Genome Downloaded from www.nrcresearchpress.com by Det Kongelige Bibliotek: Nationalbibliotek og Kbenhavns Universitetsbibliotek on 11/27/17 For personal use only.
978
timated. The availability of vouchered specimens from this study will be critical in linking all new and unclear BIN clusters to species and new descriptions. Therefore, this SEAKEYS DNA barcoding project will contribute towards the estimation of marine biodiversity in South Africa.
Barcode of wildlife project Kenya: role of biorepositories and DNA barcode reference library in wildlife crime prosecution Ann N. Mwaura and Beatrice N. Khayota Centre for Biodiversity, National Museums of Kenya, Kenya. Corresponding author: Ann N. Mwaura (email:
[email protected]).
Background: Kenya is a partner country in the Barcode of Wildlife Project (BWP). The Barcode of Wildlife Project Kenya (BWPK) aimed to construct a barcode reference library of endangered flora and fauna for law enforcement in wildlife crime, with National Museums of Kenya (NMK) and the Kenya Wildlife Service (KWS) as lead institutions. NMK is a repository of live and voucher plant and animal specimens, while KWS is the enforcement and management agency. BWPK selected 200 priority species of national importance and conservation concern (frequently encountered in court cases and protected by law), CITES-listed and look-alike species. Specimens were sourced from existing repositories, botanic gardens, private collections, and from nature. Results: Training in DNA barcoding chain analysis was undertaken; Standard operating procedures (SOPs) for field collection and laboratory analysis were developed. Over 1000 “barcodes” have been generated and submitted to GenBank. Plant voucher specimens for these barcodes are deposited in East Africa Herbarium and NMK Botanic Garden. Animal e-vouchers and vouchers for small mammals, fish, reptiles, invertebrates, birds and amphibians are deposited in respective collections at NMK. These voucher specimens can be revisited in case of doubt on viability of reference library. They also serve as reference points for identification of exhibits. Sub-sampled tissues and genomic DNA are maintained at NMK. Significance: Identification of wildlife exhibits and verification based on the created barcode reference library were successful. The expert evidence generated is being used in Kenyan courts for wildlife crime prosecution, and two convictions have been secured. More exhibits are undergoing identification and this will lead to more convictions. Increasing sequences on Kenyan wildlife is vital in the development of a reference library of species in wildlife crime, with enhanced capacity to use DNA-based methods to combat wildlife crime in Kenya.
Developing DNA barcode reference library for aphid species in Pakistan Muhammad T.D. Naseem1 and Muhammad D. Ashfaq2 1Agriculture
Entomology, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan. 2Centre for Biodiversity Genomics, University of Guelph, Guelph, ON N1G 2W1, Canada. Corresponding author: Muhammad T.D. Naseem (email:
[email protected]).
Background: Aphids (Hemiptera: Aphididae) are important crop pests and disease vectors, but their correct identification to species is a challenge. Sequence variation in the mitochondrial cytochrome c oxidase I (COI-5=) (DNA barcode) gene has proved effective for the identification of insect species. The success of DNA barcoding for species identification relies on the availability of reference barcode libraries, which are lacking for the aphid fauna of Pakistan. Results: This study employed morphology to identify 809 aphids collected in Pakistan and analyzed their DNA barcodes to validate species identification and develop a reference library. The sequences were submitted to the Barcode of Life Data System (BOLD), where they were assigned to Barcode Index Numbers (BINs), species proxies. Morphology identified 743 aphids to 40 species, while the other 66 could be assigned only to the genus or the family (Aphididae). Three species (Periphyllus lyropictus, Aphis nasturtii, Aphis astragalina) were found for the first time in Pakistan. The BIN system assigned the 809 sequences to 52 BINs, that
Genome Vol. 60, 2017
were supported by neighbour-joining analysis and Bayesian inference. Conspecific barcode distances ranged from 0% to 10.2% (mean=0.2%), while congeneric ranged from 0.4% to 10.3% (mean=7.3%). Analysis suggested that specimens with >3.0% intraspecific divergence actually involved a species complex. In fact, sequences for three major pests (Aphis gossypii, Sitobion avenae, and Aphis craccivora) showed deep intraspecific divergences, pointing towards existence of cryptic species complexes. Haplotype analysis including global barcode data for seven virusvector aphid species (Acyrthosiphon pisum, Aphis spiraecola, A. gossypii, Myzus persicae, Rhopalosiphum maidis, Rhopalosiphum padi, S. avenae) showed a significant genetic variation among regional populations. Significance: The study compiles the first DNA barcode reference library for the aphids of Pakistan, providing means for sequencebased species identification of regional aphid fauna. Haplotype analysis of virus-vector species at a global scale has significance for understanding disease spread by aphid genotypes.
