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South African nose flies (Diptera, Calliphoridae, Rhiniinae): taxonomy, diversity, distribution and biology

- Thomas-Cabianca, Arianna, Villet, Martin H, Martínez-Sánchez, Anabel, Rojo, Santos

Authors: Thomas-Cabianca, Arianna , Villet, Martin H , Martínez-Sánchez, Anabel , Rojo, Santos
Date: 2023
Subjects: To be catalogued
Language: English
Type: text , article
Identifier: http://hdl.handle.net/10962/441400 , vital:73884 , 10.3897/BDJ.11.e72764
Description: Rhiniinae (Diptera, Calliphoridae) is a taxon of nearly 400 known species, many of them termitophilous. Approximatelly 160 valid species in 16 genera are Afrotropical, with over 60 of them occurring in South Africa. The taxonomy of this group is outdated, as most studies of the South African taxa were conducted 40 to 70 years ago (mostly by Salvador Peris and Fritz Zumpt). Published information on their biology and ecology is also scarce.
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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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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.
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Revision of the Afrotropical genus Fainia Zumpt, 1958, with notes on the morphology of Rhiniidae subfamilies (Diptera, Oestroidea)

- Thomas-Cabianca, Arianna, Martínez-Sánchez, Anabel, Villet, Martin H, Rojo, Santos

Authors: Thomas-Cabianca, Arianna , Martínez-Sánchez, Anabel , Villet, Martin H , Rojo, Santos
Date: 2021
Subjects: To be catalogued
Language: English
Type: text , article
Identifier: http://hdl.handle.net/10962/441446 , vital:73889 , 10.3897/zookeys.1033.58539
Description: The taxonomy and diversity of Fainia Zumpt, 1958, an exclusive Afrotropical genus, had not been reviewed recently. The genus included six nominal species, but the status of several of them was debated. Identification of most Fainia species depends on characters of the male terminalia; females are poorly known and, in several cases, are not adequately diagnosed. We conducted a taxonomic revision of the genus and generated identification tools. Based on the study of type material and specimens available in entomological collections in Africa and Europe, we recognise here three of the six species as valid (F. albitarsis (Macquart, 1846), F. elongata (Bezzi, 1908) and F. inexpectata Zumpt, 1973). We also provide an identification key to both sexes, redescriptions of the species, updated distribution records and high resolution photographs of males’ and females’ habitus and male terminalia. The description of Fainia kagerana Lehrer, 2007a nom. nud. is an invalid nomenclatural act in terms of ICZN Article 13.1. 1. Based on examinations of their holotypes, F. sambura Lehrer, 2008 syn. nov. is proposed as a junior synonym of F. albitarsis; F. kirinyaga Lehrer, 2007b syn. nov. is proposed as a junior synonym of F. inexpectata; and Fainia giriama Lehrer, 2007b is moved from the genus Fainia to the genus Rhinia Robineau-Desvoidy, as Rhinia giriama (Lehrer, 2007b) comb. nov.. We propose two apomorphies that support the status of the subfamily Rhiniinae.
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Habitat requirements affect genetic variation in three species of mayfly (Ephemeroptera, Baetidae) from South Africa:

- Taylor, Chantal L, Barker, Nigel P, Barber-James, Helen M, Villet, Martin H, Pereira-da-Conceicoa, Lyndall L

Authors: Taylor, Chantal L , Barker, Nigel P , Barber-James, Helen M , Villet, Martin H , Pereira-da-Conceicoa, Lyndall L
Date: 2020
Language: English
Type: text , article
Identifier: http://hdl.handle.net/10962/149314 , vital:38824 , https://doi.org/10.3897/zookeys.936.38587
Description: This study investigates genetic diversity in three species of Ephemeroptera, one eurytopic and therefore widespread (Afroptilum sudafricanum) and two stenotopic and thus endemic (Demoreptus natalensis and Demoreptus capensis) species, all of which co-occur in the southern Great Escarpment, South Africa. Mitochondrial DNA was analysed to compare the genetic diversity between the habitat generalist and the two habitat specialists. Afroptilum sudafricanum showed no indication of population genetic structure due to geographic location, while both Demoreptus species revealed clear genetic differentiation between geographic localities and catchments, evident from phylogenetic analyses and high FST values from AMOVA.
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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.
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The uses of Chrysomya megacephala (Fabricius, 1794)(Diptera: Calliphoridae) in forensic entomology:

