Y-chromosomal Adam

In human genetics, Y-chromosomal most recent common ancestor (YMRCA; informally also known as Y-chromosomal Adam) refers to the most recent common ancestor (MRCA) from whom all currently living people are descended patrilineally. The term YMRCA reflects the fact that the Y chromosomes of all currently living 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" (mtMRCA, named for the matrilineal transmission of mtDNA), the most recent woman from whom all living humans are descended matrilineally.

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). In 2013, the discovery of a previously unknown Y-chromosomal haplogroup was announced,[1] which resulted in a slight adjustment of the estimated age of the human YMRCA.[2]

Current estimates of the Y-TMRCA (time to most recent common male ancestor) range around 200,000 to 300,000 years ago, consistent with the emergence of anatomically modern humans and overlapping with age estimates for the mtMRCA (matrilinear MRCA).[3]

By definition, it is not necessary that the YMRCA and the mtMRCA should have lived at the same time,[4][5] even though current (as of 2014) estimates suggest the possibility that the two individuals may well have been roughly contemporaneous (albeit with uncertainties ranging in the tens of thousands of years).[6]

Y-chromosomal data taken from a neanderthal from El Sidrón, Spain produced a Y-TMRCA of 588ka for neanderthal and Homo sapiens patrilineages, dubbed ante Adam. [7]

Definition

Main article: MRCA

The existence of a YMRCA for any given human population is a consequence of the fact that every human being has a biological father, and that every human male inherits his Y chromosome from his biological father. We assume quite reasonably that every man inherited his Y chromosome from some common ancestor (say, the first creature to have a Y chromosome). So there had to be a male who was the last one from whom all men inherit their Y chromosome. (It is not a logical necessity that that male was a Homo sapiens however.)

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.[8] His other male contemporaries also have descendants alive today, but not, by definition, through solely patrilineal descent.

Due to the definition via the "currently living" population, the identity of a MRCA, and by extension of the human YMRCA, 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 YMRCA forward in time. Such an event could be due to the total extinction of several basal haplogroups.[4] The same holds for the concepts of matrilineal and patrilineal MRCAs: it follows from the definition of YMRCA 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 YMRCA 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 YMRCA is not permanently fixed to a single individual, and the YMRCA for any given population would himself have been part of a population which had its own, more remote, YMRCA.

Age estimate

In addition to the tendency of the title of YMRCA to shift forward in time, the estimate of the YMRCA'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 YMRCA was:

Method

The time when YMRCA lived is determined by applying a molecular clock to human Y-chromosomes. In contrast to mitochondrial DNA, 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.[9]

Methods of estimating the age of the YMRCA 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 YMRCA 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 YMRCA'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.

Estimates

Current (as of 2015) estimates for the age for the YMRCA are roughly compatible with the estimate for the emergence of anatomically modern humans some 200,000 years ago (200 kya), although there are substantial uncertainties.

Early estimates published during the 1990s ranged between roughly 200 and 300 kya,[10] Such estimates were later substantially corrected downward, as in Thomson et al. 2000,[9] which proposed an age of about 59,000. This date suggested that the YMRCA lived about 84,000 years after his female counterpart mtMRCA (the matrilineal most recent common ancestor), who lived 150,000–200,000 years ago.[11] 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 YMRCA.[12][13]

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.[14] 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.[15] or again as high as 180 to 200 kya.[16] Also in 2013, Poznik et al. reported the YMRCA 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.[17] 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.[6][18]

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. 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 YMRCAs 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.[3]

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.[19] 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.[20] 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.[19][20]

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.[20]

Likely geographic origin

Further information: Haplogroup A (Y-DNA)

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 YMRCA living in the general region of "Central-Northwest Africa".[21]

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. [22] The 2013 report of haplogroup A00 found among the Mbo people of western present-day Cameroon is also compatible with this picture.[1]

The revision of Y-chromosomal phylogeny since 2011 has affected estimates for the likely geographical origin of YMRCA 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 TMRCA ("time to MRCA") to at least twice its current estimate. However, the discovery of a neanderthal Y-chromosome by Mendez et al. [7] 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.

