- Title
- Detecting and removing sample contamination in phylogenomic data: an example and its implications for Cicadidae phylogeny (Insecta Hemiptera).
- Creator
- Owen, Christopher L, Marshall, David C, Wade, Elizabeth J, Meister, Russ, Goemans, Geert, Kunte, Krushnamegh, Moulds, Max, Hill, Kathy, Villet, Martin H, Pham, Thai-Hong, Kortyna, Michelle, Lemmon, Emily M, Lemmon, Alan R, Simon, Chris
- Subject
- To be catalogued
- Date
- 2022
- Type
- text
- Type
- article
- Identifier
- http://hdl.handle.net/10962/440749
- Identifier
- vital:73809
- Identifier
- https://doi.org/10.1093/sysbio/syac043
- Description
- Contamination of a genetic sample with DNA from one or more nontarget species is a continuing concern of molecular phylogenetic studies, both Sanger sequencing studies and next-generation sequencing studies. We developed an automated pipeline for identifying and excluding likely cross-contaminated loci based on the detection of bimodal distributions of patristic distances across gene trees. When contamination occurs between samples within a data set, a comparison between a contaminated sample and its contaminant taxon will yield bimodal distributions with one peak close to zero patristic distance. This new method does not rely on a priori knowledge of taxon relatedness nor does it determine the causes(s) of the contamination. Exclusion of putatively contaminated loci from a data set generated for the insect family Cicadidae showed that these sequences were affecting some topological patterns and branch supports, although the effects were sometimes subtle, with some contamination-influenced relationships exhibiting strong bootstrap support. Long tip branches and outlier values for one anchored phylogenomic pipeline statistic (AvgNHomologs) were correlated with the presence of contamination.
- Format
- 20 pages, pdf
- Language
- English
- Relation
- Systematic Biology, Owen, C.L., Marshall, D.C., Wade, E.J., Meister, R., Goemans, G., Kunte, K., Moulds, M., Hill, K., Villet, M., Pham, T.H. and Kortyna, M., 2022. Detecting and removing sample contamination in phylogenomic data: an example and its implications for Cicadidae phylogeny (Insecta: Hemiptera). Systematic Biology, 71(6), pp.1504-1523, Systematic Biology volume 71 number 6 1504 1523 2022 1076-836X
- Rights
- Publisher
- Rights
- Use of this resource is governed by the terms and conditions of the Oxford Academic Journals Open Access Policy Statement (https://academic.oup.com/journals/pages/open_access)
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Collections
Villet, Martin Herrer (Prof)
SDG 15. Life On Land
RU Department of Zoology and Entomology
| Thumbnail | File | Description | Size | Format | |||
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| View Details Download | SOURCE1 | Detecting and Removing Sample Contamination in Phylogenomic Data.pdf | 2 MB | Adobe Acrobat PDF | View Details Download |