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J Man
10-01-2014, 09:02 PM
For a long time there has been a debate about when mtDNA haplogroup H spread into Europe. For quite some time geneticists thought that haplogroup H originated in Iberia during the LGM and pre-dated the spread of agriculture into the continent. Now we know from the numerous ancient DNA samples that have been obtained from European pre-agricultural Upper Paleolithic and Mesolithic remains that it was not H that was dominant among those ancient hunter-gatherers but U. As far as I know there is only really one confirmed H sample from Mesolithic Europe and it comes from Karelia. There are also possibly a few from either Upper Paleolithic or Mesolithic Iberia bu these seem to be debatable. Many think now that most of the H in Europe today started to expand into the continent during the Neolithic with farming populations who ultimately have their origins in the Near East. We need to look at H subclades though instead of just plain old H like we do with the U subclades such as U5. U4, U2, etc as each subclade has a different history. It does seem likely now that a lot of the H subclades present in Europe today spread around and experienced large population growths with Neolithic or later farming populations however I think there is a chance that some types of H were present in parts of Europe during the Upper Paleolithic or Mesolithic. We need more ancient samples to know for sure.

Thoughts?

alan
10-01-2014, 11:01 PM
I am curious about the medical/selective advantages or H.

J Man
10-01-2014, 11:55 PM
I am curious about the medical/selective advantages or H.

It appears that there may have been at least some considering that it has become the most common mtDNA haplogroup in Europe by far.

Jean M
10-02-2014, 12:19 PM
I am curious about the medical/selective advantages of H.

The only one I know of is better recovery from sepsis, but I can't say that I have really scoured the literature. I may have mentioned that geneticist Mike Hammer told me that there were signs of strong selective pressure in favour of H, though there was no paper published on this.

J Man
10-02-2014, 03:23 PM
H1 and H3 are both common subclades of H in Europe. It seems likely that they may have spread around with the Bell Beaker culture especially H1.

alan
10-02-2014, 04:33 PM
Here is a possibly daft thought. Beaker people - large round heads=harder to give birth to for a population with pelvises used to narrow smaller heads. Therefore advantage in sepsis becomes a big one.

Heber
10-02-2014, 09:27 PM
I see similarities between the migrations of my H1c1 and it's defining mutations back to H and my Y R1b-DF21 and it's defining mutations back to R1b-L11. They both appear to be associated with the extreme expansion of R1b and H through the later Neolithic to the Age of Metals and the expansion of Bell Beaker.
Their success could be related to a societal advantage linked to the development of an embryonic Proto Celtic clan organisation system with competitive advantages such as metal workers, elite warriors, knowledge and spiritual (Druidic and Filiadh), founder effect, maritime and fluvial navigation and the advantages conferred by dairy produce.

http://www.pinterest.com/gerardcorcoran/h1c1/

lgmayka
10-03-2014, 02:05 AM
H1 and H3 are both common subclades of H in Europe. It seems likely that they may have spread around with the Bell Beaker culture especially H1.
In a study of 180 Lithuanians (http://www.ebiblioteka.lt/resursai/LMA/Acta%20medica%20Lituanica/A-01-1.pdf), only 3 (1.7%) belonged to H1, and only 8 (4.4%) belonged to H3. But 83 (46.1%) belonged to H (total all clades).

J Man
10-03-2014, 08:53 PM
In a study of 180 Lithuanians (http://www.ebiblioteka.lt/resursai/LMA/Acta%20medica%20Lituanica/A-01-1.pdf), only 3 (1.7%) belonged to H1, and only 8 (4.4%) belonged to H3. But 83 (46.1%) belonged to H (total all clades).

Yes that is true and we know that when it comes to autosomal genetics Lithuanians have some of the highest if not the highest amounts of Mesolithic European ancestry.

palamede
10-08-2014, 03:41 PM
As Maju remarked (see below), there is a great similarity in the development of haplogroup M and haplogroup H, They have more than 50 branches and a lot more of subbranches after 2 or 3 mutations (specially under H1 which is certainly one of the first mutations appeared in H tree) , and we observe the surviving branches only. This suppose a possibility of large and quick expansion in large empty areas.

There is also an analogy in their relations with concurrent haplogroups : M versus N, H versus U .

