ArticleBiology2013
Parsimony and model-based analyses of indels in avian nuclear genes reveal congruent and incongruent phylogenetic signals.
Article in Biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
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- Tactile bill-tip organs in seabirds suggest conservation of a deep avian symplesiomorphy.Biology letters · 2024Article
- Genome and life-history evolution link bird diversification to the end-Cretaceous mass extinction.Science advances · 2024Article
- Deep learning for predicting 16S rRNA gene copy number.Scientific reports · 2024Article
- Evolution and expression patterns of the neo-sex chromosomes of the crested ibis.Nature communications · 2024Article
- Genomes, fossils, and the concurrent rise of modern birds and flowering plants in the Late Cretaceous.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- The consequences of craniofacial integration for the adaptive radiations of Darwin's finches and Hawaiian honeycreepers.Nature ecology & evolution · 2020Article
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- Mass estimation of extinct taxa and phylogenetic hypotheses both influence analyses of character evolution in a large clade of birds (Telluraves).Proceedings. Biological sciences · 2019Article
- Comparative genomics sheds light on the predatory lifestyle of accipitrids and owls.Scientific reports · 2019Article
- Verbalizing phylogenomic conflict: Representation of node congruence across competing reconstructions of the neoavian explosion.PLoS computational biology · 2019Article
- Comparative analysis of the vertebral pneumatization in pterosaurs (Reptilia: Pterosauria) and extant birds (Avialae: Neornithes).PloS one · 2019Article
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- Reconstruction of avian ancestral karyotypes reveals differences in the evolutionary history of macro- and microchromosomes.Genome biology · 2018Article
- Filtering nucleotide sites by phylogenetic signal to noise ratio increases confidence in the Neoaves phylogeny generated from ultraconserved elements.Molecular phylogenetics and evolution · 2018Article
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- Molecular characterization ofInternational journal for parasitology. Parasites and wildlife · 2017Article
- Conserved Nonexonic Elements: A Novel Class of Marker for Phylogenomics.Systematic biology · 2017Article
- Early Paleocene landbird supports rapid phylogenetic and morphological diversification of crown birds after the K-Pg mass extinction.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
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Authors and funding
15 authors.
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No grant is acknowledged in the PubMed record.
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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