Resolving taxonomic ambiguity and cryptic speciation of species of Hypotrigona through morphometrics and DNA barcoding Nelly N. Ndungu,1 Nkoba Kiatoko,1 Catherine L. Sole,2 Christian W. Pirk,2 Yusuf A. Abdullahi,2 Suresh K. Raina,1 and Daniel K. Masiga3 1African
Reference Laboratory for Bee Health, International Centre for Insect Physiology and Ecology (icipe), Kenya. of Zoology and Entomology University of Pretoria, University of Pretoria, South Africa. 3Molecular Biology and Bioinformatics Unit, International Centre for Insect Physiology and Ecology (icipe), Kenya. Corresponding author: Nelly N. Ndungu (email:
[email protected]). 2Department
Background: Stingless bees are important pollinators of cultivated and wild plants, contributing significantly to biodiversity and food security. Understanding pollinator–plant interactions is essential to secure these ecosystems services. The use of morphological features in the identification of stingless bees in the genus Hypotrigona is extremely difficult due to many similarities among species resulting in taxonomic ambiguity. Here, we apply both traditional morphometrics and DNA barcoding as complementary tools for the identification of three species of Hypotrigona: Hypotrigona gribodoi, H. ruspolii, and H. araujoi. Results: Our results show that morphometrics separates H. gribodoi and H. ruspolii from H. araujoi; however, there is an overlap between H. gribodoi and H. ruspolii. On the other hand, DNA barcoding separates the three species reliably and consistently. However, there is lower genetic divergence between H. araujoi and H. gribodoi from Kakamega (1.4%) than between H. gribodoi collected from Kakamega and H. gribodoi from Mwingi (4.3%). The low genetic distance between H. araujoi and H. gribodoi suggests hybridization, while the high intraspecific distance in H. gribodoi strongly suggests cryptic speciation within this species. Significance: The combined use of morphometrics and molecular taxonomic approaches (DNA barcoding) provides a convenient, robust, and reliable way to identify species of Hypotrigona. The high intraspecific divergence highlights the need for a thorough revision of H. gribodoi.
Identification of stingless bees (Hymenoptera: Apidae) in Kenya using morphometrics and DNA barcoding Nelly N. Ndungu,1 Nkoba Kiatoko,1 Marc Ciosi,2 Daisy Salifu,3 Damaris Nyansera,1 Daniel K. Masiga,4 and Suresh K. Raina1 1African
Reference Laboratory for Bee Health, International Centre for Insect Physiology and Ecology (icipe), Kenya. of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, United Kingdom. 3Biostatistics Unit, International Centre for Insect Physiology and Ecology (icipe), Kenya. 4Molecular Biology and Bioinformatics Unit, International Centre for Insect Physiology and Ecology (icipe), Kenya. Corresponding author: Nelly N. Ndungu (email:
[email protected]). 2Institute
Background: Stingless bees are important pollinators of wild plants and crops. The identity of stingless bee species in Africa has not been fully documented. The present study explored the utility of morphoPublished by NRC Research Press