In the first expansion in Eurasia, according to the repartition of clades and subclades, M preceded N certainly and altogether the calculation of coalescence dates gives N older than M (M is 4 mutations below L3 , 1 in HVR, 3 in coding region, N is 5 mutations below in the coding region) . Same thing but a lot stronger difference for H comparing to U (U is a direct branch from R with 3 coding mutations , H is 5 mutations below R,1 in HVR, 4 in the coding region, but through 2 nodes R0 and HV). The difference of H and U is 1 mutation in HVR and 1 in coding, the average age difference should be about 4-8,000 years.
But the calculated difference for coalescence times of U and H is about 30-35,000 years, statistically a weak probability, but not impossible.

Generally, the given explanation is a quick occurence of mutations (quicker than the average occurence) between R and U and for H a slow occurence in the 5 mutations between R and H. For me, This difference cannot be issued below H because the large number of mutations guarantees that the mutations below H and in its sub-branches must follow all the probability curve of mutation occurences with the respect of the average rate, Although Maju had a different opinion (see below).

An other opinion of mine , the occurences of new branches followed the curve of probability, if by exemple an average rate of 1 mutation every 3500 years, some branches (like H1 probably ) appeared soon after H in less than 3500 years, the occurences of half of the branches were more than 3500 years and some could appear after some multiples of 3500 years. we cannot say the time of H* lived on, maybe until present.

Here is Maju hypothese in 2013 for the lack of depth of the tree of hg H (I don't know his nowadays state of mind, except he seems in a discouragement phase, maybe for financial difficulties) . I should say I cannot know if his reasonments were valid or not. The majority doesn't agree with Maju opinions about chronology, but Maju is one of the most profoundt and erudite bloggers.


Maju text on May 5, 2013 at 12:26 AM http://forwhattheywereweare.blogspot.fr/2013/04/brotherton-2013-cherry-picking-evidence.html:

"There's no way to estimate with any certainty the age of mtDNA haplogroups. But within my main hypothesis it is more likely for a large haplogroup to "freeze" for long because of drift than for a small one. Hence it's more convenient to look at the mutations from the common root, in this case R.

H is the second largest haplogroup by number of basal mutations after M, that implies an explosive expansion at its origin (and at the formation of some derived branches like H1). The star-like structure of H tells us that it was not a minor lineage infiltrating behind the lines, so to say, but that it was very dominant when it coalesced instead. It can only be compared in all the human genome to the explosion of M, which represents most likely the arrival of Homo sapiens to South Asia.
........
IMO H expanded with Aurignacian while it's possible that U variants did with Gravettian. It could also be the other way around or a more complex scenario but something like that. Aurignacian colonization offered H the kind of open expansive scenario that can justify its hyper-star-like structure. However Gravettian was also very vigorous, so I remain cautious on that."
.................

"Those mutations did not (nor could in any sensible molecular-clock-o-logic interpretation) accumulate that fast: I estimate that each mtDNA c.r. mutation takes an average of c. 2,500 years to coalesce, quite more in the case of H, which has shorter stems. So in all that time you can expect maybe one mutation to happen per branch at most, probably zero in most branches. It is saying: the HV-H transition (2 c.r. mutations) was frozen for 40,000 years and then suddenly all those mutations happened and accumulated in just a few thousand years, maybe centuries only.

And never mind what happened elsewhere, for example in Iberia, where we see at least some of those clades (H1b, H6, H3...) already present much earlier. "

palamede
10-09-2014, 08:25 AM
I said "the occurences of half of the branches were more than 3500 years" . Here I considered the median age is equal to the average age . In this case, it is almost true but the shame of the probability curve and therefore for H with about 100 surviving branches and numerous removed branches, the curve of the branch births is the same (and probably almost the same for H1 branches) and the half way value must be slightly lower than the average value, but this doesn't change anything in the reasoning.

In Maju logic, the genetic derive through the numerous bottlenecks of H and its branches involves the disappearence of a lot of recent mutations (because a weak number of individus), it is true certainly, but I don't know it it could be an explanation for a weakness in the global coalescence age of the haplogroup H. It needs to be better statistician than me to answer this problem. It is a good problem for the amateurs of statistic mathematic. In an other post, I remind Maju said he did convincing simulations with a statistician.

An other good problem for the amateurs of statistic mathematic is to calculate the probability of late birth age of a first mutation in H* until present and the number of remaining H* from the birth of the haplogroup H.

