Y-chromosomal Adam

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Y chromosome phylogenetic tree with major branches represented by Y-DNA haplogroups (obsolete)

In human genetics, Y-chromosomal Adam (Y-MRCA) is an informal name given to the most recent common ancestor (MRCA) from whom all currently living people are descended patrilineally (tracing back only along the paternal or male lines of their family tree). However, the title is not permanently fixed on a single individual (see below).

Y-chromosomal Adam is named after the biblical Adam, but the bearer of the chromosome was not the only human male alive during his time.[1] His other male contemporaries also have descendants alive today, but not, by definition, through solely patrilineal descent.

The age for the Y-MRCA has been variously estimated as 188,000,[2] 270,000,[3] 306,000,[4] and 142,000 years.[5] A paper published in March 2013 reported an older estimate of 338,000 years.[6] Then two simultaneous reports in August 2013 provide younger estimates, one suggested 180,000 to 200,000 years,[7] and another, based on the genome sequence of nine different populations, indicated the age between 120,000 and 156,000 years.[8]

Analogous to Y-chromosomal Adam, Mitochondrial Eve is the woman from whom all living humans are descended matrilineally, who lived about 140,000 to 200,000 years ago in Africa. The estimate is based on inherited mtDNA through mothers. Theoretically, it is not necessary to believe that Y-chromosomal Adam and Mitochondrial Eve should have lived at the same time.[9][10] However, more recent findings (2013) suggest the possibility that the two individuals may well have been contemporaneous.[11]

Definition[edit]

The existence of a Y-chromosomal Adam was determined by 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. Y-chromosomal Adam 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 Y-chromosomal Adam'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.

The existence of Y-chromosomal Adam was confirmed by a worldwide sample[which?] of Y chromosomes that included persons from all continents. A number of Y-chromosome lineages, or haplogroups, from Africa were found to be the most divergent from each other, and non-African lineages were determined to be subsets of a few lineages found in Africa. This suggested that Africa was the most likely home of Y-chromosomal Adam.

Not a fixed individual[edit]

Different MRCAs (Most Recent Common Ancestor)

The title "Y-chromosomal Adam" is not permanently fixed on a single individual. It follows from the definition of Y-chromosomal Adam 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-chromosomal Adam" 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.

Once a lineage has died out it is irretrievably lost and this mechanism can thus only shift the title of "Y-chromosomal Adam" forward in time. Such an event could be due to the total extinction of several basal haplogroups.[9]

In addition to the ability of the title of Y-chromosomal Adam to shift forward in time, the estimate of Y-chromosomal Adam'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 Y-chromosomal Adam 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.

Family tree[edit]

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.[12] 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.

However, one paper[5] placed this event around 142,000 years ago (see below for subsequent findings). 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.[13] 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.[12][13]

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.[13]

Origin[edit]

Initial studies implicated East Africa and Southern Africa as the likely sources of human Y-chromosome diversity. This was because the basal lineages, Haplogroup A and Haplogroup B achieve their highest frequencies in these regions. But according to Cruciani et al. 2011, the most basal lineages have been detected in West, Northwest and Central Africa. 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 from Niger. Haplogroup A1b was identified in three Bakola pygmies from Southern Cameroon and one Algerian Berber. Cruciani et al. 2011 suggest a Y-chromosomal Adam, living somewhere in Central-Northwest Africa, fits well with the data.[13]

In November 2012, a study by Scozzari et al. reinforced "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".[14]

Divergences discovered in 2013 and nomenclature[edit]

A discovery published in March 2013 proposed that Haplogroup A1b be renamed Haplogroup A0 and announced an earlier divergence, which it dubbed Haplogroup A00.[15]

The discovery emerged after an African American man[6] submitted his DNA for commercial genealogical analysis by Family Tree DNA.[16] His Y-chromosome was quite different from all Y-chromosomes known at the time. A group led by Michael F. Hammer investigated. They named his haplogroup A00 (so named as it separated from other extant lineages prior to the renamed Haplogroup A0's separation), and later testing in Cameroon found this haplogroup also included a small number of Mbo males, though the first subject's Y-chromosome was the most genetically distinct in terms of number of mutations.[6] The age of Adam was estimated from the mutations within the Y-chromosome genome (based on known mutation rates), and was found to be in excess of the estimated age of the current Mitochondrial Eve and the oldest known fossils of anatomically modern humans.[6]

Two reports in August 2013 suggest much younger ages,[17] and in fact, suggest that both Y-chromosomal Adam and Mitochondrial Eve could have lived at the same time.[11] In one, Italian geneticists led by Paolo Francalacci from the Università di Sassari 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 human through paternal lineage.[7] In the other study, led by Stanford University School of Medicine geneticists 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, they estimated the age of Mitochondrial Eve to about 99,000 and 148,000 years.[8] This would imply that the discrepancies between the age of male and female MRCA are reconcilable.[18] However, these two studies did not take into consideration the recently discovered Haplogroup A00, which puts the "true Y-chromosome Adam" much further back in time.[17]

Time frame[edit]

