(Click to enlarge)
Friday, July 9, 2010
Monday, June 28, 2010
Facts and Common Misconceptions
- No, haplogroups are not the same as haplotypes.
- Yes, all people living today fall into one of 18 main Y-DNA haplogroups on their paternal line, and one of 26 main mtDNA haplogroups on their maternal line.
- No, haplogroups will not show if you are related to someone (unless you count distant relationships from thousands of years ago).
- Yes, once you know your haplogroup, you will be able to view how your haplogroup migrated out of Africa and retrace their migration routes.
- No, haplogroups will not add people to your family tree or allow you to trace your surname (that’s the job of STR haplotypes).
- No, haplogroups will not tell you precise migration routes, it will show a broad migration route and population distribution.
- No, if you and someone else belong to the same haplogroup, it does not mean that you are closely related.
- Yes, once you know your haplogroup, you can often fine tune your branch of the haplogroup tree through subclade testing.
- No, you cannot confirm your haplogroup through STR testing or HVR1 testing. A Y-DNA STR test and HVR1 test will often allow you to predict your haplogroup, but only a SNP backbone test will confirm the prediction.
- No, SNP backbone testing will not give you information about sub-clades. It will confirm your haplogroup. Once your haplogroup has been confirmed, a subclade panel test for your particular haplogroup will trace your subclade.
- Yes, STR testing can give predictions for haplogroups and even some sub-clades, but the backbone test can only confirm the haplogroup, not the sub-clade.
- Yes, subclades are determined through SNP subclade testing (once your haplogroup has been confirmed)
- No, your haplogroup will not tell you if you are Welsh or Irish. It will not tell you your ethnicity. Although there are associations between ethnic groups and haplogroups, you must remember that haplogroups represent deep ancestry, tracing events from tens of thousands of years ago. It does not tell you what your ancestors have been up to over the last few hundred years (that’s the job of Y-DNA STR markers, and applications such as Surname Projects, which will be the topic of another blog).
- Yes, all people living in the world today are connected in the human phylogenetic tree. Just like how all people belong to a certain blood group i.e. A, B, AB, O which can be determined through testing, all people also belong to a certain haplogroup which is unique to their ancestry, and their haplogroup type can be determined through genetic genealogy testing.
Tuesday, February 23, 2010
Phylogenetic tree of human Y-chromosome haplogroups observed in Eurasians
click to enlarge
A couple of things I notice on the chart:
- R2 is shown as younger than R1/R1a/R1b, which I think is probably true.
- An Asian source for all Europeans - excluding haplogroup E.
The Human Genetic History of South Asia
Partha P. Majumder
Summary:
South Asia — comprising India, Pakistan, countries in the sub-Himalayan region and Myanmar — was one of the first geographical regions to have been peopled by modern humans. This region has served as a major route of dispersal to other geographical regions, including southeast Asia. The Indian society comprises tribal, ranked caste, and other populations that are largely endogamous. As a result of evolutionary antiquity and endogamy, populations of India show high genetic differentiation and extensive structuring. Linguistic differences of populations provide the best explanation of genetic differences observed in this region of the world. Within India, consistent with social history, extant populations inhabiting northern regions show closer affinities with Indo-European speaking populations of central Asia that those inhabiting southern regions. Extant southern Indian populations may have been derived from early colonizers arriving from Africa along the southern exit route. The higher-ranked caste populations, who were the torch-bearers of Hindu rituals, show closer affinities with central Asian, Indo-European speaking, populations.
Current Biology, Volume 20, Issue 4, R184-R187, 23 February 2010
Full article (link)
Summary:
South Asia — comprising India, Pakistan, countries in the sub-Himalayan region and Myanmar — was one of the first geographical regions to have been peopled by modern humans. This region has served as a major route of dispersal to other geographical regions, including southeast Asia. The Indian society comprises tribal, ranked caste, and other populations that are largely endogamous. As a result of evolutionary antiquity and endogamy, populations of India show high genetic differentiation and extensive structuring. Linguistic differences of populations provide the best explanation of genetic differences observed in this region of the world. Within India, consistent with social history, extant populations inhabiting northern regions show closer affinities with Indo-European speaking populations of central Asia that those inhabiting southern regions. Extant southern Indian populations may have been derived from early colonizers arriving from Africa along the southern exit route. The higher-ranked caste populations, who were the torch-bearers of Hindu rituals, show closer affinities with central Asian, Indo-European speaking, populations.
