muthama muasya university of cape town application of dna barcoding in plant taxonomy, eastern...

Muthama Muasya

University of Cape Town

Application of DNA barcoding in plant taxonomy, Eastern Africa

Experience

Role in biodiversity studiesIdentificationNamingClassification

Relevance to CBDArticle 7: Identification & monitoring of biodiversity (Ecosystem & habitats, species & communities, genes)

FacilitiesHerbaria with representative material

Plant taxonomy in Eastern Africa

Global plant diversity

Kier et al. 2005; J. Biogeography

•C. 12,000 species in Eastern Africa•Loss of biodiversity great

Rarity of Eastern Africa FloraKueper et al 2004.

•Hotspots of plant endemism•Gaps exists in current plant knowledge

Status of taxonomy in Eastern Africa

•Regional Floras & local checklists

•Phenetics (overall similarity)

•Phylogenetics (shared common ancestry; DNA data)

Value of barcode data

•Plant identification

•Phylogenetic position for ‘new’ plant material

•Use of barcode data in classification and evolutionary studies

Isolepis endemics on East African mountains

I. kilimanjarica

I. meruensis

I. keniensis

Example: Isolepis studies

Mt. Kenya

Mt. Meru

Australia

SA

SA

SA

SA

Tropical

temperate

Barcoding: Challenges for E. Africa

•Taxonomic teaching/practice not using DNA•Lack of molecular facilities, capacity•Expense

Do we really need the initiative now?

Barcoding: Opportunities for E. Africa

•Large flora, endemics, unique lineages•Alpha taxonomy, herbarium collections•Active taxonomic groups/teaching•Ongoing projects offer entry point (e.g. Seeds for life, RPSUD, eastern arc & coastal forests , afro-temperate flora, Albertine Rift)•One BIOTA project proposing barcoding trees of Kakamega & Budongo forests next year•International funding goodwill now

Cyperus_involucratus TCTTTCTAATTTCCTGTGGATTTTTACAT-CCACCATTTTCTTTCTATAGTAATGAAAATGCTCTTGGCTCGACATAATTTGTTCTGTTCAAAAACCC----AATTTCTAATTTCTATT-----AGGTTGTCCGTAAACAGTACACGATGGAGCTCG----------AAGTTTGATTTTTTTA---------TCAAACAAGGGAAAGAATCTAGGGTTAGTGATAATTCAATT----AATTCTAATTAATTTAGACCAATTTTGTAAGTATA-TCTTAGTATCAGAATCAGAAA---AAAA-TACAATTCGAACAAG--------AAAAAAA--A--------TAGAAAGTGAAATTGTTGG-----AAACTGGTAAAA---CTATTCTGATTTTAAGGTGGAACGGGAATGAATCCTTCGTATTTATTTTATA------TTATAAAGAAGGAAATCAAAAAGAAGGG-GTGTTGCTTTCCCTTTGAAAGGAATAAAGGTCTTCAAAATAAATTTATAAACCTAAAGATTCCAAAAAGAAAAAAGAAAGGATTCCG-AACAAGAAAATACTTTTTT-AA-TTATCTCAAC-----AGTGTAATTGGATCAAATTGACAAATCTAAAAAGGGT----AGAGATATGACACACACAAAAGAGTTTAGAGACAGCTCAAGAAATTCTTTCA-----TAAGGATTTATG---------AACTTT-----CTAAAAATTTTTTATTTAACTTGAGTCATGAGTAAAAAAAA---TATTATGATATTTTTTTATA---------TAACGAAAAGGAAAAAGGA-CTCTATTTGAATCATAGTATAATTCATGATTTTCTGAGTCCATTTTGCA-----TTCTATACAGAAATTTGAATTATTTTTCTTGAGCCGTATGAGGTGAAAATTTCATTTACGTTTCTAGGGGGA-CTTTTTTT-ATC-ATAYAATGTGCCCATCTAAA----------- [855]

Cyperus_laevigatus CCCGTCTAATTTTCTGTGGATTTTTACAT-CCACCATTTTCTTTCTATAGTAATGAAAATGCTCTTGGCTCGACATAATTTGTTCTGTTCAAAAAGCC----AATTTCTAATTTCTATT-----AGGTTGTCCGTAAACAGTACATGATGGAGCTCG----------AAGTTTGATTTTTTTA---------TCAAACAAGGGAAAGAATCTAGGGTTAGTGATAATTCAATT----AATTCTAATTAATTTAGACCAATTTTGTAAGTATA-TCTTAGTATCAGAATCAGAAA---AAAA-TACAATTTGAACAAG--------AAAAAAA-AA--------TATAAAGTGAAATTCTTGG-----AAACTGGTAAAA---CTATTCTGATTTTAAGGTGGAACGGGAATGAATCCTTCGTATTTATTTTATA-----------AAGAAGGAAATCAAAAAGAAGGG-GTGTTGCTTTCCCTTTGAAAGGAATAAAGGTCTTCAAAATAA-TTTCTAAACCTAAAGATTCCAAAAAGAAAAAAGAAAGGATTCCGGAACAAGAAAATACTTTTTT-AAATTATCTCAAC-----AGTGTAATTCGATCAAATTGACAAATCTAAAAAGGTT----AGAGATAAAACAAACA-AAAAGAGTTTAGAGACAGCTCAAGAAATTCTTTCA-----TAAGGATTTATG---------AACTTT-----CTAAAAATTTTTTATTTAACTTGAGTCATGAGTAAAAAAAA---TATTATGAATTTTGTATATA---------TAACGTAAAGGAAAAGGGA-CTCTATTTGAATCATAGTATAATTCATGAATTTATGAG?????????????????????????????????????????????????????????????????????????????????????????????????-???????????????????????------------ [857]

•Barcoding of plant diversity in the hotspot e.g. afro-alpine zones•Collaboration- local & international

Way forward

•Barcoding of plant diversity in hotspots e.g. afro-alpine zones; taxon specific (grasses)•Collaboration- local & international

Way forward

Actual implementation

•Sample collection (herbarium/museums tissue, supplementary fieldwork)

•Set up labs (PCR machines, etc)

•Laboratory data generation

•Incorporation of data into databank

•Using the databank to serve taxonomic & broader community

Outputs

•DNA barcode data

•Voucher specimens & curation

•DNA lab capacity

•Student training, publications

Asante sana

•Organisers•Colleagues (S. Masinde, G. Mwachala, P. Muthoka, R Cowan; M van der Bank)