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Population Genetics Establishing relationships, similarities & differences within the human genome. Discuss genetics & human microbiology.

DNA Haplogroups (R1a, R1b, I, ect...)

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Old Sunday, June 19th, 2005   #1
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Post DNA Haplogroups (R1a, R1b, I, ect...)

I recently had a 'Y' DNA test done and found that my direct male line -- through the 'Y' DNA is of the R1b Haplogroup. My direct male line is native to the Isle of Skye, Scotland -- and before that is speculation at this point.

I was hoping someone could discuss with me the R1b Haplogroup specifically. Is this 'Celtic' DNA? ..... or from the European mainland?

I would also like to hear discussion of the other Haplogroups.

Thanks
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Old Monday, June 20th, 2005   #2
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Post Re: DNA Haplogroups (R1a, R1b, I, ect...)

Quote:
Originally Posted by Ljót-fulfr
I recently had a 'Y' DNA test done and found that my direct male line -- through the 'Y' DNA is of the R1b Haplogroup. My direct male line is native to the Isle of Skye, Scotland -- and before that is speculation at this point.

I was hoping someone could discuss with me the R1b Haplogroup specifically. Is this 'Celtic' DNA? ..... or from the European mainland?

I would also like to hear discussion of the other Haplogroups.

Thanks
Hi.

I hope this will help:

HAPLOGROUP ASSIGNMENTS: Grey bands in the table identify the haplogroups to which Family Tree DNA has assigned the haplotypes that follow each band. The initial assignments are made on the basis of probability.Most of the time these are *suggested* results and require a haplogroup test to know for certain.



The haplogroup designations are those established by the Y Chromosome Consortium (YCC) in 2002. The YCC system permits greater precision in defining haplogroups than previous systems. One familiar predecessor system used the categories HG1, HG2 and HG3 to classify most individuals of European origin. HG1 identified the haplogroup that is now called R1b in the YCC system; HG2 identified a haplogroup that is now largely classified as “I” (upper case “i”, the alphabetic character, and not the numeral “1”), but which also includes haplogroups that are now differentiated in the YCC system; and HG3 identified the haplogroup now called R1a.



The old HG classification system has the potential to be misleading.





HAPLOGROUP DEFINITIONS: Family Tree DNA provided the following thumbnail summaries of the different haplogroups



B

Haplogroup B is one of the oldest Y-chromosome lineages in humans. Haplogroup B is found exclusively in Africa. This lineage was the first to disperse around Africa. There is current archaeological evidence supporting a major population expansion in Africa approximately 90-130 thousand years ago. It has been proposed that this event may have spread Haplogroup B throughout Africa. Haplogroup B appears at low frequency all around Africa, but is at its highest frequency in Pygmy populations.

C

Haplogroup C is found throughout mainland Asia, the south Pacific, and at low frequency in Native American populations. Haplogroup C originated in southern Asia and spread in all directions. This lineage colonized New Guinea, Australia, and north Asia, and currently is found with its highest diversity in populations of India.

C3

The C3 lineage is believed to have originated in southeast or central Asia. This lineage then spread into northern Asia, and then into the Americas.

J

Haplogroup J is found at highest frequencies in Middle Eastern and north African populations where it most likely evolved. This marker has been carried by Middle Eastern traders into Europe, central Asia, India, and Pakistan.

J2

This lineage originated in the northern portion of the Fertile Crescent where it later spread throughout central Asia, the Mediterranean, and south into India. As with other populations with Mediterranean ancestry this lineage is found within Jewish populations. The Cohen modal lineage is found in Haplogroup J2.

I

The I, I1, and I1a lineages are nearly completely restricted to northwestern Europe. These would most likely have been common within Viking populations. One lineage of this group extends down into central Europe.

I1b

This line was derived within Viking / Scandinavian populations in northwest Europe and has since spread down into southern Europe where it is present at low frequencies.

R1a

The R1a lineage is believed to have originated in the Eurasian Steppes north of the Black and Caspian Seas. This lineage is believed to have originated in a population of the Kurgan culture, known for the domestication of the horse (approximately 3000 B.C.E.). These people were also believed to be the first speakers of the Indo-European language group. This lineage is currently found in central and western Asia, India, and in Slavic populations of Eastern Europe.

R1b

Haplogroup R1b is the most common haplogroup in European populations. It is believed to have expanded throughout Europe as humans re-colonized after the last glacial maximum 10-12 thousand years ago. This lineage is also the haplogroup containing the Atlantic modal haplotype.

