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. 2013 Mar 13;2(1):419-44.
doi: 10.3390/biology2010419.

Parsimony and model-based analyses of indels in avian nuclear genes reveal congruent and incongruent phylogenetic signals

Tamaki Yuri  1 , Rebecca T Kimball  2 , John Harshman  3 , Rauri C K Bowie  4 , Michael J Braun  5 , Jena L Chojnowski  6 , Kin-Lan Han  7 , Shannon J Hackett  8 , Christopher J Huddleston  9 , William S Moore  10 , Sushma Reddy  11 , Frederick H Sheldon  12 , David W Steadman  12 , Christopher C Witt  12 , Edward L Braun  13
Affiliations

Parsimony and model-based analyses of indels in avian nuclear genes reveal congruent and incongruent phylogenetic signals

Tamaki Yuri et al. Biology (Basel). .

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.

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Figures

Figure 1
Figure 1
Estimate of avian phylogeny based upon nucleotide sequence data (maximum likelihood [ML] tree using the GTR+I+Γ model) and the higher-level classification described in the text. Nodes with 100% support are indicated with an asterisk. Red asterisks indicate nodes with 100% support that define supra-ordinal clades with extensive independent corroboration (see below). Coloring conventions here will be used in all trees, and named supra-ordinal clades are indicated using letters below branches (see Table 1 for details).
Figure 2
Figure 2
Branch lengths estimated from gap data (using the CFNv+Γ model) plotted against branch lengths from all nucleotide data (estimated using the GTR+I+Γ model). Branch length estimates for specific nucleotide partitions (introns, coding exons and 3' untranslated regions [UTRs]) are presented for comparison of relative rates (next page).
Figure 3
Figure 3
Estimates of avian phylogeny obtained using 12,030 gap characters obtained using (a) ML analyses with the CFNv+Γ model and (b) the maximum parsimony (MP) criterion. Orders were collapsed when monophyletic to simplify the trees. Bootstrap support on terminal branches reflects the support of those orders; orders represented by a single taxon are indicated using “(1)”. There were a limited number of rearrangements relative to the nucleotide topology within orders, most without bootstrap support. We highlighted the topology for the order Galliformes, because the gap topology included a clade with bootstrap support that conflicts with multiple nuclear gene regions [8,83] and morphology [84].
Figure 4
Figure 4
Branch length heterogeneity evident in the (a) optimal nucleotide tree (based upon the GTR+I+Γ model) and (b) the optimal gap tree (based upon the CFNv+Γ model).
Figure 5
Figure 5
(a) Comparison of bootstrap support in trees based on all gap characters and gap characters >1-bp in length. Bipartitions that appeared well supported (≥70% bootstrap) by one analysis and poorly supported (<50% bootstrap) in the other are shaded. Numbers correspond to the following bipartitions: 1. Ardea-Cochlearius-Eudocimus; 2. Alisterus-Psittacula; 3. Chalcopsitta-Platycercus; and 4. Picodynastornites. (b) Comparison of bootstrap support for analyses using all gap characters and RY-coded nucleotide data. The same numbers of informative characters were used in each of these analyses (next page).
Figure 6
Figure 6
Combined evidence estimate of the avian tree of life. A partitioned ML analysis was conducted using the GTR+I+Γ model for the nucleotide partition and the CFNv+Γ model for the gap partition. Arrows indicate nodes defining supra-ordinal clades where bootstrap support increased or decreased by more than 10% relative to the nucleotide analysis (Figure 1). The combined evidence topology for Columbiformes was congruent with the gap topology instead of the nucleotide topology (inset; bootstrap values are reported for combined analysis [above branches] and for gap characters [below branches]).
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