REPORT ONDEFRA PROJECT CR 0404
“UK BIODIVERSITY INDICATORS – DEVELOPMENT OF AN INDICATOR OF GENETIC DIVERSITY IN SELECTED FARM BREEDS”
Beatriz Villanueva, Rami Sawalha, Tim Roughsedge, Elisenda Rius and John Woolliams
1. BACKGROUND TO PROJECT
In 2002, the UK along with all other Parties to the UN Convention on Biological Diversity (CBD), made a commitment to ‘achieve by 2010 a significant reduction of the current rate of biodiversity loss at the national, regional and global level as a contribution to poverty alleviation and to the benefit of all life on earth’. This targetwas subsequently endorsed at the World Summit on Sustainable Developmentand the United Nations General Assembly and was incorporated as a new target under the Millennium Development Goals. The CBD Conference of the Parties decided that in order to assess progress at the global level towards the 2010 target, and to communicate effectively about trends in biodiversity, a limited number of indicators of biodiversity need to be developed and used for a global assessment. These indicators should use existing data sources.
Genetic diversity in livestock species is an important component of biodiversity. In November 2006, Defra and the rural affairs departments of the Devolved Administrationspublished their National Action Plan on Farm Animal Genetic Resources (FAnGR) and in March 2008, they launched the National Standing Committee for FAnGR to oversee the implementation of the plan. One important aspect in the monitoring of trends in FAnGR is to produce a biodiversity indicator for them. This has been recognised also in the set of biodiversity indicators for the UK published by Defra ( in June 2007.
In contrast to wild species, livestock species have been managed and selected by humans for centuries and this has resulted in a considerable number of breeds in each species. The diversity of native livestock breeds, each with their adaptations to particular environments, plays an important role in shaping the ecosystems within the UK supporting other natural wild diversity, e.g., in invertebrates and landscape diversity. The partition of the diversity both within and between breeds is unique to farmlivestock and some companion (e.g., dogs) animal species (although an analogous situation may exist with crop species), and the selection that has formed it, needs to be taken into account when developing the indicator.
Within this project we calculated an indicator of genetic diversity for farm animals following the methodology previously proposed by Villanueva et al., (2007). The method results in an indicator that is sensitive to i) genetic variation within breeds, as it is based on the effective population size (Ne), and ii) what is happening to breeds most at risk of disappearing. It uses existing data sources and can be obtained simply, given a set of guidelines. The indicator initially proposed was the species average Ne for the lower 10% tail of the distribution of Ne across breeds.The lower 10% was chosen because it provided a good compromise between giving high weight to the breeds most at risk, without being too sensitive to events surrounding a single breed. In other words, given that the challenge is to indicate within a single statistic the state of diversity both between and within breeds, the indicator responds negatively (i.e. goes down) when breeds become extinct (here Ne = 0) or when management within breeds deteriorates. It will be sensitive to those breeds most at risk and insensitive to events in breeds where Ne remains high.A new recommendation arising from this project is that this percentage may need to be increased if the number of breeds with available information is low.
For each species, Villanueva et al., (2007) proposed that the biodiversity indicator is calculated in the following way: i) estimate Ne for each breed; ii) calculate the distribution of breed Ne values; iii) find the average Ne for the lower tail of the distribution.
2. OBJECTIVES OF THE PROJECT
The general aim of this project is to produce an agreed indicator of genetic diversity, based on effective population sizes, in farm animals. The specific objectives are:
- To identify the availability of data for evaluating the proposed indicator.
- To produce a draft indicator and associated descriptive text.
- To consult scientific and policy making communities to agree any refinements or amendments to the indicator.
- To revise and present the indicator and associated text description and data specifications.
3. REVIEW OF OBJECTIVE 1: TO IDENTIFY THE AVAILABILITY OF DATA FOR EVALUATING THE PROPOSED INDICATOR
The initial step to develop the indicator is to identify the information available for estimating Ne for all native breeds of cattle and sheep, as listed in the UK Country Report (Defra, 2002). These include 59 sheep breeds (Table 1) and 36 cattle(Table 2) breeds. Ideally, Ne is estimated from pedigree data. However, for breeds for which pedigree information is not available, an estimate of Ne can be obtained from the numbers of parents and proportions of animals selected.
3.1. Information requested
A letter (Appendix 1) with some background information to the project (Appendix 2) was submitted to all breed societies of native breeds at the beginning of the project requesting the information needed for computing the indicator. For breeds with electronic pedigree files we requested an electronic copy of pedigree records or written permission to obtain pedigree files from the agent holding the records. For breeds without electronic pedigree files we requested estimates of the i) number of breeding males used each year; ii) number of breeding females used each year; iii) average number of years of active breeding for males; and iv) average number of years of active breeding for females.
