Population analysis of the Mastiff breed Genetic analysis of the Kennel Club pedigree records of the UK Mastiff 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 Mastiff 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: Mastiff Figure 1: Number of registrations by year of birth Trend of registrations over year of birth (1980-2014) = 0.52 per year (with a 95% confidence interval of -4.29 to 5.32). 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 79 41 35 7 2 1 2.26 1.6 77.22 50.63 29.11 16.46 1981 163 45 32 23 4 2 5.09 4.84 81.6 58.28 29.45 22.09 1982 268 58 38 23 5 5 7.05 5.73 78.36 55.97 30.22 16.42 1983 225 54 37 17 5 1 6.08 4.68 82.22 52 25.78 13.78 1984 275 62 46 23 4.5 1 5.98 5.34 81.82 57.82 32.73 16.36 1985 226 52 36 26 5 1 6.28 5.26 79.65 53.1 30.53 18.58 1986 310 73 44 23 5.5 1 7.05 5.66 80.65 52.9 25.81 14.19 1987 330 74 46 38 5.5 1 7.17 7.08 81.82 56.36 34.55 20 1988 280 63 38 41 5 2 7.37 8.53 82.86 62.14 41.07 26.07 1989 397 70 50 26 6 1 7.94 6.4 79.85 55.67 27.71 17.88 1990 348 70 49 20 6 1 7.1 4.87 78.16 47.41 24.43 10.92 1991 401 66 46 49 6 5 8.72 9.05 79.8 58.35 35.41 21.95 1992 389 68 46 43 6 5 8.46 8.21 79.69 57.84 34.7 18.77 1993 371 70 44 25 6 2 8.43 6.63 79.78 54.99 23.72 12.67 1994 458 92 53 54 7 5 8.64 8.73 78.17 54.59 32.97 24.24 1995 483 88 56 35 7 7 8.63 6.22 74.53 49.28 27.33 16.15 1996 498 88 48 42 8.5 3 10.38 8.33 76.71 51 29.52 15.66 1997 472 85 55 36 7 1 8.58 7.85 81.14 54.87 33.9 21.82 1998 537 88 51 44 8 7 10.53 9.24 79.14 55.49 30.73 20.67 1999 572 96 61 33 8 8 9.38 7.39 78.5 53.32 27.27 15.38 2000 484 84 60 34 6 3 8.07 7.27 79.75 54.55 31.4 20.45 2001 484 88 58 29 6.5 6 8.34 6.17 77.48 50.41 27.07 16.12 2002 414 75 49 38 7 1 8.45 7.15 79.95 52.66 28.74 15.22 2003 571 95 60 32 7.5 1 9.52 8 80.04 55.52 29.07 15.76 2004 435 74 47 39 7 1 9.26 8.53 81.84 57.01 32.87 17.47 2005 510 74 48 75 7.5 7 10.63 11.57 78.63 55.29 34.51 21.18 2006 411 77 50 28 8 1 8.22 6.68 80.78 54.01 27.74 17.76 2007 403 72 53 29 6 3 7.6 5.63 78.91 48.88 25.06 16.63 2008 253 51 41 37 5 1 6.17 6.49 83 57.31 32.41 21.74 2009 270 53 37 31 4 1 7.3 7.25 83.7 61.11 35.19 20 2010 187 42 38 18 3.5 1 4.92 4.35 85.03 57.22 29.95 17.65 2011 143 38 32 16 2.5 1 4.47 4.3 86.71 58.74 30.77 20.98 2012 166 43 33 16 2 1 5.03 4.82 89.16 59.04 26.51 18.07 2013 168 43 30 19 1.5 1 5.6 5.96 91.07 67.86 30.36 21.43 2014 101 25 24 11 2.5 1 4.21 3.36 83.17 54.46 20.79 10.89 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) = 3.36 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 = 70.5 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 202 308.6 393.4 512.4 477.6 369.4 153 Total #sires 114 122 144 184 176 149 124 Max #progeny 83 94 141 100 96 116 27 Mean #progeny 8.8509 12.582 13.646 13.864 13.563 12.376 6.1532 Median #progeny 5.5 9 8 8 8 8 3 Mode #progeny 1 1 2 1 1 1 1 SD #progeny 11.289 13.964 17.182 16.948 17.375 15.303 6.7872 Skew #progeny 3.3017 2.7374 4.045 2.5531 2.6858 3.1925 1.4904 Total #dams 183 227 270 337 317 268 169 Max #progeny 42 30 31 37 50 31 17 Mean #progeny 5.5137 6.793 7.2815 7.5697 7.5142 6.8881 4.5148 Median #progeny 4 6 6 6 6 6 3 Mode #progeny 1 2 5 4 1 1 1 SD #progeny 5.4871 5.4029 5.4482 5.8014 6.4197 5.2512 3.9703 Skew #progeny 2.6685 1.5118 1.3716 1.7409 2.2358 1.5386 1.1041 Rate of inbreeding 0.033648-0.01639 0.027808-0.00698 0.018201-0.02323-0.03018 Generation interval 3.1905 3.3069 3.3767 3.2254 3.3653 3.2998 3.8738 Effective pop size 14.86 n/a 17.98 n/a 27.471 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 The rate of inbreeding in this breed has remained relatively steady but moderately high 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 eased a little (the tail of the blue distribution shortening 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