Q3

Haplogroup Q3 is the only lineage strictly associated with native American populations. This haplogroup is defined by the presence of the M3 mutation (also known as SY103). This mutation occurred on the Q lineage 8-12 thousand years ago as the migration into the Americas was underway. There is some debate as to on which side of the Bering Strait this mutation occurred, but it definitely happened in the ancestors of the Native American peoples.








GENETIC DISTANCE: A table of genetic distances between the different participants in the DNA Project is in development and will be added to this page in a future update.



In almost all cases, any two members of a haplogroup or subclade—even those with different surnames—will share a more recent common ancestor than either one of them will share with a member of a predecessor haplogroup from which their haplogroup ultimately derives. Thus any R individual will be share a more recent common ancestor with another R than with a Q. Similarly, an R and a Q will share a more recent common ancestor than either will share with either an I or a J. Similarly, an I and a J will share a common ancestor more recent than the one either of them shares with an R or a Q.



These relationships can be seen here in the table of haplogroup relationships established by the Y-Chromosome Consortium. This is a large file that will be slow to load over dial-up connections. It is recommended that interested individuals download and save the PDF version (over five megs) in order to have it available for ready reference on their own computers. The full report from which this table is taken can be accessed here.
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Last edited by visigodo : Monday, June 20th, 2005 at 12:18 PM.
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Old Tuesday, July 26th, 2005   #3
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Post I1b*

I1b*

High-Resolution Phylogenetic Analysis of Southeastern Europe (SEE) Traces Major Episodes of Paternal Gene Flow Among Slavic Populations




The Peopling of Modern Bosnia-Herzegovina:
Y - chromosome Haplogroups in the Three Main Ethnic Groups



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Old Tuesday, July 26th, 2005   #4
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Post Re: DNA Haplogroups (R1a, R1b, I, ect...)

R1b originally comes from what is now Russia.

There are different types in Europe...including what can be termed as the Balto-Slavic, north Germanic, south Germanic, and western European.
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Old Tuesday, July 26th, 2005   #5
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Post Re: DNA Haplogroups (R1a, R1b, I, ect...)

Quote:
Originally Posted by Ljót-fulfr
I recently had a 'Y' DNA test done and found that my direct male line -- through the 'Y' DNA is of the R1b Haplogroup. My direct male line is native to the Isle of Skye, Scotland -- and before that is speculation at this point.

I was hoping someone could discuss with me the R1b Haplogroup specifically. Is this 'Celtic' DNA? ..... or from the European mainland?

I would also like to hear discussion of the other Haplogroups.

Thanks
You are likely of indigenous British ancestry. Here are some additional links if you are interested. Haplogroup R1b was previously known as Haplogroup 1 which can be confusing when reading some of the older research:

Genes link Celts to Basques

Genetic evidence for different male and female roles during cultural transitions in the British Isles

English and Welsh are races apart

Y Chromosome Evidence for Anglo-Saxon Mass Migration

Chromosomes Sketch New Outline of British History

A Y Chromosome Census of the British Isles

Geographical, Linguistic, and Cultural Influences on Genetic Diversity: Y-Chromosomal Distribution in Northern European Populations

Y-Chromosomal Diversity in Europe Is Clinal and Influenced Primarily by Geography, Rather than by Language
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Old Tuesday, July 26th, 2005   #6
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Post Re: DNA Haplogroups (R1a, R1b, I, ect...)

Quote:
Originally Posted by Polak
R1b originally comes from what is now Russia.
What research shows that R1b originated in Russia?
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Old Wednesday, July 27th, 2005   #7
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Post Re: DNA Haplogroups (R1a, R1b, I, ect...)

Quote:
Originally Posted by Vetinari
What research shows that R1b originated in Russia?

The very latest research.

It shows that the Russian, Polish and Baltic R1b is the most diverse.

Diversity in R1b drops as one moves from Russia to western Europe.

The Atlantic R1b is the least diverse, suggesting that it's also the youngest.
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Old Wednesday, July 27th, 2005   #8
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Post Re: DNA Haplogroups (R1a, R1b, I, ect...)

Do you have the study?

I'm inclined to believe this model is correct.
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Old Wednesday, July 27th, 2005   #9
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Post Re: DNA Haplogroups (R1a, R1b, I, ect...)

Quote:
Originally Posted by SouthernBoy
Do you have the study?

I'm inclined to believe this model is correct.

No, that map is wrong.


