Any human geneticists here?

[Sauron]

Just curious - I have some questions about haplotype grouping.

Isn't Roland98 an expert in genetics? I can't remember if that's the field or not.

[viscousmemories]

Roland98 is an epidemiologist, so she knows a lot about genetics. Unfortunately she's rarely around these days, so you might have to track her down at her blog (http://scienceblogs.com/aetiology/) to ask her a question. TomJoe is a microbiologist too, so he could probably help as well. The Lone Ranger is very knowledgeable about genetics too. Can't think of any others off the top of my head, but I just woke up.

[TomJoe]

I stayed at a Holiday Inn Express last night ...

[viscousmemories]

Speaking of microbes?

[Roland98]

I'm not an "expert" in genetics, but I certainly use a lot of it in my research (not any directly on human haplotypes, but analysis of those is used a lot in infectious disease epi, in examining susceptibility to different pathogens, for instance). What's your question?

[Sauron]

I'm not an "expert" in genetics, but I certainly use a lot of it in my research (not any directly on human haplotypes, but analysis of those is used a lot in infectious disease epi, in examining susceptibility to different pathogens, for instance). What's your question?

I just finished receiving my results from the National Geographic sponsored Genographic Project (https://www3.nationalgeographic.com/genographic/) - Human Migration, Population Genetics, mapping DNA, etc.

They have a recorded video analysis that goes along with the results. According to National Geographic, apparently my mitochondrial DNA puts me in haplogroup - J, J*. That haplogroup originated in the Middle East around 40,000 years ago and is common to southern Europe, Anatolia, the Mideast, among Bedouin tribes, the Fertile Crescent area, and the Indus River valley. I found all that surprising, because I my mother's lineage is European, with some native American from a paternal grandfather.

Here is a map (http://www.scs.uiuc.edu/~mcdonald/WorldHaplogroupsMaps.pdf#search=%22%22mitochondrial%20DNA%22%20J%20haplogroup%22) of European Y-haplogroups and mtDNA haplogroups.

The maps for haplogroup J concentrations in Europe vary, depending upon whether you're looking at the Y haplogroup or the mtDNA haplogroup. Since I'm dealing with mtDNA here instead of Y, am I misinterpreting the data with regard to origins?

I'm also going to do the Y-DNA analysis as soon as the kit arrives.

[BDS]

Strange.

I thought you were a member of the Mayar, servants of the Valar, and an immortal race just below them in power.

[LadyShea]

That's a cool project. If I still had disposable income I would by the kit and participate. Please tell us more, Sauron, about your report.

[TomJoe]

Here is a map (http://www.scs.uiuc.edu/%7Emcdonald/WorldHaplogroupsMaps.pdf#search=%22%22mitochondrial%20DNA%22%20J%20haplogroup%22) of European Y-haplogroups and mtDNA haplogroups.

The maps for haplogroup J concentrations in Europe vary, depending upon whether you're looking at the Y haplogroup or the mtDNA haplogroup. Since I'm dealing with mtDNA here instead of Y, am I misinterpreting the data with regard to origins?

I'm also going to do the Y-DNA analysis as soon as the kit arrives.

Interesting project. Looking at the mtDNA map, haplogroup J appears to be the third/fourth most frequent haplogroup throughout most of Europe.

According to this report (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16960846&query_hl=1&itool=pubmed_docsum), haplogroup J is the 3rd most common.

Reading that paper (attached), I could design an MLGT (multilocus genotype) assay to do that. It'd be quicker and more cost effective than that primer extension assay they do.

Also, mitochondria are passed down from mother to offspring, so your paternal grandfather wouldn't factor into the equation at all. It would depend on what your mother's mother was, and what her mother was, and what her mother was ... etc etc.

[D. Scarlatti]

the National Geographic sponsored Genographic Project (https://www3.nationalgeographic.com/genographic/) ...

Cool ... an online project that involves pricking your finger rather than fingering your prick.

[Roland98]

Like Tom said, mtDNA is passed down the maternal line (it comes along with the egg, though very occcasionally it's been found from the father). Y chromosomal analysis can tell you more about the paternal lineage (though obviously, not your mother's side of it, at least not with your Y chromosome). There are drawbacks and limitations to each technique, though, and you may get slightly different results from the mtDNA than from genomic DNA, etc.

[Sauron]

Strange.

I thought you were a member of the Mayar, servants of the Valar, and an immortal race just below them in power.

Previously, true:
Sauron has regained much of his former strength. He cannot yet take physical form, but his spirit has lost none of its potency.

Times change, though. Now:
In an attempt to take physical form, Sauron, Lord of the Rings, accidentally gets his dumbass self trapped in the body of a rather ordinary 44 year old white male. The Lord of Middle Earth is mega-pissed.....

