Detecting population structure and recent demographic history in endangered livestock breeds: The case of the Italian autochthonous donkeys

Animal Genetics

Volumn 44, Issue 1, 2013, Pages 69-78

  Colli, L ^a   Perrotta, G ^b   Negrini, R ^a   Bomba, L ^a   Bigi, D ^c   Zambonelli, P ^c   Verini Supplizi, A ^d   Liotta, L ^e   Ajmone Marsan, P ^a  

^a UNIVERSITÀ CATTOLICA DEL SACRO CUORE   (Italy)

^b Laboratorio di Genetica e Servizi LGS   (Italy)

^c UNIVERSITY OF BOLOGNA   (Italy)

^d UNIVERSITY OF PERUGIA   (Italy)

^e UNIVERSITY OF MESSINA   (Italy)

Author keywords

autochthonous breeds; donkey; Equus asinus; Italy; microsatellite

Indexed keywords

MICROSATELLITE DNA;

ALLELE; ANIMAL; ANIMAL HUSBANDRY; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; CELL NUCLEUS; DEMOGRAPHY; ENVIRONMENTAL PROTECTION; GENETIC VARIABILITY; GENETICS; HORSE; ITALY; POPULATION DENSITY;

ALLELES; ANIMAL HUSBANDRY; ANIMALS; BAYES THEOREM; CELL NUCLEUS; CONSERVATION OF NATURAL RESOURCES; DEMOGRAPHY; EQUIDAE; GENETIC VARIATION; ITALY; MICROSATELLITE REPEATS; MODELS, GENETIC; POPULATION DENSITY;

ANIMALIA; EQUUS ASINUS;

EID: 84872070797     PISSN: 02689146     EISSN: 13652052     Source Type: Journal    
DOI: 10.1111/j.1365-2052.2012.02356.x     Document Type: Article

References (44)

