Hostname: page-component-78c5997874-mlc7c Total loading time: 0 Render date: 2024-11-20T05:29:29.515Z Has data issue: false hasContentIssue false
  • English
  • Français

A model to infer the demographic structure evolution of endangered donkey populations

Published online by Cambridge University Press:  16 May 2017

F. J. Navas ,
J. Jordana ,
J. M. León ,
C. Barba  and
J. V. Delgado
F. J. Navas*
Affiliation:
Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Córdoba, Spain The Worldwide Donkey Breeds Project, Faculty of Veterinary Sciences, University of Córdoba, 14071 Córdoba, Spain
J. Jordana
Affiliation:
Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
J. M. León
Affiliation:
Centro Agropecuario Provincial de Córdoba, Diputación Provincial de Córdoba, 14071 Córdoba, Spain
C. Barba
Affiliation:
Department of Animal Production, Faculty of Veterinary Sciences, University of Córdoba, 14071 Córdoba, Spain
J. V. Delgado
Affiliation:
Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Córdoba, Spain
*
†E-mail: [email protected]
Get access

Abstract

Stemming from The Worldwide Donkey Breeds Project, an initiative aiming at connecting international researchers and entities working with the donkey species, molecularly tested pedigree analyses were carried out to study the genetic diversity, structure and historical evolution of the Andalusian donkey breed since the 1980s to infer a model to study the situation of international endangered donkey breeds under the remarkably frequent unknown genetical background status behind them. Demographic and genetic variability parameters were evaluated using ENDOG (v4.8). Pedigree completeness and generation length were quantified for the four gametic pathways. Despite mean inbreeding was low, highly inbred animals were present in the pedigree. Average coancestry, relatedness, and non-random mating degree trends were computed. The effective population size based on individual inbreeding rate was about half when based on individual coancestry rate. Nei’s distances and equivalent subpopulations number indicated differentiated farms in a highly structured population. Although genetic diversity loss since the founder generations could be considered small, intraherd breeding policies and the excessive contribution of few ancestors to the gene pool could lead to narrower pedigree bottlenecks. Long average generation intervals could be considered when reducing inbreeding. Wright’s fixation statistics indicated slight inbreeding between farms. Pedigree shallowness suggested applying new breeding strategies to reliably estimate descriptive parameters and control the negative effects of inbreeding, which could indeed, mean the key to preserve such valuable animal resources avoiding the extinction they potentially head towards, making the present model become an international referent when assessing endangered donkey populations.

Keywords

assendangered breedgenetic diversityinbreedingpopulation genetics
Type
Research Article
Information
animal , Volume 11 , Issue 12 , December 2017 , pp. 2129 - 2138
Copyright
© The Animal Consortium 2017 