[Sauron]

Like Tom said, mtDNA is passed down the maternal line (it comes along with the egg, though very occcasionally it's been found from the father). Y chromosomal analysis can tell you more about the paternal lineage (though obviously, not your mother's side of it, at least not with your Y chromosome). There are drawbacks and limitations to each technique, though, and you may get slightly different results from the mtDNA than from genomic DNA, etc.


Right.

But why would the geographic distribution of Y-chromosome haplogroup J be different from the geographic distribution of mtDNA haplogroup J?

If they're the same haplogroup, shouldn't they have the same geographic ranges and distributions? :chin:

[Sauron]

Here is a map (http://www.scs.uiuc.edu/%7Emcdonald/WorldHaplogroupsMaps.pdf#search=%22%22mitochondrial%20DNA%22%20J%20haplogroup%22) of European Y-haplogroups and mtDNA haplogroups.

The maps for haplogroup J concentrations in Europe vary, depending upon whether you're looking at the Y haplogroup or the mtDNA haplogroup. Since I'm dealing with mtDNA here instead of Y, am I misinterpreting the data with regard to origins?

I'm also going to do the Y-DNA analysis as soon as the kit arrives.

Interesting project. Looking at the mtDNA map, haplogroup J appears to be the third/fourth most frequent haplogroup throughout most of Europe.

According to this report (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16960846&query_hl=1&itool=pubmed_docsum), haplogroup J is the 3rd most common.

Reading that paper (attached), I could design an MLGT (multilocus genotype) assay to do that. It'd be quicker and more cost effective than that primer extension assay they do.

Also, mitochondria are passed down from mother to offspring, so your paternal grandfather wouldn't factor into the equation at all. It would depend on what your mother's mother was, and what her mother was, and what her mother was ... etc etc.


Superb research skills, TomJoe. I looked for an hour and couldn't find either of these documents.

[Sauron]

That's a cool project. If I still had disposable income I would by the kit and participate. Please tell us more, Sauron, about your report.

LadyShea, send me a PM and I'll give you the access code to read the report. There's nothing identifying about it, and no way to trace it back to me. But it does come with some interactive maps and you can watch the video presentation if you like.

[The Lone Ranger]

Right.

But why would the geographic distribution of Y-chromosome haplogroup J be different from the geographic distribution of mtDNA haplogroup J?

If they're the same haplogroup, shouldn't they have the same geographic ranges and distributions? :chin:
Remember that the Y-chromosome grouping are different from the mtDNA groupings.

Say, for the sake of argument, that every one of your male ancestors for the past 20 generations was from Sweden, and so was every one of your female ancestors. If your great-great ... grandfather in Generation #21 (a big Viking type) happened to marry a woman of Middle Eastern stock, then, since you inherit mtDNA only from the female lineage (to a first approximation, anyway) and Y-chromosomes only from the male lineage, your Y-chromosome DNA will indicate that you're of Northern European stock and your mtDNA will indicate that you're of Middle Eastern stock -- even though you'd have to go back 21 generations to find an ancestor of Middle Eastern stock.


It's far too easy to misinterpret data from studies such as this. Indeed, given the amount of inbreeding between human populations (especially European populations), my personal opinion is that such studies are virtually useless. Trying to infer migration patterns from studies of a single haplotype is a more or less pointless exercise. Geneticists who're trying to do this sort of thing look at many genes, not just one.

The only thing such a study can really tell you is that there's been a considerable amount of interbreeding within your ancestry. That shouldn't be news to anyone.

Cheers,

Michael

[TomJoe]

Right.

But why would the geographic distribution of Y-chromosome haplogroup J be different from the geographic distribution of mtDNA haplogroup J?

If they're the same haplogroup, shouldn't they have the same geographic ranges and distributions? :chin:
Remember that the Y-chromosome grouping are different from the mtDNA groupings.


Correct. An mtDNA "J" haplogroup is not the same as a Y-chromosome "J" haplogroup. They're two different sets of DNA, not related in any way. The naming convention is the same, but that's about it.

[Sauron]

If anyone's still interested in this, I now have my paternal y-chromosome results back from National Geographic.

My father is from haplogroup I1a, common to Northwest Europe. This lineage has been called the "Wodan" lineage, for its clustering in Scandinavia and the North Sea / Baltic Sea.

I have a question for TomJoe and Roland98 and Lone Ranger or anyone else with skills in this area - can someone tell me what this (http://www.familytreedna.com/forum/archive/index.php?t-3494.html)means for me, since I share the I1a DYS19=15 value?

For I1a DYS19=15 the modal for the east Sami counts for 57% (highest ever obsverved) of the haplotypes while it only covers 23% for Finns in Raitio and 8% in for Finns in Lappalainen 2006. Its therefore unlikely that Sami I1a among the east Sami may have come from the Finns, rather it seems it may have come along the Norwegian coast.

