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Mitochondrial DNA

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Proyecto ADN Puertorriqueño - Our R1b Diagrams

Proyecto ADN

de
  Apellidos Puertorriqueños  

updated 11-12-2005

Haplogroup R1b

In order to better visualize the clusters into which our R1b members fall, we present analyses of their haplotype sequences in three formats. These are
1) a network analysis of their haplotype sequences (STRs) producing a phylogenetic tree by the Median Joining method
2) a Haplotree produced using various tools including
   -Whit Athey's yHaplogroup Predictor
   -Dean McGee's yDNA Utility Comparison Tool
   -FTDNA ToolTip
   -Phylip Phylogenetic Software and

-Mega 3.1 Phylogenetic/ Network software for producing graphs and diagrams

    from Phylip  data trees
and finally, 

3) a radiating haplotree/phylogram using the same applications mentioned in #2.

For many people who are new to genetic genealogy, interpreting their results may be very frustrating. Visual aids of haplotype sequences are very helpful in assisting members comprehend their relationship to each other whether it be a relationship in far more ancient times or in a genealogical time frame. The first diagram is a Phylogenetic tree produced with Fluxus Network of those R1b member haplotype results received as of July 2005. The latter two diagrams below use the TMRCA (Time to Most Recent Common Ancestor) data generated by the yUtility Comparison Tool and the Haplogroup R1b sequences of all those members who belong to R1b (both SNP tested and estimated) and whose results have been received to date. This data was then loaded into the Phylip progam for further analysis and the diagram were produced using Mega Phylogenetic software. The branch length and stems are measured in terms of years.

Note: This is a geographic project and as such, we remind you that the  surname anarchy practiced in Spain and later Puerto Rico since before 1492 until about the beginning of the 19th century was such that these individuals' most ancient paternal ancestors' surname in Spain may actually have been very different than it is now. The memory of this often has been lost over time. However, for others who are long time researchers, it is not. Many of these old family surnames have been researched to the 16th century. Approximately 68% of Spaniards belong to Haplogroup R1b.  This is not unexpected since Iberia was one of the primary refuges during the LGM (Last Glacial Maximum). In fact, overall, there is representation from almost every haplogroup in our project.

  The largest influx of Spaniards to Borikén or Borinquén (Puerto Rico) after the colonization was from the regions of Castile, Galicia, Valencia, Asturia, Navarra, the Vascondados (Basque country), Aragón, Catalunya, Santander, the Canary and the Balearic Islands. Additinonally, there have been immigrants from Ireland, Corsica, Italy, Flanders and France throughout its history.