See also

References

  1. 1 2 Mendez, Fernando; Krahn, Thomas; Schrack, Bonnie; Krahn, Astrid-Maria; Veeramah, Krishna; Woerner, August; Fomine, Forka Leypey Mathew; Bradman, Neil; Thomas, Mark; Karafet, Tatiana M.; Hammer, Michael F. (7 March 2013). "An African American paternal lineage adds an extremely ancient root to the human Y chromosome phylogenetic tree" (PDF). American Journal of Human Genetics 92 (3): 454–9. doi:10.1016/j.ajhg.2013.02.002. PMC 3591855. PMID 23453668. (primary source)
  2. ↑ "The 'extremely ancient' chromosome that isn't: a forensic bioinformatic investigation of Albert Perry's X-degenerate portion of the Y chromosome". EJHG 22 (9): 1111–6. 2014. doi:10.1038/ejhg.2013.303. PMID 24448544. 'Y-Chromosomal Adam Lived 208,300 Years Ago, Says New Study', Sci-News.com, 23 January 2014.
  3. 1 2 Karmin et al., "A recent bottleneck of Y chromosome diversity coincides with a global change in culture", Genome Research (2015), doi:10.1101/gr.186684.114. "we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192–307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47–52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males."
  4. 1 2 Dawkins (2005-09-02). The Ancestor's Tale. ISBN 9780618619160.
  5. ↑ Blaine Bettinger (20 July 2007). "Mitochondrial Eve and Y-chromosomal Adam". The Genetic Genealogist.
  6. 1 2 Cann RL (2013). "Genetics. Y weigh in again on modern humans". Science 341 (6145): 465–467. doi:10.1126/science.1242899. PMID 23908212.
  7. 1 2 Mendez L. et al., "The Divergence of Neandertal and Modern Human Y Chromosomes", The American Journal of Human Genetics (2016), Volume 98, Issue 4, 728 - 734 (http://dx.doi.org/10.1016/j.ajhg.2016.02.023).
  8. ↑ Takahata, N (January 1993). "Allelic genealogy and human evolution". Mol. Biol. Evol. 10 (1): 2–22. PMID 8450756.
  9. 1 2 Thomson, J.; et al. (2000). "Recent common ancestry of human Y chromosomes: Evidence from DNA sequence data". PNAS 97 (13): 6927–9. doi:10.1073/pnas.97.13.6927. PMC 34361. PMID 10860948.
  10. ↑ Hammer MF (1995). "A recent common ancestry for human Y chromosomes". Nature 378 (6555): 376–378. doi:10.1038/378376a0. PMID 7477371. Dorit RL, Akashi H, Gilbert W (1995). "Absence of polymorphism at the ZFY locus on the human Y chromosome". Science 268 (5214): 1183–1185. doi:10.1126/science.7761836. PMID 7761836. Huang W, Fu YX, Chang BH, Gu X, Jorde LB, Li WH (1998). "Sequence variation in ZFX introns in human populations". Mol Biol Evol 15 (2): 138–142. doi:10.1093/oxfordjournals.molbev.a025910. PMID 9491612.
  11. ↑ "Genetic 'Adam never met Eve'". BBC News. 2000-10-30. Retrieved 2013-03-08.
  12. ↑ Stone; et al. (2007). "Fundamentals of Human Evolution". Genes, Culture and Human Evolution. ISBN 1-4051-3166-7.
  13. ↑ Cavalli-Sforza, Luigi Luca (2007). "Human Evolution and Its Relevance for Genetic Epidemiology" (PDF). Annual Review of Genomics and Human Genetics 8: 1–15. doi:10.1146/annurev.genom.8.080706.092403. PMID 17408354.
  14. ↑ Cruciani, Fulvio; Trombetta, Beniamino; Massaia, Andrea; Destro-Bisol, Giovanni; Sellitto, Daniele; Scozzari, Rosaria (2011). "A Revised Root for the Human Y Chromosomal Phylogenetic Tree: The Origin of Patrilineal Diversity in Africa". The American Journal of Human Genetics 88 (6): 814–8. doi:10.1016/j.ajhg.2011.05.002. PMC 3113241. PMID 21601174.
  15. ↑ Francalacci P, Morelli L, Angius A, Berutti R, Reinier F, Atzeni R, Pilu R, Busonero F, Maschio A, Zara I, Sanna D, Useli A, Urru MF, Marcelli M, Cusano R, Oppo M, Zoledziewska M, Pitzalis M, Deidda F, Porcu E, Poddie F, Kang HM, Lyons R, Tarrier B, Gresham JB, Li B, Tofanelli S, Alonso S, Dei M, Lai S, Mulas A, Whalen MB, Uzzau S, Jones C, Schlessinger D, Abecasis GR, Sanna S, Sidore C, Cucca F (2013). "Low-pass DNA sequencing of 1200 Sardinians reconstructs European Y-chromosome phylogeny". Science 341 (6145): 565–569. doi:10.1126/science.1237947. PMID 23908240.
  16. ↑ Poznik GD, Henn BM, Yee MC, Sliwerska E, Euskirchen GM, Lin AA, Snyder M, Quintana-Murci L, Kidd JM, Underhill PA, Bustamante CD (2013). "Sequencing Y chromosomes resolves discrepancy in time to common ancestor of males versus females". Science 341 (6145): 562–565. doi:10.1126/science.1237619. PMID 23908239.
  17. ↑ University of Michigan Health System (1 August 2013). "The when and where of the Y: Research on Y chromosomes uncovers new clues about human ancestry". ScienceDaily. Retrieved 10 August 2013.
  18. ↑ Rathi A (2 August 2013). Genetic Adam and Eve may have walked on Earth at the same time "Genetic Adam and Eve may have walked on Earth at the same time" Check |url= value (help). ars technica. Condé Nast. Retrieved 10 August 2013.
  19. 1 2 Karafet TM, Mendez FL, Meilerman MB, Underhill PA, Zegura SL, Hammer MF (2008). "New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree". Genome Research 18 (5): 830–8. doi:10.1101/gr.7172008. PMC 2336805. PMID 18385274.
  20. 1 2 3 Fulvio Cruciani, Beniamino Trombetta, Andrea Massaia, Giovanni Destro-Biso, Daniele Sellitto y Rosaria Scozzari 2011, A Revised Root for the human Y-chromosomal Phylogenetic Tree: The Origin of Patrilineal Diversity in Africa
  21. ↑ In a sample of 2204 African Y-chromosomes, 8 chromosomes belonged to either haplogroup A1b or A1a. Haplogroup A1a was identified in two Moroccan Berbers, one Fulbe, and one Tuareg person from Niger. Haplogroup A1b was identified in three Bakola pygmies from Southern Cameroon and one Algerian Berber. Cruciani et al. 2011
  22. ↑ "the hypothesis of an origin in the north-western quadrant of the African continent for the A1b haplogroup, and, together with recent findings of ancient Y-lineages in central-western Africa, provide new evidence regarding the geographical origin of human MSY diversity". Scozzari R; Massaia A; D'Atanasio E; Myres NM; Perego UA; et al. (2012). Caramelli, David, ed. "Molecular Dissection of the Basal Clades in the Human Y Chromosome Phylogenetic Tree". PLoS ONE 7 (11): e49170. doi:10.1371/journal.pone.0049170. PMC 3492319. PMID 23145109.

