Data from: Species limits and phylogenomic relationships of Darwin’s finches remain unresolved: potential consequences of a volatile ecological setting

Island biotas have become paradigms for illustrating many evolutionary
processes. The fauna of the Galapagos Islands includes several taxa that
have been focal points for evolutionary studies. Perhaps their most famous
inhabitants, Darwin’s finches, represent a go-to icon when thinking about
how species originate and adapt to the environment. However, unlike other
adaptive radiations, past morphological and molecular studies of Darwin’s
finches have yielded inconsistent hypotheses of species limits and
phylogenetic relationships. Expecting that idiosyncrasies of prior data
and analytic methods explained different proposed classifications, we were
surprised to observe that three new phylogenetic hypotheses derived mostly
from the same genomics data were topologically inconsistent. We found that
the differences between some of these genomics trees were as great as one
would expect between two random trees with the same number of taxa. Thus,
the phylogeny of Darwin’s finches remains unresolved, as it has for more
than a century. A component of phylogenetic uncertainty comes from unclear
species limits, under any species concept, in the ground finches
(Geospiza) and tree finches (Camarhynchus). We suggest that past authors
should have tested the species limits of Lack, rather than uncritically
accepting them. In fact, the impressive amount of genomics data do not
provide unambiguous hypotheses of the number of species of Geospiza or
Camarhynchus, although they imply greater species diversity than Lack’s
taxonomy. We suggest that insufficient sampling of species populations
across islands (35.6% for morphometrics and 20.4% for genomics) prevents
accurate diagnoses of species limits. However, it is unknown whether
samples from a greater number of islands might result in bridging
differences between species, or reveal many new ones. We conclude that
attempts to interpret patterns of variation among the finches under
standard evolutionary paradigms have obscured some major messages, most
specifically the ongoing reciprocal interactions between geographic
isolation and lineage divergence, and dispersal and gene flow caused by
the volatile ecological conditions in the islands. Although the finches
provide textbook examples of natural selection, better understanding of
species limits and a robust phylogenetic hypothesis are required to
corroborate past hypotheses of speciation and adaptive radiation in the
finches of the Galapagos.