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Saturday, August 3, 2019

Recent African origin of modern humans

From Wikipedia, the free encyclopedia

Successive dispersals of      Homo erectus (yellow),      Homo neanderthalensis (ochre) and      Homo sapiens (red).
 
Expansion of early modern humans from Africa through the Near East
 
Map of the migration of modern humans out of Africa, based on mitochondrial DNA. Colored rings indicate thousand years before present.

In paleoanthropology, the recent African origin of modern humans, also called the "Out of Africa" theory (OOA), recent single-origin hypothesis (RSOH), replacement hypothesis, or recent African origin model (RAO), is the dominant model of the geographic origin and early migration of anatomically modern humans (Homo sapiens). It follows the early expansions of hominins out of Africa, accomplished by Homo erectus and then Homo neanderthalensis

The model proposes a "single origin" of Homo sapiens in the taxonomic sense, precluding parallel evolution of traits considered anatomically modern in other regions, but not precluding multiple admixture between H. sapiens and archaic humans in Europe and Asia. H. sapiens most likely developed in the Horn of Africa between 300,000 and 200,000 years ago. The "recent African origin" model proposes that all modern non-African populations are substantially descended from populations of H. sapiens that left Africa after that time. 

There were at least several "out-of-Africa" dispersals of modern humans, possibly beginning as early as 270,000 years ago, including 215,000 years ago to at least Greece, and certainly via northern Africa about 130,000 to 115,000 years ago. These early waves appear to have mostly died out or retreated by 80,000 years ago.

The most significant "recent" wave took place about 60,000–70,000 years ago, via the so-called "Southern Route", spreading rapidly along the coast of Asia and reaching Australia by around 65,000–50,000 years ago, while Europe was populated by an early offshoot which settled the Near East and Europe less than 55,000 years ago.

In the 2010s, studies in population genetics have uncovered evidence of interbreeding between H. sapiens and archaic humans in Eurasia and Oceania but not in Africa, which means that all non-African modern population groups, while mostly derived from early H. sapiens, are to a lesser extent also descended from regional variants of archaic humans.

Proposed waves

Layer sequence at Ksar Akil in the Levantine corridor, and discovery of two fossils of Homo sapiens, dated to 40,800 to 39,200 years BP for "Egbert",and 42,400–41,700 BP for "Ethelruda"
 
"Recent African origin," or Out of Africa II, refers to the migration of anatomically modern humans (Homo sapiens) out of Africa after their emergence at c. 300,000 to 200,000 years ago, in contrast to "Out of Africa I", which refers to the migration of archaic humans from Africa to Eurasia roughly 1.8 to 0.5 million years ago. 

Since the beginning of the 21st century, the picture of "recent single-origin" migrations has become significantly more complex, not only due to the discovery of modern-archaic admixture but also due to the increasing evidence that the "recent out-of-Africa" migration took place in a number of waves spread over a long time period. As of 2010, there were two main accepted dispersal routes for the out-of-Africa migration of early anatomically modern humans: via the "Northern Route" (via Nile Valley and Sinai) and the "Southern Route" via the Bab al Mandab strait.
  • Posth et al. (2017) suggest that early Homo sapiens, or "another species in Africa closely related to us," might have first migrated out of Africa around 270,000 years ago.
  • Finds at Misliya cave, which include a partial jawbone with eight teeth, have been dated to around 185,000 years ago. Layers dating from between 250,000 and 140,000 years ago in the same cave contained tools of the Levallois type which could put the date of the first migration even earlier if the tools can be associated with the modern human jawbone finds.
  • An Eastward Dispersal from Northeast Africa to Arabia 150,000–130,000  years ago based on the finds at Jebel Faya dated to 127,000 years ago (discovered in 2011). Possibly related to this wave are the finds from Zhirendong cave, Southern China, dated to more than 100,000 years ago. Other evidence of modern human presence in China has been dated to 80,000 years ago.
  • The most significant dispersal took place around 60–70,000 years ago via the so-called Southern Route, either before or after the Toba event, which happened between 69,000 and 77,000 years ago. This dispersal followed the southern coastline of Asia, and reached Australia around 65,000-50,000 years ago. Western Asia was "re-occupied" by a different derivation from this wave around 50,000 years ago, and Europe was populated from Western Asia beginning around 43,000 years ago.
  • Wells (2003) describes an additional wave of migration after the southern coastal route, namely a northern migration into Europe at circa 45,000 years ago. However, this possibility is ruled out by Macaulay et al. (2005) and Posth et al. (2016), who argue for a single coastal dispersal, with an early offshoot into Europe.

Northern Route dispersal

Anatomically Modern Humans known archaeological remains in Europe and Africa, directly dated, calibrated carbon dates as of 2013.
 
Beginning 135,000 years ago, tropical Africa experienced megadroughts which drove humans from the land and towards the sea shores, and forced them to cross over to other continents.

Modern humans crossed the Straits of Bab el Mandab in the southern Red Sea, and moved along the green coastlines around Arabia, and thence to the rest of Eurasia. Fossils of early Homo sapiens were found in Qafzeh cave in Israel and have been dated 80,000 to 100,000 years ago. These humans seem to have either become extinct or retreated back to Africa 70,000 to 80,000 years ago, possibly replaced by southbound Neanderthals escaping the colder regions of ice-age Europe. Hua Liu et al. analyzed autosomal microsatellite markers dating to about 56,000 years ago. They interpret the paleontological fossil as an isolated early offshoot that retracted back to Africa.

The discovery of stone tools in the United Arab Emirates in 2011 at the Faya-1 site in Mleiha, Sharjah, indicated the presence of modern humans at least 125,000 years ago, leading to a resurgence of the "long-neglected" North African route.

