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
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
Pigs vs people: the use of pigs as analogues for humans in forensic entomology and taphonomy research
- Matuszewski, Szymon, Hall, Martin J R, Moreau, Gaétan, Schoenly, Kenneth G, Tarone, Aaron M, Villet, Martin H
- Authors: Matuszewski, Szymon , Hall, Martin J R , Moreau, Gaétan , Schoenly, Kenneth G , Tarone, Aaron M , Villet, Martin H
- Date: 2019
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/140557 , vital:37898 , DOI: 10.1007/s00414-019-02074-5
- Description: Most studies of decomposition in forensic entomology and taphonomy have used non-human cadavers. Following the recommendation of using domestic pig cadavers as analogues for humans in forensic entomology in the 1980s, pigs became the most frequently used model cadavers in forensic sciences. They have shaped our understanding of how large vertebrate cadavers decompose in, for example, various environments, seasons and after various ante- or postmortem cadaver modifications. They have also been used to demonstrate the feasibility of several new or well-established forensic techniques. The advent of outdoor human taphonomy facilities enabled experimental comparisons of decomposition between pig and human cadavers. Recent comparisons challenged the pig-as-analogue claim in entomology and taphonomy research. In this review, we discuss in a broad methodological context the advantages and disadvantages of pig and human cadavers for forensic research and rebut the critique of pigs as analogues for humans. We conclude that experiments using human cadaver analogues (i.e. pig carcasses) are easier to replicate and more practical for controlling confounding factors than studies based solely on humans and, therefore, are likely to remain our primary epistemic source of forensic knowledge for the immediate future. We supplement these considerations with new guidelines for model cadaver choice in forensic science research.
- Full Text:
- Date Issued: 2019
- Authors: Matuszewski, Szymon , Hall, Martin J R , Moreau, Gaétan , Schoenly, Kenneth G , Tarone, Aaron M , Villet, Martin H
- Date: 2019
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/140557 , vital:37898 , DOI: 10.1007/s00414-019-02074-5
- Description: Most studies of decomposition in forensic entomology and taphonomy have used non-human cadavers. Following the recommendation of using domestic pig cadavers as analogues for humans in forensic entomology in the 1980s, pigs became the most frequently used model cadavers in forensic sciences. They have shaped our understanding of how large vertebrate cadavers decompose in, for example, various environments, seasons and after various ante- or postmortem cadaver modifications. They have also been used to demonstrate the feasibility of several new or well-established forensic techniques. The advent of outdoor human taphonomy facilities enabled experimental comparisons of decomposition between pig and human cadavers. Recent comparisons challenged the pig-as-analogue claim in entomology and taphonomy research. In this review, we discuss in a broad methodological context the advantages and disadvantages of pig and human cadavers for forensic research and rebut the critique of pigs as analogues for humans. We conclude that experiments using human cadaver analogues (i.e. pig carcasses) are easier to replicate and more practical for controlling confounding factors than studies based solely on humans and, therefore, are likely to remain our primary epistemic source of forensic knowledge for the immediate future. We supplement these considerations with new guidelines for model cadaver choice in forensic science research.
- Full Text:
- Date Issued: 2019
Connectivity through allochthony: Reciprocal links between adjacent aquatic and terrestrial ecosystems in South Africa
- Richoux, Nicole B, Moyo, Sydney, Chari, Lenin D, Bergamino, Leandro, Carassou, Laure, Dalu, Tatenda, Hean, Jeffrey W, Sikutshwa, Likho, Gininda, Simphiwe, Magoro, Mandla L, Perhar, Gurbir, Ni, Felicity, Villet, Martin H, Whitfield, Alan K, Parker, Daniel M, Froneman, P William, Arhonditsis, George, Craig, Adrian J F K
- Authors: Richoux, Nicole B , Moyo, Sydney , Chari, Lenin D , Bergamino, Leandro , Carassou, Laure , Dalu, Tatenda , Hean, Jeffrey W , Sikutshwa, Likho , Gininda, Simphiwe , Magoro, Mandla L , Perhar, Gurbir , Ni, Felicity , Villet, Martin H , Whitfield, Alan K , Parker, Daniel M , Froneman, P William , Arhonditsis, George , Craig, Adrian J F K
- Date: 2015
- Subjects: To be catalogued
- Language: English
- Type: text , report
- Identifier: http://hdl.handle.net/10962/438363 , vital:73454 , ISBN 978-1-4312-0679-7 , https://wrcwebsite.azurewebsites.net/wp-content/uploads/mdocs/2186-1-15.pdf
- Description: An important aspect of the dynamics of nutrients and pollutants in natural systems is captured in the concept of allochthony, founded on the observation that nutrients and energy in a variety of forms are transferred between adjacent habitats, com-munities and ecosystems that are not routinely considered as connected. Different forms of nutrients and energy move across the conceptual boundaries of habitats via organisms’ activities or physical processes such as wind or water currents, and these transfers can represent important food subsidies. Such cross-partition ecolog-ical subsidies can augment the nutritional condition, biomass and biodiversity of communities, particularly where local production (or autochthony) alone may be inadequate to support local food webs. Furthermore, organic subsidies can influ-ence population dynamics, community interactions and ecosystem processes, and can represent dominant flux inputs in ecosystem budgets. Our intention was to ex-plore organic nutrient fluxes in relation to a primarily lotic (i.e. flowing) aquatic sys-tem at the scale of a hydrological catchment.