The letter emphasized that the data received will be i) treated in the strictest confidence; and ii) used solely for the purpose of calculating the indicator. In return for providing the requested information individual breed societies will receive an individual copy of the indicator highlighting the information contributed by their individual breeds.
Contact details (breed secretaries, postal and email addresses and telephones) were provided initially by the National Sheep Association and by the National Beef Association and later updated by Grassroots Systems Ltd.
3.2. Responses
A substantial effort was made to obtain the information required. Very few breed societies responded initially to the letter and following up individual societies has required a considerable amount of time. A total of 31 sheep and 20 cattle breedsocieties have provided information.The Scottish Blackface breed society responded but they consider that the information required for computing the indicator is not available for this breed. In addition, information on numbers of breeding animals for Chillingham cattle, a feral breed not represented by a breed society,was provided by ProfStephen Hall (member of the National Standing Committee on Farm Animal Genetic Resources).There is not reliable information for the Swona breed, another feral cattle breed. In total,responses obtained represent53% of sheep, and 58% of cattle breeds native to the UK.The information provided by breed societiesfor sheep and cattle breeds is indicated in Tables 1 and 2, respectively.
Breeds using the Grassroots system. A very good response rate was obtained from these breeds (19 of the 22 sheep breeds using Grassroots and 10 of the 14 cattle breeds haveprovided information).
Rare Breed Survival Trust (RBST).A good response was also obtained from the RBST, the breed society for 8 breeds (Boreray, Castlemilk Moorit, Manx Loaghtan, Norfolk Horn, North Ronaldsay, Portland, Soay and Whitefaced Woodland). The RBST uses the Grassroots system.
Breeds supported by The Sheep Trust. Of all the 17 breeds geographically isolated and supported by The Sheep Trust (Badger Face Welsh, Bluefaced Leicester, Brecknock Hill, Cheviot, Dalesbred, Derbyshire Gritstone, Exmoor Horn, Herdwick, Jacob, Lonk, North Country Cheviot, Romney, Rough Fell, Shetland, South Wales Mountain, Welsh Hill Speckled, Welsh Mountain), only two of them (the Bluefaced Leicester and the Herdwick breeds) provided information. One of them (Bluefaced Leicester) uses the Grassroots system. In general, breeds supported by The Sheep Trust that have not responded do not have electronic pedigree files (Amanda Carson, personal communication). It is expected that the information needed for these breeds (or at least for some of them) could be obtained from a paper currently under peer review in the journal ‘Livestock Science’. This paper describes the results for 12 breeds from the “Endemism” survey conducted in 2007 by Amanda Carson with the purpose of investigating geographical isolation, but the information can not be release until publication. Some Sheep Trust breeds do undertakepedigree and performance recording through Signet (Bluefaced Leicester,North Country Cheviot, SouthWalesMountain and Welsh Hill Speckled) although often for only a small number of flocks, relative to the size of the breed.
Breeds performing routine genetic evaluations in the UK.There are 16 UK native sheep breeds and 13 cattle breeds for which routine genetic evaluations are performed through Edinburgh Genetic Evaluation Services (EGENES). Sheep breeds include Beulah, Bluefaced Leicester, Border Leicester, Dorset, Hampshire Down, Leicester Longwool, Llandovery Hill, Lleyn, Meatlinc, North Country Cheviot, Oxford Down, Scottish Blackface, Shropshire,Suffolk, Welsh Hill Speckled, Wiltshire Horn. Cattle breeds include Ayrshire,British White, Devon, Galloway, Guernsey (together with Guernsey Island), Highland, Jersey,Jersey Island,Lincoln Red,Red Poll,Shorthorn (dairy), Sussex and Welsh Black. All cattle breeds and about half of the sheep breeds have responded.
Breeds performing routine genetic evaluations in Australia.There are four cattle breeds for which routine genetic evaluations are performed through the Agricultural Business Research Institute (ABRI). These are Aberdeen Angus, Beef Shorthorn, Hereford and South Devon. Only South Devonresponded positively.
3.3. Information received
A total of 21 sheep and 19 cattle breeds that responded had pedigree data (Tables 1 and 2). This excludes BlackWelshMountain sheep as only sire (but not dam) information is recorded. Pedigree files were provided by Grassroots (18 sheep and 10 cattle breeds), by EGENES (3 sheep and 8 cattle breeds) and by ABRI (1 cattle breed). For breeds with pedigree files in both Grassroots and Signet/EGENES systems the Grassroots files were used as Grassroots pedigrees aremore complete than Signet/EGENES pedigrees (for most beef cattle and sheep breeds, Signet/EGENES files only contain information on flocks/herds that are performance recorded).
