Deep-Time Demographic Inference Suggests Ecological Release as Driver of Neoavian Adaptive Radiation
Abstract
:1. Introduction
2. Materials and Methods
3. Results
4. Discussion
4.1. Estimates of Ne
4.2. Caveats in the Estimation of Ne
4.2.1. Accuracy of Ne Estimates
4.2.2. Homoplasy and Sequence Alignment
4.2.3. Biases Associated with Relaxed Clock Analyses
4.2.4. Generation Length
4.2.5. Taxon Sampling Bias
4.2.6. Other Potential Biases
4.3. Ecological Theory of Adaptive Radiation
4.4. Comparison to Extant Birds
5. Conclusions and Future Directions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Data Type 1 | MP-EST* | TENT |
---|---|---|
Indels | ||
>100 bp indels | 0.8326 | 0.8323 |
>50 bp indels | 0.807 | 0.8061 |
>10 bp indels | 0.6703 | 0.6685 |
>2 bp indels | 0.6129 | 0.6111 |
all indels | 0.617 | 0.6152 |
Gene trees | ||
1938 loci | ||
nucleotides | 0.6300 | 0.6286 |
unweighted indels | 0.5613 | 0.5592 |
weighted indels | 0.5550 | 0.5528 |
nucleotides + unweighted indels | 0.6274 | 0.6253 |
nucleotides + weighted indels | 0.6248 | 0.6230 |
2515 loci | ||
nucleotides | 0.6109 | 0.6091 |
unweighted indels | 0.5476 | 0.5453 |
nucleotides + unweighted indels | 0.6090 | 0.6063 |
Indels | |||||
≥100 bp | ≥50 bp | ≥10 bp | ≥2 bp | all | |
Median | 646,358 | 613,876 | 1,397,245 | 1,703,268 | 1,763,134 |
Upper Quartile | 1,203,937 | 1,354,148 | 3,205,650 | 4,135,471 | 3,547,585 |
Gene Trees | |||||
1938 loci | |||||
nts | unwt indels | wt25 indels | nts + unwt indels | nts + wt25 indels | |
Median | 421,623 | 992,529 | 1,034,323 | 406,267 | 447,136 |
Upper Quartile | 1,262,357 | 2,293,435 | 2,480,454 | 1,107,612 | 1,139,726 |
2515 loci | |||||
Median | 493,796 | 1,125,470 | — 1 | 499,080 | — 1 |
Upper Quartile | 1,431,494 | 2,631,364 | — 1 | 1,244,437 | — 1 |
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Houde, P.; Braun, E.L.; Zhou, L. Deep-Time Demographic Inference Suggests Ecological Release as Driver of Neoavian Adaptive Radiation. Diversity 2020, 12, 164. https://doi.org/10.3390/d12040164
Houde P, Braun EL, Zhou L. Deep-Time Demographic Inference Suggests Ecological Release as Driver of Neoavian Adaptive Radiation. Diversity. 2020; 12(4):164. https://doi.org/10.3390/d12040164
Chicago/Turabian StyleHoude, Peter, Edward L. Braun, and Lawrence Zhou. 2020. "Deep-Time Demographic Inference Suggests Ecological Release as Driver of Neoavian Adaptive Radiation" Diversity 12, no. 4: 164. https://doi.org/10.3390/d12040164