some human groups are parental to other groups and that these groups represent ] groups to their descent groups. For example, under the ] theory the human population in Africa is paraphyletic to all other human groups because it represents the ancestral group from which all non-African populations derive, but more than that, non-African groups only derive from a small non-representative sample of this African population. This means that all non-African groups are more closely related to each other and to some African groups (probably east Africans) than they are to others, and further that the migration out of Africa represented a ], with much of the diversity that existed in Africa not being carried out of Africa by the emigrating groups. Under this scenario, human populations do not have equal amounts of local variability, but rather diminished amounts of diversity the further from Africa any population lives. Long and Kittles find that rather than 85% of human genetic diversity existing in all human populations, about 100% of human diversity exists in a single African population, whereas only about 70% of human genetic diversity exists in a population derived from New Guinea. Long and Kittles argued that this still produces a global human population that is genetically homogeneous compared to other mammalian populations.<ref name="LongKittles">{{cite journal | vauthors = Long JC, Kittles RA | title = Human genetic diversity and the nonexistence of biological races | journal = Human Biology | volume = 75 | issue = 4 | pages = 449–71 | date = August 2003 | pmid = 14655871 | doi = 10.1353/hub.2003.0058 | s2cid = 26108602 }}</ref>

=== Archaic admixture ===
{{Main|Archaic human admixture with modern humans}}
Anatomically modern humans interbred with Neanderthals during the ]. In May 2010, the ] presented genetic evidence that ] took place and that a small but significant portion, around 2–4%, of Neanderthal admixture is present in the DNA of modern Eurasians and Oceanians, and nearly absent in sub-Saharan African populations.<ref>{{Cite journal|last1=Harris|first1=Kelley|last2=Nielsen|first2=Rasmus|date=June 2016|title=The Genetic Cost of Neanderthal Introgression|journal=Genetics|volume=203|issue=2|pages=881–891|doi=10.1534/genetics.116.186890|issn=0016-6731|pmc=4896200|pmid=27038113}}</ref><ref>{{Cite journal|last1=Wall|first1=Jeffrey D.|last2=Yang|first2=Melinda A.|last3=Jay|first3=Flora|last4=Kim|first4=Sung K.|last5=Durand|first5=Eric Y.|last6=Stevison|first6=Laurie S.|last7=Gignoux|first7=Christopher|last8=Woerner|first8=August|last9=Hammer|first9=Michael F.|last10=Slatkin|first10=Montgomery|date=May 2013|title=Higher Levels of Neanderthal Ancestry in East Asians than in Europeans|journal=Genetics|volume=194|issue=1|pages=199–209|doi=10.1534/genetics.112.148213|issn=0016-6731|pmc=3632468|pmid=23410836}}</ref>

Between 4% and 6% of the genome of ] (represented by the Papua New Guinean and Bougainville Islander) appears to derive from ]s – a previously unknown hominin which is more closely related to Neanderthals than to Sapiens. It was possibly introduced during the early migration of the ancestors of Melanesians into Southeast Asia. This history of interaction suggests that Denisovans once ranged widely over eastern Asia.<ref name="Reich et al.">
{{cite journal | vauthors = Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, Viola B, Briggs AW, Stenzel U, Johnson PL, Maricic T, Good JM, Marques-Bonet T, Alkan C, Fu Q, Mallick S, Li H, Meyer M, Eichler EE, Stoneking M, Richards M, Talamo S, Shunkov MV, Derevianko AP, Hublin JJ, Kelso J, Slatkin M, Pääbo S | display-authors = 6 | title = Genetic history of an archaic hominin group from Denisova Cave in Siberia | journal = Nature | volume = 468 | issue = 7327 | pages = 1053–60 | date = December 2010 | pmid = 21179161 | pmc = 4306417 | doi = 10.1038/nature09710 | bibcode = 2010Natur.468.1053R }}</ref>

Thus, Melanesians emerge as one of the most archaic-admixed populations, having Denisovan/Neanderthal-related admixture of ~8%.<ref name="Reich et al." />

In a study published in 2013, Jeffrey Wall from University of California studied whole sequence-genome data and found higher rates of introgression in Asians compared to Europeans.<ref name="wall">{{cite journal | vauthors = Wall JD, Yang MA, Jay F, Kim SK, Durand EY, Stevison LS, Gignoux C, Woerner A, Hammer MF, Slatkin M | display-authors = 6 | title = Higher levels of neanderthal ancestry in East Asians than in Europeans | journal = Genetics | volume = 194 | issue = 1 | pages = 199–209 | date = May 2013 | pmid = 23410836 | pmc = 3632468 | doi = 10.1534/genetics.112.148213 }}</ref> Hammer et al. tested the hypothesis that contemporary African genomes have signatures of gene flow with archaic human ancestors and found evidence of archaic admixture in the genomes of some African groups, suggesting that modest amounts of gene flow were widespread throughout time and space during the evolution of anatomically modern humans.<ref name="hammer">{{cite journal | vauthors = Hammer MF, Woerner AE, Mendez FL, Watkins JC, Wall JD | title = Genetic evidence for archaic admixture in Africa | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 108 | issue = 37 | pages = 15123–8 | date = September 2011 | pmid = 21896735 | pmc = 3174671 | doi = 10.1073/pnas.1109300108 | bibcode = 2011PNAS..10815123H | doi-access = free }}</ref>

A study published in 2020 found that the ] and ] populations of West Africa derive between 2% and 19% of their genome from an as-yet unidentified archaic hominin population that likely diverged before the split of modern humans and the ancestors of Neanderthals and Denisovans,<ref name="Durvasula">{{cite journal | vauthors = Durvasula A, Sankararaman S | title = Recovering signals of ghost archaic introgression in African populations | journal = Science Advances | volume = 6 | issue = 7 | date = February 2020 | pages = eaax5097 | doi = 10.1126/sciadv.aax5097| pmid = 32095519 | pmc = 7015685 | bibcode = 2020SciA....6.5097D | doi-access = free }}</ref> potentially making these groups the most archaic-admixed human populations identified yet.

==Categorization of the world population==
]
]
{{See also|Race (human classification)|Race and genetics}}
New data on human genetic variation has reignited the debate about a possible biological basis for categorization of humans into races. Most of the controversy surrounds the question of how to interpret the genetic data and whether conclusions based on it are sound. Some researchers argue that self-identified race can be used as an indicator of geographic ancestry for certain ].

Although the genetic differences among human groups are relatively small, these differences in certain genes such as ], ], ], called ]s (AIMs) nevertheless can be used to reliably situate many individuals within broad, geographically based groupings. For example, computer analyses of hundreds of polymorphic loci sampled in globally distributed populations have revealed the existence of genetic clustering that roughly is associated with groups that historically have occupied large continental and subcontinental regions (Rosenberg ''et al.'' 2002; Bamshad ''et al.'' 2003).

Some commentators have argued that these patterns of variation provide a biological justification for the use of traditional racial categories. They argue that the continental clusterings correspond roughly with the division of human beings into ]; ]ans, ]s, ]s, ]s and ]ns; ]ns, ]s, ] and ]s; and other inhabitants of ] (Melanesians, ] & Australian Aborigines) (Risch ''et al.'' 2002). Other observers disagree, saying that the same data undercut traditional notions of racial groups (King and Motulsky 2002; Calafell 2003; Tishkoff and Kidd 2004<ref name=Tishkoff04/>). They point out, for example, that major populations considered races or subgroups within races do not necessarily form their own clusters.

