dna barcoding publications - fapesp · laurus nobilis sm-s.n. lindera benzoin k-16947 litsea cubeba...

DNA Barcoding Publications

How many Speciesare there on Earth?

Sir Robert May

Science 1988

Ernst Haeckel

Described Species

= 10,000 spp.

1,562,000 spp.

Mammals

= 10,000 spp.4,500 spp.

Birds

= 10,000 spp.9,500 spp.

Reptiles

= 10,000 spp.6,500 spp.

Amphibians

= 10,000 spp.4,000 spp.

Fish

= 10,000 spp.22,000 spp.

Echinoderms

= 10,000 spp.6,000 spp.

Molluscs

= 10,000 spp.70,000 spp.

Worms and kind

= 10,000 spp.12,000 spp.

Insects

= 10,000 spp.840,000 spp.

Arachnids

= 10,000 spp.75,000 spp.

Crustaceans

= 10,000 spp.30,000 spp.

Other Arthropods

= 10,000 spp.10,000 spp.

Flatworms

= 10,000 spp.15,000 spp.

Rotifers and Nematodes

= 10,000 spp.15,000 spp.

Jellyfish and kind

= 10,000 spp.9,500 spp.

Other Invertebrates

= 10,000 spp.13,000 spp.

Sponges

= 10,000 spp.9,000 spp.

Fungi

= 10,000 spp.70,000 spp.

Flowering Plants

= 10,000 spp.230,000 spp.

Other Plants

= 10,000 spp.26,000 spp.

Algae and other Protists

= 10,000 spp.80,000 spp.

Bacteria and Archaea

= 10,000 spp.5,000 spp.

Ignorance Index

Ignorance Index

7%65%

90%

90%

88%

97%

15%80% 80%

99%

93%

87%

Species Accumulation Curves

Bacteria

The Tricorder

http://www.bolnet.ca

DNA - “The Code of Life”

Jansen & Hebert

14812–14817 PNAS October 12, 2004 vol. 101

no. 41

CBoL

http://www.barcoding.si.edu/

Philosophical Transactions: Biological SciencesIssue: Volume 360, Number 1462 / October 29, 2005

http://www.barcodinglife.org

BOLs

• BarcodeBlog http://phe.rockefeller.edu/barcode/blog

• BOLI-Barcode of Life Initiative www.dnabarcodes.org

• BOLInfoNET-Barcode of Life InfoNET www.bolinfonet.org

• BOLNET-Canadian Barcode of Life Network www.bolnet.ca

• CBOL-Consortium for the Barcode of Life www.barcoding.si.edu

• CCDB-Canadian Centre for DNA Barcoding www.dnabarcoding.ca

• ECBOL-European Consortium for the Barcode of Life www.ecbol.org

• iBOL-International Barcode of Life www.ibolproject.org

• NBOL-Barcode of Life NL www.dnabarcoding.nl

http://phe.rockefeller.edu/barcode/blog

http://www.dnabarcodes.org

http://www.bolinfonet.org

http://www.bolnet.ca

http://www.barcoding.si.edu

http://www.dnabarcoding.ca

http://www.ecbol.org

http://www.ibolproject.org

http://www.dnabarcoding.nl

Campaigns

• ABBI www.barcodingbirds.org

• AllLeps-Lepidoptera Barcode of Life www.lepbarcoding.org

• Bee-BOL www.bee-bol.org

• CMarZ-Census of Marine Zooplankton www.cmarz.org

• FISH-BOL-Fish Barcode of Life www.fishbol.org

• Barcoding Invasive and Pest Species barcoding.si.edu/INBIPS.htm

• MarBOL-Marine Barcode of Life www.marinebarcoding.org

• MBI-Mosquito Barcode Initiative

• PolarBOL-Polar Barcode of Life www.polarbarcoding.org

• QBOL-Quarantine Barcode of Life www.qbol.org

• TBI-Tephritid Barcode Initiative

http://www.barcodingbirds.org

http://www.lepbarcoding.org

http://www.bee-bol.org



http://www.cmarz.org

http://www.fishbol.org

http://barcoding.si.edu/INBIPS.htm

http://www.marinebarcoding.org

http://www.polarbarcoding.org

http://www.qbol.org

Plants?

Consortium for the Genetic Identification of

Neotropical Plants

Cassio van den Berg- Brasil

Gerardo Salazar – México

Santiago Madriñán – Colombia

Consortium for the Genetic Identification of

Neotropical Plants

Cassio van den Berg- Brasil

Gerardo Salazar – México

Santiago Madriñán – Colombia

http://ArBOL.uniandes.edu.co



4

No of species in CTFS plots

4

Indets

Overall Indets

Sampling Priorities

AvailabilityPlots

DNA Banks

Usetimber

medicinalfood

ComplexTaxonomy

UniqueEcosystems

Resources

• Interested botanical community

• Active molecular laboratories

• Botanical Gardens

• Well-established Forestry Networks w/ Permanent Plots

20 Forest Plots in 15 CountriesMore than 75 Partner Institutions Worldwide

Center for Tropical Forest Science (CTFS)

59

RainFor

Proof of Concept Papers

Projects at the “Laboratorio de Botánica y Sistemática”

• Sensitivity Tests

– Families with complex taxonomy

– Large genera

– Recently evolved floras

Lauraceae

• Big family

• Largely understudied

• VERY difficult to id.

