Wednesday, October 8, 2008

How To Read HAM DNA Phylograms


How To Read
HAM DNA Phylograms
Oct 7, 2008




The HAM Country Poll for October has so far returned (from 100 % of the people voting) that they do not know "How To" interpret the HAM DNA Project phylogenetic charts. That was a surprise to me.
I have been posting these charts to HAM Country for years now, trying to keep them up to date with the new data as it arrives. I have received almost no requests to explain how to interpret these charts. I thought most of the folks would know how to read these charts.

Let me take the opportunity to try to remedy that. I have posted a 7 minute video to You Tube in order to explain "How To" read the HAM DNA Phylograms. And, I will go over the basics here.

Once you are familiar with phylograms, it should be easy to read. The charts are intended to tell you what the Y-DNA data tells you, pretty much at a glance.


I can remember some years back when I asked Dean McGee to add his TMRCA data in PHYLIP format. He has graciously provided that.
I'd hate to think that HAM genealogists still do not know how to use the data that he has so generously provided for us.

The main points to remember about a phylogenetic chart are:

- The software is only solely on the DNA data. The only input to the chart is the DNA data.
- The software will automatically try to organize the data into "groups."
- The chart is created from the TMRCA
data, which means a mutation rate has been applied. That means we have a timeline.
- In order to get an idea of how related two individuals may be, simply follow the
timeline back to the vertical line that connects the two.
- The software should automatically sort by Haplotype Group.

The graphs in use at HAM Country are always created with a few basic tools:

1) Dean McGee's Y-DNA Comparison Utility.
2) The PHYLIP software program called "kitsch."
3) and MEGA tree viewing software

There are other software packages that could be used to create charts, but the results may vary. I have selected these programs for their ease of use, ease of interpretation, and best of all, they are free for use by the general public. I have seen and used software that is much more difficult to use, and also software that is much more difficult to interpret. And the results from these particular packages are reasonably accurate when used properly.

Geneticists have used similar charts many time in the past in order to describe their data at a glance. The term "Phylo" means "name," and the basic concept is to create a chart based upon the kit number or name of the individual and also based upon some time driven mechanism.

The objective of the charts is to create a time driven chart, based upon the kit number (or name of the individual), using only the DNA data as input.

The first thing to remember is that since the graphs are based upon the Time to Most Recent Common Ancestor (or TMRCA),

In order to get an idea of how related two individuals may be, simply follow the timeline back to the vertical line that connects the two.

Here's an example of how related Conrad (kit # 112972) is to the other participants:







Following the line traced in purple back to the vertical line (that he has in common with the others) tells you that in order to connect to Conrad, the kits need to go back in time some 16,825 years.








The graph will also try to group similar kits into "Groups." The following picture shows HAM DNA Group #2 hi-lited in cyan:







Because the connecting (vertical) lines are not far from the present, the chart indicates that you do not have to go very far back in time to connect. So, you should find the HAM DNA Groups next to each other on the chart.








And finally, you should notice that the Haplotype Group is automatically sorted such that those in the same Haplotype Group will be next to each other on the chart.


That's about all there is to reading the HAM DNA Phylogenetic charts. The charts try to display all of the data for the HAM DNA Project together on on a picture that should be easy to understand.

Feel free to rate or comment on the
You Tube video that I have posted to explain "How To" read the HAM DNA Phylograms.

see also:

Instructions for creating a Phylogenetic Chart
Dean McGee's Y-DNA Comparison Utility
PHYLIP software package
MEGA tree viewing software
HAM DNA Project Phylogenetic charts







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