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Author Topic: The coming of the Greeks to Provence and Corsica: Y-chromosome models  (Read 587 times)
Curtis Pigman(Pigmon)
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« on: November 18, 2012, 06:07:01 PM »

Having found some rather close matches in the Greek y-DNA project I found some other results that astonished me!  In Genebase there is a feature that is actually very useful.  On their indigenous DNA tab you can compare your alleles with population studies.  Here is their definition of RMI:  

RMI (Relative Match Index): A measure of how closely your Y-DNA STR haplotype matches those of a defined population group as compared to all other population groups in the comparison. For example, a RMI of 100 means that you are 100 times more likely to belong to that population set as compared to the rest of the populations.

I have used this before and getting an RMI of 61 with Tyrol, Austria I thought that was pretty high.  There are new studies on there and here are the results I found today:

Indigenous Y-DNA Search

The Y-DNA of Curtis Pigman was compared to a dataset of 2 populations in 1 journal using 6 Y-DNA STR markers. The closest matches in a set of 2 populations are listed in the table below:
Smyrna, Greece    
RMI: 290.18
Phocaea, Greece    
RMI: 209.82

Appendix 4: Raw Comparison Results

The results of this comparison are based on the following raw analysis data:

Matches at a Genetic Distance of 0:
Population Set    # Matches    Population Size    Match %
Phocaea, Greece    1    26    3.85%
Smyrna, Greece    1    45    2.22%

Matches at a Genetic Distance of 1:
Population Set    # Matches    Population Size    Match %
Smyrna, Greece    5    45    11.11%
Phocaea, Greece    1    26    3.85%

Matches at a Genetic Distance of 2:
Population Set    # Matches    Population Size    Match %
Smyrna, Greece    8    45    17.78%

Matches at a Genetic Distance of 3:
Population Set    # Matches    Population Size    Match %
Smyrna, Greece    6    45    13.33%
Phocaea, Greece    3    26    11.54%

Matches at a Genetic Distance of 4:
Population Set    # Matches    Population Size    Match %
Phocaea, Greece    5    26    19.23%
Smyma, Greece    3    45    6.67%

Here is a link to the peer reviewed study:

The coming of the Greeks to Provence and Corsica: Y-chromosome models of archaic Greek colonization of the western Mediterranean

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3068964/?tool=pubmed

« Last Edit: November 18, 2012, 06:16:02 PM by Curtis Pigman(Pigmon) » Logged

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OConnor
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« Reply #1 on: November 19, 2012, 07:26:58 AM »

using only 6 str's?..which 6 were used?
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M42+, M45+, M526+, M74+, M89+, M9+, M94+, P108+, P128+, P131+, P132+, P133+, P134+, P135+, P136+, P138+, P139+, P14+, P140+, P141+, P143+, P145+, P146+, P148+, P149+, P151+, P157+, P158+, P159+, P160+, P161+, P163+, P166+, P187+, P207+, P224+, P226+, P228+, P229+, P230+, P231+, P232+, P233+, P234+, P235+, P236+, P237+, P238+, P239+, P242+, P243+, P244+, P245+, P280+, P281+, P282+, P283+, P284+, P285+, P286+, P294+, P295+, P297+, P305+, P310+, P311+, P312+, P316+, M173+, M269+, M343+, P312+, L21+, DF13+, M207+, P25+, L11+, L138+, L141+, L15+, L150+, L16+, L23+, L51+, L52+, M168+, M173+, M207+, M213+, M269+, M294+, M299+, M306+, M343+, P69+, P9.1+, P97+, PK1+, SRY10831.1+, L21+, L226-, M37-, M222-, L96-, L193-, L144-, P66-, SRY2627-, M222-, DF49-, L371-, DF41-, L513-, L555-, L1335-, L1406-, Z251-, L526-, L130-, L144-, L159.2-, L192.1-, L193-, L195-, L96-, DF21-, Z255-, DF23-, DF1-, Z253-, M37-, M65-, M73-, M18-, M126-, M153-, M160-, P66-

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Curtis Pigman(Pigmon)
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« Reply #2 on: November 19, 2012, 09:06:08 AM »

DYS447
DYS448
DYS449
DYS454
DYS455
DYS460 / GATA A7 1

I believe they used several more but the comparison uses only six.

Here is a small portion from the link:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3068964/?tool=pubmed

All 89 samples from Anatolian Greeks were genotyped using 29 Y-chromosome binary polymorphisms in a sequential manner using Y tree branching patterns to infer upstream haplogroup status. The following binary markers were genotyped: YAP, M35, V13, M78, M123, M34, M102, M9, M70, M74, M198, M269, M304, M497, M12, M241, M205, Page55, M67, M92, M530, M258, M253, M436, M223, P37.2, M423, M406, and M530. M497, Page55, Page94, and M530 are newly listed SNPs whose specifications are listed in Additional file 3: Supplemental Table S3. Binary marker genotyping was done by RFLP assay, DHPLC or direct sequencing. Each of the Phokaia and Smyrna samples were typed at 37 YSTRs listed in Additional file 4: Supplemental Table S4.