I think if the half way is 3000 years and 1000 first mutations (we are in the Paleolithic with very weak populations) and 100 remaining branches. According to the duration after the birth of the haplogroup

duration________first mutations______remaining branches ____cumul
3,000 years______500 __________________30_______________30____For remaining branches, I suppose later the branch birth, higher the rate of survivings.
6,000 years______250___________________20_______________ 50
9,000 years______125___________________16_______________ 66
12,000_ _________62___________________12______________78__ ___after this line, the average occurence is more aleatory than the values I take.
15,000 __________32?___________________9?______________87 ?
18,000___________16?___________________6?_________ _____93?
24,000____________4____________________?__________ _____?
27,000____________?____________________?__________ ____100?
30,000____________?____________________?__________ ____100?
33,000____________?____________________?__________ ____100?
36,000____________?____________________?__________ ____100?

But as the branches of haplogroups M, some branches could have a coalescence age a lot lower than the age of their first mutation.

Judith
10-03-2016, 08:05 PM
Loogvali http://mbe.oxfordjournals.org/content/21/11/2012.short states that H is unusual in being so bushy, namely so many new branches. certainly the timeline with the Neolithic population expansion is fortunate.
Behar gives about 2500 years as the mutation time in the H (esp H4 sub clade), and the mutation time as measured by pedigrees is also 2500 years. So there is no difference between phylogenetic rate and pedigree so that means that there is no purifying selection. So ther must be some genetic benefit.
Without cleanliness, disinfectants and antibiotics a resistance to septis is a huge one which could compensate for other deterious effects. Childbirth for example would be safer, and to leave many descendants that is a benefit.

Heber
10-03-2016, 08:30 PM
Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans
Paul Brotherton, Wolfgang Haak, [...], and The Genographic Consortium

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3978205/

Ancient DNA reveals key stages in the formation of Central European mitochondrial genetic diversity
Guido Brandt, Wolfgang Haak, [...], and The Genographic Consortium

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4039305/

"12. Archaeogenetic and Palaeogenetic Evidence for Metal Age Mobility
in Europe
Maria Pala, Pedro Soares, & Martin B. Richards 321
part III: Linguistics"

Genome wide SNP analysis of global populations.*
PC Analysis depicting relationships between mtDNA haplogroups frequency variation in modern day West Eurasian populations and samples from Early Neolithic to Early Bronze Age showing West to East cline.
Detailed analysis of mtDNA H and the Brotherton and Brandt papers.
Expansion of H with Bell Beaker from Iberia.
Possible arrival of Yamnays Package in SW Europe in time for expansion of Maritine Bell Beaker from Iberia

The Haplogroups H enigma
Haak, Brandt, Brotherton
Clear signal of expansion of H from Iberia to Central Europe but without population replacement, concistant with infiltration, small enclaves that were settled by carriers of the Beaker complex. Confirmed by large scale 2000+ Bell Beaker samples for non metric dental traits (Desideri).

"Modelling post Neolithic demographic changes
Nevertheless the indications from what is a now quiet a large mtDNA sample that Early Neolithic Central European mtDNAs had unusually low levels of haplogroups H suggest that something significant happened to affect the distribution of this haplogroups in the Late Neolithic. And if the source for H1 and H3 is indeed south-west Europe then Iberia may be implicated in subsequent dispersals into Central Europe that may match the archeological evidence for the spread of the Beaker complex...."

http://www.oxbowbooks.com/oxbow/celtic-from-the-west-3.html

Judith
10-04-2016, 11:04 AM
I don't want to repeat the arguments over Celtic from the west, but that does not explain how high some H haplo groups are in the isolated populations of the Caucuses and also the middle east, such as Lebanon. I accept the argument that H1 and H3 were in Iberia and expanded from there with the BellBeakers. But other H clades such as H4 do not follow this trend. I know it is boring and less Eurocentric but I think H started in the Fertile Crescent and had spread across Europe in different directions for different sub clades with the Neolithic

REWM
10-04-2016, 09:20 PM
This is what 23andme has for H4.

Haplogroup H4 Migration

Origin: Haplogroup H, the parent of H4, originated in the Near East and spread throughout Europe after the peak of the Ice Age. H4 branched off approximately 12,000 years ago in the Black Sea region and spread into Eastern Europe, eventually making its way as far west as the British Isles.

Highlight: H4 is most common in Poland today, but it may have spread in part through Viking women.

Example Populations: Polish, Irish, Arabs

I.M.T. Rautavuori
10-29-2016, 11:08 AM
There is also the possibility that some of the haplogroups came to the Iberian Peninsula via North Africa after LGM, whilst all the other subgroups may have come directly from Near East. Maternal lineages H1, H3 and H13 are very likely from the Iberian. The North African route seems to be often overlooked as an optional explanation.

