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
Key for the identification of third instar larvae of African blowflies (Diptera Calliphoridae) of forensic importance in death investigations
- Szpila, Krzysztof, Williams, Kirstin A, Soszyńska, Agnieszka, Ekanem, Mfon, Heyns, Marise, Dinka, Mergi D, Villet, Martin H
- Authors: Szpila, Krzysztof , Williams, Kirstin A , Soszyńska, Agnieszka , Ekanem, Mfon , Heyns, Marise , Dinka, Mergi D , Villet, Martin H
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/440761 , vital:73810 , https://doi.org/10.1016/j.forsciint.2023.111889
- Description: Blowfly larvae are the insects primarily responsible for the active stage of decomposition of exposed vertebrate remains and are the most frequently collected entomological evidence during forensic investigations of death. The necrophagous calliphorids in continental Africa that consistently develop on large vertebrate carrion include 11 species belonging to four genera: Calliphora, Chrysomya, Hemipyrellia and Lucilia. Most of these species are widespread in Africa and frequently reported on large animal carcasses and carrion and human corpses. A few keys have been compiled for identification of their third instar larvae, but none of them covers the complete set of taxa. Therefore, we provide a new comprehensive key with original illustrations of all taxonomically significant characters. The key is based on characters that should be easily observable even in poorly equipped local laboratories and is a reliable taxonomic tool for material collected in either urban or rural areas where synanthropic species predominate. However, it should be used with some caution in areas with relatively pristine natural habitats, where additional carrion-breeding species may occur. The publication of the key will significantly facilitate both medical and forensic entomological research and practice in Africa.
- Full Text:
- Date Issued: 2022
- Authors: Szpila, Krzysztof , Williams, Kirstin A , Soszyńska, Agnieszka , Ekanem, Mfon , Heyns, Marise , Dinka, Mergi D , Villet, Martin H
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/440761 , vital:73810 , https://doi.org/10.1016/j.forsciint.2023.111889
- Description: Blowfly larvae are the insects primarily responsible for the active stage of decomposition of exposed vertebrate remains and are the most frequently collected entomological evidence during forensic investigations of death. The necrophagous calliphorids in continental Africa that consistently develop on large vertebrate carrion include 11 species belonging to four genera: Calliphora, Chrysomya, Hemipyrellia and Lucilia. Most of these species are widespread in Africa and frequently reported on large animal carcasses and carrion and human corpses. A few keys have been compiled for identification of their third instar larvae, but none of them covers the complete set of taxa. Therefore, we provide a new comprehensive key with original illustrations of all taxonomically significant characters. The key is based on characters that should be easily observable even in poorly equipped local laboratories and is a reliable taxonomic tool for material collected in either urban or rural areas where synanthropic species predominate. However, it should be used with some caution in areas with relatively pristine natural habitats, where additional carrion-breeding species may occur. The publication of the key will significantly facilitate both medical and forensic entomological research and practice in Africa.
- Full Text:
- Date Issued: 2022
Season and environment modulate aquatic invertebrates’ responses to trout and indigenous fishes in three South African mountain streams
- Bellingan, Terence A, Hugo, Sanet, Villet, Martin H, Weyl, Olaf L F
- Authors: Bellingan, Terence A , Hugo, Sanet , Villet, Martin H , Weyl, Olaf L F
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/441487 , vital:73893 , https://doi.org/10.3389/fenvs.2022.1004939
- Description: Introduced organisms are seen as one of the greatest threats to resource sustainability worldwide, and aquatic macroinvertebrates are regarded as good indicators of the health of water resources. To explore these two perspectives, the responses of macroinvertebrate faunas to native and introduced fishes in three headwater tributaries of the Keiskamma River system, South Africa, were examined by comparing potential indicator communities in reaches considered to be fishless, reaches invaded by introduced salmonid species, and reaches containing native fishes. Patterns in the macroinvertebrate faunal assemblage data were driven strongly by season and flow rate, and less strongly by the presence of insectivorous fishes and biotope availability, a finding in parallel with several similar studies from the region. This affirms that aquatic macroinvertebrate faunas are responsive indicators of both environmental and biotic factors and leaves room for further studies to resolve the effects of non-native fish in the Keiskamma River system and other similar systems from South Africa.
- Full Text:
- Date Issued: 2022
- Authors: Bellingan, Terence A , Hugo, Sanet , Villet, Martin H , Weyl, Olaf L F
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/441487 , vital:73893 , https://doi.org/10.3389/fenvs.2022.1004939
- Description: Introduced organisms are seen as one of the greatest threats to resource sustainability worldwide, and aquatic macroinvertebrates are regarded as good indicators of the health of water resources. To explore these two perspectives, the responses of macroinvertebrate faunas to native and introduced fishes in three headwater tributaries of the Keiskamma River system, South Africa, were examined by comparing potential indicator communities in reaches considered to be fishless, reaches invaded by introduced salmonid species, and reaches containing native fishes. Patterns in the macroinvertebrate faunal assemblage data were driven strongly by season and flow rate, and less strongly by the presence of insectivorous fishes and biotope availability, a finding in parallel with several similar studies from the region. This affirms that aquatic macroinvertebrate faunas are responsive indicators of both environmental and biotic factors and leaves room for further studies to resolve the effects of non-native fish in the Keiskamma River system and other similar systems from South Africa.
- Full Text:
- Date Issued: 2022
The first ‘Grylloblattida’of the family Liomopteridae from the Middle Permian in the Onder Karoo, South Africa (Insecta Polyneoptera)
- Cawood, Rebecca, Nel, Andre, Garrouste, Romaine, Moyo, Sydney, Villet, Martin H, Prevec, Rosemary
- Authors: Cawood, Rebecca , Nel, Andre , Garrouste, Romaine , Moyo, Sydney , Villet, Martin H , Prevec, Rosemary
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/440723 , vital:73807 , https://hal.science/mnhn-04019993/
- Description: Here we describe a new genus and four new species of the extinct ‘Grylloblattida’: Liomopteridae Sellards, 1909: Liomopterum connexus Cawood and Nel, n. sp., Liomopterum daenerys Cawood and Nel, n. sp., Colubrosopterum karooensis Cawood and Nel, n. gen., n. sp., and Paraliomopterum sp. The fossil wings were collected from a new Middle Permian locality near Sutherland, Northern Cape, South Africa, with the horizon close to the Ecca-Beaufort Group contact in the southern Karoo Basin.
- Full Text:
- Date Issued: 2022
- Authors: Cawood, Rebecca , Nel, Andre , Garrouste, Romaine , Moyo, Sydney , Villet, Martin H , Prevec, Rosemary
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/440723 , vital:73807 , https://hal.science/mnhn-04019993/
- Description: Here we describe a new genus and four new species of the extinct ‘Grylloblattida’: Liomopteridae Sellards, 1909: Liomopterum connexus Cawood and Nel, n. sp., Liomopterum daenerys Cawood and Nel, n. sp., Colubrosopterum karooensis Cawood and Nel, n. gen., n. sp., and Paraliomopterum sp. The fossil wings were collected from a new Middle Permian locality near Sutherland, Northern Cape, South Africa, with the horizon close to the Ecca-Beaufort Group contact in the southern Karoo Basin.
- Full Text:
- Date Issued: 2022
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