Is there a way to calculate a ten generation COI on pedigree database? - Page 1

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by Snowleaf on 14 February 2017 - 10:02

Is there a way to calculate a ten generation COI on pedigree database? Preferably Hardiman's? And, being new to the game, am I correct in assuming that I need to add up the different values given in the Wright's / Hardiman's columns respectively in order to get the total COI for a given dog?

Thanks! Love this tool!
susie

by susie on 14 February 2017 - 22:02

First of all, I don´t think it´s possible, but 10 generations in dogs is like around 250 years in humans.
That´s a very long time...and even if you are able to trace back 10 generations you will never know which genes ( 50:50 ) were inherited to the next generation. The COI may show the overall percentage, but never the single traits you are looking for.
For instance breeder x bred a litter because of working ability of sire and dam, breeder y bought a puppy out of this litter, but selected for color, not for working ability - out of this litter breeder z bought a puppy, and he selected for size or coat, and so on...
During the same time all these breeders ( 10 generations = thousands of breeders ) not only used one dog, but two ( sire and dam ). That´s a lot of unknown blood...and you will not be able to point out one ancestor for one trait, simply too many variables.

by Snowleaf on 15 February 2017 - 07:02

Thank your for your answer! I'm aware of the data, and of the fact that we're talking probabilities. However, I'm not primarily interested in linebreeding, but in avoiding inbreeding. With Australian Shepherds, we have about 300 foundation dogs, and in the early days there were a lot of linebred dogs and favorite studs. Thus, in order to preserve the genetic vitality and heterozygotism of the present day Aussie, it is recommended to go back ten generations in order to get a clear idea of which dogs to mate. Referring to C.S. Sharp on Ashgi.org here, in case you're interested in reading up on that.

In my case, when I go back five generations, the COI is null. However, in generation 6 and 7 the first common ancestors begin to appear, and if you go back ten generations, you find like 6, 7, 10 times the same dog. I just want to know the ratio for each possible stud in order to select for greatest homozygosity.

As for the mantra of linebreeding: Statistically there is no correlation between success in shows and linebreeding. Historically (in the case of Dalmations, at least, which were used for a study) there were just as many outcrossed winners as there were linebred ones.

Oli (admin)

by Oli on 15 February 2017 - 19:02

Hi, There is a reason that 7 is the limit. With dogs that have 100% lineage for 10 generations, the system needs to do massive calculations (including power of and squared) for 7,257,600 dogs. Since the last generation (10th) still needs to check 5 generations back, (according to the formula). Of course there aren't that many dogs in the system, but it shows the scale. Of course its the same dog for most parts as you go up, but checks need to be done

Since web crawlers and harvesters show no respect (they are about 93% of all traffic, humans around 7%), I had to limit it to 7 generations and still keep the calculations fairly fast. This is done in real-time, every time the page is viewed (or generations changed).

I could add the ability to go to 10, 15, 20 . but it would have to be extremely limited and only very few persons could use it due to the strain on the database. So, this is possible. I just need to put down heavy guidelines on who can use it and when.

 

I checked out this dog: Crazy-River-Enjo with 10 generations, it took the system (and it's a powerful setup) 50! seconds to calculate the stuff.  This is a lot for an open system. Any user could simply drown the server for every body by simply asking for that information 100 times a second.

 

This was the result:

 

 