- Full Text:
- Date Issued: 2015
- Authors: Richoux, Nicole B , Moyo, Sydney , Chari, Lenin D , Bergamino, Leandro , Carassou, Laure , Dalu, Tatenda , Hean, Jeffrey W , Sikutshwa, Likho , Gininda, Simphiwe , Magoro, Mandla L , Perhar, Gurbir , Ni, Felicity , Villet, Martin H , Whitfield, Alan K , Parker, Daniel M , Froneman, P William , Arhonditsis, George , Craig, Adrian J F K
- Date: 2015
- Subjects: To be catalogued
- Language: English
- Type: text , report
- Identifier: http://hdl.handle.net/10962/438363 , vital:73454 , ISBN 978-1-4312-0679-7 , https://wrcwebsite.azurewebsites.net/wp-content/uploads/mdocs/2186-1-15.pdf
- Description: An important aspect of the dynamics of nutrients and pollutants in natural systems is captured in the concept of allochthony, founded on the observation that nutrients and energy in a variety of forms are transferred between adjacent habitats, com-munities and ecosystems that are not routinely considered as connected. Different forms of nutrients and energy move across the conceptual boundaries of habitats via organisms’ activities or physical processes such as wind or water currents, and these transfers can represent important food subsidies. Such cross-partition ecolog-ical subsidies can augment the nutritional condition, biomass and biodiversity of communities, particularly where local production (or autochthony) alone may be inadequate to support local food webs. Furthermore, organic subsidies can influ-ence population dynamics, community interactions and ecosystem processes, and can represent dominant flux inputs in ecosystem budgets. Our intention was to ex-plore organic nutrient fluxes in relation to a primarily lotic (i.e. flowing) aquatic sys-tem at the scale of a hydrological catchment.
- Full Text:
- Date Issued: 2015
Human myiasis in rural South Africa is under-reported
- Kuria, Simon K, Villet, Martin H, Kingu, H J C, Dhaffala, A
- Authors: Kuria, Simon K , Villet, Martin H , Kingu, H J C , Dhaffala, A
- Date: 2015
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/442425 , vital:73983 , https://www.ajol.info/index.php/samj/article/view/114028
- Description: Background. Myiasis is the infestation of live tissue of humans and other vertebrates by larvae of flies. Worldwide, myiasis of humans is seldom reported, although the trend is gradually changing in some countries. Reports of human myiasis in Africa are few. Several cases of myiasis were recently seen at the Mthatha Hospital Complex, Mthatha, Eastern Cape Province, South Africa (SA).
- Full Text:
- Date Issued: 2015
- Authors: Kuria, Simon K , Villet, Martin H , Kingu, H J C , Dhaffala, A
- Date: 2015
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/442425 , vital:73983 , https://www.ajol.info/index.php/samj/article/view/114028
- Description: Background. Myiasis is the infestation of live tissue of humans and other vertebrates by larvae of flies. Worldwide, myiasis of humans is seldom reported, although the trend is gradually changing in some countries. Reports of human myiasis in Africa are few. Several cases of myiasis were recently seen at the Mthatha Hospital Complex, Mthatha, Eastern Cape Province, South Africa (SA).
- Full Text:
- Date Issued: 2015
Cryptic variation in an ecological indicator organism: mitochondrial and nuclear DNA sequence data confirm distinct lineages of Baetis harrisoni Barnard (Ephemeroptera: Baetidae) in Southern Africa
- Pereira-da-Conceicoa, Lyndall L, Price, Benjamin W, Barber-James, Helen M, Barker, Nigel P, de Moor, Ferdy C, Villet, Martin H
- Authors: Pereira-da-Conceicoa, Lyndall L , Price, Benjamin W , Barber-James, Helen M , Barker, Nigel P , de Moor, Ferdy C , Villet, Martin H
- Date: 2012
- Language: English
- Type: Article
- Identifier: vital:6535 , http://hdl.handle.net/10962/d1005976 , https://dx.doi.org/10.1186/1471-2148-12-26
- Description: Baetis harrisoni Barnard is a mayfly frequently encountered in river studies across Africa, but the external morphological features used for identifying nymphs have been observed to vary subtly between different geographic locations. It has been associated with a wide range of ecological conditions, including pH extremes of pH 2.9–10.0 in polluted waters. We present a molecular study of the genetic variation within B. harrisoni across 21 rivers in its distribution range in southern Africa.
