Small steps lead to big initiatives: Pakistan reaffirms support for iBOL by launching PakBOL

Small steps lead to big initiatives: Pakistan reaffirms support for iBOL by launching PakBOL

Small steps lead to big initiatives: Pakistan reaffirms support for iBOL by launching PakBOL

From economically important insect species to plants to food security, Pakistani researchers are working to barcode all life in their country through a national initiative - PakBOL.

PakBOL inauguration with Margaux McDonald, Canada’s Senior Trade Commissioner in Pakistan (left) and Dr. Ghazala Yasmin, Vice Chancellor of Women University Mardan.

PHOTO CREDIT: Hina Jabeen

With continued interest in documenting native biodiversity and cognizance about the applications of barcode data, the scientific community in Pakistan has reiterated its support for the iBOL Consortium and its new venture BIOSCAN by launching the national initiative, Pakistan Barcode of Life (PakBOL).

PakBOL launched in the presence of more than 120 scientists, academicians, students, and other stakeholders in biodiversity and pest management sciences who gathered in Islamabad for the 3rd international conference on “Empowering Nation through Science” organized by the Women University Mardan.

PakBOL attended by Pakistani representatives from 15 universities and several government and non-government organizations
PHOTO CREDIT: Hina Jabeen

The two-day conference was attended by Pakistani representatives from 15 universities and several government and non-government organizations including Higher Education Commission, Directorate of Biodiversity, Ministry of Climate Change, Pakistan Agricultural Research Council, Pakistan Atomic Energy Commission, and Dairy Science Park.

International delegates were also in attendance, including the Canadian High Commission Islamabad, Oxford Brooks University (UK), International Foundation of Science (Sweden), Organization for Women in Science for Developing Countries (Italy), Centre for Biodiversity Genomics (Canada).

Pakistan has been an active member of iBOL since it joined the consortium in 2011, generating more than 50,000 barcode records. Over the last eight years, these efforts have provided coverage for 6,300 animal BINs (proxy for species) and 350 plant species.

Researchers sampling in the foothills of Kashmir, Pakistan.
PHOTO CREDIT: Muhammad Ashfaq

But the amount of barcode data generated so far pales in comparison with the species richness and size (882,000 km2) of the country. Most of the barcoding work in Pakistan has been carried out by a few labs with 99% of the generated data representing arthropods.

The very first barcoding project in Pakistan “Sequencing DNA barcodes of economically important insect species of Pakistan” conducted jointly by the National Institute for Biotechnology and Genetic Engineering, Pakistan, and the University of Guelph, Canada, successfully introduced DNA barcoding to the country producing 5,000 barcodes within the first year of its launch (2010 – 2012).

Although the resources available for the project were inadequate for large-scale barcode coverage of the country’s arthropod fauna, the project helped to create understanding among local researchers about barcoding science. The subsequent financial support from the International Development Research Centre (IDRC), through the University of Guelph, helped Pakistani researchers expand barcoding activities in the country, generate barcode data from other organisms including plants, and develop national networking opportunities. This helped Pakistan become a National Node in iBOL’s first research program BARCODE 500K and contributed to the documentation of biodiversity on the planet.

With continued interest in DNA barcoding research, Pakistan has formally joined as a member nation of the iBOL Consortium to participate in its global initiative – BIOSCAN. Pakistan is already participating in the Global Malaise Program led by the Centre for Biodiversity Genomics in Guelph and, with the launch of BIOSCAN, it plans to expand this program to all the ecoregions in the country. 

Participating in the Global Malaise Program from Lahore, Pakistan.
PHOTO CREDIT: Shahbaz Ahmad 

Balochistan University of Information Technology, Engineering and Management Sciences (BUITEMS), Quetta is leading the efforts to organize a network of universities and research organizations; their aim is to promote and strengthen barcoding research in Pakistan to achieve the goal of documenting all fauna and flora in the country.

Several universities in Pakistan, including BUITEMS, the University of Sargodha, GC University Lahore, University of Swat, University of Sindh Jamshoro, GC University Faisalabad, University of Rawalakot Azad Kashmir, Punjab University Lahore, LCWU Lahore, and Quaid-e-Azam University Islamabad have been involved in barcoding research but lack a common platform to coordinate barcoding activities. PakBOL will provide that platform to the barcoding community in Pakistan to coordinate efforts to achieve their common goal.

An initiative taken eight years ago with a small project on barcoding pest insects has now expanded to a national effort with a much broader goal – barcoding all life in Pakistan. And PakBOL aims to achieve just that!

