DNA barcoding of forensically important flies in the Western Cape, South Africa

Genome ◽  
2018 ◽  
Vol 61 (12) ◽  
pp. 823-828 ◽  
Author(s):  
Tenielle Cooke ◽  
Kyle Kulenkampff ◽  
Marise Heyns ◽  
Laura Jane Heathfield
Keyword(s):  
South Africa ◽  
Dna Barcoding ◽  
Dna Sequences ◽  
The Body ◽  
Western Cape ◽  
Accurate Identification ◽  
Intraspecific Divergence ◽  
Post Mortem Interval ◽  
Interspecific Divergence

Forensic entomology aids the determination of post mortem interval based on arthropods associated with a deceased body. This relies on the accurate identification of insects that visit the body, particularly first colonisers such as Calliphoridae (Diptera). Traditional species identification though morphological keys can be challenging as immature or closely related specimens can look similar. Some of these challenges have been overcome through “DNA barcoding”, which involves the sequencing of informative regions within a species’ DNA and comparison to a database of reference sequences. However, reference DNA sequences of blow fly species in South Africa is currently limited. In this study, adult blow flies representing four species common to the Western Cape, South Africa (Chrysomya chloropyga, Chrysomya albiceps, Chrysomya marginalis, Lucilia sericata) were examined using morphological keys and DNA barcoding of two regions: COI and ITS2. These DNA sequences were then used as references for the successful identification of seven unknown immature specimens. Intraspecific divergence showed a maximum of 0.36% and 2.25% for COI and ITS2, respectively; interspecific divergence showed a minimum of 6.14% and 64.6% for COI and ITS2, respectively. According to these results, COI and ITS2 have sufficient discriminatory power for species-level identification for the four species studied.

The use of human resource information systems in two retail organisations in the Western Cape, South Africa

2017 ◽  
Vol 1 (2) ◽  
Author(s):  
Emmanuel Udekwe ◽  
Andre C. De la Harpe
Keyword(s):  
South Africa ◽  
Information Systems ◽  
Human Resources ◽  
Human Resource ◽  
The Body ◽  
Retail Industry ◽  
Successful Implementation ◽  
Western Cape ◽  
Report Generation ◽  
Resource Information

Orientation: The retail industry is the largest contributor to employment and the gross domestic product (GDP) in the Western Cape, South Africa. The management of human resources in this very competitive industry is a high priority for all retailers. The successful implementation, maintenance and use of human resource information systems (HRISs) are an integral part of many retailers.Research purpose: Human resource information systems are difficult to implement and maintain, and as a result, organisations cannot effectively utilise these systems to their benefit. The purpose of this paper is to explore the factors affecting the implementation, maintenance and use of HRISs in two retail organisations in the Western Cape.Motivation of study: Many retailers find it difficult to apply and utilise HRISs to their benefit and to the systems’ full potential. This study explores the challenges retailers are facing when implementing, maintaining and using HRISs.Research design, approach and method: Multiple case studies were used to conduct the research. Data were collected through a semi-structured questionnaire using interviews. Twenty-one interviews were conducted in the two retail companies to gain an understanding of the use of HRISs within these organisations. The data were analysed using a thematic method of analysis. The units of analysis were the Human Resources and the Information Technology departments of both companies. The units of observation were (21) purposively selected employees in the two mentioned departments of both retail organisations.Main findings: This research shows an under-utilisation of the HRIS in both companies as a result of poor data quality, lack of adequate training and the high cost of implementing and maintaining the system. There is a gap in terms of data analytics and report generation. This gap leads to the under-utilisation of the HRISs preventing the retailers to optimise the benefits of the HRIS.Practical and managerial implications: For organisations to reap benefits from HRISs, a change management strategy and a rigorous training programme are needed that will focus on the implemented maintenance and improved usage of these systems.Contribution: The contribution of the study includes proposed guidelines for the effective and efficient use of HRISs. The study further contributes to the body of knowledge in shedding light on the implementation, maintenance and use of HRISs in the retail industry in the Western Cape, South Africa.

Steinernema citrae n. sp. (Rhabditida: Steinernematidae), a new entomopathogenic nematode from South Africa

Nematology ◽  
2011 ◽  
Vol 13 (5) ◽  
pp. 569-587 ◽  
Author(s):  
Nomakholwa F. Stokwe ◽  
Antoinette P. Malan ◽  
Khuong B. Nguyen ◽  
Rinus Knoetze ◽  
Louwrens Tiedt
Keyword(s):  
South Africa ◽  
New Species ◽  
Body Length ◽  
Entomopathogenic Nematode ◽  
Tail Length ◽  
Morphological Characters ◽  
The Body ◽  
Infective Juvenile ◽  
Western Cape ◽  
Citrus Orchards

