masaki miya 1 and mutsumi nishida 2 1 natural history museum and institute, chiba evolutionary...
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Masaki Miya1 and Mutsumi Nishida2 1 Natural History Museum and Institute, Chiba
Evolutionary History of Fishes: An Overview Based on >1000 Whole Mitochondrial
Genome Sequences
2 Ocean Research Institute, University of Tokyo
Second International Barcode of Life Conference18–20 September 2007 in Taipei
Actinopterygii(27,580 spp.)
48.7%
Agnatha(108 spp.) Chondrichthyes
(980 spp.)
“Basal Sarcopterygii”(8 spp.)
Amphibia(6002 spp.)
10.6%
Reptilia(7483 spp.)
13.2%
Aves(9924 spp.)
17.5%
Mammal(4554 spp.)
8.0%
Sarcopterygii(27,971 spp.)
Ray-finned fish in vertebrates
Origin of ray-finned fish
Agnatha
Chondrichthyes
Sarcopterygii420 Mya
Actinopterygii
4289 genera453 families
44 orders
extant ray-finned fish
27,580 spp.
The knowns and unknowns
Paleozoic Mesozoic Cenozoic
1.When2.Where3.Howray-fiinned fishes have diversified during these 420 Myr
???
common ancestor
The late Silurian420 Mya
A summary of the initial stage
4. Gene rearrangement as a new phylogenetic marker• Inoue et al. (2000) J. Mol. Evol. 52: 311–320
3. Ability of mitogenomic data for controversial issues• Inoue et al. (2001) Mol. Phylogenet. Evol. 20: 275–285
2. Use of mitogenomic data in phylogenetic analysis• Miya & Nishida (2000) Mol. Phylogenet. Evol. 17: 437–455
1. Development of the new method• Miya & Nishida (1999) Mar. Biotechnol. 1: 416–426
Resolution of the higher-level relationships of ray-finned fish (Actinopterygii)
Resolution of the higher-level relationships of ray-finned fish (Actinopterygii)
Four separate analyses: An overview
Otocephala
• Saitoh et al. (2003) J. Mol. Evol. 56: 464–472• Ishiguro et al. (2005) J. Fish Biol. 67: 561–569• Lavoué et al. (2005). Mol. Phyl. Evol. 37: 165–177• Saitoh et al. (2006) J. Mol. Evol. 63: 826–841• Lavoué et al. (2007). Mol. Phyl. Evol. 43:1096–1105
6864 spp.
Basal Actinopterygii• Inoue et al. (2003) Mol. Phyl. Evol. 26: 110–120• Inoue et al. (2004) Mol. Phyl. Evol. 32: 274–286
10 spp.
34 spp.
217 spp.
801 spp.
Basal Euteleostei
• Ishiguro et al. (2003) Mol. Phyl. Evol. 27: 476–481
322 spp.
Higher Teleostei
• Miya et al. (2001) Mol. Biol. Evol. 18: 1993–2009• Miya et al. (2003) Mol. Phyl. Evol. 26: 121–138• Miya et al. (2005) Biol. J. Linn. Soc. 85: 289–306• Mabuchi et al. (2007) BMC Evol. Biol. 7: 10• Kawahara et al. (2007) Mol. Phyl. Evol. (in press)
321 spp.
219 spp.
272 spp.
535 spp.
209 spp.
13,866 spp.
common ancestor
The late Silurian420 Mya
Paleozoic Mesozoic Cenozoic
4289 genera453 families
44 orders
extant ray-finned fish
27,580 spp.
Evolutionary Mitogenomics of Fishes (EMFish)
1. 16,500 bp x 327 spp.2. Phylogenetic analysis3. Divergence time estimation4. Macroevolutionary analysis
EMFish: Some statistics
906Number of species***
1045Total number
88Other groups/individuals**
957Our research group
1. Number of whole mitogenome sequences*
* As of 9 August 2007 ** From NCBI database*** Excluding duplicated species
(3.7%)90624,618Species
(79.3%)383482Family
(18.3%)7784,257Genus
2. Taxonomic coverage of the data
ProportionSeq**Numbers*Rank
* Nelson (1994) ** Including unpubl. data
4289 genera453 families
44 orders
extant ray-finned fish
27,580 spp.
