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37%
35%
8%
7%
6%4%
2% 1%Arthropoda (phylum)
Mollusca (phylum)
Cnidaria (phylum)
Echinodermata (phylum)
Chordata (phylum)
Annelida (phylum)
Bryozoa (phylum)
4 others (phylum)
SEAKEYS: unlocking foundational marine biodiversity
knowledge in South Africa using DNA barcoding1,2Monica Mwale, 2G. Gouws, 3J Landschoff, 3JA Toms, 3CL Griffiths and 4K. Sink
1National Zoological Gardens of South Africa, PO BOX 754, Pretoria 0001, South Africa. 2South African Institute for Aquatic Biodiversity, P/Bag 105, Grahamstown, South Africa
3Zoology Department, Marine Biology Research Centre, University of Cape Town, Rondebosch, South Africa4South African National Biodiversity Institute, Kirstenbosch Research Centre, Cape Town, South Africa
783
ABSTRACT
The information on the biodiversity of most southern African marine ecosystems is limited1. The development of comprehensive databases is
therefore critical to support the effective monitoring of marine ecosystems and species for the implementation of evidence-based policy and
conservation management for sustainable use. The SEAKEYS project funded by the DST/NRF/SANBI Foundational Biodiversity Knowledge and
Information research funding Programme (FBIP) therefore aims to unlock fundamental biodiversity information using DNA barcoding to generate
species records and distribution databases for priority ecosystems and groups.
Funding Sources/Acknowledgements
1. DST/NRF/SANBI Foundational Biodiversity Knowledge
2. Dr Kerry Sink – SANBI
3. Yonela Sithole (MSc)
4. BOLD team
5. IZIKO museums
To describe and undertake associated genetic (DNA barcoding),
systematic and ecological research for;
Priority taxa: harvested, habitat forming, indicator, threatened and
potentially invasive species.
Priority ecosystems: with key ecosystem services and those that are
particularly sensitive to fishing, mining and other impacts.
The research aims to support biodiversity assessments and evidence-
based decision making and effective marine biodiversity.
References
1. Branch GM, Griffiths CL, Branch ML, Beckley LE. 1994. Two Oceans: A Guide to the
Marine Life of Southern Africa. David Phillip Publishers (Pty) Ltd, South Africa, pp 1-456
2. Reece JS. 2010. Phylogenetics and phylogeography of moray eels (Muraenidae). PhD
thesis, Washing University, St. Louis, pp 1-112.
3. Reece JS, Bowen BW, Smith DG, Larson A. 2010a. Molecular phylogenetics of moray
eels (Muraenidae) demonstrates multiple origins of a shell-crushing jaw (Gymnomuraena,
Echidna) and multiple colonizations of the Atlantic Ocean. Molecular Phylogenetics and
Evolution 57: 829-835.
4. Castle PHJ, McCosker JE. 1986. Family Muraenidae. In: Smith MM, Heemstra PC (eds),
Smiths’ Sea Fishes. MacMillan, South Africa, pp 165-176.
RESULTS
DNA barcodes of 573 specimens of coastal marine fishes and
invertebrates from 128 nominal species
Collected from the cool-temperate, warm-temperate and sub-tropical
bioregions and offshore (Agulhas Bank) in South Africa, mascarene
plateau and Inhaca Island in southern Mozambique.
These specimens included invasive, commercially important, rare,
threatened and endangered species. Average COI sequence
divergences within species, genera and families were moderate to high
at 1.76%, 20.0% and 23.5% respectively.
The barcode-gap analysis indicated that 14 species were indistinct,
while 23 had high intraspecific distances (>2%) due to either deep
divergences or cryptic speciation.
An additional 12 species had very low interspecific variation suggesting
misidentifications or a need for taxonomic evaluation.
The 138 Barcode Index Numbers (BIN) identified included 93
concordant assignments.
17 singletons specimens that will require more sampling for
species verification.
AIMS & OBJECTIVES
Figure 1: Summary of taxa analysed from SeaKeys project.
Graph show diversity among fishes (e.g. endemic species of
Cafforgobius).
High levels of genetic variation
Taxonomically discordant BINS (28) with good sample sizes (5-65
samples) were re-analysed and corrected using the DNA barcode.
Example: Genetic variation of Gymnothorax undulatus
(Anguilliformes: Muraenidae) in the WIO
G. undulatus is an Indo-Pacific species defined by presence of
irregular brown rectangular spots with reticulated pattern1,2,4
Taxonomic status is unclear and the species is highly misidentified
and confused with other Indo-Pacific species3,4.
This was observed in both DNA barcode data and morphological
analysis.
Southern African marine taxa are very
diverse, with more species to be discovered.
BINs are higher than the number of
identified species.
The vouchered specimens from this study will
be critical in linking all new and unclear BIN
clusters to species and new descriptions.
Thus more holotype and type locality
barcodes will become vital.
Barcodes consistent with good morphological
identifications for species.
Therefore, this project will contribute towards
the estimation of marine biodiversity in South
Africa.
Figure 2: DNA barcoding (COI) ML tree and WIO colour
morphs of G. undulatus in the WIO (Top: South Africa, Middle:
Seychelles, Bottom: FISHBASE distribution map.
SIGNIFICANCE
Email: [email protected]
GG07-A080 G. undulatus SA
HM09-091 Gymnothorax sp. SA
GG07-A079 G. undulatus SA
GG07-A088 G. undulatus SA
GG07-A089 G. undulatus SA
HM09-064 G. undulatus SA
Smith-41.24 1 G. undulatus SA
HM09-065 G. undulatus SA
Clade 2
T-355 G. griseus
T-453 G. chilospilus
KNY2011/164 Gymnothorax sp. EA
RB09-144 Gymnothorax sp. Moz
RB09-104 Gymnothorax sp. Moz
DB11-103 G. undulatus SA
T-341 G. rueppellii
T-340 G. rueppellii
MAL226 G. undulatus Arc
LS07-0793 G. undulatus EA
LS07-0638 G. undulatus EA
T-346 G. undulatus Sey
T-421 G. undulatus Sey
T-422 G. undulatus Sey
Clade 1
CB10-351 Gymnothorax sp. EA
GG07-A050 G. flavimarginatus
RB10-A014 G. flavimarginatus
JX242970 G. flavimarginatus
JX242970 G. flavimarginatus
AB695709 G. undulatus Jap
AB695707 G. undulatus Jap
AB695708 G. undulatus Jap
Clade 3
AB695653 G. thyrsoideus
AB695651 G. thyrsoideus
AB695652 G. thyrsoideus
JX242971 G. fuscomaculatus
JX242968 G. chilospilus
AB695696 G. chilospilus
AB695695 G. chilospilus
AB695694 G. chilospilus
AB695649 G. pictus
AB695650 G. pictus
AB695648 G. pictus
JX242976 G. pictus
AB702979 S. tigrina
AB702972 S. tigrina
AB702973 S. tigrina
AB702976 S. tigrina92
100
100
100
100
95
100
100
100
88
100
99
87
100
98
85100
100
99
0.02
Clade 2
Clade 2
Clade 3