Current Biology, Volume 20, Issue 4, R184-R187, 23 February 2010
Full article (link)
Friday, February 19, 2010
Jews of Haplogroup R2
Haplogroup R2 is rather rare outside India, where it accounts for about 90% of all men on Earth having R2. In India it has been observed in about 10% of male population, in Pakistan – about 7-8%. In Tadzhikistan, neighboring India, haplogroup R2 is met in about 6% of the population. Some singular percentage of population having R2 can be met in the area of Caucasus, among Azerbaidzhanians, Armenians, Georgians, Chechens. It is conjectured that in these areas haplogroup R2 was introduced by the Gypsies, who carry haplogroup R2 with frequency of more than 50% of their population. The next main haplogroup in the Gypsies is H, as it was described in the preceding paper in this issue with an example of Bulgarian Gypsies. It is surmised that haplogroup R2 was originated some 25 thousand years ago.
The Gypsies have brought haplogroup R2 to Europe in medieval times, some 500-700 years ago, apparently first to Bulgaria, Germany and Austria (under the Gypsies names of Sinti and Roma), and then spread over Europe. This haplogroup was recently found among the Jews, and immediately it was suggested by the scholars that it came from the Khazars. No justifications and no time estimates were given.
Recently (Sengupta et al, 2006) a large set of Indian and Pakistani haplotypes was published, including more than 900 haplotypes. 81 of them belonged to haplogroup R2. Since as many as 21 of identical six-marker haplotypes (the base haplotypes) from those 81 are observed, as follows
14-12-23-10-10-14
it is rather obvious that these haplotypes cannot be too old. Indeed, ln (81/21)/0.0096 = 141 generations (163 with correction for back mutations) to a common ancestor. All 81 haplotypes contain 108 mutations from the above base haplotype, which gives 108/81/0.0096 = 139 generations (161 with correction for back mutations). It is a practically absolute fit, indicating that it was a single ancestor who originated the lineage of R2 haplogroup in India 4,000 years BP.
However, it seems that the actual time of origination of R2 haplogroup was much earlier. The R2 section of YSearch data base contains 34 haplotypes of individuals. Half of them are ethnic Indians, plus some Scotts, French, Italians, Armenians. Twelve individuals have names of their predecessors as Abraham, Isaac, Lebe, Mordecai, etc., and some of them presented supplementary information indicating that they are Ashkenazi Jews. The most frequent 6-marker haplotype among those 39 individuals is
14-12-23-10-10-14
which is exactly the same as that the base haplotype of haplogroup R2 in India- Pakistan, shown above. However, if to remove the Jewish haplotypes (which, as it is shown below, are derived from a recent ancestor), the remaining 22 haplotypes contain 35 mutations, that translates into 198 generations from a common ancestor. In 22 of the 12-marker haplotypes there were 101 mutations, which give 236 generations from a common ancestor. In 7 of the 37-marker haplotypes amount of mutations in the 12-, 25- and 37-marker panels corresponded to 282, 259 and 207 generations to a common ancestor. These four figures being averaged give 246±32 generations, that is about 6,200±800 years to a common ancestor of the non-Jewish individuals of R2 haplogroup in YSearch database. This might be a good indication that haplogroup R2 had originated not in India, since the Indian R2 haplogroups were derived from a significantly “younger” ancestor who lived about 4,000 years BP (see above), that is some 2,000 years later that an older bearer of the R2 haplogroup. In any case, this question needs more detailed studies.
And when a common ancestor of the Jews of haplogroup R2 had lived?
The most frequent 12-marker haplotype among those 34 individuals, Jewish and not, is
14-23-14-10-13-20-12-12-11-14-10-29
which is exactly the same as that for the Jewish individuals of haplogroup R2 in YSearch database.
Let us now consider the Jewish haplotypes in more detail.
6-marker haplotypes
11 of the 12 Jewish R2 haplotypes are identical to each other (Fig. 50), and their
6-marker base (ancestral) haplotype is
14-12-23-10-10-14
that is the same as the most popular among known bearers of R2 haplogroup in India and elsewhere in the world.
Figure 50. The 6-marker haplotype tree for 12 Jewish haplotypes of haplogroup R2. A “commercial” set (YSearch database)
Formally, 11 base haplotypes out of 12 give ln(12/11)/0.0096 = 9 generations, and one mutation in all twelve 6-marker haplotypes gives 1/12/0.0096 = 9 generations to a common ancestor, and the identity of these figures point out at a single ancestor for all 12 individuals in the set of their 6-marker haplotypes. However, as it has happened before, this tentative conclusion should be examined with more extended haplotypes. It is too often when 6-marker haplotypes, particularly in small haplotype sets, do not reveal mutations which occur in more extended panels of the haplotype.
