Mitochondrial haplogroup origin dating & placing, is it actually that reliable?

[Saetro]

The Seven Daughters of Eve (2001) by Bryan Sykes is a good introductory book on human mitochondrial DNA, while methods of studying mitochondrial genomes have advanced greatly since the 2000s. When he wrote these bestselling popular science books on human genetics, peer-reviewed scientific papers on human mitochondrial DNA were hardly available. There are limitations in calculating the mtDNA substitution rate based on fossil calibration or archaeological evidence. To circumvent the problem, Fu et al. (2013) calculated the human mtDNA substitution rate directly from complete mitochondrial genomes of ten ancient modern humans, for which reliable radiocarbon dates are available.

"Blood of the Isles" reads now like dated science.
I also read "7 daughters of Eve" when it came out, but now it reads like fiction: maybe one of Kipling's Just So stories.
Can still be inspiring these days, but not for everyone.

Fu's paper is wonderful.
Just after it came out there were comments that these 10 samples did not represent the branch that they knew and so on.
(Probably still tucked away in this forum. Look for old posts.)
So Fu (2013) is still not regarded as the last word.

The important point is that averages represent groups, but we each test as individuals who can be widely deviant from the average.

[Judith]

Blood of the Isles was one of the first books I read too. An easy read and inspired me to learn more. The original scientific papers are hard work and you may only understand the introduction and discussion the first time through but I have more on each reading. Even the papers are overtaken virtually every year this is a field which is developing fast.
Use google scholar to find the papers and the use cited by to find papers which build on it.
Depending which haplogroup you are looking for you will find lots or just some information. Mtdna H is the most difficult because authors just report H and all H clades are NOT the same.
Also useful are ftdna projects where you can read without joining and Eupedia has been mentioned. Treat all with a pinch of salt. There are more blogs with opinion than facts.

[TuaMan]

These estimates are not pseudoscience, but should be taken with due caution.

Hey Mega, question for you (or anyone else who knows, feel free to chime in as well) -

In this paper, if you look at tables 2 and 3 with the mtDNA coalescence ages, you notice there's a big discrepancy for many mtdna between the "observed age" and the "expected age." For example if you look at mtdna X, the authors calculated an observed age of 31.9 kya, versus an expected age of 66.6 kya. Why the massive difference between the two? I tried skimming the paper to find out how they calculated observed vs expected and if they mention anything about reconciling the two but I couldn't find anything.

[Megalophias]

In this paper, if you look at tables 2 and 3 with the mtDNA coalescence ages, you notice there's a big discrepancy for many mtdna between the "observed age" and the "expected age." For example if you look at mtdna X, the authors calculated an observed age of 31.9 kya, versus an expected age of 66.6 kya. Why the massive difference between the two? I tried skimming the paper to find out how they calculated observed vs expected and if they mention anything about reconciling the two but I couldn't find anything.

In this paper they are trying to figure out where haplogroup N spread from, and the idea is that the haplogroup N subclades should be older near where the expansion began, and younger as they get further away. The model they are testing assumes the expansion began in East Africa (Djibouti) at the age of L3, and ended in Australia at the age of haplogroup S, so the further away from Djibouti the haplogroup is centred, the younger the expected age will be. Since haplogroup X is found in West Eurasia and Africa, it is close to the presumed starting point, and so according to this model its expected age is very old.

So the expected age is just a feature of this model calculated based on distance from Africa, it is not anything applicable outside of this paper. The observed age is the actual genetic TMRCA of the haplogroup. There is a big gap between them because haplogroup X didn't originate immediately after Out-of-Africa, the model is a poor fit.

[TuaMan]

The observed age is the actual genetic TMRCA of the haplogroup. There is a big gap between them because haplogroup X didn't originate immediately after Out-of-Africa, the model is a poor fit.

Hmm, I get that TMRCA of 30,000 kya means its most recent coalescence is way too young for OOA, but isn't X a primary branch of N, which is at least 60,000 years old? So couldn't X also have formed nearer to 60,000 years ago shortly after the coalescence of N, but just went through a big bottleneck until 30,000 years ago when it began its first real expansion?

[Megalophias]

Yes, that's right. X would have formed (by definition) when N coalesced, since it is a primary branch of N, and then must have had a long period without growth.

The idea is that the *average* age of haplogroup expansion (not just considering one case) should be greater in the areas first colonized by modern humans. This does not necessarily make sense, though. For instance West Asia and North Africa were quite arid, so they could have had smaller population sizes and more bottlenecks during the Ice Age than relatively warm and moist South and Southeast Asia, regardless of where modern humans reached first.