[Listener]

I find the thread fascinating.

Forgive a few homespun thoughts - I'm no expert! :chin:

I've no idea if our mitochondrial DNA has any relevance to our appearance but I suspect that it hasn't - so even if we are descended (by the female line) from a very distinctive looking "dowager" we are going to look like the results of mixing all the couples involved in our ancestry.

Precisely the same (I think) will apply to the male line and the Y chromosome. What we look like will be a function of our autosomes (non-sex-chromosomes) so again, having the Y chromosome that we have is not going to make a scrap of difference to our appearance.

If Goliath of Gath produced offspring with an African Pygmy then any son would have his Y chromosome and her mitochondrial DNA and they would look like a "first cross".

The chances are that this Y chromosome and the mitochondrial DNA will be split up in the next generation (unless a son breeds with a close relative of his mother e.g. her sister or his sister)

The distinctive appearance of the "first cross" will (most probably) be lost as generation after generation gets autosomes from the local population until individuals just look like natives of their particular region.

If you follow the male line though, all the men will have Goliath's Y chromosome. If you follow the female line, all the women will have that African pygmy's mitochondrial DNA.

To learn anything at all from DNA types you need to sample entire populations and study the distribution statistically - individuals can't really learn anything from their own DNA.

There was a T.V. documentary about "blood of the vikings" where the incidence of a particular Y chromosome was taken as an indicator of the distribution of viking settlers in the British isles. The men with that particular Y chromosome didn't have to look a bit like vikings, they would look like the product of all their male ancestors' "wives".

Perhaps the real experts will let me know if I've got the gist right and what I've missed?

[The Lone Ranger]

If anyone's still interested in this, I now have my paternal y-chromosome results back from National Geographic.

My father is from haplogroup I1a, common to Northwest Europe. This lineage has been called the "Wodan" lineage, for its clustering in Scandinavia and the North Sea / Baltic Sea.

I have a question for TomJoe and Roland98 and Lone Ranger or anyone else with skills in this area - can someone tell me what this (http://www.familytreedna.com/forum/archive/index.php?t-3494.html)means for me, since I share the I1a DYS19=15 value?

For I1a DYS19=15 the modal for the east Sami counts for 57% (highest ever obsverved) of the haplotypes while it only covers 23% for Finns in Raitio and 8% in for Finns in Lappalainen 2006. Its therefore unlikely that Sami I1a among the east Sami may have come from the Finns, rather it seems it may have come along the Norwegian coast.


I'm no human geneticist, so I'm not particularly familiar with the naming conventions.

The yDNA Haplogroup I Subclade I1a seems to trace back to a common ancestor who lived somewhere on the Iberian Peninsula (Spain or Portugal) roughly 15,000 years ago, toward the tail end of the last Ice Age. His descendants spread north, perhaps following the retreating ice, and the I1a group is common in Scandinavia. It's also common in the British Isles, Germany, and much of the rest of northern Europe. This would be consistent with the founding population leaving remnant populations behind as they moved northward. A possible migration pathway would be northward through France and Britain (during the last Ice Age, the sea level was low-enough that the British Channel was dry land, so you could simply walk from France to Britain), then across northern Europe to what's today Scandinavia.


The Sami people are indigenous to what's today northern Sweden, Finland, Norway, and parts of Russia. There are several different genetic haplotypes in the Sami people that are rarely found in other peoples, and tracing of the yDNA markers leads to the conclusion that they're derived from Iberian stock of around the time of the last Ice Age (unsurprising -- that's where the I1a group comes in), but that the majority of yDNA markers are of eastern European origin.

After the Sami people wound up in Scandinavia, the relatively unchanging nature of their genetic makeup suggests relatively little genetic mixing with other groups. They may have had migrants moving out and spreading their genes to other parts of Europe, but very few outsiders were coming in to that region and bringing new genes with them, apparently.

Apparently, you're descended from a group of people who moved into Scandinavia toward the end of the last Ice Age, and then stayed put, remaining surprisingly isolated (genetically speaking, at least) from the rest of Europe.

Cheers,

Michael

[The Lone Ranger]

I find the thread fascinating.

Forgive a few homespun thoughts - I'm no expert! :chin:

I've no idea if our mitochondrial DNA has any relevance to our appearance but I suspect that it hasn't - so even if we are descended (by the female line) from a very distinctive looking "dowager" we are going to look like the results of mixing all the couples involved in our ancestry.

Precisely the same (I think) will apply to the male line and the Y chromosome. What we look like will be a function of our autosomes (non-sex-chromosomes) so again, having the Y chromosome that we have is not going to make a scrap of difference to our appearance.

If Goliath of Gath produced offspring with an African Pygmy then any son would have his Y chromosome and her mitochondrial DNA and they would look like a "first cross".

