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