Upload
betty-hill
View
219
Download
0
Tags:
Embed Size (px)
Citation preview
DNA barcoding-at-sea on Polarstern ANTXXXIV-1DNA barcoding-at-sea on Polarstern ANTXXXIV-1
TEAM DNA (left to right): Christina Folker, Paola Batta Lona, Leo Blanco Bercial, Lisa Nigro, Rob Jennings, Ann Bucklin, CJ Sweetman
Zooplankton BarcodesSargasso Sea & Eastern Atlantic
GroupSpecies Known
Individuals Submitted
Species Submitted
DNA Extracted
Individuals Barcoded
Species Barcoded
Individuals Barcoded
Species Barcoded
CNIDARIA Hydromedusae 842 0 0 0 0 0 12 8 Siphonophora 160 0 0 0 0 0 50 50 Scyphozoa 161 0 0 0 0 0 5 5CRUSTACEA 0 Amphipoda 400 42 27 31 9 9 22 17 Copepoda 2,000 686 162 298 26 15 96 46 Euphausiidae 86 144 23 79 16 6 23 11 Ostracoda 169 540 77 161 99 45 156 58 Other crustacea xx 54 6 4 0 0 10 8MOLLUSCA 0 Gastropoda 144 225 44 114 53 20 96 37 Cephalopoda 370 19 16 15 12 11 23 20Nemertea 99 3 1 1 1 1 3 2ANNELIDA 0 Polychaeta 110 0 0 0 0 0 5 3CHAETOGNATHA 93 67 18 33 12 5 28 11
TOTAL 4,634 1,780 374 736 228 112 529 310
Both Cruises to DateEastern Atlantic
DNA Barcoding Steps & Errors
1) Identify specimen
2) Extract DNA
3) PCR mtCOI barcode
4) Sequence DNA
5) Edit / align sequences
6) Validate barcode
7) Submit to database
Wrong specimen - specimen incorrectly identified - specimen incorrectly labeled
No DNA - bug dead too long before preservation - DNA cooked under microscope - DNA cooked during sample shipment
PCR fails - PCR primers don’t match species - PCR protocol not optimal for species - too much or too little DNA
Sequence fails - mis-priming in sequencing reaction
Incorrect sequence - pseudogene of mtCOI - duplication / translocation of mtCOI - contamination with exogenous DNA - contamination from symbiont, gut
Eastern Atlantic Barcodes
228 individuals, 112 speciesNeighbor Joining algorithm, Kimura-2-Parameter distances, Bootstrap 1000X
Amphipods 9 ind, 9 spp
Ostracods
99 ind, 45 spp, 65%
Gastropods 46 ind, 17 spp
Copepods26 ind, 15 spp, 95%
Gastropods 7 ind, 3 spp, 100%
Cephalopods12 ind, 11 spp, 72%
Nemerteans1 ind, 1 sp
Euphausiids 16 ind, 6 spp
Chaetognaths 12 ind, 5 spp, 96%
0.1
99
100
95100
Zooplankton BarcodesSargasso Sea & Eastern Atlantic
529 individuals, 310 speciesNeighbor Joining algorithm, Kimura-2-Parameter distances
0.1
Copepods96 ind, 46 spp, 98%
Gastropods77 ind, 27 spp
Gastropods19 ind, 10 spp, 99%
Cephalopods 23 ind, 20 spp, 99 %
Polychaetes 5 ind, 3 spp, 99%
Nemerteans3 indiv, 2 spp
Amphipods 22 ind, 17 spp, 61%
Ostracods 156 ind, 58 spp, 99%
Other Crustacea 10 ind, 8 spp, 75%
Siphonophores50 ind, 50 spp
Hydromedusae 12 ind, 8 spp
Scyphzoa 5 ind, 5 spp
Chaetognaths 28 ind, 11 spp, 90%
Euphausiids23 ind, 11 spp, 85%
99
100
98
Barcoding Euphausiids
193 individuals, 40 speciesNeighbor Joining algorithm, Kimura-2-Parameter distances, bootstrapped 1000X
N. atla
ntica(
15)
N. micropsN. tenella(4)
N. gracilis(3)N. megalops(4)
N. difficilis(5)
T. monacantha(6)
S. abbreviatum(4)
S. carinatum(5)
S. elongatum(4)
S. longicorne(3)S. affine(3)
S. suhmii(6)
T. longipes(2)T. ocu l atu m
T. spinifera(6)
N. s
exsp
inos
um (4
) N
. fle
xipe
s(4)
T. o
rient
alis
(3)
S. m
axim
um(3
) B
. am
blyo
ps
T. o
btusif
rons(5
)
T. aequalis(16)
N. australis(2)
N. simplex
M. norvegica
T. gregaria(3)
T. macrura(3)
T. tricuspidata(3)
E. tenera(6) E. lammellibrachea(7)
E. sibogae(3) E. distinguenda(9)
E. gibboides(6)
E. brevis(4)
E. eximia(2)
E. brevis(14)
E. mutica(2)
E. americana(2)
E. krohnii(14)
0.05
Euphausia
Thysanoessa
Nyctiphanes
Meganyctiphanes
Thysanopoda
Stylocheiron
Nematobrachion
Nematoscelis
Bentheuphausia
Tessarobrachion
98
99
99
100% bootstrap
Barcoding Taxonomic Experts
Martin AngelOstracods
Francesc Pagès (dec.)Siphonophores
Janet Bradford-Grieve Sigrid SchieldCopepods
Russ HopcroftGastropods
Uwe PiatkowskiCephalopods
Dhugal LyndseyAmphipods
Annelies Pierrot-BultsChaetognaths
Peter Wiebe Fred BuccholtzEuphausiids