- Badenhorst, Rozane, Villet, Martin H

Authors: Badenhorst, Rozane , Villet, Martin H
Date: 2018
Language: English
Type: text , article
Identifier: http://hdl.handle.net/10962/140631 , vital:37905 , DOI: 10.1080/20961790.2018.1426136
Description: Chrysomya megacephala (Fabricius, 1794) occurs on every continent and is closely associated with carrion and decaying material in human environments. Its abilities to find dead bodies and carry pathogens give it a prominence in human affairs that may involve prosecution or litigation, and therefore forensic entomologists. The identification, geographical distribution and biology of the species are reviewed to provide a background for approaches that four branches of forensic entomology (urban, stored-product, medico-criminal and environmental) might take to investigations involving this fly.
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Species identification of adult African blowflies (Diptera: Calliphoridae) of forensic importance:

- Lutz, Lena, Williams, Kristin A, Villet, Martin H, Ekanem, Mfon

Authors: Lutz, Lena , Williams, Kristin A , Villet, Martin H , Ekanem, Mfon
Date: 2017
Language: English
Type: text , article
Identifier: http://hdl.handle.net/10962/140620 , vital:37904 , DOI: 10.1007/s00414-017-1654-y
Description: Necrophagous blowflies can provide an excellent source of evidence for forensic entomologists and are also relevant to problems in public health, medicine, and animal health. However, access to useful information about these blowflies is constrained by the need to correctly identify the flies, and the poor availability of reliable, accessible identification tools is a serious obstacle to the development of forensic entomology in the majority of African countries. In response to this need, a high-quality key to the adults of all species of forensically relevant blowflies of Africa has been prepared, drawing on high-quality entomological materials and modern focus-stacking photomicroscopy. This new key can be easily applied by investigators inexperienced in the taxonomy of blowflies and is made available through a highly accessible online platform. Problematic diagnostic characters used in previous keys are discussed.
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Dung beetle (Coleoptera Scarabaeoidea) assemblages in the western Italian Alps: benchmark data for land use monitoring

- Tocco, Claudia, Villet, Martin H

Authors: Tocco, Claudia , Villet, Martin H
Date: 2016
Subjects: To be catalogued
Language: English
Type: text , article
Identifier: http://hdl.handle.net/10962/441361 , vital:73879 , 10.3897/BDJ.4.e10059
Description: Traditional agro-pastoral practices are in decline over much of the Alps (MacDonald et al. 2000), leading to shrub and tree encroachment, and this represents one of the main threats for the conservation of alpine biodiversity, as many plant and animal species are dependent on the presence of semi-natural open habitats. However, quantifying this environmental change and assessing its impact on biodiversity may be difficult, especially in the context of sparse historical survey data. The accessibility of contemporary data about local biodiversity surveys in general, and indicator taxa in particular, is an essential consideration for planning future evaluations of conservation status in the Alps and for conservation plans that use ecological indicators to monitor temporal changes in biodiversity. Dung beetles are important ecosystem service providers (Nichols et al. 2008) that have been assessed as a good ecological indicator taxon in several studies (reviewed by Nichols and Gardner 2011), and although the Alps is perhaps one of the best-studied regions in respect of dung beetles, there are still only eight readily-accessible publications. We have augmented and comprehensively reviewed the data from these publications.
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Monitoring of invertebrate and fish recovery following river rehabilitation using rotenone in the Rondegat River

- Weyl, Olaf L F, Barrow, S, Bellingan, Terence A, Dalu, Tatenda, Ellender, Bruce R, Esler, K, Impson, D, Gouws, Jeanne, Jordaan, M, Villet, Martin H, Wasserman, Ryan J, Woodford, Darragh J

Authors: Weyl, Olaf L F , Barrow, S , Bellingan, Terence A , Dalu, Tatenda , Ellender, Bruce R , Esler, K , Impson, D , Gouws, Jeanne , Jordaan, M , Villet, Martin H , Wasserman, Ryan J , Woodford, Darragh J
Date: 2016
Subjects: To be catalogued
Language: English
Type: text , article
Identifier: http://hdl.handle.net/10962/442411 , vital:73982 , https://www.wrc.org.za/wp-content/uploads/mdocs/2261.pdf
Description: Fish invasions have been cited as a primary threat to imperilled South African fishes and other aquatic fauna. As a result, the management and control of alien invasive species is a legislated priority in South Africa. From a river rehabilitation perspective, eradicating alien fish allows for the rehabilitation of several kilometres of river, with very significant benefits for the endangered fish species present and for the associated aquatic biota. In South Africa, the piscicide rotenone is one of the preferred methods for achieving eradication.
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Optimising design and effort for environmental surveys using dung beetles (Coleoptera: Scarabaeidae):