12-marker haplotypes
Indeed, a move to the 12-marker tree (Fig. 51) immediately shows that there are two groups of the Jewish haplotypes, with an “older” and a “younger” haplotypes, descending from the same ancestor. Half of all 12 haplotypes still represent the base (ancestral) haplotype
14-23-14-10-13-20-12-12-11-14-10-29
Since their other mutations will be revealed by moving to more extended haplotypes, an estimate of a time span to the common ancestor based on the 12- marker haplotypes will be only tentative.
Figure 51. The 12-marker haplotype tree for 12 Jewish haplotypes of haplogroup R2. A “commercial” set (YSearch database)
This 12-marker base haplotype is exactly the same as the most frequent 12- marker haplotype in YSearch database, only one-third of which represent the Jewish haplotypes.
6 base haplotypes from the total 12 Jewish haplotypes would point to 29 generations to a common ancestor, since ln(12/6)/0.024 = 29. The other 6 haplotypes contain 15 mutations with respect to the above base haplotype. This would lead to 15/12/0.024 = 52 generations to a common ancestor. This mismatch (29 and 52) indicates that there were more than just one common ancestor for the Jews in R2 haplogroup. In fact, Fig. 51 makes it rather obvious.
As it turned out, many more mutations have occurred in the 13-37 marker panel of the distant branch, which distinctly separates the two branches. However, even the 12-marker tree shows the principal separation of the two groups of haplotypes.
37-marker haplotypes
The 37-marker haplotype tree is shown in Fig. 52. It reveals a striking feature of R2 Jewish haplotypes. Though there are only 7 haplotypes on the tree, they clearly show that Jewish R2 haplotypes splits indeed into two quite distant groups. Statistics is insufficient to perform detailed analysis, however, there are still enough data available to make some principal conclusions. One group of haplotypes, which are located on the right-hand side of the tree (Fig. 52) and much closer to the trunk of the tree (that is, to the present times), has the same 12- marker base haplotype as shown immediately above and in the Table, and corresponds to the group of the base haplotypes around the 12-marker tree (Fig. 51). This 4-haplotype branch has only 9 mutations with respect to the base 37- marker haplotype, and refers to a common ancestor who lived only 26 generations BP, 650±50 years ago, in the 14th century.
Figure 52. The 37-marker haplotype tree for 7 Jewish haplotypes of haplogroup R2. A “commercial” set (YSearch database)
Another group of Jewish R2 haplotypes, represented with three distant haplotypes on the left-hand side in Fig. 52, shows a base 12-marker haplotype (the 37-marker haplotype is shown in the Table):
14-23-14-10-13-20-12-12-10-13-10-31
It turned out that these three haplotypes (the left-hand side in Fig. 52) have only two mutations in their 37-marker haplotypes, that is among 111 alleles. This formally places their common ancestor only 7 generations BP, that is about two hundred years ago. All three are relatives within seven generations.
Overall, there are 21 mutations between these two base (ancestral) haplotypes in the 37-marker format. This means that these two haplotypes are separated by thousands of years of separate mutations, and, more specifically, this separation is approximately equivalent to 305 generations between the two, that is about 7,600 years. This places their common ancestors about 4,200 years BP, and fits pretty well with the common ancestor of Indian R2 haplogroup of 4,000 years BP, see above. It is very likely that the both lineages, “young” and the ancient one, are derived from the Gypsies in Europe. The “young” is traced down to the invasion time or a bottleneck time to the Jewish community, and the “older” is traced down to the ancient common ancestor in India. At any rate, both Jewish ancestral haplotypes, shown above in their 12-marker format and in the Table 2 in a 37-marker format are derived from two quite unrelated individuals, whose haplotypes had evolved from the very initial survivors in haplogroup R2, but traced down in millennia apparently to India, through the Gypsies.
Some historical conjectures
Here is a plausible story of the Jewish haplotypes of R2 haplogroup. Its ancestral haplotype
14-23-14-10-13-20-12-12-11-14-10-29
shown here in the 12-marker format, is about 4,200 years old, that corresponds to the age of this haplotype in India (see above). This haplotype had arrived to Europe apparently with the Gypsies, in the Medieval times, some 800 years BP, and got into the Jewish community. About 30-40% of the present day Jews, bearers of R2 haplogroup, are direct descendant of those Gypsies, or the Indians, on that matter. Approximately 650 years ago, apparently during the Black Plague times, in the 14th century, a bearer of this haplogroup, albeit in the mutated form had survived and fled to the Eastern Europe. This was a bottleneck for this particular haplotype. Close to half of present day Jews are descendants of that individual.
This story is a mirror one of the Jewish Q haplotypes story (see the preceding section). Apparently, the 14th century, the Black Plague times, created a number of bottleneck situations for the Jews of a number of haplotypes, and not for the Jews only.