1. Aranguren-Méndez J., Jordana J., &, Gõmez M., (2001) Genetic diversity in Spanish donkey breeds using microsatellite DNA markers. Genetics Selection Evolution 33, 433-42.
2. Aranguren-Méndez J., Gõmez M., &, Jordana J., (2002) Hierarchical analysis of genetic structure in Spanish donkey breeds using microsatellite markers. Heredity 89, 207-11.
3. ™ pour la génétique des populations. Laboratoire Génome, Populations, Interactions CNRS UMR 5000, Université de Montpellier II, Montpellier (France). Web site: http://www.genetix.univ-montp2.fr/genetix/genetix.htm
4. Benzécri J.P., (1973) L'analyse des Donnèes: T.2, L'analyse des Correspondances. Dunoud, Paris.
5. Beretti V., Zanon A., Soffiantini C.S., &, Sabbioni A., (2005) Preliminary results about morphological and demographic traits of Romagnolo donkey. Annali della Facoltà di Medicina Veterinaria di Parma 25, 131-44.
6. Berthouly C., Do Ngoc D., Thévenon S., Bouchel D., Nhu Van T., Danes C., Grosbois V., Hoang Thanh H., Vu Chi C., &, Maillard J.C., (2009) How does farmer connectivity influence livestock genetic structure? A case-study in a Vietnamese goat population. Molecular Ecology 18, 3980-91.
7. Cañõn J., Checa M.L., Carleos C., Vega-Pla J.L., Vallejo M., &, Dunner S., (2000) The genetic structure of Spanish Celtic horse breeds inferred from microsatellite data. Animal Genetics 31, 39-48.
8. Cherchi R., (2005) Asino Sardo. Atti del 1° Convegno Nazionale sull'asino. Grosseto, Italy, 28-29 May 2005. (In Italian).
9. Cosseddu G.M., Fraghì A., Mura L., Carta A., Cherchi R., &, Pau S., (2001) Genetic relationships among donkey populations living in Sardinia. An analysis using molecular markers. Ippologia 2, 25-33.
10. Di Trapani D., (2005) Asino di Pantelleria. Atti del 1° Convegno Nazionale sull'asino. Grosseto, Italy, 28-29 May 2005. (In Italian).
11. Excoffier L., Smouse P., &, Quattro J., (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131, 479-91.
12. Excoffier L., Laval G., &, Schneider S., (2005) arlequin ver. 3.0. An integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online 1, 47-50. Web site: http://cmpg.unibe.ch/software/ arlequin3.
13. FAO (2010) DAD-IS website: http://dad.fao.org/
14. Goudet J., (2001) fstat. A program to estimate and test gene diversities and fixation indices. Version 2.9.3. Web site: http://www.unil.ch/izea/ softwares/fstat.html
15. Huson D.H., &, Bryant D., (2006) Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution 23 (2), 254-67.
16. Iamartino D., Bruzzone A., Lanza A., Blasi M., &, Pilla F., (2005) Genetic diversity of Southern Italian goat populations assessed by microsatellite markers. Small Ruminant Research 57, 249-55.
17. Impeduglia R., (2005) Asino Amiatino. Atti del 1° Convegno Nazionale sull'asino. Grosseto, Italy, 28-29 May 2005. (In Italian).
18. Ivankovic A., Kavar T., Caput P., Mioc B., Pavic V., &, Dovc P., (2002) Genetic diversity of three donkey populations in the Croatian coastal region. Animal Genetics 33, 169-77.
19. Jordana J., Folch P., &, Sanchez A., (1999) Genetic variation (protein markers and microsatellites) in endangered Catalonian donkeys. Biochemical Systematics and Ecology 27, 791-8.
20. Jordana J., Folch P., &, Aranguren J.A., (2001) Microsatellite analysis of genetic diversity in the Catalonian donkey breed. Journal of Animal Breeding and Genetics 118, 57-63.
21. Krüger K., Gaillard C., Stranzinger G., &, Rieder S., (2005) Phylogenetic analysis and species allocation of individual equids using microsatellite data. Journal of Animal Breeding and Genetics 122 (Suppl. 1), 78-86.
22. Kugler W., Grunenfelder H.P., &, Broxham E., (2008) Donkey breeds in Europe. Inventory, Description, Need for Action, Conservation. Report 2007-2008.
23. Lorenzen E.D., Arctander P., &, Siegismund H.R., (2008) High variation and very low differentiation in wide ranging plains zebra (Equus quagga): insights from mtDNA and microsatellites. Molecular Ecology 17, 2812-24.
24. Marchi E., &, Mascheroni E., (1925) Zootecnia Speciale. UTET, Torino, Italy. (in Italian).
25. Montana G., (2006) Statistical methods in genetics. Briefings in Bioinformatics 7 (3), 297-308.
26. Moodley Y., Baumgarten I., &, Harley E.H., (2006) Horse microsatellites and their amenability to comparative equid genetics. Animal Genetics 37, 258-61.
27. Moodley Y., &, Harley E.H., (2005) Population structuring in mountain zebras (Equus zebra): the molecular consequences of divergent demographic histories. Conservation Genetics 6, 953-68.
28. Nei M., (1987) Molecular Evolutionary Genetics. Columbia University Press, New York, NY, USA.
29. Paladino S., (2005) Asino Ragusano. Atti del 1° Convegno Nazionale sull'asino. Grosseto, Italy, 28-29 May 2005. (In Italian).
30. Pellecchia M., Colli L., Bigi D., Zambonelli P., Verini Supplizi A., Liotta L., Negrini R., &, Ajmone-Marsan P., (2007) Mitochondrial DNA diversity of five Italian autochthonous donkey breeds. Proceedings of the XVII National A.S.P.A. Congress. Alghero (SS, Italy), 29 May-1 June 2007. Italian Journal of Animal Science, 6 (Suppl. 1), 185.
31. Pritchard J.K., Stephens M., &, Donnelly P., (2000) Inference of population structure using multilocus genotype data. Genetics 155, 945-59.
32. Rebbeck C.A., Jones O.R., &, Tsai I.J., (2008) simco: A program to automate the comparison of multiple structure runs. Web site: http://cran.r-project.org/web/packages/simco/index.html
33. Reynolds J., Weir B.S., &, Cockerham C.C., (1983) Estimation for the coancestry coefficient: basis for a short-term genetic distance. Genetics 105, 767-79.
34. Rice W.R., (1989) Analyzing tables of statistical tests. Evolution 43, 223-5.
35. Rosenberg N.A., (2004) distruct: a program for the graphical display of population structure. Molecular Ecology Notes 4, 137-8. Web site: http://rosenberglab.bioinformatics.med.umich.edu/distruct.html
36. Rosenberg N.A., Pritchard J.K., Weber J.L., Cann H.M., Kidd K.K., Zhivotovsky L.A., &, Feldman M.W., (2002) Genetic structure of human populations. Science 298, 2381-5.
37. Salza G., (2006) L'asino Romagnolo, in sella tra biodiversità e tempo libero. Agricoltura 34 (6), 18-20 (in Italian).
38. Slatkin M., (1991) Inbreeding coefficients and coalescence times. Genetics Research (Camb.) 58, 167-75.
39. Starkey P., &, Starkey M., (2000) Regional and world trends in donkey populations. In:, Starkey P., &, Fielding D,. (eds) Donkeys, People and Development. A resource book of the Animal Traction Network for Eastern and Southern Africa (ATNESA), ACP-EU Technical Centre for Agricultural and Rural Cooperation (CTA), Wageningen, The Netherlands, 247 p. ISBN 92-9081-219-2. website: http://www.atnesa.org
40. Van Oosterhout C., Hutchinson W.F., Wills D.P.M., &, Shipley P., (2004) micro-checker: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes 4, 535-8.
41. Vranova M., Alloggio I., Qablan M., Vyskocil M., Baumeisterova A., Sloboda M., Putnova L., Vrtkova I., Modry D., &, Horin P., (2011) Genetic diversity of the class II major histocompatibility DRA locus in European, Asiatic and African domestic donkeys. Infection, Genetics and Evolution 11 (5), 1136-41.
42. Weir B.S., &, Cockerham C.C., (1984) Estimating F-statistics for the analysis of population structure. Evolution 38, 1358-70.
43. Wright S., (1965) The interpretation of population structure by F-statistics with special regard to systems of mating. Evolution 19, 395-420.
44. Zumbo A., Di Rosa A., Rundo Sotera A., &, Portolano B., (2004) Demographic, genealogical and morphological characterization of Pantelleria donkey. Archivio Veterinario Italiano 55 (6), 41-9 (in Italian).