The use of COI barcodes for molecular identification of forensically important fly species in Germany

Boehme, Petra; Amendt, Jens; Zehner, Richard

doi:10.1007/s00436-011-2767-8

Cited by 80 publications

(49 citation statements)

References 23 publications

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“…Sin embargo algunos estudios sugieren que a pesar de que la región COI es sin duda de gran utilidad para la identificación de especies de importancia forense, no todas las especies se pueden identificar adecuadamente con este marcador (Wells y Williams, 2007;Harvey et al, 2008;Boehme et al, 2012). Por esta razón, otros genes (o fragmentos de genes), como la región ITS2, también han sido postulados como buenos marcadores (Nelson et al, 2008;.…”

Section: Discussionunclassified

ITS2 para la identificación de Califóridos (Diptera: Calliphoridae) de importancia forense en Colombia

2016

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RESUMENLa entomología forense es una disciplina que utiliza insectos para obtener información útil en la determinación del intervalo postmortem (IPM). Las moscas de la familia Calliphoridae son muy utilizadas en entomología forense, sin embargo, su identificación a nivel de especie puede dificultarse cuando el individuo se encuentra incompleto o en estadio inmaduro. En el presente trabajo, se evaluó el potencial de la región ITS2 del genoma nuclear para la identificación de especies de Calliphoridae en Colombia utilizando tres aproximaciones: comparando distancias genéticas utilizando la metodología de códigos de barra, haciendo una reconstrucción filogenética, y con enzimas de restricción (PCR-RFLPs). Se secuenciaron un total de 520 pb en 44 individuos pertenecientes a 16 especies. Se calcularon los valores de distancia intraespecífica e interespecíficas utilizando el modelo K2P. Los valores de distancia intraespecífica oscilaron entre 0 y 0,252 %, mientras que las distancias interespecíficas fluctuaron entre 3,6 y 18,9 %, evidenciándose que esta técnica puede ser utilizada como código de barras genético en la identificación de especies de la familia Calliphoridae. Tanto en los análisis de Neighbour-Joining como en los análisis bayesianos el 90 % de los géneros presentan una monofilia sustentada en probabilidad posterior de 0,89 a 1. En todos los casos la especie Blepharicnema splendens agrupa con el género Lucilia. Con base en las secuencias obtenidas se utilizó la aplicación NEBCutter para identificar cuatro enzimas de restricción las cuales se probaron en el laboratorio y se comprobó su utilidad para la identificación rápida de especies de Calliphoridae en Colombia.Palabras clave: códigos de barra genéticos, enzimas de restricción, intervalo post-mortem, genoma nuclear. ABSTRACTForensic entomology is a discipline that uses insects to obtain useful information for the determination of the postmortem interval (PMI). Flies of the family Calliphoridae are extensively used for this purpose, however, the identification of these flies can be difficult when the individual is not an adult or when it is incomplete. In the present work, we tested the utility of the ITS2 region of the nuclear genome for the identification of Calliphoridae species in Colombia using three approaches: comparing genetic distances using the barcoding methodology, with a phylogenetic reconstruction, and with PCR-RFLPs. We sequenced 520 bp in 44 individuals belonging to 16 species of califorids. Intraspecific and interspecific distance values were calculated using the K2P model. The intraspecific distance values ranged between 0 and 0.252 %, while the interspecific distance values ranged between 3.6 and 18.9 %, indicating that this gene can be used as a genetic barcode for the identification of species of the Calliphoridae family. Both the Neighbour-Joining and Bayesian analyses recovered 90 % of the genera as monophyletic, with pp values between 0.89 and 1. Blepharicnema splendens was always recovered within the Lucilia genera. Based on the o...