Racial categories are also undermined by findings that genetic variants which are limited to one region tend to be rare within that region, variants that are common within a region tend to be shared across the globe, and most differences between individuals, whether they come from the same region or different regions, are due to global variants.<ref name="pmid33350384">{{cite journal |vauthors=Biddanda A, Rice DP, Novembre J| title=A variant-centric perspective on geographic patterns of human allele frequency variation. | journal=eLife | year= 2020 | volume= 9 | issue= | pages= | pmid=33350384 | doi=10.7554/eLife.60107 | pmc=7755386 | doi-access=free }}</ref> No genetic variants have been found which are ] within a continent or major region and found nowhere else.<ref name="pmid32193295">{{cite journal |vauthors=Bergström A, McCarthy SA, Hui R, Almarri MA, Ayub Q, Danecek P | display-authors=etal| title=Insights into human genetic variation and population history from 929 diverse genomes. | journal=Science | year= 2020 | volume= 367 | issue= 6484 | pages= | pmid=32193295 | doi=10.1126/science.aay5012 | pmc=7115999 }}</ref>


Furthermore, because human genetic variation is clinal, many individuals affiliate with two or more continental groups. Thus, the genetically based "biogeographical ancestry" assigned to any given person generally will be broadly distributed and will be accompanied by sizable uncertainties (Pfaff ''et al.'' 2004). Furthermore, because human genetic variation is clinal, many individuals affiliate with two or more continental groups. Thus, the genetically based "biogeographical ancestry" assigned to any given person generally will be broadly distributed and will be accompanied by sizable uncertainties (Pfaff ''et al.'' 2004).


In many parts of the world, groups have mixed in such a way that many individuals have relatively recent ancestors from widely separated regions. Although genetic analyses of large numbers of loci can produce estimates of the percentage of a person's ancestors coming from various continental populations (Shriver ''et al.'' 2003; Bamshad ''et al.'' 2004), these estimates may assume a false distinctiveness of the parental populations, since human groups have exchanged mates from local to continental scales throughout history (Cavalli-Sforza ''et al.'' 1994; Hoerder 2002). Even with large numbers of markers, information for estimating admixture proportions of individuals or groups is limited, and estimates typically will have wide CIs (Pfaff ''et al.'' 2004). In many parts of the world, groups have mixed in such a way that many individuals have relatively recent ancestors from widely separated regions. Although genetic analyses of large numbers of loci can produce estimates of the percentage of a person's ancestors coming from various continental populations (Shriver ''et al.'' 2003; Bamshad ''et al.'' 2004), these estimates may assume a false distinctiveness of the parental populations, since human groups have exchanged mates from local to continental scales throughout history (Cavalli-Sforza ''et al.'' 1994; Hoerder 2002). Even with large numbers of markers, information for estimating admixture proportions of individuals or groups is limited, and estimates typically will have wide ]s (Pfaff ''et al.'' 2004).

=== Genetic clustering ===
{{Main|Human genetic clustering}}
Genetic data can be used to infer population structure and assign individuals to groups that often correspond with their self-identified geographical ancestry. Jorde and Wooding (2004) argued that "Analysis of many loci now yields reasonably accurate estimates of genetic similarity among individuals, rather than populations. Clustering of individuals is correlated with geographic origin or ancestry."<ref name=Jorde04/> However, identification by geographic origin may quickly break down when considering historical ancestry shared between individuals back in time.<ref>{{Cite journal|last1=Albers|first1=Patrick K.|last2=McVean|first2=Gil|date=2018-09-13|title=Dating genomic variants and shared ancestry in population-scale sequencing data|url=https://www.biorxiv.org/content/early/2018/09/13/416610|journal=bioRxiv|volume=18|issue=1|language=en|pages=416610|doi=10.1101/416610|pmid=31951611|pmc=6992231|doi-access=free}}</ref>

An analysis of ] ] data from the ] (Phase II) and ] Human Genome Diversity Panel samples was published in 2009.
The study of 53 populations taken from the HapMap and CEPH data (1138 unrelated individuals) suggested that ] may shape the human genome much more slowly than previously thought, with factors such as migration within and among continents more heavily influencing the distribution of genetic variations.<ref name="coop2009">{{cite journal | vauthors = Coop G, Pickrell JK, Novembre J, Kudaravalli S, Li J, Absher D, Myers RM, Cavalli-Sforza LL, Feldman MW, Pritchard JK | display-authors = 6 | title = The role of geography in human adaptation | journal = PLOS Genetics | volume = 5 | issue = 6 | pages = e1000500 | date = June 2009 | pmid = 19503611 | pmc = 2685456 | doi = 10.1371/journal.pgen.1000500 | editor1-last = Schierup | editor1-first = Mikkel H. | doi-access = free }}
See also: {{cite news | url = https://www.washingtonpost.com/wp-dyn/content/article/2009/06/21/AR2009062101726_pf.html | title = Among Many Peoples, Little Genomic Variety | newspaper = ] | date = 22 June 2009 | access-date = 25 June 2009 | first=David | last=Brown | name-list-style = vanc }}.
{{cite web| title= Geography And History Shape Genetic Differences in Humans | url= https://www.sciencedaily.com/releases/2009/06/090605091157.htm | publisher=] | date= 7 June 2009 | access-date = 25 June 2009}}.</ref>
A similar study published in 2010 found strong genome-wide evidence for selection due to changes in ecoregion, diet, and subsistence
particularly in connection with polar ecoregions, with foraging, and with a diet rich in roots and tubers.<ref name=Hancock2010>{{cite journal | vauthors = Hancock AM, Witonsky DB, Ehler E, Alkorta-Aranburu G, Beall C, Gebremedhin A, Sukernik R, Utermann G, Pritchard J, Coop G, Di Rienzo A | display-authors = 6 | title = Colloquium paper: human adaptations to diet, subsistence, and ecoregion are due to subtle shifts in allele frequency | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 107 | pages = 8924–30 | date = May 2010 | issue = Suppl 2 | pmid = 20445095 | pmc = 3024024 | doi = 10.1073/pnas.0914625107 | bibcode = 2010PNAS..107.8924H | doi-access = free }}</ref> In a 2016 study, ] of genome-wide data was capable of recovering previously-known targets for positive selection (without prior definition of populations) as well as a number of new candidate genes.<ref>{{cite journal | vauthors = Duforet-Frebourg N, Luu K, Laval G, Bazin E, Blum MG | title = Detecting Genomic Signatures of Natural Selection with Principal Component Analysis: Application to the 1000 Genomes Data | journal = Molecular Biology and Evolution | volume = 33 | issue = 4 | pages = 1082–93 | date = April 2016 | pmid = 26715629 | pmc = 4776707 | doi = 10.1093/molbev/msv334 | arxiv = 1504.04543 }}</ref>

=== Forensic anthropology ===
]s can assess the ancestry of skeletal remains by analyzing skeletal morphology as well as using genetic and chemical markers, when possible.<ref>{{Cite journal|last1=Cunha|first1=Eugénia|last2=Ubelaker|first2=Douglas H.|date=2019-12-23|title=Evaluation of ancestry from human skeletal remains: a concise review|journal=Forensic Sciences Research|volume=5|issue=2|pages=89–97|doi=10.1080/20961790.2019.1697060|issn=2096-1790|pmc=7476619|pmid=32939424}}</ref> While these assessments are never certain, the accuracy of skeletal morphology analyses in determining true ancestry has been estimated at 90%.<ref>{{Cite journal|last1=Thomas|first1=Richard M.|last2=Parks|first2=Connie L.|last3=Richard|first3=Adam H.|date=July 2017|title=Accuracy Rates of Ancestry Estimation by Forensic Anthropologists Using Identified Forensic Cases|url=https://pubmed.ncbi.nlm.nih.gov/28133721/|journal=Journal of Forensic Sciences|volume=62|issue=4|pages=971–974|doi=10.1111/1556-4029.13361|issn=1556-4029|pmid=28133721|s2cid=3453064}}</ref>
] showing average admixture of five North American ethnic groups. Individuals that self-identify with each group can be found at many locations on the map, but on average groups tend to cluster differently.]]

=== Gene flow and admixture ===
{{Main|Gene flow}}
Gene flow between two populations reduces the average genetic distance between the populations, only totally isolated human populations experience no gene flow and most populations have continuous gene flow with other neighboring populations which create the clinal distribution observed for most genetic variation. When gene flow takes place between well-differentiated genetic populations the result is referred to as "genetic admixture".

