DNA barcoding of forensically important blow flies (Diptera: Calliphoridae) within the Western Cape of South Africa

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dc.contributor.advisorHeathfield, Laura
dc.contributor.advisorHeyns, Marise
dc.contributor.authorKulenkampff, Kyle Sieghard
dc.date.accessioned2020-05-06T12:05:01Z
dc.date.available2020-05-06T12:05:01Z
dc.date.issued2019
dc.date.updated2020-05-06T01:41:40Z
dc.description.abstractIn forensic entomology, determining species identity is a crucial step towards estimating post mortem interval. DNA barcoding can aid in the identification of unknown forensically relevant species, and this requires the comparison of DNA barcodes to reference data from known species. However, there is a lack of DNA barcode reference data of forensically relevant Calliphoridae species in the Western Cape (South Africa). DNA barcodes were generated for the COI and ITS2 markers for 41 forensically relevant Calliphoridae specimens, representing seven species from six localities in the Western Cape: Chrysomya albiceps (n = 3), Chrysomya chloropyga (n = 8), Chrysomya marginalis (n = 5), Chrysomya megacephala (n = 7), Hemipyrellia fernandica (n = 1), Lucilia cuprina (n = 8) and Lucilia sericata (n = 9). This data was combined with that from Cooke et al. (2018) (n = 40), and subjected to rigorous statistical and phylogenetic analyses. Phylogenetic analysis which combined data for both COI and ITS2 barcodes returned monophyletic clades for each species with increased support when compared to using each barcode individually. This combined dataset was able to discriminate between L. cuprina and L. sericata with full support (100% pP), which was not achieved previously. DNA barcodes were evaluated for intra- and inter-specific variance as well as haplotype patterning. No haplotype patterning was observed for either barcodes across sampled localities. Lastly, a single-blinded approach was used to assess the dataset, whereby DNA barcodes from ‘unknown’ specimens were correctly identified using this reference data. These identifications were more accurate than those using GenBank® or BOLD, highlighting the importance of using locally relevant reference data. This study has contributed new data pertaining to DNA barcodes for seven Calliphoridae species, which was previously scarce for the Western Cape, and this has directly contributed to an improvement in the accuracy of local species identification.
dc.identifier.apacitationKulenkampff, K. S. (2019). <i>DNA barcoding of forensically important blow flies (Diptera: Calliphoridae) within the Western Cape of South Africa</i>. (). ,Faculty of Health Sciences ,Department of Pathology. Retrieved from en_ZA
dc.identifier.chicagocitationKulenkampff, Kyle Sieghard. <i>"DNA barcoding of forensically important blow flies (Diptera: Calliphoridae) within the Western Cape of South Africa."</i> ., ,Faculty of Health Sciences ,Department of Pathology, 2019. en_ZA
dc.identifier.citationKulenkampff, K.S. 2019. DNA barcoding of forensically important blow flies (Diptera: Calliphoridae) within the Western Cape of South Africa. . ,Faculty of Health Sciences ,Department of Pathology. en_ZA
dc.identifier.ris TY - Thesis / Dissertation AU - Kulenkampff, Kyle Sieghard AB - In forensic entomology, determining species identity is a crucial step towards estimating post mortem interval. DNA barcoding can aid in the identification of unknown forensically relevant species, and this requires the comparison of DNA barcodes to reference data from known species. However, there is a lack of DNA barcode reference data of forensically relevant Calliphoridae species in the Western Cape (South Africa). DNA barcodes were generated for the COI and ITS2 markers for 41 forensically relevant Calliphoridae specimens, representing seven species from six localities in the Western Cape: Chrysomya albiceps (n = 3), Chrysomya chloropyga (n = 8), Chrysomya marginalis (n = 5), Chrysomya megacephala (n = 7), Hemipyrellia fernandica (n = 1), Lucilia cuprina (n = 8) and Lucilia sericata (n = 9). This data was combined with that from Cooke et al. (2018) (n = 40), and subjected to rigorous statistical and phylogenetic analyses. Phylogenetic analysis which combined data for both COI and ITS2 barcodes returned monophyletic clades for each species with increased support when compared to using each barcode individually. This combined dataset was able to discriminate between L. cuprina and L. sericata with full support (100% pP), which was not achieved previously. DNA barcodes were evaluated for intra- and inter-specific variance as well as haplotype patterning. No haplotype patterning was observed for either barcodes across sampled localities. Lastly, a single-blinded approach was used to assess the dataset, whereby DNA barcodes from ‘unknown’ specimens were correctly identified using this reference data. These identifications were more accurate than those using GenBank® or BOLD, highlighting the importance of using locally relevant reference data. This study has contributed new data pertaining to DNA barcodes for seven Calliphoridae species, which was previously scarce for the Western Cape, and this has directly contributed to an improvement in the accuracy of local species identification. DA - 2019 DB - OpenUCT DP - University of Cape Town KW - Biomedical Forensic Science LK - https://open.uct.ac.za PY - 2019 T1 - DNA barcoding of forensically important blow flies (Diptera: Calliphoridae) within the Western Cape of South Africa TI - DNA barcoding of forensically important blow flies (Diptera: Calliphoridae) within the Western Cape of South Africa UR - ER - en_ZA
dc.identifier.urihttps://hdl.handle.net/11427/31810
dc.identifier.vancouvercitationKulenkampff KS. DNA barcoding of forensically important blow flies (Diptera: Calliphoridae) within the Western Cape of South Africa. []. ,Faculty of Health Sciences ,Department of Pathology, 2019 [cited yyyy month dd]. Available from: en_ZA
dc.language.rfc3066eng
dc.publisher.departmentDepartment of Pathology
dc.publisher.facultyFaculty of Health Sciences
dc.subjectBiomedical Forensic Science
dc.titleDNA barcoding of forensically important blow flies (Diptera: Calliphoridae) within the Western Cape of South Africa
dc.typeMaster Thesis
dc.type.qualificationlevelMasters
dc.type.qualificationnameMPhil
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