January 08, 2014

New chronology of Y chromosome phylogeny (Scozzari et al. 2013)

The authors infer a Y chromosome mutation rate of 0.64 x 10e-9 via the autosomal mutation rate. This is in-between two other mutation rates recently published and lower than the only known direct measurement of this quantity.

The issue of mutation rate calibration also popped up in the A00 paper where two different ages for the A00 clade (209 vs. 338ky) were inferred using either the direct or autosomally-adjusted rate.

The Y chromosome mutation rate needs to be studied further; in any case, the relative age estimates should be useful regardless of this issue.

Genome Res. 2014 Jan 6. [Epub ahead of print]

An unbiased resource of novel SNP markers provides a new chronology for the human Y chromosome and reveals a deep phylogenetic structure in Africa.

Scozzari R et al.

Abstract

The phylogeography of the paternally-inherited MSY has been the subject of intense research. However, sequence diversity and the ages of the deepest nodes of the phylogeny remain largely unexplored due to the severely biased collection of SNPs available for study. We characterized 68 worldwide Y chromosomes by high-coverage next generation sequencing, including 18 deep-rooting ones, and identified 2,386 SNPs, 80% of which were novel. Many aspects of this pool of variants resembled the pattern observed among genome-wide de novo events, suggesting that in the MSY a large proportion of newly arisen alleles have survived in the phylogeny. Some degree of purifying selection emerged in the form of an excess of private missense variants. Our MSY tree recapitulated the previously known topology, but the relative lengths of major branches were drastically modified and the associated node ages were remarkably older. We found significantly different branch lengths when comparing the rare deep-rooted A1b African lineage with the rest of the tree. Our dating results and phylogeography led to the following main conclusions: 1) patrilineal lineages with ages approaching those of early AMH fossils survive today only in central-western Africa; 2) only a few evolutionarily successful MSY lineages survived between 160 and 115 kya; 3) an early exit out of Africa (before 70 kya), which fits recent western Asian archaeological evidence, should be considered. Our experimental design produced an unbiased resource of new MSY markers informative for the initial formation of the anatomically modern human gene pool, i.e. a period of our evolution which had been previously considered to be poorly accessible with paternally-inherited markers.

Link

10 comments:

andrew said...

It is nice to see greater precision in the Y-DNA evidence to bring the genetic evidence closer to the archaeological evidence for the appearance of the earliest modern humans and for Out of Africa (although the dates would match even better if the directly measured mutation rate were used).

The very close proximity of the split of the C, E and F clade from the B clade, to the split of the C clade from the F clade, is notable. It implies perhaps that C, E, F each went their separate ways almost immediately following Out of Africa at the same time - C to non-West Asia, E to Africa, and F staying in West Asia.

But, we can't tell if the DE split came later, like the I and P split within F, or if that was an almost identical fourth branch of the dispersing Eurasians. The lack of D clade samples is the biggest disappointment of the otherwise very exciting and helpful paper.

Still, this timing tends to persuade me that E is an almost immediate back migration from West Asia to Africa from the founding Out of Africa population, rather than a clade with African origins.

The fact that the most basal Y-DNA lineages are found in central-western Africa rather than in East Africa where the oldest modern human skeletal remains have been found is also interesting, although a variety of different narratives could explain this result.

One could have an East African origin followed by dispersal that was replaced elsewhere in more congenial environments for modern humans. One could have had an origin anywhere in Africa with the oldest modern humans preserved only in East Africa due to optimal preservation conditions with the oldest Y-DNA clades replaced elsewhere in more congenial environments for moder humans. Or, central-west Africa could be a modern human Eden. Surely, there are other plausible scenarios as well.

Daniel Szelkey said...

If the timing on this paper is correct then C, and DE began in the same place.

Which means that either.
A. C and DE began somewhere in asia. DE did not go extinct in asia and niether did C. Certian variants of DE survived as D clades and possibly as E clades, as E is present in asia,and has been for a long time.
B. C and DE began in Africa, where macro-haplogroup C became extinct, and certian variants and DE survived in as E clades but not D, as no D is found in any populations of africa, or anywhere near africa.

http://press.princeton.edu/chapters/haywood/s2_9519.pdf
shows old cililizations .
Since the sea levals where differnet it is possible that DE and C and F pre-G did not began in asia or africa but in the ocean, which is why they may have lost some diversity.

terryt said...

"3) an early exit out of Africa (before 70 kya), which fits recent western Asian archaeological evidence, should be considered".

I agree with Andrew, it is encouraging to see that being more and more accepted.

"1) patrilineal lineages with ages approaching those of early AMH fossils survive today only in central-western Africa"

Once more we see evidence supporting a West Afrian origin for the basal modern human Y-DNA.

