Data Types and the Phylogeny of Neoaves
Abstract
:Simple Summary
Abstract
1. Introduction
- (1)
- (2)
2. Methods
2.1. Dataset Construction
2.2. Analysis of Base Composition
2.3. Phylogenetic Analyses
3. Results
3.1. Base Composition and the Impact of RY Coding
3.2. Different Data Types within the Prum Dataset Yield Distinct Topologies
3.3. RY Coding also Affects Species Tree Analyses
4. Discussion
4.1. The Role of Data Types in Phylogenomic Analyses
4.2. Implications for Avian Phylogeny
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Acknowledgments
Conflicts of Interest
References
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Data Type | Sites | %A | %C | %G | %T | %GC |
---|---|---|---|---|---|---|
Coding data | ||||||
Exon c1 | Invariant | 29.6 | 21.1 | 31.4 | 17.9 | 52.5 |
Informative | 31.0 | 26.4 | 24.7 | 17.9 | 51.1 | |
Exon c2 | Invariant | 33.3 | 23.7 | 15.9 | 27.0 | 39.6 |
Informative | 31.0 | 29.1 | 22.4 | 17.5 | 51.5 | |
Exon c3 | Invariant | 17.0 | 21.6 | 43.4 | 17.9 | 65.0 |
Informative | 23.8 | 26.0 | 22.4 | 27.8 | 48.4 | |
Non-coding data | ||||||
Intron | Invariant | 29.0 | 14.6 | 21.7 | 34.7 | 36.3 |
Informative | 26.4 | 19.9 | 20.5 | 33.2 | 40.4 | |
UTR | Invariant | 26.6 | 16.4 | 20.3 | 36.6 | 36.7 |
Informative | 29.1 | 19.4 | 22.0 | 29.5 | 41.4 | |
Intergenic | Invariant | 31.3 | 18.8 | 22.0 | 27.8 | 40.8 |
Informative | 30.2 | 20.8 | 21.3 | 27.6 | 42.1 |
RY (AG-CT) | SW (GC-AT) | KM (GT-AC) | ||||
---|---|---|---|---|---|---|
Data Type | Inf Sites 1 | Variation 2 | Inf Sites 1 | Variation 2 | Inf Sites 1 | Variation 2 |
Coding exons | ||||||
Exon c1 | 11,374 | 0.39% | 23,325 | 1.29% | 21,170 | 0.37% |
Exon c2 | 6958 | 0.32% | 13,774 | 1.17% | 14,531 | 0.35% |
Exon c3 | 37,673 | 0.56% | 87,299 | 2.56% | 87,755 | 0.32% |
Non-coding data | ||||||
Introns | 22,510 | 0.25% | 31,014 | 0.73% | 30,780 | 0.29% |
UTRs | 7654 | 0.40% | 12,522 | 1.23% | 12,383 | 0.32% |
Intergenic | 310 | 1.90% | 648 | 3.24% | 638 | 1.28% |
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Braun, E.L.; Kimball, R.T. Data Types and the Phylogeny of Neoaves. Birds 2021, 2, 1-22. https://doi.org/10.3390/birds2010001
Braun EL, Kimball RT. Data Types and the Phylogeny of Neoaves. Birds. 2021; 2(1):1-22. https://doi.org/10.3390/birds2010001
Chicago/Turabian StyleBraun, Edward L., and Rebecca T. Kimball. 2021. "Data Types and the Phylogeny of Neoaves" Birds 2, no. 1: 1-22. https://doi.org/10.3390/birds2010001
APA StyleBraun, E. L., & Kimball, R. T. (2021). Data Types and the Phylogeny of Neoaves. Birds, 2(1), 1-22. https://doi.org/10.3390/birds2010001