Wednesday, August 17, 2011

Sounding the Depths goes paperback

Sounding the Depths, the "blog-book" discussed in the previous post, is now complete in eighteen chapters, readable either online -- or as a beautifully bound paperback, available for purchase via CreateSpace or Amazon.com. 

The paperback contains the complete text, but does not contain most of the figures (photos, maps, diagrams, etc.) or any of the audio and video links. For the convenience of hard copy readers, I've added two pages to the book blog, one containing the Audio-Visual Examples, another containing the Figures. (Both links can be found directly under the Blog Archive at http://soundingthedepths.blogspot.com/.)
 
The paperback, priced at $18.00, can be ordered from either CreateSpace or Amazon. (If you order from CreateSpace I'll get a larger commission, but you'll get free shipping from Amazon with an order of $25 or more.)
 
Many portions of Sounding the Depths are based on materials originally posted on this blog, so the book should be of interest to anyone regularly reading here. 

5 comments:

German Dziebel said...

Hi Victor, hope you're well. Just a heads-up regarding a recent out-of-Asia reinterpretation of mtDNA and Y-Dna tree (http://biorxiv.org/content/early/2017/01/18/101410), with my commentary in which I touch on polyphony distributions (http://anthropogenesis.kinshipstudies.org/2017/01/world-science-en-route-from-out-of-africa-to-out-of-america-first-stop-is-out-of-asia/).

DocG said...

Thanks, German. Sounds interesting. I'll look into this.

DocG said...

Ok, German, I skimmed through the paper and also your commentary on your blog. It's all very intriguing, but also completely over my head, as so many highly technical issues are raised, the sort of thing that only very experienced population geneticists would be in a position to evaluate.

All I can say is that Out of Africa is supported by the great preponderance of population genetic studies, reinforced by a wealth of archaeological research. And by "preponderance" I mean literally thousands of papers, many of which I've downloaded, read over (as best I could) and stored on my handy dandy laptop. What impresses me especially are the many highly detailed phylogenetic trees that have been produced that tend so strongly to support OOA. While there are certainly exceptions, and mysteries that have not yet been resolved, I'd think it would be very difficult to replace this huge body of evidence with something so totally different. If some multiregional model were closer to the truth, it's very hard to understand how such detailed trees could have been produced in the first place. The trees presented in the paper you cite are decidedly bare of details.

In any case, it's not for me to pass judgement on such a technical paper and I look forward to reading responses from those actually in a position to meaningfully evaluate it. I'm wondering whether it hasn't yet been peer reviewed because there is some problem with it or simply because there hasn't yet been time for the peer review process to have been completed. In any case thanks for sharing this very interesting new development.

German Dziebel said...

What's interesting about their study is that they combined Multiregional (autosomally) with Single Origin (uniparental markers). It's just Single Origin but not out of Africa, but out of Asia. How the two interact is not 100% clear to me but it's progress for both the Multiregional camp (mostly extinct in the West but well and alive in the East) and the Single Origin camp.

The quantity of phylogenies generated in support of out-of-Africa is not surprising to me. Academia is a machine and lots of graduate students in genetics wanted jobs, so they kept generating phylogenies and ran analyses. I don't want to sound caustic but I witnessed this happening.

What this team did is that they asked a question: how reliable are our inferences regarding which state (out of 2) is ancestral and which one is derived. If you compare (as I did) human mtDNA stem mutations (those that define the main clades such as N, R, L3, etc.) with those found on Denisovan and Neanderthal sequences, you see that sometimes African mutations match D and N and sometimes non-African mutations match D and N. This team decided that mtDNA (and Y-DNA) are too variable to know which state is ancestral in which species. So they went by the most common and least chaotic mutations that are found among modern humans. It turned out that non-African sequences have alleles that are most widely spread among humans (both in Africa and outside of Africa). As one enters Africa, this common fund begins to deteriorate: L3 will have all of them, but L4, L2, L3, L0 and L1 will have fewer and fewer of those pan-human alleles. Sometimes those new alleles would match those we see on Neanderthal and Denisovan sequences. This team says it's homoplasy or adaptive convergence because in so many case we MUST conclude that those matches (e.g. between more downstream haplogroups such as mtDNA C1 and Denisovans, which I compared myself) are homoplastic. So why use a double standard for "stem" mutations vs. "downstream" mutations? Plus no one has found any African sequences in the most ancient Eurasian aDNA samples, so the African sequences must have evolved within Africa from those ancient Eurasian sequences.

The rest of my observations are on my website.

I have no doubt that they are going to face difficulties getting published in the U.S. They flip so many things (diversity comes from admixture, modern African genomes are more like Neandertal and Denisovan genomes, mtDNA trees are rooted in East Asia), and academia is not set up to handle such controversies in a constructive manner. I'm just glad the "peers" who are not part of the "peer review" now get a chance to see for themselves what the authors have put together.

German Dziebel said...

Victor, FYI: Shi Huang's most recent response to my question about the mtDNA phylogeny, Johnson et al. 1983 and an out-of-Asia alternative. http://biorxiv.org/content/early/2017/01/18/101410