Comparing ultraconserved elements and exons for phylogenomic analyses of Middle American cichlids: When data agree to disagree

Choosing among types of genomic markers to be used in a phylogenomic study
can have a major influence on the cost, design, and results of a study.
Yet few attempts have been made to compare categories of next-generation
sequence markers limiting our ability to compare the suitability of these
different genomic fragment types. Here we explore properties of different
genomic markers to find if they vary in the accuracy of component
phylogenetic trees and to clarify the causes of conflict obtained from
different datasets or inference methods. As a test case, we explore the
causes of discordance between phylogenetic hypotheses obtained using a
novel dataset of ultraconserved elements (UCEs) and a recently published
exon dataset of the cichlid tribe Heroini. Resolving relationships among
heroine cichlids has historically been difficult, and the processes of
diversification and colonization of Middle America and the Greater
Antilles are not yet well understood. Despite differences in
informativeness and levels of gene tree discordance between UCEs and
exons, the resulting phylogenomic hypotheses generally agree on most
relationships. The independent datasets disagreed in areas with low
phylogenetic signal that were overwhelmed by noise and non-phylogenetic
signals. For UCEs, high levels of incomplete lineage sorting (ILS) seem to
be a major cause of noise, whereas, for exons, non-phylogenetic signal may
be caused by a reduced number of highly informative loci. This paucity of
informative loci in exons might be due to heterogeneous substitution rates
that are problematic to model (i.e., computationally restrictive)
resulting in systematic errors that UCEs (being less informative
individually but more uniform) are less prone to. These results generally
demonstrate the robustness of phylogenomic methods to accommodate genomic
markers with different biological and phylogenetic properties. However, we
identify common and unique pitfalls of different categories of genomic
fragments when inferring enigmatic phylogenetic relationships.