Inbreeding in a closed dog population
Nm = number of fathers in that year, Nf corresponding number of mothers
F-average = average inbreeding level of individuals born in that year. a. Make a scatterplot with a two lines, one for inbreeding and one for relatedness.
a-average = average additive genetic relatedness among individuals born in that year. Put year on the x-axis.
Generation interval equals 4 years.
year Nm Nf F-average a-average deltaF/year dF-expected/gen ½delta_a/year 0.3
1970 80 237 0 0.013179
1971 54 245 0 0.019104 0.25
1972 76 277 0 0.010384
1973 77 234 0 0.019219 0.2
1974 82 263 0.0013 0.034211 0.0013 0.00199967541501 0.00756876271
1975 69 256 0.0023 0.034356 0.00100130169 0.0022998754529 7.35693255E-05 0.15 F-average
1976 95 238 0.0014 0.029783 -0.0009020748 0.00184099955772 -0.00232655229 a-average
1977 88 258 0.0115 0.037329 0.01011415982 0.00190495066949 0.0038302982 0.1
1978 83 294 0.0092 0.050598 -0.0023267577 0.00193119416441 0.00676073494
1979 76 243 0.0083 0.054747 -0.0009083569 0.00215914013429 0.00212809628
0.05
1980 92 257 0.0154 0.065342 0.00715942321 0.00184507697513 0.00544691364
1981 99 267 0.0234 0.069258 0.00812512696 0.00173079105663 0.00202399828
0
1982 78 238 0.0198 0.071171 -0.0036862584 0.0021277741866 0.00099074868 1960 1970 1980 1990 2000 2010 2020
1983 74 284 0.0192 0.083037 -0.00061212 0.00212933003426 0.00615200634
1984 86 274 0.0267 0.084739 0.00764681892 0.00190969275166 0.00088780334 b. Calculate the realized rate of inbreeding in each year between 1974 and 2015, and its average per year.
1985 83 236 0.0312 0.088233 0.00462344601 0.00203568511333 0.00182410177 Do this by adding a column to the data set.
1986 90 258 0.0324 0.093562 0.00123864575 0.00187338501292 0.00278775664 See column F.
1987 91 263 0.0294 0.091856 -0.0031004547 0.00184891154473 -0.0008951244
1988 83 281 0.0278 0.110021 -0.0016484649 0.00195086395404 0.00951993861 c. From your answer to question b, calculate the average rate of inbreeding per generation.
1989 76 255 0.0357 0.112124 0.00812590002 0.00213493292054 0.0011124623 Generation interval is assumed to be 4 years.
1990 67 244 0.0389 0.120673 0.00331846936 0.00237796672376 0.00452842657 dF/generation = L * dF/year = 4 * 0.002794 = 0.011177
1991 81 287 0.0328 0.114043 -0.0063468942 0.00197874994623 -0.00352773793 This is greater than 1% per generation, hence, this is a high rate of inbreeding.
1992 92 287 0.0415 0.121129 0.00899503722 0.00179423572186 0.00375697314
1993 75 257 0.0517 0.122285 0.01064162754 0.00215304798962 0.00061559699 d. Calculate the expected rate of inbreeding per generation in years 1974-2015. For this you need
1994 79 259 0.0598 0.129371 0.00854160076 0.00206490396364 0.00377339354 the number of sires and dams per generation. You may assume that the number of distinct sires and dams
1995 87 249 0.0578 0.147315 -0.002127207 0.00193878964132 0.00959250516 per generation is approximately equal to the number of sires and dams per year. (Note: this assumption
1996 67 274 0.0545 0.149829 -0.0035024411 0.00232187602135 0.00135714304 is mostly not correct in reality, with a real pedigree, you could calculate the actual number of distinct
1997 88 288 0.0781 0.154183 0.02496033845 0.00185448232323 0.00235338317 parents in a generation). Add a column with the expected inbreeding rate of inbreeding per generation.
