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Recent advances in molecular phylogenies of actinopterygian fishes

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... Ray-finned Fishes DeepFin will Advance The Phylogeny of Fishes A Research Coordination Network To promote fish phylogenetics (resolve the fish tree!) – PowerPoint PPT presentation

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Title: Recent advances in molecular phylogenies of actinopterygian fishes


1
Recent advances in molecular phylogenies of
actinopterygian fishes
  • Guillermo Ortí
  • University of Nebraska, USA

2
Molecular Systematics of Ray-finned Fishes
3
DeepFin will Advance The Phylogeny of Fishes A
Research Coordination Network
  1. To promote fish phylogenetics (resolve the fish
    tree!)
  2. To develop cyberinfrastructure, a portal for fish
    phylogenetics (www.deepfin.org) with networking
    tools and interconnected relational databases
  3. To develop educational material to foster
    education on fish biodiversity, fish evolution,
    and current knowledge on the phylogenetic
    relationships of fishes

4
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5
DeepFin will Advance The Phylogeny of Fishes A
Research Coordination Network
  • To promote fish phylogeneticshow far are we from
    the tree of all fishes??
  • Integrate all sources of information
  • Morphology
  • Genetics
  • Paleontology

6
Issues with molecular phylogenies based on a
single gene or few loci
  • Low resolution or low support (characters v taxa)
  • Conflicts among trees inferred from different
    loci.
  • Analytical reasons (base compositional bias /
    long branch attraction / heterotachy).

7
GC at the 3rd codon position of RAG 1
Muraenesox
Gonostoma
Albuliformes
Ogcocephalus
galaxiids
Colisa
Elops
Engraulis
Arnoglossus
Trigla
scorpaenids
Albula
Sparus
Gasterosteus
Megalops
Mean
1
Zeus
Lophiiformes
Basal neoteleosts
0.5
Paracanthop.
Elopomorpha
Ostariophysi
Acanthopterygii
Protacanthop.
0
Basal actinop.
Polypteriformes
Stomiiformes
Osteoglosso.
Clupeomorpgha
Elasmobranchii
Tetrapoda
8
Issues with molecular phylogenies based on a
single gene or few loci
  • Low resolution or low support (characters v taxa)
  • Conflicts among trees inferred from different
    loci.
  • Biological reasons (gene tree vs. organismal tree)

9
Gene trees within organismal trees
Lineage sorting
Gene duplication
Horizontal transfer
10
Phylogenomics use many (genome-scale) loci to
infer phylogeny
  • Large number of characters will increase
    statistical power
  • Analysis of many independent loci may reduce
    systematic error
  • Genome-scale nuclear gene markers will be more
    likely to represent organismal evolution

11
How to collect phylogenomic data (from multiple
loci)
  • Using available genome databases (model
    organisms)
  • Sequencing cDNA/EST libraries
  • Directly amplify and sequence target fragments
    from genomic DNA using universal nuclear markers

How can we find new universal nuclear gene
markers???
12
Three criteria to choose good nuclear gene
markers
  1. Orthologous genes should be easy to identify and
    amplify in all taxa of interest. To minimize the
    chance of mistaken paralogy, we seek only
    single-copy genes (so, what about gene
    duplications?)

Chenhong Li (UNL) and Guoqing Lu (UN-Omaha)
13
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14
Three criteria to choose good nuclear gene
markers
  • 2) The amplicon (i.e. target sequences
    amplified by the PCR primers) should be of
    reasonable size (exons gt800 bp).

15
Three criteria to choose good nuclear gene
markers
  • 3) The gene should be reasonably conserved,
    so universal primers can be designed and the
    sequences can be easily aligned.

16
  • If we agree with these 3 criteria (single copy,
    long exon, reasonable conservation) for good
    nuclear makers, randomly testing genes provides
    a poor chance to finding a good marker
    (additional criteria are possible)
  • Directly apply the 3 criteria to screen genomes
    of two model organisms, zebrafish (Danio rerio)
    and pufferfish (Takifugu rubripes).

17
Scheme of our marker-developing strategy 130
candidate loci were identified in silico
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Distribution of 109 candidate markers in
zebrafish chromosomes
109 are located on 24 of the 25 chromosomes (21
with no location information). Chi-square test
did not reject the Poisson distribution of these
markers (p0.0746).
21
Summary of the 130 candidate loci
  • Size range from 802 bp to 5811 bp in zebrafish.
  • Base composition GC content ranges from 41.6 to
    63.9 in zebrafish.
  • Identity of these markers between zebrafish and
    pufferfish ranges from 77.3 to 93.2.

22
Experimental test of the candidate markers
  • A random sample of 15 candidate markers was
    examined in 52 ray-finned fish taxa (40/47 orders
    of Actinopterygii).
  • PCR primers were designed to conserved regions
    (nested PCR strategy)
  • 10 out of the 15 markers tested were successfully
    amplified by PCR from genomic DNA in most taxa

