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.
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- 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.
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Out of Africa?: a dated molecular phylogeny of the cicada tribe Platypleurini Schmidt (Hemiptera: Cicadidae), with a focus on African genera and the genus Platypleura Amyot and Audinet‐Serville
- Price, Benjamin W, Marshall, David C, Barker, Nigel P, Simon, Chris, Villet, Martin H
- Authors: Price, Benjamin W , Marshall, David C , Barker, Nigel P , Simon, Chris , Villet, Martin H
- Date: 2019
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/140704 , vital:37911 , DOI: 10.1111/syen.12360
- Description: The Platypleurini is a large group of charismatic cicadas distributed from Cape Agulhas in South Africa, through tropical Africa, Madagascar, India and eastern Asia to Japan, with generic diversity concentrated in equatorial and southern Africa. This distribution suggests the possibility of a Gondwanan origin and dispersal to eastern Asia from Africa or India. We used a four-gene (three mitochondrial) molecular dataset, fossil calibrations and molecular clock information to explore the phylogenetic relationships of the platypleurine cicadas and the timing and geography of their diversification. The earliest splits in the tribe were found to separate forest genera in Madagascar and equatorial Africa from the main radiation, and all of the Asian/Indian species sampled formed a younger clade nested well within the African taxa.
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- Authors: Price, Benjamin W , Marshall, David C , Barker, Nigel P , Simon, Chris , Villet, Martin H
- Date: 2019
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/140704 , vital:37911 , DOI: 10.1111/syen.12360
- Description: The Platypleurini is a large group of charismatic cicadas distributed from Cape Agulhas in South Africa, through tropical Africa, Madagascar, India and eastern Asia to Japan, with generic diversity concentrated in equatorial and southern Africa. This distribution suggests the possibility of a Gondwanan origin and dispersal to eastern Asia from Africa or India. We used a four-gene (three mitochondrial) molecular dataset, fossil calibrations and molecular clock information to explore the phylogenetic relationships of the platypleurine cicadas and the timing and geography of their diversification. The earliest splits in the tribe were found to separate forest genera in Madagascar and equatorial Africa from the main radiation, and all of the Asian/Indian species sampled formed a younger clade nested well within the African taxa.
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Patterns and processes underlying evolutionary significant units in the Platypleura stridula L. species complex (Hemiptera: Cicadidae) in the Cape Floristic Region, South Africa
- Price, Benjamin W, Barker, Nigel P, Villet, Martin H
- Authors: Price, Benjamin W , Barker, Nigel P , Villet, Martin H
- Date: 2007
- Language: English
- Type: Article
- Identifier: vital:6964 , http://hdl.handle.net/10962/d1012027
- Description: Cicadas have been shown to be useful organisms for examining the effects of distribution, plant association and geographical barriers on gene flow between populations. The cicadas of the Platypleura stridula species complex are restricted to the biologically diverse Cape Floristic Region (CFR) of South Africa. They are thus an excellent study group for elucidating the mechanisms by which hemipteran diversity is generated and maintained in the CFR. Phylogeographical analysis of this species complex using mitochondrial DNA Cytochrome Oxidase I (COI) and ribosomal 16S sequence data, coupled with preliminary morphological and acoustic data, resolves six clades, each of which has specific host-plant associations and distinct geographical ranges. The phylogeographical structure implies simultaneous or near-simultaneous radiation events, coupled with shifts in host-plant associations. When calibrated using published COI and 16S substitution rates typical for related insects, these lineages date back to the late Pliocene - early Pleistocene, coincident with vegetation change, altered drainage patterns and accelerated erosion in response to neotectonic crustal uplift and cyclic Pleistocene climate change, and glaciation-associated changes in climate and sea level.
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- Authors: Price, Benjamin W , Barker, Nigel P , Villet, Martin H
- Date: 2007
- Language: English
- Type: Article
- Identifier: vital:6964 , http://hdl.handle.net/10962/d1012027
- Description: Cicadas have been shown to be useful organisms for examining the effects of distribution, plant association and geographical barriers on gene flow between populations. The cicadas of the Platypleura stridula species complex are restricted to the biologically diverse Cape Floristic Region (CFR) of South Africa. They are thus an excellent study group for elucidating the mechanisms by which hemipteran diversity is generated and maintained in the CFR. Phylogeographical analysis of this species complex using mitochondrial DNA Cytochrome Oxidase I (COI) and ribosomal 16S sequence data, coupled with preliminary morphological and acoustic data, resolves six clades, each of which has specific host-plant associations and distinct geographical ranges. The phylogeographical structure implies simultaneous or near-simultaneous radiation events, coupled with shifts in host-plant associations. When calibrated using published COI and 16S substitution rates typical for related insects, these lineages date back to the late Pliocene - early Pleistocene, coincident with vegetation change, altered drainage patterns and accelerated erosion in response to neotectonic crustal uplift and cyclic Pleistocene climate change, and glaciation-associated changes in climate and sea level.
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Revision of the genus Xiphoscelis Burmeister 1842 (Coleoptera Scarabaeidae Cetoniinae), with description of two new species and notes on its phylogeny and ecology
- Perissinotto, Renzo, Villet, Martin H, Stobbia, P
- Authors: Perissinotto, Renzo , Villet, Martin H , Stobbia, P
- Date: 2003
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/442293 , vital:73973 , https://doi.org/10.1080/03946975.2003.10531184
- Description: Recent field work has shown that the genus Xiphoscelis Burmeister 1842 contains at least three species. The type species is re-described, and two new species are described, based on adult morphology. The distribution of all three Xiphoscelis species is mapped, and a phylogeny is proposed for the genus. Ecological data are presented and discussed in the context of the previously-reported association of members of this genus with termites.
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- Authors: Perissinotto, Renzo , Villet, Martin H , Stobbia, P
- Date: 2003
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/442293 , vital:73973 , https://doi.org/10.1080/03946975.2003.10531184
- Description: Recent field work has shown that the genus Xiphoscelis Burmeister 1842 contains at least three species. The type species is re-described, and two new species are described, based on adult morphology. The distribution of all three Xiphoscelis species is mapped, and a phylogeny is proposed for the genus. Ecological data are presented and discussed in the context of the previously-reported association of members of this genus with termites.
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