Linebreeding - 10 generations Inbreeding coefficient
Father - Mother Who Wright's Hardiman's
4 - 5 Scrap's Rusty Luger 00.39% 02.34%
        ↳5 - 6         ↳Gannon's Scrap's of Blue    
            ↳6 - 7             ↳Black Powder's Image    
            ↳6 - 7             ↳Nomad's Little Scrapper    
        ↳5 - 6         ↳Rabrega's Rusty Memorie    
            ↳6 - 7             ↳She Ain't Ez    
            ↳6 - 7             ↳ASCA Ch Downeast Courageous    
                ↳7 - 8                 ↳Blue Lad Boomarang Flashfire CDX    
                    ↳8 - 9                     ↳Beauwood's Panda Bear    
                        ↳9 - 10                         ↳Beauwood's Calgari Bear    
                    ↳8 - 9                     ↳ASCA CH Blue Lad Rocky Road    
                        ↳9 - 10                         ↳ASCA Ch Blue Lad Texas Ranger CD TD    
                        ↳9 - 10                         ↳ASCA Ch Copper Canyon Sandstorm of Blue Lad CD TD    
                ↳7 - 8                 ↳Downeast Yankee's Shadow    
                    ↳8,10 - 9                     ↳Ch. Robinsons Bonnie Blue Yankee CD    
                    ↳8,10 - 9                     ↳ASCA Ch Moonshine of Windermere HOF    
4 - 5 Lanbria Larky Yascal 00.39% 04.30%
        ↳5 - 6         ↳Jokers Wild Sapphire Sampson    
            ↳6 - 7             ↳Somercrest's Holly Baleau    
            ↳6 - 7             ↳ASCA Ch Master Charge of Windermere    
                ↳7,8,9 - 8                 ↳ASCA Ch Westwind's Miss Moonglow CD #1 A.S. HOF    
                    ↳8,9,10 - 9                     ↳Ch. Tophands Lisa CDX UD    
                        ↳9,10,10 - 10                         ↳Miller's Molina of Flintridge    
                ↳7,8,9 - 8                 ↳ASCA Ch Sun's Mark of Windermere CD    
        ↳5 - 6         ↳Gold Nugget's Crimson Delilah    
            ↳6 - 7,10             ↳ASCA Ch Nelson's Phoebe of Gold Nugget CD STDds    
                ↳7 - 8                 ↳Nelson's Magic Dust    
                    ↳8 - 9                     ↳Ch. Higgins Maggie    
                        ↳9 - 10                         ↳Las Rocosa Aunt Jemima    
                        ↳9 - 10                         ↳Schueller's Irish Whiskey    
                ↳7 - 8                 ↳Ch. Tri Ivory Baked Alaska CDX    
5 - 6 Aust. Ch. By Popular Demand of Cimarron 00.10% 01.37%
        ↳6 - 7         ↳ASCA Ch Cimarron's Light The Way    
            ↳7 - 8             ↳Aust. Ch. Cimarron's Talk of the Town    
                ↳8 - 9                 ↳Cimarron's Tiger Lily    
                    ↳9 - 10                     ↳ASCA Ch ASCA Ch Marquis You Better Believe It    
                    ↳9 - 10                     ↳ASCA Ch Natassia of Cobber    
                ↳8 - 9                 ↳Ch. ASCA Ch Las Rocosa Adam    
                    ↳9 - 10                     ↳L7 Good Time Charlie    
                    ↳9 - 10                     ↳ASCA Ch Las Rocosa Justa Sinner    
            ↳7 - 8,9             ↳ASCA Ch Peachcreek's Razzle Dancer HOF    
