Wednesday, January 22, 2014

Updated I-L160 tree

We've had several sets of Geno 2.0 results and I have updated the tree for I-L160 (which is called I2a1b at FTDNA, it's part of I-M26 "Sardinian").

I've added CTS787 to the tree for the first time. I had omitted it on some earlier trees, it was thought to be equivalent to Z118. But now we have a person who is CTS787+ and negative for all downstream SNPs including Z118.

It's also become clear that there is a large and complex group of people who are PF4088+ and CTS11338-. There are several SNPs that have been found in this group, but so far they have each been found in only one family: L1299, PF5084, CTS8386. There are 8 people so far with PF4088+ CTS11338- results and they have 67 and 111 STR markers that are quite different from each other.

The top tree is thanks to Zdenko Markovic and the handwritten tree is my own--Bernie

Top level SNPs in I-P37.2

Click on tree to enlarge. There are five main branches of I-P37.2 and this tree shows how they are related:
the M423+ branch is CTS595-
and the other four branches (L1286, L880, L1294 and M26) are all CTS595+.

We still need to sort out these four CTS595+ branches. It's possible that PF3983 will be useful: we know that three branches are PF3983+ (these three branches are L880, L1294 and M26) but we aren't sure what the status of PF3983 is for the L1286 group. (We know that the M423 branch is PF3983-). But we have been unable to determine a PF3983 result for L1286 at Geno 2.0 or FTDNA, probably L1286+ people
have some mutation in the area of PF3983 that is interfering with the test.

Eventually we will have full Y/Big Y sequencing for all of these groups that will help us figure out the rest of the branching pattern. We have  multiple Big Y tests in progress for people in L621, L161, L233 and M26 but none for the other groups which are all much rarer.

We already have at least one Geno 2.0 result for every group except I-L1295 "France-Scotland", and we have learned a lot from Geno 2.0, especially for the L621, L161 and M26 groups. At this point I think we have learned most of what there is to learn from Geno 2.0, and I am recommending it mainly for people in the I-L160 group (which is part of M26).

(The top tree is thanks to Zdenko Markovic and the handwritten tree is my own--Bernie)

Friday, January 3, 2014

(from Sept 2013) Tree for I-L160

(from Sept 2013) Main branches of I-M26

All known I-M26 is either F1915+ or L672+. I-L672 is by far the larger group.

I-L672 can be L160+, PF6947+ or can be I-L672*, with the * meaning no known additional derived SNPs beyond L672.
I-L160 is by far the biggest group, and it has at least 10 SNP defined branches of its own, see the separate L160 tree.
I-PF6947 is a small group known only from Ireland.
All of the I-L672* "France" and "DYS413=19,22" groups and most or all of the "generic" group are more recently related to I-PF6947, not I-L160. We know this from 111 marker results, they share some distinctive marker values, in particular DYS532=9.

(from July 2013) Geno 2.0 Results for I-M26 Maltese gentleman

We now have a Geno 2.0 CSV file for someone with paternal ancestry from Malta (an island in the Mediterranean, between Africa and Sicily/Italy). He clearly is related to the I-M26 people in Sardinia. The question I have is, does he have recent ancestry from Sardinia/Sicily/Italy, or has his paternal line been in Malta for thousands of years?

(from July 2013) L160 Tree with Geno 2.0 SNPs, updated and simplified

We have nine Geno 2.0 results for I-L160 which fall into eight different subgroups. Unless one of your relatives or close matches have done Geno 2.0, it's impossible to predict what group you will belong to. And it's very likely that we will discover new groups when more I-L160 people do Geno 2.0. All of the SNPs on this tree are included in the Geno 2.0 test which costs $199, and they all can be ordered at FTDNA for $39 each. But you would need to order at least two SNPs and probably many more, so Geno is probably a better idea.