Quote:
Variations of R1b Ydna in Europe: Distribution and Origins.

A.A.Foster. 13 March, 2005.


Based on the differences and diversity of the alleles of R1b's DYS390 locus, there is evidence that there are four regional variants of the R1b sub-haplogroup in Europe. These are:
(i) Baltic-Russian. (ii) NorthSea-Baltic. (iii) Alpine-South German. (iv) Atlantic.

In Central and Western Europe, north of its great mountain ranges - The Pyrenees, Alps, and others - the major rivers flow northwest and northwards to the Atlantic, the North Sea and the Baltic. Only the Danube, which flows eastwards from the Northern Alpine regions to the Black sea, follows a different pattern. Extrapolating from data available within the online "YHRD" database (¹, see below) suggested all variants of R1b in Europe, as pre-historic hunter-gatherers, entered Europe from the east, and migrated and expanded along rivers and coastlines, and across the ridgeways of high ground, eventually to reach the Baltic, North Sea, Mediterranean and Atlantic coastlines.

The mean frequency for DYS390=24 within the whole of the "YHRD" European database is about 59% of the R1b DYS390 population. In Iberia and France, and in the more remote areas of the British Isles, it averages almost 70% and reaches 80%. But in the Baltic regions the frequency is consistently low: it averages only 33% throughout the Baltic States, about 43% in the Netherlands, and 47% in Baltic Germany. The lowest European percentage (29%) is to be found in Moscow, Russia. An even lower frequency, of 22%, can be found in Asian Khazakstan.

Complete R1b data from the "YHRD" database, indicated that, after an earlier existence in Asian Khazakstan, all European variants of R1b shared an existence in Russia ( in the region of Kazan, on the Volga river at about 55° North and 50° East), and that, later they separated and expanded into two major migrations ( a westward migration to the Russian-Baltic region, and a south-western migration to the Black Sea area and then further, westwards, to the Alpine-South German region). Eventually, a North Sea-Baltic migration evolved from the Russian-Baltic expansion; and an Atlantic migration evolved from the Alpine-South German variant.

Baltic--Russian R1b:
Research showed that the greatest diversity of R1b's DYS 390 locus is within the Russian-Baltic region. The data suggested that the Russian-Baltic variant migrated/expanded from the Kazan region of Russia westwards to Moscow, and then to the Baltic States of Finland, Estonia, Lithuania, Latvia & Poland.
In this Baltic-Russian area, a sample of 159 haplotypes showed the R1b DYS390 percentages to be:

DYS 390=25. 28.9%;
DYS 390=24. 32.7%;
DYS 390=23. 32.1%;
DYS 390=22. 3.1%

Diversity: 68.6% (²)

North Sea-Baltic R1b:
Within the North Sea-Baltic area (Northern Germany, Denmark, Netherlands and
Norway) a sample of 1,227 haplotypes showed the R1b DYS390 percentages to be:

DYS 390=25... 10.1%.
DYS 390=24... 46.6%.
DYS 390=23... 38.1%.
DYS 390=22... 3.7%.

Diversity: 61.5% (²)

These percentages were less diverse than in the Russian-Baltic area - supporting the likelihood of an R1b migration/expansion from east to west along the Baltic coast. The coastal parts of the North Sea-Baltic region had more R1b diversity than in Norway and in the (German) Elbe river cities, indicating a further migration - from "Greater Frisia"(³) northwards to Norway and southwards into the Saxon lands alongside the Elbe.(4) Ultimately, North Sea-Baltic R1bs invaded England and other parts of British Isles during the period 450 to 1,000AD as part of the Germanic-speaking Anglo-Saxon and Danish Viking invasion forces.

Alpine-South German R1b:
Analysis of the Yhrd data for this region indicates a migration/expansion path from Kiev (Ukraine - Russia), westwards along the River Danube (2,850 km), and north/westwards along the Rhine (1,320 km) to the North Sea. Politically, this whole region includes today's Ukraine, Romania, Hungary, Austria and Switzerland, Rhineland Germany, and Southern Holland. Except for the exception given below, a sample of 1,296 haplotypes revealed the R1b percentages for this region were uniform at:

DYS 390=25... 8.3%.
DYS 390=24... 57.9%.
DYS 390=23... 30.1%.
DYS 390=22... 2.6%.

