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

Abstract

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 1421 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.

Figure 1

(A) Map of the Iberian Peninsula showing the Iberian desman distribution range in grey. The study area is indicated with a red square. (B) Enlarged map showing the localities of the Iberian desmans used in this work. Each sampled individual is represented with different symbols for males (squares) and females (circles). The numbers indicate the localities (1: Aiaiturrieta-Ataun; 2: Amundarain-Zaldibia; 3: Leitzaran-Berastegi; 4: Erasote-Leitza; 5: Urumea; 6: Elama-Artikutza; 7: Ameztia-Labaien; 8: Ezpelura-Urrotz; 9: Sasoaran-Eugi; 10: Olazar-Eugi; 11: Aritzakun; and 12: Urrobi-Auritz). Red lines delimit the three main river basins: Cantabrian at the northwest, Adur at the northeast, and Ebro at the south. Populations 1 and 2 are possibly extinct. Human population nuclei with more than 500 inhabitants are indicated in dark gray. The map was constructed using QGIS 2.14. The distribution range of Galemys pyrenaicus was generated using information from different sources^,. The coastline shapefile was downloaded from Natural Earth (https://www.naturalearthdata.com). The shapefiles of the shaded relief map, rivers, main river basins, and human population nuclei were downloaded from Instituto Geográfico Nacional (https://www.ign.es). The river shapefile for France was obtained from DIVA-GIS (https://www.diva-gis.org).

Figure 2

Principal component analysis of the Iberian desman individuals. Each locality is represented with a different color. The locality code, which can be found in the legend of Fig. 1, is also indicated.

Figure 3

Map of the Iberian desmans with their inbreeding coefficients, estimated with RELATED, represented using a color scale. The map was constructed as indicated in the legend to Fig. 1.

Figure 4

Maps plotting networks of related individuals detected by KING. Line thickness is proportional to the relatedness coefficient of the connected Iberian desmans. The map was constructed as indicated in the legend to Fig. 1.

Figure 5

Boxplots of relatedness coefficients obtained using RELATED and KING for the analysis of replicates of the same individual and samples of different individuals.