Talk:Haplogroup X (mtDNA)

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[edit] Altaia

I've pulled this paragraph:

Nevertheless, Derenko's study asserts that the recent European admixture cannot explain the presence of haplogroup X in the Altaians. Hence, these study allow us to suggest that haplogroup X was the part of the ancestral gene pool for Altaian populations, being found both in northern and southern Altaians. As shown by computer analysis, this DNA sequence is not a late European admixture. Rather, the Altai variant X is ancient and can be close to the ancestral form of the variants of contemporary Europeans and Amerinds. The mtDNA studies have shown that both northern and southern Altaians exhibit all four Asian and American Indian–specific haplogroups (A–D). Therefore, they may represent the populations which are most closely related to New World indigenous groups. The candidate source population for American Indian mtDNA haplotypes therefore may include the populations originating in the regions to the southwest and southeast of Lake Baikal, including the Altay Mountain region. The presence of X mtDNAs in Altaians is generally consonant with the latter conclusion.

Derenko's 2001 conclusions were drawn from tests for key markers on the Altay samples; it is essentially superseded by Reidla's 2003 work, based on much more extensive sequencing of samples from all known Haplogroup X populations. It confirms that the Altaian Hg X samples, given the subclade X3e, have a different ancesty to the most commonly found subclades in Europe. Rather, subclade X3e is particularly associated with the South Caucausus, where it is estimated to have arisen in about 10,000 BC. But the detailed similarity of the Altaian sequences suggest that they share a common ancestor much later than this, very unlikely to have been earlier than 4,700 BC. In contrast, subclade X2a is estimated to have been separately developing in North America, isolated from all the other subclades, since 16,000 BC; and it is as different to X2e as it is to any other subclades.

The ancestors of the X2a subclade might have passed through Altaia on their journey to North America. But the modern-day X2e samples are essentially irrelevant to this question - they have nothing to say about it, neither one way nor the other. Jheald 10:48, 14 September 2006 (UTC).

[edit] A discussion on some hypotheses + possible additions to this article

I think that some important points may be missing here:

a) Let us first assume that mtDNA haplogroup X arrived in North America and the Caribbean from Europe, carried by individuals of the Solutrean culture, which is almost identical to the Clovis one, circa 16000 YBP. This event is perfectly possible, and certainly not unheard of even among Palaeolithic peoples. At any rate, if there were such an arrival of populations distinct from those of the main migrations that subsequently brought mtDNA haplogroups C, D, B and A to the Americas along with the widespread Y-chromosome haplogroup Q (and possibly an earlier YAP haplogroup, reportedly found in isolated pockets, besides the obviously latecomer C with Na-Dene speakers), we might also expect a different Y-DNA haplogroup, distinct from Q, to have been carried along through the male population. The question is, where is it, and crucially, what Y-chromosome haplogroup would it be, specifically? X-carrying populations do not generally differ from other Amerind populations when it comes to the paternal side: they almost exclusively present Q or C. Have the earlier paternal line(s) been wiped out by the incoming Q-carrying warrior groups? Interestingly, the estimated time of arrival of Y-DNA Haplogoup Q to the Americas is of ~14.000 years, shortly after the hypothesized arrival of X-carrying groups. That might explain the limited geographical extent of haplogroup X and the absence of a Y-DNA migratory counterpart: before it could spread westwards and southwards, another population wave came along, eliminating much of the male subjects and subsuming the female population. This might not be unique of the populations carrying haplogroup X, since haplogroups C and D (belonging to macrohaplogroup M) have expansion times significantly greater than that calculated for Y-chrom. haplogroup Q. Can this be explained by the suspected divergence in the “genetic clocks” of mtDNA and Y-chromosome? Maybe it is not necessary, since the time estimated for the arrival of mtDNA haplogroup A agrees almost perfectly with Y-DNA haplogroup Q. So, on the other hand, the A haplogroup dominant in North America and decreasing in frequency toward the south would be the latecomer alongside haplogroup Q (probably in the same migration wave), and all other mtDNA haplogroups would have arrived earlier, in distinct migrations and in groups whose male population has been all but replaced by the more recent wave.

