Phylogenomic analysis of the beetle suborder Adephaga with comparison of tailored and generalized ultraconserved element probe performance
Corresponding Author
Grey T. Gustafson
Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, U.S.A.
Biodiversity Institute, University of Kansas, Lawrence, KS, U.S.A.
Correspondence: Grey T. Gustafson, Department of Ecology and Evolutionary Biology, Biodiversity Institute, University of Kansas, Lawrence, KS, U.S.A. E-mail: [email protected]Search for more papers by this authorStephen M. Baca
Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, U.S.A.
Biodiversity Institute, University of Kansas, Lawrence, KS, U.S.A.
Search for more papers by this authorAlana M. Alexander
Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
Search for more papers by this authorAndrew E. Z. Short
Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, U.S.A.
Biodiversity Institute, University of Kansas, Lawrence, KS, U.S.A.
Search for more papers by this authorCorresponding Author
Grey T. Gustafson
Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, U.S.A.
Biodiversity Institute, University of Kansas, Lawrence, KS, U.S.A.
Correspondence: Grey T. Gustafson, Department of Ecology and Evolutionary Biology, Biodiversity Institute, University of Kansas, Lawrence, KS, U.S.A. E-mail: [email protected]Search for more papers by this authorStephen M. Baca
Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, U.S.A.
Biodiversity Institute, University of Kansas, Lawrence, KS, U.S.A.
Search for more papers by this authorAlana M. Alexander
Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
Search for more papers by this authorAndrew E. Z. Short
Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, U.S.A.
Biodiversity Institute, University of Kansas, Lawrence, KS, U.S.A.
Search for more papers by this authorABSTRACT
Adephaga is the second largest suborder of beetles (Coleoptera) and they serve as important arthropod predators in both aquatic and terrestrial ecosystems. The suborder is divided into Geadephaga comprising terrestrial families and Hydradephaga for aquatic lineages. Despite numerous studies, phylogenetic relationships among the adephagan families and monophyly of the Hydradephaga itself remain in question. Here we conduct a comprehensive phylogenomic analysis of the suborder using ultraconserved elements (UCEs). This study presents the first in vitro test of a newly developed UCE probe set customized for use within Adephaga that includes both probes tailored specifically for the suborder, alongside generalized Coleoptera probes previously found to work in adephagan taxa. We assess the utility of the entire probe set, as well as comparing the tailored and generalized probes alone for reconstructing evolutionary relationships. Our analyses recovered strong support for the paraphyly of Hydradephaga with whirligig beetles (Gyrinidae) placed as sister to all other adephagan families. Geadephaga was strongly supported as monophyletic and placed sister to a clade composed of Haliplidae + Dytiscoidea. Monophyly of Dytiscoidea was strongly supported with relationships among the dytiscoid families resolved and strongly supported. Relationships among the subfamilies of Dytiscidae were strongly supported but largely incongruent with prior phylogenetic estimates for the family. The results of our UCE probe comparison showed that tailored probes alone outperformed generalized probes alone, as well as the full combined probe set (containing both types of probes), under decreased taxon sampling. When taxon sampling was increased, the full combined probe set outperformed both tailored probes and generalized probes alone. This study provides further evidence that UCE probe sets customized for a focal group result in a greater number of recovered loci and substantially improve phylogenomic analysis.
Open Research
Data availability
Raw Illumina reads used for this study are deposited at the NCBI SRA under BioProject ID PRJNA577889. The full Adephaga 2.9Kv1 UCE probe set is available on Dryad (https://doi.org/10.5061/dryad.2f62927). The phyluce software pipeline is available from https://github.com/faircloth-lab/phyluce and the additional scripts used in this paper from https://github.com/laninsky/UCE_processing_steps; https://github.com/laninsky/reference_aligning_to_established_loci/tree/master/phase_everyone; https://github.com/laninsky/beetles/blob/master/downsampled_dataset/generate_downsampled.R.
