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Thread: SNP's and Haplogroups

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    Default SNP's and Haplogroups

    -What are haplogroups?

    The topic of haplogroups is becoming an increasing source of interest with those that have received their Y-chromosome haplotypes. This is because your haplotype can give you hints to your ancient origins.

    We’ve all seen illustrations that show the evolutionary branches of primates, and how millions of years ago, chimpanzees, gorillas, gibbons, and orang-utans diverged off from our primate family tree.


    Man (hominids) went off in a different evolutionary direction, and there have been several different lines that have since died off, Neanderthals being a notable example. With his origins in Africa, modern man has spread himself around the globe. As he did so, he adapted to his surroundings. These adaptations can be seen in the lightened skin colour due to the lack of sun away from the equator, stockier build as observed in peoples in the Arctic regions to maintain body-heat, and better oxygen absorption capability as seen in inhabitants of mountainous, oxygen-poor regions.

    Migration of humans over time (dates are in years before present)


    Over time, many mutations in the DNA strand have occurred. The Y-chromosome, whose main job is just to turn on the male baby switch, has also picked up mutations of a particular type as time has passed. This type of mutation is called a SNP (or Single Nucleotide Polymorphism). This is quite a simply where one letter of the DNA strand is changed to another letter (e.g. T changes to a A).



    These SNP’s are so rare as to be considered unique and are passed down faithfully from father to son. Because of this, they have been used to define several broad groups into which every male in the world can be placed in. These broad groups are called ‘haplogroups’.

    As man has migrated around the world over time, these haplogroups can be used to trace their paths. This is incredibly useful and is an extra tool used alongside archaeological and linguistic data.


    Because some haplotypes (from STR tests) are found to be common within particular haplogroups, it is very often possible to make a prediction of what your haplogroup is from your haplotype.

    Where it becomes interesting for genealogists is that they can gain some insight into their very ’deep’ ancestry – i.e. thousands of years ago – of their direct paternal ancestors.


    For example, when it comes to Europe, the haplogroups observed can be broadly split into two groups, Palaeolithic and Neolithic.

    The first image (Map 1) shows Palaeolithic Europe 18,000 years ago in the grip of the last ice age. Glacial ice 2km thick covers much of Northern Europe and the Alps. Sea levels are approx. 125m lower than today and the coastline differs slightly from the present day. For example, Britain and Ireland would have been connected to continental Europe (not shown on map).

    Map 1 - Ice age Europe (18,000 years ago)


    The air would have been on average 10-12 degrees cooler and much more arid. In between the ice and the tree line, drought-tolerant grasses and dunes would have dominated the landscape.

    The Neanderthals would have died out around 14,000 years ago leaving the nomadic hunter-gatherer Cro-Magnon (modern man) to pursue the animals of the time. Due to the cold and the need for food, the populations of the day waited the ice age out in the three locations shown on the map. These were the Iberian Peninsula, the Balkans and the Ukraine.

    These people were skilled in flint-knapping techniques and various tools such as end-scrapers for animal skins and burins for working wood and engraving were common. Cave painting using charcoal had been around for a couple of thousand years although at this time they were now more subtle than mere outline drawings. These artistic expressions are significant as it shows that people are able to obtain some leisure time. Whether this is ‘art for art’s sake’ or objects of ritual is not known.


    If we fast forward to 12,000 years ago (Map 2), the ice has retreated and the land has become much more supportive to life. Many animal species have returned to inhabit the land, although the snake, harvest mouse and mole never made it as far as Ireland before the land bridges re-flooded (ever wondered why there are no snakes in Ireland?).

    Map 2- spread of Haplogroups R1b, I and R1a (12,000 years ago)


    The three groups of humans had taken refuge for so long that their DNA had naturally picked up mutations, and consequently can be defined into different haplogroups. As they spread from these refuges, Haplogroups R1b, I and R1a propagated across Europe.

    - Haplogroup R1b is common on the western Atlantic coast as far as Scotland.
    - Haplogroup I is common across central Europe and up into Scandinavia.
    - Haplogroup R1a is common in eastern Europe and has also spread across into central Asia and as far as India and Pakistan.

    These three major haplogroups account for approx 80% of Europe's present-day population.


    Around 8,000 years ago (Map 3), the Neolithic peoples of the Middle East that had developed the new technology of agriculture began moving into Europe. There were several haplogroups involved, mainly E3b, F, J2 and G2.

