Phylogeny of Rhynchium and Its Related Genera (Hymenoptera: Eumeninae) Based on Universal Single-Copy Orthologs and Ultraconserved Elements
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Sampling and Sequencing
2.2. Genome Assembly and Matrix Generation
2.3. Phylogenetic Analyses
2.4. Hypothesis Testing
2.5. Divergence Time Analyses
3. Results
3.1. Genome Assembly and Matrix Generation
3.2. Phylogenetic Relationships among the Rhynchium Genera Group
3.3. Molecular Dating of the Rhynchium Genera Group
4. Discussion
4.1. Sources of Gene Tree Discordance
4.2. Phylogenetic Relationships
4.3. Effects of Continental Drifts on the Distribution of Rhynchium Genera Group
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Species | Accession Number | Average Read Coverage (X) | BUSCO Completeness (%) | The Number of Scaffolds | Assembly Size (Mb) | Max Read Length (kb) | N50 Scaffold (kb) | GC (%) |
---|---|---|---|---|---|---|---|---|
Rhynchium brunneum | SAMN36845277 | 78.85 | 94.6 | 42,348 | 194.79 | 1170.58 | 134.32 | 37.24 |
Rhynchium quinquecinctum | SAMN36845333 | 78.26 | 94.0 | 48,619 | 196.27 | 1281.6 | 105.73 | 37.24 |
Allorhynchium argentatum | SAMN36845335 | 84.95 | 95.3 | 49,682 | 180.81 | 894.85 | 160.54 | 37.27 |
Allorhynchium chinense | SAMN36845336 | 72.63 | 91.5 | 187,058 | 211.49 | 318.76 | 23.39 | 36.31 |
Anterhynchium (A.) abdominale | SAMN36845337 | 83.57 | 94.0 | 60,405 | 183.79 | 586.96 | 63.68 | 38.61 |
Anterhynchium (A.) mellyi | SAMN36845339 | 90.69 | 94.7 | 23,487 | 169.37 | 842.5 | 112.22 | 38.66 |
Anterhynchium (Dirhynchium) flavomarginatum | SAMN36845338 | 86.10 | 94.4 | 23,366 | 178.40 | 786.82 | 74.28 | 37.83 |
Anterhynchium (Dirhynchium) coracinum | SAMN36845334 | 86.89 | 94.3 | 21,837 | 176.77 | 739.09 | 68.99 | 37.69 |
Pararrhynchium septemfasciatus feanus | SAMN36845341 | 100.40 | 95.6 | 15,712 | 152.99 | 4723.7 | 670.26 | 38.53 |
Pararrhynchium venkataramani | SAMN36845340 | 85.82 | 92.5 | 51,762 | 178.97 | 728.23 | 51.56 | 38.76 |
Matrix | Average Missing Taxa per Locus (%) | Number of Loci | Number of Sites | Missing Sites (%) | Average Locus Length |
---|---|---|---|---|---|
USCO50 | 2.99 | 5714 | 3,467,928 | 3.19 | 606.92 |
USCO90 | 1.05 | 5115 | 2,945,110 | 1.18 | 575.78 |
USCO100 | 0 | 4398 | 2,423,609 | 0.01 | 551.07 |
UCE60 | 2.56 | 2138 | 2,396,740 | 2.56 | 1121.02 |
UCE90 | 0.77 | 1928 | 2,159,911 | 0.85 | 1120.29 |
UCE100 | 0 | 1726 | 1,933,308 | 0.24 | 1120.11 |
Matrix | Partitioning | GHOST | ASTRAL | PMSF |
---|---|---|---|---|
USCO50 | T1 | T1 | T2 | T1 |
USCO90 | T1 | T1 | T2 | T1 |
USCO100 | T1 | T1 | T1 | T1 |
UCE60 | T1 | T2 | T2 | - |
UCE90 | T1 | T2 | T2 | - |
UCE100 | T1 | T2 | T2 | - |
Topologies | logL | deltaL | bp-RELL | P-WKH | P-WSH | P-AU |
---|---|---|---|---|---|---|
T1 | −8,408,349.19 | 964.1 | 0 * | 0 * | 0 * | 2.88 × 10−6 |
T2 | −8,407,385.093 | 0 * | 1 | 1 | 1 | 1 |
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Dai, M.; He, S.-L.; Chen, B.; Li, T.-J. Phylogeny of Rhynchium and Its Related Genera (Hymenoptera: Eumeninae) Based on Universal Single-Copy Orthologs and Ultraconserved Elements. Insects 2023, 14, 775. https://doi.org/10.3390/insects14090775
Dai M, He S-L, Chen B, Li T-J. Phylogeny of Rhynchium and Its Related Genera (Hymenoptera: Eumeninae) Based on Universal Single-Copy Orthologs and Ultraconserved Elements. Insects. 2023; 14(9):775. https://doi.org/10.3390/insects14090775
Chicago/Turabian StyleDai, Min, Shu-Lin He, Bin Chen, and Ting-Jing Li. 2023. "Phylogeny of Rhynchium and Its Related Genera (Hymenoptera: Eumeninae) Based on Universal Single-Copy Orthologs and Ultraconserved Elements" Insects 14, no. 9: 775. https://doi.org/10.3390/insects14090775