- Full Text:
- Date Issued: 2012
- Authors: Pereira-da-Conceicoa, Lyndall L , Price, Benjamin W , Barber-James, Helen M , Barker, Nigel P , de Moor, Ferdy C , Villet, Martin H
- Date: 2012
- Language: English
- Type: Article
- Identifier: vital:6535 , http://hdl.handle.net/10962/d1005976 , https://dx.doi.org/10.1186/1471-2148-12-26
- Description: Baetis harrisoni Barnard is a mayfly frequently encountered in river studies across Africa, but the external morphological features used for identifying nymphs have been observed to vary subtly between different geographic locations. It has been associated with a wide range of ecological conditions, including pH extremes of pH 2.9–10.0 in polluted waters. We present a molecular study of the genetic variation within B. harrisoni across 21 rivers in its distribution range in southern Africa.
- Full Text:
- Date Issued: 2012
African carrion ecosystems and their insect communities in relation to forensic entomology
- Authors: Villet, Martin H
- Date: 2011
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/442439 , vital:73984 , http://www.globalsciencebooks.info/Online/GSBOnline/OnlinePT_5_1.html
- Description: African carrion communities contain representatives of the same families that occur in carrion communities on other continents. Checklists and identification guides are tabulated, and the natural histories of core members of the terrestrial community are outlined. Because of strong phylogenetic trends in the biology of the families, the species are effectively ecological surrogates of their relatives elsewhere. These phylogenetic trends also allow the definition of a set of guilds of functionally equivalent species that unify the study of carrion communities world-wide, and a revised suite of guilds is described with both synecological and forensic purposes in mind. Although the decomposition process has been arbitrarily subdivided into stages, they have little direct relation to the dynamics of the carrion community, and should be treated as landmarks rather than phases. Community turnover follows a qualitatively predictable succession, with the greatest species richness and diversity around the ecotone-like transition from ‘wet-phase’ to ‘dry-phase’ carrion habitats. These habitats are differentiated along interacting ecological gradients of dietary quality, competition, and risk of predation, which are important to the core guilds. Competition and predation have strong effects on population dynamics of community members, but link particular species only weakly, so that the succession pattern largely reflects the autecology of the individual species. Discrete waves of species are absent, which increases the temporal resolution, and therefore the forensic value, of the succession as a ‘clock’. The forensic significance of various aspects of community and trophic dynamics are discussed, and means of applying ecological theory to investigations are reviewed.
- Full Text:
- Date Issued: 2011
- Authors: Villet, Martin H
- Date: 2011
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/442439 , vital:73984 , http://www.globalsciencebooks.info/Online/GSBOnline/OnlinePT_5_1.html
- Description: African carrion communities contain representatives of the same families that occur in carrion communities on other continents. Checklists and identification guides are tabulated, and the natural histories of core members of the terrestrial community are outlined. Because of strong phylogenetic trends in the biology of the families, the species are effectively ecological surrogates of their relatives elsewhere. These phylogenetic trends also allow the definition of a set of guilds of functionally equivalent species that unify the study of carrion communities world-wide, and a revised suite of guilds is described with both synecological and forensic purposes in mind. Although the decomposition process has been arbitrarily subdivided into stages, they have little direct relation to the dynamics of the carrion community, and should be treated as landmarks rather than phases. Community turnover follows a qualitatively predictable succession, with the greatest species richness and diversity around the ecotone-like transition from ‘wet-phase’ to ‘dry-phase’ carrion habitats. These habitats are differentiated along interacting ecological gradients of dietary quality, competition, and risk of predation, which are important to the core guilds. Competition and predation have strong effects on population dynamics of community members, but link particular species only weakly, so that the succession pattern largely reflects the autecology of the individual species. Discrete waves of species are absent, which increases the temporal resolution, and therefore the forensic value, of the succession as a ‘clock’. The forensic significance of various aspects of community and trophic dynamics are discussed, and means of applying ecological theory to investigations are reviewed.