Member R1b Haplotype Sequences

DYS# Kit * H a p l o 3 9 3 3 9 0 1 9 3 9 1 3 8 5 a 3 8 5 b 4 2 6 3 8 8 4 3 9 3 8 9 | 1 3 9 2 3 8 9 | 2 4 5 8 4 5 9 a 4 5 9 b 4 5 5 4 5 4 4 4 7 4 3 7 4 4 8 4 4 9 4 6 4 a 4 6 4 b 4 6 4 c 4 6 4 d 4 6 0 G A T A H 4 Y C A I I a Y C A I I b 4 5 6 6 0 7 5 7 6 5 7 0 C D Y a C D Y b 4 4 2 4 3 8 26079 R1b 12 23 14 10 11 14 12 12 12 13 13 28                                                   19672 R1b 12 24 14 10 11 14 12 12 11 13 13 29 17 9 10 11 11 26 14 19 30 15 15 17 17 11 11 19 23 16 16 19 15 38 40 12 12 18689 R1b 12 24 14 10 11 14 12 12 12 13 13 29 17 9 9 11 12 26 15 20 29 15 15 16 17 10 11 19 23 15 16 19 18 36 37 12 12 25234 R1b 13 22 14 10 13 15 11 14 11 14 11 30 15 8 9 8 11 22 16 20 28 12 14 15 15 10 10 19 21 14 14 15 18 34 36 12 10 14087 R1b 13 23 14 11 11 14 12 12 11 13 13 29 17 9 10 11 11 25 14 19 29 15 16 17 17 11 11 19 23 15 14 16 17 36 37 12 12 42631 R1b 13 23 14 11 11 14 12 12 12 13 13 29                                                   41475 R1b 13 23 14 12 11 14 12 13 14 13 13 28 16 9 10 11 11 26 15 18 30 15 15 16 17                         14851 R1b 13 23 16 11 12 14 12 14 11 14 13 30 14 9 9 11 11 26 15 18 27 13 14 14 16 11 11 18 23 15 17 18 16 34 35 11 11 16451 R1b 13 23 16 11 12 14 12 14 11 14 13 30 14 9 9 11 11 26 15 18 27 13 14 14 16 11 11 18 23 15 17 18 16 35 35 11 11 30232 R1b 13 24 13 11 12 14 12 12 12 13 14 29                                                   N10849 R1b 13 24 14 10 11 13 12 12 11 13 13 29                                                   14344 R1b 13 24 14 10 11 14 12 12 12 13 13 29                                                   16611 R1b 13 24 14 10 11 14 13 12 12 13 14 28                                                   14085 R1b 13 24 14 11 11 14 12 12 11 13 12 29                                                   30881 R1b 13 24 14 11 11 14 12 12 11 13 13 29 16 9 9 11 11 25 15 19 30 15 15 16 17 12 11 19 23 15 15 18 17 35 37 13 12 19509 R1b 13 24 14 11 11 14 12 12 11 13 13 29 17 9 10 11 11 25 14 19 29 15 16 17 17 11 11 19 23 15 15 16 17 36 38 12 12 12101 R1b 13 24 14 11 11 14 12 12 12 12 13 28 18 9 9 11 11 25 15 18 28 15 15 17 17                         00043 R1b 13 24 14 11 11 14 12 12 12 13 13 29 17 9 10 11 11 25 14 19 29 15 17 17 17                         24541 R1b 13 24 14 11 11 14 12 12 12 13 13 29 17 9 10 11 11 25 15 19 29 15 15 16 17 10 10 19 19 15 15 18 17 35 36 12 10 35662 R1b 13 24 14 11 11 14 12 12 12 14 13 30                                                   N10968 R1b 13 24 14 11 11 14 12 12 12 14 13 30                                                   39372 R1b 13 24 14 11 11 14 12 12 13 13 13 29 16 9 10 11 11 25 14 19 29 15 15 17 17                         11639 R1b 13 24 14 11 11 14 12 12 13 13 13 29 17 9 9 11 11 25 15 18 29 14 15 16 17                         40448 R1b 13 24 14 11 11 14 12 12 13 13 14 29                                                   19961 R1b 13 24 14 11 12 14 11 12 12 14 13 30                                                   42951 R1b 13 24 14 11 12 14 12 12 12 13 13 29 17 9 10 10 11 25 15 19 31 15 15 15 17                         14094 R1b 13 24 14 11 12 15 12 12 13 13 13 29 17 9 9 11 11 23 15 20 30 14 15 15 17                         29829 R1b 13 24 15 11 11 14 12 12 12 13 13 29 17 9 9 11 11 25 14 19 30 15 15 17 17                         24204 R1b 13 24 15 11 11 14 12 12 12 13 13 29 18 9 10 11 11 25 14 18 28 15 16 17 00  11 10 22 23 16 15 18 17 35 39 12 12 14082 R1b 13 25 13 11 11 14 12 12 12 13 14 30 16 9 10 11 11 25 15 19 30 15 15 16 17                         24074 R1b 13 25 14 10 11 14 12 12 12 13 13 29 18 9 9 12 11 25 15 20 29 14 15 16 17 10 11 19 23 15 15 19 17 38 39 12 12 39563 R1b 13 25 14 10 11 15 13 12 12 13 13 28 18 9 10 11 11 24 15 19 30 15 15 17 17                         14585 R1b 13 25 14 11 11 13 12 12 12 14 13 31                                                   00135 R1b 13 25 14 11 11 14 12 12 11 13 13 29 17 9 9 11 11 25 14 20 29 14 15 15 17 11 11 19 23 15 15 19 16 34 35 12 12 N1972 R1b 13 25 14 11 11 15 12 12 13 14 13 30                                                   23683 R1b 13 25 14 11 11 15 12 12 13 14 13 30 17 9 9 11 11 25 14 18 31 15 15 15 17                         33074 R1b 13 25 14 11 11 15 12 12 13 14 13 30 17 9 9 11 11 25 14 18 31 15 15 17 17 12 10 19 23 16 15 19 17 37 38 12 12 N2638 R1b 13 25 15 10 12 13 11 12 12 13 13 29                                                   41262 R1a 13 25 16 11 11 15 12 12 10 12 11 30 15 9 10 11 11 25 14 20 32 12 13 14 16 11 12 19 23 15 16 18 19 33 40 13 11 29818 R1a 13 25 17 11 11 15 12 12 10 13 11 31                                                   25135 R1b 13 27 14 11 11 14 12 12 12 13 13 29                                                   19400 R1b 14 24 14 10 11 14 12 12 13 14 13 30                           11 11 19 23 17 13 17 18 38 39 11 12 12319 R1b 14 24 14 10 11 14 12 12 13 14 13 30 20 9 10 11 11 25 15 20 30 14 14 16 18                         20732 R1b 14 24 14 11 11 16 12 12 11 13 13 29 18 9 9 11 11 27 14 18 29 15 15 17 17 11 11 19 23 16 14 19 18 35 36 12 12