"Which means that either.
A. C and DE began somewhere in asia".

That seems the most likely of the two scenarios you propose.

"Still, this timing tends to persuade me that E is an almost immediate back migration from West Asia to Africa from the founding Out of Africa population, rather than a clade with African origins".

Yes. I'm beginning to be convinced.

"The fact that the most basal Y-DNA lineages are found in central-western Africa rather than in East Africa where the oldest modern human skeletal remains have been found is also interesting, although a variety of different narratives could explain this result".

But 'different narratives' are not necessary. We could just accept the findings as they are in the absence of evidence to the contrary. Although it is fairly apparent that the basal modern hukan mt-DNA originated in East africa it is by no means impossible that the two lines originated in different regions.

"The very close proximity of the split of the C, E and F clade from the B clade, to the split of the C clade from the F clade, is notable. It implies perhaps that C, E, F each went their separate ways almost immediately following Out of Africa at the same time - C to non-West Asia, E to Africa, and F staying in West Asia".

I remember somewhere recently F suffered a long period of isolation after the CF split, presumably in West Asia. As F almost certainly moved east through South Asia I took this as implying that option was not as readily available as most believe. That in turn implies C and D did not move east through South Asia.

eurologist said...

The new timing estimates are certainly very welcome, given archaeological evidence. I would still add at least ~10% to the times stated, which would make the I/P (IJ/KLT?) separation pre-Toba, which makes a lot more sense.

Dr. Clyde Winters said...

Scozzari et al, conclusion that"an early exit out of Africa (before 70 kya), which fits recent western Asian archaeological evidence is incongruent with the archaeological evidence. This inturn makes the idea of a back migration of y-chromosomes E and R, and mtDNA M1 impossible.

The whole idea about a back migration of y-chromosomes from West Asia, back into Africa, given the origination dates for these genes is inconsistent with the archaeological evidence which indicates that amh in western Eurasia, date to the expansion of the Aurignacian culture. And as a result, dating the origin of y-chromosomes E, R, and mtDNA M1 in Eurasia prior to 30kyr is not supported by the archaeological evidence. The archaeological evidence does not place amh in the Levant and Eastern Europe before 30kyr.

Granted, the OOA amh population found in Qafzeh cave and Skhul are associated with Neanderthals and date between 100kyr and 90kyr. This population was very small and amh appear to have disappeared in the Levant, shortly thereafter, until between 30-20kyr. The dominant population in Europe , prior to 30kya was Neanderthal.


Trenton W. Holliday,in "Evolution at the Crossroads: Modern Human Emergence in Western Asia, American Anthropologist,102(1) [2000], tested the hypothesis that if modern Africans had dispersed into the Levant from Africa , "tropically adapted hominids" would be represented in the archaeological history of theLavant,especially in relation to the Qafzeh-Skhul hominids. This researcher found that the Qafzeh-Skhul hominids (20,000-10,000),were assigned to the Sub-Saharan population (SSP), along with the Natufians samples (4000 BP). Holliday also found African fauna in the area.

Holliday confirmed his hypothesis that the replacement of the Neanderthal people were Sub-Saharan Africans. This shows that there were no European types in the Middle East Between 20,000-4,000BP. Moreover, we clearly see from the archaeology the continuity between African culture from Nubia to the Levant.

Below are a few quotes from the paper by Holliday they show that the at this time was SSP dominated Southwest Asia.

"In this light, some of the more robust assignments (albeit not 95% of the Qafzeh-Skhul hominids to the sub-Saharan African sample e.g., Qafzeh 8 at 85%, Skhul 4 at 71%) are remarkable indeed" (p. 62).

"The Qafzeh-Skhul hominids have sometimes been refered to as "Proto-CroMagnons" (e.g., Howell 1957; Vandermeersch 1996) because of their presumed similarity to the famous Aurignacian-associated hominids from Western Europe....Specifically [Brace], he notes that "in both the details of its dental and craniological size and from Qafzeh is an unlikely proto-Cro-Magnon, but it makes a fine model for the ancestors of modern sub-Saharan Africans"(p.63).

"taken as a whole, the work of Tchernov seems to support the findings of the current research that the Qafzeh-Skhul hominids have their origins in Africa, while the Neanderthals are from cold to temperate biomes"(p.64).

"The current study demonstrates African-like affinities in the body shape of the Qafzeh-Skhul hominids. This finding is consistent with craniofacial evidence (Brace 1996) and with zooarchaeological data indicating the presence of African fauna at Qafzeh (Rabinovich and Tchernov 1995; Tchernov 1988, 1992)" (p.64).