b) But then what if a X-carrying population had crossed from Western Eurasia through the Siberian Steppes and later the same Steppes were depopulated by Ice-age geological events? I have seen a study suggesting that a gigantic lake might have formed in Central Siberia – effectively causing depopulation – and that would mean that the current haplogroups could have arrived later and would explain the missing link. This would also better account for the absence of an “outlier” mtDNA haplogroup with geographical variation in the Americas without corresponding outlying Y-DNA groups, since the dominant Y-DNA group in the Americas, Q, is present in both ends of Siberia (with those sequences most similar to a majority of Amerindian Q subgroups being found precisely at the frontier of Western Eurasia, among Samoyedic populations). Alternatively, though, the occurrence of extreme geological events in parts of Siberia might explain the absence of archeological remains similar to those of Solutrean and Clovis cultures, and so obscure this link also on the material level, although I personally believe that this is probably unlikely. At any rate, however, this second hypothesis apparently fails to explain the extremely limited geographical occurrence of haplogroup X, when compared to the more common C, D, B and A, even considering genetic drift or bottleneck effects, as well as the already mentioned divergence in coalescence times. What do you think? There are many more issues here, of course, and a better clarification of these questions by genetics would have wide-reaching consequences for the history of Palaeolithic migrations. This article, as well as all the related articles, should address these issues as well, and I believe that some of the above mentioned facts should be somehow included. Before, though, I’d have to search my files and in the papers for some specific references. Would also appreciate if you know of any other studies that might somehow add up to the discussion and be mentioned in the main article.

[edit] Origin of Haplogroup X

I thought Haplogroup X originated in the Middle East, not Asia? 67.83.173.186 20:06, 12 August 2007 (UTC)


The article states now that "Other suggestions which do not involve boats state that a population of Ukranian origin possessing haplogroup X migrated rapidly eastward across Russia as a single group, ultimately crossing the Bering land bridge and entering North America. This group left few people behind, as evidenced by the scarcity of Haplogroup X within Asia" with a reference to an article mtDNA haplogroup X: An ancient link between Europe/Western Asia and North America? . But the article does not contain such information. Instead, it states: "Given the apparent absence of haplogroup X in modern eastern and northern Asia, it is difficult to define a source population for haplogroup X in the Americas" and presumes different possible ways of how haplogroup X occurs in mtDNA of Native Americans. One of possible ways is indeed "that this mtDNA was brought to Beringia/America by the eastward migration of an ancestral Caucasian population, of which no trace has so far been found in the mtDNA gene pool of modern Siberian/eastern Asian populations", but there is no mention of "a population of Ukrainian origin", which along with the Russians and Russia came to exist a few thousand years later. I presume that the story about Ukrainians and Russia and haplogroup X is an original research and should be corrected. A.I.K. (talk) 15:34, 2 May 2008 (UTC)

[edit] Why is X stronger in North American populations than in Europe?

After reading the article I was confused by the stated percentages and "origins" of Haplogroup X. It's stated that certain populations of Algonquins in North America display a 25% presence of this genetic marker while only 2% of Europe's population displays it. Seeing that Europe has a much larger population and documented history of Paleolithic interaction throughout the European Continent, why has the X gene lost prominence?. Shouldn't there be at least a 20% presence of X within the European population in general? Also, since there is no conclusive evidence that Solutreans contained this genetic marker how can it be assumed that they even had the X gene?--208.54.15.161 19:17, 22 August 2007 (UTC)

Different Haplogroups. X2a in North America is not the same as the X strain in Europe. Can anyone find a source for the 25% figure anyway? Dougweller 16:36, 30 October 2007 (UTC)

Please read the entries: founder effect and genetic drift. They are self-explainatory (I hope). --Sugaar (talk) 11:44, 6 June 2008 (UTC)

[edit] Recent Research pointing to a Beringian 'Standstill'

Research published this year argues for a founding population travelling through and remaining in Beringia for some time. I'm not sure how this affects this article. The American Journal of Human Genetics, Volume 82, Issue 3, 583-592, 3 March 2008, Mitochondrial Population Genomics Supports a Single Pre-Clovis Origin with a Coastal Route for the Peopling of the Americas Nelson J.R. Fagundes, Ricardo Kanitz, Roberta Eckert, Ana C.S. Valls, Mauricio R. Bogo, Francisco M. Salzano, David Glenn Smith, Wilson A. Silva, Marco A. Zago, Andrea K. Ribeiro-dos-Santos, Sidney E.B. Santos, Maria Luiza Petzl-Erler and Sandro L. Bonatto

PLoS ONE. 2007 Sep 5;2(9) Beringian standstill and spread of Native American founders. Tamm E, Kivisild T, Reidla M, Metspalu M, Smith DG, Mulligan CJ, Bravi CM, Rickards O, Martinez-Labarga C, Khusnutdinova EK, Fedorova SA, Golubenko MV, Stepanov VA, Gubina MA, Zhadanov SI, Ossipova LP, Damba L, Voevoda MI, Dipierri JE, Villems R, Malhi RS.