                ↳8 - 9,10                 ↳ASCA Ch Briarbrook's Broadway Joe    
                    ↳9 - 9,10                     ↳ASCA Ch Fieldmaster's Nik Nak    
                    ↳9 - 10                     ↳ASCA Ch Fieldmaster's Cast the Die    
                ↳8 - 9,10                 ↳ASCA Ch Briarbrook's Song and Dance HOF CD    
                    ↳9 - 10                     ↳Aristocrats Lady Sings the Blues HOF    
        ↳6 - 7         ↳Aust. Ch. Brigadoon's Gotcha    
            ↳7 - 8             ↳ASCA Ch Windswept of Windermere CD HOF    
            ↳7 - 8             ↳CH ASCA Brigadoon's One Arrogant Dude HOF    
                ↳8 - 9                 ↳ASCA Ch Patchworks River Fog    
                    ↳9 - 9,9,10,10                     ↳Ch. Tri Ivory Ruff Rider CD    
                    ↳9 - 9,9,10,10                     ↳ASCA CH Windsong's Foggi Notion HOF    
                        ↳10 - 10,10                         ↳ASCA Ch Hoyt's Wildwood Flower    
6,8,10 - 7,9,10,10,10 Ch. Tri Ivory Yankee Dandy CDX 00.02% %
        ↳7,9 - 8,10         ↳Ealand's Nemo Blue Chips CDX    
        ↳7,9 - 8,10         ↳Tri-Me Yanks PJ CDX    
            ↳8,10 - 9             ↳Peterson's Trixie    
                ↳9 - 10                 ↳Rulisons Blue    
                ↳9 - 10                 ↳Rulisons Rip    
            ↳8,10 - 9             ↳Peterson's Damn Yankee    
                ↳9 - 10                 ↳Hahn's Phoebe    
6,8,10 - 8,9,9,10,10 ASCA CH Arrogance of Heatherhill CDX STDD HOF 00.01% %
        ↳7,9 - 9,10,10         ↳ASCA CH Sweet Seasons of Heatherhill    
            ↳8,8,10 - 10             ↳Mc CORKLES BLUE TULE FOG    
8,8 - 7 WTCH CH Silverledge Slide Me Five HOF 00.01% %
        ↳9,9 - 8         ↳CH Taylor's Luke the Drifter CDX    
            ↳10,10 - 9             ↳Wood's Stubbie    
            ↳10,10 - 9             ↳Bjork's Chula    
        ↳9,9 - 8         ↳Silverledge Mindy Taylor    
            ↳10,10 - 9             ↳Taylor's Calamity Jane CD    
7,8,8,9,9,9,10,10 - 8,9,9,9,9,9,10,10,10,10,10,10,10 Ch. Windermere's Sunshine of Bonnie Blu CDX HOF 00.01% %
        ↳8,9,9,9,10,10,10 - 9,10,10,10,10,10,10,10         ↳Wildhagen's Thistle of Flintridge HOF    
            ↳9,10,10,10 - 10             ↳Sisler's John    
8,9,9,10,10,10,10,10,10,10 - 8,9,9,9,10,10,10,10,10,10,10,10,10,10,10,10 ASCA Ch Fieldmaster of Flintridge HOF 00.00% %
9 - 7 CH Tri-Ivory Roquefort of Higgins CD 00.00% %
        ↳10 - 8         ↳Patch-Work Isis    
8,8 - 8,8 ASCA CH Slash V Little Rock CD HOF 00.00% %
        ↳9,9 - 9,9         ↳ASCA Ch Slash V Rocky Top    
            ↳10,10 - 10,10             ↳George's Dago Rojo    
            ↳10,10 - 10,10,10             ↳Keep's Waltzing Matilda    
        ↳9,9 - 9,9         ↳Myrup's Gabby    
            ↳10,10 - 10,10             ↳Moody's Barrocho    
10 - 7,7,9,10,10 Ch. Copper Canyons Caligari CD 00.00% %
8,9,9,10,10,10,10,10,10,10 - 9,10 Hartnagle's Fritzie Taylor 00.00% %
8,9,10,10,10,10,10 - 9,10,10,10 ASCA Ch Las Rocosa Leslie #1 A.S., CD OTDs CWDg 00.00% %
9 - 8,10 ASCA Ch Vanlandingham's Ebony Lace CD OTDd HOF 00.00% %