Supporting Information
| Filename | Description |
|---|---|
| syen12413-sup-0001-TableS1.xlsxExcel 2007 spreadsheet , 1.1 MB |
Table S1. Taxon sampling, voucher IDs, BioSample accession numbers, and summary metrics for each taxon including contigs identified after assembly, total UCE loci recovered, mean coverage, and missing data percentage for the 50% and 70% complete data matrices. Additionally, information on the total number of sites and variable sites for general loci and tailored loci are available here. |
| syen12413-sup-0002-Supinfo.pdfPDF document, 449.3 KB |
Figure S1. Results of maximum likelihood analysis on concatenated, aligned, unpartitioned 50% complete data matrix. Values at nodes are bootstrap support. Figure S2. Results of maximum likelihood analysis on concatenated, aligned, SWSC-EN partitioned 50% complete data matrix. Values at nodes are bootstrap support. Figure S3. Results of Bayesian inference on concatenated, aligned, unpartitioned 50% complete data matrix. Values at nodes are posterior probability. Figure S4. Results of astral coalescent-based analysis of gene trees generated from 50% complete data matrix. Values at nodes are posterior probability. Figure S5. Results of svdquartets-based analysis on aligned gene trees generated from 50% complete data matrix. Values at nodes are multilocus bootstrap support. Figure S6. Results of maximum likelihood analysis on concatenated, aligned, unpartitioned 70% complete data matrix. Values at nodes are bootstrap support. Figure S7. Results of maximum likelihood analysis on concatenated, aligned, SWSC-EN partitioned 70% complete data matrix. Values at nodes are bootstrap support. Figure S8. Results of Bayesian inference on concatenated, aligned, unpartitioned 70% complete data matrix. Values at nodes are posterior probability. Figure S9. Results of astral coalescent-based analysis of gene trees generated from 70% complete data matrix. Values at nodes are posterior probability. Figure S10. Results of svdquartets-based analysis on aligned gene trees generated from 70% complete data matrix. Values at nodes are multilocus bootstrap support. Figure S11. Results of maximum likelihood analysis for Baca taxa × Baca loci treatment. Values at nodes are bootstrap support. Figure S12. Results of maximum likelihood analysis for Baca taxa × Gustafson loci treatment. Values at nodes are bootstrap support. Figure S13. Results of maximum likelihood analysis for Baca taxa × full loci treatment. Values at nodes are bootstrap support. Figure S14. Results of maximum likelihood analysis with SWSC-EN partitioning for Baca taxa × Baca loci treatment. Values at nodes are bootstrap support. Figure S15. Results of maximum likelihood analysis with SWSC-EN partitioning for Baca taxa × Gustafson loci treatment. Values at nodes are bootstrap support. Figure S16. Results of maximum likelihood analysis with SWSC-EN partitioning for Baca taxa × full loci treatment. Values at nodes are bootstrap support. Figure S17. Results of Bayesian inference for Baca taxa × Baca loci treatment. Values at nodes are posterior probability. Figure S18. Results of Bayesian inference for Baca taxa × Gustafson loci treatment. Values at nodes are posterior probability. Figure S19. Results of Bayesian inference for Baca taxa × full loci treatment. Values at nodes are posterior probability. Figure S20. Results of astral coalescent-based analysis for Baca taxa × Baca loci treatment. Values at nodes are posterior probability. Figure S21. Results of astral coalescent-based analysis for Baca taxa × Gustafson loci treatment. Values at nodes are posterior probability. Figure S22. Results of astral coalescent-based analysis for Baca taxa × full loci treatment. Values at nodes are posterior probability. Figure S23. Results of svdquartets-based analysis for Baca taxa × Baca loci treatment. Values at nodes are multilocus bootstrap support. Figure S24. Results of svdquartets-based analysis for Baca taxa × Gustafson loci treatment. Values at nodes are multilocus bootstrap support. Figure S25. Results of svdquartets-based analysis for Baca taxa × full loci treatment. Values at nodes are multilocus bootstrap support. Figure S26. Results of maximum likelihood analysis for full taxa × Baca loci treatment. Values at nodes are bootstrap support. Figure S27. Results of maximum likelihood analysis for full taxa × Gustafson loci treatment. Values at nodes are bootstrap support. Figure S28. Results of maximum likelihood analysis with SWSC-EN partitioning for full taxa × Baca loci treatment. Values at nodes are bootstrap support. Figure S29. Results of maximum likelihood analysis with SWSC-EN partitioning for full taxa × Gustafson loci treatment. Values at nodes are bootstrap support. Figure S30. Results of Bayesian inference for full taxa × Baca loci treatment. Values at nodes are posterior probability. Figure S31. Results of Bayesian inference for full taxa × Gustafson loci treatment. Values at nodes are posterior probability. Figure S32. Results of astral coalescent-based analysis for full taxa × Baca loci treatment. Values at nodes are posterior probability. Figure S33. Results of astral coalescent-based analysis for full taxa × Gustafson loci treatment. Values at nodes are posterior probability. Figure S34. Results of svdquartets-based analysis for full taxa × Baca loci treatment. Values at nodes are multilocus bootstrap support. Figure S35. Results of svdquartets-based analysis for full taxa × Gustafson loci treatment. Values at nodes are multilocus bootstrap support. Table S2. Presence/absence of indicator clades across different replicates (columns) and phylogenetic reconstruction methods/taxon sampling levels (rows) for the 100 replicates of 'Gustafson loci' down sampled to 305 loci |
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
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