R-L21 Phylogenetic Network Analysis

[MJost]

I complied the various (50) subclade Modals from L21 using 111 marker haplotypes where I could create a modal. I ran these actual and speculative varieties modals through my modified version of McGee which has an option to use Heinila's 2012 mutation rates on each marker vs not using an average rate across the 111 markers. This PDF has the output from Fluxus using 111 markers removing DYS464's to remove some of the errant results. I was required to use unique names so I used numbers 101 to 15O and provided a Note tag on the PDF with the associated Clade Names.

In the next few pages, I provided McGee's Genetic Distances and TRMCA using Probability of 1-Sigma (68.27%) at 30 years / generation using all 111 markers. With these pages show the Clade's names and I showed the GD's sorted lowest to highest from L21.

And on the last page I ran a Phylogram using SplitsTree4 diagram.

Click 'File' on the Google Menu bar and download the PDF. Open and you can rotate each page as needed to view properly.

L21Modals111mFluxus-x464-05072013MJost.pdf

https://docs.google.com/file/d/0By9Y3jb2fORNNlNjV0JjaF9rMjA/edit?usp=sharing

I was interested if Fluxus, using 111 markers, could tease out the varieties associated near known clades. So branches such as DF23# (added in the entire variety as referenced by the # sign) lineage has mutated into a completely different set of allele values and placed it on a different section of the tree.

MJost

[MJost]

I have have taken almost 200 HTs that are classified in MikeW's L21 spreadsheet as Z' varieties and calculated the TRMCAs at 30 years per Generation from the L21 root modal using my modified McGee's 111 Y Utility using all STRs and using the actual Marko Heinila’s 2012 mutation rates applied per each STR (not an average of all the markers applied to each STR)rates.

I ran a SplitsTree PHYLIP package for inferring phylogenetic relationships on these HTs. Next I show the exact haplotypes used in a table.

I then ran the McGee output into a Phylogenetic Network software available from Fluxus Technology and its output shows the Root ball and clusters the expanded outward. (I may build the full tree on this one but it takes hours to do by hand).

And the next page is the Fluxus TMRCA of all these 196 HTs calculating the TMRCA of 2,729 years before present with a standard deviation about one sigma which states that all haplotypes ran will fit into a plus or minus range of 103 years from 2,729 years.

This is the calculation from Fluxus and it is not mine. All I supplied was the 102 years per Mutation using 111 markers at 30 years per generation.

I then ran my TMRCA Estimator using 111 Bird's stable STRs for comparison.

https://docs.google.com/file/d/0By9Y3jb2fORNWUxLQnJPYzdJQ0k/edit?usp=sharing

MJost