DOI: 10.5061/dryad.dc82gp3
title: Data from: Species limits and phylogenomic relationships of Darwin’s finches remain unresolved: potential consequences of a volatile ecological setting

description: 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.
description: L2015 - Darwin's
 finches phylogenyTreefile in newick
 format (topology) with 1.0 branch lengths reconstructed from Lamichhaney
 et al. 2015 https://www.nature.com/articles/nature14181dfinches_2015br.nwkL2016 - Darwin's finches phylogenyTreefile in newick format (topology) with 1.0 branch lengths reconstructed from Lamichhaney et al. 2016 http://science.sciencemag.org/content/352/6284/470dfinches_2016bbr.nwkL2018 - Darwin's finches phylogenyTreefile in newick format (topology) with 1.0 branch lengths reconstructed from Lamichhaney et al. 2018 http://science.sciencemag.org/content/359/6372/224dfinches_2018br.nwkSimulated trees 24 taxa1000 pure-birth trees with 24 terminal taxa simulated with phytools0.6-44 (Revell 2012)simtrees24.treSimulated trees 26 taxa1000 pure-birth trees with 26 terminal taxa simulated with phytools0.6-44 (Revell 2012)simtrees26.treSimulated RF distances 24 taxaRobinson-Foulds (1981) “RF” symmetrical distance matrix between simulated trees with 24 taxa using phytools0.6-44 (Revell 2012) and phangorn2.4.0 (Schliep 2011).simRF24.txtSimulated RF distances 26 taxaRobinson-Foulds (1981) “RF” symmetrical distance matrix between simulated trees with 26 taxa using phytools0.6-44 (Revell 2012) and phangorn2.4.0 (Schliep 2011).simRF26.txtSimulated KF distances 24 taxaKuhner- Felsenstein (1994) “KF” distance matrix between simulated trees with 24 taxa using phytools0.6-44 (Revell 2012) and phangorn2.4.0 (Schliep 2011).simKF24.txtSimulated KF distances 26 taxaKuhner- Felsenstein (1994) “KF” distance matrix between simulated trees with 26 taxa using phytools0.6-44 (Revell 2012) and phangorn2.4.0 (Schliep 2011).simKF26.txtSimulated PD distances 24 taxaPath “PD” distances (Steel and Penny 1993) distance matrix between simulated trees with 24 taxa using phytools0.6-44 (Revell 2012) and phangorn2.4.0 (Schliep 2011).simPD24.txtSimulated PD distances 26 taxaPath “PD” distances (Steel and Penny 1993) distance matrix between simulated trees with 26 taxa using phytools0.6-44 (Revell 2012) and phangorn2.4.0 (Schliep 2011).simPD26.txt