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[QUOTE]Originally posted by Clyde Winters: [QB] [QUOTE]Originally posted by Doug M: [qb] [QUOTE]Originally posted by capra: [qb] [QUOTE]Originally posted by Doug M: If we believe the Saharan pump theory, then as populations "pulsed" in waves through the Sahara during various wet phases they may have had unique lineages that were spawned and then left Africa as a result of later dry phases.[/QUOTE]Which waves of what are tied to which specific, actual wet phases, though?[/qb][/QUOTE]The only way to find out is more data from the Sahara, not just using the same reference populations along the coasts of North Africa. I guess what I am saying is ultimately a lot of the problem right now is the limited sample sets they use to model "North Africa" DNA. If most samples are from sites close to the coast then of course you are likely to see "mixture" with populations from outside Africa. But all populations in North Africa don't live close to the coasts. And during the various wet/dry phases it is not only likely that there are 'extinct' lineages representing populations that died out in the area, but also other "connector" lineages that are not represented in the DNA of modern "reference" populations along the coasts. [QUOTE]Originally posted by capra: [qb] [QUOTE]From the way it looks in the current distribution TO ME, U6 was much more wide spread at a very early point of time between Africa, the Near East and Europe. It could be that the populations carrying these lineages were part of a wave of Africans pushing out across North Africa into the Levant in Europe over 40,000 years ago.[/QUOTE]It could, is there any archaeological evidence that indicates such a wave? Modern human populations were already well established outside Africa by then, and of course were still doing fine in Africa, so there is no reason to favour Africa -> Eurasia or Eurasia -> Africa a priori. [/qb][/QUOTE]This isn't about what is greater or lesser in terms of geography. Firstly this is more an issue of semantics. Populations moving out of Africa 50 to 60 thousand years ago or even 40,000 years ago in Eurasia, were not closely similar in appearance to modern populations in the same areas. This is why calling them "Eurasian" is misleading. It would take a long time for "Eurasians" to diverge from Africans in terms of phenotype. But ultimately the point I am making is that they are guessing where these lineages arose because there are so many gaps. And that is what I mean by "waves". So if you set the clock back to 50,000 years ago, what I am saying is there would be a solid chunk of North Africa, the Near East and Europe with populations carrying U lineages, as part of an expansion or "wave" of populations carrying said lineage. Over time many of those populations moved or died out and other lineages became dominant in those areas. So what you see today is only a remnant of that ancient genetic expansion. It is hard to tell clearly where exactly a lineage like U arose in that scenario. The only thing they are doing is just assuming that any remains they find going back in time carrying a specific lineage represents the "origin point" of that lineage which does not have to be true. For example the example of U6 in Romania from the 35,000 year old remains there. [QUOTE]Originally posted by capra: [qb] [QUOTE]That said the more confusing part to me is why there aren't more 'downstream' lineages of L found in "sub saharan" Africa given that they are the oldest human lineages. Somehow it makes no sense that humans outside of Africa who are less than 100,000 years old have all the downstream lineages J,M,N, U R and so forth while populations in Africa are still carrying only L lineages.[/QUOTE]There is no 'only L', all those Eurasian lineages are sub-branches of L3 and no more or less 'downstream' than lineages in Africa which are labelled 'L'. There is no such thing as haplogroup L apart from all the others. The terminology originated when the phylogeny as still poorly understood. I suppose you will interpret this as a conspiracy, but in any case understand that, say, L4b2 is equivalent in age and phylogenetic position to R, and L3a to M. [/qb][/QUOTE]I am just saying the terminology as currently used to distiguish "African" (meaning L lineages) from (Non-African) (NON L or M and N derived lineages)is a bit misleading. Again note the topic of the thread and the way "African" DNA is seen as synonymous with "Sub Saharan" DNA as if the rest of Africa is "Non African" in terms of DNA. Such semantics only reinforces this idea of a "split" in the DNA tree going back to the tree found in the Laziridis papers which put OOA populations on a Non African branch. And to be clear, there is no "conspiracy" here. Many papers openly and bluntly suggest that the "Neanderthal interlude" is the reason for modeling the human DNA tree this way. Implying that "Eurasians" are separated from "Africans" by Neanderthal or Denisovan or whatever mixture. And the idea of North African DNA being "Eurasian" and not "African" is the subject of many other papers as well. Meaning it is hard to show the true genetic relationship and where various major branches arose with a model that claims a 'hard split' between African and Eurasian DNA and back migration into North Africa, which would effectively erase most direct evidence of any OOA lineages moving out of Africa. But again, they are using a limited set of "reference" samples for North Africa which produces this flawed model. They don't even have or use reference populations from Northern Sudan and Upper Egypt as reference populations in the "North African" data set. [QUOTE]Originally posted by capra: [qb] [QUOTE]Dead end referring to populations who carried genetic branches or lineages that died out because the populations carrying them died out. And those dead end branches go back 300,000 years or more to include even older hominid types that we don't know about.