Hostname: page-component-586b7cd67f-r5fsc Total loading time: 0 Render date: 2024-11-24T06:07:46.208Z Has data issue: false hasContentIssue false
  • English
  • Français

Effective population sizes in cattle, sheep, horses, pigs and goats estimated from census and herdbook data

Published online by Cambridge University Press:  10 May 2016

S. J. G. Hall
S. J. G. Hall*
Affiliation:
Livestock Diversity Ltd, 3 Cross O’Cliff Hill, Lincoln LN5 8PN, UK
*
†E-mail: [email protected]
Get access

Abstract

Accurate measures of effective population sizes (Ne) in livestock require good quality data and specialized skills for their computation and analysis. Ne can be estimated by Wright’s equation Ne=4MF/(M+F) (M, F being sires and dams, respectively), but this requires assumptions which are often not met. Total census sizes Nc of livestock breeds are collated globally. This paper investigates whether estimates of Ne can be made from Nc; this would facilitate conservation monitoring. Some Ne methodologies avoid the assumptions of Wright’s equation and permit measurement, rather than estimation, of Ne. Those considered here employ, respectively, linkage disequilibrium (LD) of single-nucleotide polymorphisms (yielding Ne(LD)), and genealogical analysis (rate of increase of inbreeding, DF), yielding Ne(DF). Considering breeds of cattle, sheep, horses, pigs and goats for which Nc and either Ne(LD) or Ne(DF) are known (totals of 203 breeds and 321 breeds, respectively), proportionality has been investigated between Nc and these measures of Ne. Ne(LD) was found to increase with Nc, significantly in sheep and horses, less so in cattle, but not at all in pigs. Ne(DF) was correlated with log10(Nc) in cattle, sheep and horses (53, 56, 43 breeds, respectively). Ne(LD) was correlated in cattle (73 breeds) and pigs (31 breeds) with the log10 transformation of Ne as calculated by Wright’s equation. Further verification and refinement are needed, particularly of census data, but credible predictions of Ne are obtainable by applying the following multipliers to log10(Nc): cattle 17.61, sheep 97.72, horse 70.78. For cattle and pigs, multiplying log10(Ne(Wright)) by, respectively, 40.69 and 60.09, also gives credible predictions. Such census-based estimates of Ne could in principle be generated by non-specialists and are likely to be suited to audits of conservation activity when financial resources or availability of data are limiting. The ratio Ne/Nc varied among species with an overall median value of 0.03, less than a tenth of that typically observed in wild mammals. Characteristics were also investigated of a distinct herdbook-based methodology, namely the development of Wright’s equation to take into account variances of progeny numbers to yield what has been termed here Ne (Hill). Comparison of these values with Ne (Wright) could help to identify breeds with breeding structures conducive or inimical to genetic conservation. However, Ne(Hill) requires breed-specific values for these variances, and this restricts its applicability.

