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Thread: New DNA Papers - General Discussion Thread

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    New DNA Papers - General Discussion Thread

    Isn't this the author which conducted the mtDNA analysis of the Rostov-on-Don Scythians? Hopefully YDNA will follow.

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    Quote Originally Posted by parasar View Post
    About 80000 years for mtdNA M and 85000 years for mtDNA N
    Thank you for the link, parasar. However, I do not see where you have got these figures for the TMRCA of mtDNA haplogroup M and the TMRCA of mtDNA haplogroup N. Within macrohaplogroup N, the present study seems to deal with only the subclades B and P, which share a common ancestor more recent than that of haplogroup N as a whole (either haplogroup R or a subgroup of haplogroup R that contains B, P, and probably also R0'HV).

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    Quote Originally Posted by Ebizur View Post
    Thank you for the link, parasar. However, I do not see where you have got these figures for the TMRCA of mtDNA haplogroup M and the TMRCA of mtDNA haplogroup N. Within macrohaplogroup N, the present study seems to deal with only the subclades B and P, which share a common ancestor more recent than that of haplogroup N as a whole (either haplogroup R or a subgroup of haplogroup R that contains B, P, and probably also R0'HV).
    Those were my ballpark estimates for the upper bounds (the authors connect them using dotted lines) from "Figure 6. Schematic of Haplogroups and Coalescence Times for Haplogroups Found in Oceania, Based on Bayesian Phylogenetic Analyses and Mutation Rates"

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    Quote Originally Posted by alan View Post
    Just notice this

    http://www.plosone.org/article/info%...l.pone.0096074

    7.36% unassigned M269 could theoretically be M269*, L23xL51, L51*, L11* etc so I wouldnt get too worked up about that figure.
    In the world of R1b-M269*, L23xL51, L51*, L11*, 7.36% will get some attention. Hopefully good. The study published the STRs of 119 Y samples of all haplogroups.
    Table S3. Y-Chromosome STRs haplotypes and SNPs analysis results for the newly-typed samples of the present study (N=119)

    It looks like out of five M269*, L23xL51, L51*, L11*" haplotypes, four are most likely R1b-Z2103 or R1b-PF7563 of some sort and one is a L51 or L11.
     
    Code:
    Pop.	DYS393	DYS390	DYS19	DYS391	DYS385a	DYS385b	DYS439	DYS389I	DYS392	DYS389II  DYS458  DYS437  DYS448  GATAH4  DYS456  DYS438  DYS635  HG-SNP
    
    CS	12	24	14	11	10	14	12	13	13	29	18	15	19	12	15	12	23	R-M269(xP311)
    CS	12	23	14	11	11	14	12	13	13	29	17	15	19	12	16	12	23	R-M269(xP311)
    EN	13	25	14	11	12	15	12	13	13	29	16	15	19	12	17	12	23	R-M269(xP311)
    TP	12	23	14	11	11	14	13	13	13	29	16	15	19	12	15	12	23	R-M269(xP311)
    TP	12	23	14	11	11	14	12	14	15	29	17	15	19	12	15	12	23	R-M269(xP311)
    EN	13	23	14	11	14	16	11	13	13	30	16	14	19	12	15	11	23	R-M343(xM269,M18)
    Can anybody figure out if that is a L51, L11, PF7589?Z2118 or what?
    Map from study


    Citation: Sarno S, Boattini A, Carta M, Ferri G, Alų M, et al. (2014) An Ancient Mediterranean Melting Pot: Investigating the Uniparental Genetic Structure and Population History of Sicily and Southern Italy. PLoS ONE 9(4): e96074. doi:10.1371/journal.pone.0096074
    Last edited by Joe B; 05-03-2014 at 05:28 AM.
    YFull R1b-M269>L23>Z2103>Z2106>Z2108>Y14512>Y20971>Y22199, ISOGG R1b1a1a2a2c1b Y14416, FTDNA R-M64

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    About 5% L23xL51 is not really a major surprise. The relatively significant amount of this in southern Italy has been noted before. I tend to think we should look Balkans-ward to explain it but I am not an expert on this clade.

    Quote Originally Posted by Joe B View Post
    In the world of R1b-M269*, L23xL51, L51*, L11*, 7.36% will get some attention. Hopefully good. The study published the STRs of 119 Y samples of all haplogroups.
    Table S3. Y-Chromosome STRs haplotypes and SNPs analysis results for the newly-typed samples of the present study (N=119)

    It looks like out of five M269*, L23xL51, L51*, L11*" haplotypes, four are most likely R1b-Z2103 or R1b-PF7563 of some sort and one is a L51 or L11.
     