Admixture mapping is a technique used to study how genetic variants cause differences in disease rates between population.<ref name="Winkler_2010">{{cite journal | vauthors = Winkler CA, Nelson GW, Smith MW | title = Admixture mapping comes of age | journal = Annual Review of Genomics and Human Genetics | volume = 11 | pages = 65–89 | year = 2010 | pmid = 20594047 | doi = 10.1146/annurev-genom-082509-141523 | pmc = 7454031 | url = https://zenodo.org/record/1234977 }}</ref> Recent admixture populations that trace their ancestry to multiple continents are well suited for identifying genes for traits and diseases that differ in prevalence between parental populations. African-American populations have been the focus of numerous population genetic and admixture mapping studies, including studies of complex genetic traits such as white cell count, body-mass index, prostate cancer and renal disease.<ref name = "Bryc_2009">{{cite journal | vauthors = Bryc K, Auton A, Nelson MR, Oksenberg JR, Hauser SL, Williams S, Froment A, Bodo JM, Wambebe C, Tishkoff SA, Bustamante CD | display-authors = 6 | title = Genome-wide patterns of population structure and admixture in West Africans and African Americans | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 107 | issue = 2 | pages = 786–91 | date = January 2010 | pmid = 20080753 | pmc = 2818934 | doi = 10.1073/pnas.0909559107 | bibcode = 2010PNAS..107..786B | doi-access = free }}</ref>

An analysis of phenotypic and genetic variation including skin color and socio-economic status was carried out in the population of Cape Verde which has a well documented history of contact between Europeans and Africans. The studies showed that pattern of admixture in this population has been sex-biased (involving mostly matings between European men and African women) and there is a significant interaction between socioeconomic status and skin color, independent of ancestry.<ref name = "pmid_23226471">{{cite journal | vauthors = Beleza S, Campos J, Lopes J, Araújo II, Hoppfer Almada A, Correia e Silva A, Parra EJ, Rocha J | display-authors = 6 | title = The admixture structure and genetic variation of the archipelago of Cape Verde and its implications for admixture mapping studies | journal = PLOS ONE| volume = 7 | issue = 11 | pages = e51103 | year = 2012 | pmid = 23226471 | pmc = 3511383 | doi = 10.1371/journal.pone.0051103 | bibcode = 2012PLoSO...751103B | doi-access = free }}</ref> Another study shows an increased risk of ] complications after transplantation due to genetic variants in human leukocyte antigen (HLA) and non-HLA proteins.<ref name="pmid_23213535">{{cite journal | vauthors = Arrieta-Bolaños E, Madrigal JA, Shaw BE | title = Human leukocyte antigen profiles of Latin American populations: differential admixture and its potential impact on hematopoietic stem cell transplantation | journal = Bone Marrow Research | volume = 2012 | pages = 1–13 | year = 2012 | pmid = 23213535 | pmc = 3506882 | doi = 10.1155/2012/136087 | doi-access = free }}</ref>

== Health ==
{{See also|Race and health}}

Differences in ] contribute to group differences in the incidence of some ], and they may contribute to differences in the incidence of some common diseases.<ref name="Categorization of humans in biomedi">{{cite journal | vauthors = Risch N, Burchard E, Ziv E, Tang H | title = Categorization of humans in biomedical research: genes, race and disease | journal = Genome Biology | volume = 3 | issue = 7 | pages = comment2007 | date = July 2002 | pmid = 12184798 | pmc = 139378 | doi = 10.1186/gb-2002-3-7-comment2007 | doi-access = free }}</ref> For the monogenic diseases, the frequency of causative alleles usually correlates best with ancestry, whether familial (for example, ] among the Pennsylvania ]), ethnic (] among ] populations), or geographical (hemoglobinopathies among people with ancestors who lived in malarial regions). To the extent that ancestry corresponds with racial or ethnic groups or subgroups, the incidence of monogenic diseases can differ between groups categorized by race or ethnicity, and health-care professionals typically take these patterns into account in making diagnoses.<ref>{{cite journal | vauthors = Lu YF, Goldstein DB, Angrist M, Cavalleri G | title = Personalized medicine and human genetic diversity | journal = Cold Spring Harbor Perspectives in Medicine | volume = 4 | issue = 9 | pages = a008581 | date = July 2014 | pmid = 25059740 | pmc = 4143101 | doi = 10.1101/cshperspect.a008581 }}</ref>

Even with common diseases involving numerous genetic variants and environmental factors, investigators point to evidence suggesting the involvement of differentially distributed alleles with small to moderate effects. Frequently cited examples include ] (Douglas ''et al.'' 1996), ] (Gower ''et al.'' 2003), ] (Fernandez ''et al.'' 2003), and ] (Platz ''et al.'' 2000). However, in none of these cases has allelic variation in a susceptibility gene been shown to account for a significant fraction of the difference in disease prevalence among groups, and the role of genetic factors in generating these differences remains uncertain (Mountain and Risch 2004).

Some other variations on the other hand are beneficial to human, as they prevent certain diseases and increase the chance to adapt to the environment. For example, mutation in ] gene that protects against ]. CCR5 gene is absent on the surface of cell due to mutation. Without CCR5 gene on the surface, there is nothing for ] viruses to grab on and bind into. Therefore, the mutation on CCR5 gene decreases the chance of an individual's risk with AIDS. The mutation in CCR5 is also quite common in certain areas, with more than 14% of the population carry the mutation in ] and about 6–10% in ] and ].<ref>{{cite journal | vauthors = Limborska SA, Balanovsky OP, Balanovskaya EV, Slominsky PA, Schadrina MI, Livshits LA, Kravchenko SA, Pampuha VM, Khusnutdinova EK, Spitsyn VA | display-authors = 6 | title = Analysis of CCR5Delta32 geographic distribution and its correlation with some climatic and geographic factors | journal = Human Heredity | volume = 53 | issue = 1 | pages = 49–54 | year = 2002 | pmid = 11901272 | doi = 10.1159/000048605 | s2cid = 1538974 }}</ref>

]

Apart from mutations, many genes that may have aided humans in ancient times plague humans today. For example, it is suspected that genes that allow humans to more efficiently process food are those that make people susceptible to obesity and diabetes today.<ref>{{cite journal | vauthors = Tishkoff SA, Verrelli BC | title = Patterns of human genetic diversity: implications for human evolutionary history and disease | journal = Annual Review of Genomics and Human Genetics | volume = 4 | issue = 1 | pages = 293–340 | year = 2003 | pmid = 14527305 | doi = 10.1146/annurev.genom.4.070802.110226 }}</ref>

] of ] has proposed that self-identified race/ethnic group could be a valid means of categorization in the US for public health and policy considerations.<ref>
{{cite journal | vauthors = Tang H, Quertermous T, Rodriguez B, Kardia SL, Zhu X, Brown A, Pankow JS, Province MA, Hunt SC, Boerwinkle E, Schork NJ, Risch NJ | display-authors = 6 | title = Genetic structure, self-identified race/ethnicity, and confounding in case-control association studies | journal = American Journal of Human Genetics | volume = 76 | issue = 2 | pages = 268–75 | date = February 2005 | pmid = 15625622 | pmc = 1196372 | doi = 10.1086/427888 }}</ref><ref name="Categorization of humans in biomedi"/> A 2002 paper by ]'s group makes a similar claim: "The structure of human populations is relevant in various epidemiological contexts. As a result of variation in frequencies of both genetic and nongenetic risk factors, rates of disease and of such phenotypes as adverse drug response vary across populations. Further, information about a patient's population of origin might provide health care practitioners with information about risk when direct causes of disease are unknown."<ref>{{cite journal | vauthors = Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, Feldman MW | title = Genetic structure of human populations | journal = Science | volume = 298 | issue = 5602 | pages = 2381–5 | date = December 2002 | pmid = 12493913 | doi = 10.1126/science.1078311 | bibcode = 2002Sci...298.2381R | s2cid = 8127224 }}</ref> However, in 2018 ] released a study arguing against genetically essentialist ideas of health disparities between populations stating environmental variants are a more likely cause<ref></ref>

== Genome projects and organizations ==
{{Further|:Category:Human genome projects}}
Human ] are ] endeavors that determine or study the structure of the ]. The ] was a landmark genome project.

