Population analysis of the Maltese breed Genetic analysis of the Kennel Club pedigree records of the UK Maltese 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 Maltese 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: Maltese Figure 1: Number of registrations by year of birth Trend of registrations over year of birth (1980-2014) = 15.32 per year (with a 95% confidence interval of 9.10 to 21.55). 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 110 93 65 5 1 1 1.69 1.09 70.91 48.18 26.36 11.82 1981 327 190 99 16 3 1 3.3 2.72 79.51 54.43 28.44 16.82 1982 498 232 120 15 3 2 4.15 3.11 76.91 52.21 26.71 15.06 1983 492 246 125 19 3 2 3.94 3.17 78.46 53.25 29.07 16.26 1984 522 243 138 24 2 1 3.78 3.59 80.46 58.62 32.95 18.97 1985 427 220 125 12 3 2 3.42 2.37 76.11 49.65 26.23 13.82 1986 508 239 127 24 3 1 4 3.6 79.72 55.51 31.69 17.52 1987 429 218 124 17 3 1 3.46 2.82 78.32 52.91 27.51 17.02 1988 459 223 125 20 3 1 3.67 2.9 76.69 50.98 28.32 15.9 1989 624 243 127 39 3 2 4.91 5.13 80.45 58.81 34.94 20.67 1990 575 230 111 31 4 3 5.18 4.84 80 56.87 31.48 21.04 1991 581 234 136 25 3 2 4.27 3.79 77.97 53.53 30.98 19.45 1992 530 215 131 23 3 2 4.05 4.03 78.3 56.98 35.09 23.02 1993 446 180 111 25 3 4 4.02 3.35 75.56 51.35 28.7 19.28 1994 524 198 118 19 3 3 4.44 3.27 76.34 51.34 26.72 15.65 1995 525 199 112 18 4 1 4.69 3.36 76.76 49.52 25.14 16 1996 486 194 116 26 3 2 4.19 4.39 80.04 58.44 36.83 23.25 1997 533 195 116 33 3 3 4.59 4.65 78.99 56.85 34.52 22.14 1998 571 209 107 31 4 2 5.34 4.54 78.11 52.54 29.25 17.51 1999 436 163 106 16 3 3 4.11 3.27 75.92 51.83 30.05 16.97 2000 398 166 111 15 3 2 3.59 2.64 74.87 49.25 26.38 17.84 2001 370 152 104 12 3 3 3.56 2.13 71.35 45.68 21.89 12.97 2002 423 155 100 23 3 2 4.23 3.77 76.83 52.96 31.44 20.57 2003 378 152 103 16 3 1 3.67 2.94 77.51 53.17 28.04 16.4 2004 381 156 99 20 3 1 3.85 3.21 79.79 53.81 28.87 17.06 2005 416 157 95 18 3 1 4.38 3.97 81.49 58.17 33.17 18.51 2006 443 162 99 19 4 2 4.47 3.21 76.52 49.21 26.19 15.35 2007 609 219 119 21 4 2 5.12 4.09 80.13 54.19 27.42 16.09 2008 644 225 143 23 3 1 4.5 4.37 81.21 58.23 33.39 20.34 2009 870 274 143 30 4 3 6.08 5.25 79.2 55.4 29.08 18.28 2010 857 280 159 39 4 2 5.39 5.2 80.4 56.13 31.39 20.42 2011 1053 356 208 26 3 3 5.06 4.48 79.96 55.75 30.48 17.85 2012 1082 341 213 32 4 3 5.08 4.86 78.47 55.36 32.62 22 2013 1143 365 210 33 4 4 5.44 5.26 78.83 56.87 33.42 21.7 2014 1155 343 178 58 4 3 6.49 6.28 77.84 54.37 31.26 20.17 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) = 3.61 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 = 135.9 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 389.8 489.4 531.2 510.2 390 596.4 1058 Total #sires 275 314 298 297 276 321 503 Max #progeny 50 91 73 82 42 96 181 Mean #progeny 7.08 7.7898 8.9094 8.5859 7.058 9.2866 10.511 Median #progeny 4 5 6 5 5 5 6 Mode #progeny 1 1 1 2 1 1 1 SD #progeny 7.6788 9.4798 10.48 10.037 7.3388 10.936 14.05 Skew #progeny 2.0544 3.7373 3.0126 2.9531 2.0653 2.8475 5.0068 Total #dams 604 667 623 602 521 647 1092 Max #progeny 13 15 22 25 18 22 25 Mean #progeny 3.2235 3.6672 4.2616 4.2359 3.739 4.6074 4.8416 Median #progeny 3 3 3 3 3 4 4 Mode #progeny 1 2 3 2 1 2 3 SD #progeny 2.404 2.6969 3.1348 3.2094 2.6956 3.4869 3.3571 Skew #progeny 1.4629 1.4222 1.543 1.7794 1.621 1.5464 1.3258 Rate of inbreeding 0.019921 0.002288 0.018118 0.010492 0.006032-0.01388-0.00792 Generation interval 3.1138 3.4983 3.8841 3.8003 3.9684 3.6716 3.361 Effective pop size 25.099 218.55 27.596 47.653 82.886 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 and 1990s. This represents a genetic bottleneck, with genetic variation lost from the population. However, since the late-1990s 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