Can the standard "Young Earth Creationist" model be falsified by genetics alone?

lol, just like that? I don't think so.If 36 individuals have 6662 mutations detected in 8,97 Mb, how then can figure 2 be claiming that 36 individuals have 12240 mutations in 3.2 Mb?? This makes no sense.
'After restricting our analysis to 8.97 Mb of the unique male-specific Y sequence, we identified 6662 high-confidence variants, including single-nucleotide polymorphisms (SNPs), multi-nucleotide polymorphisms (MNPs), and indels. '
"After QC and validation, we extracted 6662 high-confidence variants (i.e., sites that differ from the Y chromosome reference sequence), including both SNPs and indels, from 8.97 Mb of unique Y sequence"
"We assigned ancestral states to 6271 of the variants and then constructed a rooted parsimony-based phylogenetic tree containing all 6662 variants (tree 1) (Supplemental Fig. 1)"(note - tree 1 has no 3.2 Mb restrictions)6662 mutations are found in 8.97 Mb , if we divide that among 36 individuals we get 185.06 mutations in each individual. Multiply this by 6.58 to represent the whole Y chromosome, and we have 1217 germline mutations per Y-chromosome per individual.At 225 generations, and at a mutation rate of 4.6 per generation in the Y-chromosome, we get to 1025 expected mutations. 1217 found, 1025 expected. Obviously we can get a better match if we adjust the generation time or the 1.5 x 10(-8) mutation rate, both variables are uncertain.I'm not swearing by this either because various areas of even the y chromosome collect mutations at far higher rates and so this whole study is not a definite reflection on germline mutations in the rest of the genome.Edited by mindspawn, : No reason given.Edited by mindspawn, : No reason given.Edited by mindspawn, : No reason given.

Fig. 2 doesn't claim that. Hardly surprising. You made it up! You're doing the same as usual. Making a basic mistake, then doing lots of calculations that will end out wrong because of that mistake (like on the other thread, when you made calculations as if the whole genome is coding genes when only ~1.5% is).The number of mutations divided by the 36 people doesn't mean anything when you're looking for the distance to the common Y ancestor of all of them, because most will have a more recent Y ancestor as well. You can see this on the trees.To illustrate. We take you, your second cousin, also a mindspawn, another very distant mindspawn cousin, and another guy from your own ethnic group. We look at a 8.97Mbp section of the 4 Y-chromosomes, and we find 1,200 SNPs difference from a genome like that of individual "A". You, being the great mathematician of the group says: "There are four of us. 1200 divided by 4 equals 300, therefore we are each of us about ~300 mutations away from the common ancestor." In fact, on 8.97 Mbp, the average is over 900.Do you now see what you're getting wrong?