        ↳10 - 9         ↳Mansmith's Mei Mei    
        ↳10 - 9         ↳ASCA Ch Sundown's Maize of Bonnie-Blu    
9,9 - 8 ASCA CH Jones Reddy Teddy HOF SCHH I OTD-CDS CDX #1 A.S. 00.00% %
        ↳10,10 - 9         ↳Davies Ginger Red    
        ↳10,10 - 9         ↳Piz Little Joe    
8,9,9,10,10,10,10,10,10,10,10,10,10,10,10,10,10 - 9,9,10,10 Taylor's Whiskey 00.00% %
        ↳9,10,10 - 10,10         ↳Manskers Anna Lee    
        ↳9,10,10 - 10,10         ↳Lamar's (Mansker's) Turk    
8,10 - 9,10,10,10 Ch. Tri Ivory Here Cum Da Fuzz CD 00.00% %
        ↳9,9 - 9,10,10         ↳Farrington's Buster Ivory UD    
            ↳10,10 - 10             ↳Wiles Annie Oakley    
            ↳10,10 - 10             ↳Wiles One Too Many    
        ↳9 - 10         ↳Farrington's Punkin CDX    
8,10 - 9,10 Evan's Bonnie Blue Chips 00.00% %
8,10 - 9,10 ASCA Ch Evan's Regal Spice 00.00% %
        ↳9 - 10         ↳Leavitt's Patches    
8,8,9,9,10 - 9,9,10,10,10 Blue Heather of Windermere HOF 00.00% %
        ↳9,9,9,10,10,10,10,10,10,10 - 8,8,9,10,10,10,10,10         ↳George's Red Rustler HOF    
            ↳10,10,10 - 9,9,10             ↳Ginther's Rusty    
            ↳10,10,10 - 9,9,10             ↳Ginther's Red Velvet    
        ↳9,9,10,10 - 10,10         ↳Wilsons Little Annie UD    
9,10 - 8,8,10 HOF, ASCA CH Hot Toddy of Emerald Isle 00.00% %
        ↳10 - 9,9         ↳ASCA Ch Hopscotch of Adelaide    
8,8,8,8,9,9,9,10,10,10,10 - 9,9,10,10,10,10,10,10,10,10 ASCA Ch Wildhagen's Dutchman of Flintridge CDX, PC, HOF 00.00% %
9,9 - 8,8,9,9,9,9,10,10,10 ASCA CH Fieldmasters Three Ring Circus 00.00% %
        ↳10,10,10 - 9,9,10,10,10,10,10         ↳Whispering Pines of Flintridge    
10 - 8,8,10 Quaglinos Miss Pooh 00.00% %
9,9,9,9,9,10,10,10,10,10 - 9,10,10,10,10,10,10,10 Ch. Herdsman of Flintridge 00.00% %
        ↳10,10,10,10,10,10,10,10 - 10,10         ↳Heard's Blue Spice of Flintridge    
        ↳10,10,10,10,10 - 10,10,10,10         ↳Cactus of Flintridge    
9,9,10,10,10,10,10,10,10 - 9,10,10,10,10,10 Heard's Salt of Flintridge 00.00% %
        ↳10,10,10 - 10         ↳Harper's Old Smokey (NSDR Reg.)    
9,9,10,10,10,10,10,10,10,10 - 9,9,10,10,10,10,10 ASCA Ch Las Rocosa Shiloh HOF 00.00% %
        ↳10,10 - 10,10         ↳Boehmer's Four Man    
9,9,9,9,9,9,10,10,10,10,10 - 9,10,10,10,10,10,10 Heard's Savor of Flintridge 00.00% %
        ↳10,10,10,10,10,10,10 - 10         ↳Nettesheim's Twinkle    
10,10 - 9 ASCA Ch Little Abner of Flintridge 00.00% %
9 - 10 ASCA Ch Yankee Clipper of Wingmont HOF 00.00% %
9,9,10,10 - 10,10 Martins Red Fudge 00.00% %
9,10,10,10 - 10,10 ASCA CH Heard's Chili of Flintridge 00.00% %
9,10,10,10,10,10 - 10 ASCA Ch Shanahan's Phantom 00.00% %
9,9,9,9,9,10,10 - 10 Hartnagle's Hud 00.00% %
9,10,10,10,10,10,10,10 - 10 Taylor's Buena 00.00% %
10 - 9 ASCA Ch Slash V Frosted Fudge 00.00% %
10,10,10,10,10,10,10 - 10,10 Hosmer's Jill 00.00% %
10 - 10 ASCA Ch Laurel of Flintridge 00.00% %
10 - 10 Bar Lazy K's Red Hot Chili 00.00% %
10 - 10,10 Ch. Adelaides Scotsman of Windermere 00.00% %
10 - 10 ASCA Ch Freedom of Flintridge 00.00% %

