Talk:Macro-haplogroup L

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For discussion concerning the origins of this article see Talk:Haplogroup L (mtDNA).--Andrew Lancaster (talk) 08:52, 5 February 2010 (UTC)

Clade or paragroup?

I see from this edit that the article has a problem which needs to be cleared up. Is L a paragroup or a clade? The way the article has been edited in recent times has led more to the direction of saying that L defined most logically actually includes M and N, which would make it a clade. My original switch from using "pagragroup" to "clade" was just making the article consistent. If however it does not include M and N then it is indeed a paragroup. Instead of just reverting back and forth on one word the article apparently needs to be adjusted concerning whether L has two meaning or not.--Andrew Lancaster (talk) 10:19, 9 February 2010 (UTC)

I would describe haplogroup L as simply as a haplogroup, or a macrohaplogroup. Strictly speaking haplogroup L isn't a paragroup because it's subclades have known downstream mutations. Though there once was a haplogroup L* that harbored no downstream mutations, but this lineage either went extinct or now possesses downstream mutations. Haplogroups M and N are sometimes referred to as L3M and L3N respectively just to emphasize that the terms "M" and "N" are mainly for convenience. The paragroup for M and N would be L3*(xM, xN). Wapondaponda (talk) 14:11, 9 February 2010 (UTC)

I like your logic, but haplogroup names are a result of the historical sequence of discoveries, and this means they are not always as nice as they would be if you could turn back time. Isn't Maulucioni correct to say that the term L is also used in a way which excludes L? If so then there is no pointing pretending otherwise. If the subject has a broad and narrow sense then surely it is not impossible to cover this?--Andrew Lancaster (talk) 14:48, 10 February 2010 (UTC)

Reviewing, I see that the term “paragroup” is used by Y chromosome consortium to distinguish the groups it recognizes as Y-DNA haplogroups from those that belong to a major haplogroup, but that are not yet well defined because of their mutations, and this is why their paraphyletic condition. In short, to Y-Consortium the term paragroup is contrary to the term haplogroup, it is represented by an asterisk (*) and it isn’t just a synonymous to paraphyletic group.

Instead, in mitochondrial DNA the term paragroup is not used in its nomenclature, and the asterisk is used to include the whole clade and sometimes is used ambiguously.

In Biology, “clade” is a synonymous to “monophyletic group”; but, the nomenclature created to define the mtDNA and Y-DNA haplogroups is full of paraphyletic groups, therefore they are not clades; this is the case of macro-haplogroups. For instance, K (mtDNA) descends from U, and, when we talk about the frequency of U, it excludes K, which has its own frequency. To us, this is absolutely normal, because we are used to work with paraphyletic groups. But, to a biologist who is a cladistic taxonomy follower, and therefore does not believe in the true value of paraphyletic groups, this nomenclature might seem unacceptable and he would propose that the name “K” should be changed, maybe being renamed U9 or Uk. I think that "paragroup" might be an appropriate term for these cases. --Maulucioni (talk) 04:01, 14 February 2010 (UTC)

The YCC has standardized nomenclature for the y-chromosome, but there isn't yet been a consortium that deals with mtDNA nomenclature. As a result mtDNA nomenclature lacks standardization [1] . For the YCC, a paragroup indicates the lack of downstream mutations. This also means that the paragroup represents the ancestral state of a lineage. Some interpret this ancestral lineage as being representative of the whole clade since all subclades would have evolved mutations on the ancestral lineage. There is some inconsistency in nomenclature, for example:

Brehm et al. 2002 state the paragroup L3* (which constitutes the paraphyletic cluster harbouring all other L3 mtDNAs not grouped into the Eurasian haplogroups M or N)

Whereas Behar et al. 2008 state]:

"The term African Hg L(xM,N) is used to describe all mtDNA Haplogroups but (L3)M and (L3)N. We reserve the term branch to describe the two evolving sides of the root and have labeled them L0 and L1′2′3′4′5′6 (L1′5) "

Salas 2002 also uses "paraphyletic group" or "paragroup" and in this case "paragroup L1" is equivalent to Macro-haplogroup L (mtDNA).

In summary the paragroup or "*" nomenclature is used to represent ancestral lineages that lack known or specific mutations. But these ancestral lineages are sometimes used to represent the whole clade. Wapondaponda (talk) 07:33, 14 February 2010 (UTC)

Either I am missing something or there are two alternatives which it would be good if you guys good choose between: 1. Treat L as a paragroup, which excludes M and N or 2. (Muntuwandi would need to make sure he has a source) write the article so that it is clearly mentioned that there are two senses of the term, one being a paragroup and one not. Am I wrong?--Andrew Lancaster (talk) 13:20, 15 February 2010 (UTC)

So far the only paragroup that excludes M and N that has been referenced with "*" notation is L3* and not L*. To exclude M and N, the "X" notation is typically used eg "Hg L(xM,N)". In short the "X" notation is used to exclude specific mutations regardless of their location in the phylogeny whereas the "*" notation is used to denote a paragroup. Since a paragroup is believed to represent the ancestral state it can be used to represent the whole clade. So I would say that * means two different things, but actually these two different things are actually the same. This is because all mutations form subclades of the paragroup. I believe that it is appropriate to give an explanation of the two senses in the article and also in the "paragroup" article. Wapondaponda (talk) 14:20, 15 February 2010 (UTC)

