Irish Type 2 – Kane

Exploring the origins of the Eóganachta-type Kanes.

Category Archives: Phylogenetic Tree

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R-FGC11134 Experimental Tree

A new resource has been added to the site, which is the current draft tree for R-FGC11134. Unlike previous versions I’ve created this one removes all variants falling in the palindromic arms, the DYZ19 repeat region, or occur in a known STR. It represents the tree most likely to appear on the ISOGG Y-DNA Haplogroup R chart.

All variants are found in at least two samples and to date have sufficient genetic distance to be accepted. It’s just a matter of creating the support matrices and submitting the draft for acceptance.

The experimental tree may be found here: F-FGC11134 Experimental Tree

The document will be published as part of the update process for the R-P312 and Subclades quick test matrix also hosted on this domain. Eventually the two will be merged into a single tree concept with kits shown at their terminal testing level on the tree. While the matrix concentrates on R-P312 it does present those kits from reference samples outside the group. All of these are used to track recurrent variants outside R-FGC11134.

The matrix can be found here: R-P312 & Subclades Matrix

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R-P312 Combo BAM Matrix

Over the last year I have been experimenting with using the GATK to analyze the BAM results of FGC11134 men. This has resulted in a very detailed tree for the DF13 subclade. With the experience and newer versions of the software a new workflow has been established to enable hundreds of kits to be efficiently processed and reported.

An important part of the process has always been to maintain a few outgroup samples. These help to draw the line between a variant under FGC11134 and possibly upstream. Using the batch calling functions in GATK allows automated extraction of the ancestral calls, which normally requires a trip to IGV or the like to manually read.

The R-P312 Combo BAM matrix contains a summary of all variants found in the cohort. Each location reports an average confidence for the SNP or INDEL. Then each kit’s read depth are charted for the location. Ancestral calls are marked with a rose colored background and a negative read depth. Derived calls are marked with a green colored background and read depth. When there are alignment issues a heterozygous read is possible. In these cases the depth of both alleles is reported with an amber background.

Any NGS tester under the R haplogroup may submit their BAM for the R-P312 Combo Bam Matrix. Once analysis is complete they will be added to the appropriate haplogroup cluster. Upon inclusion in the workbook they can filter for their truly private high-quality variants, and compare with their near matches.

Individuals wishing to submit their Big Y results should use the “Share BAM” button to create a temporary link, which should then be sent to the email address on the README tab. Full Genomes customers can share their kit with the same address. By doing so you agree to allow analysis and comparison by other researchers interested in the R haplogroup. The file is also available to the individuals responsible for maintaining the ISOGG Y DNA Tree.

Later articles will detail how the R-P312 Combo BAM matrix is generated and some useful examples of how one might look at their results.

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The Evolving Y-DNA Tree

The FGC11134 tree has grown in radical bounds over the year of 2014. Through the dedicated testing efforts of 65 people, the Y-DNA tree under FGC11134 has burst in to leaf. There are now 50 branches and terminal leafs shared by at least two individuals where this time last year only three existed.

On reflection this is still just the start of our exploration for the purposes of genetic genealogy. Only a handful of the terminal leafs are truly surname specific, and we still are not to the point we can definitely tie dates to branches. More testing will eventually bring us to the point where this may become more feasible.

Of interest is that A804 seems to hold significance for the Irish Type 2 Cain/Kane/Keanes. It’s been observed that some of these individuals possess an O’Donoghue-like signature. A804 indeed was found in three O’Donoghue Big Y kits and now one of the CTS4466 Kanes has Sanger tested positive for this SNP as well.

Those who would be interested in this early medieval era SNP can test for it at YSEQ. A804 is available individually or as part of the R1b-FGC11134 Panel (including CTS4466.) Doing so will help to draw an understanding when the men carrying a variation of the Catháin surname split off from those carrying O’Donoghue.

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ISOGG Y Tree Updates

Over the past few months the FGC11134, CTS4466 Plus and R1b-South Irish projects have been combing through over 70GB of raw data searching for the branching structure of the genetic tree under CTS4466. All of that work has paid off as the ISOGG Y tree has been updated based on our research and collaborative efforts.

The reorganization starts with FGC11134 taking the R1b1a2a1a2c1c from L96. As the common ancestor to both L96 and CTS4466 this decreases the number of known branches of DF13 in the 2013 tree. Under CTS4466 we now have 3 major branches before S1121. But it is S1121 that is of most interest to the Irish Type 2 Kanes. Currently at the R1b1a2a1a2c1c2* this is as deep as two of the Kane testers have moved in the accepted tree.

S1121 currently has 6 known branches which should be added over the next month or so, but none of these appear to be the branch where the group is hiding. An NGS test from Full Genomes Corp is expected sometime around Christmas. This should lead to the discovery of the Kane’s distinct branch.

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Growing the Irish Type 2 Kane Phylogentic Tree

As previously noted there are a large number of men who have tested STR markers at FTDNA bearing a signature of the CTS4466 SNP. Of these three of these closest to the middle of the phylogentic tree have tested CTS4466 positive, and two of those S1121 positive. This helps to establish the accuracy of the prediction from STR markers alone.

At this time one of these individuals has a DNA sample undergoing Next Generation Sequencing at Full Genomes Corporation. These results should be returned in the next three months. After comparing with the existing Big Y tests for CTS4466, this will show where the next round of SNP testing should be focused.

A more direct option is to find a second volunteer from the identified list take the Big Y test. Should any of the central kits listed in the phylogentic tree be interested, they should contact me through the Cain Surname project for details.

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R1b-CTS4466 Phylogenetic Tree

The current Big Y-based phylogenetic tree for the R1b-CTS4466 haplogroup appears above. The level between DF13 and CTS4466 is a new discovery from Full Y testing. The Big Y VCFs are not reporting FGC11134, but we can find the variant in the current BAM results. This location seems to be equivalent to S7942, which was found in the Chromo2 results. Further testing is needed to confirm this however.

As previously discussed the Irish Type 2 Kanes appear to be somewhere under S1121, but the exact branch has not yet been identified. Testing at YSEQ has confirmed the B5163 sample is A150-. Results are still pending for A159, but based on the latest STR signature it is unlikely this will be a positive result either.

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Known/Suspected Irish Type 2 Kanes

The linked tree shows all known STR tested individuals with a Kane variant surname, who have a signature consistent with R1b-CTS4466>S1121. The tree is generated by finding the time to most recent ancestor estimation using the Infinite allele mutation model. The resulting matrix of generations is then processed with the Kitsch algorithm to construct a phylogenetic tree.

Individuals closer to the center are more likely related, and would have a higher probability of sharing these two SNPs with B5163. 44297 and 47795 are the most likely to be members of a different R1b-L21 subclade with overlapping signature. There are another seven samples which also fit the signature, who are known to be different R1b-L21 subclades not included in the graphic.

A limitation of the current grouping is the low number of STRs tested in the Kanes sampled. The modal number of STRs tested is 37. Five samples currently only have FTDNAs 12 base STRs tested. Only four samples are tested to 67 or more positions. The distance of relationship can be improved by increasing the level of testing in the majority of the current samples. SNP testing on the haplotypes closest to the middle of the tree would also improve the modal signature for the group, and potentially remove false positives.