Abstract :
Demographic processes leave specific genetic signatures that can be detected through the
analysis of nuclear and mitochondrial markers. Often, these signatures are very complex
to interpret due to the co-occurrence of processes that are very distinct in nature and
magnitude. In this work, we have analysed the footprint of past bottlenecks in the gene
pool of Azpi Gorri goats, a Basque breed in a critical status of conservation because of
dramatic reductions in its census. A sample of Azpi Gorri goats was analysed by sequencing
the mitochondrial control region (N = 24) and genotyping 29 autosomal microsatellites
(N = 50). Contrary to our expectations, the analysis of nuclear and mitochondrial markers
showed that the Azpi Gorri breed has retained a considerable level of genetic diversity. Even
more, conflicting results were obtained when trying to detect bottleneck genetic signatures
through the calculation of R2 and Fu’s FS statistics (mitochondrial data) and by performing
Bottleneck and M P VAL analyses (microsatellite data). Cryptic bottleneck genetic signatures
might be relatively frequent in domestic species because population declines are
usually smooth and sustained, rather than drastic and instantaneous, and also because
many concomitant factors, such as population subdivision, selection and migration, can
alter their shape
