Population analysis of the Boxer breed Genetic analysis of the Kennel Club pedigree records of the UK Boxer population has been carried out with the aim of estimating the rate of loss of genetic diversity within the breed and providing information to guide a future sustainable breeding strategy. The population statistics summarised provide a picture of trends in census size, the number of animals used for breeding, the rate of inbreeding and the estimated effective population size. The rate of inbreeding and estimated effective population size indicate the rate at which genetic diversity is being lost within the breed. The analysis also calculates the average relationship (kinship) among all individuals of the breed born per year and is used to determine the level of inbreeding that might be expected if matings were made among randomly selected dogs from the population (the expected rate of inbreeding). Summary of results The analysis utilises the complete computerised pedigree records for the current UK Kennel Club registered Boxer population, and statistics were calculated for the period 1980-2014. 1
Figure 1: a plot of number of registrations by year of birth, indicative of any changing trend in popularity of the breed, followed by the yearly trend in number of animals registered (and 95% confidence interval). Breed: Boxer Figure 1: Number of registrations by year of birth Trend of registrations over year of birth (1980-2014) = 71.72 per year (with a 95% confidence interval of -10.10 to 153.54). 2
Table 1: census statistics by year, including sire use statistics. Table 1: by year (1980-2014), the number of registered puppies born, by the number of unique dams and sires; maximum, median, mode, mean and standard deviation of number of puppies per sire; and the percentage of all puppies born to the most prolific 50%, 25%, 10% and 5% of sires. year #born #dams #sires puppies per sire %puppies sired by most prolific sires max median mode mean sd 50% sires 25% sires 10% sires 5% sires 1980 889 588 335 20 2 1 2.65 2.89 80.88 59.73 36.45 23.85 1981 3168 1091 499 122 3 1 6.35 10.83 86.33 68.34 45.49 31.72 1982 4052 1201 542 141 4 1 7.48 11.87 85.12 65.97 43.51 30.08 1983 4948 1403 575 177 4 1 8.61 14.35 86.05 68.88 47.82 33.91 1984 5230 1515 620 159 4 2 8.44 13.36 86.12 67.82 45.76 32.1 1985 5120 1519 629 103 4 1 8.14 11.8 86.33 68.5 45.37 30.27 1986 5141 1527 692 109 4 2 7.43 10.71 85.74 67.65 44.39 29.94 1987 4894 1454 659 104 4 2 7.43 10.3 84.41 64.75 41.3 28.36 1988 4818 1396 657 104 4 2 7.33 10.6 84.72 66.13 43.63 29.76 1989 6939 1481 678 111 7 6 10.23 12.9 82.04 61.82 39.53 26.66 1990 6540 1316 617 188 7 5 10.6 13.71 81.22 61.04 39.16 26.38 1991 6615 1276 612 154 7 5 10.81 13.08 80.68 60.35 37.26 25.2 1992 7430 1468 679 105 7 7 10.94 13.91 81.8 62.93 41.17 27.25 1993 7922 1504 650 155 7 6 12.19 15.79 82.39 63.57 40.94 27.11 1994 8725 1679 710 206 7 4 12.29 16.7 82.96 64.65 42.26 28.29 1995 9210 1762 769 116 7 6 11.98 14.18 81.21 62.57 39.22 24.97 1996 10100 1952 851 128 7 5 11.87 15.34 82.23 63.68 41.35 28.23 1997 10901 2062 945 166 7 5 11.54 16.28 81.81 63.25 43.12 30.24 1998 10245 1922 924 131 7 6 11.09 14.08 81.09 61.83 40.11 27.55 1999 9713 1840 878 151 7 6 11.06 14.29 80.72 61.64 40.47 27.85 2000 9737 1832 905 123 7 7 10.76 12.64 80.28 60.37 38.09 25.22 2001 8962 1702 877 125 7 6 10.22 11.6 79.68 59.26 37.15 24.86 2002 9190 1726 807 128 7 5 11.39 13.63 81.38 61.48 38.59 24.98 2003 9420 1757 851 122 7 4 11.07 13.65 80.94 61.7 39.2 26.5 2004 9739 1787 861 183 7 7 11.31 14.44 80.22 60.42 38.57 25.85 2005 9413 1719 825 180 7 6 11.41 15.25 81.48 61.76 39.77 27.2 2006 9264 1685 829 116 7 6 11.17 13.01 80.18 60.63 38.71 25.05 2007 7830 1442 790 148 7 5 9.91 11.82 80.38 60.1 38.52 25.76 2008 7247 1320 721 112 7 6 10.05 11.34 79.21 57.94 36.14 24.08 2009 5974 1105 631 129 7 6 9.47 10.7 78.89 57.25 36.02 24 2010 5310 982 537 75 7 6 9.89 10.27 80 58.32 35.01 22.24 2011 5245 973 506 104 7 5 10.37 11.95 81.28 61.09 38.42 24 2012 4568 839 461 97 7 5 9.91 11.03 80.36 59.57 36.45 22.96 2013 3866 689 390 60 7 7 9.91 9.46 79.57 57.58 33.32 20.9 2014 4006 676 334 78 8 6 11.99 12.07 79.43 58.64 34.37 21.89 3
Generation interval: the mean average age (in years) of parents at the birth of offspring which themselves go on to reproduce. Mean generation interval (years) = 3.67 Figure 2: a plot of the annual mean observed inbreeding coefficient (showing loss of genetic diversity), and mean expected inbreeding coefficient (from random mating ) over the period 1980-2014. Expected inbreeding is staggered by the generation interval and, where >2000 animals are born in a single year, the 95% confidence interval is indicated. Figure 2: Annual mean observed and expected inbreeding coefficients 4