Abstract During a survey for entomopathogenic nematodes in citrus orchards throughout South Africa, a new species of Steinernema was isolated from a citrus orchard on Rietkloof farm, near the town of Piketberg in the Western Cape Province, South Africa. The nematode was isolated from soil using the Galleria-baiting technique. Steinernema citrae n. sp. is characterised by the following morphological characters: third-stage infective juvenile with a body length of 754 (623-849) μm, distance from head to excretory pore of 56 (49-64) μm, tail length of 71 (63-81) μm, and ratio E value of 110 (85-132). The lateral pattern for the new species is 2, 7, 8, 6, 4, 2 and is not typical for the genus. Steinernema citrae n. sp. is closely related the feltiae-group. The body length of the IJ is close to that of S. texanum and S. weiseri, though it differs in body diam., the length of the pharynx and E%. The male of S. citrae n. sp. differs from S. feltiae in the length and shape of the spicule and body diam. Steinernema citrae n. sp. differs from all species in the feltiae-group in the morphology of the vulva, as it has a single flapped, low, epiptygma. It also differs from the most closely related species, S. feltiae, as there is no interbreeding between the two species. In addition, the new nematode differs from other species of the feltiae-group by characteristics of the ITS and D2D3 regions of its rDNA.

Morphology and DNA barcodes reveal the presence of the non-native land planarian Obama marmorata (Platyhelminthes : Geoplanidae) in Europe

2015 ◽  
Vol 29 (1) ◽  
pp. 12 ◽  
Author(s):  
Domingo Lago-Barcia ◽  
Fernando A. Fernández-Álvarez ◽  
Lisandro Negrete ◽  
Francisco Brusa ◽  
Cristina Damborenea ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Geographic Origin ◽  
Original Description ◽  
Neotropical Region ◽  
Morphological Evidence ◽  
Intraspecific Divergence ◽  
Interspecific Divergence ◽  
Allochthonous Species ◽  
First Time ◽  
Land Planarian

We report for the first time the occurrence of Obama marmorata in the Iberian Peninsula as an introduced species from the Neotropical Region. The species is also reported for the first time in Argentina. The identification was made on the basis of morphological evidence. The divergence levels of a fragment of the mitochondrial cytochromec oxidaseI gene from Argentinean and Iberian samples were studied. The morphology of samples from the two regions was the same and matched the original description of the species. A DNA barcoding matrix was constructed using new sequences from O. marmorata and sequences of related species taken from GenBank. Among the Geoplanidae, interspecific divergence ranged between 3.3 and 14.4%, while intraspecific divergence percentages were 0–1.2%, signalling the presence of a DNA barcoding gap. All O. marmorata sequences, irrespective of their geographic origin, form a well supported clade with an intraspecific divergence of 0–0.9 (average = 0.4%). These results indicate the utility of DNA barcoding to discover allochthonous species in this group of organisms.

Use of entomotoxicology in estimating post-mortem interval and determining cause of death

2017 ◽  
Vol 295 ◽  
pp. 56-63
Author(s):  
Joanna Stojak ◽  
Keyword(s):  
Cause Of Death ◽  
Current Knowledge ◽  
The Body ◽  
Toxic Substances ◽  
Post Mortem ◽  
Toxicological Analysis ◽  
Post Mortem Interval ◽  
The Impact

Entomotoxicology allows the estimation of the post-mortem interval and the determination of the cause of death in cases in which the corpse has decomposed and the tissues necessary for toxicological analysis are no longer available. Obtaining information about toxic substances potentially present in the body is possible by isolation of larvae and pupae of true flies (Diptera) and/or adult forms of, e.g., beetles (Coleoptera) present on or near the corpse. This article was intended to summarize the current knowledge in the field of entomotoxicology, including examples from the literature, and to present the impact of selected toxic substances and medicines on the development of necrophagous larvae of insects.

scholarly journals Challenging species delimitation in Collembola: cryptic diversity among common springtails unveiled by DNA barcoding

2012 ◽  
Vol 26 (6) ◽  
pp. 470 ◽  
Author(s):  
D. Porco ◽  
A. Bedos ◽  
Penelope Greenslade ◽  
C. Janion ◽  
D. Skarżyński ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Functional Groups ◽  
Species Delimitation ◽  
Sequence Divergence ◽  
Cryptic Diversity ◽  
Congeneric Species ◽  
Nuclear Marker ◽  
Accurate Identification ◽  
Intraspecific Divergence

Collembola is one of the major functional groups in soil as well as a model taxon in numerous disciplines. Therefore the accurate identification of specimens is critical, but could be jeopardised by cases of cryptic diversity. Several populations of six well characterised species of springtails were sequenced using the COI barcode fragment as a contribution to the global Collembola barcoding campaign. Each species showed high intraspecific divergence, comparable to interspecific sequence divergence values observed in previous studies and in 10 congeneric species barcoded here as a reference. The nuclear marker, 28S, confirmed all the intraspecific lineages found with COI, supporting the potential specific status of these entities. The implications of this finding for taxonomy and for disciplines relying on species names, such as evolution and ecology, are discussed.

scholarly journals Identifying Chinese species of Gammarus (Crustacea: Amphipoda) using DNA barcoding

