Background: Parasites are evolutionary hitchhikers whose phylogenies often track the evolutionary history of their
hosts. Incongruence in the evolutionary history of closely associated lineages can be explained through a variety of
possible events including host switching and host independent speciation. However, in recently diverged lineages
stochastic population processes, such as retention of ancestral polymorphism or secondary contact, can also
explain discordant genealogies, even in fully co-speciating taxa. The relatively simple biogeographic arrangement
of the Galápagos archipelago, compared with mainland biomes, provides a framework to identify stochastic and
evolutionary informative components of genealogic data in these recently diverged organisms.
Results: Mitochondrial DNA sequences were obtained for four species of Galápagos mockingbirds and three
sympatric species of ectoparasites - two louse and one mite species. These data were complemented with nuclear
EF1a sequences in selected samples of parasites and with information from microsatellite loci in the mockingbirds.
Mitochondrial sequence data revealed differences in population genetic diversity between all taxa and varying
degrees of topological congruence between host and parasite lineages. A very low level of genetic variability and
lack of congruence was found in one of the louse parasites, which was excluded from subsequent joint analysis of
mitochondrial data. The reconciled multi-species tree obtained from the analysis is congruent with both the
nuclear data and the geological history of the islands.
Conclusions: The gene genealogies of Galápagos mockingbirds and two of their ectoparasites show strong
phylogeographic correlations, with instances of incongruence mostly explained by ancestral genetic polymorphism.
A third parasite genealogy shows low levels of genetic diversity and little evidence of co-phylogeny with their
hosts. These differences can mostly be explained by variation in life-history characteristics, primarily host specificity
and dispersal capabilities. We show that pooling genetic data from organisms living in close ecological association
reveals a more accurate phylogeographic history for these taxa. Our results have implications for the conservation
and taxonomy of Galápagos mockingbirds and their parasites.