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DNA Barcoding in the Genome Era

The Second International Barcoding of Life Conference. ( 16-21 September 2007, Taipei, Taiwan). DNA Barcoding in the Genome Era. Ya-ping Zhang Kunming Institute of Zoology Chinese Academy of Sciences Yunnan University. Sinocyclocheilus grahami. Challenge: loss of biodiversity and expert .

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DNA Barcoding in the Genome Era

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  1. The Second International Barcoding of Life Conference (16-21 September 2007, Taipei, Taiwan) DNA Barcoding in the Genome Era Ya-ping Zhang Kunming Institute of Zoology Chinese Academy of Sciences Yunnan University

  2. Sinocyclocheilus grahami

  3. 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?

  4. DNA Barcoding 2002 First proposal of “DNA Taxonomy” by Tautz et al 2003 First proposal of a DNA barcoding system based on Mitochondrial Cytochrome C Oxidase Subunit 1 (COI) sequence diversity by Hebert et al Mar, 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 May, 2004 Establishment of Consortium for the Barcode of Life, CBOL Feb, 2005The First International Barcode Conference in London

  5. Total Barcode Records • Total Barcode Records 303,359 • http://www.boldsystems.org/views/login.php Kingdoms of Life Barcoded Formally Described Species With Barcodes 31,763

  6. Barcoding in China NSFC ? MOST? National Basic Research Program of China (973 Program) My laboratory animal DNA bank

  7. Diagnosis of described species and Discovery of new species Plant Barcoding (nuclear ITS, Plastid trnH-psbA intergenic spacer, rbcL) (flowering plants) (land plants) Fungi and Algae Barcoding (mitochondrial COI) Fungi Barcoding (Penicillium: 0.06% intraspecific and 5.6% interspecific divergence) Algae Barcoding (Red Macroalgae: 0.5% vs. 4.5-13.6%) (Alaria: 1% vs. 2.2-4.7%)

  8. Animal Barcoding (mitochondrial COI) Vertebrates Barcoding …… (birds: 0.43% intraspecific and 7.93% interspecific) (amphibians: 7-14% intraspecific) (fish: 0.39% vs. 9.93%) (primates: 0.3% vs. 5.88%) Invertebrates Barcoding (moths: 0.25% vs. 6.5%) (ants: 8.51% interspecific) (mayflies: 1% vs. 18%) (Lepidoptera: 0.17-0.46% vs. 4.41-6.02%) (spiders: 1.4% vs. 16.4%) ……

  9. Delimiting Cryptic Species

  10. Can we build a bridge between BOL and TOL in genome era? Goal? Technology? Cost? 10 million species

  11. Vences et al. 2005 Hajibabaei et al. 2007

  12. 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 ……

  13. Should CBOL recommend additional mitochondrial DNA fragments? Nuclear Pseudogenes Phylogenetic signal Root vs tip? Can we harvest without too much additional investment?

  14. In Genome Era: Taking advantage of the completely sequenced genomes An assessment of candidate mt barcoding genes by phylogenetic analysis of complete mitochondrial genome sequences Ursidae (bear) family as a test case

  15. 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

  16. Analyses give the rough appearance of relatively superior performance ofCO1, ND5, ND4, CYTB, 16SrRNA,andND2genes Recommendation?

  17. Introgression Nuclear Pseudogenes Identifying 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 group Chinese 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)