Estimated effective population size: the rate of inbreeding (slope or steepness of the observed inbreeding in Figure 2) is used to estimate the effective population size of the breed. The effective population size is the number of breeding animals in an idealised, hypothetical population that would be expected to show the same rate of loss of genetic diversity (rate of inbreeding) as the breed in question. It may be thought of as the size of the gene pool of the breed. Below an effective population size of 100 (inbreeding rate of 0.50% per generation) the rate of loss of genetic diversity in a breed/population increases dramatically (Food & Agriculture Organisation of the United Nations, Monitoring animal genetic resources and criteria for prioritization of breeds, 1992). An effective population size of below 50 (inbreeding rate of 1.0% per generation) indicates the future of the breed many be considered to be at risk (Food & Agriculture Organisation of the United Nations, Breeding strategies for sustainable management of animal genetic resources, 2010). Where the rate of inbreeding is negative (implying increasing genetic diversity in the breed), effective population size is denoted n/a. Estimated effective population size = 80.9 NB - this estimate is made using the rate of inbreeding over the whole period 1980-2014 5
Table 2: a breakdown of census statistics, sire and dam usage and indicators of the rate of loss of genetic diversity over 5 year periods (1980-4, 1985-9, 1990-4, 1995-9, 2000-4, 2005-9, 2010-14). Rate of inbreeding and estimated effective population size for each 5-year block can be compared with the trend in observed inbreeding in Figure 2. Table 2: by 5-year blocks, the mean number of registrations; for sires the total number used, maximum, mean, median, mode, standard deviation and skewness (indicative of the size of the tail on the distribution) of number of progeny per sire; for dams the total number used, maximum, mean, median, mode, standard deviation and skewness of number of progeny per dam; rate of inbreeding per generation (as a decimal, multiply by 100 to obtain as a percentage); mean generation interval; and estimated effective population size. years 1980-1984 1985-1989 1990-1994 1995-1999 2000-2004 2005-2009 2010-2014 Mean #registrations 3657.4 5382.4 7446.4 10034 9409.6 7945.6 4599 Total #sires 1528 1968 1878 2551 2540 2254 1335 Max #progeny 592 303 692 666 504 488 277 Mean #progeny 11.961 13.674 19.822 19.666 18.522 17.625 17.224 Median #progeny 4 5 8 8 8 8 8 Mode #progeny 1 2 5 5 5 6 6 SD #progeny 28.933 27.109 37.694 39.423 34.209 31.21 27.009 Skew #progeny 9.5152 5.1757 6.5183 6.8009 5.969 5.5205 4.0972 Total #dams 4290 5431 5083 6671 6229 5291 3048 Max #progeny 27 27 42 39 40 47 40 Mean #progeny 4.2601 4.9551 7.3236 7.5203 7.5515 7.5084 7.544 Median #progeny 3 4 6 6 6 6 6 Mode #progeny 1 3 5 6 5 6 6 SD #progeny 3.3928 3.6587 4.9443 5.1096 4.9052 5.0727 5.1467 Skew #progeny 1.8363 1.6527 1.5444 1.537 1.4144 1.6759 1.6567 Rate of inbreeding 0.016284 0.014761 0.002362 0.0026 0.007649-0.00035-0.00786 Generation interval 3.3656 3.4123 3.6665 3.5825 3.8462 3.9164 3.9248 Effective pop size 30.705 33.874 211.68 192.29 65.368 n/a n/a 6
Figure 3: a histogram ( tally distribution) of number of progeny per sire and dam over each of the seven 5-year blocks above. A longer tail on the distribution of progeny per sire is indicative of popular sires (few sires with a very large number of offspring, known to be a major contributor to a high rate of inbreeding). Figure 3: Distribution of progeny per sire (blue) and per dam (red) over 5-year blocks (1980-4 top, 2010-14 bottom). Vertical axis is a logarithmic scale. 7
Comments As with most breeds, the rate of inbreeding was at its highest in this breed in the 1980s. This represents a genetic bottleneck, with genetic variation lost from the population. However, since then the rate of inbreeding has slowed and even declined slightly, implying maintenance and even some replenishment of genetic diversity (possibly through the use of imported animals). There appears to be extensive use of popular dogs as sires in this breed (the tail of the blue distribution in figure 3). It should be noted that, while animals imported from overseas may appear completely unrelated, this is not always the case. Often the pedigree available to the Kennel Club is limited in the number of generations, hampering the ability to detect true, albeit distant, relationships. 8