[/QUOTE]Yes, certainly. [QUOTE]According to SNPS haplogroups which are the age of the first extinction event tend to be around 45–50 kya. Haplogroups of the second extinction event seemed to diverge 32–35 kya according to Mal'ta. The ground zero extinction event appears to be Toba during which haplogroup CDEF* appeared to diverge into C, DE and F. C and F have almost nothing in common while D and E have plenty in common.[/QUOTE]I'm not sure what you have in mind by the second extinction event, but I agree with you that the timing of Toba does match suspiciously well with the break-up of CDEF. This was followed by the severe cold and aridity of MIS 4/the Early Pleniglacial, so whatever population growth began after Toba (if that's really what we are seeing in the phylogeny) could have been arrested by the climate for some time, depending where they were actually located of course. I don't know why you say D and E have a lot in common and C and F don't? Seems like the opposite to me. [QUOTE]Note that my theory surrounding the process of the spread of the U lineages also applies to M and N as well and many other lineages. All of these lineages arose in the same time frame: 40 - 50 KYA. Which is odd.[/QUOTE]The very rapid growth of M and N (and R), as well as C, D, and F (and K), ending with a great many basal branches spread out across most of the globe, can hardly be the result of anything but the population boom of modern humans expanding rapidly outside of Africa, so it makes perfect sense that they would all date to about the same time at the beginning of the Upper Palaeolithic. That E, and several basal branches of L3, are about the same age, likely means they were linked to the same cause, whatever exactly that was. Could be tied to the climate getting milder and wetter beginning about 60 000 years ago, though obviously that can't be the whole story. [/qb][/QUOTE]The question is where did this massive bottleneck occur? Did it occur in Syria? Iraq? Arabia? Central Asia? That is my point. If all these lineages spread from the same point and it was NOT in Africa then where was it? Because I assume it represents a bottlenecked population holed up in some refuge as a result of climate or other natural factors. Finding this site would be key to understanding what happened. But again all of these paths lead back to some major bottleneck population from which all these branches split. So they couldn't have been going in all directions if they were part of a large bottleneck after OOA. But it could be that this bottleneck was closer to Africa as well. We see evidence of it but nobody knows where it occurred. Hence the recent papers on "Basal Eurasian" which attempts to identify that bottlenecked population but in a very clumsy way IMO: [QUOTE] “This deep lineage of non-African ancestry branched off before all the other non-Africans branched off from one another,” he said. “Before Australian Aborigines and New Guineans and South Indians and Native Americans and other indigenous hunter-gatherers split, they split from Basal Eurasians. This reconciled some contradictory pieces of information for us.”[/QUOTE] https://hms.harvard.edu/news/new-branch-added-european-family-tree [QUOTE]Originally posted by capra: [qb] [QUOTE]But calling these wandering populations of Africans in Eurasia "Eurasians" is misleading. These were Africans genetically and physically.[/QUOTE]They were genetically more related to modern Eurasians than to modern Africans, naturally, and physically there is no reason why they would be closer to modern Africans than to other tropical populations such as Papuans. They were the ancestors of Eurasians, they had undergone a bottleneck that made them genetically distinctive, they lived in Eurasia, and the whole point of names is to distinguish things - so we can call them ancestral Eurasians. Your complaining about it makes no sense to anyone else. [/qb][/QUOTE]This isn't about their relationship to modern populations. The point is that semantically the label makes no sense. Those populations and all their genes originated in Africa. We label populations and genetic lineages based on where they came from not where they wind up later. And obviously all these populations originated in Africa. That is why I am saying it is misleading. None of these populations would resemble "modern" Eurasians in most cases. And all "Eurasians" don't look the same today either. But ultimately my reading of the relevant papers says that the mixture with Neanderthals and other hominid species is the reason for this hard distinction between "Eurasian" and "African". So we have a bottleneck and during that major bottleneck a lot of mixture occurred with other hominids meaning the populations leaving from that point weren't "African" anymore, as they would have been before that which would have been the initial OOA population. [QUOTE]Originally posted by capra: [qb] [QUOTE]The problem is nobody has been able to find any remains from the populations in the time frame of 40,000 to 50,000 years ago. And certainly no DNA has been extracted from such remains.