The 'tubenosed' seabirds of the Procellariiformes are notoriously hard to identify and hide many cryptic relationships within their similar sizes, colourations and adaptations.
During the recent history of the shearwaters, for instance, their reliance on nesting on oceanic islands has resulted in them being very susceptible to extinction during climate changes since the glacial period, and several subfossil forms and extinct species have been unearthed. Human-derived causes - particularly habitat destruction, hunting and competition with invasive species - have also been responsible for the disappearance of shearwater species. At least five species are known to have become extinct in the last 10,000 years, among them two forms from the Canary Islands.
In some respects fortunately, the two Canary Islands fossils - 'Lava Shearwater' Puffinus olsoni and 'Dune Shearwater' P holeae - have been well-preserved enough for ancient DNA to be extracted, and this has now been used by a Spanish academic team to partially reconstruct a phylogeny for Puffinus species.
Fossil and subfossil finds show that the two extinct species bred simultaneously with Manx and Barolo Shearwaters P baroli, though each fossil is found in different situations, indicating differences in breeding behaviour or choice of nest site, possibly even separation by season as in the Madeiran Storm-petrel Oceanodroma castro complex.
It has been believed that the various Puffinus groups of species may be grouped together due to convergent features, as the group has mostly been classified according to morphological features, and the new work seems to confirm this.
Unfortunately, the fragmentary gene samples of 'Dune Shearwater' (the oldest) did not produce any results, but 'Lava Shearwater', despite being notably physically smaller than Manx, is apparently its sister species, though the basal part of the relationship is not entirely resolved. Balearic and Yelkouan Shearwaters also cluster together in a sister clade to Manx, as do Barolo and Audubon's Shearwaters.
Another notable cluster was a largely southern ocean clade consisting of Short-tailed P tenuirostris, Great P gravis, Sooty P griseus, Pink-footed P creatopus, Flesh-footed P carneipes, Buller's P bulleri and Wedge-tailed P pacificus Shearwaters. There is a strong argument for separating these species into a new genus, as they are less closely related to other Puffinus than Calonectris, the genus that contains Cory's Shearwater complex. Calonectris is nested within Puffinus genetically, demonstrating that Puffinus should either be all-embracing, or split into at least two genera to reflect these relationships.
The associations of the various 'Audubon's', 'Little' and other shearwater taxa found in the Pacific were less resolved, though Atlantic Audubon's may actually be separate from its current superficially similar Pacific 'subspecies'. The authors don't discuss these forms at all, despite apparently splitting all as separate species.
It is hoped that more serviceable examples of 'Dune Shearwater' DNA can be extracted, and that further genetic comparisons can be done to resolve the ancestry of all these groups and produce a complete lineage.
Ramirez, O, Illera, J C, Rando, J C, Gonzalez-Solis, J, Alcover, J A and Lalueza-Fox, C. (2010) Ancient DNA of the Extinct Lava Shearwater (Puffinus olsoni) from the Canary Islands Reveals Incipient Differentiation within the P. puffinus Complex. PLoS ONE 5: e16072. doi:10.1371/journal.pone.0016072