The time when Y-chromosomal Adam 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 and as a consequence, reduced the accuracy of Y-chromosome mutation rate estimates.[19] Initial studies, such as Thomson et al. 2000,[19] proposed that Y-chromosomal Adam lived about 59,000 years ago. This date suggested that Y-chromosomal Adam lived about 84,000 after his female counterpart Mitochondrial Eve, who lived 150,000–200,000 years ago.[20] 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 dates of Adam and Eve 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 doesn't 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 Y-chromosomal Adam.[21][22]

The 2011 study by Cruciani et al. suggested that Y-chromosomal Adam lived about 142,000 years ago, significantly earlier than the 59,000 years ago estimate proposed by Thomson et al. 2000. The older TMRCA 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. According to the study, determining the precise date when Y-chromosomal Adam lived depends on the accuracy of the mutation rate used. But the repositioning of the MRCA from the root of Haplogroups A and BT to the root of Haplogroups A1b and A1a still entails that Y-chromosomal Adam is older than previously estimated. According to Cruciani et al., the much older date is easier to reconcile with models of human origins.[13]

A March 2013 paper claimeed that a previously unknown, very distinct Y chromosome from African-Americans had been found which pushed back further the estimated Y-MRCA to 338,000 years ago (237,000 to 581,000 years ago with 95% confidence).[6] The conclusion was contradicted[23] by a follow-up paper which argues that the statistical and analytical techniques employed were vitiated by methodological defects that produced an inflated back-dating for the lineage, which in the researchers' estimation averages out rather to 208,300 (163,900 to 260,200).[24] Subsequent studies published in August 2013 dated the MRCA of Y chomosomes excluding lineages A00, A0, and A1a to about 120,000 to 200,000 years.[7][8][18] In March 2014 the MRCA of lineages excluding A00 was estimated to about 200,000 years.[25]

See also[edit]

References[edit]

  1. ^ Takahata, N (January 1993). "Allelic genealogy and human evolution". Mol. Biol. Evol. 10 (1): 2–22. PMID 8450756. 
  2. ^ Hammer MF (1995). "A recent common ancestry for human Y chromosomes". Nature 378 (6555): 376–378. doi:10.1038/378376a0. PMID 7477371. 
  3. ^ 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. 
  4. ^ 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. 
  5. ^ a b 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. 
  6. ^ a b c d e 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". American Journal of Human Genetics 92 (3): 454–9. doi:10.1016/j.ajhg.2013.02.002. PMC 3591855. PMID 23453668.  (primary source)
  7. ^ a b c 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. 
  8. ^ a b c 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. 
  9. ^ a b Dawkins (2005-09-02). The Ancestor's Tale. ISBN 9780618619160. 
  10. ^ Blaine Bettinger (20 July 2007). "Mitochondrial Eve and Y-chromosomal Adam". The Genetic Genealogist. 
  11. ^ a b Cann RL (2013). "Genetics. Y weigh in again on modern humans". Science 341 (6145): 465–467. doi:10.1126/science.1242899. PMID 23908212. 
  12. ^ a b 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. 
  13. ^ a b c d e 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
  14. ^ 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. 
  15. ^ Mendez; F. L. et al. "Supplemental Data: An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree". The American Journal of Human Genetics 92. 
  16. ^ Barras, Colin (6 March 2013). "The father of all men is 340,000 years old". New Scientist. Retrieved 7 March 2013. 
  17. ^ a b 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". ars technica. Condé Nast. Retrieved 10 August 2013. 
  18. ^ a b 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. 
  19. ^ a b 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. 
  20. ^ "Genetic 'Adam never met Eve'". BBC News. 2000-10-30. Retrieved 2013-03-08. 
  21. ^ Stone et al. (2007). "Fundamentals of Human Evolution". Genes, Culture and Human Evolution. ISBN 1-4051-3166-7. 
  22. ^ Cavalli-Sforza, Luigi Luca (2007). "Human Evolution and Its Relevance for Genetic Epidemiology". Annual Review of Genomics and Human Genetics 8: 1–15. doi:10.1146/annurev.genom.8.080706.092403. PMID 17408354. 
  23. ^ 'Y-Chromosomal Adam Lived 208,300 Years Ago, Says New Study,' Sci-News.com, 23 January 2014.
  24. ^ "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. 
  25. ^ Scozzari, Rosaria; Massaia, Andrea; Trombetta, Beniamino; Bellusci, Giovanna; Myers, Natalie; Noveletto, Andrea; Cruciani, Fulvio (March 2014). "An unbiased resource of novel SNP markers provides a new chronology for the human Y chromosome and reveals a deep phylogenetic structure in Africa". Genome Research 24 (3): 535–44. doi:10.1101/gr.160788.113. PMC 3941117. PMID 24395829.  (primary source)

Further reading[edit]

External links[edit]

Evolutionary tree of human Y-chromosome DNA (Y-DNA) haplogroups
MRC Y-ancestor
A00 A0'1'2'3'4
A0 A1'2'3'4
A1 A2'3'4
A2'3 A4=BCDEF
A2 A3 B CDEF
DE CF
D E C F
GHIJKLT
G HIJKLT
H IJKLT
IJ KLT (K)
I J LT(K1) K (K2)
L T MPS (K2b) X (K2a)
MS P NO
M S QR N O
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.