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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)