In Oman, a site was discovered by Bien Joven in 2011 containing more than 100 surface scatters of stone tools belonging to the late Nubian Complex, known previously only from archaeological excavations in the Sudan. Two optically stimulated luminescence age estimates placed the Arabian Nubian Complex at approximately 106,000 years old. This provides evidence for a distinct stone age technocomplex in southern Arabia, around the earlier part of the Marine Isotope Stage 5.

According to Kuhlwilm and his co-authors, Neanderthals contributed genetically to modern humans then living outside of Africa around 100,000 years ago: humans which had already split off from other modern humans around 200,000 years ago, and this early wave of modern humans outside Africa also contributed genetically to the Altai Neanderthals. They found that "the ancestors of Neanderthals from the Altai Mountains and early modern humans met and interbred, possibly in the Near East, many thousands of years earlier than previously thought". According to co-author Ilan Gronau, "This actually complements archaeological evidence of the presence of early modern humans out of Africa around and before 100,000 years ago by providing the first genetic evidence of such populations." Similar genetic admixture events have been noted in other regions as well.

In China, the Liujiang man (Chinese: 柳江人) is among the earliest modern humans found in East Asia. The date most commonly attributed to the remains is 67,000 years ago. High rates of variability yielded by various dating techniques carried out by different researchers place the most widely accepted range of dates with 67,000 BP as a minimum, but do not rule out dates as old as 159,000 BP. Liu, Martinón-Torres et al. (2015) claim that modern human teeth have been found in China dating to at least 80,000 years ago.

Southern Route dispersal

Coastal route

Red Sea crossing
 
By some 50-70,000 years ago, a subset of the bearers of mitochondrial haplogroup L3 migrated from East Africa into the Near East. It has been estimated that from a population of 2,000 to 5,000 individuals in Africa, only a small group, possibly as few as 150 to 1,000 people, crossed the Red Sea. The group that crossed the Red Sea travelled along the coastal route around Arabia and Persia to India, which appears to have been the first major settling point. Wells (2003) argued for the route along the southern coastline of Asia, across about 250 kilometres (155 mi), reaching Australia by around 50,000 years ago. 

Today at the Bab-el-Mandeb straits, the Red Sea is about 20 kilometres (12 mi) wide, but 50,000 years ago sea levels were 70 m (230 ft) lower (owing to glaciation) and the water was much narrower. Though the straits were never completely closed, they were narrow enough to have enabled crossing using simple rafts, and there may have been islands in between. Shell middens 125,000 years old have been found in Eritrea, indicating the diet of early humans included seafood obtained by beachcombing.

The dating of the Southern Dispersal is a matter of dispute. It may have happened either pre- or post-Toba, a catastrophic volcanic eruption that took place between 69,000 and 77,000 years ago at the site of present-day Lake Toba. Stone tools discovered below the layers of ash disposed in India may point to a pre-Toba dispersal but the source of the tools is disputed. An indication for post-Toba is haplo-group L3, that originated before the dispersal of humans out of Africa and can be dated to 60,000–70,000 years ago, "suggesting that humanity left Africa a few thousand years after Toba". New research showing slower than expected genetic mutations in human DNA was published in 2012, indicating a revised dating for the migration to between 90,000 and 130,000 years ago.

Western Asia

A fossil of a modern human dated to 54,700 years ago was found in Manot Cave in Israel, named Manot 1, though the dating was questioned by Groucutt et al. (2015).

South-Asia and Australia

It is thought that Australia was inhabited around 65,000–50,000 years ago. As of 2017, the earliest evidence of humans in Australia is at least 65,000 years old, while McChesney stated that
...genetic evidence suggests that a small band with the marker M168 migrated out of Africa along the coasts of the Arabian Peninsula and India, through Indonesia, and reached Australia very early, between 60,000 and 50,000 years ago. This very early migration into Australia is also supported by Rasmussen et al. (2011).
Fossils from Lake Mungo, Australia, have been dated to about 42,000 years ago. Other fossils from a site called Madjedbebe have been dated to at least 65,000 years ago.

East Asia

Tianyuan man from China has a probable date range between 38,000 and 42,000 years ago, while Liujiang man from the same region has a probable date range between 67,000 and 159,000 years ago. According to 2013 DNA tests, Tianyuan man is related "to many present-day Asians and Native Americans". Tianyuan is similar in morphology to Minatogawa Man, modern humans dated between 17,000 and 19,000 years ago and found on Okinawa Island, Japan.

Europe

According to Macaulay et al. (2005), an early offshoot from the southern dispersal with haplogroup N followed the Nile from East Africa, heading northwards and crossing into Asia through the Sinai. This group then branched, some moving into Europe and others heading east into Asia. This hypothesis is supported by the relatively late date of the arrival of modern humans in Europe as well as by archaeological and DNA evidence. Based on an analysis of 55 human mitochondrial genomes (mtDNAs) of hunter-gatherers, Posth et al. (2016) argue for a "rapid single dispersal of all non-Africans less than 55,000 years ago."

Genetic reconstruction

Mitochondrial haplogroups

Within Africa

Map of early diversification of modern humans according to mitochondrial population genetics.
 
The first lineage to branch off from Mitochondrial Eve was L0. This haplogroup is found in high proportions among the San of Southern Africa and the Sandawe of East Africa. It is also found among the Mbuti people. These groups branched off early in human history and have remained relatively genetically isolated since then. Haplogroups L1, L2 and L3 are descendants of L1–L6, and are largely confined to Africa. The macro haplogroups M and N, which are the lineages of the rest of the world outside Africa, descend from L3. L3 is about 84,000 years old, while haplogroups M and N are about 63,000 years old. The relationship between such gene trees and demographic history is still debated when applied to dispersals.

Of all the lineages present in Africa, only the female descendants of one lineage, mtDNA haplogroup L3, are found outside Africa. If there had been several migrations, one would expect descendants of more than one lineage to be found. L3's female descendants, the M and N haplogroup lineages, are found in very low frequencies in Africa (although haplogroup M1 populations are very ancient and diversified in North and North-east Africa) and appear to be more recent arrivals. A possible explanation is that these mutations occurred in East Africa shortly before the exodus and became the dominant haplogroups thereafter by means of the founder effect. Alternatively, the mutations may have arisen shortly afterwards.