Fish-BOL: character and taxon samplings
Correct estimation of genetic diversity (≈ species diversity)
Fish-BOL
655 bp x 4123 spp. = 2.7 Mb
4289 genera453 families
44 orders
extant ray-finned fish
27,580 spp.
EMFish: character and taxon samplings
Correct estimation of gene tree (≈ species phylogeny)
EMFish
16,500 bp x 327 spp. = 5.4 Mb
Fish-BOLNumber of “leaves”
EMFishTopology of “branches”
Paleozoic Mesozoic Cenozoic
Molecular Phylogeny
Divergence Time
Rates of Diversification
New Insights into Evolutionary History
4289 genera453 families
44 orders
extant ray-finned fish
27,580 spp.
common ancestor
The late Silurian420 Mya
New insights into evolutionary history
EMFishFish-BOL
Masaki Miya1 & Mutsumi Nishida2
Evolutionary Genomics of Fishes: A New Perspective Based on Whole Mitochondrial
Genome Sequences from >1000 species
1 Natural History Museum & Institute, Chiba2 Ocean Research Institute, University of Tokyo
Second International Barcode of Life Conference18–20 September 2007 in Taipei
Schematic figure of a cell
Size (human) 3.0 × 108 bp 16,500 bp (redundant) (compact)
Number of genes 30,000 13
Mode of inheritance Mendelian maternal(recombination) (no recombination)
Mode of variations
DNA substitutions/indels substitutions/indels
Gene duplications/indels/translocations
Chromosome same as above + inversion ––
Genome polyploidy ––
Homology assessment difficult easy
Evolutionary rate slow–fast medium–fast
Nuclear vs. mitochondrial genomes
Features Nuc Mito
Configuration linear circular
Development of the new method
1. Long PCRs
3. Direct cycle sequencing
2. Full-nested short PCRs
Long PCR product #1
Long PCR product #2
Miya & Nishida (1999) Mar. Biotechnol. 1: 416–426
Sister-group of the SalmonidaeSister of the Salmonidae
Sister-group of the SalmonidaeSister of the Salmonidae
A project summary—1. Published studies
1–4. Foundation of mitochondrial (phylo)genomics of fishes (10 published papers)
5. Higher-level relationships of Actinopterygii• Miya et al. (2001) Mol. Biol. Evol. 18: 1993–2009. First attempt at resolving higher teleostean
relationships• Inoue et al. (2003) Mol. Phylogenet. Evol. 26: 110–120 . Basal actinopterygian relationships• Miya et al. (2003) Mol. Phylogenet. Evol. 26: 121–138. Analysis of 100 mitogenomes of higher
teleosts• Saitoh et al. (2003) J. Mol. Evol. 56: 464–472. Ostariophysan phylogeny and evolution• Ishiguro et al. (2003) Mol. Phylogenet. Evol. 27: 476–488. Basal euteleostean relationships• Inoue et al. (2004) Mol. Phylogenet. Evol. 32: 274–286. Mitogenomic evidence for the
elopomorph monophyly• Lavoué et al. (2005) Mol. Phylogenet. Evol. 37: 165–177. Gonorynchiform phylogeny within the
Otocelphala• Ishiguro et al. (2005) J. Fish Biol. 67: 561–569. Phylogenetic position of Sundasalangidae• Miya et al. (2005) Biol. J. Linn. Soc. 85: 289–306. Phylogenetic position of toadfish in higher
actinopterygians
A project summary—1. (continued)
5. Higher-level relationships of Actinopterygii (continued)
• Saitoh et al. (2006) J. Mol. Evol. 63: 826–841. Higher-level relationships of the Cypriniformes.• Mabuchi et al. (2007) BMC Evol. Biol. 7: 10. Polyphyly of the Labroidei.• Lavoué et al. (2007) Mol. Phylogenet. Evol. 43: 1096–1105. Higher-level relationships of the
Clupeiformes.• Yamanoue et al. (2007) Mol. Phylogenet. Evol. (In press.) Phylogenetic position of
Tetraodontiformes.• Miya et al. (2007) Ichthyol. Res. 54 (In press.) Phylogenetic position of Stylephoridae.• Kawahara et al. (2007) Mol. Phylogenet. Evol. (In press.) Polyphyly of the Gasterosteiformes.