There are 36 individuals, and they do have about 340 mutations each. The link isn't clear whose DNA was tested against to count the variations.Here are some general questions I have regarding the certainty of your claims:A) Knowing that they do not have the DNA of Y chromosome Adam , they must have defined variants as variations between humans within the study. Which focuses my attention on the 285 differences and 185 differences between the Haplogroup A individual and the rest. This is where the bulk of the differences lie, but compared against what ancestral DNA? If compared with eachother, surely the number of differences would be the same between two individuals. ie 285 differences. Why 185/285? Could you kindly explain that to me , because that is where the bulk of your differences lie.They refer to a chimpanzee as a reference point, if this is the source of the variation, that makes the first 185/285 variants completely irrelevant. (Figure 1 "chimpanzee reference F")
"First, we used all the 6662 sites in 36 individuals to construct a haplogroup tree, which was rooted using the chimpanzee Y sequence. "B) They included non-Germline mutations in their study, which distorts the figures. Even in those where they could have logically eliminated the somatic mutations, they still chose to include them in the study:
"An additional source of biological error is the mutations that occur somatically in the donor or during cell culture, which are relevant here since all sequences were derived from lymphoblastoid cell lines. We can estimate this number from the sequences of the three-generation family. The grandfather and father carry 13 and 11 specific variants, respectively, two of which are absent from the grandfather but present in the father and transmitted to all his sons and are thus likely to represent in vivo de novo mutations, while the remaining 22 are likely to be somatic"C) I quoted a Wikipedia article indicating that mutations on the Y-chromosome are about 4.8 times more common in the Y-chromosome. This was approximate, but it is generally known that Y-chromosome germline mutations are far more prolific than elsewhere. Have you any definitive studies on mutation rates specifically in the Y-chromosome that can help your case? It seems to be general consensus that Y-chromosome mutation rates need to be more fully established.D) Some regions of the Y-chromosome are more prone to mutations than other regions, are you sure that the following sequences do not contain excessive mutation rates:M32, M190, M220, M144, M202, M305, M219, P97http://www.uni-koeln.de/...ertation/diss/khalid_arhzaouy.pdf
"Up to now, more than 20 unique p97 missense mutations have been identified with codon 155 being a mutation hot spot"http://www.accessexcellence.com/WN/SUA05/ychrom.php
"We hope to be able to confirm an African origin by looking at another segment of the Y chromosome that is mutating slightly faster than our original segment, which could reveal subtle regional genetic differences," he said."Your link from the opening post was an accurate reflection of population movement. I believe it is premature to use it as a reflection on the number of generations since the common male ancestor, given the uncertainties surrounding the variations detected and the uncertainties of generation times and mutation rates. Mutation rates are especially fickle taking into account that even lifestyle can effect germline mutation rates. The lifestyles of early man (eg Neanderthal) were vastly different. Hoping you can provide more definite information.Edited by mindspawn, : No reason given.

What nucleotide diversity would reflect a bottleneck? Have you or Jar any estimate or evidence of the type of nucleotide diversity that would reflect a bottleneck? Anything?

There cannot be a fixed number. The diversity expected would increase with time after the bottleneck. And surely mutation rates vary among organisms.

Yes, but there are lots of overlaps, so Fig. 2 certainly does not claim the 12,240 mutations that you said it did. A human Y-reference, then they are compared to each other. I see your point, but you're wrong about the 285 differences. The difference between "A" and the other individuals is usually over 600. That's easily established by counting. But I understand what's puzzling you. It's how they assign the mutations without having an outgroup, and it's probable that they do use the chimps to decide this. However, we can ignore that and just concentrate on the differences. Once we've identified over 600 differences between two individuals on 3.2Mbp, we've blown out Noah on even the highest plausible mutation rates (see below). Fig. 1 just shows some points where the chimp Y matches ours, and points where it doesn't. That's got nothing to do with the mutations that differ between human beings. They are certainly not counting the differences between humans and chimps! The point is that there are 470 points of difference there, then there are the added mutations when the other "Y"s diverge. Why didn't you read on from the bit you quoted?

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This observation of two germline mutations in two transmissions of 8.97 Mbp is consistent with the expectation of ∼0.6 mutations in two transmissions (0.3 variants observed per meiosis in 10.5 Mbp) (Xue et al. 2009). In addition, the sons carry from zero to 17 individual-specific variants each. If we assume that all the nontransmitted variants are somatic, we can estimate an upper limit to the number of somatic variants at eight per individual (three SNPs per individual). These somatic variants are thus highly enriched for indels compared with total variants (42 of 67 compared with 699 of 6595; P < 0.001, Fisher exact test). Three somatic SNPs per individual would have a negligible effect on the analyses presented.

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You can see that 3 somatic SNPs on the 8.97Mbp makes a negligible difference (an individual 950 SNPs away from the Y ancestor would be 947 instead). On the 3.2Mbp chart, there would be an average of only one somatic per. person. Your Wikipedia article says:

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The human Y chromosome is particularly exposed to high mutation rates due to the environment in which it is housed. The Y chromosome is passed exclusively through sperm, which undergo multiple cell divisions during gametogenesis. Each cellular division provides further opportunity to accumulate base pair mutations. Additionally, sperm are stored in the highly oxidative environment of the testis, which encourages further mutation. These two conditions combined put the Y chromosome at a greater risk of mutation than the rest of the genome.[10] The increased mutation risk for the Y chromosome is reported by Graves as a factor 4.8.[10] However, her original reference obtains this number for the relative mutation rates in male and female germ lines for the lineage leading to humans.

