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John James Wilson

Application of DNA barcodes


in Southeast Asia
10 15 million
animal species 1.4 million
animal species
described

2 2.5 million
animal species

1000 species
A segment of DNA unique to a species

DNA barcode
Hebert et al. 2003; Hebert et al. 2004; dnalc.org
International Barcode of Life

ibol.org
1. DNA barcoding is very technical?

Museum collections
Fieldwork
Sing, Syaripuddin, Wilson. 2016. Malayan Nature Journal

2. DNA barcoding is expensive?

US$0.03 US$0.71
US$0.31 US$5.86
Museum collections
Fieldwork
Wong et al. 2015. Bulletin of Entomological Research

3. Species recognised with DNA barcodes


are not real?

Barcode Index Numbers (BIN) provide


stable, persistent, interoperable identifiers
Wilson et al. 2016. Conservation Biology
DNA barcoding in TEA:
why not?
2003 Biological Identifications Using DNA Barcodes Barcoding workshop
2016
2005 1st BoL London Naresuan University, Thailand
2nd BoL Taipei 2017 7th BoL Kruger
2007
Indo-Malayan Birds (ABBI)
NUS, Singapore
FISHBOL workshop
DNA barcoding in
2009
USM, Penang, Malaysia Southeast Asia
3rd BoL Mexico City

2011 4th BoL Adelaide

Barcoding workshop/seminar/meeting
UM, Kuala Lumpur, Malaysia
2013
5th BoL Kunming

Asian Fish Biodiversity Conference


USM, Penang, Malaysia
Society Conservation Biologists (Asia)
2014 Melaka, Malaysia
DNA profiling and barcoding workshop
Forest Research Institute Malaysia
2015 6th BoL Guelph
Wilson et al. 2016. Conservation Biology
DNA barcoding in Tropical East Asia
Birds (Luczon et al. 2013) Crabs (Rosly et al. 2013)
Fishes (Mat Jafar et al. 2012) Parasitic wasps (Butcher et al. 2012)
Blackflies (Pramual et al. 2010) Earthworms (Bantoawong et al. 2011)
Bats (Lim et al. 2017) Butterflies (Wilson et al. 2013)
Applications of DNA barcodes in
Southeast Asia?

DNA barcoding of sites:


biodiversity inventory

DNA barcoding for monitoring and


assessments of target species
Zieritz et al. 2016. Science of the Total Environment

Inventory difficult species


Casas et al. 2017. Mitochondrial DNA A

Inventory difficult species

Mindanao

Barcoded of the
species of Odonata
Wilson et al. 2014. J Asia-Pacific Entomol; Jisming-See et al. 2016. Genome

Inventory difficult species


Jaturas et al. 2016. Mito DNA A; Sukantamala et al. 2016. Mito DNA A

Inventory important vectors


Muslimin et al. 2015. JVATTD; Moktar et al. 2016a., 2016b. J Med Ent

Inventory important parasites


Cigarette beetle

Clogmia albipunctatus

Brown
Widow
Spider
Rapid biodiversity inventory

Global Malaise Trap Program


biodiversitygenomics.net/projects/gmp/

Global Malaise Trap Program


Brandon-Mong et al. 2015. Bulletin of Entomological Research

Malaise trap metabarcoding


BULK DNA EXTRACT BULK PCR

ILLUMINA HTS
Brandon-Mong et al. 2015. Bulletin of Entomological Research

Malaise trap metabarcoding


Brandon-Mong et al. In Review. Bulletin of Entomological Research

Malaise trap metabarcoding


Urban Park
Reserve
Forest

Oil Palm Plantation


Wilson et al. In Review. Molecular Ecology Resources

Malaise trap metatranscriptomics?


Raw reads & BLAST Quality Filtering & Clustering

Malaysia
Syaripuddin, Sing, Wilson. 2015. Trop Con Sci; Wilson et al. 2015. BDJ

Non-lethal DNA sampling


Wilson et al. 2015. BDJ; Jisming-See, Sing, Wilson. 2016. Genome

Non-lethal DNA sampling


Syaripuddin et al. 2014. Ecotox; Wilson et al. 2014. Gen Mol Res

Non-lethal DNA sampling


When forests are flooded
toxic methylmercury enters
terrestrial food webs
Wilson et al. In review. Mitochondrial DNA A

Environmental DNA
Wilson et al. In review. Mitochondrial DNA A

Environmental DNA
Lee, Sing & Wilson. 2015. PLOS ONE; Lee et al. 2016. Genome

Blowfly-derived DNA
Lee, Sing & Wilson. 2015. PLOS ONE

Blowfly-derived DNA
Mammal DNA persists in blowfly
guts for ~72hrs
Blowflies disperse ~1km per day
Our primer set amplifies 205bp
5-COI mini barcode
90% amplification success for
mammal dataset
Lee et al. 2016. Genome

Blowfly-derived DNA

VS.
Lee et al. 2016. Genome

Blowfly-derived DNA
Blowflies
outperform
traditional
methods nets,
scat, traps,
cameras
Bats, rats, cattle,
boar detected
Lee et al. 2016. Genome

Blowfly-derived DNA
Lim et al. In Review. Urban Ecosystems

Trophic relationships
Agriculture
Forest Urban
Lim et al. In Preparation.

Trophic relationships
DNA barcoding is
a team effort
South
China
DNA
Barcoding
Center