There are numerous related projects that deal with genetic variation (or variation in the encoded proteins), e.g. organized by the following organizations:

* ] (HUGO) -- organizes activities around human genome sequencing, including variants
* ] (HGVS) -- develops nomenclatural standards for human genetic variants
* HGVS Variant Nomenclature Committee (HVNC) -- maps and organizes variant nomenclature


==Physical variation in humans== == See also ==
* ]
{{further|]}}
* ]
{{Template:Biasutti skin color map|float=right}}
* ]
* ]
* ]
* ]
* ]
* ]
* ]
* ]


===Regional===
The distribution of many physical traits resembles the distribution of genetic variation within and between human populations (] 1996; Keita and Kittles 1997). For example, ∼90% of the variation in human head shapes occurs within every human group, and ∼10% separates groups, with a greater variability of head shape among individuals with recent African ancestors (Relethford 2002).
* ]
* ]
* ]
* ]
* ]
*]


===Projects===
A prominent exception to the common distribution of physical characteristics within and among groups is skin color. Approximately 10% of the variance in skin color occurs within groups, and ~90% occurs between groups (Relethford 2002). This distribution of skin color and its geographic patterning—with people whose ancestors lived predominantly near the equator having darker skin than those with ancestors who lived predominantly in higher latitudes—indicate that this attribute has been under strong selective pressure. Darker skin appears to be strongly selected for in equatorial regions to prevent sunburn, skin cancer, the photolysis of folate, and damage to sweat glands (Sturm ''et al.'' 2001; Rees 2003). A leading hypothesis for the selection of lighter skin in higher latitudes is that it enables the body to form greater amounts of vitamin D, which helps prevent rickets (Jablonski 2004). Evidence for this includes the finding that
* ]
a substantial portion of the differences of skin color between Europeans and Africans resides in a single gene, ] the threonine-111 allele of which was found in 98.7 to 100% among several European samples, while the alanine-111 form was found in 93 to 100% of samples of Africans, East Asians and Indigenous Americans (Lamason ''et al.'' 2005). However, the vitamin D hypothesis is not universally accepted (Aoki 2002), and lighter skin in high latitudes may correspond simply to an absence of selection for dark skin (Harding ''et al.'' 2000). ] which serves as the pigment, is located in the ] of the skin, and is based on ] ].


== References ==
Because skin color has been under strong selective pressure, similar skin colors can result from convergent adaptation rather than from genetic relatedness. Sub-Saharan Africans, tribal populations from southern India, and Indigenous Australians have similar skin pigmentation, but genetically they are no more similar than are other widely separated groups. Furthermore, in some parts of the world in which people from different regions have mixed extensively, the connection between skin color and ancestry has been substantially weakened (Parra ''et al.'' 2004). In Brazil, for example, skin color is not closely associated with the percentage of recent African ancestors a person has, as estimated from an analysis of genetic variants differing in frequency among continent groups (Parra ''et al.'' 2003).
{{reflist}}


== Further reading ==
Considerable speculation has surrounded the possible adaptive value of other physical features characteristic of groups, such as the constellation of facial features observed in many eastern and northeastern Asians (Guthrie 1996). However, any given physical characteristic generally is found in multiple groups (Lahr 1996), and demonstrating that environmental selective pressures shaped specific physical features will be difficult, since such features may have resulted from sexual selection for individuals with certain appearances or from genetic drift (Roseman 2004).
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* {{cite journal | vauthors = Zietkiewicz E, Yotova V, Gehl D, Wambach T, Arrieta I, Batzer M, Cole DE, Hechtman P, Kaplan F, Modiano D, Moisan JP, Michalski R, Labuda D | title = Haplotypes in the dystrophin DNA segment point to a mosaic origin of modern human diversity | journal = American Journal of Human Genetics | volume = 73 | issue = 5 | pages = 994–1015 | date = November 2003 | pmid = 14513410 | pmc = 1180505 | doi = 10.1086/378777 }}
* {{cite journal | vauthors = Pennisi E | author-link = Elizabeth Pennisi | title = Breakthrough of the year. Human genetic variation | journal = Science | volume = 318 | issue = 5858 | pages = 1842–43 | date = December 2007 | pmid = 18096770 | doi = 10.1126/science.318.5858.1842 | doi-access = free }}
* {{cite book | vauthors = Ramachandran S, Tang H, Gutenkunst RN, Bustamante CD |year=2010 |chapter=Genetics and Genomics of Human Population Structure | veditors = Speicher MR, Antonarakis SE, Motulsky AG |title=Vogel and Motulsky's Human Genetics: Problems and Approaches |edition=4th |publisher=] |isbn=978-3-540-37653-8 }}
{{refend}}


== External links ==
==References==
{{Commons category|Human genetic diversity}}
* Altmüller J, Palmer LJ, Fischer G, Scherb H, Wjst M (2001) Genomewide scans of complex human diseases: true linkage is hard to find. Am J Hum Genet 69:936–950
*
* Aoki K (2002) Sexual selection as a cause of human skin colour variation: Darwin's hypothesis revisited. Ann Hum Biol 29:589–608
* Bamshad, Michael; Wooding, Stephen; Salisbury, Benjamin A.; Stephens, J. Claiborne (2004). Deconstructing The Relationship Between Genetics And Race. ''Nature Reviews Genetics'' 5, 598&ndash;609.
* Bamshad M, Wooding SP (2003) Signature of natural selection in the human genome. Nat Rev Genet 4:99–111
* Bamshad MJ, Wooding S, Watkins WS, Ostler CT, Batzer MA, Jorde LB (2003) Human population genetic structure and inference of group membership. Am J Hum Genet 72:578–589
* Cann, Rebecca, M. Stoneking, A. Wilson 1987 "Mitochondrial DNA and Human Evolution" in ''Nature'' 325(January) 31-36.
* Cardon LR, Abecasis GR (2003) Using haplotype blocks to map human complex trait loci. Trends Genet 19:135–140
* Cavalli-Sforza LL, Feldman MW (2003) The application of molecular genetic approaches to the study of human evolution. Nat Genet Suppl 33:266–275
* Collins FS (2004) What we do and don't know about "race," "ethnicity," genetics and health at the dawn of the genome era. Nat Genet 36:S13–S15
* Collins FS, Green ED, Guttmacher AE, Guyer MS, for the US National Human Genome Research Institute (2003) A vision for the future of genomics research. Nature 422:835–847
* Ebersberger I, Metzler D, Schwarz C, Pääbo S (2002) Genomewide comparison of DNA sequences between humans and chimpanzees. Am J Hum Genet 70:1490–1497
* Edwards, AW (2003). Human genetic diversity: Lewontin's fallacy ''Bioessays'' 25, 798&ndash;801.
* Foster MW, Sharp RR (2004) Beyond race: towards a whole-genome perspective on human populations and genetic variation. Nat Rev Genet 5:790–796
* Foster MW, Sharp RR, Freeman WL, Chino M, Bernsten D, Carter TH (1999) The role of community review in evaluating the risks of human genetic variation research. Am J Hum Genet 64:1719–1727
* Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, Liu-Cordero SN, Rotimi C, Adeyemo A, Cooper R, Ward R, Lander ES, Daly MJ, Altshuler D (2002) The structure of haplotype blocks in the human genome. Science 296:2225–2229
* Harding RM, Healy E, Ray AJ, Ellis NS, Flanagan N, Todd C, Dixon C, Sajantila A, Jackson IJ, Birch-Machin MA, Rees JL (2000) Evidence for variable selective pressures at MC1R. Am J Hum Genet 66:1351–1361
* Ingman M, Kaessmann H, Pääbo S, Gyllensten U (2000) Mitochondrial genome variation and the origin of modern humans. Nature 408:708–713
* International HapMap Consortium (2003) The International HapMap Project. Nature 426:789–796
* ——— (2004) Integrating ethics and science in the International HapMap Project. Nat Rev Genet 5:467–475
* International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921
* Jorde LB, Bamshad M, Rogers AR (1998) Using mitochondrial and nuclear DNA markers to reconstruct human evolution. BioEssays 20:126–136
* Jorde LB, Watkins WS, Bamshad MJ, Dixon ME, Ricker CE, Seielstad MT, Batzer MA (2000a) The distribution of human genetic diversity: a comparison of mitochondrial, autosomal, and Y-chromosome data. Am J Hum Genet 66:979–988
* Jorde LB, Watkins WS, Kere J, Nyman D, Eriksson AW (2000b) Gene mapping in isolated populations: new roles for old friends? Hum Hered 50:57–65
* Jorde, Lynn B.; Wooding, Stephen P. (2004). Genetic variation, classification and race. ''Nature Genetics'' 36, S28&ndash;S33.
* Kaessmann H, Heissig F, von Haeseler A, Pääbo S (1999) DNA sequence variation in a non-coding region of low recombination on the human X chromosome. Nat Genet 22:78–81
* Kaessmann H, Wiebe V, Weiss G, Pääbo S (2001) Great ape DNA sequences reveal a reduced diversity and an expansion in humans. Nat Genet 27:155–156
* Lewontin RC (1972) The apportionment of human diversity. Evol Biol 6:381–398
* Mountain JL, Risch N (2004) Assessing genetic contributions to phenotypic differences among "racial" and "ethnic" groups. Nat Genet Suppl 36:S48–S53
* Pääbo S (2003) The mosaic that is our genome. Nature 421:409–412
* Sankar P, Cho MK (2002) Toward a new vocabulary of human genetic variation. Science 298:1337–1338
* Sankar P, Cho MK, Condit DM, Hunt LM, Koenig B, Marshall P, Lee SS, Spicer P (2004) Genetic research and health disparities. JAMA 291:2985–2989
* Serre D, Pääbo S (2004) Evidence for gradients of human genetic diversity within and among continents. Genome Res 14:1679–1685
* Weiss KM (1998) Coming to terms with human variation. Annu Rev Anthropol 27:273–300
* Weiss KM, Terwilliger JD (2000) How many diseases does it take to map a gene with SNPs? Nat Genet 26:151–157
* Yu N, Jensen-Seaman MI, Chemnick L, Kidd JR, Deinard AS, Ryder O, Kidd KK, Li WH (2003) Low nucleotide diversity in chimpanzees and bonobos. Genetics 164:1511–1518
* Zi&eogon;tkiewicz E, Yotova V, Gehl D, Wambach T, Arrieta I, Batzer M, Cole DEC, Hechtman P, Kaplan F, Modiano D, Moisan J-P, Michalski R, Labuda D (2003) Haplotypes in the dystrophin DNA segment point to a mosaic origin of modern human diversity. Am J Hum Genet 73:994–1015