2009 ◽  
Vol 55 (2) ◽  
pp. 158-164 ◽  
Author(s):  
Zhong-e Hou ◽  
Zhu Li ◽  
Shu-qiang Li
Keyword(s):  
Cryptic Species ◽  
Dna Barcoding ◽  
Cytochrome C Oxidase ◽  
Neighbor Joining ◽  
Cytochrome C Oxidase I ◽  
Widespread Species ◽  
Intraspecific Divergence ◽  
Gammarus Lacustris ◽  
Interspecific Divergence ◽  
Identification Of Species

Abstract Using a standard cytochrome c oxidase I sequence, DNA barcoding has been shown to be effective to distinguish known species and to discover cryptic species. Here we assessed the efficiency of DNA barcoding for the amphipod genus Gammarus from China. The maximum intraspecific divergence for widespread species, Gammarus lacustris, was 3.5%, and mean interspecific divergence reached 21. 9%. We presented a conservative benchmark for determining provisional species using maximum intraspecific divergence of Gammarus lacustris. Thirty-one species possessed distinct barcode clusters. Two species were comprised of highly divergent clades with strong neighbor-joining bootstrap values, and likely indicated the presence of cryptic species. Although DNA barcoding is effective, future identification of species of Gammarus should incorporate DNA barcoding and morphological detection.

scholarly journals DNA barcoding reveals the diversity of sharks in Guyana coastal markets

2017 ◽  
Vol 15 (4) ◽  
Author(s):  
Matthew A. Kolmann ◽  
Ahmed A. Elbassiouny ◽  
Elford A. Liverpool ◽  
Nathan R. Lovejoy
Keyword(s):  
Dna Barcoding ◽  
Accurate Determination ◽  
Total Sample ◽  
Artisanal Fishing ◽  
Species Identity ◽  
Sustainable Fisheries ◽  
International Union ◽  
Accurate Identification ◽  
Fundamental Challenge

ABSTRACT A fundamental challenge for both sustainable fisheries and biodiversity protection in the Neotropics is the accurate determination of species identity. The biodiversity of the coastal sharks of Guyana is poorly understood, but these species are subject to both artisanal fishing as well as harvesting by industrialized offshore fleets. To determine what species of sharks are frequently caught and consumed along the coastline of Guyana, we used DNA barcoding to identify market specimens. We sequenced the mitochondrial co1 gene for 132 samples collected from six markets, and compared our sequences to those available in the Barcode of Life Database (BOLD) and GenBank. Nearly 30% of the total sample diversity was represented by two species of Hammerhead Sharks (Sphyrna mokarran and S. lewini), both listed as Endangered by the International Union for Conservation of Nature (IUCN). Other significant portions of the samples included Sharpnose Sharks (23% - Rhizoprionodon spp.), considered Vulnerable in Brazilian waters due to unregulated gillnet fisheries, and the Smalltail Shark (17% - Carcharhinus porosus). We found that barcoding provides efficient and accurate identification of market specimens in Guyana, making this study the first in over thirty years to address Guyana’s coastal shark biodiversity.

Steinernema jeffreyense n. sp. (Rhabditida: Steinernematidae), a new entomopathogenic nematode from South Africa

2015 ◽  
Vol 90 (3) ◽  
pp. 262-278 ◽  
Author(s):  
A.P. Malan ◽  
R. Knoetze ◽  
L.R. Tiedt
Keyword(s):  
South Africa ◽  
New Species ◽  
Dna Sequences ◽  
First Generation ◽  
Galleria Mellonella ◽  
Entomopathogenic Nematode ◽  
The Body ◽  
Its Rdna ◽  
28S Rdna ◽  
Cross Hybridization

AbstractDuring a non-targeted survey for entomopathogenic nematodes in South Africa, a new species of Steinernema was isolated from a soil sample collected from underneath a guava tree, close to the shore at Jeffrey's Bay. The nematode was isolated by means of the insect-baiting technique using last-instar larvae of Galleria mellonella. It is described herein as Steinernema jeffreyense n. sp. The nematode can be separated from other described, closely related species in terms of the morphological and morphometric characteristics of the different life stages, and in terms of the characterization and phylogeny of DNA sequences of the internal transcribed spacer (ITS) rDNA of the 18S gene, and of the D2D3 region of the 28S rDNA gene. The new species is placed molecularly in the arenarium–glaseri–karii–longicaudatum group characterized by the following morphological characters: infective third-stage juvenile with a body length of 926 (784–1043) μm, distance from head to excretory pore of 87 (78–107) μm, tail length of 81 (50–96) μm, with an E% of 109 (86–169), and eight evenly spaced ridges (i.e. nine lines) in the middle of the body. First-generation males have a spicule length of 88 (79–95) μm and gubernaculum length of 57 (51–61) μm. Male mucron is absent in both generations. First-generation females have an asymmetrical protuberance and a short, double-flapped epiptygmata, with both flaps directed to the front. The tail of the first-generation female is shorter than the anal body width, with a mucron on the dorsal tail tip, with D% = 78 (59–99). Cross-hybridization with S. khoisanae, S. tophus and S. innovationi showed the new species to isolate reproductively from the others. The analyses of ITS rDNA and D2D3 sequence of the 18S and 28S rDNA genes support the studied nematode isolate to be a valid new species belonging to the ‘glaseri’ group (Clade V).

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