Keywords

effective population sizelivestockconservationvariance of family sizeherdbook
Type
Research Article
Information
animal , Volume 10 , Issue 11 , November 2016 , pp. 1778 - 1785
Copyright
© The Animal Consortium 2016 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Bohmanova, J, Sargolzaei, M and Schenkel, FS 2015. Characteristics of linkage disequilibrium in North American Holsteins. BMC Genomics 11, 421.CrossRefGoogle Scholar
Bruford, MW, Ginja, C, Hoffmann, I, Joost, S, Orozco-terWengel, P, Alberto, F, Amaral, A, Barbato, M, Biscarini, F, Colli, L, Costa, M, Curik, I, Duruz, S, Ferenčaković, M, Fischer, D, Fitak, R, Groeneveld, LF, Hall, SJG, Hanotte, O, Hassan, F, Helsen, P, Iacolina, L, Kantanen, J, Leempoel, K, Lenstra, JA, Ajmone-Marsan, P, Masembe, C, Megens, H-J, Miele, MJ, Neuditschko, M, Nicolazzi, EL, Pompanon, F, Roosen, J, Sevane, N, Smetko, A, Štambuk, A, Streeter, I, Stucki, S, Supakorn, C, Telo da Gama, L, Tixier-Boichard, M, Wegmann, D and Zhan, X 2015. Prospects and challenges for the conservation of farm animal genomic resources, 2015-2025. Frontiers in Genetics 6, 109.CrossRefGoogle ScholarPubMed
Caballero, A 1994. Developments in the prediction of effective population size. Heredity 73, 657–679.CrossRefGoogle ScholarPubMed
Cervantes, I, Goyache, F, Molina, A, Valera, M and Gutiérrez, JP 2008. Application of individual increase in inbreeding to estimate realized effective sizes from real pedigrees. Journal of Animal Breeding and Genetics 125, 301–310.CrossRefGoogle ScholarPubMed
Corbin, LJ, Liu, AYH, Bishop, SC and Woolliams, JA 2012. Estimation of historical effective population size using linkage disequilibria with marker data. Journal of Animal Breeding and Genetics 129, 257–270.CrossRefGoogle ScholarPubMed
Flury, C, Tapio, M, Sonstegard, TS, Drögemüller, C, Leeb, T, Simianer, H, Hanotte, O and Rieder, S 2010. Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium. Journal of Animal Breeding and Genetics 127, 339–347.CrossRefGoogle ScholarPubMed
Food and Agricultural Organization of the United Nations 1998. Secondary guidelines for development of national Farm Animal Genetic Resources management plans. Management of small populations at risk. Food and Agricultural Organization of the United Nations, Rome, Italy. Retrieved on 30 January 2016 from http://www.fao.org/ag/againfo/programmes/es/lead/toolbox/Indust/sml-popn.pdf Google Scholar
Frankham, R 1995. Effective population size/adult population size ratios in wildlife: a review. Genetical Research 66, 95–107.CrossRefGoogle Scholar
Gandini, GC, Ollivier, L, Danell, B, Distl, O, Georgoudis, A, Groeneveld, E, Martyniuk, E, van Arendonk, JAM and Woolliams, JA 2004. Criteria to assess the degree of endangerment of livestock breeds in Europe. Livestock Production Science 91, 173–182.CrossRefGoogle Scholar
Garrido, LR, Birchmeier, AN, Munilla, S. and Cantet, RJC 2008. Estimation of effective population size using bivariate discrete distributions for modeling family size in beef cattle. Livestock Science 117, 43–51.CrossRefGoogle Scholar
Habier, D, Götz, K-U and Dempfle, L 2009. Breeding programme for Piétrain pigs in Bavaria with an estimation of genetic trends and effective population size. Livestock Science 123, 187–192.CrossRefGoogle Scholar
Hall, SJG 2013. Development of co-ordinated in situ and ex situ UK Farm Animal Genetic Resources conservation strategy and implementation guidance. Defra Research Project GC0146. Department of Food and Rural Affairs, UK and Livestock Diversity Ltd, London and Lincoln. Retrieved on 30 January 2016 from http://randd.defra.gov.uk/Default.aspx?Menu=Menu&Module=ProjectList&Completed=0&ContractorID=2153 Google Scholar
Harmegnies, N, Farnir, F, Davin, F, Buys, N, Georges, M and Coppieters, W 2006. Measuring the extent of linkage disequilibrium in commercial pig populations. Animal Genetics 37, 225–231.CrossRefGoogle ScholarPubMed
Hartwig, S, Wellmann, R, Hamann, H and Bennewitz, J 2013. Description of genetic variability of Vorderwald, Hinterwald and Limpurg cattle via pedigree analysis. Züchtungskunde 85, 270–288.Google Scholar
Hasler, H, Flury, C, Menet, S, Haase, H, Leeb, T, Simianer, H, Poncet, PA and Rieder, S 2011. Genetic diversity in an indigenous horse breed – implications for mating strategies and the control of future inbreeding. Journal of Animal Breeding and Genetics 128, 394–406.CrossRefGoogle Scholar
Herrero-Viedma, E, Megens, H-J, Groenen, MAM, Ramis, G, Bosse, M, Perez-Enciso, M and Crooijmans, RPMA 2013. Conservation genomic analysis of domestic and wild pig populations from the Iberian Peninsula. BMC Genetics 14, 106.CrossRefGoogle Scholar
Hill, WG 1979. A note on effective population size with overlapping generations. Genetics 92, 317–322.CrossRefGoogle ScholarPubMed