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That last sentence means the figure isn't the relative difference between the Y chromosome and the rest. As I pointed out in an earlier post, nearly half of the rest of the genetic material also comes from the father. If the male germline is about 5 times more vulnerable to mutation than the female germline, then the ratio of the Y to the rest would be ~5:3, not 5 to 1, because the Y is always passed male to male, and the other stuff is only passed through males half of the time.But it doesn't matter, because we would assume the highest plausible mutation rate for the falsification anyway. So, it would be more than 5 times the rate for the whole genome.For example, we take the 13 generation pedigree study:

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The latter could be placed in different positions on the pedigree and led to a mutation-rate measurement of 3.0 10^-8mutations/nucleotide/generation (95% CI: 8.9 10⁻⁹—7.0 10⁻⁸), consistent with estimates of 2.3 10⁻⁸—6.3 10⁻⁸mutations/nucleotide/generation for the same Y-chromosomal region from published human-chimpanzee comparisons depending on the generation and split times assumed.

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As you can see, their actual rate is 3.0 10⁻⁸ ,but the top end of their 95% confidence level is 7.0 10⁻⁸
For purposes of falsification, we could raise that to 10 10⁻⁸
That way we're 99% sure it isn't higher. Bear in mind that some modern estimates for the whole genome are as low as 1.1 10⁻⁸Work that out for the whole non-recombining Y for 200 generations and you get less than 1200 SNPs. Even at that very high mutation rate, the Y ancestor would be over 900 generations ago. So, with more than 99% confidence (because the gap is big) we've falsified the standard YEC model.As for hotspots, they certainly exist, and that's one of the reasons that modern techniques which can search millions of bp are much more reliable than older ones. 2.9% of the SNPs were recurring mutations, and the researchers eliminated these before making the 3.2 Mbp chart, so it doesn't actually contain any likely "hot" mutations. That didn't make much difference, as you can see that the numbers of SNPs on the 3.2Mbp chart and the number on the 8.97Mbp chart are approximately proportional to the respective sizes of the sample. If you want to include Neanderthal as descendants of Noah, you're in even worse trouble. Remember this paper.
An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree: The American Journal of Human GeneticsThere's one basal Y haplogroup that wasn't included in our 36 individuals because it has only just been discovered. This diverges from the rest of us by far more than individual "A". And the Neanderthal "Y" will differ even more.

Historical bottlenecks have been identified in some mammals. Cheetahs and North American pumas are two examples. But South American pumas are very diverse.I'll find you some papers when I've got time. I gave you one on elephant diversity a couple of times already on other threads.

My bad, I should have phrased the question, what evidence would reveal a long term bottleneck 4500 years ago, considering that the number of alleles would increase over time. I agree that short term bottlenecks a few hundred years old are detected (cheetahs/bison), but how would one detect long-term bottlenecks?

I know short term bottlenecks can be detected, how would long term bottlenecks be detected considering large population can collect literally hundreds of thousands of alleles in 4500 years?I believe it can be done, but only through the type of DNA analysis as in the opening post. When various individuals of a widespread species are limited to only a few original mutation sequences, we can then count the number of originals in the population. mtDNA analysis could eventually determine whether mankind does only have four original women as the ark story requires.

