Genome Evolution and the Future of Phylogenomics of Non-Avian Reptiles
Abstract
:Simple Summary
Abstract
1. Introduction
2. Non-Avian Reptiles Are Highly Variable in Physical Traits with Strong Links to the Genome
3. Substantial Variation in Genome Size and Karyotype among Non-Avian Reptiles
4. Dynamic Features of Sequence Composition in Non-Avian Reptiles
5. Summary of Available Reference Genomes for Non-Avian Reptiles
6. Why Are There So Few Genomes of Non-Avian Reptiles?
7. First-Generation Phylogenomic Data Acquisition: Reduced Representation Approaches
8. Genome-Scale Phylogenomics: In Silico Investigation of Markers Extracted from Whole Genomes
9. Allele Phasing Is a Much-Neglected Component of Most Phylogenomic Workflows
10. New Reptile Genomes Will Fuel the Future of Reptile Phylogenomics and Genome-Phenotype Discovery via Comparative Genomics
11. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Study | Taxon | Type of Loci | # of Loci | # Samples | Depth of Divergences |
---|---|---|---|---|---|
Ashman et al., 2018 [209] | lizards | exons | 547 | 64 | shallow |
Blair et al., 2022 [210] | lizards | UCEs | 3157 | 34 | shallow |
Blom et al., 2017 [211] | lizards | exons | 2840 | 28 | shallow |
Blom et al., 2019 [212] | lizards | exons | 2457 | 135 | shallow |
Bragg et al., 2018 [213] | lizards | exons | 2364 | 123 | shallow-deep |
Brennan et al., 2021 [214] | lizards | AHEs | 388 | 103 | shallow-deep |
Bryson et al., 2017 [215] | lizards | UCEs | 3282 | 58 | shallow |
Domingos et al., 2017 [216] | lizards | AHEs | 422 | 30 | shallow |
Freitas et al., 2022 [217] | lizards | exons | 625 | 69 | shallow |
Garcia-Porta et al., 2019 [218] | lizards | AHEs + other | 6593 (324 AHEs + 6269 other) | 262 | shallow-deep |
Grummer et al., 2018 [219] | lizards | UCEs + exons | 589 (541 UCEs + 44 exons) | 29 | shallow |
Morando et al., 2020 [220] | lizards | UCEs + exons | 588 (540 UCEs + 44 exons) | 26 | deep |
Moritz et al., 2018 [149] | lizards | exons | 1636 | 56 | shallow |
Panzera et al., 2017 [221] | lizards | UCEs | 581 (538 UCEs + 43 exons) | 16 | higher |
Ramírez-Reyes et al., 2020 [222] | lizards | RAD-seq | 78,970–549,193 | 90 | shallow |
Reilly et al., 2022a [223] | lizards | exons | 709 | 99 | shallow-deep |
Reilly et al., 2022b [224] | lizards | exons | 1154 | 104 | shallow |
Reynolds et al., 2022 [225] | lizards | UCEs | 4055 | 82 | shallow-deep |
Rodriguez et al., 2018 [226] | lizards | UCEs | 2690 | 119 | shallow-deep |
Schools et al., 2022 [227] | lizards | UCEs | 5060 | 30 | higher |
Singhal et al., 2018 [228] | lizards | exons | 2668 | 25 | shallow |
Skipwith et al., 2019 [229] | lizards | UCEs | 4268 | 290 | shallow-deep |
Tucker et al., 2017 [230] | lizards | AHEs | 316 | 16 | shallow |
Wood et al., 2020 [231] | lizards | UCEs | 772–4715 | 42 | deep |
Zozaya et al., 2022 [232] | lizards | exons | 1429 | 33 | shallow |
Bernstein and Ruane 2022 [233] | snakes | AHEs + UCEs + other | 1–642 UCEs, 1–39 AHEs, 2–11 other | 156 | shallow-deep |
Blair et al., 2019 [234] | snakes | UCEs | 3384 | 54 | shallow |
Chen et al., 2017 [235] | snakes | AHEs | 304 | 88 | shallow |
Esquerré et al., 2020 [236] | snakes | AHEs | 376 | 50 | deep |
Hallas et al., 2022 [237] | snakes | RAD-seq | 22,289–48,867 | 49 | shallow |
Li et al., 2022 [238] | snakes | exons + other | 3023 (1948 exons + 1948 other) | 24 | deep |
Myers et al., 2022 [239] | lizards | RAD-seq | 2950 | 74 | shallow |
Natusch et al., 2021 [240] | snakes | AHEs | 421 | 19 | shallow |
Nikolakis et al., 2022 [241] | snakes | UCEs | 3383–4146 | 43 | shallow |
Ruane and Austin 2017 [242] | snakes | UCEs | 2318 | 10 | deep |
Burbrink et al., 2020 [243] | squamates | AHEs | 394 | 289 | deep |
Singhal et al., 2021 [244] | squamates | AHEs + UCEs + other | 5462 (372 AHEs + 5052 UCEs + 38 other) | 92 | deep |
Streicher and Wiens 2017 [245] | squamates | UCEs | 2738 | 24 | deep |
Shaffer et al., 2017 [246] | turtles | UCEs + other | 539 | 24 | deep |
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Card, D.C.; Jennings, W.B.; Edwards, S.V. Genome Evolution and the Future of Phylogenomics of Non-Avian Reptiles. Animals 2023, 13, 471. https://doi.org/10.3390/ani13030471
Card DC, Jennings WB, Edwards SV. Genome Evolution and the Future of Phylogenomics of Non-Avian Reptiles. Animals. 2023; 13(3):471. https://doi.org/10.3390/ani13030471
Chicago/Turabian StyleCard, Daren C., W. Bryan Jennings, and Scott V. Edwards. 2023. "Genome Evolution and the Future of Phylogenomics of Non-Avian Reptiles" Animals 13, no. 3: 471. https://doi.org/10.3390/ani13030471
APA StyleCard, D. C., Jennings, W. B., & Edwards, S. V. (2023). Genome Evolution and the Future of Phylogenomics of Non-Avian Reptiles. Animals, 13(3), 471. https://doi.org/10.3390/ani13030471