    Map 3 - spread of Neolithic haplogroups (from 8,000 years ago)


    These Neolithic haplogroups came in several waves over time and are found predominantly along the Mediterranean coast. Around 20% of the present-day population are from these Neolithic haplogroups. What is interesting to note is that the agricultural technology spread much further than the people who first 'invented' it.

    A little later, around 4,500 years ago, Haplogroup N3 began moving across from west of the Ural mountains. Haplogroup N3 follows closely the spread of the Finno-Ugric languages.

    Source

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    I think more attention should also be focused on the MT-DNA haplogroups as well.

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    Quote Originally Posted by Brynhild View Post
    I think more attention should also be focused on the MT-DNA haplogroups as well.
    This is true. Only looking at the y-DNA certainly gives you a skewed view of the genetic input in an area. For example, both the Faeroe Islands and Iceland have very significant levels of distinctly Scottish mt-DNA markers, whereas the y-DNA markers are almost entirely Scandinavian. Looking at the two of these together gives us a better picture of where the mates for many of these vikings came from.

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    Default R1b1b2a1a (P310/L11)

    The vast majority of Western European R1B subclades are found down stream of this subclade, which is defined by SNP P310. This Clade is found down stream R1b1b2 which is defined by the SNP mark M269, which in turn is responsible for the vast majority of all European R1b derived Subclades. The current proposed age of R1b1b2 is now deemed to be only 5000 – 8000 years old, as opposed to past estimations which held that the clade was around in Europe before the last Ice-age. R1b1b2a1a is dominated by two Subclades, R1b1b2a1a1 (U106/S21) and R1b1b2a1a2 (P312).

    R1b1b2a1a1 (U106)

    This subclade is defined by the SNP marker U106/S21, and accounts for over 25% of European R1b according to current research. R1b1b2a1a1 and its subsequent subclades are mainly founnd in at their highest frequencies in the ‘Historically Germanic’ area’s, their frequencies decline the further East and South you venture.

    R1b1b2a1a1 as percentage of total Y-Dna by Nation

    Netherlands 37.2%
    Austria ` 22.7% (comparatively small sample size)
    England 21.4%
    Germany 20.5%
    Denmark 17.7%
    Czech Republic 13.9%
    Switzerland 13.3%
    Poland 08.2%
    Russia 07.2%
    France 07.1%
    Ireland 05.9%
    Italy 03.5%
    Turkey 00.4%

    Source: http://www.cmj.hr/2007/48/4/17696299.htm

    U106 Subclades

    R1b1b2a1a1a – Defined by U198/S29, found in low levels in; Netherlands(2.1%), Germany(1.8%), England(1.4%), Denmark(0.9%) and Russia(1.8)%.

    R1b1b2a1a1c – Defined by L1/S26, found in low levels in Germany and England.

    R1b1b2a1a1d – Defined by L48/S162, this Subclade is responsible for the bulk of R1b1b2a1a1 (U106) Subclades.

    The Map below shows U106/S21(orange), S29(brown) and remaining R1b(pale yellow) has a percentage of Y-Dna Haplogroups in various Nations.

    Click image for larger version. 

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    R1b1b2a1a2 (P312)

    This Subclade has been viewed to account for one half of all European R1b1b2, it is found all over Europe but is mainly concentrated in Western Europe.
    P312 Subclades

    R1b1b2a1a2b – Defined by M153, this Subclade is found in high numbers amongst the Basques and Gascons, with a lower amount throughout Iberia.

    R1b1b2a1a2c – Defined by M167, this subclade is found in relatively high numbers in both the Basques and Catalans. In the rest of Spain, plus France, Netherlands, Germany and England, it is found at below 5%.

    R1b1b2a1a2d – Defined by U152/S28, this subclade reaches its peak in the alpine area’s, which has led some to associate the subclade with the ‘La Tene Culture’. Out side of Switzerland, Southern Germany and Northern Italy it drops in number dramatically in all directions.

    R1b1b2a1a2e – Defined by L21. Current tests results indicate this subclade being fairly common in Ireland, Britain, Northern France, Germany and Scandinavia, but rare in Iberia and Italy.

    R1b1b2a1a2f2 – Defined by M222, this subclade is heavily associated with Ireland and Scotland, especially northern Ireland. It is also quite abundant in Western Ireland.