Diversity: 55.7% (²)

With the Alpine-South German group, a small sub-sample of 122 haplotypes in the eastern Danube area, showed only 53% DYS390 =24, and 13% for DYS 390=25. This higher diversity supported the notion of a migration path of the Alpine-South German group from the east, and its heightened DYS390=25 in the eastern Danube area suggests that this variant may well have split from the Russian-Baltic variant near to its source in central Russia.

Atlantic R1b:
This variant is found on the Atlantic coast, in Iberia, France and in the more remote parts of Ireland and Scotland. In order to obtain more accurate data on the
aboriginal/indigenous Scots/Irish, data was extracted from Capelli et al, (5) for Pitlochry and Oban in the Scots Highlands, and from Castlereigh in Central Ireland.

In the Atlantic region, R1b's DYS=390 showed the least diversity. A sample of 1,516 haplotypes showed its R1b's DYS390 percentages to be:

DYS 390=25... 10.4%.
DYS 390=24... 69.7%.
DYS 390=23... 17.8%.
DYS 390=22... 1.1%.

Diversity: 46.1% (²)

The origin of this sub-population is unclear, but its lack of DYS390 diversity makes it the "youngest" R1b in Europe. Some data suggested that it may have split from the Alpine-South German variant in the region of Albania, and then subsequently expanded, westwards, along the Mediterranean coast to Iberia.
Methodology:
The YHRD R1b sub-populations were identified by carrying out a geographic search based on the selection of DYS 392=13, within Europe. A repeat geographical selection, selecting DYS392=13 and combining it, alternatively, with DYS390=25,24,23 & 22 revealed the frequencies of each of DYS390's alleles. After analysis, these were aggregated into the four variant groups. The frequencies of DYS390=26 and 21 were so low that they could be ignored as being statistically irrelevant to this study.
The age of R1b?
If the allele DYS390=24 was the original modal value for all four R1b variants, then the Russian-Baltic group has been mutating either at least twice-as-long or twice-as-fast as the Atlantic one. About 30% of the Atlantic group's DYS390 does not have an allele of 24, while within the Russian-Baltic group this figure increases to 68%. Perhaps the Russian-Baltic variant never did have the well-known Atlantic Modal Haplotype where DYS390=24. But in either case, the difference in allele frquencies highlights that the populations are not homogenous. Differing alleles at the same locus position can be measured to show how diverse is the locus, and such increased locus diversity is a sign of a population's increased age (since its foundation or since it was isolated with a reduced amount of genetic diversity).

A simple application of the different levels of diversity of the four variants to the known archaeology of the Atlantic countries suggests that the ages of the variants, since separation from an earlier, parent type, may, approximately, be as follows:
Atlantic group c.14-18,000 ybp;
Alpine-South German c.18,000 - 22,000 ybp;
NorthSea-Baltic c. 21,000- 25,000 ybp, and
Russian-Baltic possibly c. 24,000 - 28,000 ybp.
More work needs to be done on this aspect, and on the question of where the variant R1bs may have existed during the Last Glacial Maximum.
References:
*1* The YHRD database can be found at www.yhrd.org and it is maintained by the Institute of Legal Medicine, Charite' - University Medicine Berlin.
*2* Diversity has been calculated using Simpson's Index of Diversity, 1-D, expressed as a percentage where 100% represents complete diversity and 0% represents complete homogenity. The maximum diversity of 4 alleles, comprising a total of 100% of those occurring at a locus, cannot exceed 75%. This would be achieved when all four alleles have the same frequency of occurrence, i.e 25%.
*3* "Greater Frisia" was coined by Dr Ken Nordtvedt, during 2004, to describe the North Sea coastal region of the Northern Netherlands and Southern Denmark, after he detected that the frequency of the R1b combination DYS390=23 and DYS391=11, was unexpectedly high in this region. See, Ken Nordtvedt's R1b Sub-Clade at www.worldfamilies.net/Tools/R1b.html
*4* Data from Sweden was excluded from both Baltic groups. Some of its data accords with them, but other data suggests that Sweden and Polish Gdansk may have received a later input of Central European R1bs from Bohemia. These R1bs might have been intermingled with the later inruption of R1as northwards across the Baltic.
*5* Capelli et al, A Y-Chromosome Census of the British Isles, Current Biology, Elsevier Science Ltd. 2003
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Old Wednesday, July 27th, 2005   #10
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Post Re: DNA Haplogroups (R1a, R1b, I, ect...)