Read more about Pakistan:

DNA BARCODING WILD FLORA IN PAKISTAN’S FORESTS

Preserving voucher specimens and creating a virtual herbarium to understand and protect some of the oldest living trees on the planet.

UNIVERSITY OF SINDH JAMSHORO BARCODES GRASSHOPPERS IN PAKISTAN’S THAR DESERT

Tracking the shift of non-pests to crop pests, a phenomenon accelerated by anthropogenic pressures in the Thar Desert.

Written by

Muhammad Ashfaq

Muhammad Ashfaq

Centre for Biodiversity Genomics, University of Guelph

June 10, 2019

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University of Sindh Jamshoro Barcodes Grasshoppers in Pakistan’s Thar Desert

University of Sindh Jamshoro Barcodes Grasshoppers in Pakistan’s Thar Desert

University of Sindh Jamshoro Barcodes Grasshoppers in Pakistan’s Thar Desert

Tracking the shift of non-pests to crop pests, a phenomenon accelerated by anthropogenic pressures in the Thar Desert.
The Thar Desert is considered the seventh largest desert in the world and the third largest in Asia. Although this desert is rich in unique biodiversity, efforts to explore and analyze its fauna and flora have been minimal. The desert harbours some important crop pests, particularly orthopterans, by providing them alternate host plants, overwintering space, and environments for reproduction. The region provides favourable soil and environmental conditions for the survival of Acridids (grasshoppers and locusts). In particular, it supports the reproduction, development, and outbreak of the desert locust; the gregarious phase of locusts results in attacks on neighbouring regions that cause severe loss to crops and forests.

Cattle grazing in the Thar region.
Photo credit: Ahmed Ali Samejo

Around 20,000 orthopterans have been described in the world including 1,750 from India, but the number of known species in Pakistan is merely 161. Our recent surveys of the Thar region have revealed 29 species of grasshoppers that are new to the country indicating the rich grasshopper diversity of this desert.

With expanding agricultural fields, overgrazing and desertification, and changing ecological conditions, biodiversity is also changing. These changes are pushing non-pests to become crop pests, a phenomenon that warrants further investigation using reliable identification methods. An effective, preventive management strategy of these pests relies on an improved knowledge of their biology and ecology, and on more efficient monitoring and control techniques. The Department of Zoology at the University of Sindh Jamshoro has taken initiative to document and understand the grasshopper fauna in the Thar Desert by coupling DNA barcoding with conventional taxonomy.

Field surveys in the Thar Desert with Kumar, Riffat, & Samejo (left to right).
PHOTO CREDIT: Ahmed Ali Samejo

With funding support from the Higher Education Commission (HEC) Pakistan, the department plans to develop a DNA barcode reference library for grasshoppers in the Thar Desert of Pakistan. Grasshopper collection and specimen identification is already in progress and, so far, 2,334 specimens have been identified to 22 species while the identity of 300 specimens is yet to be resolved. After the front-end processing (data-basing, imaging, tissue sampling) at the University of Sindh Jamshoro is complete, the identified specimens will be barcoded at the Centre for Biodiversity Genomics, University of Guelph.

This is the first effort towards understanding grasshopper diversity in the Thar using DNA methods and developing a reliable reference library for this important group of pest insects. The generated data will not only be used for the rapid identification of grasshoppers and locusts, it will also provide a useful tool for pest management and biodiversity conservation.

Written by

Riffat Sultana

Riffat Sultana

Department of Zoology, University of Sindh Jamshoro, Pakistan

April 7, 2019
PDF
https://doi.org/10.21083/ibol.v9i1.5491

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Read more about Pakistan:

SMALL STEPS LEAD TO BIG INITIATIVES: PAKISTAN REAFFIRMS SUPPORT FOR IBOL BY LAUNCHING PAKBOL

From economically important insect species to plants to food security, Pakistani researchers are working to barcode all life in their country through a national initiative – PakBOL.

DNA BARCODING WILD FLORA IN PAKISTAN’S FORESTS

Preserving voucher specimens and creating a virtual herbarium to understand and protect some of the oldest living trees on the planet.

Don't Miss Out!

Subscribe to the iBOL Barcode Bulletin for updates on DNA barcoding efforts, the iBOL Consortium, and more.