{{Human group differences}}
==See also==
{{Human genetics}}
*]
{{Population genetics}}
{{Personal genomics}}
{{Breakthrough of the Year}}


{{DEFAULTSORT:Human Genetic Variation}}
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Latest revision as of 20:54, 9 December 2024

Genetic diversity in human populations "Human biodiversity" redirects here. For the far-right movement promoting scientific racism, see Human Biodiversity Institute.

A graphical representation of the typical human karyotype
The human mitochondrial DNA

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.

No two humans are genetically identical. Even monozygotic twins (who develop from one zygote) have infrequent genetic differences due to mutations occurring during development and gene copy-number variation. Differences between individuals, even closely related individuals, are the key to techniques such as genetic fingerprinting.

The human genome has a total length of approximately 3.2 billion base pairs (bp) in 46 chromosomes of DNA as well as slightly under 17,000 bp DNA in cellular mitochondria. In 2015, the typical difference between an individual's genome and the reference genome was estimated at 20 million base pairs (or 0.6% of the total). As of 2017, there were a total of 324 million known variants from sequenced human genomes.

Comparatively speaking, humans are a genetically homogeneous species. Although a small number of genetic variants are found more frequently in certain geographic regions or in people with ancestry from those regions, this variation accounts for a small portion (~15%) of human genome variability. The majority of variation exists within the members of each human population. For comparison, rhesus macaques exhibit 2.5-fold greater DNA sequence diversity compared to humans. These rates differ depending on what macromolecules are being analyzed. Chimpanzees have more genetic variance than humans when examining nuclear DNA, but humans have more genetic variance when examining at the level of proteins.

The lack of discontinuities in genetic distances between human populations, absence of discrete branches in the human species, and striking homogeneity of human beings globally, imply that there is no scientific basis for inferring races or subspecies in humans, and for most traits, there is much more variation within populations than between them. Despite this, modern genetic studies have found substantial average genetic differences across human populations in traits such as skin colour, bodily dimensions, lactose and starch digestion, high altitude adaptions, drug response, taste receptors, and predisposition to developing particular diseases. The greatest diversity is found within and among populations in Africa, and gradually declines with increasing distance from the African continent, consistent with the Out of Africa theory of human origins.

The study of human genetic variation has evolutionary significance and medical applications. It can help scientists reconstruct and understand patterns of past human migration. In medicine, study of human genetic variation may be important because some disease-causing alleles occur more often in certain population groups. For instance, the mutation for sickle-cell anemia is more often found in people with ancestry from certain sub-Saharan African, south European, Arabian, and Indian populations, due to the evolutionary pressure from mosquitos carrying malaria in these regions.

New findings show that each human has on average 60 new mutations compared to their parents.

Causes of variation

Further information: Recent human evolution

Causes of differences between individuals include independent assortment, the exchange of genes (crossing over and recombination) during reproduction (through meiosis) and various mutational events.

There are at least three reasons why genetic variation exists between populations. Natural selection may confer an adaptive advantage to individuals in a specific environment if an allele provides a competitive advantage. Alleles under selection are likely to occur only in those geographic regions where they confer an advantage. A second important process is genetic drift, which is the effect of random changes in the gene pool, under conditions where most mutations are neutral (that is, they do not appear to have any positive or negative selective effect on the organism). Finally, small migrant populations have statistical differences – called the founder effect – from the overall populations where they originated; when these migrants settle new areas, their descendant population typically differs from their population of origin: different genes predominate and it is less genetically diverse.

In humans, the main cause is genetic drift. Serial founder effects and past small population size (increasing the likelihood of genetic drift) may have had an important influence in neutral differences between populations. The second main cause of genetic variation is due to the high degree of neutrality of most mutations. A small, but significant number of genes appear to have undergone recent natural selection, and these selective pressures are sometimes specific to one region.

Measures of variation

Genetic variation among humans occurs on many scales, from gross alterations in the human karyotype to single nucleotide changes. Chromosome abnormalities are detected in 1 of 160 live human births. Apart from sex chromosome disorders, most cases of aneuploidy result in death of the developing fetus (miscarriage); the most common extra autosomal chromosomes among live births are 21, 18 and 13.

Nucleotide diversity is the average proportion of nucleotides that differ between two individuals. As of 2004, the human nucleotide diversity was estimated to be 0.1% to 0.4% of base pairs. In 2015, the 1000 Genomes Project, which sequenced one thousand individuals from 26 human populations, found that "a typical genome differs from the reference human genome at 4.1 million to 5.0 million sites … affecting 20 million bases of sequence"; the latter figure corresponds to 0.6% of total number of base pairs. Nearly all (>99.9%) of these sites are small differences, either single nucleotide polymorphisms or brief insertions or deletions (indels) in the genetic sequence, but structural variations account for a greater number of base-pairs than the SNPs and indels.

As of 2017, the Single Nucleotide Polymorphism Database (dbSNP), which lists SNP and other variants, listed 324 million variants found in sequenced human genomes.