That's easy! Just examine the DNA of humans and see if there are significant changes pre- and post-4500 years ago. One of the marks of a bottleneck is a reduction of diversity. Even worse, the ark scenario would, by necessity, involve an absolute break in mtDNA types with worldwide repopulation from Near Eastern types.One of the skeletons I excavated in the western US had a particular mtDNA haplotype that persisted from 5300 years ago to the present in the same area! The Native American consultant on the project turned out to have the same exact haplotype!So there is evidence of direct continuity across the date biblical experts give for the flood. (You're so far out in left field on the dating issue there is no way to take your dating estimates seriously so we're sticking to the real dates.)But wait! There's more! There is a site in southern Alaska named On Your Knees Cave, which has a skeleton dated to 10,000 years. It is linked to a number of living individuals by a rare mtDNA haplotype. Again, there is evidence of direct continuity across the date biblical experts give for the flood.And still more!

Analysis of mitochondrial DNA (mtDNA) variation has permitted the reconstruction of the ancient migrations of women. This has provided evidence that our species arose in Africa about 150,000 years before present (YBP), migrated out of Africa into Asia about 60,000 to 70,000 YBP and into Europe about 40,000 to 50,000 YBP, and migrated from Asia and possibly Europe to the Americas about 20,000 to 30,000 YBP.

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http://www.bec.ucla.edu/papers/Wallace_23.5.05_3.pdf

Hmmm. No mentions of bottlenecks or drastic changes there.Whoa, now you have to deal with mtDNA continuity for over 150,000 years! Oh, noes! No breaks from an imaginary flood?Maybe you're just flat-out wrong, eh?

But wait, there's more.For any of the Biblical Flood stories to be true you also need to find the same 4500 year ago genetic break in cows and coyotes and buffalo and wolves and sheep and goats and ravens and doves and lions and tigers and bears and ohmys and ...

surely the overlaps were actually counted. If each individual was compared against a reference (like a chimp) then the same snp's would show again and again in closely related individuals. Where does the document show that repeat snp's at the same locus were not counted? You could be right, but you are not necessarily correct here, I need you to show me. Haha, no. Its a chimp.
"We extracted the ancestral allele for each position that was variable in humans (assumed to be the allele present in chimpanzee) using the Ensembl-Compara pipeline (Vilella et al. 2009), release 66, and obtained calls for 6271 of the total number of 6662 variable sites (Fig. 1; Supplemental Table S2)." I don't see the 600 differences, where are you counting?
But they are comparing to a chimp, which means we have to ignore the first 185 mutations as irrelevant.The rest are compared between humans, but which of the humans has the originally correct ancestral sequence? We don't know, just because they vary from the chimp, and vary from eachother, does not mean there were mutations. So its fair to divide any differences between two compared individuals by 2, half the differences coming from each individual. Fair enough. Ok let's check your maths based on 10 x 10-8 (per generation?) in the y-chromosome.
This amounts to 5.9 per generation in the y-chromosome.
Looking at figure 2, like I said we have to halve the differences measured directly between the humans, not knowing which human actually had the mutations. Variants are not mutations unless you know who has the ancestral DNA.
So we get an approximate average of 180 /2 = 90. Multiply by 18 and we have 1620 .At 250 generations of 5.9 mutations, we should expect 1475. Pretty close!!We just have to factor in Neanderthals breathing lots of firesmoke and eating red meat and sun exposure and smoking weed, and we make up the difference. (amongst many other possibilities) Makes some sense, I enjoyed your comparison between the 2 regions, but of course does not eliminate the possibility that they inadvertently chose a hotspot area.ps Im battling to find your 8.97mb figures in the document, can you point me somewhere please?