Iberomaurusian cultural connection between North Africa and Iberian Peninsula. '... haplogroups H, JT, U6 and V were identified ...'
http://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-14-109

Heber
10-29-2016, 12:09 PM
There is also the possibility that some of the haplogroups came to the Iberian Peninsula via North Africa after LGM, whilst all the other subgroups may have come directly from Near East. Maternal lineages H1, H3 and H13 are very likely from the Iberian. The North African route seems to be often overlooked as an optional explanation.

Iberomaurusian cultural connection between North Africa and Iberian Peninsula. '... haplogroups H, JT, U6 and V were identified ...'
http://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-14-109

Interesting theory. Others have explored the Green Sahara route.

http://blogs.sapo.pt/cloud/file/eb6b52b82097d41dfa0e5797a2fa7945/olympusmons/2016/From%20Shulaveri%20to%20Bell%20beaker.pdf

http://www.nature.com/scitable/knowledge/library/green-sahara-african-humid-periods-paced-by-82884405

http://ngm.nationalgeographic.com/2008/09/green-sahara/gwin-text.html

http://www.pbs.org/program/skeletons-sahara/

http://anthropology.msu.edu/anp363-ss13/2013/02/06/the-lost-tribes-of-the-green-sahara/

Kings College London has an interesting mapping research project on the "Peopling of the Green Sahara"

http://www.kcl.ac.uk/sspp/departments/geography/people/academic/drake/Research/When-fish-swam-the-Sahara.aspx

https://www.leverhulme.ac.uk/sites/default/files/Publications/May2016.pdf

http://www.kcl.ac.uk/sspp/departments/geography/people/academic/drake/Research/The-Sahara-Megalakes-Project/The-Sahara-Megalakes-Project.aspx

http://www.sciencedirect.com/science/article/pii/S0277379114002728

Green Sahara

http://pin.it/o6zqJeT

Isidro
10-29-2016, 01:16 PM
There is also the possibility that some of the haplogroups came to the Iberian Peninsula via North Africa after LGM, whilst all the other subgroups may have come directly from Near East. Maternal lineages H1, H3 and H13 are very likely from the Iberian. The North African route seems to be often overlooked as an optional explanation.



There is no doubt that there was a connection between Africa and the Iberian Peninsula after the LGM.

https://helenastm.wordpress.com/2015/05/14/el-neolitico-puerta-de-la-civilizacion-the-documentary/

Quote: "The second one, “Yacimiento del Campo de Hockey”, is an interesting Neolithic site in a place that was an island thousand of years before. It has an interesting necropolis where have been found individual burials, pretty well conserved in full anatomical connection and with some exotics materials. These things bring interesting questions and thoughts like that obviously they had to have some external contact by sea, but how was the navigation? The burials are interesting too, although it’s a late Neolithic site you can’t find group or megalithic burials (only a couple can be consider like that). Apart from this, at the first sight, anthropologists said that the population of the site seem to have african features. This is still on study and waiting for DNA analysis results that will tell us more interesting things."

I did watch the documentary in Arqueomania, they did mention the African influence permeating the Campos de Hockey burial site, there seem to be little confusion about the skeletons:

http://www.historiayarqueologia.com/2016/09/el-neolitico-puerta-de-la-civilizacion.html

RCO
10-29-2016, 05:02 PM
No substantial news after this article - Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans
http://www.nature.com/articles/ncomms2656#introduction

A very pioneer article from 2005 without sequence - Using ancient DNA to examine genetic continuity at the Mesolithic-Neolithic transition in Portugal
Helen Chandler Bryan Sykes João Zilhão
http://www.bris.ac.uk/archanth/staff/zilhao/dna2005.pdf

An analysis of genetic distances indicates that the
Portuguese Neolithic and Mesolithic groups studied here
represent different genetic populations. While it must be
noted that this observation is based on a very small
Mesolithic sample size, this finding implies genetic dis-
continuity between the hunter-gatherer and early farming
populations. A discontinuity at the Neolithic transition is
consistent with the Maritime Pioneer Colonisation model
for the arrival of farming in Portugal (Zilhão 1993, Zilhão
2001). In this model, agricultural enclaves were formed by
groups of leap-frogging sea-faring colonists who moved
around the Mediterranean coast.

Heber
11-06-2016, 12:15 AM
To understand mtDNA H it is useful to look at its ancestor HV.