Single nucleotide polymorphisms

DNA molecule 1 differs from DNA molecule 2 at a single base-pair location (a C/T polymorphism).
Main article: Single nucleotide polymorphism

A single nucleotide polymorphism (SNP) is a difference in a single nucleotide between members of one species that occurs in at least 1% of the population. The 2,504 individuals characterized by the 1000 Genomes Project had 84.7 million SNPs among them. SNPs are the most common type of sequence variation, estimated in 1998 to account for 90% of all sequence variants. Other sequence variations are single base exchanges, deletions and insertions. SNPs occur on average about every 100 to 300 bases and so are the major source of heterogeneity.

A functional, or non-synonymous, SNP is one that affects some factor such as gene splicing or messenger RNA, and so causes a phenotypic difference between members of the species. About 3% to 5% of human SNPs are functional (see International HapMap Project). Neutral, or synonymous SNPs are still useful as genetic markers in genome-wide association studies, because of their sheer number and the stable inheritance over generations.

A coding SNP is one that occurs inside a gene. There are 105 Human Reference SNPs that result in premature stop codons in 103 genes. This corresponds to 0.5% of coding SNPs. They occur due to segmental duplication in the genome. These SNPs result in loss of protein, yet all these SNP alleles are common and are not purified in negative selection.

Structural variation

Main article: Structural variation

Structural variation is the variation in structure of an organism's chromosome. Structural variations, such as copy-number variation and deletions, inversions, insertions and duplications, account for much more human genetic variation than single nucleotide diversity. This was concluded in 2007 from analysis of the diploid full sequences of the genomes of two humans: Craig Venter and James D. Watson. This added to the two haploid sequences which were amalgamations of sequences from many individuals, published by the Human Genome Project and Celera Genomics respectively.

According to the 1000 Genomes Project, a typical human has 2,100 to 2,500 structural variations, which include approximately 1,000 large deletions, 160 copy-number variants, 915 Alu insertions, 128 L1 insertions, 51 SVA insertions, 4 NUMTs, and 10 inversions.

Copy number variation

Main article: Copy number variation

A copy-number variation (CNV) is a difference in the genome due to deleting or duplicating large regions of DNA on some chromosome. It is estimated that 0.4% of the genomes of unrelated humans differ with respect to copy number. When copy number variation is included, human-to-human genetic variation is estimated to be at least 0.5% (99.5% similarity). Copy number variations are inherited but can also arise during development.

A visual map with the regions with high genomic variation of the modern-human reference assembly relatively to a Neanderthal of 50k has been built by Pratas et al.

Epigenetics

Epigenetic variation is variation in the chemical tags that attach to DNA and affect how genes get read. The tags, "called epigenetic markings, act as switches that control how genes can be read." At some alleles, the epigenetic state of the DNA, and associated phenotype, can be inherited across generations of individuals.

Genetic variability

Main article: Genetic variability

Genetic variability is a measure of the tendency of individual genotypes in a population to vary (become different) from one another. Variability is different from genetic diversity, which is the amount of variation seen in a particular population. The variability of a trait is how much that trait tends to vary in response to environmental and genetic influences.

Clines

Main article: Cline (biology)

In biology, a cline is a continuum of species, populations, varieties, or forms of organisms that exhibit gradual phenotypic and/or genetic differences over a geographical area, typically as a result of environmental heterogeneity. In the scientific study of human genetic variation, a gene cline can be rigorously defined and subjected to quantitative metrics.

Haplogroups

Main article: Haplogroup

In the study of molecular evolution, a haplogroup is a group of similar haplotypes that share a common ancestor with a single nucleotide polymorphism (SNP) mutation. The study of haplogroups provides information about ancestral origins dating back thousands of years.

The most commonly studied human haplogroups are Y-chromosome (Y-DNA) haplogroups and mitochondrial DNA (mtDNA) haplogroups, both of which can be used to define genetic populations. Y-DNA is passed solely along the patrilineal line, from father to son, while mtDNA is passed down the matrilineal line, from mother to both daughter or son. The Y-DNA and mtDNA may change by chance mutation at each generation.

Variable number tandem repeats

Main article: Variable number tandem repeat

A variable number tandem repeat (VNTR) is the variation of length of a tandem repeat. A tandem repeat is the adjacent repetition of a short nucleotide sequence. Tandem repeats exist on many chromosomes, and their length varies between individuals. Each variant acts as an inherited allele, so they are used for personal or parental identification. Their analysis is useful in genetics and biology research, forensics, and DNA fingerprinting.

Short tandem repeats (about 5 base pairs) are called microsatellites, while longer ones are called minisatellites.

History and geographic distribution

Map of the migration of modern humans out of Africa, based on mitochondrial DNA. Colored rings indicate thousand years before present.
Genetic distance map by Magalhães et al. (2012)
See also: Human evolutionary genetics § Modern humans, and Recent human evolution

Recent African origin of modern humans

The recent African origin of modern humans paradigm assumes the dispersal of non-African populations of anatomically modern humans after 70,000 years ago. Dispersal within Africa occurred significantly earlier, at least 130,000 years ago. The "out of Africa" theory originates in the 19th century, as a tentative suggestion in Charles Darwin's Descent of Man, but remained speculative until the 1980s when it was supported by the study of present-day mitochondrial DNA, combined with evidence from physical anthropology of archaic specimens.

According to a 2000 study of Y-chromosome sequence variation, human Y-chromosomes trace ancestry to Africa, and the descendants of the derived lineage left Africa and eventually were replaced by archaic human Y-chromosomes in Eurasia. The study also shows that a minority of contemporary populations in East Africa and the Khoisan are the descendants of the most ancestral patrilineages of anatomically modern humans that left Africa 35,000 to 89,000 years ago. Other evidence supporting the theory is that variations in skull measurements decrease with distance from Africa at the same rate as the decrease in genetic diversity. Human genetic diversity decreases in native populations with migratory distance from Africa, and this is thought to be due to bottlenecks during human migration, which are events that temporarily reduce population size.

A 2009 genetic clustering study, which genotyped 1327 polymorphic markers in various African populations, identified six ancestral clusters. The clustering corresponded closely with ethnicity, culture and language. A 2018 whole genome sequencing study of the world's populations observed similar clusters among the populations in Africa. At K=9, distinct ancestral components defined the Afroasiatic-speaking populations inhabiting North Africa and Northeast Africa; the Nilo-Saharan-speaking populations in Northeast Africa and East Africa; the Ari populations in Northeast Africa; the Niger-Congo-speaking populations in West-Central Africa, West Africa, East Africa and Southern Africa; the Pygmy populations in Central Africa; and the Khoisan populations in Southern Africa.

In May 2023, scientists reported, based on genetic studies, a more complicated pathway of human evolution than previously understood. According to the studies, humans evolved from different places and times in Africa, instead of from a single location and period of time.

Population genetics

See also: Population genetics

Because of the common ancestry of all humans, only a small number of variants have large differences in frequency between populations. However, some rare variants in the world's human population are much more frequent in at least one population (more than 5%).

Genetic variation
Genetic variation of Eurasian populations showing different frequency of West- and East-Eurasian components.

It is commonly assumed that early humans left Africa, and thus must have passed through a population bottleneck before their African-Eurasian divergence around 100,000 years ago (ca. 3,000 generations). The rapid expansion of a previously small population has two important effects on the distribution of genetic variation. First, the so-called founder effect occurs when founder populations bring only a subset of the genetic variation from their ancestral population. Second, as founders become more geographically separated, the probability that two individuals from different founder populations will mate becomes smaller. The effect of this assortative mating is to reduce gene flow between geographical groups and to increase the genetic distance between groups.

The expansion of humans from Africa affected the distribution of genetic variation in two other ways. First, smaller (founder) populations experience greater genetic drift because of increased fluctuations in neutral polymorphisms. Second, new polymorphisms that arose in one group were less likely to be transmitted to other groups as gene flow was restricted.