Southern Route and haplogroups M and N

Results from mtDNA collected from aboriginal Malaysians called Orang Asli indicate that the hapologroups M and N share characteristics with original African groups from approximately 85,000 years ago, and share characteristics with sub-haplogroups found in coastal south-east Asian regions, such as Australasia, the Indian subcontinent and throughout continental Asia, which had dispersed and separated from their African progenitor approximately 65,000 years ago. This southern coastal dispersal would have occurred before the dispersal through the Levant approximately 45,000 years ago. This hypothesis attempts to explain why haplogroup N is predominant in Europe and why haplogroup M is absent in Europe. Evidence of the coastal migration is thought to have been destroyed by the rise in sea levels during the Holocene epoch. Alternatively, a small European founder population that had expressed haplogroup M and N at first, could have lost haplogroup M through random genetic drift resulting from a bottleneck (i.e. a founder effect).

The group that crossed the Red Sea travelled along the coastal route around Arabia and Persia until reaching India. Haplogroup M is found in high frequencies along the southern coastal regions of Pakistan and India and it has the greatest diversity in India, indicating that it is here where the mutation may have occurred. Sixty percent of the Indian population belong to Haplogroup M. The indigenous people of the Andaman Islands also belong to the M lineage. The Andamanese are thought to be offshoots of some of the earliest inhabitants in Asia because of their long isolation from the mainland. They are evidence of the coastal route of early settlers that extends from India to Thailand and Indonesia all the way to Papua New Guinea. Since M is found in high frequencies in highlanders from New Guinea and the Andamanese and New Guineans have dark skin and Afro-textured hair, some scientists think they are all part of the same wave of migrants who departed across the Red Sea ~60,000 years ago in the Great Coastal Migration. The proportion of haplogroup M increases eastwards from Arabia to India; in eastern India, M outnumbers N by a ratio of 3:1. Crossing into Southeast Asia, haplogroup N (mostly in the form of derivatives of its R subclade) reappears as the predominant lineage. M is predominant in East Asia, but amongst Indigenous Australians, N is the more common lineage. This haphazard distribution of Haplogroup N from Europe to Australia can be explained by founder effects and population bottlenecks.

Autosomal DNA

A 2002 study of African, European and Asian populations, found greater genetic diversity among Africans than among Eurasians, and that genetic diversity among Eurasians is largely a subset of that among Africans, supporting the out of Africa model. A large study by Coop et al. (2009) found evidence for natural selection in autosomal DNA outside of Africa. The study distinguishes non-African sweeps (notably KITLG variants associated with skin color), West-Eurasian sweeps (SLC24A5) and East-Asian sweeps (MC1R, relevant to skin color). Based on this evidence, the study concluded that human populations encountered novel selective pressures as they expanded out of Africa. MC1R and its relation to skin color had already been discussed by Liu, Harding et al. (2000), p. 135. According to this study, Papua New Guineans continued to be exposed to selection for dark skin color so that, although these groups are distinct from Africans in other places, the allele for dark skin color shared by contemporary Africans, Andamanese and New Guineans is an archaism. Endicott et al. (2003) suggest convergent evolution. A 2014 study by Gurdasani et al. indicate that higher genetic diversity in Africa was caused by relatively recent Eurasian migrations into Africa.

Pathogen DNA

Another promising route towards reconstructing human genetic genealogy is via the JC virus (JCV), a type of human polyomavirus which is carried by 70–90 percent of humans and which is usually transmitted vertically, from parents to offspring, suggesting codivergence with human populations. For this reason, JCV has been used as a genetic marker for human evolution and migration. This method does not appear to be reliable for the migration out of Africa, in contrast to human genetics, JCV strains associated with African populations are not basal. From this Shackelton et al. (2006) conclude that either a basal African strain of JCV has become extinct or that the original infection with JCV post-dates the migration from Africa.

Admixture of archaic and modern humans

Evidence for archaic human species (descended from Homo heidelbergensis) having interbred with modern humans outside of Africa, was discovered in the 2010s. This concerns primarily Neanderthal admixture in all modern populations except for Sub-Saharan Africans but evidence has also been presented for Denisova hominin admixture in Australasia (i.e. in Melanesians, Aboriginal Australians and some Negritos).

The rate of admixture of Neanderthal admixture to European and Asian populations as of 2017 has been estimated at between about 2–3%.

Archaic admixture in some Sub-Saharan African populations hunter-gatherer groups (Biaka Pygmies and San), derived from archaic hominins that broke away from the modern human lineage around 700,000 years, was discovered in 2011. The rate of admixture was estimated at around 2%. Admixture from archaic hominins of still earlier divergence times, estimated at 1.2 to 1.3 million years ago, was found in Pygmies, Hadza and five Sandawe in 2012. From an analysis of Mucin 7, a highly divergent haplotype that has an estimated coalescence time with other variants around 4.5 million years BP and is specific to African populations is inferred to have been derived from interbreeding between African modern and archaic humans.

Stone tools

In addition to genetic analysis, Petraglia et al. also examines the small stone tools (microlithic materials) from the Indian subcontinent and explains the expansion of population based on the reconstruction of paleoenvironment. He proposed that the stone tools could be dated to 35 ka in South Asia, and the new technology might be influenced by environmental change and population pressure.

History of the theory

Classical paleoanthropology

The frontispiece to Huxley's Evidence as to Man's Place in Nature (1863): the image compares the skeleton of a human to other apes.
 
The cladistic relationship of humans with the African apes was suggested by Charles Darwin after studying the behaviour of African apes, one of which was displayed at the London Zoo. The anatomist Thomas Huxley had also supported the hypothesis and suggested that African apes have a close evolutionary relationship with humans. These views were opposed by the German biologist Ernst Haeckel, who was a proponent of the Out of Asia theory. Haeckel argued that humans were more closely related to the primates of South-east Asia and rejected Darwin's African hypothesis.

