Detecting and removing sample contamination in phylogenomic data: an example and its implications for Cicadidae phylogeny (Insecta Hemiptera).
- 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
- Authors: 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
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/440749 , vital:73809 , 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.
- Full Text:
- Date Issued: 2022
- Authors: 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
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/440749 , vital:73809 , 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.
- Full Text:
- Date Issued: 2022
A molecular phylogeny of the cicadas (Hemiptera: Cicadidae) with a review of tribe and subfamily classification:
- Marshall, David C, Moulds, Max, Hill, Kathy B R, Price, Benjamin W, Wade, Elizabeth J, Owen, Christopher L, Goemans, Geert, Marathe, Kiran, Sarkar, Vivek, Cooley, John R, Sanborn, Allen F, Kunte, Krushnamegh, Villet, Martin H, Simon, Chris
- Authors: Marshall, David C , Moulds, Max , Hill, Kathy B R , Price, Benjamin W , Wade, Elizabeth J , Owen, Christopher L , Goemans, Geert , Marathe, Kiran , Sarkar, Vivek , Cooley, John R , Sanborn, Allen F , Kunte, Krushnamegh , Villet, Martin H , Simon, Chris
- Date: 2018
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/140601 , vital:37902 , DOI: 10.11646/zootaxa.4424.1.1
- Description: A molecular phylogeny and a review of family-group classification are presented for 137 species (ca. 125 genera) of the insect family Cicadidae, the true cicadas, plus two species of hairy cicadas (Tettigarctidae) and two outgroup species from Cercopidae. Five genes, two of them mitochondrial, comprise the 4992 base-pair molecular dataset. Maximum-likelihood and Bayesian phylogenetic results are shown, including analyses to address potential base composition bias. Tettigarcta is confirmed as the sister-clade of the Cicadidae and support is found for three subfamilies identified in an earlier morphological cladistic analysis. A set of paraphyletic deep-level clades formed by African genera are together named as Tettigomyiinae n. stat. Taxonomic reassignments of genera and tribes are made where morphological examination confirms incorrect placements suggested by the molecular tree, and 11 new tribes are defined (Arenopsaltriini n. tribe, Durangonini n. tribe, Katoini n. tribe, Lacetasini n. tribe, Macrotristriini n. tribe, Malagasiini n. tribe, Nelcyndanini n. tribe, Pagiphorini n. tribe, Pictilini n. tribe, Psaltodini n. tribe, and Selymbriini n. tribe). Tribe Tacuini n. syn. is synonymized with Cryptotympanini, and Tryellina n. syn. is synonymized with an expanded Tribe Lamotialnini. Tribe Hyantiini n. syn. is synonymized with Fidicinini. Tribe Sinosenini is transferred to Cicadinae from Cicadettinae, Cicadatrini is moved to Cicadettinae from Cicadinae, and Ydiellini and Tettigomyiini are transferred to Tettigomyiinae n. stat from Cicadettinae. While the subfamily Cicadinae, historically defined by the presence of timbal covers, is weakly supported in the molecular tree, high taxonomic rank is not supported for several earlier clades based on unique morphology associated with sound production.
- Full Text:
- Date Issued: 2018
- Authors: Marshall, David C , Moulds, Max , Hill, Kathy B R , Price, Benjamin W , Wade, Elizabeth J , Owen, Christopher L , Goemans, Geert , Marathe, Kiran , Sarkar, Vivek , Cooley, John R , Sanborn, Allen F , Kunte, Krushnamegh , Villet, Martin H , Simon, Chris
- Date: 2018
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/140601 , vital:37902 , DOI: 10.11646/zootaxa.4424.1.1
- Description: A molecular phylogeny and a review of family-group classification are presented for 137 species (ca. 125 genera) of the insect family Cicadidae, the true cicadas, plus two species of hairy cicadas (Tettigarctidae) and two outgroup species from Cercopidae. Five genes, two of them mitochondrial, comprise the 4992 base-pair molecular dataset. Maximum-likelihood and Bayesian phylogenetic results are shown, including analyses to address potential base composition bias. Tettigarcta is confirmed as the sister-clade of the Cicadidae and support is found for three subfamilies identified in an earlier morphological cladistic analysis. A set of paraphyletic deep-level clades formed by African genera are together named as Tettigomyiinae n. stat. Taxonomic reassignments of genera and tribes are made where morphological examination confirms incorrect placements suggested by the molecular tree, and 11 new tribes are defined (Arenopsaltriini n. tribe, Durangonini n. tribe, Katoini n. tribe, Lacetasini n. tribe, Macrotristriini n. tribe, Malagasiini n. tribe, Nelcyndanini n. tribe, Pagiphorini n. tribe, Pictilini n. tribe, Psaltodini n. tribe, and Selymbriini n. tribe). Tribe Tacuini n. syn. is synonymized with Cryptotympanini, and Tryellina n. syn. is synonymized with an expanded Tribe Lamotialnini. Tribe Hyantiini n. syn. is synonymized with Fidicinini. Tribe Sinosenini is transferred to Cicadinae from Cicadettinae, Cicadatrini is moved to Cicadettinae from Cicadinae, and Ydiellini and Tettigomyiini are transferred to Tettigomyiinae n. stat from Cicadettinae. While the subfamily Cicadinae, historically defined by the presence of timbal covers, is weakly supported in the molecular tree, high taxonomic rank is not supported for several earlier clades based on unique morphology associated with sound production.
- Full Text:
- Date Issued: 2018
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