Achilli A, Perego UA, Bravi CM, Coble MD, Kong QP, et al. (2008) The Phylogeny of the Four Pan-American MtDNA Haplogroups: Implications for Evolutionary and Disease Studies. PLoS ONE 3(3)

The American Journal of Human Genetics article says "Here we show, by using 86 complete mitochondrial genomes, that all Native American haplogroups, including haplogroup X, were part of a single founding population, thereby refuting multiple-migration models."--Doug Weller (talk) 08:27, 14 March 2008 (UTC)

The AJGH paper is very interesting. The skyline plot of likely effective population size, and the scenario of a long bottleneck period before a marked expansion, looks very plausible. However, I think the word "refute" is a bit strong. I can't see anything in the paper to show that the Solutrean hypothesis is impossible -- I don't think they have enough data to say. IMO a fairer summary would be to say that the paper demonstrates that the Solutrean hypothesis is not necessary to expain the present distribution of Haplogroup X2a, regionally concentrated in a few areas in North America, and apparently absent in Asia.
The evidence from Haplogroups A, B, C and D is of a founder population with an effective population size of about 1,000 females becoming separated from an ancestral population in Asia for a period of about 5,000 years, before undergoing a rapid population expansion soon after the end of the last LGM. The haplotype X2a data also fits this scenario, with a similar coalescence time. The present geographical distribution is compatible with it initially having been present at a much lower frequency than the other four haplogroups, so that in most descendent populations it has not been preserved; except for a few areas, where by chance it may have been stronger in the initial founder population and then "surfed" a subsequent sudden range expansion.
But it seems to me that that same scenario - with that same timescale - would apply equally well to the Solutrean hypothesis. The real problems AFAICS with the Solutrean hypothesis are different: namely, if one accepts it, why didn't any other "European" mtDNA haplogroups come over too? And why doesn't it seem to be accompanied by any corresponding Y-DNA "European" haplogroups?
So it seems to me the paper does a persuasive job of showing the Solutrean hypothesis is unnecessary. But I don't think the argumentation is developed to actually refute it - at least, not in the paper itself. Jheald (talk) 09:51, 14 March 2008 (UTC)
Ineresting point. It's fascinating that suddenly we have several papers, all arguing for a Pre-Clovis migration with a Beringian standstill. I don't think the AJGH paper was just aimed at the Solutrean hypothesis, but it certainly targets it. The sentence "Our results strongly support the hypothesis that haplogroup X, together with the other four main mtDNA haplogroups, was part of the gene pool of a single Native American founding population; therefore they do not support models that propose haplogroup-independent migrations, such as the migration from Europe posed by the Solutrean hypothesis" might be more to your liking. I rarely think 'refute' is final anyway.--Doug Weller (talk) 10:41, 14 March 2008 (UTC)

[edit] X2a

according to the article linked,

"if we assume that the two complete Native American X sequences (from one Navajo and one Ojibwa) began to diverge while their common ancestor was already in the Americas, we obtain a coalescence time of 18,000 ± 6,800 YBP, implying an arrival time not later than 11,000 YBP."

this leaves open the question whether the ancestor of X2a reached America together with the main migration across the Bering straight, or at a later date around the LGM. dab (𒁳) 11:36, 30 October 2007 (UTC)

[edit] Science on Wikipedia

I've just changed two occurances of BC to BP. Am I wrong? Is there a Wikipedian rule I don't know about, suggesting a Christ-centric view of the scientific world? I'm a Christian myself, and some of my colleagues are giving us a bad name by realistically trying to hijack science ... I try to not impose my beliefs on others, and feel this is important. —Preceding unsigned comment added by 207.138.32.33 (talk) 22:08, 9 May 2008 (UTC)

That's very good of you, I wish everyone was like that. WP:styleguide is what you want:

"Either CE and BCE or AD and BC can be used—spaced, undotted (without periods) and upper-case. Choose either the BC-AD or the BCE-CE system, but not both in the same article. AD appears before or after a year (AD 1066, 1066 AD); the other abbreviations appear after (1066 CE, 3700 BCE, 3700 BC). The absence of such an abbreviation indicates the default, CE-AD. It is inappropriate for a Wikipedia editor to change from one style to another unless there is some substantial reason for the change; the Manual of Style favors neither system over the other. Uncalibrated (bce) radiocarbon dates: Do not give uncalibrated radiocarbon dates (represented by the lower-case bce unit, occasionally bc or b.c. in some sources), except in directly quoted material, and even then include a footnote, a [square-bracketed editor's note], or other indication to the reader what the calibrated date is, or at least that the date is uncalibrated. Calibrated and uncalibrated dates can diverge surprisingly widely, and the average reader does not recognize the distinction between bce and BCE-BC."

When I last read that I realised I've seen several cases recently of BP being incorrectly used.
The earliest relevant version uses BC, so that is the way it should be (to my regret as in archaeology and history BCE/CE is used more and more).--Doug Weller (talk) 08:12, 10 May 2008 (UTC)