The chances are that this Y chromosome and the mitochondrial DNA will be split up in the next generation (unless a son breeds with a close relative of his mother e.g. her sister or his sister)

The distinctive appearance of the "first cross" will (most probably) be lost as generation after generation gets autosomes from the local population until individuals just look like natives of their particular region.

If you follow the male line though, all the men will have Goliath's Y chromosome. If you follow the female line, all the women will have that African pygmy's mitochondrial DNA.

To learn anything at all from DNA types you need to sample entire populations and study the distribution statistically - individuals can't really learn anything from their own DNA.

There was a T.V. documentary about "blood of the vikings" where the incidence of a particular Y chromosome was taken as an indicator of the distribution of viking settlers in the British isles. The men with that particular Y chromosome didn't have to look a bit like vikings, they would look like the product of all their male ancestors' "wives".

Perhaps the real experts will let me know if I've got the gist right and what I've missed?


That's pretty-much accurate.

Mitochondrial DNA has to do with the fact that mitochondria are, in effect, smaller cells living inside our body cells. They have their own DNA and reproduce independently of the rest of the cell. So, their DNA is quite separate from the nuclear DNA that determines your hair color, eye color, etc. (Strictly speaking, mitochondria are ancient bacterial cells that invaded larger cells; the arrangement turned out to be mutually beneficial. This is what the evidence strongly suggests, anyway.)

Since mitochondrial DNA is inherited only from your mother and Y-chromosome DNA is inherited only from and by males, mDNA and yDNA will continually be mixed and remixed in a family's history. So, you can indeed track mDNA only through the female line (males, of course, inherit mDNA, but cannot pass it on to their children, so every male is a "dead end" as far as mDNA is concerned). Similarly, since only males inherit Y chromosomes, yDNA can be traced only along the male line.


So, knowing that you have the mDNA from some particular group certainly doesn't imply that you'll resemble members of that group, given that there could have been a great deal of interbreeding in your lineage. It only means that your great, great ... great grandmother was from that group.

In the example I gave above, if your grandsire 30 generations back was Norse and he happened to marry a Middle-Eastern woman who then gave birth to your 29th-generation grandmother, who gave birth to your 28th-generation grandmother and so on, your mDNA is of Middle-Eastern origin, even though you'd have to go back 30 generations to find an ancestor of Middle-Eastern extraction.

The same sort of thing could be done with a yDNA analysis. That's why, as mentioned, knowing an individual's haplotypes really doesn't say very much.




Look at it this way. You inherit 1/2 of your nuclear DNA from each parent. That means you inherit 1/4 of your nuclear DNA from each grandparent, 1/8 of your nuclear DNA from each great-grandparent, and so forth.

If, 30 generations ago, your direct maternal ancestor was Middle-Eastern, while every other relative you've had since then was Norse, then you have "Middle-Eastern" mDNA. So what? The odds are overwhelmingly against you having inherited even a single gene of nuclear DNA from that 30-generations-back grandmother. So, though you have "Middle-Eastern" mDNA, you most-certainly will not look like you're of Middle-Eastern descent, because you won't have any Middle-Eastern nuclear DNA.

Cheers,

Michael

[fragment]

The yDNA Haplogroup I Subclade I1a seems to trace back to a common ancestor who lived somewhere on the Iberian Peninsula (Spain or Portugal) roughly 15,000 years ago, toward the tail end of the last Ice Age. His descendants spread north, perhaps following the retreating ice, and the I1a group is common in Scandinavia. It's also common in the British Isles, Germany, and much of the rest of northern Europe. This would be consistent with the founding population leaving remnant populations behind as they moved northward. A possible migration pathway would be northward through France and Britain (during the last Ice Age, the sea level was low-enough that the British Channel was dry land, so you could simply walk from France to Britain), then across northern Europe to what's today Scandinavia.
To attempt to put things in perspective (in my own amateur way), at the time of the last glacial maximum, about 18,000 years ago, the Iberian peninsula and southern France were the only places in western Europe where humans lived. This area did get pretty cold in winter, but there was plenty of large game for them to hunt. They left (http://en.wikipedia.org/wiki/Lascaux) pictures (http://en.wikipedia.org/wiki/Altamira_%28cave%29).

As the climate warmed up, the ice receded and ecological zones moved northwards. With the genetic picture TLR gives, it sounds like the Sami are partly descended from people who followed the climate they had thrived in and the animals they hunted through northern Europe until they reached the Arctic and could go no further. As TLR notes, some of their descendants remained behind along the way, and interbred with other groups of people who came later.

There's some links about Sami genetics on the wiki page (http://en.wikipedia.org/wiki/Sami_people). TLR's advice about not reading too much into mtDNA and Y-DNA seems wise, though.