    Code:
    Pop.	DYS393	DYS390	DYS19	DYS391	DYS385a	DYS385b	DYS439	DYS389I	DYS392	DYS389II  DYS458  DYS437  DYS448  GATAH4  DYS456  DYS438  DYS635  HG-SNP
    
    CS	12	24	14	11	10	14	12	13	13	29	18	15	19	12	15	12	23	R-M269(xP311)
    CS	12	23	14	11	11	14	12	13	13	29	17	15	19	12	16	12	23	R-M269(xP311)
    EN	13	25	14	11	12	15	12	13	13	29	16	15	19	12	17	12	23	R-M269(xP311)
    TP	12	23	14	11	11	14	13	13	13	29	16	15	19	12	15	12	23	R-M269(xP311)
    TP	12	23	14	11	11	14	12	14	15	29	17	15	19	12	15	12	23	R-M269(xP311)
    EN	13	23	14	11	14	16	11	13	13	30	16	14	19	12	15	11	23	R-M343(xM269,M18)
    Can anybody figure out if that is a L51, L11, PF7589?Z2118 or what?
    Map from study


    Citation: Sarno S, Boattini A, Carta M, Ferri G, Alų M, et al. (2014) An Ancient Mediterranean Melting Pot: Investigating the Uniparental Genetic Structure and Population History of Sicily and Southern Italy. PLoS ONE 9(4): e96074. doi:10.1371/journal.pone.0096074

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    Maybe I missed it but I can't find where they explain/discuss the "resequencing" methodology shown in the figures.
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    Quote Originally Posted by MitchellSince1893 View Post
    Maybe I missed it but I can't find where they explain/discuss the "resequencing" methodology shown in the figures.
    I believe they are comparing STR calculations with those using SNPs, however as you said they did not specify which mutation rate /paper they used for SNPs. SNPs mutation rates thus far derived have a number of intrinsic assumptions that could make them prone to errors, however one of them, the one derived using the clovis individual might be more accurate for small populations that expanded like the native americans did. In any case, this paper fails to take into account the non-linearity of the Short Tandem Repeats with the repeat number, amongst other assumptions. That is, that the germline mutation rates for SNPs do not provide the substitution rates, and the observed mutation rates on father-son pairs might be prone to overestimating the mutability of STRs, as it is empirically observed that the mutability increases as a function of the repeat number for many loci, and it appears that a logistic fit, seems to be the best fit for many of the loci.

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    This aligns with the hypothesis that both Paleoamericans and Native Americans derive from a single source population
    ...

    'Modern Native Americans closely resemble people of China, Korea, and Japan,' James Chatters, lead author on the study, said, 'but the oldest American skeletons do not.'
    They have longer, narrower crania than later Native Americans, and smaller, shorter faces, too - more closely resembling modern peoples of Africa, Australia, and the Southern Pacific Rim....

    The earliest modern human bones unearthed to date are pieces of human skull from ‘the Cave of the Monkeys’ in Laos that are up to 63,000-years-old.
    This could imply that the EDAR mutation first occurred in the Americas and swept out of there, as it could hardly have arisen independently in the Americas and in East Asia.

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    Fascinating story.

    From the above BBC article:

    To reach the natural amphitheatre, divers had to swim almost 1km (0.6 miles) through a water-filled tunnel.


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    Quote Originally Posted by parasar View Post
    Inferring human population size and separation history from multiple genome sequences
    http://biorxiv.org/content/early/201...1/005348?rss=1
    As always, there is the issue of calibrating the results. The paper says:
    ---
    Our results are scaled to real times using a mutation rate of 1.25×10-8 per nucleotide per generation, as proposed recently [16] and supported by several direct mutation studies [14-16]. Using a value of 2.5×10-8 as was common previously [44, 45] would halve the times. This would bring the midpoint of the out-of-Africa separation to an uncomfortably recent 30-40kya, but more concerningly it would bring the separation of Native American ancestors (MXL) from East-Asian populations to 5-10kya, inconsistent with the paleontological record [25, 26]. We suggest that the establishment and spread of the Native American populations may provide a good time point for calibrating population genetic demographic models.
    ---
    This is not entirely convincing, since:

    - There is considerable evidence of some continuing gene flow between the Old and New Worlds after the initial Beringian crossing. I am still skeptical of the recently popular claim that "Mongoloid" characteristics arose independently in the Old and New Worlds.

    - Unlike the authors, I am not "uncomfortable" with some gene flow in and out of Africa continuing until 30,000 B.C. and beyond.
    Last edited by lgmayka; 05-22-2014 at 10:51 PM.

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