    R1b1b2a1a2f4 – Defined by L226/S168, it is found throughout Ireland, especially Western and Central Ireland.


    Other R1b Maps

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    Default Haplogroup I

    Haplogroup I represents around 20% of the European population, it is found in a majority of European nataions yet yet is virtually absent outside of Europe, leading most academics to believe that Haplogroup I is indigenous to Europe. It is currently held that the most recent common ancestor for this Clade lived some 21 000 years ago, this estimated age puts the appearance of I roughly at the onset of the Last Glacial Maximum. It diverged into two large European Subclades, I1(M253) and I2(M438).

    Click image for larger version. 

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    Click image for larger version. 

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    I1(M253)

    This subclade is deemed to have risen around 4-6000 years ago, it is strongly associated with the ‘Historical Germanic’ populations. It reaches a peak of 40+% saturation in an area covering Sweden, Denmark, most of Norway and Western Finalnd. The percentage drops has one moves further away from these area’s; Northern Germany, Netherlands and Northern England around 15%, Southern Germany and Southern England around 10%. Northern France is around 5%.
    I1 has various subclades, unfortunately, these have not received the same amount of study as say, R1b, so not as much information is available for commentary.
    One particular subclade, I1b defined by SNP M227, is found almost exclusively in low numbers amongst the Baltic and Slavic populations.

    Click image for larger version. 

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    I2(M438)

    This subclade produced three important subclades, I2a1(M26), I2a2 (M423) and I2b(M436/P214/S33), covering varying populations throughout Europe.

    I2a1(M26)

    This subclade is believed to be greater than 4000 years old and it makes up a staggering 40% of the Sardinian Population. Significant frequencies have been found in the Basque Country, Castile and other parts of Spain. Outside of Sardinia, Iberia and Southwest France are very low values are recorded, in Eastern Europe it is virtually absent.

    The map below shows the distribution of both I2a1 and I2a2
    Click image for larger version. 

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    I2a2 (M423)

    This subclade reaches its peak in both Croatia and Bosnia, exceeding 50% in frequency. It is common in Slavic Countries, normally forming the Second or Third most numerous Haplotype found. This subclade also features significantly in Romania, Hungary and the remaining Balkland nations. It is viewed to be at least 3600 years old.

    Click image for larger version. 

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    I2b(M436/P214/S33)
    This subclade has a strong correlation to I1, except in Northern Norway, Northern Sweden and Finland. This has led to geneticists connecting the two subclades to the ‘Historical Germanic’ populations. Its highest frequencies are attained in the Netherlands(6%), Denmark(5%), Germany(4.5%), England(4.5%) and Belgium(4%). It falls to very low frequencies the once you move further East and South.

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    Updated map of R1b :


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    Quote Originally Posted by Iberia View Post
    Updated map of R1b :

    Intresting that the strongest concentration of R1b in Norway is in the areas of Western and Southern Norway were there is a strong presence of Atlantids and Paleo-Atlantids.



    If I remember correctly the highest frequency for R1b in Norway was in 'Mřre og Romsdal' and 'Sogn og Fjordane'.

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    Quote Originally Posted by Pallantides View Post
    Intresting that the strongest concentration of R1b in Norway is in the areas of Western and Southern Norway were there is a strong presence of Atlantids and Paleo-Atlantids.



    If I remember correctly the highest frequency for R1b in Norway was in 'Mřre og Romsdal' and 'Sogn og Fjordane'.
    R1b in Norway table :


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    From Eupedia
    R1b is the most common haplogroup in Western Europe, reaching over 80% of the population in Ireland, the Scottish Highlands, western Wales, the Atlantic fringe of France and the Basque country. It is also common in Anatolia and around the Caucasus, in parts of Russia and in Central and South Asia. Besides the Atlantic and North Sea coast of Europe, hotspots include the Po valley in north-central Italy (over 70%), the Ossetians of the North Caucasus (over 40%) and nearby Armenia (35%), the Bashkirs of the Urals region of Russia (50%), Turkmenistan (over 35%), the Hazara people of Afghanistan (35%), the Uyghurs of North-West China (20%) and the Newars of Nepal (11%). R1b-V88, a subclade specific to sub-Saharan Africa, is found in 60 to 95% of men in northern Cameroon.

    R1b map on 23andMe


    R1b1


    R1b1b2

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    delete
    Last edited by Pallantides; 08-28-2010 at 01:58 AM.

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