- Tocco, Claudia, Quinn, Danielle, Midgley, John M, Villet, Martin H

Authors: Tocco, Claudia , Quinn, Danielle , Midgley, John M , Villet, Martin H
Date: 2016
Language: English
Type: text , article
Identifier: http://hdl.handle.net/10962/140670 , vital:37908 , DOI: 10.4039/tce.2016.48
Description: In biological monitoring, deploying an effective standardised quantitative sampling method, optimised by trap design and sampling effort, is an essential consideration. To exemplify this using dung beetle (Coleoptera: Scarabaeidae: Scarabaeinae and Aphodiinae) communities, three pitfall trap designs (un-baited (TN), baited at ground level (flat trap, TF), and baited above the trap (hanging trap, TH)), employed with varying levels of sampling effort (number of traps = 1, 2, 3… 10; number of days = 1, 2, 3), were evaluated for sampling completeness and efficiency in the Eastern Cape, South Africa. Modelling and resampling simulation approaches were used to suggest optimal sampling protocols across environmentally diverse sites. Overall, TF recovered the greatest abundance and species richness of dung beetles, but behavioural guilds showed conflicting trends: endocoprids preferred TH while paracoprids and telocoprids preferred TF. Resampling simulation of trap type and the two components of sampling effort suggested that six TF traps left for three days was most efficient in obtaining a representative sample and allowed differentiation between trap types, allowing the improved efficiency to be recognised. The effect of trap type on non-target specimens, particularly ants, was also investigated. TF and TH caught almost no by-catch, which is ethically desirable.
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Phylogenetic radiation of the greenbottle flies (Diptera, Calliphoridae, Luciliinae).

- Williams, Kristin A, Lamb, Jennifer, Villet, Martin H

Authors: Williams, Kristin A , Lamb, Jennifer , Villet, Martin H
Date: 2016
Subjects: To be catalogued
Language: English
Type: text , article
Identifier: http://hdl.handle.net/10962/441431 , vital:73887 , 10.3897/zookeys.568.6696
Description: The subfamily Luciliinae is diverse and geographically widespread. Its four currently recognised genera (Dyscritomyia Grimshaw, 1901, Hemipyrellia Townsend, 1918, Hypopygiopsis Townsend 1916 and Lucilia Robineau-Desvoidy, 1830) contain species that range from saprophages to obligate parasites, but their pattern of phylogenetic diversification is unclear. The 28S rRNA, COI and Period genes of 14 species of Lucilia and Hemipyrellia were partially sequenced and analysed together with sequences of 11 further species from public databases. The molecular data confirmed molecular paraphyly in three species-pairs in Lucilia that hamper barcode identifications of those six species. Lucilia sericata and Lucilia cuprina were confirmed as mutual sister species. The placements of Dyscritomyia and Hypopygiopsis were ambiguous, since both made Lucilia paraphyletic in some analyses. Recognising Hemipyrellia as a genus consistently left Lucilia s.l. paraphyletic, and the occasionally-recognised (sub)genus Phaenicia was consistently paraphyletic, so these taxa should be synonymised with Lucilia to maintain monophyly.
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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.
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A review of the alderfly genus Leptosialis Esben-Petersen (Megaloptera, Sialidae) with description of a new species from South Africa

- Price, Benjamin W, Liu, Xingyue, de Moor, Ferdy C, Villet, Martin H

Authors: Price, Benjamin W , Liu, Xingyue , de Moor, Ferdy C , Villet, Martin H
Date: 2012
Subjects: To be catalogued
Language: English
Type: text , article
Identifier: http://hdl.handle.net/10962/441461 , vital:73891 , https://zookeys.pensoft.net/articles.php?id=2856
Description: The monotypic South African alderfly genus Leptosialis Esben-Petersen, 1920 is reviewed and Leptosialis africana Esben-Petersen, 1920 is redescribed. In the process a new species of alderfly Leptosialis necopinata sp. n. from the Eastern Cape and KwaZulu-Natal provinces of South Africa is recognised and described. Within Sialidae the new species most closely resembles Leptosialis africana. A key to the two species of Leptosialis using both adult and larval characters is provided.
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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.
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