Cattle domestication from wild aurochsen was among the most important innovations during the Neolithic agricultural revolution. The available genetic and archaeological evidence points to at least two major sites of domestication in India and in the Near East, where zebu and the taurine breeds would have emerged independently. Under this hypothesis, all present-day European breeds would be descended from cattle domesticated in the Near East and subsequently spread during the diffusion of herding and farming lifestyles. We present here previously undescribed genetic evidence in contrast with this view, based on mtDNA sequences from five Italian aurochsen dated between 7,000 and 17,000 years B.P. and >1,000 modern cattle from 51 breeds. Our data are compatible with local domestication events in Europe and support at least some levels of introgression from the aurochs in Italy. The distribution of genetic variation in modern cattle suggest also that different south European breeds were affected by introductions from northern Africa. If so, the European cattle may represent a more variable and valuable genetic resource than previously realized, and previous simple hypotheses regarding the domestication process and the diffusion of selected breeds should be revised.

Animal domestication was a major step forward in human prehistory, contributing to the emergence of more complex societies. At the time of the Neolithic transition, zebu cattle (Bos indicus) were probably the most abundant and important domestic livestock species in Southern Asia. Although archaeological evidence points toward the domestication of zebu cattle within the Indian subcontinent, the exact geographic origins and phylogenetic history of zebu cattle remains uncertain. Here, we report evidence from 844 zebu mitochondrial DNA (mtDNA) sequences surveyed from 19 Asiatic countries comprising 8 regional groups, which identify 2 distinct mitochondrial haplogroups, termed I1 and I2. The marked increase in nucleotide diversity (P < 0.001) for both the I1 and I2 haplogroups within the northern part of the Indian subcontinent is consistent with an origin for all domestic zebu in this area. For haplogroup I1, genetic diversity was highest within the Indus Valley among the three hypothesized domestication centers (Indus Valley, Ganges, and South India). These data support the Indus Valley as the most likely center of origin for the I1 haplogroup and a primary center of zebu domestication. However, for the I2 haplogroup, a complex pattern of diversity is detected, preventing the unambiguous pinpointing of the exact place of origin for this zebu maternal lineage. Our findings are discussed with respect to the archaeological record for zebu domestication within the Indian subcontinent.

Recently different studies have formalized the way in which it is possible to obtain coancestry coefficients from molecular information (Caballero and Toro 2002; Eding and Meuwissen 2001) by applying Malécot's (1948) definition of kinship to marker genes, though referring it to identity-by-state instead of identity-by-descent (Caballero and Toro 2002). The molecular coancestry between two individuals, i and j, is the probability that two randomly sampled alleles from the same locus in two individuals are identical by state. Because of its straightforward relationship with genealogical coancestry, this parameter has been shown to have interesting properties that may be used for conservation purposes (Eding et al. 2002; Toro et al., 2002; 2003). Moreover, molecular coancestry can be used to assess genetic diversity within and between populations (Eding and Meuwissen 2001). Using simulated data, Eding and Meuwissen (2001) showed that molecular coancestry has some interesting properties, namely that average kinship between populations becomes constant very quickly after population fission, causing between-population diversity to remain constant. This property allows researchers using molecular coancestry information to study the genetic relationships between populations (Álvarez et al. 2005; Caballero and Toro 2002; Fabuel et al. 2004).

Summary: The aim of this work is to highlight the need of monitoring small populations to conserve their genetic variability by using a set of parameters to characterize both the structure of populations and management practices. As a representative example we analyse the pedigree information of the endangered Xalda sheep breed of Asturias. The herdbook of Xalda sheep included a total of 805 animals and 62 herds. The number of founders was 329. Nowadays, there are 562 live animals and 26 active herds. The breed is in risk of losing genetic diversity because of the abusive use of certain individuals as parents. The effective number of founder animals is 81.1. The effective number of founder herds is 9.9. The average value of inbreeding in the whole Xalda population was 1.5%. The average relatedness (AR) coefficient reached 1.8% in the whole pedigree. The genetic representation of the lines of founders is unbalanced. Inbreeding trends and effective size do not provide realistic information concerning the risk of loss of diversity as a result of the shallowness of the genealogical information. We suggest the monitoring of the breed using AR to unbalance the genetic contributions of specific individuals, equalizing the genetic representation of the founders and lines in the population. In addition, AR can suggest the introduction of new, under‐represented animals in herds showing high average AR values relative to the population. Our results can be useful to improve the development of conservation initiatives involving open herdbooks to avoid the risk of loss of genetic diversity caused by incorrect management practices.