- Full Text:
- Date Issued: 2011
Report of the multidisciplinary investigation of differentiation and potential hybridisation between two Yellowfish species Labeobarbus Kimberleyensis and L. Aeneus from the Orange-Vaal system
- Bloomer, Paulette, Villet, Martin H, Bills, Ian R, Van der Bank, F Herman, Jones, Nick, Walsh, Gina
- Authors: Bloomer, Paulette , Villet, Martin H , Bills, Ian R , Van der Bank, F Herman , Jones, Nick , Walsh, Gina
- Date: 2007
- Language: English
- Type: Report
- Identifier: vital:7162 , http://hdl.handle.net/10962/d1011937
- Description: From the executive summary]: The relationships within and between two yellowfish species, Labeobarbus aeneus (smallmouth yellowfish) and L. kimberleyensis (largemouth yellowfish) from the Orange-Vaal system were investigated through three independently conducted studies of the same material collected from the Sak River (the type locality of L. aeneus), the upper Orange River at Aliwal North and the lower Orange River at Pella and Onseepkans.
- Full Text:
- Date Issued: 2007
- Authors: Bloomer, Paulette , Villet, Martin H , Bills, Ian R , Van der Bank, F Herman , Jones, Nick , Walsh, Gina
- Date: 2007
- Language: English
- Type: Report
- Identifier: vital:7162 , http://hdl.handle.net/10962/d1011937
- Description: From the executive summary]: The relationships within and between two yellowfish species, Labeobarbus aeneus (smallmouth yellowfish) and L. kimberleyensis (largemouth yellowfish) from the Orange-Vaal system were investigated through three independently conducted studies of the same material collected from the Sak River (the type locality of L. aeneus), the upper Orange River at Aliwal North and the lower Orange River at Pella and Onseepkans.
- Full Text:
- Date Issued: 2007
Karyology of the redfin minnows, genus Pseudobarbus Smith, 1841 (Teleostei: Cyprinidae): one of the evolutionarily tetraploid lineages of South African barbines
- Naran, Daksha, Skelton, Paul H, Villet, Martin H
- Authors: Naran, Daksha , Skelton, Paul H , Villet, Martin H
- Date: 2006
- Language: English
- Type: Article
- Identifier: vital:6770 , http://hdl.handle.net/10962/d1008063
- Description: The karyotypes of six species of Pseudobarbus Smith, 1841, namely P. afer (Peters, 1864), P. asper (Boulenger, 1911), P. burchelli Smith, 1841, P. burgi (Boulenger, 1911), P. phlegethon (Barnard, 1938) and P. tenuis (Barnard, 1938), were examined by conventional Giemsa staining and described. All six karyotypes have 2n = 100 chromosomes, dominated by biarmed chromosomes, as does the only other member of the genus, P. quathlambae (Barnard, 1938). Sex-related intraspecific karyotype variation was not found. The shared chromosome numbers and general similarity of the karyotypes (FN = 186–192) provide a new synapomorphy to support their monophyly, which is already indicated by anatomical and mtDNA markers. Karyotype evolution within the genus has been accompanied by chromosomal inversions and centromeric shifts. Comparison of the diploid number found in Pseudobarbus with other African barbine cyprinines, which have in the region of 2n=50 and lower FNs, suggests a tetraploid evolutionary origin of the genus, possibly by allotetraploidy.
- Full Text:
- Date Issued: 2006
- Authors: Naran, Daksha , Skelton, Paul H , Villet, Martin H
- Date: 2006
- Language: English
- Type: Article
- Identifier: vital:6770 , http://hdl.handle.net/10962/d1008063
- Description: The karyotypes of six species of Pseudobarbus Smith, 1841, namely P. afer (Peters, 1864), P. asper (Boulenger, 1911), P. burchelli Smith, 1841, P. burgi (Boulenger, 1911), P. phlegethon (Barnard, 1938) and P. tenuis (Barnard, 1938), were examined by conventional Giemsa staining and described. All six karyotypes have 2n = 100 chromosomes, dominated by biarmed chromosomes, as does the only other member of the genus, P. quathlambae (Barnard, 1938). Sex-related intraspecific karyotype variation was not found. The shared chromosome numbers and general similarity of the karyotypes (FN = 186–192) provide a new synapomorphy to support their monophyly, which is already indicated by anatomical and mtDNA markers. Karyotype evolution within the genus has been accompanied by chromosomal inversions and centromeric shifts. Comparison of the diploid number found in Pseudobarbus with other African barbine cyprinines, which have in the region of 2n=50 and lower FNs, suggests a tetraploid evolutionary origin of the genus, possibly by allotetraploidy.
