A recent study reported that Basques do not constitute a genetically distinct population, and that Basques from Spanish and French provinces do not show significant genetic similarity. These conclusions disagree with numerous previous studies, and are not consistent with the historical and linguistic evidence that supports the distinctiveness of Basques. In order to further investigate this controversy, we have genotyped 83 Spanish Basque individuals and used these data to infer population structure based on more than 60,000 single nucleotide polymorphisms of several European populations. Here, we present the first high-throughput analysis including Basques from Spanish and French provinces, and show that all Basques constitute a homogeneous group that can be clearly differentiated from other European populations.

Major histocompatibility complex class II locus DRB variation was investigated by single-strand conformation polymorphism analysis and sequence analysis in the two subspecies of Pyrenean chamois (Rupicapra pyrenaica) endemic to the Iberian Peninsula. Low levels of genetic variation were detected in both subspecies, with seven different alleles in R. p. pyrenaica and only three in the R. p. parva. After applying the rarefaction method to cope with the differences in sample size, the low allele number of parva was highlighted. The low allelic repertoire of the R. p. parva subspecies is most likely the result of bottlenecks caused by hunting pressure and recent parasitic infections by sarcoptic mange. A phylogenetic analysis of both Pyrenean chamois and DRB alleles from 10 different caprinid species revealed that the chamois alleles form two monophyletic groups. In comparison with other Caprinae DRB sequences, the Rupicapra alleles displayed a species-specific clustering that reflects a large temporal divergence of the chamois from other caprinids, as well as a possible difference in the selective environment for these species.

Primers based on GenBank sequences of the ovine tumour necrosis factor (TNF)-alpha gene were designed to amplify a 273-bp fragment comprising part of the fourth exon and the 3' untranslated region (UTR) of the ovine TNF-alpha gene. Five different single-strand conformational polymorphism (SSCP) patterns were detected in a number of unrelated animals and three different alleles were identified and sequenced. These alleles differed in one deletion and one single nucleotide polymorphism (SNP) and were named TNF*01, TNF*02 and TNF*03. These alleles corresponded to three sequences previously characterized by other groups. In the population analysis, no significant differences were found in the frequencies of the Latxa and Rasa breeds. This is the first description of allelic variation in the ovine TNF-alpha gene.