The second Jewish R2 haplotype
14-23-14-10-13-20-12-12-10-13-10-31
in the 12-marker format, got to the Jewish community quite recently, merely two hundred years ago. It is very different from the first one. Its three bearers lived in the 19th century in Hungary, Romania and Lithuania. Their current descendants probably do not know that they are rather close relatives. Two of them differ by only 3 mutations in their 66-marker haplotypes.
From
Origin of the Jews via DNA Genealogy
Anatole A. Klyosov
The Gypsies have brought haplogroup R2 to Europe in medieval times, some 500-700 years ago, apparently first to Bulgaria, Germany and Austria (under the Gypsies names of Sinti and Roma), and then spread over Europe. This haplogroup was recently found among the Jews, and immediately it was suggested by the scholars that it came from the Khazars. No justifications and no time estimates were given.
Recently (Sengupta et al, 2006) a large set of Indian and Pakistani haplotypes was published, including more than 900 haplotypes. 81 of them belonged to haplogroup R2. Since as many as 21 of identical six-marker haplotypes (the base haplotypes) from those 81 are observed, as follows
14-12-23-10-10-14
it is rather obvious that these haplotypes cannot be too old. Indeed, ln (81/21)/0.0096 = 141 generations (163 with correction for back mutations) to a common ancestor. All 81 haplotypes contain 108 mutations from the above base haplotype, which gives 108/81/0.0096 = 139 generations (161 with correction for back mutations). It is a practically absolute fit, indicating that it was a single ancestor who originated the lineage of R2 haplogroup in India 4,000 years BP.
However, it seems that the actual time of origination of R2 haplogroup was much earlier. The R2 section of YSearch data base contains 34 haplotypes of individuals. Half of them are ethnic Indians, plus some Scotts, French, Italians, Armenians. Twelve individuals have names of their predecessors as Abraham, Isaac, Lebe, Mordecai, etc., and some of them presented supplementary information indicating that they are Ashkenazi Jews. The most frequent 6-marker haplotype among those 39 individuals is
14-12-23-10-10-14
which is exactly the same as that the base haplotype of haplogroup R2 in India- Pakistan, shown above. However, if to remove the Jewish haplotypes (which, as it is shown below, are derived from a recent ancestor), the remaining 22 haplotypes contain 35 mutations, that translates into 198 generations from a common ancestor. In 22 of the 12-marker haplotypes there were 101 mutations, which give 236 generations from a common ancestor. In 7 of the 37-marker haplotypes amount of mutations in the 12-, 25- and 37-marker panels corresponded to 282, 259 and 207 generations to a common ancestor. These four figures being averaged give 246±32 generations, that is about 6,200±800 years to a common ancestor of the non-Jewish individuals of R2 haplogroup in YSearch database. This might be a good indication that haplogroup R2 had originated not in India, since the Indian R2 haplogroups were derived from a significantly “younger” ancestor who lived about 4,000 years BP (see above), that is some 2,000 years later that an older bearer of the R2 haplogroup. In any case, this question needs more detailed studies.
And when a common ancestor of the Jews of haplogroup R2 had lived?
The most frequent 12-marker haplotype among those 34 individuals, Jewish and not, is
14-23-14-10-13-20-12-12-11-14-10-29
which is exactly the same as that for the Jewish individuals of haplogroup R2 in YSearch database.
Let us now consider the Jewish haplotypes in more detail.
6-marker haplotypes
11 of the 12 Jewish R2 haplotypes are identical to each other (Fig. 50), and their
6-marker base (ancestral) haplotype is
14-12-23-10-10-14
that is the same as the most popular among known bearers of R2 haplogroup in India and elsewhere in the world.
Formally, 11 base haplotypes out of 12 give ln(12/11)/0.0096 = 9 generations, and one mutation in all twelve 6-marker haplotypes gives 1/12/0.0096 = 9 generations to a common ancestor, and the identity of these figures point out at a single ancestor for all 12 individuals in the set of their 6-marker haplotypes. However, as it has happened before, this tentative conclusion should be examined with more extended haplotypes. It is too often when 6-marker haplotypes, particularly in small haplotype sets, do not reveal mutations which occur in more extended panels of the haplotype.
12-marker haplotypes
Indeed, a move to the 12-marker tree (Fig. 51) immediately shows that there are two groups of the Jewish haplotypes, with an “older” and a “younger” haplotypes, descending from the same ancestor. Half of all 12 haplotypes still represent the base (ancestral) haplotype
14-23-14-10-13-20-12-12-11-14-10-29
Since their other mutations will be revealed by moving to more extended haplotypes, an estimate of a time span to the common ancestor based on the 12- marker haplotypes will be only tentative.
