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Human sex-determining chromosomes:
X chromosome (left) and the much smaller Y chromosome.
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Geneticists Discover the Oldest Known Genetic Branch of the Human Y Chromosome
March 7, 2013 by Staff
Geneticists at the University of Arizona have discovered an African American Y chromosome with lineage that diverged from previously known Y chromosomes about 338,000 ago, pushing back the time the last common Y chromosome ancestor lived by almost 70 percent.
UA geneticists have discovered the oldest known genetic branch of the human Y chromosome – the hereditary factor determining male sex.
The new divergent lineage, which was found in an individual who submitted his DNA to Family Tree DNA, a company specializing in DNA analysis to trace family roots, branched from the Y chromosome tree before the first appearance of anatomically modern humans in the fossil record.
“Our analysis indicates this lineage diverged from previously known Y chromosomes about 338,000 ago, a time when anatomically modern humans had not yet evolved,” said Michael Hammer, an associate professor in the University of Arizona’s department of ecology and evolutionary biology and a research scientist at the UA’s Arizona Research Labs. “This pushes back the time the last common Y chromosome ancestor lived by almost 70 percent.”
Unlike the other human chromosomes, the majority of the Y chromosome does not exchange genetic material with other chromosomes, which makes it simpler to trace ancestral relationships among contemporary lineages. If two Y chromosomes carry the same mutation, it is because they share a common paternal ancestor at some point in the past. The more mutations that differ between two Y chromosomes the farther back in time the common ancestor lived.
Originally, a DNA sample obtained from an African American living in South Carolina was submitted to the National Geographic Genographic Project. When none of the genetic markers used to assign lineages to known Y chromosome groupings were found, the DNA sample was sent to Family Tree DNA for sequencing. Fernando Mendez, a postdoctoral researcher in Hammer’s lab, led the effort to analyze the DNA sequence, which included more than 240,000 base pairs of the Y chromosome.
Hammer said “the most striking feature of this research is that a consumer genetic testing company identified a lineage that didn’t fit anywhere on the existing Y chromosome tree, even though the tree had been constructed based on perhaps a half-million individuals or more. Nobody expected to find anything like this.”
About 300,000 years ago - the time the Neanderthals are believed to have split from the ancestral human lineage. It was not until more than 100,000 years later that anatomically modern humans appear in the fossil record. They differ from the more archaic forms by a more lightly built skeleton, a smaller face tucked under a high forehead, the absence of a cranial ridge and smaller chins.
Hammer said the newly discovered Y chromosome variation is extremely rare. Through large database searches, his team eventually was able to find a similar chromosome in the Mbo, a population living in a tiny area of western Cameroon in sub-Saharan Africa.
“This was surprising because previously the most diverged branches of the Y chromosome were found in traditional hunter-gatherer populations such as Pygmies and the click-speaking KhoeSan, who are considered to be the most diverged human populations living today.”
“Instead, the sample matched the Y chromosome DNA of 11 men, who all came from a very small region of western Cameroon,” Hammer said. “And the sequences of those individuals are variable, so it’s not like they all descended from the same grandfather.”
Hammer cautions against popular concepts of “mitochondrial Eve” or “Y- hromosome Adam” that suggest all of humankind descended from exactly one pair of humans that lived at a certain point in human evolution.
“There has been too much emphasis on this in the past,” he said. “It is a misconception that the genealogy of a single genetic region reflects population divergence. Instead, our results suggest that there are pockets of genetically isolated communities that together preserve a great deal of human diversity.”
Still, Hammer said, “It is likely that other divergent lineages will be found, whether in Africa or among African-Americans in the U.S. and that some of these may further increase the age of the Y chromosome tree.”
He added: “There has been a lot of hype with people trying to trace their Y chromosome to different tribes, but this individual from South Carolina can say he did it.”
The study came about by combined efforts of a private business, Family Tree DNA, the efforts of a citizen scientist, Bonnie Schrack, and the research capabilities at the UA.
Publication: Fernando L. Mendez, et al., “An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree,” The American Journal of Human Genetics, 28 February 2013; doi:10.1016/j.ajhg.2013.02.002
Source: Daniel Stolte, Univeristy of Arizona News
Image: Univeristy of Arizona News
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Y-chromosomal Adam
From Wikipedia, the free encyclopedia
In human genetics, Y-chromosomal Adam (Y-MRCA) is the most recent common ancestor (MRCA) from whom all living people are descended patrilineally (tracing back only along the paternal (male) lines of their family tree). Recent studies report that Y-chromosomal Adam lived as early as around 142,000 years ago.[1] Older studies estimated Y-MRCA as recent as 60,000 years ago.[2]
All living humans are also descended matrilineally from Mitochondrial Eve who is thought to have lived earlier, about 190,000–200,000 years ago. Y-chromosomal Adam and Mitochondrial Eve need not have lived at the same time nor at the same place. A 2013 paper reported that a previously unknown lineage had been found, which pushed the estimated Y-MRCA back to 338,000 years ago.[3]
Nomenclature
Y-chromosomal Adam is named after the biblical Adam. This may lead to a misconception that he was the only human male alive during his time, even though he co-existed with other human males,[4] including, perhaps, his own father who was not the "most recent". However, unlike himself and his paternal line, each of his male contemporaries failed to produce a direct unbroken male line to all males living today.
