Post on 16-Jan-2016
DNA Barcoding in the Genome Era
Ya-ping ZhangKunming Institute of Zoology
Chinese Academy of Sciences
Yunnan University
The Second International Barcoding of Life Conference(16-21 September 2007, Taipei,
Taiwan)
Sinocyclocheilus grahami
Challenge: loss of biodiversity and expert
Known biodiversity 1.7million named species of plants and animals
Estimated biodiversity 10 million species
How many named species can be identified by experts now and future?
How many experts will survive in future?
2002 First proposal of “DNA Taxonomy” by Tautz et al2003 First proposal of a DNA barcoding system based on Mitochondrial Cytochrome C Oxidase Subunit 1 (COI) sequence diversity by Hebert et alMar, 2003 A meeting titled “Taxonomy and DNA” in Cold Spring Harbor, USA
Jul, 2003 Accession to the website “http:www.barcodeoflife.org/”Sep, 2003 A meeting titled “Taxonomy, DNA and the Barcode of Life” in Cold Spring Harbor, USA
DNA Barcoding
May, 2004 Establishment of Consortium for the Barcode of Life, CBOL
Feb, 2005 The First International Barcode Conference in London
Total Barcode Records
Kingdoms of Life Barcoded
Total Barcode Records 303,359http://www.boldsystems.org/views/login.php
Formally Described Species With Barcodes 31,763
Barcoding in China
NSFC ?
MOST?National Basic Research Program of China (973 Program)
My laboratory
animal DNA bank
Diagnosis of described species and Discovery of new species
Plant Barcoding(nuclear ITS, Plastid trnH-psbA intergenic sp
acer, rbcL)(flowering plants) (land plants)
Fungi and Algae Barcoding(mitochondrial COI)
(Penicillium: 0.06% intraspecific and 5.6% interspecific divergence)
(Alaria: 1% vs. 2.2-4.7%) (Red Macroalgae: 0.5% vs. 4.5-13.6%)
Fungi Barcoding
Algae Barcoding
Vertebrates Barcoding
Invertebrates Barcoding
(mitochondrial COI)
(amphibians: 7-14% intraspecific)
(birds: 0.43% intraspecific and 7.93% interspecific)
(moths: 0.25% vs. 6.5%)
(fish: 0.39% vs. 9.93%)
(ants: 8.51% interspecific)
(spiders: 1.4% vs. 16.4%)
(mayflies: 1% vs. 18%)
(primates: 0.3% vs. 5.88%)
(Lepidoptera: 0.17-0.46% vs. 4.41-6.02%)
Animal Barcoding
……
……
Delimiting Cryptic Species
Can we build a bridge between BOL and TOL in genome era?
Goal?
Technology?
Cost? 10 million species
Hajibabaei et al. 2007
Vences et al. 2005
Phylogenetic signals
DNA Barcoding for Australia’s fish species: Phylogenetic signals for four major clusters
DNA Barcoding for Big-headed flies: Phylogenetic signals for four main species groups ……
Should CBOL recommend additional mitochondrial DNA fragments?
Nuclear Pseudogenes
Phylogenetic signal
Root vs tip?
Can we harvest without too much additional investment?
An assessment of candidate mt barcoding genes by phylogenetic analysis of complete mitochondrial genome sequences
In Genome Era: Taking advantage of the completely sequenced genomes
Ursidae (bear) family as a test case
The bear family Ursidae includes eight species and has been suggested to be classified into three genera: Ailuropoda (giant panda), Tremarctos (spectacled bear), and Ursus (brown, polar, sloth, sun, and Asiatic and American black bears)
The family Ursidae represents a typical example of rapid evolutionary radiation and recent speciation events, dating back to mid-Miocene about 20 million years ago.
Analyzing the complete mt genome sequences from all eight closely related bear species not only provides a robust Ursidae phylogenetic framework but evaluates the evolutionary rates and performance of individual mtDNA genes
Analyses give the rough appearance of relatively superior performance of CO1, ND5, ND4, CYTB, 16SrRNA, and ND2 genes
Recommendation?