The 51 samples from areas near Neolithic sites in Provence had derived alleles for the following markers: V13, M34, Page94, M253, M438, M497, M530, M67, M198 and M269. In order to compare the selected 51 Neolithic samples to a larger Provence set, 368 subjects from the departments of Provence: Var (n = 68), Bouche-du-Rhone (n = 209), Vaucluse (n = 60) and Alps-de-Haute-Provence (n = 31) whose surname was blindly determined to be of French origin, were genotyped for E-V13, M406, Page94, M423, M269 and all the following J-lineages: M304, Page55, M267, M12, M410, M67, M530 and M92 as well as ten YSTRs for the J and E-V13 derived samples. DYS445 was typed in M530 derived samples (Schrack B.E., Athey T.W., Wilson J.F., 2006, The American Society of Human Genetics. Abstract). The 323 samples from Corsica were only typed for E-V13.

An AMOVA [23] was performed using Arlequin 2000 [24] to test the population affinities of the two Anatolian Greek samples to three mainland Greek samples (Nea Nikomedeia, Sesklo/Dimini, Lerna/Franchthi Cave), and four regions of Turkey (western Aegean, Marmara, central Anatolia and Mediterranean Turkey) [25]. Furthermore a Multidimensional Scaling analysis (MDS) (SPSS 18.0) was performed using the Fst measure as a distance metric across the 9 populations. An AMOVA comparing the effects of geography (Asia Minor vs. Mainland Greece) and religion/language (Christian/Greek vs. Muslim/Turkish) was also calculated using these 9 populations.

To analyze the impact of the attested Greek colonization of Provence, an admixture analysis [26] was conducted using a Basque population (n = 116) [27] as an indigenous (non-Neolithic pre-Greek) source population and the Phokaia/Smyrna data as the Greek colonizing source represented by E-V13 frequency. As a signal of putative Neolithic immigration to Provence, central Anatolian and Mediterranean Turkey data [25] were used. Specifically the following markers M92, M406 and J2a-(DYS445 = 6) were chosen as indicative of Neolithic ancestry. The frequencies of M92 and J2a-(DYS445 = 6) in the Basque population were estimated from their YSTR pattern [27]. In order to assess the degree of E-V13 affinity, a 8 loci YSTR network using Phokaia, Smyrna, Provence and Corsica samples was constructed [28]. Networks were constructed by the median joining method using Network 4.5.0.2, where ε = 0 and microsatellite loci were weighted proportionally to the inverse of the repeat variance observed in each haplogroup[29]. Coalescent times for E-V13 based on the following 8 loci DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393 and DYS439 were computed using the methodology of Zhivotovsky et al.[30] as modified according to Sengupta et al.[31]. A microsatellite evolutionary effective mutation rate of 6.9 × 10-4 per 25 years was used [30].
« Last Edit: November 19, 2012, 09:22:56 AM by Curtis Pigman(Pigmon) » Logged

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Curtis Pigman(Pigmon)
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« Reply #3 on: November 19, 2012, 10:39:52 AM »

I re-ran the analysis at 8 markers
DYS426
DYS447
DYS449
DYS454
DYS456
DYS459a
DYS459b
DYS462

and came up with this:

The Y-DNA of Curtis Pigman was compared to a dataset of 2 populations in 1 journal using 8 Y-DNA STR markers. The closest matches in a set of 2 populations are listed in the table below:
Smyma, Greece    
RMI: 294.05
Phocaea, Greece    
RMI: 205.95
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acekon
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« Reply #4 on: November 19, 2012, 04:03:07 PM »

I re-ran the analysis at 8 markers
DYS426
DYS447
DYS449
DYS454
DYS456
DYS459a
DYS459b
DYS462


Perhaps you can try some more slow markers from the list below, it looks like you have only used 2 slow markers
 
DYS426-slow
DYS447-med
DYS449-fast
DYS454-slow
DYS456-fast
DYS459a-med
DYS459b-med
DYS462-med

according to:

http://archiver.rootsweb.ancestry.com/th/read/GENEALOGY-DNA/2008-06/1213590779
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Curtis Pigman(Pigmon)
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« Reply #5 on: November 19, 2012, 08:47:49 PM »

I re-ran the analysis at 8 markers
DYS426
DYS447
DYS449
DYS454
DYS456
DYS459a
DYS459b
DYS462


Perhaps you can try some more slow markers from the list below, it looks like you have only used 2 slow markers
 
DYS426-slow
DYS447-med
DYS449-fast
DYS454-slow
DYS456-fast
DYS459a-med
DYS459b-med
DYS462-med

according to:

http://archiver.rootsweb.ancestry.com/th/read/GENEALOGY-DNA/2008-06/1213590779
I wish I could!  Unfortunately it doesn't work that way on the Genebase tool.  They chose 8 of the markers from my data to compare with their markers.
« Last Edit: November 20, 2012, 10:14:37 AM by Curtis Pigman(Pigmon) » Logged

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