Oli (admin)

by Oli on 15 February 2017 - 21:02

Explanation:  Hardiman's formula only applies to 5 generation while Wright's requires the coefficient of every ancestor, which is why Hardiman's stops calculating after Generation 5

by Snowleaf on 16 February 2017 - 16:02

Thanks for the reply and the explanation, I see your point, and the calculation is indeed impressive! Wow, only 7 % humans? That's creepy! I truly appreciate your effort, and the database is such a great tool! :-) I've looked into several different breeder-software-products these days, but none are as satisfying, especially given the fact that I'd need to first type in all the data that is already online on your site. Since I'm a very small breeder with only two dogs and no intention of becoming bigger, that seems like a lot of effort, especially since I'd only need the ten generations COI in order to find a sire for a planned mating every other year... I wonder – perhaps you could offer the possibility to run 10G on request? Maybe charge a small fee or something? I'm sure I'd appreciate that very much...!!! But thanks anyway for your efforts!

p.s. I tried to read up on Hardiman, but the math is quite complex. Do I get this right that with Hardiman you don't need to do a COI with more than five generations in order to get a "real" percentage of inbreeding? Even if, say, the common ancestors don't show up in the first five but only in generation nine or so? Does Hardiman take that into account? The Hardiman coefficient comes up with a much higher rate of inbreeding in your example, I added up the Wright percentages and the Hardiman's, and the first says only 0,93 as opposed to 7,01.

At any rate it seems as if the latter generations really don't seem to contribute much to the calculation of the COI. Which is strange, since C.S. Sharpe from Ashgi argues otherwise. According to her, seven generations is misleading in some cases.
Oli (admin)

by Oli on 16 February 2017 - 17:02

Hi,

I will look into allowing users to use a higher number.

This page explains the difference really well: COEFFICIENT OF INBREEDING

Excerpt:

Wright's Equation is haphazardly calculated to any number of generations, whereas Hardiman's Method is always calculated to five generations.

 

by Snowleaf on 16 February 2017 - 18:02

Thanks! :-) The Link: That's the page I found, too. I made it about halfway down, lol... but I'll give it another try now.

susie

by susie on 16 February 2017 - 19:02

Oli's example may seem to show a lot of linebreeding but never forget: only in the "10. generation" there are 1024 dogs - 10 times the same dog out of 1024 f.e. is less than 1 percent - and those 10 breedings won't do us the favor to produce clones ... And thousands of different breeders won't select for the same traits...

by Snowleaf on 16 February 2017 - 22:02

Ok, it's been a long time since I took maths (or biology...)lessons, so correct me if I'm wrong: A dog has about 20.000 genes (Nature, DOI: 10.1038/nature04338) and 1024 forebears in the tenth generation, each of which will pass on half of his genes, i.e. a maximum of 10.000 genes to the next generation. If this number were distributed equally, that would mean 20.000 divided by 1024, i.e. we're talking about around 20 genes which each forebear might have contributed to a given dog's genetic makeup. Of course some ancestors will have contributed more and some less, but since a lot of these genes are homozygous anyway, what with a given race having a reduced gene-pool, wouldn't it make sense to avoid mixing two close lines? At least that's what C.S.Sharpe argues (http://www.ashgi.org/home-page/genetics-info/faq/genetics#):

"Aren’t genes several generations back too diluted to worry about?

The idea that genes get “diluted” across the generations is a common misconception. The genes don’t dilute, but every ancestor on average passes half of whatever genes it had to its offspring – one from each gene pair. Statistically, a dog will have half of a parent’s genes, a quarter of a grandparent’s, an eighth of a great-grandparent’s and so on. In actuality it may have more or less than that number but in most cases whatever came down will hover around those amounts. A dog five generations back statistically only passes on 3.13% of its genes. Chances are low that your dog has any particular one of that ancestor’s approximately 20 thousand genes; however he almost certainly has a few. After all, 3.13% of 20 thousand is just over 626 genes.

If a dog appears in a pedigree multiple times, then it is more likely that its genes will be passed on. If you have enough 3.13%’s from the same dog and maybe a 6.5% for an appearance on the 4th generation the percentage of genes contributed can add up even though that dog doesn’t show up on a 3-generation printed pedigree. This is a “percentage of ancestry” calculation. Such calculations do not take in to account the fact that different ancestors that are close kin are likely to be carrying many of the same genes so a line-bred pedigree is apt to have more transmission of the same genes down the generations than would be apparent if you only look at how many times a particular dog shows up."

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