A DNA Barcoding Review of the Entomofauna of Egypt

A DNA Barcoding Review of the Entomofauna of Egypt

A DNA Barcoding Review of the Entomofauna of Egypt

From insect diversity to pests to forensics, DNA barcoding plays a vital role in Egyptian biodiversity conservation and legislative protection efforts.
Egyptian hornet wasp (Vespa orientalis) predating on Dermaptera (Labidura sp.).
PHOTO CREDIT: Mohamed Gamal

Egypt has more than 23,587 identified plant and animal species in addition to thousands of algae, bacteria, and viruses1, and this unique biodiversity contributes to Egypt’s economy and supports the welfare of its citizens. Agricultural production accounts for more than 10 per cent of Egypt’s GDP while tourism revenues from marine activities on the Red Sea represent more than 30 billion LE annually. Protecting threatened species such as dolphins, sharks, and dugong contribute by more than 61 million LE per year and the marine fish production is estimated to be worth 5 billion LE2. Therefore, Egypt has paid particular attention to the conservation and legislative protection of its natural heritage.

Joining its International Barcode of Life (iBOL) partners, Egypt has been using DNA barcoding to better understand and plan for protection of biodiversity. So far, Egypt has published 20,980 DNA barcode sequence records, 25 per cent (5,368) of which have species names that represent 695 species.

In this review, we present an overview of the DNA barcoding carried out on the Egyptian entomofauna and introduce current advances of this promising technique. This review focuses on three main areas that highlight studies investigating insect diversity and distribution, insects in forensic applications as well as pest and parasite dynamics.

Insect diversity and distribution: DNA barcoding has been used to investigate the genetic diversity of Egyptian wasp populations with a wide geographical range3. Three species, Vespa orientalis, Polistes bucharensis, and Polistes mongolicus were accurately identified by their DNA barcodes with the COI phylogenetic signal revealing interesting insights across Jordan, Giza, Cyprus, and Greece. Despite the wide geographical range, only minor genetic diversity was observed among populations of the three wasp species, indicating unrestricted gene flow. 

DNA barcoding has also been used in a larger-scale insect diversity investigation in the understudied Saharo-Arabian zoogeographic region, revealing significant heterogeneity between Egypt, Pakistan, and Saudi Arabia4. The year-long deployment of Malaise traps in these countries collected 53,092 specimens, including 18,391 from Egypt. The DNA barcode sequences revealed the occurrence of 3,682 BINs belonging to 254 families. These results reflect the high species richness of the area, encouraging further research into biodiversity monitoring for the region.

Insects in forensic applications: The Egyptian Forensic Medicine Authority, the leading authority on forensic medicine in Egypt, handles a relatively large number of cases annually and relies on laboratories for assistance with molecular techniques to ensure fast and reliable identification of species of forensic interest (e.g. necrophagous insects). To date, few studies in Egypt have evaluated the use of DNA barcoding in the identification and establishment of reference libraries for insect species of important post-mortem interval indication.

PHOTO CREDIT: Samy Zalat

Egyptian records of blow flies (Calliphoridae). Maggots (larva) are scavengers and adults are plant visitors.

PHOTO CREDIT: Ramadan Mounir

Aly & Wen5 studied the applicability of a 296-bp cytochrome c oxidase I (COI) sequence as a reliable mitochondrial genetic marker for the identification of forensically important flies following previous research showing the efficacy of a short COI marker in this group6. The study analyzed 16 species of blowflies (Calliphoridae), flesh flies (Sarcophagidae), and house flies (Muscidae) originating from Egypt and China and concluded that a shorter COI fragment is simple, cheap, and reproducible but lacks agreement with traditional morphological classification. In a follow-up investigation, Aly7 examined the reliability of long (1173-bp) vs. short (272-bp) COI markers for 18 species of the same 3 dipteran families from Egypt and China. The results indicated that the longer COI marker performed better than the shorter marker for dipterous identification due to better monophyletic separation and concordance with taxonomic classifications.

A more in-depth survey of the genetic diversity of forensically important blowflies (Calliphoridae) revealed numerous haplotypes among 158 specimens collected from four locations in Egypt (Giza, Dayrout, Minya, and North Sinai)8. Three particularly important species (Chrysomya albiceps, Chrysomya , Chrysomya marginalis) were well-differentiated using COI supporting its use for subfamily-, genera-, and species-level identification of blowflies.

Most importantly for forensics use, COI is highly effective at identifying different developmental stages of forensically important flies, including larvae, pupae, and even empty, otherwise difficult to identify morphologically. Five different species of Diptera and their immature stages from Alexandria, Egypt including Chrysomya albiceps, Chrysomya megacephala, Calliphora vicina, Lucilia sericata, and Ophyra capensis, were correctly identified using mitochondrial DNA markers9.

