I love a good debate so I anticipate this conversation will be lively. As intent and tone can be misleading in written form, please take any comments as constructive and collegial. My tone can sometimes come off as brusk in written form.
Let us examine the arguments you have presented here:
First your hypothesis, not theory, is just that a hypothesis. Nothing wrong with a hypothesis. OOA is just a hypothesis. Lets talk about the scientific method a second. A hypothesis goes through rounds and rounds of repeated testing and refinement over and over again before it has reached the status of theory and then even more to become a scientific law (this takes years to decades to never). Your idea has not gone through any of this yet and is at best a well supported, in your opinion, hypothesis.
The 44k years, your stating, is on the low end of the range for the event, presuming it was a singular event. This work was done by the Reich laboratory—one of the top labs in the world for ancient genetics. [www.sciencedirect.com] A quote from this paper: “we estimate 44,000–54,000 years ago for Denisovan admixture.” “We caution that the nominal date estimate of 1,000 ± 8 generations ago for Denisovan admixture and 1,121 ± 16 generations ago for Neanderthal admixture are likely to be biased. One source of bias arises from the fact that errors in the genetic map can produce systematic underestimates of dates inferred based on linkage disequilibrium;”
Now this range really overlaps with archeology and DNA evidence show a date range of 47-55 KYA: This initial settlement of Australia occurred between 47–55 KYA, based on the dating of archaeological sites dispersed throughout the continent3,4,5,6,7, and the analysis of contemporary Aboriginal Australian DNA8,9,10,11,12,13,14,15,16,17,18.”
Genetic diveristy has been studied in world wide populations: [med.stanford.edu]
“We compared SNP haplotype heterozygosity across populations and found, consistent with
earlier reports (22), that it is highest in sub-Saharan Africa and decreases steadily with
distance from this region (Fig. 3B). “ “This trend is consistent with a serial
founder effect, a scenario in which population expansion involves successive migration of a
small fraction of individuals out of the previous location, starting from a single origin in sub-
Saharan Africa.” That is a fairly solid statement-note equivocal at all. Now they did not study Australians in this study-but did study Melanesian and Papaun. However, other studies demonstrate that these three groups are on the same clade-with Australians showing some level of isolation of Melanesians and Papaun for the past 30K years.
Using statistical based analysis like Structure, frappe, ADMIXTURE, etcc all show the same thing. Here is one (of many) example see supplemental figure 5: [www.nature.com] All OOA populations are closer to each other than to SSA (K=2). These genetic analyses then consistently split populations into Africa, Eurasia, East asia (K=3) These splits crudely demonstrate how deep the genetic split between populations is. This is all backed up by multiple independent statistical analysis of multiple different genetic features. Not a single one shows genetics coming out of Australia or New Guinea or Melanesia. NOT a single test—ever.
The same testing that could demonstrate admixture very fine structure differentiation in the british isles. That can identify where regionally people come from in the world. NOT ONE.
bf_”Tere is no meaningful evidence that all mtDNA and Y chromosomal data roots in Africa not Australia. ….... This is a huge and wild assumption.”
This is neither unsupported nor is it a wild assertion. Your seemingly of the belief that you need ancient dna to fix the origin of our species. If you waiting for that, you will probably never have an answer, ancient DNA from tropics and subtropics is hard to come by and we may well have met a limit with ~500K years even under better conditions—the DNA just becomes too contaminated and tooo degraded. This may change in the future, but probably not a lot.
Pre-10 years ago, all we had to go on was fundamental population biology and the study of phylogeny and phylo-geography. Well established and well tested methodologies. Have you read the book the Seven Daughters of Eve? Another book that places these complex topics in a way accessible to the lay person. You have heard of mitochondrial eve? With a root of mitochondrial DNA (L0) being around 2180-200k years old and predominantly only L3 daughter mtDNA found outside of africa and sister lineages L1 (east africa), L2, L4, L5, L6 found in africa (an really no where else except a bit in Near east and populations from Slave trade) . This places, firmly, the root of mitochondrial DNA evolution in Africa—there is no debate on this.
