Methodological challenges in the genomic analysis of an endangered mammal population with low genetic diversity

Recently, populations of various species with very low genetic diversity
have been discovered. Some of these persist in the long term, but others
could face extinction due to accelerated loss of fitness. In this work, we
characterize 45 individuals of one of these populations, belonging to the
Iberian desman (Galemys pyrenaicus). For this, we used the ddRADseq
technique, which generated 1,421 SNPs. The heterozygosity values of the
analyzed individuals were among the lowest recorded for mammals, ranging
from 26 to 91 SNPs/Mb. Furthermore, the individuals from one of the
localities, highly isolated due to strong barriers, presented extremely
high inbreeding coefficients, with values above 0.7. Under this scenario
of low genetic diversity and elevated inbreeding levels, some individuals
appeared to be almost genetically identical. We used different methods and
simulations to determine if genetic identification and parentage analysis
were possible in this population. Only one of the methods, which does not
assume population homogeneity, was able to identify all individuals
correctly. Therefore, genetically impoverished populations pose a great
methodological challenge for their genetic study. However, these
populations are of primary scientific and conservation interest, so it is
essential to characterize them genetically and improve genomic
methodologies for their research.