- Full Text:
- Date Issued: 2006
Influence of grazing by large mammals on the spider community of a Kenyan savanna biome
- Warui, Charles M, Villet, Martin H, Young, T P, Jocqué, R
- Authors: Warui, Charles M , Villet, Martin H , Young, T P , Jocqué, R
- Date: 2005
- Language: English
- Type: Article
- Identifier: vital:6889 , http://hdl.handle.net/10962/d1011649 , http://0-www.bioone.org.wam.seals.ac.za/doi/10.1636/CT05-43.1
- Full Text:
- Date Issued: 2005
- Authors: Warui, Charles M , Villet, Martin H , Young, T P , Jocqué, R
- Date: 2005
- Language: English
- Type: Article
- Identifier: vital:6889 , http://hdl.handle.net/10962/d1011649 , http://0-www.bioone.org.wam.seals.ac.za/doi/10.1636/CT05-43.1
- Full Text:
- Date Issued: 2005
A fuzzy classification technique for predicting species' distributions: applications using invasive alien plants and indigenous insects
- Robertson, Mark P, Villet, Martin H, Palmer, Anthony R
- Authors: Robertson, Mark P , Villet, Martin H , Palmer, Anthony R
- Date: 2004
- Language: English
- Type: text , Article
- Identifier: vital:6897 , http://hdl.handle.net/10962/d1011659 , http://dx.doi.org/10.1111/j.1366-9516.2004.00108.x
- Description: A new predictive modelling technique called the fuzzy envelope model (FEM) is introduced. The technique can be used to predict potential distributions of organisms using presence-only locality records and a set of environmental predictor variables. FEM uses fuzzy logic to classify a set of predictor variable maps based on the values associated with presence records and combines the results to produce a potential distribution map for a target species. This technique represents several refinements of the envelope approach used in the BIOCLIM modelling package. These refinements are related to the way in which FEMs deal with uncertainty, the way in which this uncertainty is represented in the resultant potential distribution maps, and the way that these maps can be interpreted and applied. To illustrate its potential use in biogeographical studies, FEM was applied to predicting the potential distribution of three invasive alien plant species (Lantana camara L., Ricinus communis L. and Solanum mauritianum Scop.), and three native cicada species (Capicada decora Germar, Platypleura deusta Thun. and P. capensis L.) in South Africa, Lesotho and Swaziland. These models were quantitatively compared with models produced by means of the algorithm used in the BIOCLIM modelling package, which is referred to as a crisp envelope model (the CEM design). The average performance of models of the FEM design was consistently higher than those of the CEM design. There were significant differences in model performance among species but there was no significant interaction between model design and species. The average maximum kappa value ranged from 0.70 to 0.90 for FEM design and from 0.57 to 0.89 for the CEM design, which can be described as 'good' to 'excellent' using published ranges of agreement for the kappa statistic. This technique can be used to predict species' potential distributions that could be used for identifying regions at risk from invasion by alien species. These predictions could also be used in conservation planning in the case of native species.
- Full Text:
- Date Issued: 2004
- Authors: Robertson, Mark P , Villet, Martin H , Palmer, Anthony R
- Date: 2004
- Language: English
- Type: text , Article
- Identifier: vital:6897 , http://hdl.handle.net/10962/d1011659 , http://dx.doi.org/10.1111/j.1366-9516.2004.00108.x
- Description: A new predictive modelling technique called the fuzzy envelope model (FEM) is introduced. The technique can be used to predict potential distributions of organisms using presence-only locality records and a set of environmental predictor variables. FEM uses fuzzy logic to classify a set of predictor variable maps based on the values associated with presence records and combines the results to produce a potential distribution map for a target species. This technique represents several refinements of the envelope approach used in the BIOCLIM modelling package. These refinements are related to the way in which FEMs deal with uncertainty, the way in which this uncertainty is represented in the resultant potential distribution maps, and the way that these maps can be interpreted and applied. To illustrate its potential use in biogeographical studies, FEM was applied to predicting the potential distribution of three invasive alien plant species (Lantana camara L., Ricinus communis L. and Solanum mauritianum Scop.), and three native cicada species (Capicada decora Germar, Platypleura deusta Thun. and P. capensis L.) in South Africa, Lesotho and Swaziland. These models were quantitatively compared with models produced by means of the algorithm used in the BIOCLIM modelling package, which is referred to as a crisp envelope model (the CEM design). The average performance of models of the FEM design was consistently higher than those of the CEM design. There were significant differences in model performance among species but there was no significant interaction between model design and species. The average maximum kappa value ranged from 0.70 to 0.90 for FEM design and from 0.57 to 0.89 for the CEM design, which can be described as 'good' to 'excellent' using published ranges of agreement for the kappa statistic. This technique can be used to predict species' potential distributions that could be used for identifying regions at risk from invasion by alien species. These predictions could also be used in conservation planning in the case of native species.