BF-“……...Just on the contrary, the oldest M and N haplogroups are detected in southern China and Australasia instead of India, ……….. ages of M and N haplogroups run, against to expectation, westwards with younger haplogroup ages going to Africa.” [www.biorxiv.org] –“
This is an interesting paper and I will need to read it further. But it is a pre-published paper and will likely change before it is published. Regardless, An exit and a return of L3 lineages into africa. Discussed more below.
BF- “…..HgL3 and both HgM & HgN are closely related, they are considered to have emerged at essentially the same time…....”
L3 is defined by 3 main mutations that distinguish it from of it “”mother” L3,4. (http://www.phylotree.org). The mutations are also present within N that has an 5 additional mutations AND M with 4 additional mutations-different from N. The most parsimonious explanation is that they had a common origin. Look here for a reassessment of the timing of divergence for these mtDNA lines: www.ncbi.nlm.nih.gov/pmc/articles/PMC3322232/
look at the supplemental file for dates:
The current best date for L3 is 67kya +/- 4 ky
The current best date for M is 49Kya +/- 1.8ky
The current best date for N is 59kya +/- 2ky
The coalescent ages reported in the biorxiv paper of the mtDNA groups L3, M and N do not align with the seminal work I referenced above. Not to rely to heavily on an authoritative argument here-the paper I reference was done by basically the best mtDNA experts there are in the field. Antonio Torroni , Silva are just the best at this work. Indeed V Cabrera is not a complete neophyte in this area. And has earlier published work showing L3 emerging from africa—disseminating across eurasia just north of the caspian and going across and down into SE asia. Later a dissemination of M1 comes back into western eurasia and africa during the paleolithic. Several other lines suggest a Paleolithic expansion from Near east/Arabia into East Africa and perhaps North africa During the Lgm.
A temporary tangent: During the LGM the carrying capacity of Arabian Glacial Refuges was decreased (Rose, 2010) which correlates with a population expansion outward and into Africa dating to ~23,000 years ago (Gandini et al. 2016, Hodgson et al. 2014, Fernandes et al. 2012, Henn et al. 2012). The first introgression of Near Eastern genetics in Western Eurasia is seen in DNA extracted from ~18,700 year old toe bone of a female in the El-Miron Cave found in Cantabria Spain and associated with the Magdalenian culture (Fu et al. 2016; Figure 4). This female was geographically located where the population with Solutrean technology existed and is only 2-400 years past the end of the Solutrean period (Cascalheira and Bicho 2015). Approximately 63% of the El-Miron individual’s genome came from a Paleolithic Hunter Gatherer population dating to ~36,000 year ago (cal. C14 years BP) and the remaining 37% came from a population with deeply ancestral Near Eastern genetics (Fu et al. 2016). The source of the Near Eastern genetics in the El Miron genetic grouping has not been directly assessed, but closely related Near Eastern genetics from a Neolithic individual excavated in Loschbour Germany best matches with contemporary Saudi Arabian populations (Lazaridis et al. 2016). The Near Eastern genetics within El-Miron are modeled to be ancestral to Loschbour with a gap of ~11,000 years (Lazaridis et al. 2014). Therefore, autosomal genetics place people from the same geographical range from which the X2 mtDNA haplogroup originated (Fernandes et al. 2012) and within a possible time frame to spread into Iberia during the LGM (Figure 4). Interestingly, the Southern Arabian regions had a long tradition of bifacial lithic technologies with leaf-like blades present before and during the LGM (Rose 2010).
Back to mtDNA and M1. An expansion out of SE asia would well explain the range and depth of Denisovian heritage—M and Denisovan genetics being mostly Eastern. Makes sense they spread at the same time. A coalescence date pf ~49Kya falls well within the range of introgression of Denisovan genes into AMH and the time frame for archeology evidence of settlement of Australia. It all fits rather nicely.