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

Boichard, D, Maignel, L and Verrier, E 1997. The value of using probabilities of gene origin to measure genetic variability in a population. Genetics Selection Evolution 29, 5–23.CrossRefGoogle Scholar
Caballero, A and Toro, MA 2000. Interrelations between effective population size and other pedigree tools for the management of conserved populations. Genetics Research 75, 331–343.CrossRefGoogle ScholarPubMed
Cassell, B, Adamec, V and Pearson, R 2003. Effect of incomplete pedigrees on estimates of inbreeding and inbreeding depression for days to first service and summit milk yield in Holsteins and Jerseys. Journal of Dairy Science 86, 2967–2976.CrossRefGoogle ScholarPubMed
Cecchi, F, Ciampolini, R, Ciani, E, Matteoli, B, Mazzanti, E, Tancredi, M and Presciuttini, S 2006. Demographic genetics of the endangered Amiata donkey breed. Italian Journal of Animal Science 5, 387–391.CrossRefGoogle Scholar
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
Cervantes, I, Goyache, F, Molina, A, Valera, M and Gutierrez, JP 2011. Estimation of effective population size from the rate of coancestry in pedigreed populations. Journal of Animal Breeding and Genetics 128, 56–63.CrossRefGoogle ScholarPubMed
Colleau, JJ and Sargolzaei, M 2008. A proximal decomposition of inbreeding, coancestry and contributions. Genetics Research 90, 191–198.CrossRefGoogle ScholarPubMed
Fernández, J, Meuwissen, THE, Toro, MA and Mäki-Tanila, A 2011. Management of genetic diversity in small farm animal populations. Animal 5, 1684–1698.CrossRefGoogle ScholarPubMed
Folch, P and Jordana, J 1998. Demographic characterization, inbreeding and maintenance of genetic diversity in the endangered Catalonian donkey breed. Genetics Selection Evolution 30, 1–7.CrossRefGoogle Scholar
Frankham, R, Ballou, JD and Briscoe, DA 2010. Introduction to conservation genetics. Cambridge University Press, Cambridge, UK.CrossRefGoogle Scholar
Gutiérrez, JP, Cervantes, I and Goyache, F 2009. Improving the estimation of realized effective population sizes in farm animals. Journal of Animal Breeding and Genetics 126, 327–332.CrossRefGoogle ScholarPubMed
Gutiérrez, JP, Marmi, J, Goyache, F and Jordana, J 2005. Pedigree information reveals moderate to high levels of inbreeding and a weak population structure in the endangered Catalonian donkey breed. Journal of Animal Breeding and Genetics 122, 378–386.CrossRefGoogle Scholar
Halbert, ND, Gogan, PJP, Hedrick, PW, Wahl, JM and Derr, JN 2012. Genetic population substructure in Bison at Yellowstone National Park. Journal of Heredity 103, 360–370.CrossRefGoogle ScholarPubMed
James, JW 1977. A note on selection differential and generation length when generations overlap. Animal Science 24, 109–112.CrossRefGoogle Scholar
Kugler, W, Grunenfelder, HP and Broxham, E 2008. Donkey breeds in Europe: inventory, description, need for action, conservation; report 2007/2008. Monitoring Institute for Rare Breeds and Seeds in Europe, St. Gallen, Switzerland. Retrieved on 4 October 2016 from https://www.americanmuleassociation.org/s/donkey_breeds.pdf.Google Scholar
Lacy, RC 1989. Analysis of founder representation in pedigrees: founder equivalents and founder genome equivalents. Zoo Biology 8, 111–123.CrossRefGoogle Scholar
Leroy, G, Mary-Huard, T, Verrier, E, Danvy, S, Charvolin, E and Danchin-Burge, C 2013. Methods to estimate effective population size using pedigree data: examples in dog, sheep, cattle and horse. Genetics Selection Evolution 45, 1–10.CrossRefGoogle ScholarPubMed
Lutaaya, E, Misztal, I, Bertrand, JK and Mabry, JW 1999. Inbreeding in populations with incomplete pedigrees. Journal of Animal Breeding and Genetics 116, 475–480.CrossRefGoogle Scholar
Maignel, L, Boichard, D and Verrier, E 1996. Genetic variability of French dairy breeds estimated from pedigree information. Interbull 14, 49–54.Google Scholar
Melé, M, Javed, A, Pybus, M, Zalloua, P, Haber, M, Comas, D, Netea, MG, Balanovsky, O, Balanovska, E, Jin, L, Yang, Y, Pitchappan, RM, Arunkumar, G, Parida, L, Calafell, F and Bertranpetit, J, the Geographical Consortium 2012. Recombination gives a new insight in the effective population size and the history of the old world human populations. Molecular Biology and Evolution 29, 25–30.CrossRefGoogle ScholarPubMed
Meuwissen, THE 1999. Operation of Conservation Schemes. In Genebanks and the conservation of farm animal genetic resources (ed. JK Oldenbroek), 91 p. DLO Institute for Animal Science and Health, Lelystad, the Netherlands.Google Scholar
Meuwissen, THE and Luo, Z 1992. Computing inbreeding coefficients in large populations. Genetics Selection Evolution 24, 305–313.CrossRefGoogle Scholar
Meuwissen, THE and Woolliams, JA 1994. Effective sizes of livestock populations to prevent a decline in fitness. Theoretical and Applied Genetics 89, 1019–1026.CrossRefGoogle ScholarPubMed
Nei, M 1987. Molecular evolutionary genetics. Columbia University Press, New York, USA.CrossRefGoogle Scholar
Oldenbroek, JK 1999. Genebanks and the conservation of farm animal genetic resources. DLO Institute for Animal Science and Health, Lelystad, The Netherlands.Google Scholar
Quaresma, M, Martins, AMF, Rodrigues, JB, Colaço, J and Payan-Carreira, R 2014. Pedigree and herd characterization of a donkey breed vulnerable to extinction. Animal 8, 354–359.CrossRefGoogle ScholarPubMed
Rizzi, R, Tullo, E, Cito, AM, Caroli, A and Pieragostini, E 2011. Monitoring of genetic diversity in the endangered Martina Franca donkey population. Journal of Animal Science 89, 1304–1311.CrossRefGoogle ScholarPubMed
Santana, ML and Bignardi, AB 2015. Status of the genetic diversity and population structure of the Pêga donkey. Tropical Animal Health and Production 47, 1573–1580.CrossRefGoogle ScholarPubMed
SPSS Statistics 2008. SPSS statistics for windows, version 17.0. SPSS Inc, Chicago, IL, USA.Google Scholar
Wright, S 1969. Evolution and the genetics of populations (volume 2: the theory of gene frequencies. University of Chicago Press, Chicago, IL, USA.Google Scholar