Populations in Africa tend to have lower amounts of linkage disequilibrium than do populations outside Africa, partly because of the larger size of human populations in Africa over the course of human history and partly because the number of modern humans who left Africa to colonize the rest of the world appears to have been relatively low. In contrast, populations that have undergone dramatic size reductions or rapid expansions in the past and populations formed by the mixture of previously separate ancestral groups can have unusually high levels of linkage disequilibrium

Distribution of variation

Human genetic variation calculated from genetic data representing 346 microsatellite loci taken from 1484 individuals in 78 human populations. The upper graph illustrates that as populations are further from East Africa, they have declining genetic diversity as measured in average number of microsatellite repeats at each of the loci. The bottom chart illustrates isolation by distance. Populations with a greater distance between them are more dissimilar (as measured by the Fst statistic) than those which are geographically close to one another. The horizontal axis of both charts is geographic distance as measured along likely routes of human migration. (Chart from Kanitz et al. 2018)

The distribution of genetic variants within and among human populations are impossible to describe succinctly because of the difficulty of defining a "population," the clinal nature of variation, and heterogeneity across the genome (Long and Kittles 2003). In general, however, an average of 85% of genetic variation exists within local populations, ~7% is between local populations within the same continent, and ~8% of variation occurs between large groups living on different continents. The recent African origin theory for humans would predict that in Africa there exists a great deal more diversity than elsewhere and that diversity should decrease the further from Africa a population is sampled.

Phenotypic variation

Further information: Phenotype § Phenotypic variation

Sub-Saharan Africa has the most human genetic diversity and the same has been shown to hold true for phenotypic variation in skull form. Phenotype is connected to genotype through gene expression. Genetic diversity decreases smoothly with migratory distance from that region, which many scientists believe to be the origin of modern humans, and that decrease is mirrored by a decrease in phenotypic variation. Skull measurements are an example of a physical attribute whose within-population variation decreases with distance from Africa.

The distribution of many physical traits resembles the distribution of genetic variation within and between human populations (American Association of Physical Anthropologists 1996; Keita and Kittles 1997). For example, ~90% of the variation in human head shapes occurs within continental groups, and ~10% separates groups, with a greater variability of head shape among individuals with recent African ancestors (Relethford 2002).

A prominent exception to the common distribution of physical characteristics within and among groups is skin color. Approximately 10% of the variance in skin color occurs within groups, and ~90% occurs between groups (Relethford 2002). This distribution of skin color and its geographic patterning – with people whose ancestors lived predominantly near the equator having darker skin than those with ancestors who lived predominantly in higher latitudes – indicate that this attribute has been under strong selective pressure. Darker skin appears to be strongly selected for in equatorial regions to prevent sunburn, skin cancer, the photolysis of folate, and damage to sweat glands.

Understanding how genetic diversity in the human population impacts various levels of gene expression is an active area of research. While earlier studies focused on the relationship between DNA variation and RNA expression, more recent efforts are characterizing the genetic control of various aspects of gene expression including chromatin states, translation, and protein levels. A study published in 2007 found that 25% of genes showed different levels of gene expression between populations of European and Asian descent. The primary cause of this difference in gene expression was thought to be SNPs in gene regulatory regions of DNA. Another study published in 2007 found that approximately 83% of genes were expressed at different levels among individuals and about 17% between populations of European and African descent.

Wright's fixation index as measure of variation

The population geneticist Sewall Wright developed the fixation index (often abbreviated to FST) as a way of measuring genetic differences between populations. This statistic is often used in taxonomy to compare differences between any two given populations by measuring the genetic differences among and between populations for individual genes, or for many genes simultaneously. It is often stated that the fixation index for humans is about 0.15. This translates to an estimated 85% of the variation measured in the overall human population is found within individuals of the same population, and about 15% of the variation occurs between populations. These estimates imply that any two individuals from different populations may be more similar to each other than either is to a member of their own group. "The shared evolutionary history of living humans has resulted in a high relatedness among all living people, as indicated for example by the very low fixation index (FST) among living human populations." Richard Lewontin, who affirmed these ratios, thus concluded neither "race" nor "subspecies" were appropriate or useful ways to describe human populations.

Wright himself believed that values >0.25 represent very great genetic variation and that an FST of 0.15–0.25 represented great variation. However, about 5% of human variation occurs between populations within continents, therefore FST values between continental groups of humans (or races) of as low as 0.1 (or possibly lower) have been found in some studies, suggesting more moderate levels of genetic variation. Graves (1996) has countered that FST should not be used as a marker of subspecies status, as the statistic is used to measure the degree of differentiation between populations, although see also Wright (1978).

Jeffrey Long and Rick Kittles give a long critique of the application of FST to human populations in their 2003 paper "Human Genetic Diversity and the Nonexistence of Biological Races". They find that the figure of 85% is misleading because it implies that all human populations contain on average 85% of all genetic diversity. They argue the underlying statistical model incorrectly assumes equal and independent histories of variation for each large human population. A more realistic approach is to understand that some human groups are parental to other groups and that these groups represent paraphyletic groups to their descent groups. For example, under the recent African origin theory the human population in Africa is paraphyletic to all other human groups because it represents the ancestral group from which all non-African populations derive, but more than that, non-African groups only derive from a small non-representative sample of this African population. This means that all non-African groups are more closely related to each other and to some African groups (probably east Africans) than they are to others, and further that the migration out of Africa represented a genetic bottleneck, with much of the diversity that existed in Africa not being carried out of Africa by the emigrating groups. Under this scenario, human populations do not have equal amounts of local variability, but rather diminished amounts of diversity the further from Africa any population lives. Long and Kittles find that rather than 85% of human genetic diversity existing in all human populations, about 100% of human diversity exists in a single African population, whereas only about 70% of human genetic diversity exists in a population derived from New Guinea. Long and Kittles argued that this still produces a global human population that is genetically homogeneous compared to other mammalian populations.

Archaic admixture

Main article: Archaic human admixture with modern humans

Anatomically modern humans interbred with Neanderthals during the Middle Paleolithic. In May 2010, the Neanderthal Genome Project presented genetic evidence that interbreeding took place and that a small but significant portion, around 2–4%, of Neanderthal admixture is present in the DNA of modern Eurasians and Oceanians, and nearly absent in sub-Saharan African populations.

Between 4% and 6% of the genome of Melanesians (represented by the Papua New Guinean and Bougainville Islander) appears to derive from Denisovans – a previously unknown hominin which is more closely related to Neanderthals than to Sapiens. It was possibly introduced during the early migration of the ancestors of Melanesians into Southeast Asia. This history of interaction suggests that Denisovans once ranged widely over eastern Asia.

Thus, Melanesians emerge as one of the most archaic-admixed populations, having Denisovan/Neanderthal-related admixture of ~8%.

In a study published in 2013, Jeffrey Wall from University of California studied whole sequence-genome data and found higher rates of introgression in Asians compared to Europeans. Hammer et al. tested the hypothesis that contemporary African genomes have signatures of gene flow with archaic human ancestors and found evidence of archaic admixture in the genomes of some African groups, suggesting that modest amounts of gene flow were widespread throughout time and space during the evolution of anatomically modern humans.

A study published in 2020 found that the Yoruba and Mende populations of West Africa derive between 2% and 19% of their genome from an as-yet unidentified archaic hominin population that likely diverged before the split of modern humans and the ancestors of Neanderthals and Denisovans, potentially making these groups the most archaic-admixed human populations identified yet.

Categorization of the world population

Chart showing human genetic clustering
Individuals mostly have genetic variants which are found in multiple regions of the world. Based on data from "A unified genealogy of modern and ancient genomes".
See also: Race (human classification) and Race and genetics

New data on human genetic variation has reignited the debate about a possible biological basis for categorization of humans into races. Most of the controversy surrounds the question of how to interpret the genetic data and whether conclusions based on it are sound. Some researchers argue that self-identified race can be used as an indicator of geographic ancestry for certain health risks and medications.

Although the genetic differences among human groups are relatively small, these differences in certain genes such as duffy, ABCC11, SLC24A5, called ancestry-informative markers (AIMs) nevertheless can be used to reliably situate many individuals within broad, geographically based groupings. For example, computer analyses of hundreds of polymorphic loci sampled in globally distributed populations have revealed the existence of genetic clustering that roughly is associated with groups that historically have occupied large continental and subcontinental regions (Rosenberg et al. 2002; Bamshad et al. 2003).