[/QUOTE]Huh? Do you mean in Africa? Ust' Ishim man from Siberia is ~45 000 years old. [/qb][/QUOTE]Of course, that is true but we can't depend on one man from Siberia to fully flesh out the DNA tree unfortunately. Not only that but the significance of this man was the amount of Neanderthal DNA found in him. Yes that is important for our knowledge of the past, but again modern science is trying to do a lot in terms of theoretical models of ancient DNA history with limited hard data. But ultimately at this point this DNA only reinforces the idea of OOA populations being bottle necked and then having a lot of admixture with other hominids as the distinguishing marker for "Eurasians" versus "Africans"...... "Basal Eurasian" only comes up much later as a result of less than expected Neanderthal mixture in Neolithic populations related to the spread of farming, which begs the question is this a result of later African gene flow or something else. Also this bottleneck plus neanderthal mixture model kind of contradicts the Southern vs Northern migration route into Asia. Meaning if the Northern and Southern routes were separated by thousands of miles and involved different populations at different times, how could they all be related to a single "bottle necked" population outside of Africa somewhere? Sure it could have happened but depending on where this theoretical "bottle necked" refuge was it would be hard for the Southern route to have started in Africa or Arabia. [QUOTE] A key issue in the estimation of OoA dates using autosomal data is that the Yoruba of West Africa are commonly used as the reference point for AMH departure from East Africa, despite mtDNA and autosomal studies indicating a deep time separation of West and East African populations.98 Furthermore, many approaches assume that modern human groups are related via a simple bifurcating tree, which is likely an over simplistic view of human history. Another fundamental problem with many of the estimates used to date divergence times is that they are highly dependent on the choice of mutation rate, which can be estimated using a wide number of different approaches that often yield disparate values. The accumulation of heritable changes in the genome has traditionally been calculated from the divergence between humans and chimpanzees at pseudogenes, assuming a divergence time of around 6–7 million years ago (phylogenetic mutation rate 2.5 × 10−8/base/generation). With the advent of deep sequencing, it is now possible to directly calculate the mutation rate among present-day humans from parent-offspring trios. Using this method, the mutation rate has been estimated at 1.2 × 10−8/base/generation, half of the phylogenetic mutation rate, thus doubling the estimated divergence dates of Africans and suggesting that events in human evolution have occurred earlier than suggested previously.98–104 More recently, Harris reported that the rate of mutation has likely not been stable since the origin of modern humans, revealing higher mutation rates (particularly in the transition 5′-TCC-3′ to 5′-TTC-3′) in Europeans relative to African or Asian populations thus suggesting it may be too simplistic to assume the mutation rate is consistent across different populations.105 In addition to this, there is also considerable uncertainty in terms of the effect of paternal age at time of conception in the mutation rate with respect to ancestral populations.102 Recent work has attempted to mitigate some of these difficulties by instead calibrating estimates against fine-scale meiotic recombination maps. Using eight diploid genomes from modern non-Africans, Lipson et al calculated a mutation rate of 1.61 ± 0.13 × 10−8, which falls between phylogenetic and pedigree-based approaches.106 aDNA is becoming another major tool in appropriate calibration of mutation rate estimates and is likely to greatly refine our understanding of population divergence times, as it allows direct comparison of present-day and accurately dated ancient human DNA. For example, Fu et al used 10 whole mtDNA sequences from ancient AMHs spanning Europe and East Asia from 40 kya to directly estimate the mtDNA substitution rates based on a tip calibration approach. Using an amended mitochondrial substitution rate of 1.57 × 10−8, they dated the last major gene flow between Africans and non-Africans to 95 kya.107 Later work utilized high coverage aDNA from a 45,000-year-old western Siberian individual called Ust’-Ishim and a technique based on modeling the number of substitutions in relation to the PSMC inferred history, which led to slightly higher estimates of 1.3–1.8 × 10−8 per base per generation.108 It is likely that an increasing availability of ancient samples from different time periods will assist in further refining these estimates.[/QUOTE] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4844272/ [/qb][/QUOTE]The Yoruba came from the Levant before they settled in Nigeria. I am sure that researchers maskout much of the Yoruba genome to get the results they are looking for. Sadly, we will never know the truth until someone reveals the actual genetic makeup of the Yoruba. [/QB][/QUOTE]
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