Intro to Pedigree Analysis and COI

Info and discussion about the Pedigree Analysis and Coefficient of Inbreeding (COI) functions.

Intro to Pedigree Analysis and COI

Postby dmeyer » Sat Nov 29, 2008 6:05 pm

The Red Wattle Project web site provides some pedigree analysis features including the calculation of Wright's Coefficient Of Inbreeding (COI). These features are accessed using a page called Pedigree Analysis. There is a link to it on the Members Home page.

Following is an explanation of the Pedigree Analysis features:

The form near the top of the Pedigree Analysis page lets you enter either the reg # for an animal, or reg #s for the sire and dam of a hypothetical mating. When you submit the form with valid reg #s the page will reload and show a summary of the pedigree analysis for the animal(s) you provided. Click any of the blue ">" buttons (or the link text to their right) to see a detailed report on that part of the analysis. Here's a brief description of how this works and what the reports show:

a. When you first submit the reg #(s) to analyze, the software generates a temporary table in the database containing info about all the ancestors in the database for that animal (or mating). When you click the various reports later, the temporary table will be used unless the base animal(s) changed, in which case a new table will be generated.

b. The first 4 reports are the results of basic queries run on the temporary table of ancestors:
b.1. Total Ancestors Found: this shows a list (table) of all the ancestors found in the database for the base animal(s). This is equivalent to an n-generation pedigree but in list format. The number of generations to analyze is currently not limited, so it will search back as far as the data in the database goes. I can put a limit on the number of generations to analyze in case the database gets to be so large that the program runs out of either the horsepower or memory needed to do the analysis.
b.2. Unique Ancestors: This is a subset of the data for b.1. that doesn't show any ancestors that appear more than once in the pedigree.
b.3. Common Ancestors: This shows the animals from b.1. that are not unique and shows a count of how many times each appears in the pedigree.
b.4. Duplicate Ancestors: This essentially shows all the animals from b.1. that are not shown in b.2.

c. The reports in b. above use some notation that might need to be explained:
c.1. The "Gen" column shows what generation of the pedigree the animal is in.
c.2. The "Label" column indicates the exact position in the pedigree of the animal. For example, "SD" means the base animal's Sire's Dam (or grandmother on the father's side.)
c.3. You can use the "Customize Ancestors Report" link at the upper left of the page to select from a list of available fields the fields you want to show in the report. You can also click the heading of most columns in the report to re-sort the table by that field (then click again to re-sort in the opposite direction.)
c.4. Use the "Pedigree Analysis" link at the upper right to return to the analysis summary page for the animal or mating you are analyzing.

d. The Inbreeding Loop Analysis function will analyze the pedigree data to find all inbreeding loops. An inbreeding loop is a path from an animal down (left) the pedigree to a base animal then back up (right) the pedigree ending on the same animal that you started from. These loops are used in the next step to calculate the COI. The report shows you a list of all the loops that were found. Loops going through the base animal will directly influence the base animal's COI. Other loops will only impact the base animal's COI if they affect the COI of another animal that is in a loop through the base animal.

Here are a few examples that I found interesting:
e.1. Reg # 1125 "Bill" -- Go to the Pedigree Analysis page and enter 1125 in the top box of the form and click the top Go button. The page should reload showing the analysis summary. Click the little blue "P" button above the results table to bring up the pedigree for Bill. Note that Bill is the offspring of full siblings. Click your browser's Back button to return to the summary page and take a look at some of the reports. Use the "Pedigree Analysis" link at the upper right of the detailed reports to return to the summar page. Note the Inbreeding Loop Analysis for Bill shows two loops, one for the common grandfather and one for the common grandmother. Each loop contibutes 0.125 to the COI. Take a look at the COI report and you will see that in this simple case the two 0.125 numbers are simply added together to get a total COI of 0.25 for Bill.

e.2. Reg #1678 "Bertha" -- Run the analysis on Bertha and take a look at the Loop analysis. This is a more complex case that has a common ancestor (# 1394) causing several loops from the sire side to the dam side through the base animal. And there is one more loop with # 1395 as the common ancestor. This yields a total COI of 0.3125.

e.3. Reg #1724 "Candi" -- Run this analysis and look at the loop analysis. This is a very complex case with several loops through the base animal (6 loops to/from #1243, and one loop to/from #1368). And there is another loop to/from #1243 through #1368. The loop through #1368 affects the COI contribution that #1368 makes to the COI of #1724. Take a close look at the COI calculation details to see how it was figured.

If you want to read more about Wright's COI, here is a link to a web page about it that I found to give a pretty good overview:

The first example on the page above is similar to the example e.1. I gave, except it is the offspring of half-siblings, yielding half the total COI as with full siblings.

You can run a google search for "Wright Inbreeding Coefficient" and find many more pages of examples and details of how to do the calculations. Let me know if you find any good ones. I looked through the first 20 or so search results.
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