Some commentators have argued that these patterns of variation provide a biological justification for the use of traditional racial categories. They argue that the continental clusterings correspond roughly with the division of human beings into sub-Saharan Africans; Europeans, Western Asians, Central Asians, Southern Asians and Northern Africans; Eastern Asians, Southeast Asians, Polynesians and Native Americans; and other inhabitants of Oceania (Melanesians, Micronesians & Australian Aborigines) (Risch et al. 2002). Other observers disagree, saying that the same data undercut traditional notions of racial groups (King and Motulsky 2002; Calafell 2003; Tishkoff and Kidd 2004). They point out, for example, that major populations considered races or subgroups within races do not necessarily form their own clusters.

Racial categories are also undermined by findings that genetic variants which are limited to one region tend to be rare within that region, variants that are common within a region tend to be shared across the globe, and most differences between individuals, whether they come from the same region or different regions, are due to global variants. No genetic variants have been found which are fixed within a continent or major region and found nowhere else.

Furthermore, because human genetic variation is clinal, many individuals affiliate with two or more continental groups. Thus, the genetically based "biogeographical ancestry" assigned to any given person generally will be broadly distributed and will be accompanied by sizable uncertainties (Pfaff et al. 2004).

In many parts of the world, groups have mixed in such a way that many individuals have relatively recent ancestors from widely separated regions. Although genetic analyses of large numbers of loci can produce estimates of the percentage of a person's ancestors coming from various continental populations (Shriver et al. 2003; Bamshad et al. 2004), these estimates may assume a false distinctiveness of the parental populations, since human groups have exchanged mates from local to continental scales throughout history (Cavalli-Sforza et al. 1994; Hoerder 2002). Even with large numbers of markers, information for estimating admixture proportions of individuals or groups is limited, and estimates typically will have wide confidence intervals (Pfaff et al. 2004).

Genetic clustering

Main article: Human genetic clustering

Genetic data can be used to infer population structure and assign individuals to groups that often correspond with their self-identified geographical ancestry. Jorde and Wooding (2004) argued that "Analysis of many loci now yields reasonably accurate estimates of genetic similarity among individuals, rather than populations. Clustering of individuals is correlated with geographic origin or ancestry." However, identification by geographic origin may quickly break down when considering historical ancestry shared between individuals back in time.

An analysis of autosomal SNP data from the International HapMap Project (Phase II) and CEPH Human Genome Diversity Panel samples was published in 2009. The study of 53 populations taken from the HapMap and CEPH data (1138 unrelated individuals) suggested that natural selection may shape the human genome much more slowly than previously thought, with factors such as migration within and among continents more heavily influencing the distribution of genetic variations. A similar study published in 2010 found strong genome-wide evidence for selection due to changes in ecoregion, diet, and subsistence particularly in connection with polar ecoregions, with foraging, and with a diet rich in roots and tubers. In a 2016 study, principal component analysis of genome-wide data was capable of recovering previously-known targets for positive selection (without prior definition of populations) as well as a number of new candidate genes.

Forensic anthropology

Forensic anthropologists can assess the ancestry of skeletal remains by analyzing skeletal morphology as well as using genetic and chemical markers, when possible. While these assessments are never certain, the accuracy of skeletal morphology analyses in determining true ancestry has been estimated at 90%.

Ternary plot showing average admixture of five North American ethnic groups. Individuals that self-identify with each group can be found at many locations on the map, but on average groups tend to cluster differently.

Gene flow and admixture

Main article: Gene flow

Gene flow between two populations reduces the average genetic distance between the populations, only totally isolated human populations experience no gene flow and most populations have continuous gene flow with other neighboring populations which create the clinal distribution observed for most genetic variation. When gene flow takes place between well-differentiated genetic populations the result is referred to as "genetic admixture".

Admixture mapping is a technique used to study how genetic variants cause differences in disease rates between population. Recent admixture populations that trace their ancestry to multiple continents are well suited for identifying genes for traits and diseases that differ in prevalence between parental populations. African-American populations have been the focus of numerous population genetic and admixture mapping studies, including studies of complex genetic traits such as white cell count, body-mass index, prostate cancer and renal disease.

An analysis of phenotypic and genetic variation including skin color and socio-economic status was carried out in the population of Cape Verde which has a well documented history of contact between Europeans and Africans. The studies showed that pattern of admixture in this population has been sex-biased (involving mostly matings between European men and African women) and there is a significant interaction between socioeconomic status and skin color, independent of ancestry. Another study shows an increased risk of graft-versus-host disease complications after transplantation due to genetic variants in human leukocyte antigen (HLA) and non-HLA proteins.

Health

See also: Race and health

Differences in allele frequencies contribute to group differences in the incidence of some monogenic diseases, and they may contribute to differences in the incidence of some common diseases. For the monogenic diseases, the frequency of causative alleles usually correlates best with ancestry, whether familial (for example, Ellis–Van Creveld syndrome among the Pennsylvania Amish), ethnic (Tay–Sachs disease among Ashkenazi Jewish populations), or geographical (hemoglobinopathies among people with ancestors who lived in malarial regions). To the extent that ancestry corresponds with racial or ethnic groups or subgroups, the incidence of monogenic diseases can differ between groups categorized by race or ethnicity, and health-care professionals typically take these patterns into account in making diagnoses.

Even with common diseases involving numerous genetic variants and environmental factors, investigators point to evidence suggesting the involvement of differentially distributed alleles with small to moderate effects. Frequently cited examples include hypertension (Douglas et al. 1996), diabetes (Gower et al. 2003), obesity (Fernandez et al. 2003), and prostate cancer (Platz et al. 2000). However, in none of these cases has allelic variation in a susceptibility gene been shown to account for a significant fraction of the difference in disease prevalence among groups, and the role of genetic factors in generating these differences remains uncertain (Mountain and Risch 2004).

Some other variations on the other hand are beneficial to human, as they prevent certain diseases and increase the chance to adapt to the environment. For example, mutation in CCR5 gene that protects against AIDS. CCR5 gene is absent on the surface of cell due to mutation. Without CCR5 gene on the surface, there is nothing for HIV viruses to grab on and bind into. Therefore, the mutation on CCR5 gene decreases the chance of an individual's risk with AIDS. The mutation in CCR5 is also quite common in certain areas, with more than 14% of the population carry the mutation in Europe and about 6–10% in Asia and North Africa.

HIV attachment

Apart from mutations, many genes that may have aided humans in ancient times plague humans today. For example, it is suspected that genes that allow humans to more efficiently process food are those that make people susceptible to obesity and diabetes today.

Neil Risch of Stanford University has proposed that self-identified race/ethnic group could be a valid means of categorization in the US for public health and policy considerations. A 2002 paper by Noah Rosenberg's group makes a similar claim: "The structure of human populations is relevant in various epidemiological contexts. As a result of variation in frequencies of both genetic and nongenetic risk factors, rates of disease and of such phenotypes as adverse drug response vary across populations. Further, information about a patient's population of origin might provide health care practitioners with information about risk when direct causes of disease are unknown." However, in 2018 Noah Rosenberg released a study arguing against genetically essentialist ideas of health disparities between populations stating environmental variants are a more likely cause

Genome projects and organizations

Further information: Category:Human genome projects

Human genome projects are scientific endeavors that determine or study the structure of the human genome. The Human Genome Project was a landmark genome project.

There are numerous related projects that deal with genetic variation (or variation in the encoded proteins), e.g. organized by the following organizations:

  • HUman Genome Organisation (HUGO) -- organizes activities around human genome sequencing, including variants
  • Human Genome Variation Society (HGVS) -- develops nomenclatural standards for human genetic variants
  • HGVS Variant Nomenclature Committee (HVNC) -- maps and organizes variant nomenclature

See also

Regional

Projects

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