• Economically important

Species Complexes

Phylogenetic Spread

Lauraceae

accD matK ndhJ rpoB rpoC1

Actinodaphne glabra K-8202

Actinodaphne pruinosa K-8203

Aiouea dubia AN-417

Beilschmiedia pendula BCI-065681



Beilschmiedia tawa K-5519

Caryodaphnopsis cogolloy JAUM-s.n.

Cinnamomum camphora K-6469

Cinnamomum dictyoneuron K-8201

Cinnamomum obtusifolium K-8303

Cinnamomum triplinerve BCI-206711


Cinnamomum triplinerve SM-Ama-005

Cinnamomum zeylanicum K-8306

Cryptocarya triplinervis K-5522

Dodecadenia grandiflora K-5520

Endlicheria sp. 1 SM-Ama-006

Endlicheria sp. 2 SM-Ama-003

Lauraceae sp. 1 A-1535

Lauraceae sp. 2 NN-BCI?

Laurus azorica K-21989

Laurus nobilis SM-s.n.

Lindera benzoin K-16947

Litsea cubeba K-15475

Nectandra cissiflora BCI-216314




Nectandra cuspidata FC-1579

Nectandra cuspidata Gamboa-s.n.

Nectandra 'fuzzy' BCI-036152

Nectandra 'fuzzy' BCI-105750

Nectandra lineata BCI-065446

Nectandra lineata BCI-220065

Nectandra purpurea BCI-151022



Nectandra sp. 1 AN-410

Nectandra sp. 1 AN-411

Neolitsea aciculata K-17739

Ocotea callophyla SM-s.n.

Ocotea cernua BCI-206437



Ocotea floribunda HD-1166

Ocotea guianensis A-818

Ocotea oblonga BCI-309078

Ocotea oblonga BCI-403510

Ocotea puberula BCI-146684



Ocotea sp. 1 HD-1167

Ocotea whitei BCI-008086

Ocotea whitei BCI-306277

Persea americana SM-s.n.

Persea caerulea Sánchez-4911

Persea rimosa K-8204

Rhodostemonodaphne frontinoensis Brant-1387

Rhodostemonodaphne kunthiana HD-1175

Rhodostemonodaphne kunthiana Madriñán-717

Rhodostemonodaphne penduliflora SM-s.n.

Sassafras albidum K-16948

accD matK ndhJ rpoBrpoC

1

Genera 17 17 16 17 17

Species 42 40 36 42 43

Specimens 47 58 42 48 49

Sp. w/ >1

specimen5 11 6 6 6

matK

974 bp

matK

0

100

200

300

400

500

0.00

0.01

0.02

0.03

0.04

0.05

0.06

0.07

0.08

0.09

0.10

0.11

0.12

0.13

0.14

0.15

0.16

0.17

0.18

0.19

0.20

0.21

0.22

0.23

0.24

0.25

0.26

0.27

0.28

0.29

K2P Distance

Freq

uen

cy

Inter Intra

trnH-psbA

596 bp

trnH-psbA

GenBank (50)

+

Samles (43)

93 sequences

GenBank Accessions

accD matK ndhJ rpoB rpoC1 rbcLtrnH-

psbA

All GenBank 1,509 19,354 305 7,144 1,445 36,228 904

Viridiplantae 838 19,299 278 590 904 29,627 903

Lauraceae 0 158 0 0 0 9 50

matK BLAST matches

matK

GenBank (134)

+

Samples (58)

192 sequences

matK

1

3

2

GenBank (134)

+

Samples (58)

192 sequences

1

Dodecadenia?

Cryptocarya triplinervis K-5522

Match


Match

Caryodaphnopsis cogolloi JAUM-s.n.

Match

Dodecadenia grandiflora K-5520

Oh Oh!

Persea caerulea Sánchez-4911

Match


Match

Neolitsea aciculata K-17739

Match


Match


Match?

Sassafras albidum K-16948

Nectandra ''fuzzy'' BCI-105750

Match

Nectandra ''fuzzy'' BCI-036152

trnH-psbABLAST matches


Match

Caryodaphnopsis cogolloi JAUM-s.n.

Match


Match

Rhodostemonodaphne penduliflora

chingaza.uniandes.edu.co

Flora Ilustrada del

Páramo de Chingaza

Year

#

spp

.

Species Accumulation inPáramos

ITS

1047 chars.

167 variable uninformative

204 informative

Tree search aborted after 30000 trees

669 steps

CI = 0.744

Hypericum in Páramos

Obrigado!

ArBOL.uniandes.edu.co

dna barcoding publications - fapesp · laurus nobilis sm-s.n. lindera benzoin k-16947 litsea cubeba...

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