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8. Theoretical issues in molecular systematics• Simmon et al. (2004) Mol. Biol. Evol. 21: 188–199. How meaningful are posterior
probabilities in Bayesian analysis?• Simmon & Miya (2004) Mol. Phylogenet. Evol. 31: 351–362. Efficient resolution of higher-
level relationships; taxonomic sampling vs. character sampling
7. Molecular biology and evolution• Inoue et al. (2003) Mol. Biol. Evol. 20: 1911–1924. Evolution of the gulper eel mitogenomes and
analysis of lower teleostean phylogeny • Mabuchi et al. (2004) J. Mol. Evol. 59: 287–297. Evolution of pseudogenes in the scarid
mitogenomes
6. Species level phylogeny• Yamanoue et al. (2004) Ichthyol. Res. 51: 269–273. Relationships of ocean sunfishes• Minegishi et al. (2004) Mol. Phylogenet. Evol. 34: 134–146. Phylogeny and evolution of freshwater
eel genus Anguilla
continuedContinued — total, 54 papers cited >1000 times
9. Divergence time estimation• Inoue et al. (2005) Gene 349: 227–235. Divergence time of the two coelacanths• Yamanoue et al. (2006) Gene Genetic Syst. 81:29–39.
A project summary—2. Ongoing studies
1. Global analysis of phylogeny and evolution• Elasmobranch relationships based on 31 whole mitochondrial genome sequences (Shirai et al.)• Actinopterygian phylogeny and evolution based on 327 whole mitochondrial genome sequences
(Miya et al.)• Evolution of mitochondrial genomes of fishes based on the data from 250 species (Satoh et al.)
2. Local analysis of phylogeny and evolutionOsteoglossomorpha (Lavoué et al.); Anguilliformes (Inoue et al.); Clupeiformes (Lavoué et al); Cypriniformes (Miya et al.); Characiphysi (Nakatani et al.); Aulopiformes (Kawaguchi et al.); Lophiiformes (Miya et al.); Gadiformes (Satoh et al.); Pleuronectiformes (Suzuki et al.);
3. Species/population level phylogeny and evolution• Natural selection along temperature gradient in two populations of Japanese medaka (Mukai et al.)• Patterns of variation in Japanese flounder mitogenomes (Shigenobu et al.)
A project summary—3. Database
Taxonomic searchTaxonomic search
BLAST homology searchBLAST homology search
Top pageTop page
International collaborationAToL
• Grant proposal accepted for “Assembling the Tree of Life” project from NSF in August 2004
• PIs: R. L. Mayden and six US members with 16 scientists participated (including M. Miya and K. Saitoh) from 12 countries
Cypriniformes Tree of Life (CToL) Earth’s Most Diverse Clade of Freshwater Fishes QuickTime˛ Ç∆TIFFÅià≥èkǻǵÅj êLí£ÉvÉçÉOÉâÉÄǙDZÇÃÉsÉNÉ`ÉÉÇ å©ÇÈÇΩÇflÇ…ÇÕïKóvÇ≈Ç∑ÅB
• Five years project beginning from September 2004
• Grant proposal accepted for Grants-in-Aid (Scien-tific Research A) from JSPS on 18 April 2005
• PI: M. Miya; Co-PIs: M. Nishida and K. Saitoh
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Family
Tribe
Genus
Species
Cypriniformes350 genera, 3285 spp.
Phylogeny of the Cypriniformes Mitogenomic Resolution of a Big Phylogeny
• Four years project beginning from April 2005