Jones, JPG, Collen, B, Atkinson, G, Baxter, PWJ, Bubb, P, Illian, JB, Katzner, TE, Keane, A, Loh, J, McDonald-Madden, E, Nicholson, E, Pereira, HM, Possingham, HP, Pullin, AS, Rodrigues, ASL, Ruiz-Gutierrez, V, Sommerville, M and Milner-Gulland, EJ 2010. The why, what, and how of global biodiversity indicators beyond the 2010 target. Conservation Biology 25, 450–457.CrossRefGoogle ScholarPubMed
Leroy, G, Mary-Huard, T, Verrier, E, Danvy, S and Charvolin, E 2013. Methods to estimate effective population size using pedigree data: examples in dog, sheep, cattle and horse. Genetics Selection Evolution 45, 1.CrossRefGoogle ScholarPubMed
Martyniuk, E, Pilling, D and Scherf, B 2010. Indicators: do we have effective tools to measure trends in genetic diversity of domesticated animals? Animal Genetic Resources 47, 31–43.CrossRefGoogle Scholar
Meuwissen, THE 2009. Genetic management of small populations: a review. Acta Agriculturae Scandinavica, Section A – Animal Science 59, 71–79.CrossRefGoogle Scholar
Palstra, FP and Fraser, DJ 2012. Effective/census population size ratio estimation: a compendium and appraisal. Ecology and Evolution 2, 2357–2365.CrossRefGoogle ScholarPubMed
Pilling, D and Scherf, B 2010. Report of a workshop on indicators to measure trends in genetic diversity of domesticated animals, held in Rome, 9–10 February 2010. FAO, Rome, Italy. Retrieved on 30 January 2016 from http://www.fao.org/ag/againfo/programmes/en/genetics/documents/ITWG_AnGR_6/indicator_report.pdf Google Scholar
Pollott, GE 2016. The breeding structure of the British sheep industry 2012. EBLEX, Stoneleigh, Warwickshire, UK. Retrieved on 30 January 2016 from http://www.eblex.org.uk/wp/wp-content/uploads/2014/09/The-breeding-structure-of-the-British-sheep-industry-2012-180914.pdf Google Scholar
Rodriguez-Ramilo, ST, Fernández, J, Toro, MA, Hernández, D and Villanueva, B 2014. Genome-wide estimates of effective population size in the Spanish Holstein population. Poster 818. Proceedings of the 10th World Congress on Genetics Applied to Livestock Production, Vancouver, BC, Canada, 17–22 August 2014. Retrieved on 30 January 2016 from https://asas.org/wcgalp-proceedings/species-breeding-dairy-cattle-(posters).Google Scholar
Santiago, E and Caballero, A 1995. Effective size of populations under selection. Genetics 139, 1013–1030.CrossRefGoogle ScholarPubMed
Saura, M, Tenesa, A, Woolliams, JA, Fernández, A and Villanueva, B 2015. Evaluation of the linkage-disequilibrium method for the estimation of effective population size when generations overlap: an empirical case. BMC Genomics 16, 922.CrossRefGoogle ScholarPubMed
Tholen, E, Staack, J, Muller, P and Ingwersen, J 2010. Degree of endangerment of different German pig herdbook populations. Abstract 0264. Proceedings of the 9th World Congress on Genetics Applied to Livestock Production, Leipzig, Germany, 1–6 August 2010.Google Scholar
Toro, MA, Meuwissen, THE, Fernández, J, Shaat, I and Mäki-Tanila, A 2011. Assessing the genetic diversity in small farm animal populations. Animal 5, 1669–1683.CrossRefGoogle ScholarPubMed
Uimari, P and Tapio, M 2011. Extent of linkage disequilibrium and effective population size in Finnish Landrace and Finnish Yorkshire pig breeds. Journal of Animal Science 89, 609–614.CrossRefGoogle ScholarPubMed
Verrier, E, Audiot, A, Bertrand, C, Chapuis, H, Charvolin, E, Danchin-Burge, C, Danvy, S, Gourdine, JL, Gaultier, P, Guémené, D, Laloë, D, Lenoir, H, Leroy, G, Naves, M, Patin, S and Sabbagh, M 2015. Assessing the risk status of livestock breeds: a multi-indicator method applied to 178 French local breeds belonging to ten species. Animal Genetic Resources 57, 105–118.CrossRefGoogle Scholar
Verrier, E, Leroy, G, Blouin, C, Mériaux, JC, Rognon, X and Hospital, F 2010. Estimating the effective size of farm animals populations from pedigree or molecular data: a case study on two French Draught horse breeds. Proceedings of the 9th World Congress on Genetics Applied to Livestock Production, Leipzig, Germany, 1–6 August 2010. Retrieved on 30 January 2016 from https://www.researchgate.net/publication/255702131_Estimating_the_effective_size_of_farm_animals_populations_from_Pedigree_or_molecular_data_a_case_ study_on_two_French_ draught_horse_ breeds Google Scholar
Villanueva, B, Sawalha, RM, Roughsedge, T, Rius-Vilarassa, E and Woolliams, JA 2010. Development of a genetic indicator of biodiversity for farm animals. Livestock Science 129, 200–207.CrossRefGoogle Scholar
Woolliams, JA and Toro, MA 2007. Genetic contributions and inbreeding. In Utilisation and conservation of farm animal genetic resources (ed. JK Oldenbroek), pp. 147–165. Wageningen Academic Publishers, Wageningen, The Netherlands.CrossRefGoogle Scholar
Supplementary material: PDF

Hall supplementary material

Tables S1-S8 and Figures S1-S5

Download Hall supplementary material(PDF)
PDF 949.6 KB