23
Marker Exon ID PCR Fragment Size (bp) No. of PI sites Average p-distance
zic1 ENSDARE00000015655 945 344 0.156
myh6 ENSDARE00000025410 735 329 0.179
RYR3 ENSDARE00000465292 837 421 0.210
ptr ENSDARE00000145053 708 372 0.205
tbr1 ENSDARE00000055502 723 313 0.189
ENC1 ENSDARE00000367269 810 360 0.180
Gylt ENSDARE00000039808 882 510 0.211
SH3PX3 ENSDARE00000117872 708 317 0.167
plagl2 ENSDARE00000136964 690 345 0.173
sreb2 ENSDARE00000029022 987 387 0.149
24
New Data 10 genes 8025 bp 52 taxa ML tree
25
POLYPTERIFORMES
ACIPENSERIFORMES
SEMIONOTIFORMES
AMIIFORMES
OSTEOGLOSSOMORPHA
ELOPOMORPHA
CLUPEOMORPHA
OSTARIOPHYSI
PROTACANTHOPTERYGII
TELEOSTEI
STOMIIFORMES
ATELEOPODIFORMES
EUTELEOSTEI
AULOPIFORMES
MYCTOPHIFORMES
NEOTELEOSTEI
LAMPRIDIFORMES
POLYMIXIIFORMES
ACANTHOMORPHA
PARACANTHOPTERYGII
Nelson 94
ACANTHOPTERYGII
26
Basal Actinops
Polypterus
sturgeons
gars
Holostei
Amia
Teleostei
1. G. Nelson (1969) -- branchial arch morphology
27
Basal Actinops
Polypterus
gars
Holostei
Amia
Teleostei
sturgeons
2. Jessen (1973) -- pectoral anatomy
28
Basal Actinops
Polypterus
sturgeons
Amia
Teleostei
gars
3. Olsen (1984) -- skull and pectoral girdle
29
Basal Actinops
Chondrostei
Polypterus
sturgeons
gars
Amia
Teleostei
4. J. Nelson (1994) -- most reasonable
30
Basal Actinops
Polypterus
sturgeons
gars
Amia
Teleostei
5. Bemis et al (1997) -- morphology
31
Basal Actinops
Polypterus
sturgeons
gars
Amia
Teleostei
6. Lê et al (1993) -- 28S rRNA Venkatesh
et al (1999)-- 8 nuclear introns
32
Basal Actinops
Polypterus
sturgeons
gars
Holostei
Amia
Teleostei
7. Inoue et al -- mtDNA Ortí et al RAG-1, and
rhodopsin
33
Basal Actinopterygians
34
Basal Actinops
Holostei
mtDNA, 421 taxa, ME tree
35
POLYPTERIFORMES
ACIPENSERIFORMES
SEMIONOTIFORMES
AMIIFORMES
OSTEOGLOSSOMORPHA
Basal teleosts
ELOPOMORPHA
CLUPEOMORPHA
OSTARIOPHYSI
PROTACANTHOPTERYGII
TELEOSTEI
STOMIIFORMES
ATELEOPODIFORMES
EUTELEOSTEI
AULOPIFORMES
MYCTOPHIFORMES
NEOTELEOSTEI
LAMPRIDIFORMES
POLYMIXIIFORMES
ACANTHOMORPHA
PARACANTHOPTERYGII
Nelson 94
ACANTHOPTERYGII
36
Elopomorpha
10 genes 8025 bp
37
POLYPTERIFORMES
ACIPENSERIFORMES
SEMIONOTIFORMES
AMIIFORMES
OSTEOGLOSSOMORPHA
ELOPOMORPHA
CLUPEOMORPHA
Clupeo-Ostario
OSTARIOPHYSI
PROTACANTHOPTERYGII
TELEOSTEI
STOMIIFORMES
ATELEOPODIFORMES
EUTELEOSTEI
AULOPIFORMES
MYCTOPHIFORMES
NEOTELEOSTEI
LAMPRIDIFORMES
POLYMIXIIFORMES
ACANTHOMORPHA
PARACANTHOPTERYGII
Nelson 94
ACANTHOPTERYGII
38
10 genes 8025 bp
39
POLYPTERIFORMES
ACIPENSERIFORMES
SEMIONOTIFORMES
AMIIFORMES
OSTEOGLOSSOMORPHA
ELOPOMORPHA
CLUPEOMORPHA
OSTARIOPHYSI
PROTACANTHOPTERYGII
TELEOSTEI
STOMIIFORMES
ATELEOPODIFORMES
EUTELEOSTEI
AULOPIFORMES
MYCTOPHIFORMES
NEOTELEOSTEI
LAMPRIDIFORMES
POLYMIXIIFORMES
ACANTHOMORPHA
PARACANTHOPTERYGII
Nelson 94
ACANTHOPTERYGII
40
10 genes 8025 bp
41
PI, parsimony informative sites SDR, standard
deviation of substitution rates among three codon
positions CI-MP, consistency index ?, gamma
distribution shape parameter RCV, relative
composition variability. Treeness, ratio of
internal branch length to total branch length.
42
Summary
  • Gene markers that satisfied the three criteria
    are widely distributed in zebrafish genome
  • Ten out of 15 markers tested seem useful for
    phylogenetic inference. Their profiles are
    comparable to the popular RAG1 gene
  • The strategy is successful!
  • The new markers developed will help to infer the
    tree of ray-finned fishes
  • The bioinformatic tool developed can be used in
    other taxonomic groups (S similarity may vary)

43
www.deepfin.org
44
www.deepfin.org
  • Member data base (Directory) currently has 606
    records

45
www.deepfin.org
  • Literature data base currently has 800 records
  • (for members only)

46
www.deepfin.org -- Literature data base
47
www.deepfin.org
  • Literature data base upload pdf files to share
    with other members

48
  • Collaboratories a virtual environment to share
    files and information

49
www.tolweb.org
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Contribute tree pages!
55
Join DeepFin !
  • Questions, comments, suggestions?
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