Case studies: species delimitation
In Anopheles and in particular in Drosophila , the number
of species-level entities recognized was much higher than the currently
recognized number of morphospecies. All or most morphospecies were split
into multiple species (Fig. 5; Figure S24). SODA exhibited a higher
tendency to split individual morphospecies into multiple species than
tr2. In Darwin’s finches, over-splitting was also visible, especially in
the earlier-diverging species. However, we also found many morphospecies
in the genera Geospiza and Camarhynchus to be lumped into
a single species. This problem was prevalent when using tr2, but it also
occurred with SODA. In Heliconius , over-splitting was less of a
problem, but it occurred in some cases. Species-level entities mostly
corresponded to established (sub)species in which, however, some
entities were lumped (Heliconius melpomene aglaope / H. m.
amaryllis ; Heliconius melpomene melpomene [from Panama] /H. m. rosina ). Since over-splitting (or lumping in the case of
Darwin’s finches) was the overwhelming problem in almost all analyses,
we refrained from performing additional analyses with the full WGS data
(such analyses were not performed in the studies that generated the WGS
data either).