- Full Text:
- Date Issued: 2004
A proposed prioritization system for the management of invasive alien plants in South Africa
- Robertson, Mark P, Villet, Martin H, Fairbanks, Dean H K, Henderson, L, Higgins, Simon I, Hoffmann, John H, Le Maitre, David C, Palmer, Anthony R, Riggs, I, Shackleton, Charlie M, Zimmermann, Helmuth G
- Authors: Robertson, Mark P , Villet, Martin H , Fairbanks, Dean H K , Henderson, L , Higgins, Simon I , Hoffmann, John H , Le Maitre, David C , Palmer, Anthony R , Riggs, I , Shackleton, Charlie M , Zimmermann, Helmuth G
- Date: 2003
- Language: English
- Type: Article
- Identifier: vital:6911 , http://hdl.handle.net/10962/d1011872
- Description: Every country has weed species whose presence conflicts in some way with human management objectives and needs. Resources for research and control are limited, so priority should be given to species that are the biggest problem. The prioritization system described in this article was designed to assess objectively research and control priorities of invasive alien plants at a national scale in South Africa. The evaluation consists of seventeen criteria, grouped into five modules, that assess invasiveness, spatial characteristics, potential impact, potential for control, and conflicts of interest for each plant species under consideration. Total prioritization scores, calculated from criterion and module scores, were used to assess a species' priority. Prioritization scores were calculated by combining independent assessments provided by several experts, thus increasing the reliability of the rankings. The total confidence score, a separate index, indicates the reliability and availability of data used to make an assessment. Candidate species for evaluation were identified and assessed by several experts using the prioritization system. The final ranking was made by combining two separate indices, the total prioritization score and the total confidence score. This approach integrates the plant's perceived priority with an index of data reliability. Of the 61 species assessed, those with the highest ranks (Lantana camara, Chromolaena odorata and Opuntia ficus-indica) had high prioritization and high confidence scores, and are thus of most concern. Those species with the lowest ranks, for example, Harrisia martinii, Opuntia spinulifera and Opuntia exaltata, had low prioritization scores and high confidence scores, and thus are of least concern. Our approach to ranking weeds offers several advantages over existing systems because it is designed for multiple assessors based on the Delphi decision-making technique, the criteria contribute equally to the total score, and the system can accommodate incomplete data on a species. Although the choice of criteria may be criticized and the system has certain limitations, it appears to have delivered credible results.
- Full Text:
- Date Issued: 2003
- Authors: Robertson, Mark P , Villet, Martin H , Fairbanks, Dean H K , Henderson, L , Higgins, Simon I , Hoffmann, John H , Le Maitre, David C , Palmer, Anthony R , Riggs, I , Shackleton, Charlie M , Zimmermann, Helmuth G
- Date: 2003
- Language: English
- Type: Article
- Identifier: vital:6911 , http://hdl.handle.net/10962/d1011872
- Description: Every country has weed species whose presence conflicts in some way with human management objectives and needs. Resources for research and control are limited, so priority should be given to species that are the biggest problem. The prioritization system described in this article was designed to assess objectively research and control priorities of invasive alien plants at a national scale in South Africa. The evaluation consists of seventeen criteria, grouped into five modules, that assess invasiveness, spatial characteristics, potential impact, potential for control, and conflicts of interest for each plant species under consideration. Total prioritization scores, calculated from criterion and module scores, were used to assess a species' priority. Prioritization scores were calculated by combining independent assessments provided by several experts, thus increasing the reliability of the rankings. The total confidence score, a separate index, indicates the reliability and availability of data used to make an assessment. Candidate species for evaluation were identified and assessed by several experts using the prioritization system. The final ranking was made by combining two separate indices, the total prioritization score and the total confidence score. This approach integrates the plant's perceived priority with an index of data reliability. Of the 61 species assessed, those with the highest ranks (Lantana camara, Chromolaena odorata and Opuntia ficus-indica) had high prioritization and high confidence scores, and are thus of most concern. Those species with the lowest ranks, for example, Harrisia martinii, Opuntia spinulifera and Opuntia exaltata, had low prioritization scores and high confidence scores, and thus are of least concern. Our approach to ranking weeds offers several advantages over existing systems because it is designed for multiple assessors based on the Delphi decision-making technique, the criteria contribute equally to the total score, and the system can accommodate incomplete data on a species. Although the choice of criteria may be criticized and the system has certain limitations, it appears to have delivered credible results.
