Red deer populations in the Iberian glacial refugium were the main source for
postglacial recolonization and subspecific radiation in north-western Europe.
However, the phylogenetic history of Iberian red deer (Cervus elaphus
hispanicus) and its relationships with northern European populations remain
uncertain. Here, we study DNA sequences at the mitochondrial control region
along with STR markers for over 680 specimens from all the main red deer populations
in Spain and other west European areas. Our results from mitochondrial
and genomic DNA show contrasting patterns, likely related to the nature
of these types of DNA markers and their specific processes of change over time.
The results, taken together, bring support to two distinct, cryptic maternal lineages
for Iberian red deer that predated the last glacial maximum and that have
maintained geographically well differentiated until present. Haplotype relationships
show that only one of them contributed to the northern postglacial recolonization.
However, allele frequencies of nuclear markers evidenced one main
differentiation between Iberian and northern European subspecies although also
supported the structure of both matrilines within Iberia. Thus, our findings
reveal a paraphyletic nature for Iberian red deer but also its genetic identity and
differentiation with respect to northern subspecies. Finally, we suggest that
maintaining the singularity of Iberian red deer requires preventing not only
restocking practices with red deer specimens belonging to other European populations
but also translocations between both Iberian lineages.This work was partly supported by project CGL2010-17163/BOS from the Spanish MInistry of Science and by Extremadura and Andalusian Regional Goverments
