- Title
- Detecting and removing sample contamination in phylogenomic data: an example and its implications for Cicadidae phylogeny (Insecta Hemiptera).
- Creator
- Owen, Christopher L
- Creator
- Marshall, David C
- Creator
- Wade, Elizabeth J
- Creator
- Meister, Russ
- Creator
- Goemans, Geert
- Creator
- Kunte, Krushnamegh
- Creator
- Moulds, Max
- Creator
- Hill, Kathy
- Creator
- Villet, Martin H
- Creator
- Pham, Thai-Hong
- Creator
- Kortyna, Michelle
- Creator
- Lemmon, Emily M
- Creator
- Lemmon, Alan R
- Creator
- Simon, Chris
- Subject
- To be catalogued
- Date Issued
- 2022
- 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
- Format
- Language
- English
- Relation
- Systematic Biology
- Relation
- 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
- Relation
- 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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Villet, Martin Herrer (Prof)
SDG 15. Life On Land
RU Department of Zoology and Entomology
| Thumbnail | File | Description | Size | Format | |||
|---|---|---|---|---|---|---|---|
| View Details Download | SOURCE1 | Detecting and Removing Sample Contamination in Phylogenomic Data.pdf | 2 MB | Adobe Acrobat PDF | View Details Download |