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Case Study Framework - download working prototype

Based on mutation rate calculations written by Anatole Klyosov:

Paper - Mutation Rates and some historical evidence written in the Y Chromosome I. Basic Principals and Method 

Paper - DNA Genealogy, Mutation Rates, and Some Historical Evidence written in the Y Chromosome II. Walking the Map  

Additional Papers from Anatole Klyosov's Series

Mutation Rate Constants in DNA Genealogy (Y Chromosome)

1. Haplogroup Analysis - uses current FTDNA YDNA results and compares them to the current R-L21 Yahoo Groups modal haplotypes that are compiled by Alex Williamson and Mike Walsh.  These results can be found on the results webpage.

Identify the modal haplotype and genetic distance of the project members.  This data will be used to build phylogenetic trees.

Haplogroup analysis is a form of predictive analysis.  It needs to be confirmed by Deep Clade of SNP tests. 

How to determine haplogroups:

Download FTDNA YDNA results and analyze them according to the R-L21 Project Haplogroups.  Identify haplotypes belonging to the R-L21 haplogroups within a genetic distance <= 9. 

2. Build Phylogenetic trees - built into the FTDNA Case Study Framework Workbook: see Case Study Download webpage.

Using the formatted haplotype data above, identify clusters by reviewing phylogenetic trees built from different binary methods.

Build phylogenetic trees using PHYLIP software.  There are several executables that build phylogenetic trees (i.e. Neighbor and Kitsch).  Each uses a different algorithm and can be displayed through TreeView software in different graphs types.  The algorithms themselves do not predict the actual phylogenetic tree that occurred in reality.  The only way we can confirm the tree is by coordinating family histories, Gedcoms, locations and time frames.

Non-the-less the phylogenetic trees are an excellent tool.  It will be an iterative process using the different phylogenetic trees along with family histories, Gedcoms, locations and time frames.

How to build trees:

Take the FTDNA YDNA results of haplotypes by haplogroup and paste them into the McGee YDNA Utility for PHYLIP input.  Using this input data run either the Neighbor or Kitsch PHYLIP programs to get outtree output.  Import the outtree data into the TreeView program.  Find the distinct clusters.

3. Calculate Mutation Rates - click to view analysis

From identified clusters above.  If the mutation rate calculation is 'clean' it can be used to build family trees.

TMRCA calculation enables you to tell the time when two lines split for example.  This helps in determining time between close genetic matches or time from the most recent common ancestor of the haplogroup.

Use the cluster data found in the phylogenetic trees to calculate mutation rates from their Most Recent Common Ancestor.

4. Build Family trees and branches - click to view

From 'clean' results above and eventually identify septs and clans.

Using the results of iterative analysis (coordinating the building of the phylogenetic trees, Gedcoms, family histories, and locations), build the actual family trees and branches.  These results are constantly going to be updated and changed as a moving target as more information becomes available.