Further reading

External links

Wikimedia Commons has media related to Y-chromosomal Adam.
Evolutionary tree of human Y-chromosome DNA haplogroups [χ 1][χ 2]
"Y-chromosomal Adam"
A00 A0-T [χ 3]
A0 A1[χ 4]
A1a A1b
A1b1 BT
B CT
DE CF
D E C F
F1 F2 F3 GHIJK
G HIJK
H IJK
IJ K
I J LT [χ 5]  K2
L T NO [χ 6] K2b [χ 7]   K2c K2d K2e [χ 8]
N O K2b1 [χ 9]    P
M S [χ 10] Q R
  1. ↑ Van Oven M, Van Geystelen A, Kayser M, Decorte R, Larmuseau HD (2014). "Seeing the wood for the trees: a minimal reference phylogeny for the human Y chromosome". Human Mutation 35 (2): 187–91. doi:10.1002/humu.22468. PMID 24166809.
  2. ↑ International Society of Genetic Genealogy (ISOGG; 2015), Y-DNA Haplogroup Tree 2015. (Access date: 1 February 2015.)
  3. ↑ Haplogroup A0-T is also known as A0'1'2'3'4.
  4. ↑ Haplogroup A1 is also known as A1'2'3'4.
  5. ↑ Haplogroup LT (L298/P326) is also known as Haplogroup K1.
  6. ↑ Haplogroup NO (M214) is also known as Haplogroup K2a (although the present Haplogroup K2e was also previously known as "K2a").
  7. ↑ Haplogroup K2b (M1221/P331/PF5911) is also known as Haplogroup MPS.
  8. ↑ Haplogroup K2e (K-M147) was previously known as "Haplogroup X" and "K2a" (but is a sibling subclade of the present K2a, also known as Haplogroup NO).
  9. ↑ Haplogroup K2b1 (P397/P399) is similar to the former Haplogroup MS, but has a broader and more complex internal structure.
  10. ↑ Haplogroup S (S-M230) was previously known as Haplogroup K5.
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