(from July 2013) Early Branches of I-M26

Four branches of I-M26 have been known for a few years:
M26+ L672+
M26+ L277+
M26+ L277+ L247+
M26+ (L672- and L277-)

What's new is that several L672+ men and one L247+ man have completed Geno 2.0 tests. We learned that the L247+ man is ancestral for 17 SNPs that previously were thought to be equivalent to M26. Now the M26+ L672- L277- man is doing the Geno 2.0 test, and I expect that he will be on his own branch that split off even earlier, and he will be ancestral for some of the 36 SNPs that currently give results equivalent to M26.

The Mexican-American M26+ L277+ L247+ also had two new SNP results at Geno 2.0: he is F1915+ and YSC0000078+. These occur somewhere in the area of L277 or L247.

(from July 2013) M26 Men in Sardinia

It's well known that around 40% of men on the island of Sardinia belong to the I-M26 paternal haplogroup, but which subgroup? And can that tell us anything about where M26 originated? Did M26 people expand "out of Sardinia"? Or did M26 arise on the continent, and a few M26 made it to Sardinia early in its human history?

It's starting to look like the second scenario is closer to what happened. The I2a Project at Family Tree DNA (FTDNA) has around 8 I-M26 members who were born in Sardinia, or who have fathers or grandfathers born in Sardinia. From testing at FTDNA we know that they are all likely L160+, the I-L160 group is the most common group of I-M26 but there are several L160- branches known only from continental Europe and Britain and Ireland. The design of the new Genographic 2.0 test involved sequencing several men living in Sardinia, so it includes many new SNPs relevant to these men. So far, one Sardinian-American man and one Maltese ancestry man belong to the PF4190 branch of I-L160. I think probably many or most I-M26 men living in Sardinia will belong to this branch, but we will need more testing to be sure.

(from April 2013) Updated I-L160 Tree

Click on picture to enlarge. At this point we have 6 groups of L160+ (and the Z110+ group only known from 1000 Genomes Project sequences). I don't know if F1295+ and PF4088+ are the only basic branches of L160+ or if there will be more. Usually I can tell if someone belongs to Z118+ or Z106+ based on 67 marker results, but we don't have enough results to make predictions for the other groups. About 40% of L160+ belongs to Z106+, but I don't know how big the other groups will turn out to be.

F1295, PF4088  and CTS11338are available for order as individual SNPs at Family Tree DNA, but each costs $39. My recommendation is that L160+ people order the Genographic 2.0 test for $199, it will test all the SNPs on the tree above and many more (except for a few of the Z SNPs and L1299).

(from Jan 2013) I-L160 Tree

Another Geno 2.0 result this week creates another level in the I-M26 tree, and now the L160 section is so large that it requires its own diagram, see above.

Someone with paternal ancestry from the Azores is the first person at Geno 2.0 to test L160+ and PF4088-. We have one English ancestry man and one Welsh ancestry man who have L160+ PF4088+ results from Geno 2.0.

The Azorean person is also F1295+ and PF6950+. He is the first person in I-P37.2 to be derived for those SNPs. 

More later.

(from Jan 2013) I-M26 Tree

This tree includes all known SNPs in I-M26. The format is based on this tree which shows mainly Z SNPs discovered by volunteers looking at 1000 Genomes data:
There are probably millions of men belonging to I-M26, they live in Spain, Portugal, France (up to 5% of men in some parts of these countries); and in descendants of Spanish, Portuguese and Frenchmen in the Americas etc, and they also comprise about 40% of the men on the island of Sardinia.   I-M26 is found in less than 1% of men in Ireland, Great Britain, the low countries, western Germany, Switzerland, the Italian peninsula etc. but it is very characteristic of western Europe and has a long presence there (i.e. 5,000 year old I-M26 skeletons have been found in southern France and near Paris).

There are at least 11 different SNP-defined groups on my tree, but I estimate that over 90% of I-M26 men belong to the green, blue, or red groups. With 67 STR markers, almost everyone can be placed in one of the minor groups, the green group, the blue group, or one of the red groups. But we don't yet have enough results to know if there are STR patterns that can distinguish between the three red groups.