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Section: Discussionunclassified

ITS2 para la identificación de Califóridos (Diptera: Calliphoridae) de importancia forense en Colombia

2016

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“…Currently, molecular phylogenetic work based on a COI sequence gene has been extensively used (Jamnongluk et al 2003;Nakahara & Muraji 2008;Zhang et al 2010;Liu et al 2011) because of the high degree of nucleotide variation (Boehme et al 2011). Moreover, this sequence has been standardised for molecular identification in all animal species (Hebert et al 2003).…”

Section: Introductionmentioning

confidence: 98%

Molecular clock analysis on fiveBactroceraspecies flies (Diptera: Tephritidae) based on combination ofCOIandNADHsequences

et al. 2015

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This paper marks the first attempt at using the molecular clock analysis on five Malaysian Bactrocera species based on combined data of COI and ND1 to test the divergence times of species that infested 11 varieties of fruits and vegetables. A divergence tree was constructed to estimate the cryptic species among the five closely related Bactrocera species viz. B. (Bactrocera) and B. (Zeugodacus). Both subgenera evolved and diverged approximately 21.5933 million years ago (MYA). The particularly complex taxonomical status of the sister-species B. papayae and B. carambolae has been resolved using the divergence tree; the two separated from the others approximately 2.743 MYA, while B. papayae and B. carambolae distinctly diverged between 1.9619 and 2.2884 MYA. Additionally, Bactrocera dorsalis showed divergence at 4.1596 MYA and was distinctly separate from the B. papayae. Interestingly, the molecular clock results are congruent with the phylogenetic tree that was analysed using Maximum Parsimony and Bayesian Inference. Further, the taxonomical status and host utilisation of the five Bactrocera species were also briefly discussed, which indicated that B. cucurbitae (subgenus Zeugodacus) was infesting Cucurbitaceae and B. latifrons was infesting Solanaceaea, while B. dorsalis, B. carambolae and B. papaya were infesting a wide range of fruit species. Key message Divergence time of five Malaysian Bactroceran species is reported for the first time and found congruent with the results of phylogeny based on combined data of COI and ND1 markers using MP and Bayesian analyses. This finding could prove very crucial for resolving the most crucial taxonomic conflicts in Bactrocera classification, which is highly important initially in species identification for integrated pest management (IPM) programme.

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“…They are now both found in Australia, New Zealand, South Africa, large parts of Asia, Europe and North America (Waterhouse and Paramonov 1950, Rognes 1980, 1994, Norris 1990, Bishop 1991, 1995, Holloway 1991, Fischer 2000, Harvey et al 2003a, 2003b, 2008, Chen et al 2004, Heath and Bishop 2006, Park et al 2009, Liu et al 2011, Boehme et al 2012, GilArriortua et al 2013). They have each received intensive biological investigation, and it would benefit comparative studies if it could be confirmed that they are actually sister species.…”

Section: Introductionmentioning

confidence: 99%

“…The largest genus in the subfamily, Lucilia has received few quantitative phylogenetic studies (Aubertin 1933, Stevens and Wall 1996, 1997, Wells et al 2007, Park et al 2009, DeBry et al 2012, Sonet et al 2012), with research generally focusing on species of medical, veterinary or forensic interest in specific geographic regions (Stevens and Wall 2001, Chen et al 2004, Wallman et al 2005, Harvey et al 2008, Reibe et al 2009, Liu et al 2011, Boehme et al 2012, DeBry et al 2012, Nelson et al 2012, Sonet et al 2013). The most comprehensive revision of the genus was published by Aubertin (1933), who recognised 27 species.…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic radiation of the greenbottle flies (Diptera, Calliphoridae, Luciliinae)

Williams¹,

Lamb²,

Villet³

2016

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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. Analysis of a matrix of 14 morphological characters scored for adults of all genera and for most of the species included in the molecular analysis confirmed several of these findings. The different degrees of parasitism were phylogenetically clustered within this genus but did not form a graded series of evolutionary stages, and there was no particular relationship between feeding habits and biogeography. Because of the ubiquity of hybridization, introgression and incomplete lineage sorting in blow flies, we recommend that using a combination of mitochondrial and nuclear markers should be a procedural standard for medico-criminal forensic identifications of insects.

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The use of COI barcodes for molecular identification of forensically important fly species in Germany

Cited by 80 publications

References 23 publications

ITS2 para la identificación de Califóridos (Diptera: Calliphoridae) de importancia forense en Colombia

ITS2 para la identificación de Califóridos (Diptera: Calliphoridae) de importancia forense en Colombia

Molecular clock analysis on fiveBactroceraspecies flies (Diptera: Tephritidae) based on combination ofCOIandNADHsequences

Phylogenetic radiation of the greenbottle flies (Diptera, Calliphoridae, Luciliinae)

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