Fine Dissection of Human Mitochondrial DNA Haplogroup HV Lineages Reveals Paleolithic Signatures from European Glacial Refugia

"We finally observe that Italy harbors a reservoir of mtDNA diversity, with deep-rooting HV lineages often related to sequences present in the Caucasus and the Middle East. The resulting hypothesis of a glacial refugium in Southern Italy has implications for the understanding of late Paleolithic population movements and is discussed within the archaeological cultural shifts occurred over the entire continent."

The major glacial refugia recognized from geological and ecological data (in particular from the genetics and distribution of key species of animals and plants) are the Franco-Cantabrian region, the Balkan-Caucasus, and Southern Italy [36–39].

"A recent comprehensive survey of the Italian uniparental genetic landscape, comprising almost a thousand of individuals, revealed that mtDNA haplogroup HV is the lineage in Italy with the oldest coalescence, and highlighted a divergent structure between the Northern and the Southern regions of the peninsula [17]. This early signal can be paralleled with noticeable findings obtained by aDNA analysis on remains from a Mesolithic site in Sicily (Favignana, 14 kilo years ago, kya) [18]), which included a specimen assigned to haplogroup HV1. A Paleo- lithic site in Puglia (Paglicci, 28 kya) also reported data from an individual assigned to HV0 (or pre-HV/R0) [19], but such finding could not be replicated in a more recent study [20]. While haplogroup HV was recognized as a crucial component of early human dispersal in Eurasia [9,21], patterns of its internal variability have been poorly investigated in previous works, which only focused on the major clades HV4 [4], V and H [21–27]."

http://pubman.mpdl.mpg.de/pubman/item/escidoc:2237200/component/escidoc:2237199/shh242.pdf?mode=download

My best guess at the migration of my H1 and defining mutations is.

Expansion of HV from Italian Refugium (Fanti)
Expansion of H with Neolithic Cardium along Meditteranean from Levent to Iberia (Brotherton)
Expansion of H1 and H3 with copper Age Bell Beaker from SW Iberia (Brandt, Brotherton, Soares)
Expansion of H with Megalithic Culture along the Atlantic Facade (Soares)

http://pin.it/x6fBvHG

vettor
11-06-2016, 05:08 PM
To understand mtDNA H it is useful to look at its ancestor HV.

Fine Dissection of Human Mitochondrial DNA Haplogroup HV Lineages Reveals Paleolithic Signatures from European Glacial Refugia

"We finally observe that Italy harbors a reservoir of mtDNA diversity, with deep-rooting HV lineages often related to sequences present in the Caucasus and the Middle East. The resulting hypothesis of a glacial refugium in Southern Italy has implications for the understanding of late Paleolithic population movements and is discussed within the archaeological cultural shifts occurred over the entire continent."

The major glacial refugia recognized from geological and ecological data (in particular from the genetics and distribution of key species of animals and plants) are the Franco-Cantabrian region, the Balkan-Caucasus, and Southern Italy [36–39].

"A recent comprehensive survey of the Italian uniparental genetic landscape, comprising almost a thousand of individuals, revealed that mtDNA haplogroup HV is the lineage in Italy with the oldest coalescence, and highlighted a divergent structure between the Northern and the Southern regions of the peninsula [17]. This early signal can be paralleled with noticeable findings obtained by aDNA analysis on remains from a Mesolithic site in Sicily (Favignana, 14 kilo years ago, kya) [18]), which included a specimen assigned to haplogroup HV1. A Paleo- lithic site in Puglia (Paglicci, 28 kya) also reported data from an individual assigned to HV0 (or pre-HV/R0) [19], but such finding could not be replicated in a more recent study [20]. While haplogroup HV was recognized as a crucial component of early human dispersal in Eurasia [9,21], patterns of its internal variability have been poorly investigated in previous works, which only focused on the major clades HV4 [4], V and H [21–27]."

http://pubman.mpdl.mpg.de/pubman/item/escidoc:2237200/component/escidoc:2237199/shh242.pdf?mode=download

My best guess at the migration of my H1 and defining mutations is.

Expansion of HV from Italian Refugium (Fanti)
Expansion of H with Neolithic Cardium along Meditteranean from Levent to Iberia (Brotherton)
Expansion of H1 and H3 with copper Age Bell Beaker from SW Iberia (Brandt, Brotherton, Soares)
Expansion of H with Megalithic Culture along the Atlantic Facade (Soares)

http://pin.it/x6fBvHG

There is ancient H1 found in brotherton paper in Central Germany 7000 years ago - Early Neolithic times