Common Polish Clades

5-Jun-09

Peter Gwozdz

update 10-Nov-09

 

This is an index of Supplementary Data files that go along with a pair of articles published in the Fall issue of www.jogg.info.

Y-STR Mountains in Haplospace, Part I:  Methods” explains the “mountain”, or  type”, cluster analysis method.

Y-STR Mountains in Haplospace, Part II:  Application to Common Polish Y-DNA Clades” proposes STR clusters from the Polish Project as hypothetical clades.

This index is the complete list of files in this file folder.  This folder has 33 files including this index.  These files are for archive purposes, so they will not be updated.

Future updates are in a separate folder PolishCladesUpdate.

 

Many of these files have user functions or macro subroutines.

            Excel gives a virus warning when opening such files.

            You can click “Disable Macros” to view the files without the macros.

            You need to click “Enable Macros” to do new calculations using those files.

 

Type

 

Type.xls   This is the master file.  A tool for assessing STR clusters, and for improving the cluster definition, and for determining if clusters are mountain types.  Includes a “Calculator” sheet.  The “TypeRank” sheet figures the modal haplotype, rank of markers, etc.  ASD” sheet calculates age.  “Doc” sheets have explanations, instructions.  Make copies of this file for analysis of each type.

 

Polish Project Data & Results

 

PolishProject15May2009.xls   Archive copy of the data used for the articles.  Downloaded from the Polish Project at FamilyTreeDNA.com, and converted to an Excel file.

 

Evaluator15May2009.xls   Data formatted.  This is a copy of the advanced tool “Evalulator.xls” (below), with the 15 May 2009 data evaluated, in 3 sheets, using 67, 37, and 25 markers.  Close match haplotype sets are named.  Samples from family projects are marked for editing.  Documentation and the macro are deleted in this archive copy.

 

Polish12.xls   Complete list of 12 marker haplotypes, count for each.  Ysearch comparison.  This is the extended version of Table 1 submitted for publication in the article “Common Polish Y-DNA Clades”.

 

Polish9.xls  Complete list of 9 marker haplotypes.  For comparison to Pawlowski.  This is the extended version of Table 2 submitted for publication in the article “Common Polish Y-DNA Clades”.

 

Haplotypes.xls   A list of proposed modal haplotypes for the Polish Project Types, including some speculative types for experimentation.  This file has full 67 marker modal haplotypes, and also “definition” modal haplotypes.

 

YsearchURLs.xls  Universal Resource Locator Codes for checking Ysearch, selected types, using definition modal haplotypes.

 

Results15May2009.xls   Summary of all type and subtype results for the Polish Project.  Data is color coded to highlight types.  This is a copy of “Calculator.xls”, so genetic distance steps can be calculated and sorted for any type.

 

The following are copies of the tool “Type.xls” for each type identified in the Polish Project;  the Documentation sheet is deleted from the copies to save file space.

AType.xls

GType.xls

IType.xls

KType.xls

KTypeR1a1Example.xls

KTypeYsearch.xls

NType.xls

NaType.xls

PType.xls

PTypeYsearch.xls

PcType.xls

PgType.xls

R1a1Type.xls

YType.xls

ZType.xls

 

Advanced Tools

These files should be useful for any Y-STR cluster analysis

 

Calculator.xls   “Calculator” sheet calculates mutation step distance for each haplotype in a database, compared to a reference (modal) haplotype.  Several different Calculator versions.  “Masks” allow selective removal of markers.  The “Documentation” sheet has explanations, instructions.

 

Evaluator.xls   Tool for searching for sets of closely matched haplotype data.  This file has a macro, and a “Documentation” sheet.

 

HaplotypeGenerator.xls   Makes a complete list of haplotypes, for an input number of markers, and for an input maximum mutation step count.  “Haplotype Counts” sheet has a table of total possible haplotypes for each number of markers;  this is the extended version of Table 1 submitted for publication in the article “Y-STR Mountains in Haplospace”.  The “Documentation” sheet has explanations, instructions.  This file has a macro.

 

MCSMM.doc   Multi Clade Stepwise Mutation Model.  Draft of an article describing a much more complicated model for analysis of STR data.  Incomplete.  Mentioned briefly in “Y-STR Mountains in Haplospace  Provided here as ideas for further development.

 

MCSMM.xls   Multi Clade Stepwise Mutation Model.  With sample data.  The Bessel function is required for this file.  Some older versions of Excel require the “Tools, Add-Ins, Analysis ToolPac”.

 

HaplotypeCounterGenerator.xls   Needed as input for MCSMM.xls.  Counts up how many of each haplotype in a data set.  Removes all but one copy of each.  Generates the complete set of haplotypes (with zero count for those haplotypes not present in the data set).

 

Yhrd Analysis;  Polish vs Neighbors

 

YhrdMap.doc   A copy of the map indicating all the east and central European cities with data.

PtypeByCityYhrd.xls   Data.  Percent of P type by city.

YhrdReminders.html   Notes for use of the Yhrd site.

 

Polish Project Assignments

 

The Polish Project site has links to two files that I maintain, using the “mountains in haplospace” method to assign project members to types.  Here are those two links:

Documentation

List of Assignments