Genomic analysis of geographical structure and diversity in the capercaillie (Tetrao urogallus)

The capercaillie is widespread throughout the boreal forests of northern
Eurasia but faces serious conservation challenges in the southernmost
mountain ranges, where the populations are fragmented and some are
critically endangered. To develop effective conservation strategies for
these populations, it is essential to have information on both their
genetic diversity and the genetic structure of the species. In this work,
we used a reduced representation (ddRAD) genomic sequencing technique to
analyze the genetic structure of the capercaillie across its European
range and to assess the inbreeding levels in some of the most threatened
populations. Our population structure analysis suggested the existence of
two evolutionarily significant units, one formed by the two populations
from the Iberian Peninsula and the other by the populations from the rest
of Europe. Genetic diversity showed a significant decrease in the Iberian
populations with respect to the other European populations. An
isolation-with-migration model supported these results and allowed us to
estimate the parameters of the population tree. The inbreeding
coefficients estimated for the Iberian capercaillies showed relatively low
levels in the Pyrenees. However, some individuals with very high
inbreeding values were detected in the Cantabrian Mountains, suggesting
that some of its subpopulations are substantially isolated. The population
structure results and the genomic monitoring method we used to assess
inbreeding levels may be crucial for the conservation and recovery of the
most endangered capercaillie populations.