Pest and parasite dynamics: DNA barcoding has also played an important role in the identification of pests and parasites. Seventeen species of mealybug pests (Hemiptera: Pseudococcidae) have been identified by DNA barcoding specimens collected from populations infesting various crops and ornamental plants in Egypt and France10. The genetic variation found between populations of the same species using a combination of three markers (28S-D2, COI, and ITS2) and morphological examination indicated cryptic taxa that might respond differently to management strategies.

High diversity and rapid diversification were found in the head louse, Pediculus humanus (Pediculidae: Phthiraptera)11. P. humanus includes two morphologically indistinguishable subspecies: the head louse, P. humanus and the body louse, P. humanus. By analyzing sequence diversity of two mitochondrial genes (COI, cytb) in 837 specimens of Pediculus humanus from Egypt, Pakistan, and South Africa, high diversity and the occurrence of five mitochondrial lineages was revealed with implications for the spread of disease.

Conclusion: DNA barcoding of crop pests and pollinators, in addition to disease-carrying insect-vectors, will continue to be the top priority for the Egyptian government. Egypt actively enacts laws, carries out research, increases public awareness, engages local communities in the management of protected areas, and implements projects funded by Egypt and other international donors to protect biodiversity. These motivations place Egypt in a valuable position among other countries joining iBOL in support of BIOSCAN, a project that will build a global monitoring system for the planet.

References:

1. Egypt’s Fifth Biodiversity National Report (2014). Ministry of Environmental Affairs, Cairo, Egypt.

2. Coastal and marine biodiversity in Egypt (2018). United Nations Convention on Biological Diversity Conference (CBD COP14), Sharm El Sheikh. Ministry of Environment.

3. Abdel-Samie E, ElKafrawy I, Osama M, Ageez A (2018) Molecular phylogeny and identification of the Egyptian wasps (Hymenoptera: Vespidae) based on COI mitochondrial gene sequences. Egyptian Journal of Biological Pest Control. 28: 36. https://doi.org/10.1186/s41938-018-0038-z

4. Ashfaq M, Sabir JSM, El-Ansary HO, Perez K, Levesque-Beaudin V, Khan AM, Rasool A, Gallant C, Addesi Jo, Hebert PDN (2018) Insect diversity in the Saharo-Arabian region: revealing a little-studied fauna by DNA barcoding. PLoS ONE 13(7). https://doi.org/10.1371/journal.pone.0199965

5. Aly SM, Wen J (2013) Molecular identification of forensically relevant Diptera inferred from short mitochondrial genetic marker. Libyan Journal of Medicine 8:10. https://doi.org/10.3402/ljm.v8i0.20954

6. Zehner R, Amendt J, Schutt S, Sauer J, Krettek R, Povolny D. (2004) Genetic identification of forensically important flesh flies (Diptera: Sarcophagidae). International Journal of Legal Medicine 118(4): 245–247. https://doi.org/10.1007/s00414-004-0445-4

7. Aly SM (2014) Reliability of long vs short COI markers in identification of forensically important flies. Croatian Medical Journal. 55(1): 19–26. https://doi.org/10.3325/cmj.2014.55.19

8. Salem A, Adham F, Picard C (2015) Survey of the genetic diversity of forensically important Chrysomya (Diptera: Calliphoridae). Journal of Medical Entomology 52(3):320–328. https://doi.org/10.1093/jme/tjv013

9. Abdel Ghaffar HA, Moftah MZ, Favereaux A, Swidan M, Shalaby O, El Ramah S, Gamal R (2018) Mitochondrial DNA-based identification of developmental stages and empty puparia of forensically important flies (Diptera) in Egypt. Journal of Forensic Science & Medicine 4(3): 129–134. http://www.jfsmonline.com/text.asp?2018/4/3/129/242508

10. Abd-Rabou S, Shalaby H, Germain J, Ris N (2012) Identification of mealybut pest species (Hemiptera: Pseudococcidae) in Egypt and France, using a DNA barcoding approach. Bulletin of Entomological Research 102(5):515–523. https://doi.org/10.1017/S0007485312000041

11. Ashfaq M, Prosser S, Nasir S, Masood M, Ratnasingham S, Hebert PDN (2015) High diversity and rapid diversification in the head louse, Pediculus humanus (Pediculidae: Phthiraptera). Scientific Reports, 14188. https://doi.org/10.1038/srep14188

 

 

 

 

 

 

 

 

 

 

 

Written by

Samy Zalat

Samy Zalat

Zoology Department, Faculty of Science, Suez Canal University, Ismailia, Egypt.

Mona Mahmoud

Mona Mahmoud

Nature & Science Foundation, Cairo, Egypt.

April 7, 2019
PDF
https://doi.org/10.21083/ibol.v9i1.5515

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