Afghan Hound Database and Breed Information Exchange (Inbreeding Analysis) |
Inbreeding Analysis
Inbreeding occurs whenever common ancestor(s) exist on both sides of the pedigree. Many traits/characteristics are "inherited", inbreeding increases the probability of inheritance from the common ancestor(s). For further study read "Genetics For Dog Breeders" written by Roy Robinson..
Sewell Wright (a Chicago geneticist) developed an algorithm to calculate the level of inbreeding (known as the "coefficient") in a pedigree. We have implemented this algorithm in a computer program which has been validated for accuracy by the Geneticist Roy Robinson.
(The following notes are from the September 1999 KCBS Newsletter.)
What is inbreeding?
Inbreeding is commonly regarded as the mating of related individuals; especially closely related individuals, such as, brother/sister, father/daughter, mother/son. Half brother/sister, single and double first cousins matings are less close but still constitute inbreeding. The principle is that the mated individuals share one or more common ancestors.
Avoiding a degree of inbreeding is impossible as a little calculation will reveal. The number of ancestors doubles per generation, 2 in the first generation, 4 at the next and so on. By the time you get to 15 generations the number of ancestors exceeds 32,000. The numbers increase rapidly as you go back further and eventually exceed the number of dogs bred in any generation. Many of these distant ancestors will occur multiple times which constitutes a level of background inbreeding.
The total amount of inbreeding in the known pedigree can be calculated and is expressed as the "inbreeding coefficient". The rate of inbreeding per generation can also be calculated. KCBS calculates both of these for you, and in addition lists the common ancestors and shows their relative contribution to the inbreeding total.
The significance of inbreeding is that the higher the level of inbreeding the greater the probability that the individual will inherit the same gene (good or bad!) from both sire and dam because both sire and dam trace back to a common ancestor.
The KCBS Inbreeding Analysis Feature
The inbreeding analysis screen above has three panels;
1. A chart on the left which shows the inbreeding coefficient calculated to the eighth generation
2. A chart on the right which shows the rate of inbreeding calculated to the eighth generation
3. A list which shows the ancestors in ascending order and their relative contribution to the inbreeding coefficient calculated to the eighth generation.
(1) Inbreeding Coefficient - This chart displays the
amount of inbreeding, where it occurs, and how it accumulates (if it does) over several generations.
A father/daughter mating on an outbred line will result in a minimum inbreeding coefficient of 25%. The same mating on an inbred line could result in a coefficient of 40-50% due to background inbreeding. This illustrates the need to be able to identify where and by how much the inbreeding occurs.
The chart contains six bars, one for each of the generations 3-8. The first (leftmost) bar shows the inbreeding calculated to generation 3. The next bar shows the inbreeding calculated to four generations, and so on. The graph is cumulative, and the last bar (Gen 8) shows the final inbreeding coefficient.
The graph is always lowest at generation three, and highest at generation eight. The shape of the graph is of interest. For example a father/daughter mating on an outbred line will peak at the generation bar 3 and then very quickly level off because there is little background inbreeding. The same mating on an inbred line will peak at a later generation bar because of the background inbreeding and will not level off so quickly. An apparent outbreeding may show little or nothing on the graph bars for the first few generations, then, as the distant common ancestors are calculated, this will be displayed on the graph bars for the later generation(s).
The above discussion illustrates the need to look beyond the inbreeding resultant from the current mating. It may well be that the current mating is the major inbreeding source, but, as seen above, there could be significant amounts of inbreeding further back in the pedigree. In the screen shot opposite, the coefficient for generation 3 was 19%, but is increased to 29% by generation 8. In this case, the amount of background inbreeding is significant. In another case where the coefficient for generation 3 was (say) 19% but background inbreeding amounted to (say) an additional 3%, then, relatively speaking, the background inbreeding is less significant.
(2) Rate Of Inbreeding - This chart shows the rate of
inbreeding per generation for generations 3-8 and provides an indication of whether the rate of inbreeding per generation is constant, is decreasing or increasing.
Usually the rate of inbreeding per generation moves within the range of 1-5% but the graph provides for rates higher than this. As shown in the example screen shot opposite, the rate of inbreeding increased in the more recent 3rd and 4th generations as a result of this particular mating. The rate of inbreeding then drops down to a lower and fairly constant level for the remaining generations. The trend in this example is clearly upward.
(3) List Of Contributing Ancestors - The list shows the
Ancestors, ranked in ascending order based on their relative contribution to the inbreeding coefficient. The list displays the ancestor's names, the amount of inbreeding they contribute, both per generation and in total. The list also includes a column which details the ancestor's own inbreeding coefficient.
Looking at the example screen on the previous page, the subject dog's inbreeding coefficient amounted to 29.59%. Of this total, ancestor one contributed 15.70%, ancestor two 3.61%, ancestor three 1.93% etc. An observation here is that ancestor one contributed half the known inbreeding whereas ancestor two's contribution amounted to about 10% of the total. This list helps give a perspective on each ancestor's inbreeding contribution relative to the other common ancestors.
