Genomic Insights into Basal Diptera Phylogeny: The Non-Monophyletic Nature of Blephariceromorpha
Abstract
1. Introduction
2. Results
2.1. Mitogenomic and Transcriptomic Data Analysis
2.2. Phylogenetic Analyses Using Nuclear Datasets
2.3. Phylogenetic Analyses Using Mitochondrial Datasets
3. Discussion
3.1. New Insights into Phylogeny of Nematocera
3.2. Investigation of Basal Lineages in Diptera
3.3. Convergent Evolution of Larval Morphology in Blephariceromorpha
4. Materials and Methods
4.1. Sample Collection
4.2. DNA Extraction, Mitogenomes Sequencing, and Analysis
4.3. RNA Extraction, Sequencing, and Transcriptome Assembly
4.4. Matrix Construction
4.5. Phylogenetic Analysis
4.6. Analyses of Phylogenetic Discordance and Alternative Relationships
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Family | Species | Sampling Localities | mtDNA Accession | Transcriptomes Accession | Sample Sites |
---|---|---|---|---|---|
Blephariceridae | Blepharicera sp1.-QZ | Yaowang Mountain, Zhejiang, China | PQ463199 | SRR32672063 | 28°45′25.73″ N, 118°58′34.78″ E |
Blephariceridae | Blepharicera sp2.-WYM | Wuyi Mountains, Fujian, China | PQ463200 | SRR32672062 | 27°36′15.86″ N, 117°47′03.92″ E |
Blephariceridae | Blephariceridae sp1.-WYM | Wuyi Mountains, Fujian, China | PQ463201 | SRR32672061 | 27°36′05.30″ N, 117°43′56.06″ E |
Blephariceridae | Philorus sp1.-QZ | Yaowang Mountain, Zhejiang, China | PQ463208 | SRR32672057 | 28°45′25.73″ N, 118°58′34.78″ E |
Blephariceridae | Philorus sp2.-WYM | Wuyi Mountains, Fujian, China | PQ463209 | SRR32672056 | 27°36′05.30″ N, 117°43′56.06″ E |
Deuterophlebiidae | Deuterophlebia acutirhina | Wuyi Mountains, Fujian, China | PQ463202 | SRR32672060 | 27°36′05.30″ N, 117°43′56.06″ E |
Deuterophlebiidae | Deuterophlebia sp.-Dxp | Linzhi, Xizang, China | PQ463203 | N/A | 29°35′46.15″ N, 94°21′19.52″ E |
Deuterophlebiidae | Deuterophlebia sp.-DY | Ailao Mountain, Yunnan, China | PQ463204 | N/A | 23°58′13.20″ N, 101°31′37.73″ E |
Deuterophlebiidae | Deuterophlebia sp.-QZ | Yaowang Mountain, Zhejiang, China | PQ463205 | N/A | 28°45′25.73″ N, 118°58′34.78″ E |
Deuterophlebiidae | Deuterophlebia wuyiensis | Wuyi Mountains, Fujian, China | PQ463206 | SRR32672059 | 27°44′55.52″ N, 117°40′40.77″ E |
Nymphomyiidae | Nymphomyia sp.-WYM | Wuyi Mountains, Fujian, China | PQ463207 | SRR32672058 | 27°36′15.86″ N, 117°47′03.92″ E |
Type 1 | Type 2 | Loci | Site | Description | Abbreviations |
---|---|---|---|---|---|
mtDNA | NT | 13 | 7360 | 13PCGs, codon 1 and 2 | 13PCG_NT12 |
mtDNA | NT | 13 | 11,040 | 13PCGs, codon 1, 2 and 3 | 13PCG_NT123 |
mtDNA | AA | 13 | 3555 | 13PCGs | 13PCG_AA |
nDNA | AA | 2931 | 1,344,362 | Taxon occupancy 50% | AA_Matrix50 |
nDNA | AA | 2648 | 1,167,399 | Taxon occupancy 60% | AA_Matrix60 |
nDNA | AA | 2204 | 890,185 | Taxon occupancy 70% | AA_Matrix70 |
nDNA | AA | 1533 | 546,636 | Taxon occupancy 80% | AA_Matrix80 |
nDNA | AA | 469 | 133,932 | Taxon occupancy 90% | AA_Matrix90 |
nDNA | NT | 2931 | 4,033,086 | Taxon occupancy 50% | NT_Matrix50 |
nDNA | NT | 2648 | 3,502,197 | Taxon occupancy 60% | NT_Matrix60 |
nDNA | NT | 2204 | 2,670,555 | Taxon occupancy 70% | NT_Matrix70 |
nDNA | NT | 1533 | 1,639,908 | Taxon occupancy 80% | NT_Matrix80 |
nDNA | NT | 469 | 401,796 | Taxon occupancy 90% | NT_Matrix90 |
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Yang, Y.; Ren, J.; Zheng, X.; Cai, L.; Guan, J.; Cai, T.; Xu, X.; Zhen, Y. Genomic Insights into Basal Diptera Phylogeny: The Non-Monophyletic Nature of Blephariceromorpha. Int. J. Mol. Sci. 2025, 26, 5714. https://doi.org/10.3390/ijms26125714
Yang Y, Ren J, Zheng X, Cai L, Guan J, Cai T, Xu X, Zhen Y. Genomic Insights into Basal Diptera Phylogeny: The Non-Monophyletic Nature of Blephariceromorpha. International Journal of Molecular Sciences. 2025; 26(12):5714. https://doi.org/10.3390/ijms26125714
Chicago/Turabian StyleYang, Yaoming, Jiayao Ren, Xuhongyi Zheng, Lingna Cai, Jiayin Guan, Tianlong Cai, Xiaodong Xu, and Ying Zhen. 2025. "Genomic Insights into Basal Diptera Phylogeny: The Non-Monophyletic Nature of Blephariceromorpha" International Journal of Molecular Sciences 26, no. 12: 5714. https://doi.org/10.3390/ijms26125714
APA StyleYang, Y., Ren, J., Zheng, X., Cai, L., Guan, J., Cai, T., Xu, X., & Zhen, Y. (2025). Genomic Insights into Basal Diptera Phylogeny: The Non-Monophyletic Nature of Blephariceromorpha. International Journal of Molecular Sciences, 26(12), 5714. https://doi.org/10.3390/ijms26125714