- Full Text:
- Date Issued: 2003
Comparing models for predicting species' potential distributions : a case study using correlative and mechanistic predictive modelling techniques
- Robertson, Mark P, Peter, Craig I, Villet, Martin H, Ripley, Bradford S
- Authors: Robertson, Mark P , Peter, Craig I , Villet, Martin H , Ripley, Bradford S
- Date: 2003
- Language: English
- Type: Article
- Identifier: vital:6539 , http://hdl.handle.net/10962/d1005980 , http://dx.doi.org/10.1016/S0304-3800(03)00028-0
- Description: Models used to predict species’ potential distributions have been described as either correlative or mechanistic. We attempted to determine whether correlative models could perform as well as mechanistic models for predicting species potential distributions, using a case study. We compared potential distribution predictions made for a coastal dune plant (Scaevola plumieri) along the coast of South Africa, using a mechanistic model based on summer water balance (SWB), and two correlative models (a profile and a group discrimination technique). The profile technique was based on principal components analysis (PCA) and the group-discrimination technique was based on multiple logistic regression (LR). Kappa (κ) statistics were used to objectively assess model performance and model agreement. Model performance was calculated by measuring the levels of agreement (using κ) between a set of testing localities (distribution records not used for model building) and each of the model predictions. Using published interpretive guidelines for the kappa statistic, model performance was “excellent” for the SWB model (κ=0.852), perfect for the LR model (κ=1.000), and “very good” for the PCA model (κ=0.721). Model agreement was calculated by measuring the level of agreement between the mechanistic model and the two correlative models. There was “good” model agreement between the SWB and PCA models (κ=0.679) and “very good” agreement between the SWB and LR models (κ=0.786). The results suggest that correlative models can perform as well as or better than simple mechanistic models. The predictions generated from these three modelling designs are likely to generate different insights into the potential distribution and biology of the target organism and may be appropriate in different situations. The choice of model is likely to be influenced by the aims of the study, the biology of the target organism, the level of knowledge the target organism’s biology, and data quality.
- Full Text:
- Date Issued: 2003
- Authors: Robertson, Mark P , Peter, Craig I , Villet, Martin H , Ripley, Bradford S
- Date: 2003
- Language: English
- Type: Article
- Identifier: vital:6539 , http://hdl.handle.net/10962/d1005980 , http://dx.doi.org/10.1016/S0304-3800(03)00028-0
- Description: Models used to predict species’ potential distributions have been described as either correlative or mechanistic. We attempted to determine whether correlative models could perform as well as mechanistic models for predicting species potential distributions, using a case study. We compared potential distribution predictions made for a coastal dune plant (Scaevola plumieri) along the coast of South Africa, using a mechanistic model based on summer water balance (SWB), and two correlative models (a profile and a group discrimination technique). The profile technique was based on principal components analysis (PCA) and the group-discrimination technique was based on multiple logistic regression (LR). Kappa (κ) statistics were used to objectively assess model performance and model agreement. Model performance was calculated by measuring the levels of agreement (using κ) between a set of testing localities (distribution records not used for model building) and each of the model predictions. Using published interpretive guidelines for the kappa statistic, model performance was “excellent” for the SWB model (κ=0.852), perfect for the LR model (κ=1.000), and “very good” for the PCA model (κ=0.721). Model agreement was calculated by measuring the level of agreement between the mechanistic model and the two correlative models. There was “good” model agreement between the SWB and PCA models (κ=0.679) and “very good” agreement between the SWB and LR models (κ=0.786). The results suggest that correlative models can perform as well as or better than simple mechanistic models. The predictions generated from these three modelling designs are likely to generate different insights into the potential distribution and biology of the target organism and may be appropriate in different situations. The choice of model is likely to be influenced by the aims of the study, the biology of the target organism, the level of knowledge the target organism’s biology, and data quality.
- Full Text:
- Date Issued: 2003
IsiXhosa insect names from the Eastern Cape, South Africa
- Mkize, Nolwazi, Villet, Martin H, Robertson, Mark P
- Authors: Mkize, Nolwazi , Villet, Martin H , Robertson, Mark P
- Date: 2003
- Language: English
- Type: Article
- Identifier: vital:6859 , http://hdl.handle.net/10962/d1011148
- Description: We present a list of isiXhosa names for a wide diversity of South African insects, and their English translations and scientific names, to contribute to bridging the knowledge gap between rural development workers and isiXhosa speakers. We interviewed 51 people in their homes at eight sites across the Eastern Cape and also included words from a published dictionary. We found 151 insect names, and categorized them into personal, dialectal and standard categories. Response-frequency distributions of the categories of names showed that the dialectal and standard lists were essentially complete. Sample accumulation curves showed levelling-off within sites and across the whole study, demonstrating that samples were adequate. The literal translations of some names show that isiXhosa speakers relate insects either to people, to their habitat and/or to their behaviour. The list can contribute to the standardization of knowledge of insects' indigenous names in South Africa for a variety of practical applications such as agricultural training and health services.