Ancestors may contribute to the inbreeding in a single generation or over multiple generations. In the case of our example, ancestor one contributes 15.70 percent at the 3rd generation, and that is his single and full contribution. By contrast, ancestor three contributes 1.07 at the 5th generation, this increases to 1.61 at the 6th generation and totals 1.77 at the 7th generation.
Customers have enquired why an ancestor which occurs on both sides of the pedigree is not always included in the list. The explanation is that if the ancestor and an offspring both occur on both sides of the pedigree, you take the most recent common ancestor (an offspring in this case) as the common ancestor. If the ancestor and an offspring appear in the pedigree but the offspring does not appear on both sides, then the ancestor, not the offspring, counts as the common ancestor.
As explained earlier, the inbreeding coefficient total in the known pedigree is always shown under the 8th generation bar in the inbreeding coefficient graph. The contributions from the common ancestors are also totalled at the 8th generation in the list. It is relatively easy to look at the graph on a per generation basis, then glance down at the list to see which ancestors contribute at that particular generation level.
Putting it all together
The KCBS inbreeding analysis features enable you to;
· ascertain the amount of inbreeding in any given mating,
· to establish where in the pedigree the inbreeding occurs
· to identify the common ancestors and the amount they contribute to the overall inbreeding
· to ascertain the rate of inbreeding per generation and trend analysis
Understanding relationships in a complex pedigree and quantifying these relationships in terms of inbreeding values can be quite challenging. KCBS removes these complications and provides a standard set of metrics to help breeders understand the inbreeding in clear terms.
It takes a few seconds to run the inbreeding analysis program and to view the display for any individual in the database. The output (the inbreeding screen) can then be related to the actual pedigree which can prove both informative and educational. It may simply confirm your own manual calculation, or it may prove enlightening,
A popular use of the program is to do test matings and run the inbreeding analysis program to see which mating produces the inbreeding profile closest to that desired by the breeder. (NB. To do a test mating, simply click on add new record in KCBS, name the new individual something like test1, add the parents and then run the inbreeding analysis for this individual. You can repeat this test mating as many times as you wish. Simply add a new record and use a new name each time such as test1, test2 and modify the desired/potential parent/s).
You will find it interesting and revealing to view a variety of breeding relationships and to observe the resultant coefficient. You can of course take a view on what is a suitable level of inbreeding for your kennel and use your KCBS program to help you track and monitor inbreeding levels in your breeding program.
KCBS Inbreeding Export File/Make Your Own Charts
Each time you run the inbreeding analysis a file named winibd.csv is created in your C:\PDS\WIN folder. You can import this file into a spreadsheet (Excel, Lotus etc) and create your own inbreeding charts and documents.
KCBS's inbreeding analysis features are designed to compliment breeders knowledge and experience, and to provide a speedy and accurate calculation and analysis of inbreeding levels and rates for any particular mating.
NEW PEDIGREE EXTEND FEATURE
Although not strictly an inbreeding analysis tool, the new Pedigree Extend feature gives a summary and a clue to long and short term inbreeding influences in a pedigree.
This new feature counts the ancestors at any given depth of pedigree (we chose 10 generations for this example) and lists them in ascending order. There are a total of 2046 ancestors at this depth, but of course many ancestors occur multiple times, so the actual number of different ancestors is considerably less.
Here is an example of this listing;
Gen = 10; This level = 2046 Ancestors
Total Sire Dam
JALALABAD BARWALA OF CARLOWAY 88 42 46
WINSTYLE DERA KHAN 55 28 27
ZOG OF CARLOWAY 49 22 27
DANA KHAN OF CARLOWAY 43 20 23
CH YUSSEF OF CARLOWAY 42 18 24
KOHISTAN SHAHUDIN 38 19 19
JALALABAD MARANA 35 17 18
CH HORNINGSEA MAJID 35 15 20
CH MARIKA OF THREE STREAMS 28 13 15
RED PATHAN OF ALBANEY 26 14 12
DULLI KHAN OF CARLOWAY 26 14 12
HORNINGSEA TURRIDU 25 11 14
The list displays the top 20 ancestors for the chosen pedigree depth. In the above, all of the ancestors are "common" and thus figure to some extent in the inbreeding of the subject dog. You will note, in this case that the ancestors are split fairly evenly between the sire and dam side of the pedigree. Consider the next list...
Gen = 10; This level = 2046 Ancestors
Total Sire Dam
AM CH SHIRKHAN OF GRANDEUR 43 35 8
AM CAN CH BLUE BOY OF GRANDEUR 35 30 5
CH YUSSEF OF CARLOWAY 29 0 29
CH HORNINGSEA MAJID 28 1 27
JALALABAD BARWALA OF CARLOWAY 27 0 27
MAHDI OF GRANDEUR 24 21 13
AM CH OPHAAL OF CROWN CREST 22 13 9
TILUH OF CARLOWAY 20 10 20
ZOG OF CARLOWAY 17 0 17
AM CH CROWN CREST TAE JOAN 17 13 4
AM CH KARLI BEN GHAZI 17 17 0
CH PASHA OF CARLOWAY 17 0 17
There are two main differences between this list and the first one. Firstly, not all the ancestors are common to both sire and dam, so this breeding is more of an outbreeding. Secondly, where common ancestors do exist, they are not so evenly distributed between the sire and dam sides as was the case in the first list.