In summary, the association of a SSP in West Asia along with sub-saharan flora and fauna indicate that the SSP populations were not divorced from their African origin and probably took y-haplogroups E and R, plus mtDNA M1, and U to Europe if we are to accept the dates these haplogroups originated in Europe. This is supported by the fact that amh do not replace Neanderthals until after 30kya.






andrew said...

"The new timing estimates are certainly very welcome, given archaeological evidence. I would still add at least ~10% to the times stated, which would make the I/P (IJ/KLT?) separation pre-Toba, which makes a lot more sense."

Yes, these dates do seem a bit too short. Some of my key archaeological reference points are:
(1) H. Erectus evolves ca. 2000 kya
(2) H. Erectus in Indonesia ca. 1800-1900 kya.
(3) Neanderthals appear ca. 300 kya.
(4) Oldest modern human skeletal remains ca. 195 kya (therefore modern humans are at least somewhat earlier).
(5) Out of Africa ca. 120kya.
(6) Modern human skeletal remains in Levant ca. 100 kya.
(7) Minimum persistence of pre-H. Sapiens Archeulean industry in India ca. 120 kya.
(8) Youngest H. erectus remains ca. 100 kya.
(9) Modern humans present in S. India - pre-Toba ca. 75 kya or more.
(10) Modern humans in S. Africa ca. 70 kya or more.
(11) Modern humans arrive in SE Asia - 65 kya or more.
(12) Modern humans arrive in Australia and Papua New Guinea ca. 50kya.
(13) Modern humans arrive in Europe ca. 45 kya.
(14) Ancient East Asian DNA ca. 40 kya.
(15) Jomon arrive in Japan ca. 30 kya.
(16) Neanderthals extinct ca. 28 kya.
(17) Mal'ta man ca. 24 kya.
(18) Modern human reach Beringia ca. 22 kya.
(19) LGM ca. 20 kya.
(20) Neolithic begins in W. Asia ca. 10 kya.

I also operate on the working hypothesis that Y-DNA A00 is an introgression from an archaic hominin in central or west Africa that arrives in that gene pool around the same time as other archaic African DNA, and that there may have been some gap between the formation of distinct genetic populations and the uniparental genetic clades associated with those populations (although probably not too much of gap).

Using the Out of Africa 120 kya as a reference point for the split between B and CT clades, the real TMCRA ought to be around 115-125 kya (considering founder effect scenarios as well), and so the estimate may be low by as much as 25%.

terryt said...

"Some of my key archaeological reference points are:"

That all looks pretty good to me.

"dating the origin of y-chromosomes E, R, and mtDNA M1 in Eurasia prior to 30kyr is not supported by the archaeological evidence".

But some sort of modern humans must have passed through Eurasia, unless you're claiming that Australian Aborigines are not modern humans. Their presence does not actually involve 'y-chromosomes E, R, and mtDNA M1 as AAs are mostly Y-DNA C4 and mt-DNA N of various sorts. The ancestors of at least those haplogroups must have left Africa long before 30kyr. But C is descended from CF, presumably an outside-Africa haplogroup. As Andrew said:

"(12) Modern humans arrive in Australia and Papua New Guinea ca. 50kya".

"Granted, the OOA amh population found in Qafzeh cave and Skhul are associated with Neanderthals and date between 100kyr and 90kyr."

As I understand things Neanderthals are not present in the region until more recently than those dates, c. 70-60 kya. Neandertahls replaced the earlier, more modern-looking population in the region. Andrew again:

"(6) Modern human skeletal remains in Levant ca. 100 kya."

Just because modern humans don't appear in Europe 'prior to 30kyr' doesn't mean they were absent through the whole of Eurasia.

eurologist said...

Andrew,

Yes - although different studies give slightly different ages for the wettest climate in the Sahara, the peaks seem to appear between 125 and 115 kya - which means the ages should be corrected upward by ~30-45%.

GailT said...

The most recent carbon dating shows AMH in Europe by 45 kya. I accept the possibility that AMH exited Europe before 100 kya, but the key question is whether they died out, or perhaps were replaced by a more recent OoA migration. If they survived and mixed with a more recent OoA migration, it is also possible that their mtDNA and yDNA lineages were replaced. So it is possible that uniparental DNA might not preserve a record of the earliest AMH expansion, even if that population survived and mixed with later expansions.

terryt said...

"The most recent carbon dating shows AMH in Europe by 45 kya. I accept the possibility that AMH exited Europe before 100 kya, but the key question is whether they died out, or perhaps were replaced by a more recent OoA migration".

I think the obvious conclusion is the correct one. Modern humans left Africa and had become widely distributed through much of the world long before they entered Europe. In other words modern humans were outside Africa long before 45 kya.