In the Descent of Man, Darwin speculated that humans had descended from apes, which still had small brains but walked upright, freeing their hands for uses which favoured intelligence; he thought such apes were African:
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.
— Charles Darwin, Descent of Man
In 1871 there were hardly any human fossils of ancient hominins available. Almost fifty years later, Darwin's speculation was supported when anthropologists began finding fossils of ancient small-brained hominins in several areas of Africa (list of hominina fossils). The hypothesis of recent (as opposed to archaic) African origin developed in the 20th century. The "Recent African origin" of modern humans means "single origin" (monogenism) and has been used in various contexts as an antonym to polygenism. The debate in anthropology had swung in favour of monogenism by the mid-20th century. Isolated proponents of polygenism held forth in the mid-20th century, such as Carleton Coon, who thought as late as 1962 that H. sapiens arose five times from H. erectus in five places.

Multiregional origin hypothesis

The historical alternative to the recent origin model is the multiregional origin of modern humans, initially proposed by Milford Wolpoff in the 1980s. This view proposes that the derivation of anatomically modern human populations from H. erectus at the beginning of the Pleistocene 1.8 million years BP, has taken place within a continuous world population. The hypothesis necessarily rejects the assumption of an infertility barrier between ancient Eurasian and African populations of Homo. The hypothesis was controversially debated during the late 1980s and the 1990s. The now-current terminology of "recent-origin" and "Out of Africa" became current in the context of this debate in the 1990s. Originally seen as an antithetical alternative to the recent origin model, the multiregional hypothesis in its original "strong" form is obsolete, while its various modified weaker variants have become variants of a view of "recent origin" combined with archaic admixture. Stringer (2014) distinguishes the original or "classic" Multiregional model as having existed from 1984 (its formulation) until 2003, to a "weak" post-2003 variant that has "shifted close to that of the Assimilation Model".

Genetics

In the 1980s, Allan Wilson together with Rebecca L. Cann and Mark Stoneking worked on genetic dating of the matrilineal most recent common ancestor of modern human populations (dubbed "Mitochondrial Eve"). To identify informative genetic markers for tracking human evolutionary history, Wilson concentrated on mitochondrial DNA (mtDNA), passed from mother to child. This DNA material mutates quickly, making it easy to plot changes over relatively short times. With his discovery that human mtDNA is genetically much less diverse than chimpanzee mtDNA, Wilson concluded that modern human populations had diverged recently from a single population while older human species such as Neanderthals and Homo erectus had become extinct. With the advent of archaeogenetics in the 1990s, the dating of mitochondrial and Y-chromosomal haplogroups became possible with some confidence. By 1999, estimates ranged around 150,000 years for the mt-MRCA and 60,000 to 70,000 years for the migration out of Africa.

From 2000–2003, there was controversy about the mitochondrial DNA of "Mungo Man 3" (LM3) and its possible bearing on the multiregional hypothesis. LM3 was found to have more than the expected number of sequence differences when compared to modern human DNA (CRS). Comparison of the mitochondrial DNA with that of ancient and modern aborigines, led to the conclusion that Mungo Man fell outside the range of genetic variation seen in Aboriginal Australians and was used to support the multiregional origin hypothesis. A reanalysis on LM3 and other ancient specimens from the area published in 2016, showed it to be akin to modern Aboriginal Australian sequences, inconsistent with the results of the earlier study.

Y-chromosomal Adam

From Wikipedia, the free encyclopedia

In human genetics, the Y-chromosomal most recent common ancestor (Y-MRCA, informally known as Y-chromosomal Adam) is the most recent common ancestor (MRCA) from whom all currently living men are descended patrilineally. The term Y-MRCA reflects the fact that the Y chromosomes of all currently living human males are directly derived from the Y chromosome of this remote ancestor. The analogous concept of the matrilineal most recent common ancestor is known as "Mitochondrial Eve" (mt-MRCA, named for the matrilineal transmission of mtDNA), the most recent woman from whom all living humans are descended matrilineally. As with "Mitochondrial Eve", the title of "Y-chromosomal Adam" is not permanently fixed to a single individual, but can advance over the course of human history as paternal lineages become extinct.

Estimates of the time when Y-MRCA lived have also shifted as modern knowledge of human ancestry changes. In 2013, the discovery of a previously unknown Y-chromosomal haplogroup was announced, which resulted in a slight adjustment of the estimated age of the human Y-MRCA.

By definition, it is not necessary that the Y-MRCA and the mt-MRCA should have lived at the same time. While estimates as of 2014 suggested the possibility that the two individuals may well have been roughly contemporaneous (albeit with uncertainties ranging in the tens of thousands of years), the discovery of archaic Y-haplogroup has pushed back the estimated age of the Y-MRCA beyond the most likely age of the mt-MRCA. As of 2015, estimates of the age of the Y-MRCA range around 200,000 to 300,000 years ago, roughly consistent with the emergence of anatomically modern humans.

Y-chromosomal data taken from a Neanderthal from El Sidrón, Spain, produced a Y-T-MRCA of 588,000 years ago for neanderthal and Homo sapiens patrilineages, dubbed ante Adam and 275,000 years ago for Y-MRCA.

Definition

The Y-chromosomal most recent common ancestor is the most recent common ancestor of the Y-chromosomes found in currently living human males. 

