Population analysis of the Beagle breed Genetic analysis of the Kennel Club pedigree records of the UK Beagle 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 Beagle 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: Beagle Figure 1: Number of registrations by year of birth Trend of registrations over year of birth (1980-2014) = 52.72 per year (with a 95% confidence interval of 38.91 to 66.53). 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 1238 458 258 37 2 1 4.8 6.09 87.4 66.56 41.2 26.74 1981 998 351 177 56 3 1 5.64 7.34 86.27 66.03 41.38 26.85 1982 934 347 177 49 4 2 5.28 5.64 81.37 57.82 35.12 22.38 1983 905 318 159 55 4 2 5.69 6.15 82.1 58.12 33.37 21.77 1984 1025 361 166 53 4 2 6.17 7.52 82.73 61.56 39.22 25.66 1985 1040 347 177 87 4 2 5.88 8.2 81.44 58.37 37.4 26.25 1986 792 262 146 65 3 1 5.42 6.91 82.58 60.86 36.99 24.62 1987 740 234 126 77 4 1 5.87 7.95 82.97 61.62 37.16 23.38 1988 914 252 123 58 5 2 7.43 8.47 81.18 59.41 37.09 24.95 1989 1116 255 117 43 6 2 9.54 8.2 82.35 55.29 29.66 16.85 1990 1058 220 110 63 6 3 9.62 10.11 80.25 58.88 36.2 24.1 1991 1146 228 107 74 7 7 10.71 11.22 80.02 59.51 35.69 21.38 1992 927 191 88 82 6 5 10.53 12.51 80.69 61.17 38.08 23.84 1993 932 191 97 67 7 4 9.61 10.02 78 55.36 34.55 23.61 1994 811 179 91 93 6 6 8.91 11.27 80.89 58.57 35.88 26.63 1995 969 191 89 51 8 2 10.89 9.48 79.67 53.15 30.65 17.44 1996 982 196 88 99 6 4 11.16 16.32 85.23 67.11 46.84 30.55 1997 1054 204 92 93 7 6 11.46 13.45 81.59 61.67 37.19 26.38 1998 936 194 85 64 7 6 11.01 11.74 81.52 58.97 36.97 22.22 1999 1053 219 87 63 7 6 12.1 13.43 84.14 64.86 38.94 20.13 2000 865 180 78 83 6 4 11.09 15.5 85.66 67.86 45.32 30.98 2001 963 205 93 63 7 1 10.35 11.31 83.9 59.92 35.62 25.13 2002 1091 220 90 100 7 1 12.12 15.5 86.53 66.64 39.23 27.77 2003 1344 267 106 144 6.5 1 12.68 19.77 88.76 71.87 48.66 30.73 2004 1428 276 102 90 7 1 14 16.42 86.34 66.67 37.96 22.76 2005 1752 337 127 101 9 1 13.8 15.38 86.47 61.24 35.67 21.8 2006 1848 363 131 91 8 1 14.11 16.61 87.55 66.07 38.15 25.05 2007 2249 430 164 69 9 1 13.71 13.22 83.95 59.85 31.7 18.23 2008 2429 478 176 116 7 1 13.8 16.9 85.18 65.99 39.65 25.15 2009 2565 485 192 67 8 5 13.36 13.09 82.11 59.45 33.57 20.82 2010 2743 531 219 65 7 5 12.53 13.8 84.36 63.94 37.99 22.75 2011 2753 525 226 72 8 1 12.18 11.84 82.93 60.15 32.98 19.03 2012 2669 518 224 79 7 1 11.92 13.39 82.88 62.46 36.64 23.9 2013 2482 479 224 87 7 1 11.08 12.83 82.84 62.69 37.47 23.73 2014 2434 428 193 78 8 8 12.61 12.5 79.99 57.72 34.26 22.43 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) = 3.86 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 = 54.9 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 1020 920.4 974.8 998.8 1138.2 2168.6 2616.2 Total #sires 532 367 270 254 271 431 552 Max #progeny 157 294 215 299 322 310 295 Mean #progeny 9.5658 12.537 18.041 19.657 20.996 25.153 23.688 Median #progeny 4 6 8 8 7 10 11 Mode #progeny 1 1 6 6 1 1 1 SD #progeny 16.17 21.866 26.943 31.291 39.578 40.025 34.902 Skew #progeny 4.248 7.0955 3.6807 4.2954 4.0681 3.3857 3.1613 Total #dams 1241 922 672 662 787 1366 1682 Max #progeny 25 26 28 28 37 35 30 Mean #progeny 4.1007 4.9902 7.2515 7.5423 7.23 7.9363 7.7741 Median #progeny 3 4 6 6 6 7 6 Mode #progeny 1 2 4 5 6 5 6 SD #progeny 3.767 3.98 5.0044 5.1663 5.0872 5.5112 5.3013 Skew #progeny 2.139 1.5957 1.3012 1.1816 1.4297 1.2103 1.2963 Rate of inbreeding 0.023895 0.021408 0.026108 0.022154 0.0033383-0.021653 0.002224 Generation interval 3.8843 3.9049 4.508 3.6769 3.8574 3.4902 3.6676 Effective pop size 20.925 23.356 19.151 22.569 149.78 n/a 224.82 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 and 1990s. This represents a genetic bottleneck, with genetic variation lost from the population. However, since 2000 the rate of inbreeding has decreased, implying a slowdown in the rate of loss 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