Introgression Nuclear PseudogenesIdentifying Chinese Leporids (Lagomorphs, Leporidae, Lepus)Chinese leporids underwent an early and recent radiation. Members of the Chinese leporids are characterized by similar morphological characters that contribute to the problematic taxonomy of the groupChinese leporids are generally classified into nine species based on morphometric features: L. timidus (moutain hare) L. sinensi (Chinese hare) L. Mandschuricus (Manchurian hare) L. melainus (Manchurian black hare) L. capensis (Cape hare) L. oiostolus (Woolly hare) L. yarkandensis (Yarkand hare) L. hainanus (Hainan hare) L. comus (Yunnan hare)
0.02
L. oiostolus
L. comus
L. hainanus
L.timidus DAXINGANLING
84
100
97
L.Capensis SHANXIL.Capensis SHANXI
L.Capensis QINGHAIL.Capensis QINGHAIL.sinensis GANSU
L.sinensis GANSUL.sinensis GANSUL.Capensis GANSU
L.Capensis SICHUANL.sinensis GANSU
L.sinensis GANSUL.timidus XINJIANG
L.timidus XINJIANGL.timidus XINJIANG
L.mandschuricus HEILONGJIANGL.melainus JILINL.mandschuricus JILIN
L.timidus HAERBINL.mandschuricus JILIN
7594
L.Yarkandensis XINJIANGL.Yarkandensis XINJIANGL.Yarkandensis XINJIANG
L.Yarkandensis XINJIANGL.Yarkandensis XINJIANGL.Yarkandensis XINJIANG
L.Yarkandensis XINJIANGL.Yarkandensis XINJIANGL.Yarkandensis XINJIANGL.Yarkandensis XINJIANG
L.Yarkandensis XINJIANGL.Yarkandensis XINJIANG
89
76
L.timidus JILINL.timidus HAERBINL. Mandschuricus DALIAN
100
L.sinensis GUIYANGL.Capensis SHANDONGL.sinensis FUJIANL.sinensis HUNANL.Capensis SHANDONGL.Sinensis GUIYANGL.Capensis SHANDONGL.Capensis SHANDONGL.Capensis SHANDONGL.Capensis SHANDONG
L. hainanus HAINANDAOL.. europaeus L. hainanus HAINANDAOL. hainanus HAINANDAOL. hainanus HAINANDAOL. hainanus HAINANDAOL. hainanus HAINANDAOL. hainanus HAINANDAOL. hainanus HAINANDAO
100
75
87
100
L. oiostolus SICHUANL. oiostolus XIZANGL. oiostolus SICHUANL. comus YUNNANL. comus YUNNAN
L. comus YUNNANL. comus YUNNANL. comus YUNNAN
L. comus YUNNAN
L. comus YUNNAN
O. cuniculus O. collaris
60
9999
86
L. yarkandensis
L. sinensis and L. capensis mixed
L. sinensis and L. capensis mixed
L. timidus, L. mandschuricus, and L.melainus mixed
L. timidus, L. mandschuricus, and L.melainus mixed
COI (648bp; unpublished data)
DNA barcords reveal
(1) coamplification of NUMTS in six individuals of Chinese leporids
(3) non-monophyletic species in phylogenetic tree: L.sinensis and L.capensis
(2) Intraspecific divergence within L. capensis and L. sinensis were 4% and 4.5%, which were much larger than intraspecific divergence.
Mt introgression
The real challenge of identification lies with closely allied species, species pairs with very recent origins, and hybridsUsing some level of mtDNA divergence as a yardstick for species boundaries is difficult for situations: (1) in between species and subspecies, species and populations, (2) overlap of intraspecific and interspecific divergence values
0.1
mulatta 5
mulatta 6
cyclopis
mulatta 1
mulatta 3
mulatta 4
mulatta 2
1.0
1.0
1.0 1.00.93
0.95
Papio
sylvanus
arctoides 6
arctoides 3
arctoides 1,2,5
arctoides 4
fascicularis 4
fascicularis 1,2
fascicularis 3
leonina 4
silenus 2
0.66 1.0
0.960.99
1.01.0
1.0
1.0
0.9
assamensis 5
assamensis 9
assamensis 11
assamensis 7
assamensis 3
assamensis 2
thibetana 1
thibetana 2,3,4
thibetana 5
assamensis 4
assamensis 8,10
assamensis 6
assamensis 1
assamensis 12
1.0
1.0
1.0
0.89
1.0
1.0
1.0
1.0
1.0
1.0
1.0
0.99
leonina 3
leonina 2
leonina 1
silenus 1
1.0 1.0
1.0
0.81
0.55
Papio
97
sylvanus
leonina 4
leonina 2
leonina 1
leonina 3
silenus 1
silenus 2
96
100
100
100
96
76
98
53
100
mulatta 6
mulatta 5 100
98
cyclopis
mulatta 3
mulatta 1 100
mulatta 4
mulatta 252
52
arctoides 1,2,5
arctoides 6
arctoides 3
100
100fascicularis 4
fascicularis 1,2
fascicularis 3100
58
arctoides 4
100
76
assamensis 3
assamensis 4
assamensis 6
assamensis 1
assamensis 12
assamensis 2thibetana 1
thibetana 5
thibetana 2,3,4
56
assamensis 8,1081
56100
82
62
69
assamensis 5
assamensis 9
assamensis 11
assamensis 7
10071
100
Sylvanus group
fasc
icul
aris
gro
upsi
nic
a g
roup
sile
nu
s
grou
p
BI tree MP tree
Species classification should be changed?
DNA divergence is not sufficient as a sole criterion for delineating species
DNA sequence information with traditional means, e.g. morphological and ecological data
“type sequences” (i.e. a reference framework for testing species status) for barcode?
Morphologically well-defined
Geographically well-known
What kind of samples should be included for investigating species limits?
Avoiding overestimate or underestimate the DNA divergence threshold values to identify candidate speciesPhylogeny or sequence difference?
Species: sister species pairs?
Subspecies?
Populations?
Individuals?
Recommendation for sample selection?
Do we need new sequencing technology for barcoding?
What kind?
Biodiversity assessment with high throughput technology?
Acknowledgement
Dr. Li Yu
Yu-wei Li
Jiang Liu
Dr. Qing-Qing Li
Dr. Li-ping He
Thank you for your attention!