  18. L.Capensis SHANXI L.Capensis SHANXI L.sinensis GANSU L. sinensis and L. capensis mixed L.Capensis QINGHAI L.Capensis QINGHAI L.sinensis GANSU L.sinensis GANSU 97 L.Capensis GANSU L.sinensis GANSU 94 L.Capensis SICHUAN L.sinensis GANSU 75 L.timidus XINJIANG L.timidus DAXINGANLING L.timidus XINJIANG L. timidus, L. mandschuricus, and L.melainus mixed L.timidus XINJIANG L.mandschuricus HEILONGJIANG 76 L.melainus JILIN L.mandschuricus JILIN L.timidus HAERBIN L.mandschuricus JILIN L.Yarkandensis XINJIANG 89 L.Yarkandensis XINJIANG L.Yarkandensis XINJIANG L.Yarkandensis XINJIANG L.Yarkandensis XINJIANG 87 L.Yarkandensis XINJIANG L. yarkandensis L.Yarkandensis XINJIANG L.Yarkandensis XINJIANG L.Yarkandensis XINJIANG L.Yarkandensis XINJIANG L.Yarkandensis XINJIANG L.Yarkandensis XINJIANG L. timidus, L. mandschuricus, and L.melainus mixed L.timidus HAERBIN L.timidus JILIN 100 L. Mandschuricus DALIAN 60 L.sinensis GUIYANG L.Capensis SHANDONG L.sinensis FUJIAN L.sinensis HUNAN L. sinensis and L. capensis mixed L.Capensis SHANDONG 84 L.Sinensis GUIYANG L.Capensis SHANDONG L.Capensis SHANDONG L.Capensis SHANDONG L.Capensis SHANDONG L.. europaeus 100 L. hainanus HAINANDAO 75 L. hainanus HAINANDAO 100 L. hainanus HAINANDAO L. hainanus L. hainanus HAINANDAO 100 L. hainanus HAINANDAO L. hainanus HAINANDAO L. hainanus HAINANDAO L. hainanus HAINANDAO L. oiostolus SICHUAN 99 L. oiostolus XIZANG L. oiostolus SICHUAN L. oiostolus 99 L. comus YUNNAN COI (648bp; unpublished data) L. comus YUNNAN 86 L. comus YUNNAN L. comus L. comus YUNNAN L. comus YUNNAN L. comus YUNNAN L. comus YUNNAN O. cuniculus O. collaris 0.02 DNA barcords reveal (1) coamplification of NUMTS in six individuals of Chinese leporids (2) Intraspecific divergence within L. capensis and L. sinensis were 4% and 4.5%, which were much larger than intraspecific divergence. (3) non-monophyletic species in phylogenetic tree: L.sinensis and L.capensis Mt introgression

  19. The real challenge of identification lies with closely allied species, species pairs with very recent origins, and hybrids Using 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

  20. cyclopis 52 mulatta 4 mulatta 2 100 mulatta 1 mulatta 3 100 mulatta 5 mulatta 6 100 100 71 assamensis 5 assamensis 9 assamensis 11 assamensis 7 0.1 Papio Papio Sylvanus group sylvanus sylvanus fascicularis group mulatta 5 1.0 mulatta 6 1.0 100 cyclopis 0.93 1.0 mulatta 1 1.0 98 0.95 mulatta 3 1.0 mulatta 4 96 mulatta 2 arctoides 1,2,5 arctoides 6 100 0.66 1.0 arctoides 3 arctoides 6 58 arctoides 1,2,5 arctoides 3 53 0.96 arctoides 4 arctoides 4 0.99 1.0 fascicularis 4 fascicularis 4 100 1.0 fascicularis 1,2 fascicularis 1,2 100 96 1.0 fascicularis 3 fascicularis 3 assamensis 5 1.0 assamensis 9 sinica group 1.0 assamensis 11 1.0 100 assamensis 7 0.89 assamensis 3 assamensis 3 assamensis 2 56 assamensis 2 100 0.9 thibetana 1 1.0 1.0 100 97 thibetana 1 56 1.0 thibetana 5 thibetana 2,3,4 thibetana 2,3,4 76 1.0 thibetana 5 1.0 69 assamensis 4 assamensis 4 81 assamensis 8,10 assamensis 8,10 assamensis 6 assamensis 6 62 1.0 82 assamensis 1 assamensis 1 1.0 silenus group 0.99 assamensis 12 assamensis 12 leonina 4 leonina 4 100 1.0 52 leonina 2 leonina 3 1.0 100 0.81 leonina 1 leonina 2 76 leonina 3 leonina 1 0.55 98 silenus 1 silenus 1 1.0 silenus 2 silenus 2 BI tree MP tree

  21. 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

  22. “type sequences” (i.e. a reference framework for testing species status) for barcode? Morphologically well-defined Geographically well-known

  23. What kind of samples should be included for investigating species limits? Avoiding overestimate or underestimate the DNA divergence threshold values to identify candidate species Phylogeny or sequence difference? Species: sister species pairs? Subspecies? Populations? Individuals?

  24. Recommendation for sample selection?

  25. Do we need new sequencing technology for barcoding? • What kind? • Biodiversity assessment with high throughput technology?

  26. Acknowledgement Dr. Li Yu Yu-wei Li Jiang Liu Dr. Qing-Qing Li Dr. Li-ping He

  27. Thank you for your attention!

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