1998 91 241 0.0673 0.158256 -0.0117149365 0.0018922985728 0.00220636588 dF = 1/(8Nm) + 1/(8Nf)
1999 85 234 0.0658 0.160638 -0.0016082342 0.00200477626948 0.00129352356 You can calculate this in each year (column G), and then take its average
2000 75 283 0.0732 0.158125 0.00792121601 0.00210836277974 -0.00136625593 The expected rate of inbreeding per generation equals 0.002618 per generation
2001 77 243 0.0912 0.169104 0.01942166595 0.00213777991556 0.00596089804
2002 82 257 0.1023 0.174155 0.01221390845 0.00201077156686 0.0027588306 e. Is the rate of inbreeding higher or lower than expected based on the number of parents?
2003 91 266 0.0963 0.185022 -0.0066837474 0.00184355118566 0.00595176593 The rate is much higher than expected. Based on the number of parents you'd
2004 77 271 0.0912 0.190591 -0.0056434658 0.00208463123592 0.00306795577 expect 0.26%/generation (answer 3d), but the realized rate equals 1.12%/generation (answer 3c)
2005 69 266 0.1134 0.199262 0.0244278169 0.00228151901493 0.00479221882 This is probably due to the extreme use of some of the fathers
2006 84 289 0.1254 0.203717 0.01353485224 0.00192062118965 0.00247417841
2007 85 278 0.1098 0.198785 -0.0178367254 0.00192022852306 -0.00274573592 f. Looking at the plot you made under question a,
2008 70 271 0.1342 0.1976 0.02740957088 0.00224696889826 -0.00065794378 is there much inbreeding due to preferential mating of close relatives?
2009 55 264 0.1103 0.211748 -0.0276045276 0.00274621212121 0.00784980523 No, there is not. The average additive genetic relatedness is
2010 60 230 0.1266 0.209023 0.01832078229 0.0026268115942 -0.0015237482 approximately twice the average inbreeding level. This is what
2011 35 180 0.1286 0.218428 0.00228990153 0.00426587301587 0.00525105093 you expect under random mating.
2012 25 148 0.1388 0.225418 0.01170530181 0.00584459459459 0.00392341182
2013 22 121 0.1235 0.226149 -0.017765908 0.00671487603306 0.00041194529 g. To judge the permanent loss of genetic diversity, which figure would you calculate?
2014 16 90 0.1298 0.23848 0.00718767827 0.00920138888889 0.00695178324 Half of the rate of increase in mean additive genetic relatedness per generation.
2015 20 76 0.1134 0.246257 -0.0188462422 0.00789473684211 0.00441472629 This rate is the expected permanent rate of inbreeding
0.00279428032 0.00261791270277 0.0028892851
This is the BEWARE
realized This is the h. Calculate the value of your answer to question g. Is there a big
deltaF/year expected dF loss of genetic diversity?
per generation Column H gives 0.5 delta_a per year as 0.002889
Per generation this has to be multiplied by 4, giving 0.011557
This is the expected permanent rate of inbreeding
It is higher than the FAO limit of 0.5 to 1%, thus there is
considerable loss of genetic diversity
i. The number of parents give early warning signals for bottlenecks
Before you see a steep increase in inbreeding, you often see the numbers of
parents going down.
Based on the numbers of parents, are there indications of a bottleneck?
Yes, there are. In the last years, the number of fathers and mothers steeply declined.
This suggests that the breed is becoming much less popular.
This will give a lot of inbreeding in the future, but that is not yet visible in
the current inbreeding trend. Already a little in the relatedness trend.
j. Based on the above, what is your advice?
There is much more inbreeding than expected based on the number of parents
Hence, contributions of individuals must be very unequal, probably some dogs
make very large contributions to the offspring, and others very small contributions.
The dog breeding association should look into this phenomenon, and maybe
consider a maximum number of matings per dog, or at least stimulate the
breeders to use the available breeding dogs more evenly.
There is not a lot of inbreeding due to mating close relatives , so that does
not really require action.
The recent bottleneck requires attention. The breed association should try
to increase the number of dogs, e.g. to make the breed more popular
