Predicting Species Boundaries and Assessing Undescribed Diversity in Pneumocystis, an Obligate Lung Symbiont
Abstract
:1. Introduction
2. Materials and Methods
3. Results
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
mtSSU | Mitochondrial small subunit |
mtLSU | Mitochondrial large subunit |
ABGD | Automatic Barcode Gap Discovery |
GMYC | Generalized Mixed Yule Coalescent model |
PTP | Poisson Tree Processes model |
BPP | Bayesian Phylogenetics and Phylogeography |
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Delimitation Method | Inferred Pneumocystis Species | Host: Symbiont Ratio | Predicted Global Pneumocystis Species |
---|---|---|---|
ABGD | 39 | 1:0.71 | 4606 |
GMYC | 47 | 1:0.85 | 5550 |
PTP | 53 | 1:0.96 | 6259 |
BPP | 48 | 1:0.87 | 5668 |
Taxonomic Rank | Number Screened for Pneumocystis | Total in Mammalia | Percent Sampled | Pneumocystis Genetic Data Available | Percent Screened with Genetic Data | Percent Total with Genetic Data |
---|---|---|---|---|---|---|
Mammal Species | 240 | 6495 | 3.7 | 129 | 54 | 1.99 |
Mammal Genera | 142 | 1342 | 10.58 | - | - | - |
Mammal Orders | 15 | 27 | 55.56 | - | - | - |
Mammal Order | Species Screened for Pneumocystis | Total Species in Order | Percent Screened |
---|---|---|---|
Afrosoricida | 1 | 55 | 1.82 |
Artiodactyla | 7 | 359 | 1.95 |
Carnivora | 14 | 307 | 4.56 |
Chiroptera | 37 | 1447 | 2.56 |
Diprotodontia | 1 | 150 | 0.67 |
Didelphimorphia | 2 | 129 | 1.56 |
Eulipotyphlya | 17 | 564 | 3.01 |
Hyracoidea | 1 | 6 | 16.67 |
Lagomorpha | 3 | 106 | 2.83 |
Monotremata | 1 | 5 | 20 |
Perissodactyla | 1 | 18 | 5.56 |
Pilosa | 1 | 16 | 6.25 |
Primates | 35 | 516 | 6.78 |
Rodentia | 116 | 2623 | 4.42 |
Scandentia | 1 | 23 | 4.35 |
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Babb-Biernacki, S.J.; Esselstyn, J.A.; Doyle, V.P. Predicting Species Boundaries and Assessing Undescribed Diversity in Pneumocystis, an Obligate Lung Symbiont. J. Fungi 2022, 8, 799. https://doi.org/10.3390/jof8080799
Babb-Biernacki SJ, Esselstyn JA, Doyle VP. Predicting Species Boundaries and Assessing Undescribed Diversity in Pneumocystis, an Obligate Lung Symbiont. Journal of Fungi. 2022; 8(8):799. https://doi.org/10.3390/jof8080799
Chicago/Turabian StyleBabb-Biernacki, Spenser J., Jacob A. Esselstyn, and Vinson P. Doyle. 2022. "Predicting Species Boundaries and Assessing Undescribed Diversity in Pneumocystis, an Obligate Lung Symbiont" Journal of Fungi 8, no. 8: 799. https://doi.org/10.3390/jof8080799