Due to the definition via the "currently living" population, the identity of a MRCA, and by extension of the human Y-MRCA, is time-dependent (it depends on the moment in time intended by the term "currently"). The MRCA of a population may move forward in time as archaic lineages within the population go extinct: once a lineage has died out, it is irretrievably lost. This mechanism can thus only shift the title of Y-MRCA forward in time. Such an event could be due to the total extinction of several basal haplogroups. The same holds for the concepts of matrilineal and patrilineal MRCAs: it follows from the definition of Y-MRCA that he had at least two sons who both have unbroken lineages that have survived to the present day. If the lineages of all but one of those sons die out, then the title of Y-MRCA shifts forward from the remaining son through his patrilineal descendants, until the first descendant is reached who had at least two sons who both have living, patrilineal descendants. The title of Y-MRCA is not permanently fixed to a single individual, and the Y-MRCA for any given population would himself have been part of a population which had its own, more remote, Y-MRCA.

Although the informal name "Y-chromosomal Adam" is a reference to the biblical Adam, this should not be misconstrued as implying that the bearer of the chromosome was the only human male alive during his time. His other male contemporaries may also have descendants alive today, but not, by definition, through solely patrilineal descent; in other words, none of them have an unbroken male line of descendants (son's son's son's … son) connecting them to currently living people.

By the nature of the concept of most recent common ancestors, these estimates can only represent a terminus ante quem ("limit before which"), until the genome of the entire population has been examined (in this case, the genome of all living humans).

Age estimate

Estimates on the age of the Y-MRCA crucially depend on the most archaic known haplogroup extant in contemporary populations. As of 2018, this is haplogroup A00 (discovered in 2013). Age estimates based on this published during 2014–2015 range between 160,000 and 300,000 years, compatible with the time of emergence and early dispersal of Homo sapiens.

Method

In addition to the tendency of the title of Y-MRCA to shift forward in time, the estimate of the Y-MRCA's DNA sequence, his position in the family tree, the time when he lived, and his place of origin, are all subject to future revisions. 

The following events would change the estimate of who the individual designated as Y-MRCA was:
  • Further sampling of Y chromosomes could uncover previously unknown divergent lineages. If this happens, Y-chromosome lineages would converge on an individual who lived further back in time.
  • The discovery of additional deep rooting mutations in known lineages could lead to a rearrangement of the family tree.
  • Revision of the Y-chromosome mutation rate (see below) can change the estimate of the time when he lived.
The time when Y-MRCA lived is determined by applying a molecular clock to human Y-chromosomes. In contrast to mitochondrial DNA (mtDNA), which has a short sequence of 16,000 base pairs, and mutates frequently, the Y chromosome is significantly longer at 60 million base pairs, and has a lower mutation rate. These features of the Y chromosome have slowed down the identification of its polymorphisms; as a consequence, they have reduced the accuracy of Y-chromosome mutation rate estimates.

Methods of estimating the age of the Y-MRCA for a population of human males whose Y-chromosomes have been sequenced are based on applying the theories of molecular evolution to the Y chromosome. Unlike the autosomes, the human Y-chromosome does not recombine often with the X chromosome during meiosis, but is usually transferred intact from father to son; however, it can recombine with the X chromosome in the pseudoautosomal regions at the ends of the Y chromosome. Mutations occur periodically within the Y chromosome, and these mutations are passed on to males in subsequent generations. 

These mutations can be used as markers to identify shared patrilineal relationships. Y chromosomes that share a specific mutation are referred to as haplogroups. Y chromosomes within a specific haplogroup are assumed to share a common patrilineal ancestor who was the first to carry the defining mutation. (This assumption could be mistaken, as it is possible for the same mutation to occur more than once.) A family tree of Y chromosomes can be constructed, with the mutations serving as branching points along lineages. The Y-MRCA is positioned at the root of the family tree, as the Y chromosomes of all living males are descended from his Y chromosome.

Researchers can reconstruct ancestral Y chromosome DNA sequences by reversing mutated DNA segments to their original condition. The most likely original or ancestral state of a DNA sequence is determined by comparing human DNA sequences with those of a closely related species, usually non-human primates such as chimpanzees and gorillas. By reversing known mutations in a Y-chromosome lineage, a hypothetical ancestral sequence for the MRCA, Y-chromosomal Adam, can be inferred. 

Determining the Y-MRCA's DNA sequence, and the time when he lived, involves identifying the human Y-chromosome lineages that are most divergent from each other—the lineages that share the fewest mutations with each other when compared to a non-human primate sequence in a phylogenetic tree. The common ancestor of the most divergent lineages is therefore the common ancestor of all lineages.

History of estimates

Early estimates of the age for the Y-MRCA published during the 1990s ranged between roughly 200 and 300 kya, Such estimates were later substantially revised downward, as in Thomson et al. 2000, which proposed an age of about 59,000. This date suggested that the Y-MRCA lived about 84,000 years after his female counterpart mt-MRCA (the matrilineal most recent common ancestor), who lived 150,000–200,000 years ago. This date also meant that Y-chromosomal Adam lived at a time very close to, and possibly after, the migration from Africa which is believed to have taken place 50,000–80,000 years ago. One explanation given for this discrepancy in the time depths of patrilineal vs. matrilineal lineages was that females have a better chance of reproducing than males due to the practice of polygyny. When a male individual has several wives, he has effectively prevented other males in the community from reproducing and passing on their Y chromosomes to subsequent generations. On the other hand, polygyny does not prevent most females in a community from passing on their mitochondrial DNA to subsequent generations. This differential reproductive success of males and females can lead to fewer male lineages relative to female lineages persisting into the future. These fewer male lineages are more sensitive to drift and would most likely coalesce on a more recent common ancestor. This would potentially explain the more recent dates associated with the Y-MRCA.

The "hyper-recent" estimate of significantly below 100 kya was again corrected upward in studies of the early 2010s, which ranged at about 120 kya to 160 kya. This revision was due to the discovery of additional mutations and the rearrangement of the backbone of the Y-chromosome phylogeny following the resequencing of Haplogroup A lineages. In 2013, Francalacci et al. reported the sequencing of male-specific single-nucleotide Y-chromosome polymorphisms (MSY-SNPs) from 1204 Sardinian men, which indicated an estimate of 180,000 to 200,000 years for the common origin of all humans through paternal lineage. or again as high as 180 to 200 kya. Also in 2013, Poznik et al. reported the Y-MRCA to have lived between 120,000 and 156,000 years ago, based on genome sequencing of 69 men from 9 different populations. In addition, the same study estimated the age of Mitochondrial Eve to about 99,000 and 148,000 years. As these ranges overlap for a time-range of 28,000 years (148 to 120 kya), the results of this study have been cast in terms of the possibility that "Genetic Adam and Eve may have walked on Earth at the same time" in the popular press.