Quote:

Haplogroup R-M207 lineages occur at 24.1 frequency on the whole with the majority belonging to the R1-M173 sub-clade (Fig. 2). Only one R1-M173* lineage was observed in eastern region 5. All but one (R1c-M343) of the remaining R1-M173 associated lineages allocate to R1a1- M17 and R1b-P25 sub-clades with R1b3-M269 being preponderate at 14.5% overall in Turkey. Although R1b3- M269 lineages are found throughout Europe at considerable frequency (Cruciani et al. 2002), no additional PCR compatible binary markers are currently known that show additional informative subdivision within this clade. However, two
TaqI haplotypes ht15 and ht35 associated with the complex RFLP 49a,f locus, are associated with R1b3 M269 lineages. The 49a,f ht15 form is rare in Turkey but common in Iberia (Semino et al. 1996), while 49a,f ht35 representatives are distributed across Europe (Torroni et al. 1990; Santachiara-Benerecetti et al. 1993; Semino et al. 2000b) and occurs at ~10% in the Balkan region (Santachiara- Benerecetti, personal communication). In an attempt to better understand the affinity of the frequent Turkish R1b3-M269 lineages relative to other regions, we have analyzed the same battery of STR loci in 52 additional R1b3-M269 defined samples from Iberia, the Balkans, Iraq, Georgia, and Turkey that were previously determined to be 49a,f ht15 or ht35, as well as an additional 59 European R1b3-M269 derived samples. STR haplotype data for these 111 samples are given in Appendix table B. Principal component analysis of all 187 R1b3-M269 samples at ten STR loci variables reveals distributions coinciding with samples of known 49a,f ht15 and ht35 constitution (Fig. 3). Most of the Turkish samples group with the Balkan and the Caucasian 49a,f ht35 samples, while the West European samples associate with the 49a,f ht15 samples. The variance of 49a,f ht35 related chromosomes are lower in the Balkan, Caucasian and Iraqi representatives than those in Turkey (Table 4). Similarly, the variance is higher in Iberia than in Western Europe. The decreasing diversity radiating from Turkey towards Southeast Europe, Caucasus and Mesopotamia approximates similar results from Iberia tracing the recolonization of Northwest Europe by hunter-gatherers during the Holocene as suggested by others (Torroni et al. 1998; Semino et al. 2000a; Wilson et al. 2001).
In Turks R1b3-M269 and R1a1-M17 occur at 14.7% and 6.9%, respectively. In addition R1b3-M269 related YSTR variance is significantly higher than that of R1a1- M17 [F (750,350) = 1.32, P<0.01). While no micro-geographic substructure is detected in Turkey for R1b3-M269, the frequency of R1a1-M17 is higher in Eastern Turkey and its distribution significantly correlates with longitude across the nine regions (Table 3). The majority of L-M11 chromosomes occur in the most eastern regions 3 and 4 (χ2=17.99, df=8, P<0.021) and also have high levels of variance (Table 2).
Role of R1b3-M269 in the Aurignacian and Neolithic eras Haplogroup R1b3-M269 is one of the most common binary lineages observed in Turkey. The phylogenetic and spatial distribution of its equivalent in Europe (Cruciani et al. 2002), the R1-M173 (xM17) lineage for which considerable data exist (Semino et al. 2000a; Wells et al. 2001; Kivisild et al. 2003) implies that R1b3-M269 was well established throughout Paleolithic Europe, probably arriving from West Asia contemporaneous with Aurignacian culture. Although the phylogeographic pattern of R1b3-M269 lineages in Europe suggest that R1-M173* ancestors first arrived from West Asia during the Upper Paleolithic, we cannot deduce if R1b3-M269 first entered Anatolia via the Bosporus isthmus or from an opposite eastward direction. However, archeological evidence supports the view of the arrival of Aurignacian culture to Anatolia from Europe during the Upper Paleolithic rather than from the Iranian plateau (Kuhn 2002). Haplogroup R1b3-M269 occurs at 40–80% frequency in Europe and the associated STR variance suggests that the last ice age modulated R1b3-M269 distribution to refugia in Iberia and Asia Minor from where it subsequently radiated during the Late Upper Paleolithic and Holocene. The R1b3-M269 related, but opposite TaqI p49a, f ht 15 and ht35 distributions reflect the re-peopling of Europe from Iberia and Asia Minor during that period.The R1b3-M269 variances and expansion time estimates of Iberian and Turkish lineages are similar to each other (Table 2) but higher than observed elsewhere (Table 4). Low variances for R1b3-M269 lineages have also been reported for Czech and Estonian populations (Kivisild etal. 2003)
Excavating Y-chromosome haplotype strata in Anatolia
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