A Note on Matches:

Although most in our project did not know each other prior to joining, several have matched exactly on various segments of the 12, 25 and 37 marker STRs (Short Tandem Repeats).  Since many of our participants are long time genealogists in their own right, the particular paternal surname of certain lines has already been researched extensively.  In as much as Puerto Rico was isolated geographically for long periods of time both during pre and post Columbian era,  it is well known to those who have searched the parrochial books and the Archivo General de Puerto Rico that many specific family groups were extremely endogamous. It is not surprising that our members should find many more matches within our own project than outside of it.

Examples:
ID 14851 and ID 16451 - 12/12, 25/25, 36/37 markers; Different Surname
ID  N1972, ID 23683 and ID 33074 - 12/12; Same Surname
ID  23683 and ID 33074 - 24/25; Same Surname 
ID  14344 and ID 16611 - 12/12; Different Surname

Exact matches which are on the same branch in the Haplotrees are colored accordingly. 

Phylogenetic Diagram

      

Median Joining Phylogenetic Diagram produced courtesy of Network software from Fluxus Technology as described by Bandelt H-J, Forster P, Röhl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37-48

Fluxus Network Diagram for the most recent R1b results coming end of November.  We have about many members awaiting new or upgrade results to their sequences.

Radiating Haplotree

         

Traditional Haplotree Diagram

      

    Dean McGee's yDNA Utility                      Phylip Settings

• Probability - 95%                             Kitch with L, J option                        

• Mutation Rate (FTDNA)- .004       Random Seeds: 9;  11 Jumbles
  

                                                         

Although I learned how to make these diagrams by trial and error at the onset of our Puerto Rican DNA Project in the fall of 2003, I would be remiss in not mentioning two very succinct and well done descriptions on how to produce these types of phylogenetic haplotree diagrams. They can be found on my fellow ISOGG (International Society of Genetic Genealogists) member's project pages: Dave Hamm's Hamm DNA Surname Project and L. David Roper's Roper DNA Project.

       

Bibliography

Bandelt H-J, Forster P, R÷hl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37-48

S Kumar, K Tamura, and M Nei (2004) MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Briefings in Bioinformatics 5:150-163.

       

Group Comparison Chart Results

Haplogroup E3a, E3b, B

Haplogroup G,I,J,K

All Project Haplogroup R1bs      R1b 12 markers only

 

Haplogroup R1b with this specific modal haplotype

12

24

14

10

1 1

14

1 2

1 2

1 2

13

1 3

29

  Haplogroup R1b with this specific modal haplotype

13

24

14

11

1 4

11

1 1

1 2

1 2

1 2

1 3

2 9

 Haplogroup R1b with this specific modal haplotype

13

25

14

11

1 1

14

1 2

1 2

1 3

14

1 3

30

Combined Haplogroup Results

yDNA12 Results        yDNA25 Results       yDNA37 Results

Phylogenetic Diagrams 2004

 

           yDNA12                                yDNA25                       yDNA 37

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