The announcement of yet another discovery of a previously unknown lineage, haplogroup A00, in 2013, resulted in another shift in the estimate for the age of Y-chromosomal. Elhaik et al. (2014) dated it to between 163,900 and 260,200 years ago (95% CI). Karmin et al. (2015) dated it to between 192,000 and 307,000 years ago (95% CI). The same study reports that non-African populations converge to a cluster of Y-MRCAs in a window close to 50kya (out-of-Africa migration), and an additional bottleneck for non-African populations at about 10kya, interpreted as reflecting cultural changes increasing the variance in male reproductive success (i.e. increased social stratification) in the Neolithic.

Family tree

 
The revised root of the y-chromosome family tree by Cruciani et al. 2011 compared with the family tree from Karafet et al. 2008. This has been further expanded by the discoveries published by Mendez et al. in 2013.
 
Initial sequencing (Karafet et al., 2008) of the human Y chromosome suggested that two most basal Y-chromosome lineages were Haplogroup A and Haplogroup BT. Haplogroup A is found at low frequencies in parts of Africa, but is common among certain hunter-gatherer groups. Haplogroup BT lineages represent the majority of African Y-chromosome lineages and virtually all non-African lineages. Y-chromosomal Adam was represented as the root of these two lineages. Haplogroup A and Haplogroup BT represented the lineages of the two male descendants of Y-chromosomal Adam. 

Cruciani et al. 2011, determined that the deepest split in the Y-chromosome tree was found between two previously reported subclades of Haplogroup A, rather than between Haplogroup A and Haplogroup BT. Subclades A1b and A1a-T are now believed to descend directly from the root of the tree and now represent the lineages of Y-chromosomal Adam's two sons. The rearrangement of the Y-chromosome family tree implies that lineages classified as Haplogroup A do not necessarily form a monophyletic clade. Haplogroup A therefore refers to a collection of lineages that do not possess the markers that define Haplogroup BT, though Haplogroup A includes the most distantly related Y chromosomes. 

The M91 and P97 mutations distinguish Haplogroup A from Haplogroup BT. Within Haplogroup A chromosomes, the M91 marker consists of a stretch of 8 T nucleobase units. In Haplogroup BT and chimpanzee chromosomes, this marker consists of 9 T nucleobase units. This pattern suggested that the 9T stretch of Haplogroup BT was the ancestral version and that Haplogroup A was formed by the deletion of one nucleobase. Haplogroups A1b and A1a were considered subclades of Haplogroup A as they both possessed the M91 with 8Ts.

But according to Cruciani et al. 2011, the region surrounding the M91 marker is a mutational hotspot prone to recurrent mutations. It is therefore possible that the 8T stretch of Haplogroup A may be the ancestral state of M91 and the 9T of Haplogroup BT may be the derived state that arose by an insertion of 1T. This would explain why subclades A1b and A1a-T, the deepest branches of Haplogroup A, both possess the same version of M91 with 8Ts. Furthermore, Cruciani et al. 2011 determined that the P97 marker, which is also used to identify Haplogroup A, possessed the ancestral state in Haplogroup A but the derived state in Haplogroup BT.

Likely geographic origin

As current estimates on TMRCA converge with estimates for the age of anatomically modern humans and well predate the Out of Africa migration, geographical origin hypotheses continue to be limited to the African continent

According to Cruciani et al. 2011, the most basal lineages have been detected in West, Northwest and Central Africa, suggesting plausibility for the Y-MRCA living in the general region of "Central-Northwest Africa".

Scozzari et al. (2012) agreed with a plausible placement in "the north-western quadrant of the African continent" for the emergence of the A1b haplogroup. The 2013 report of haplogroup A00 found among the Mbo people of western present-day Cameroon is also compatible with this picture.

The revision of Y-chromosomal phylogeny since 2011 has affected estimates for the likely geographical origin of Y-MRCA as well as estimates on time depth. By the same reasoning, future discovery of presently-unknown archaic haplogroups in living people would again lead to such revisions. In particular, the possible presence of between 1% and 4% Neanderthal-derived DNA in Eurasian genomes implies that the (unlikely) event of a discovery of a single living Eurasian male exhibiting a Neanderthal patrilineal line would immediately push back T-MRCA ("time to MRCA") to at least twice its current estimate. However, the discovery of a neanderthal Y-chromosome by Mendez et al. suggests the extinction of neanderthal patrilineages, as the lineage inferred from the neanderthal sequence is outside of the range of contemporary human genetic variation. Questions of geographical origin would become part of the debate on Neanderthal evolution from Homo erectus.

Mitochondrial Eve

From Wikipedia, the free encyclopedia

Haplogroup L
Early diversification.PNG
Possible time of originc. 100–230 kya
Possible place of originEast Africa
Ancestorn/a
DescendantsMitochondrial macro-haplogroups L0, L1, and L5
Defining mutationsNone

In human genetics, the Mitochondrial Eve (also mt-Eve, mt-MRCA) is the matrilineal most recent common ancestor (MRCA) of all currently living humans, i.e., the most recent woman from whom all living humans descend in an unbroken line purely through their mothers, and through the mothers of those mothers, back until all lines converge on one woman.

In terms of mitochondrial haplogroups, the mt-MRCA is situated at the divergence of macro-haplogroup L into L0 and L1–6. As of 2013, estimates on the age of this split ranged at around 150,000 years ago, consistent with a date later than the speciation of Homo sapiens but earlier than the recent out-of-Africa dispersal.

