Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals

Abstract

Insertion/deletion (indel) mutations, which are represented by gaps in multiple sequence alignments, have been used to examine phylogenetic hypotheses for some time. However, most analyses combine gap data with the nucleotide sequences in which they are embedded, probably because most phylogenetic datasets include few gap characters. Here, we report analyses of 12,030 gap characters from an alignment of avian nuclear genes using maximum parsimony (MP) and a simple maximum likelihood (ML) framework. Both trees were similar, and they exhibited almost all of the strongly supported relationships in the nucleotide tree, although neither gap tree supported many relationships that have proven difficult to recover in previous studies. Moreover, independent lines of evidence typically corroborated the nucleotide topology instead of the gap topology when they disagreed, although the number of conflicting nodes with high bootstrap support was limited. Filtering to remove short indels did not substantially reduce homoplasy or reduce conflict. Combined analyses of nucleotides and gaps resulted in the nucleotide topology, but with increased support, suggesting that gap data may prove most useful when analyzed in combination with nucleotide substitutions.

Eocene fossils and the early evolution of frogmouths (Podargiformes): further specimens of Masillapodargus and a comparison with Fluvioviridavis

“…In another analysis of nuclear sequence data, Steatornithiformes and Nyctibiidae were recovered as sister taxa, with Podargiformes being the sister taxon of the remaining taxa of Strisores (Hackett et al 2008). This tree topology was also obtained in an analysis of gap characters of the same nuclear dataset (Yuri et al 2013), and an analysis of RAG-1 sequences likewise supported a clade including Podargiformes and all other Strisores except for Steatornithiformes and Nyctibiidae (Barrowclough et al 2006). An analysis of unweighted cytochrome b sequence data resulted in a sister group relationship between Steatornithiformes and Podargiformes, whereas an analysis of weighted data placed Steatornithiformes and Podargiformes as successive sister taxa of the remaining Bcaprimulgiform^birds (Mariaux and Braun 1996; see also Braun and Huddleston 2009).…”

Error in Phylogenetic Estimation for Bushes in the Tree of Life

“…Both Notopalaeognathae (the clade comprising all extant paleognathous birds except the ostrich; Yuri et al [91]) and Neoaves (the clade comprising the majority of extant bird; reviewed by Cracraft et al [92]) Both of these groups include a number of highly divergent taxa characterized by long periods with no net speciation after the initial radiation, especially if we consider the subset of Neoaves designated "Metaves" by Fain and Houde [93]. Although these examples include some subsequent speciation, they are unified by the origin of a relatively large number of lineages during a short period of time followed by limited cladogenesis (and/or substantial extinction) afterward, at least in some lineages.…”

“…The performance of phylogenetic methods has been evaluated in many ways, including mathematical analyses, simulations, and studies of "known" phylogenies (see Yuri et al [91] for a discussion regarding the limitations of the last approach). These approaches are complementary; for example, the development of modern species tree methods was motivated in part by the proof that the anomaly zone exists [23].…”

Phylogenetically vetted and stratigraphically constrained fossil calibrations within Aves

“…Phylogenetic Position of Sphenisciformes. A sister group-relationship between Sphenisciformes and Procellariiformes (Austrodyptornithes of Yuri et al, 2013) is supported by the largest published morphological (Livezey andZusi, 2006, 2007) and molecular (Hackett et al, 2008) datasets for avian phylogeny (Figure 3). Alternative hypotheses include a sister group relationship between Sphenisciformes and a core clade of 'Pelecaniformes', supported by analysis of sequence data from the beta-fibrinogen gene (Fain and Houde, 2004) and morphological characters (Mayr, 2005b); a sister group relationships between Sphenisciformes and Podicipediformes + Gaviiformes recovered by analysis of morphological data (Smith, 2010); and a sister group relationship between Sphenisciformes and Ciconiiformes recovered from some analyses of mitochondrial data (Slack et al, 2003;Harrison et al, 2004;Watanabe et al, 2006).…”