This 12-marker base haplotype is exactly the same as the most frequent 12- marker haplotype in YSearch database, only one-third of which represent the Jewish haplotypes.
6 base haplotypes from the total 12 Jewish haplotypes would point to 29 generations to a common ancestor, since ln(12/6)/0.024 = 29. The other 6 haplotypes contain 15 mutations with respect to the above base haplotype. This would lead to 15/12/0.024 = 52 generations to a common ancestor. This mismatch (29 and 52) indicates that there were more than just one common ancestor for the Jews in R2 haplogroup. In fact, Fig. 51 makes it rather obvious.
As it turned out, many more mutations have occurred in the 13-37 marker panel of the distant branch, which distinctly separates the two branches. However, even the 12-marker tree shows the principal separation of the two groups of haplotypes.
37-marker haplotypes
The 37-marker haplotype tree is shown in Fig. 52. It reveals a striking feature of R2 Jewish haplotypes. Though there are only 7 haplotypes on the tree, they clearly show that Jewish R2 haplotypes splits indeed into two quite distant groups. Statistics is insufficient to perform detailed analysis, however, there are still enough data available to make some principal conclusions. One group of haplotypes, which are located on the right-hand side of the tree (Fig. 52) and much closer to the trunk of the tree (that is, to the present times), has the same 12- marker base haplotype as shown immediately above and in the Table, and corresponds to the group of the base haplotypes around the 12-marker tree (Fig. 51). This 4-haplotype branch has only 9 mutations with respect to the base 37- marker haplotype, and refers to a common ancestor who lived only 26 generations BP, 650±50 years ago, in the 14th century.
Another group of Jewish R2 haplotypes, represented with three distant haplotypes on the left-hand side in Fig. 52, shows a base 12-marker haplotype (the 37-marker haplotype is shown in the Table):
14-23-14-10-13-20-12-12-10-13-10-31
It turned out that these three haplotypes (the left-hand side in Fig. 52) have only two mutations in their 37-marker haplotypes, that is among 111 alleles. This formally places their common ancestor only 7 generations BP, that is about two hundred years ago. All three are relatives within seven generations.
Overall, there are 21 mutations between these two base (ancestral) haplotypes in the 37-marker format. This means that these two haplotypes are separated by thousands of years of separate mutations, and, more specifically, this separation is approximately equivalent to 305 generations between the two, that is about 7,600 years. This places their common ancestors about 4,200 years BP, and fits pretty well with the common ancestor of Indian R2 haplogroup of 4,000 years BP, see above. It is very likely that the both lineages, “young” and the ancient one, are derived from the Gypsies in Europe. The “young” is traced down to the invasion time or a bottleneck time to the Jewish community, and the “older” is traced down to the ancient common ancestor in India. At any rate, both Jewish ancestral haplotypes, shown above in their 12-marker format and in the Table 2 in a 37-marker format are derived from two quite unrelated individuals, whose haplotypes had evolved from the very initial survivors in haplogroup R2, but traced down in millennia apparently to India, through the Gypsies.
Some historical conjectures
Here is a plausible story of the Jewish haplotypes of R2 haplogroup. Its ancestral haplotype
14-23-14-10-13-20-12-12-11-14-10-29
shown here in the 12-marker format, is about 4,200 years old, that corresponds to the age of this haplotype in India (see above). This haplotype had arrived to Europe apparently with the Gypsies, in the Medieval times, some 800 years BP, and got into the Jewish community. About 30-40% of the present day Jews, bearers of R2 haplogroup, are direct descendant of those Gypsies, or the Indians, on that matter. Approximately 650 years ago, apparently during the Black Plague times, in the 14th century, a bearer of this haplogroup, albeit in the mutated form had survived and fled to the Eastern Europe. This was a bottleneck for this particular haplotype. Close to half of present day Jews are descendants of that individual.
This story is a mirror one of the Jewish Q haplotypes story (see the preceding section). Apparently, the 14th century, the Black Plague times, created a number of bottleneck situations for the Jews of a number of haplotypes, and not for the Jews only.
The second Jewish R2 haplotype
14-23-14-10-13-20-12-12-10-13-10-31
in the 12-marker format, got to the Jewish community quite recently, merely two hundred years ago. It is very different from the first one. Its three bearers lived in the 19th century in Hungary, Romania and Lithuania. Their current descendants probably do not know that they are rather close relatives. Two of them differ by only 3 mutations in their 66-marker haplotypes.
From
Origin of the Jews via DNA Genealogy
Anatole A. Klyosov
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