The male analog to the "Mitochondrial Eve" is the "Y-chromosomal Adam" (or Y-MRCA), the individual from whom all living humans are patrilineally descended. As the identity of both matrilineal and patrilineal MRCAs is dependent on genealogical history (pedigree collapse), they need not have lived at the same time. As of 2013, estimates for the age Y-MRCA are subject to substantial uncertainty, with a wide range of times from 180,000 to 580,000 years ago (with an estimated age of between 120,000 and 156,000 years ago, roughly consistent with the estimate for mt-MRCA.).

The name "Mitochondrial Eve" alludes to biblical Eve. This led to repeated misrepresentations or misconceptions in journalistic accounts on the topic. Popular science presentations of the topic usually point out such possible misconceptions by emphasizing the fact that the position of mt-MRCA is neither fixed in time (as the position of mt-MRCA moves forward in time as mitochondrial DNA (mtDNA) lineages become extinct), nor does it refer to a "first woman", nor the only living female of her time, nor the first member of a "new species".

History

Early research

Early research using molecular clock methods was done during the late 1970s to early 1980s. Allan Wilson, Mark Stoneking, Rebecca L. Cann and Wesley M. Brown found that mutation in human mtDNA was unexpectedly fast, at 0.02 substitution per base (1%) in a million years, which is 5–10 times faster than in nuclear DNA. Related work allowed for an analysis of the evolutionary relationships among gorillas, chimpanzees (common chimpanzee and bonobo) and humans. With data from 21 human individuals, Brown published the first estimate on the age of the mt-MRCA at 180,000 years ago in 1980. A statistical analysis published in 1982 was taken as evidence for recent African origin (a hypothesis which at the time was competing with Asian origin of H. sapiens).

1987 publication

By 1985, data from the mtDNA of 145 women of different populations, and of two cell lines, HeLa and GM 3043, derived from a Black American and a !Kung respectively, was available. After more than 40 revisions of the draft, the manuscript was submitted to Nature in late 1985 or early 1986 and published on 1 January 1987. The published conclusion was that all current human mtDNA originated from a single population from Africa, at the time dated to between 140,000 and 200,000 years ago.

The dating for "Eve" was a blow to the multiregional hypothesis, which was being controversially discussed at the time, and a boost to the theory of the recent origin model.

Cann, Stoneking and Wilson did not use the term "Mitochondrial Eve" or even the name "Eve" in their original paper; it appears to originate with a 1987 article in Science by Roger Lewin, headlined "The Unmasking of Mitochondrial Eve." The biblical connotation was very clear from the start. The accompanying research news in Nature had the title "Out of the garden of Eden." Wilson himself preferred the term "Lucky Mother"  and thought the use of the name Eve "regrettable." But the concept of Eve caught on with the public and was repeated in a Newsweek cover story (11 January 1988 issue featured a depiction of Adam and Eve on the cover, with the title "The Search for Adam and Eve"), and a cover story in Time on 26 January 1987.

Criticism and later research

Shortly after the 1987 publication, criticism of its methodology and secondary conclusions was published. Both the dating of mt-Eve and the relevance of the age of the purely matrilineal descent for population replacement was controversially discussed during the 1990s; Alan Templeton (1997) asserted that the study did "not support the hypothesis of a recent African origin for all of humanity following a split between Africans and non-Africans 100,000 years ago" and also did "not support the hypothesis of a recent global replacement of humans coming out of Africa."

Cann, Stoneking & Wilson (1987)'s placement of a relatively small population of humans in sub-Saharan Africa was consistent with the hypothesis of Cann (1982) and lent considerable support for the "recent out-of-Africa" scenario. 

In 1999 Krings et al. eliminated problems in molecular clocking postulated by Nei (1992)[citation needed] when it was found that the mtDNA sequence for the same region was substantially different from the MRCA relative to any human sequence.

Although the original research did have analytical limitations, the estimate on the age of the mt-MRCA has proven robust. More recent age estimates have remained consistent with the 140–200 kya estimate published in 1987: A 2013 estimate dated Mitochondrial Eve to about 160 kya (within the reserved estimate of the original research) and Out of Africa II to about 95 kya. Another 2013 study (based on genome sequencing of 69 people from 9 different populations) reported the age of Mitochondrial Eve between 99 to 148 kya and that of the Y-MRCA between 120 and 156 kya.

Female and mitochondrial ancestry

Through random drift or selection the female-lineage will trace back to a single female, such as Mitochondrial Eve. In this example over five generations colors represent extinct matrilineal lines and black the matrilineal line descended from mtDNA MRCA.
 
Without a DNA sample, it is not possible to reconstruct the complete genetic makeup (genome) of any individual who died very long ago. By analysing descendants' DNA, however, parts of ancestral genomes are estimated by scientists. Mitochondrial DNA (mtDNA) and Y-chromosome DNA are commonly used to trace ancestry in this manner. mtDNA is generally passed un-mixed from mothers to children of both sexes, along the maternal line, or matrilineally. Matrilineal descent goes back to our mothers, to their mothers, until all female lineages converge. 

Branches are identified by one or more unique markers which give a mitochondrial "DNA signature" or "haplotype" (e.g. the CRS is a haplotype). Each marker is a DNA base-pair that has resulted from an SNP mutation. Scientists sort mitochondrial DNA results into more or less related groups, with more or less recent common ancestors. This leads to the construction of a DNA family tree where the branches are in biological terms clades, and the common ancestors such as Mitochondrial Eve sit at branching points in this tree. Major branches are said to define a haplogroup (e.g. CRS belongs to haplogroup H), and large branches containing several haplogroups are called "macro-haplogroups".