A total of ninesheep breed societies (including Black Welsh Mountain) that respondedhad no pedigree data whereas only one cattle breedsociety that responded had no pedigree data (in addition to Chillingham). Very few breed societies that do not maintain electronic pedigree records provided all the information specifically requested. Most breed societies responding sent their most recent flock books (usually the 2007 book). The information given in these books varies among breeds but in general includes numbers of registered animals. It should be noted that in some breeds the number of registered animals, particularly females, is a relatively small percentage of animals in the breed.
Appendix 3 provides a clearer picture of the relevance of the responses in the calculation of the indicator. Breeds are ordered by the size given in the UK Country Report (Defra, 2002). The 11 sheep breeds with the smallest census size responded. For some breeds (52 to 59 in Appendix 3) there was no available information on their census size but none of them are at risk according to the RBST ( However, calculation of the cattle indicator is more problematic. Excluding North Dairy Shorthorn (not recognised as a breed by the Dairy Shorthorn Society but listed as ‘critical’ by the RBST), two of the six smallest breeds did not respond (Vaynol and Blue Albion)and therefore they were not included when computing the indicator. It is worth mentioning that Blue Albion is not listed in the RBST Watchlist, being acknowledged as a breed made extinct by FMD in the late 1960’s. Aberdeen Angus (Original) is a breed listed as ‘critical’ by the RBST but the data are held by the Aberdeen Angus Society which did not respond positively to our request for information.
3.4. Disaggregating the indicator by country
It has been agreed that devolved administrations are not expecting an indicator per country. Instead, they are interested in seeing how livestock biodiversity is distributed within their own countries. Tables 1 and 2 identify the origins of the breeds but this does not necessarily reflect their current distribution within the UK.In an extension to this project we willassess the distribution between countries of breeds contributingto the UK indicator, with the lowest Ne (see section 5). Files received from Grassroots contain the postcode for animals in the pedigree. Postcodes will also have to be obtained for Signet/EGENES stored pedigree files.For breeds with no pedigree information societies will have to be contacted to obtain addresses of individual flocks.
Table 1.Country of origin, information provided by breed societies and agent providing pedigree information for sheep breeds.
Breed / Country of origin1 / Information provided / Agent21 / Badger Face Welsh / W
2 / Balwen / W
3 / Beulah / W / S/E
4 / BlackWelshMountain / W / Pedigree3 / GR
5 / Blackface (Scottish) / S / S/E
6 / Bluefaced Leicester / E / Pedigree / GR
7 / Border Leicester / S/E / Pedigree / GR
8 / Boreray / S / Pedigree / GR
9 / Brecknock Hill / W
10 / British Milksheep / E
11 / Cambridge / E / Numbers
12 / Castlemilk Moorit / S / Pedigree / GR
13 / Cheviot / S/E
14 / ClunForest / E / Numbers
15 / Cotswold / E / Pedigree / GR
16 / Dalesbred / E
17 / Derbyshire Gritstone / E
18 / Devon & Cornwall L'w / E
19 / Devon Closewool / E / Numbers
20 / Dorset Down / E / Numbers
21 / Dorset Horn / E
22 / Exmoor Horn / E
23 / Greyface Dartmoor / E
24 / Hampshire Down / E / Pedigree / S/E
25 / Hebridean / S / Pedigree / GR
26 / Herdwick / E / Numbers
27 / Hill Radnor / W
28 / Jacob / E/S
29 / Kerry Hill / W / Numbers
30 / Leicester Longwool / E / Pedigree / GR
31 / Lincoln Longwool / E / Pedigree / GR
32 / Llandovery Hill / W
33 / Llanwenog / W
34 / Lleyn / W / S/E
35 / Lonk / E
36 / Manx Loaghtan / IoM / Pedigree / GR
37 / Meatlinc / E / Pedigree / S/E
38 / Norfolk Horn / E / Pedigree / GR
39 / North Country Cheviot / S / S/E
40 / North Ronaldsay / S / Pedigree / GR
41 / Oxford Down / E / Pedigree / GR
42 / Portland / E / Pedigree / GR
43 / Romney / E
44 / Rough Fell / E
45 / Ryeland / E / Pedigree / GR
46 / Shetland (SSBG) / S
47 / Shropshire / E
48 / Soay / S / Pedigree / GR
49 / SouthWalesMountain / W
50 / Southdown / E / Pedigree / GR
51 / Suffolk / E / Pedigree / S/E
52 / Swaledale / E / Numbers
53 / Teeswater / E / Pedigree + Numbers / GR
54 / Welsh Hill Speckled / W
55 / WelshMountain / W
56 / Wensleydale / E / Numbers
57 / White Face Dartmoor / E
58 / Whitefaced Woodland / E / Pedigree / GR
59 / Wiltshire Horn / E
1From personal communications from Geoff Simm and Libby Henson and from Hall and Clutton-Brock (1989), Mason (1996) and breed society websites. E = England; I = Ireland; IoM = Isle of Man; S = Scotland; W = Wales.