Probably the PF4189+ group will have many more members besides the "1 English Family". But I don't know which of the three red groups will be biggest when we have done more testing. Unfortunately, some of the important tests are not offered by Family Tree DNA (Z105, Z120, CTS11338, PF4189); these are only available as part of the Geno 2.0 test at this time.

In the near future with more Geno 2.0 results we will learn much more about the three red groups. And we will learn if the PF6947+ group is a major part of the green group or not. But unfortunately Geno 2.0 will probably not teach us much more about about the green group--there is surely a SNP out there that is shared by almost all of the green group, but it hasn't been found at Geno 2.0 or in WTYs so far.

(From Dec 2012) Geno 2.0 Heat Maps

Genographic Project 2.0 heat maps for paternal haplogroup I-M26 and I-PF4189. They are exactly the same, and supposedly Sardinia doesn't have these groups. Are the I-M26 people who make up 40% of men in Sardinia considered a different, more specific haplogroup?

Click on pictures to enlarge.

(from March 2011) Z SNPs added to I-M26 Tree

Here is a drawing of the current I-M26 tree (March 2012), click on it to enlarge. I will write more later.

(from 2011) L672 placed in I-M26 Tree

Since my most recent post we have tested the new SNPs in many different I-M26 people from all the major subgroups. All were L673+ and L707+ so I think L673 and L707 are equivalent to M26. (It's possible that these SNPs and L158 and L159 are actually above M26, not equivalent. But the other major groups of I-P37.2 are ancestral (negative) for all these SNPs, there are a few small groups who have not tested all of them yet).

L672 is more interesting, some I-M26 people are L672+ and some are L673- which introduces a new level in the tree. It turns out that all the people with YCAIIa,b=11,21 (or who are close matches to these people even if they have different values) are L672+. The people who are expected to test L277+ are L672-, and these people have YCAIIa,b=18,21 and are quite different in all their markers from the L672+ people. (L277 is placed in quotes because Family Tree DNA cannot make this test work for L277+ people, but we have results from 23andMe).

(from 2011) Tree of Haplogroup I-M26

(Click on tree to enlarge)
This is a hasty phylogenetic tree I drew up showing the major groups of I-M26 (which has been known as I2a1 for the last 3 years or so). This is the group well-known for occurring in around 40% of men in Sardinia. But in the last three years we have discovered several new SNPs that split M26 into more specific groups which occur in different regions, all in westernmost Europe.

The Sardinian M26 seems to be all L160+ which makes an out of Sardinia origin unlikely. Spain and France contain most of the major groups of M26 and I think our M26 ancestors started expanding from somewhere like southern France, up the Atlantic coast to northern France, Britain and Ireland, and probably up the Rhine to Western Germany and Switzerland. A very few M26 made it to Denmark, Norway and Sweden. The single M26 I know of from Iceland has a 37 marker STR haplotype similar to some Irish M26+ L160- people. There are also a very few M26+ people from Jewish families from Poland, Belarus and Odessa, I believe most of these probably go back to Sephardic (Spanish/Portuguese Jewish) roots, and in fact some of the families have a tradition that their paternal ancestors were Sephardic.

Some specifics about the tree: the green triangles show the periods when population have been expanding, the L160+ triangle is the biggest because this group is most common. The dates when the expansions started and when the different groups split is very loosely based on Ken Nordtvedt's work but I didn't attempt to show his calculations very accurately. Not shown is M161 which was discovered before the year 2000 but has never been found in testing at Family Tree DNA or as far as I know at 23andMe. Also not shown is the Z106 SNP, this is a subset of L160+ which probably occurs in about 1/3 of Spanish L160+ and in a much smaller percentage of English and other northern L160+. The L277 SNP is placed in quotes because FTDNA has not been able to sequence the L277 area, our information on L277 comes mostly from 23andMe. Finally, there is yet another SNP called L707 which shows the same pattern so far as L672 and L673, we are currently testing all of these in the L277+ group.

(Note: in the final line of the tree picture "happened in position A or B" should be "B or C")