- Full Text:
- Date Issued: 2003
- Authors: Mkize, Nolwazi , Villet, Martin H , Robertson, Mark P
- Date: 2003
- Language: English
- Type: Article
- Identifier: vital:6859 , http://hdl.handle.net/10962/d1011148
- Description: We present a list of isiXhosa names for a wide diversity of South African insects, and their English translations and scientific names, to contribute to bridging the knowledge gap between rural development workers and isiXhosa speakers. We interviewed 51 people in their homes at eight sites across the Eastern Cape and also included words from a published dictionary. We found 151 insect names, and categorized them into personal, dialectal and standard categories. Response-frequency distributions of the categories of names showed that the dialectal and standard lists were essentially complete. Sample accumulation curves showed levelling-off within sites and across the whole study, demonstrating that samples were adequate. The literal translations of some names show that isiXhosa speakers relate insects either to people, to their habitat and/or to their behaviour. The list can contribute to the standardization of knowledge of insects' indigenous names in South Africa for a variety of practical applications such as agricultural training and health services.
- Full Text:
- Date Issued: 2003
Reproductive behaviour of Plectroctena mandibularis F. Smith (Hymenoptera: Formicidae), a ponerine ant with ergatoid queens
- Authors: Villet, Martin H
- Date: 1999
- Language: English
- Type: Article
- Identifier: vital:6890 , http://hdl.handle.net/10962/d1011650
- Description: [From the text]: The present study reports on new observations on the reproductive biology of P. mandibularis, particularly the phenology of males, mating behaviour and colony founding, that may help in deciding between alternative explanations for the occurrence of ergatoid queens in this species.
- Full Text:
- Date Issued: 1999
- Authors: Villet, Martin H
- Date: 1999
- Language: English
- Type: Article
- Identifier: vital:6890 , http://hdl.handle.net/10962/d1011650
- Description: [From the text]: The present study reports on new observations on the reproductive biology of P. mandibularis, particularly the phenology of males, mating behaviour and colony founding, that may help in deciding between alternative explanations for the occurrence of ergatoid queens in this species.
- Full Text:
- Date Issued: 1999
Clinal morphometric variation in wild honey bees (Hymenoptera: Apidae) in South Africa
- Steele, G R, Villet, Martin H, Radloff, Sarah E, Hepburn, H Randall
- Authors: Steele, G R , Villet, Martin H , Radloff, Sarah E , Hepburn, H Randall
- Date: 1998
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/442622 , vital:74015 , https://www.jstor.org/stable/2999809
- Description: As a result of side effects of the accidental dispersal of the Cape honey bee, it has become of agroeconomic importance to delineate the region within South Africa where thelytokous worker honey bees occur so that apicultural movement of bees does not exacerbate the problem. Thelytokous workers are believed to be unique to Apis mellifera capensis, so that the problem is to find morphological markers distinguishing this race from its A. m. scutellata neighbours. However, no evidence of the expected hybrid zone demarcating races could be found. Factor analysis revealed only one spherical cluster of samples. Trend surfaces of the local mean morphometric factor scores showed a cline that paralleled latitude, with distortions relating to montane and continental effects. Discriminant function analysis implicated certain mountain ranges in amplifying the effects of latitude. Trend surfaces of local intercolony factor variance showed morphometric homogeneity across most of the country. We conclude that there is only a single population of honey bees in South Africa, and that it shows climate-correlated clinal variation. If the transportation of bees for commercial apiculture is to be successfully regulated to solve the `capensis calamity', further research should focus on the geographical distribution of thelytokous workers rather than on the capensis phenotype. Such workers have a wider distribution than capensis, occurring also at high frequencies around the type locality of A. m. scutellata.
- Full Text:
- Date Issued: 1998
- Authors: Steele, G R , Villet, Martin H , Radloff, Sarah E , Hepburn, H Randall
- Date: 1998
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/442622 , vital:74015 , https://www.jstor.org/stable/2999809
- Description: As a result of side effects of the accidental dispersal of the Cape honey bee, it has become of agroeconomic importance to delineate the region within South Africa where thelytokous worker honey bees occur so that apicultural movement of bees does not exacerbate the problem. Thelytokous workers are believed to be unique to Apis mellifera capensis, so that the problem is to find morphological markers distinguishing this race from its A. m. scutellata neighbours. However, no evidence of the expected hybrid zone demarcating races could be found. Factor analysis revealed only one spherical cluster of samples. Trend surfaces of the local mean morphometric factor scores showed a cline that paralleled latitude, with distortions relating to montane and continental effects. Discriminant function analysis implicated certain mountain ranges in amplifying the effects of latitude. Trend surfaces of local intercolony factor variance showed morphometric homogeneity across most of the country. We conclude that there is only a single population of honey bees in South Africa, and that it shows climate-correlated clinal variation. If the transportation of bees for commercial apiculture is to be successfully regulated to solve the `capensis calamity', further research should focus on the geographical distribution of thelytokous workers rather than on the capensis phenotype. Such workers have a wider distribution than capensis, occurring also at high frequencies around the type locality of A. m. scutellata.
- Full Text:
- Date Issued: 1998
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