2S/E = Signet/Edinburgh Genetic Evaluation Services; GR = Grassroots Systems.
3GR provided a pedigree file but only male information is recorded.
Table 2.Country of origin, information provided by breed societies and agent providing pedigree information for cattle breeds.
Breed / Country of origin1 / Information provided / Agent21 / Aberdeen Angus / S
2 / A. Angus (orig.popn.) / S
3 / Ayrshire / S / Pedigree / S/E
4 / Beef Shorthorn / S/E
5 / Belted Galloway / S
6 / Blue Albion / E
7 / British White / E / Pedigree / GR
8 / Chillingham / E / Numbers
9 / Devon / E / Pedigree / GR
10 / Dexter / I
11 / Galloway / S / Pedigree / GR
12 / Gloucester / E
13 / Guernsey / CI / Pedigree / S/E
14 / Guernsey (Island) / CI / Pedigree / S/E
15 / Hereford / E
16 / Hereford (Original) / E
17 / Highland / S / Pedigree / S/E
18 / Irish Moiled / I / Pedigree / GR
19 / Jersey / CI / Pedigree / S/E
20 / Jersey (Island) / CI / Pedigree / S/E
21 / Lincoln Red / E / Pedigree / GR
22 / Lincoln Red (Original) / E / Pedigree / GR
23 / Longhorn / E / Pedigree / GR
24 / Luing / S / Pedigree / GR
25 / North Dairy Shorthorn3 / E
26 / Red Poll / E / Pedigree / GR
27 / Shetland / S
28 / Shorthorn (dairy) / E / Pedigree / S/E
29 / South Devon / E / Pedigree / ABRI
30 / Sussex / E / Numbers / S/E
31 / Swona4 / S
32 / Vaynol / W
33 / Welsh Black / W / Pedigree / S/E
34 / White Galloway / S
35 / WhitePark / E/S/W
36 / Whitebred (Shorthorn) / E / Pedigree / GR
1From personal communications from Geoff Simm, Libby Henson and from Hall and Clutton-Brock (1989), Mason (1996) and breed society websites. CI = Channel Islands; E = England; I = Ireland; S = Scotland; W = Wales
2ABRI = Agricultural Business Research Institute; S/E = Signet/Edinburgh Genetic Evaluation Services; GR = Grassroots Systems.
3Not recognised by the Shorthorn breed society.
4No current available information to estimate Ne.
4. REVIEW OF OBJECTIVE 2: TO PRODUCE A DRAFT INDICATOR AND ASSOCIATED DESCRIPTIVE TEXT.
Work under Objective 2 included estimation of Ne, calculation of the indicator, assessment of changes of the indicator over time and suggested presentation of the indicator in the UK biodiversity website.
4.1. Estimates of Ne for breeds for which pedigree information is available
Estimating Ne is equivalent to estimating the rate at which inbreeding accumulates per generation (i.e., the rate of inbreeding per generation or F) as Ne = 1/2F. When pedigree information is recorded, the method for estimating of F is well established (Falconer and Mackay, 1996; Simm, 1998).
The steps involved in estimating F were the following:
1. Pedigree files received contained identification codes for the animal, its sire and its dam, and the year of birth of the animal. The first step was to prepare the files to be suitable as inputs forthe software used to compute inbreeding and to check the files for consistency. SAS (2005) was used to convert identification codes received in consecutive integer numbers and to check dates of birth. The software RelaX2 (Stranden and Vuori, 2006) was used to check potential errors in the pedigree (e.g., a particular animal is both a sire and a dam).
2. The inbreeding coefficient (F) was calculated for each animal using all pedigree records (i.e., animals in the pedigree with unknown year of birth were also used) using the software RelaX2 (Stranden and Vuori, 2006). This software uses the algorithm of Meuwissen and Luo (1992) and is freely available for research use. An example of the specific input options used is given in Appendix 4. Initially, inbreeding results from RelaX2 were compared with results from two other pieces of software that use the same algorithm (RTool of Pong-Wong at University of Edinburgh and a stand-alone program of the routine of Meuwissen) for verification. All three programs produced the same results.
3. Using the F for all animals with known year of birth, the inbreeding coefficients were averaged by year of birth and plotted together with the number of animals born per year for an initial exploratory analysis. Appendices5and 6,respectively, show plots for the sheep and cattle breeds analysed.