Population analysis of the Akita breed Genetic analysis of the Kennel Club pedigree records of the UK Akita 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 Akita 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: Akita Figure 1: Number of registrations by year of birth Trend of registrations over year of birth (1980-2014) = 31.90 per year (with a 95% confidence interval of 18.19 to 45.61). 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 6 5 4 2 1.5 1 1.5 0.58 n/a n/a n/a n/a 1981 9 9 7 3 1 1 1.29 0.76 n/a n/a n/a n/a 1982 16 14 12 3 1 1 1.33 0.65 62.5 43.75 18.75 18.75 1983 45 16 12 14 1.5 1 3.75 4.16 86.67 64.44 31.11 31.11 1984 79 16 15 11 6 1 5.27 3.53 81.01 46.84 26.58 13.92 1985 249 44 34 27 5.5 1 7.32 7.3 85.14 61.45 31.73 21.29 1986 338 54 40 23 7 6 8.45 5.57 73.67 48.22 24.56 13.31 1987 502 93 56 32 7 6 8.96 6.78 76.69 52.59 28.69 16.14 1988 588 125 82 46 5 1 7.17 7.48 81.46 59.01 33.5 22.11 1989 576 112 89 23 6 6 6.47 4.42 74.65 47.22 25.87 13.19 1990 591 107 71 58 6 5 8.32 8.65 78.68 55.84 34.52 24.2 1991 495 99 80 47 5 3 6.19 5.65 74.75 48.89 27.47 17.78 1992 557 104 81 48 6 6 6.88 6.31 76.12 50.45 29.44 19.03 1993 624 113 80 27 7 7 7.8 5.81 75.16 51.44 27.72 16.03 1994 913 149 96 79 7 4 9.51 10.68 79.3 57.5 37.02 24.75 1995 969 168 103 76 6 6 9.41 11.98 80.5 60.17 39.11 27.97 1996 1400 226 133 58 7 6 10.53 11.27 79.5 58.5 36.07 25.43 1997 1345 217 137 64 8 8 9.82 9.97 76.36 53.46 35.24 23.72 1998 1496 231 144 64 7 7 10.39 9.9 75.2 53.61 31.95 22.06 1999 1417 229 168 55 7 7 8.43 6.49 73.04 49.12 27.31 16.37 2000 1475 251 170 79 7 6 8.68 8.92 76 52.81 31.25 22.44 2001 1324 236 165 47 7 7 8.02 6.47 72.43 48.11 29.38 18.88 2002 1369 241 170 59 6 6 8.05 7.26 75.16 52.59 30.39 20.38 2003 1588 269 195 75 7 6 8.14 7.42 74.43 51.01 30.54 19.46 2004 1583 271 201 31 7 6 7.88 5.6 75.24 49.08 26.34 15.48 2005 1478 257 200 34 6 6 7.39 5.41 71.85 46.82 27.06 18 2006 1320 226 171 50 7 6 7.72 5.94 73.79 48.41 26.59 17.2 2007 1284 231 173 33 6 7 7.42 5.33 74.07 49.38 26.95 15.97 2008 995 192 144 36 6 5 6.91 4.89 72.16 46.23 24.72 15.68 2009 1080 194 141 41 6 5 7.66 5.96 73.61 49.81 28.15 17.41 2010 1013 187 131 67 6 4 7.73 8.73 78.18 54.99 35.83 26.16 2011 903 181 126 48 6 5 7.17 6.79 75.53 51.83 31.34 20.16 2012 727 147 113 24 6 1 6.43 4.39 74.14 46.35 24.76 15.82 2013 610 116 84 47 6 6 7.26 6.03 73.77 48.52 26.56 16.89 2014 452 87 62 43 5 1 7.29 7.18 80.53 57.52 31.64 20.35 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) = 2.97 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 = 53.3 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 31 450.6 636 1325.4 1467.8 1231.4 741 Total #sires 42 197 259 430 592 532 334 Max #progeny 17 87 120 230 183 129 137 Mean #progeny 3.6667 11.396 12.274 15.258 12.372 11.566 11.084 Median #progeny 1 7 7 9 8 8 7 Mode #progeny 1 1 6 7 6 6 1 SD #progeny 4.2177 13.05 14.745 23.216 15.784 12.19 14.708 Skew #progeny 1.7047 2.6918 3.3229 5.3775 5.6344 3.7983 4.581 Total #dams 55 291 387 736 900 778 509 Max #progeny 16 41 46 39 36 37 37 Mean #progeny 2.8 7.7388 8.2145 9.0014 8.1411 7.9087 7.2731 Median #progeny 1 7 7 7 7 6 6 Mode #progeny 1 1 7 7 6 6 1 SD #progeny 3.7387 5.8846 6.0175 6.0466 5.6375 5.5905 5.5004 Skew #progeny 2.1795 1.5634 1.7663 1.3219 1.5726 1.7536 1.6222 Rate of inbreeding 0.0045055 0.0084401 0.0098906 0.0032266-0.0026043 0.0011977 0.018725 Generation interval 1.2588 2.6075 3.2201 3.2841 3.2927 3.5354 3.7734 Effective pop size 110.97 59.241 50.553 154.96 n/a 417.48 26.702 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 The rate of inbreeding in this breed has remained relatively steady over the whole period. This implies genetic variation is steadily being lost from the population. It appears that the extensive use of popular dogs as sires has increased since the 1980s (the tail of the blue distribution increasing 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