I agree with you both. But I think that using L to define the whole clade makes no sense; we already have the Human mitochondrial DNA haplogroup article to do so. The relevance of L is in its paraphyletic condition. --Maulucioni (talk) 04:28, 16 February 2010 (UTC)

Would it be accurate to say that the primary meaning of the term is as a paraclade, and the secondary meaning is as a real all-encompassing clade? That is my impression. Indeed I can not really recall anyone using term haplogroup L to refer to M and N. We could just mention that wherever the term is used to refer to a real clade it then includes M and N, and then give a link to the Mitochondrial Eve article as well as the one Maulucioni suggests? Can you live with that Wapondaponda?--Andrew Lancaster (talk) 09:27, 16 February 2010 (UTC)

I think the above quote from Behar et al. 2008 does actually use the term "haplogroup L" to refer to M and N when it states "The term African Hg L(xM,N) is used to describe all mtDNA Haplogroups but (L3)M and (L3)N",

Similarly Metspalu et al. 2004) also state: Furthermore, the lack of L3 lineages other than M and N (indeed, L3M and L3N) in India is more consistent with the African launch of haplogroup M

I would agree that the primary meaning of the " * " notation is a paragroup. But this is more so for the Y-chromosome as it has specifically been defined as a paragroup by the YCC. Though I recall Chandrasekar et al. 2007 use haplogroup E* as an all encompassing clade. With mtDNA, conventions are loosely followed so there is less consistency. It can either mean a paragroup or an all encompassing clade.

Chen et al. have given some description of what they mean by macrohaplogroup L* when they state:

Therefore, it is reasonable to delineate these as haplogroups and to delineate the combination of L1 and L2, delineated by the presence of the HpaI site at np 3592, as a macrohaplogroup, “L*.”

L1 and L2 now refer to L0 and L1 respectively. Wapondaponda (talk) 10:46, 16 February 2010 (UTC)

So the article should treat the paraclade as the primary meaning, but mention the other occasionally used meaning. Is this agreed?--Andrew Lancaster (talk) 19:54, 16 February 2010 (UTC)

That's right. --Maulucioni (talk) 22:20, 16 February 2010 (UTC)

«According to some researchers L lineages in Iberia are associated to Islamic invasions, while for others it may be due to more ancient processes as well as more recent ones through the introduction of these lineages by means of the modern slave trade.»

Some researchers...Whom? Lacks source. And though I believe there are still some, that´s maybe because they are outdated. And since when we can just rely on haplogroups to explain specific migrations, when we still don´t have any idea about when happened and from where exactly it happened? Speculate, that´s it. But probably we need to be updated, before do it:

http://forwhattheywereweare.blogspot.pt/2012/03/claim-that-many-african-matrilineages.html

L haplogroup is rare in Iberia and the main exact type found in Iberia was a european specific subclade of L1b that have entered with hunter-gatherer movements (not less than 11.000 years ago and very likely much older than that). Alcácer do Sal/Coruche data is based on a well known (by the locals) african community, with slave ancestry (knowns as «negros do Sado»), known to be endogamic (some families are actually isolated by govermental laws), which have nothing ethnic and local about them. They were used on a study to determine their ancestry, not to represent the locals. Some people have been using this article for not so accurate reasons. If we use the same methodology in other countries, we would end up studying african immigrants, that are much more common in numerous other European countries.

Autosomal research done on iberians, doesn´t support admixture levels that a recent slave influx would produce with these mtDNA frequencies, being them (Iberians) the ones who shared less common ancestors with other populations, for the last 2500 years, from all the European populations used on this study (only Italians got similar results):

«Spain and Portugal showing very few common ancestors with other populations over the last 2,500 years.»

http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001555

Non Caucasoid admixture also point that Iberians and Italians, have some of the lowest levels, among many European countries:

http://s1.zetaboards.com/anthroscape/topic/5354640/1/

Anthropological analysis:

Non-Mediterranean elements in the Portuguese population are rare and of little importance. A few Nordics are scattered throughout but are particularly concentrated in the north. Traces of Dinaric blood, as we have already seen, may likewise be found on the northern coast.... On the whole, there has been no absorption of non-Europoids by the Portuguese. Portugal remains, as it has been since the days of the Muge shell-fish eaters, classic Mediterranean territory.» - Carletoon S. Coon — Preceding unsigned comment added by 46.189.202.30 (talk) 01:35, 9 May 2015 (UTC)

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Article scope

"Haplogroup L" by definition includes all modern humans. Its two descendant clades are called L1-6 and L0. This page would have some potential scope if there were known carriers, ancient or modern, of L1-6* or L0*. Otherwise, the root of the phylogeny is discussed under Mitochondrial Eve, the lineage L0 is discussed under Haplogroup L0 (mtDNA), and the only possible scope left for this page would be discussion of Haplogroup L1-6 (mtDNA). --dab (𒁳) 10:02, 22 September 2019 (UTC)

After review, it may make sense to move this to the "L1-6" title. The reason is, as mentioned above, that L0 already has its own page, and "L" is equivalent to mt-Eve. --dab (𒁳) 19:03, 22 September 2019 (UTC)