Simplified Human mitochondrial phylogeny
 
The mitochondrial clade which Mitochondrial Eve defines is the species Homo sapiens sapiens itself, or at least the current population or "chronospecies" as it exists today. In principle, earlier Eves can also be defined going beyond the species, for example one who is ancestral to both modern humanity and Neanderthals, or, further back, an "Eve" ancestral to all members of genus Homo and chimpanzees in genus Pan. According to current nomenclature, Mitochondrial Eve's haplogroup was within mitochondrial haplogroup L because this macro-haplogroup contains all surviving human mitochondrial lineages today, and she must predate the emergence of L0.

The variation of mitochondrial DNA between different people can be used to estimate the time back to a common ancestor, such as Mitochondrial Eve. This works because, along any particular line of descent, mitochondrial DNA accumulates mutations at the rate of approximately one every 3,500 years per nucleotide. A certain number of these new variants will survive into modern times and be identifiable as distinct lineages. At the same time some branches, including even very old ones, come to an end, when the last family in a distinct branch has no daughters. 

Mitochondrial Eve is the most recent common matrilineal ancestor for all modern humans. Whenever one of the two most ancient branch lines dies out, the MRCA will move to a more recent female ancestor, always the most recent mother to have more than one daughter with living maternal line descendants alive today. The number of mutations that can be found distinguishing modern people is determined by two criteria: firstly and most obviously, the time back to her, but secondly and less obviously by the varying rates at which new branches have come into existence and old branches have become extinct. By looking at the number of mutations which have been accumulated in different branches of this family tree, and looking at which geographical regions have the widest range of least related branches, the region where Eve lived can be proposed.

Popular reception and misconceptions

Newsweek reported on Mitochondrial Eve based on the Cann et al. study in January 1988, under a heading of "Scientists Explore a Controversial Theory About Man's Origins". The edition sold a record number of copies.

The popular name "mitochondrial Eve", of 1980s coinage, has contributed to a number of popular misconceptions. At first, the announcement of a "mitochondrial Eve" was even greeted with endorsement from young earth creationists, who viewed the theory as a validation of the biblical creation story.

Due to such misunderstandings, authors of popular science publications since the 1990s have been emphatic in pointing out that the name is merely a popular convention, and that the mt-MRCA was not in any way the "first woman". Her position is purely the result of genealogical history of human populations later, and as matrilineal lineages die out, the position of mt-MRCA keeps moving forward to younger individuals over time. 

In River Out of Eden (1995), Richard Dawkins discussed human ancestry in the context of a "river of genes", including an explanation of the concept of Mitochondrial Eve. The Seven Daughters of Eve (2002) presented the topic of human mitochondrial genetics to a general audience. The Real Eve: Modern Man's Journey Out of Africa" by Stephen Oppenheimer (2003) was adapted into a Discovery Channel documentary.

Not the only woman

One common misconception surrounding mitochondrial Eve is that since all women alive today descended in a direct unbroken female line from her, she must have been the only woman alive at the time. However, nuclear DNA studies indicate that the size of the ancient human population never dropped below tens of thousands. Other women living during Eve's time may have descendants alive today but not in a direct female line.

Not a fixed individual over time

The definition of mitochondrial Eve is fixed, but the woman in prehistory who fits this definition can change. That is, not only can our knowledge of when and where Mitochondrial Eve lived change due to new discoveries, but the actual mitochondrial Eve can change. The mitochondrial Eve can change, when a mother-daughter line comes to an end. It follows from the definition of Mitochondrial Eve that she had at least two daughters who both have unbroken female lineages that have survived to the present day. In every generation mitochondrial lineages end – when a woman with unique mtDNA dies with no daughters. When the mitochondrial lineages of daughters of mitochondrial Eve die out, then the title of "Mitochondrial Eve" shifts forward from the remaining daughter through her matrilineal descendants, until the first descendant is reached who had two or more daughters who together have all living humans as their matrilineal descendants. Once a lineage has died out it is irretrievably lost and this mechanism can thus only shift the title of "Mitochondrial Eve" forward in time. 

Because mtDNA mapping of humans is very incomplete, the discovery of living mtDNA lines which predate our current concept of "Mitochondrial Eve" could result in the title moving to an earlier woman. This happened to her male counterpart, "Y-chromosomal Adam," when older Y lines from Africa were discovered.

Not necessarily a contemporary of "Y-chromosomal Adam"

Sometimes mitochondrial Eve is assumed to have lived at the same time as Y-chromosomal Adam (from whom all living people are descended patrilineally), and perhaps even met and mated with him. Even if this were true, which is currently regarded as highly unlikely, this would only be a coincidence. Like mitochondrial "Eve", Y-chromosomal "Adam" probably lived in Africa. A recent study (March 2013) concluded however that "Eve" lived much later than "Adam" – some 140,000 years later. (Earlier studies considered, conversely, that "Eve" lived earlier than "Adam".) More recent studies indicate that mitochondrial Eve and Y-chromosomal Adam may indeed have lived around the same time.

Not the most recent ancestor shared by all humans

Mitochondrial Eve is the most recent common matrilineal ancestor, not the most recent common ancestor. Since the mtDNA is inherited maternally and recombination is either rare or absent, it is relatively easy to track the ancestry of the lineages back to a MRCA; however, this MRCA is valid only when discussing mitochondrial DNA. An approximate sequence from newest to oldest can list various important points in the ancestry of modern human populations:
  • The human MRCA. Monte Carlo simulations suggest the MRCA was born surprisingly recently, perhaps even within the last 5,000 years, even for people born on different continents.
  • The identical ancestors point. Just a few thousand years before the most recent single ancestor shared by all living humans was the time at which all humans who were then alive either left no descendants alive today or were common ancestors of all humans alive today. In other words, "each present-day human has exactly the same set of genealogical ancestors" alive at the "identical ancestors point" in time. This is far more recent than when Mitochondrial Eve lived.
  • Mitochondrial Eve, the most recent female-line common ancestor of all living people.
  • "Y-chromosomal Adam", the most recent male-line common ancestor of all living people.

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