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Y chromosome in descendants of one human male
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All living humans are also descended matrilineally from Mitochondrial Eve who is thought to have lived earlier, about 190,000–200,000 years ago. Y-chromosomal Adam and Mitochondrial Eve need not have lived at the same time nor at the same place. A 2013 paper reported that a previously unknown lineage had been found, which pushed the estimated Y-MRCA back to 338,000 years ago.[3]
Nomenclature
Y-chromosomal Adam is named after the biblical Adam. This may lead to a misconception that he was the only human male alive during his time, even though he co-existed with other human males,[4] including, perhaps, his own father who was not the "most recent". However, unlike himself and his paternal line, each of his male contemporaries failed to produce a direct unbroken male line to all males living today.
Hypothesis
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 with the X chromosome but is transferred intact from father to son. Mutations periodically occur 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 share a common patrilineal ancestor who was the first to carry the defining mutation. 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 least unique 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 of Y chromosomes that included individuals 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 Africa was the most likely home of Y-chromosomal Adam.
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| Different MRCA's |
Variable Adam
The title "Y-chromosomal Adam" is not permanently fixed on a single individual. Because knowledge of human Y chromosomes is still incomplete, Y-chromosomal Adam's DNA sequence, his position in the family tree, the time when lived, and his place of origin, are all subject to future revisions. In addition, demographic changes during the course of human evolution would have frequently caused the title of Y-chromosomal Adam to change hands.[5] The following events would change the individual designated Y-chromosomal Adam:
- 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.
- When deep rooting haplogroups are permanently lost from the world's population, living human Y chromosomes converge on a more recent common ancestor. A Y-chromosome lineage is halted when a male dies without leaving any male offspring (although this individual may or may not have had daughters). Phenomena such as bottlenecks and genetic drift during human evolution would have caused the total extinction of several basal haplogroups. Because of these factors, the title "Y-chromosomal Adam" has changed hands numerous times.[5]
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| The revised y-chromosome family tree by Cruciani et al. 2011 compared with the family tree from Karafet et al. 2008 |
Family tree
Y-chromosomal Adam had at least two sons and two of his sons have unbroken lineages that have survived to the present day. Initial sequencing 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.[6] Y-chromosomal Adam was represented as the root of these two lineages. Haplogroup A and Haplogroup BT represented the lineages of the two sons of Y-chromosomal Adam.
However, a recent paper[1] places this event around 142,000 years ago. Cruciani et al. 2011, determined that the deepest split in the Y-chromosome tree is found between two previously reported subclades of Haplogroup A, rather than between Haplogroup A and Haplogroup BT. Subclades A1b and A1a-T, now 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.[7] 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.[6][7]
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.[7]
Origin
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.[7]
In November 2012, a new 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".[8]
Time frame
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.[9] Initial studies, such as Thomson et al. 2000,[9] proposed that Y-chromosomal Adam lived about 59,000 years ago. This date suggested that Y-chromosomal Adam lived tens of thousands of years after his female counterpart Mitochondrial Eve, who lived 150,000–200,000 years ago.[10] 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.[11][12]
The 2011 study by Cruciani et al. found that Y-chromosomal Adam lived about 142,000 years ago, significantly earlier than previous estimates, such as 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 thought. According to Cruciani et al., the much older date is easier to reconcile with models of human origins.[7]
Current Research
A 2013 paper reported that a previously unknown very distinct Y chromosome had been found, which changed the estimated Y-MRCA to 338,000 years ago (237-581 kya with 95% confidence).[3]
The discovery emerged when a relative of Albert Perry, an African American man with ancestry in the Mbo-speaking region in Cameroon[3], submitted his DNA for commercial genealogical analysis by Family Tree DNA.[13]. Perry's Y-chromosome haplogroup was named by the researchers as the A00 haplogroup (so named as it separated from other extant lineages prior to A0's separation), and later testing in Cameroon found this haplogroup also included a small number of Mbo males, though Perry's Y-chromosome was the most genetically distinct in terms of number of mutations.[3] 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.[3]
For Further Reference
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