doi:10.1111/j.1365-2052.2008.01837.x Mitochondrial DNA diversity and origins of South and Central American goats M. Amills*, O. Ramı´rez*, A. Toma `s*, B. Badaoui*, J. Marmi † , J. Acosta ‡ , A. Sa ` nchez* and J. Capote § *Departament de Cie ` ncia Animal i dels Aliments, Universitat Auto ` noma de Barcelona, Bellaterra 08193, Spain. † Institut Catala ` de Paleontologia, Universitat Auto ` noma de Barcelona, Bellaterra 08193, Spain. ‡ Fundacio ´ n Canaria-Instituto de Investigacio ´ n y Ciencia de Puerto del Rosario, Puerto del Rosario 35600, Fuerteventura, Spain. § Instituto Canario de Investigaciones Agrarias, La Laguna 38108, Tenerife, Spain Summary We have analysed the genetic diversity of South and Central American (SCA) goats by partially sequencing the mitochondrial control region of 93 individuals with a wide geographical distribution. Nucleotide and haplotype diversities reached values of 0.020 ± 0.00081 and 0.963 ± 0.0012 respectively. We have also observed a rather weak phylogeographic structure, with almost 69% of genetic variation included in the within- breed variance component. The topology of a median-joining network analysis including 286 European, Iberian, Atlantic and SCA mitochondrial sequences was very complex, with most of the haplotypes forming part of independent small clusters. SCA sequences showed a scattered distribution throughout the network, and clustering with Spanish and Portuguese sequences occurred only occasionally, not allowing the distinguishing of a clear Iberian signature. Conversely, we found a prominent cluster including Canarian, Chilean, Argen- tinian and Bolivian mitochondrial haplotypes. This result was independently confirmed by constructing a Bayesian phylogenetic tree (posterior probability of 0.97). Sharing of mito- chondrial haplotypes by SCA and Canarian goats suggests that goat populations from the Atlantic archipelagos, where Spanish and Portuguese ships en route to the New World used to stow food and supplies, participated in the foundation of SCA caprine breeds. Keywords goat, migration, mitochondrial, phylogeography, South America. Introduction A considerable effort has been devoted in the last few years to characterize the genetic diversity of African, Asian and European goats, with studies performed at both continental (Luikart et al. 2001; Can ˜o ´n et al. 2006; Naderi et al. 2007) and regional (Joshi et al. 2003; Sultana et al. 2003; Azor et al. 2005; Chen et al. 2005; Pereira et al. 2005; Sardina et al. 2006) levels. These surveys have revealed the absence of clear ties between the genetic make-up of goats and geography, with most genetic variation occurring at the within-population level. This weak phylogeographic struc- ture has been attributed to the extensive intercontinental transportation of goats in ancient times (Luikart et al. 2001; Ferna ´ndez et al. 2006). The high versatility, moderate size and hardy nature of goats made them ideal as a food resource in the lengthy commercial and exploratory jour- neys that took place in the Old World a long time ago. South and Central America (SCA) is one of the few geographical areas where the genetic diversity of goats has not been yet properly analysed. In poorly developed rural areas of SCA, goats are an important meat and milk resource, with a current census recording 38 million individuals (FAO- STAT, http://faostat.fao.org). The absence of well-managed conservation genetics programmes and the uncontrolled introgression of highly productive foreign breeds seriously threaten the future of many SCA populations that, through- out the centuries, have adapted successfully to the harsh conditions in which they were bred (Pariacote 2006). The main objective of the present study was to provide a general perspective of the phylogeographic structure and genetic variation of SCA goats at a continental level. This would be a first milestone before regional-specific analyses are con- ducted. Moreover, we were interested in understanding the Address for correspondence M. Amills, Departament de Cie ` ncia Animal i dels Aliments, Universitat Auto ` noma de Barcelona, Bellaterra 08193, Spain. E-mail: marcel.amills@uab.es Accepted for publication 7 November 2008 Ó 2009 The Authors, Journal compilation Ó 2009 International Society for Animal Genetics, Animal Genetics, 40, 315–322 315