The overlaps are shown in the tree. They don't identify the variables by looking at the chimp. That would be what you would do if you were looking for the changes since the common human chimp Y ancestor, and there would be masses. The chimp is used to determine the ancestral state. (see below). They look at each individual locus. They have to to make the trees. The overlaps are all marked on them! That's to establish the ancestral allele of the variables, not the variables themselves. It isn't necessary to do this for our falsification. I'll explain with a simpler model.You meet another guy called mindspawn. Neither of you know that much about your ancestry beyond great grandparents, but both of you have heard other family members mention a great, great, great grandfather Joe mindspawn, so you hypothesise that this might be the same character. To find out if it is, you get the same 8.97Mbp that they used in the paper of your Y chromosomes sequenced. They are compared for point mutations, and 30 differences are found. From this information, we know that 30 point mutations have occurred, and we can infer about fifteen down each line from your most recent Y ancestor.At our maximum plausible mutation rate, there would only be an average of slightly less than one mutation per.generation on this section, giving a maximum of ten on the two lines, about 5 each, back to the hypothetical common great great great grandfather from whom you would both be 5 generations removed. So, your hypotheses that the two Joe ancestors were the same person is falsified.At this point, there is no need for an outgroup comparison. What we need that for is if we want to find out which of the two lineages has mutated on which loci, and exactly how many mutations each lineage has had. In this case, we wouldn't need to use chimps. Because the two of you clearly are quite closely related, we could use any human known to be in a different haplogroup, like the African individual "A" in the study. On loci where you differ from both this individual and the other mindspawn, it shows that the mutation has happened on your branch, and where the other mindspawn differs from both, they've happened on his. From individual "A" to any of the others on the 3.2Mbp. Wrong. Once again, they only compare to the chimp to determine which lineages have mutated on the variable points, and which have the ancestral. When they compare individual "A" to individual "D", for example, there will be 610 SNP variants in that 3.2Mbp section. While they can figure that that's ~300 per. lineage, they do not know which of the 610 loci have mutated along each line, and exactly how many on each one. We don't need to know that for our falsification, but they want to know for their tree. So, they find that "A" has 285 loci that differ from "D" and the chimps, and "D" has a different 325 loci that differ from "A" and the chimps. The 185 is arrived at by finding the number of "D"s mutations that are shared by the other 34 individuals. They know very well that the 285 and the 325 are different loci. They are looking at and recording each individual one and its position, and they know that "D" is the same as the chimps on "A"'s 285 mutations, and "A" is the same as the chimps on "D"'s 325 mutations.Concentrate on my "mindspawn" example above. You don't need the outgroup to establish the mutational distance from a common "Y" ancestor between two individuals.The rest of your post is you making mistakes based on your own misunderstandings, and then making calculations based on your own mistakes, which, as usual, are completely wrong.3.2Mbp chart again for easy reference.

Ok I agree with you about the overlaps, they defined 6662 variant locations.I do disagree about the chimp though, they were comparing modern humans with the ancestral state, which under evolutionary assumptions is reflected in the chimp. So they compared humans with the chimp, which makes most of those SNPs irrelevant for our discussion, although it remains relevent for their study on population movement, because their emphasis is not to count the variations, but to determine where each set of variable SNPs are found, and the relative ancestry where the offshoots (new groups of SNPs) occurred.I don't understand your analogy at all, you seem to base your logic on a misunderstanding of my position, ie an unintended strawman argument. I wasn't inferring anything like "two Joe ancestors were the same person". I'm not sure where you get that from, maybe I expressed myself badly and you misunderstood me. No these variations are between the chimp and the humans. 285 location differences were found between the Haplogroup A individual and the chimp. At this stage we do not know if ANY of these were mutations since Y-Adam.185 location differences with the chimp were common to all 35 individuals. All 185 of these could be in the common human ancestor, at this stage we don't know if we have ANY mutations at all. Sure the locations differ with the chimp, but they could have been in the human common ancestor."We extracted the ancestral allele for each position that was variable in humans (assumed to be the allele present in chimpanzee)"Until you can acknowledge this, you will keep thinking I making mistakes, when you are making an error by denying how dramatically the chimp comparison affects your whole argument.Edited by mindspawn, : Adding quote

You still don't understand the information in the paper. You can't identify within human variations by comparing humans to chimps. The only way you can tell how far two humans are from their common Y ancestor is by comparing the same sections of their Y chromosomes, and identifying all the loci on which there are SNP polymorphisms. Each locus you find that has a difference must have had a mutation on one lineage or the other, because the common Y ancestral chromosome can't have any differences from itself, to state the obvious! So, if you find 600 differences, you know that ~300 mutations have taken place on each lineage back to the common ancestor. You do not need an outgroup for this. It could be done with you and me. Clearly, you don't understand it. Think. If we want to find out how far back you and another man share a common Y ancestor, what would we do? We would simply compare a sizeable section of your Y chromosome to his, and count the loci that are different. 30 differences would mean about 15 mutations on each lineage, and if we estimated the highest plausible mutation rate to be about one per. generation on the section searched, then we can tell that you're about 15 generations back to a common Y ancestor, and not very closely related. If we'd been trying to find out whether or not the two of you shared a common great, great, great grandfather, we'd have falsified that hypothesis, because that's only 5 generations back from each of you. There's no need for an outgroup.The Noah hypothesis at 4,500 years is easily falsified in the same way, by counting the differences between individual "A" who is in a basal haplogroup, and any of the other 35 men in the survey. You do not need an outgroup for this. No they are not. Don't make things up to comfort yourself. (see below) You couldn't be more wrong. There would have been at least 100 times as many, maybe 30,000 or more if you compared any of the individuals to a chimp. On the mutation rate used in the paper, derived from the Chinese paper, the divergence time would come out to about 6.5 million years! (It says so in the Chinese paper). Those who understand the paper know that all of them were mutations since the Y Adam. Tens of thousands of differences from the chimp would have been in all 36 individuals, if they'd looked for them. They were only looking for within human differences. When they've found them by looking within humans, they compare only those particular loci to the chimp so they can know which lineage has the mutation, and which the original. Once again, if two individuals differ on 600 loci, you know they are each about 300 mutations away from the ancestors, but you don't know which of the 600 mutations have happened on each line. That's why they look at an outgroup. They can calculate an age for the common Y ancestor without this. I know you are making mistakes. You have no idea what you're talking about. The chimp is only used when they want to find out the ancestral states of the mutations.How hard is this for you to understand? If you and I have a difference on one particular locus on the Y, we know there's been a mutation since our most recent common Y ancestor, but we don't know whether it's on your line or mine. One of us will have the mutation, and the other, the ancestral state. If we have 600 loci which are different, I'll have the mutations on ~300 and the ancestral state on ~300, and so will you. That's easy to understand. We know that without bothering with an outgroup. We need no chimps, unless we have some reason to want to know which of the 600 belong to your line, and which to mine. But without that, we know that our average is 300 from our common Y ancestor.Here the paper describes doing the high coverage of individual "A" on the 3.2Mb section.

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NA21313 High-coverage sequencing

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High-coverage sequence information was generated by amplifying 5- to 6-kb overlapping fragments by long PCR. Approximately equimolar amounts of PCR fragments were pooled and used for library preparation and paired-end sequencing (54 bp) on an Illumina GAII Genome Analyzer to obtain 475 median coverage (European Nucleotide Archive [ENA] sample accession no.: ERS006694;ENA Browser). MAQ (Li et al. 2008) was used for mapping and SNP calling in the high -coverage data. Read depth coverage (>1/2 mean depth) and mapping (consensus > 30, mapping > 63) filters reduced the raw variant calls from a total of 5684 to 2233. Subsequent filters included removal of heterozygous calls and sites that were within 4 bp of each other to create a high-confidence filtered list of 615 SNPs, none of which were discordant with the established Y phylogeny.

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They are mapping that section of his "Y" against a human "Y" reference, who is in one of the common haplogroups, like the other 35 in the survey. They find 615 polymorphisms, meaning his and the other Y differ on 615 loci. That's all we need to know for our falsification, because we can see that each must be ~300 from the common ancestor.You can see that straight away from the chart. It's exactly like my comparison of "A" to "D" in the last post. And it blows out Noah when we use the maximum plausible mutation rate.Edited by bluegenes, : typos