Heron Island, GBR

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A Primer on Phylogenetics of Holothuroids
alexander.kerr_at_aya.yale.edu
Heron Island, GBR
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Simple model of character evolution
Phylogenetic estimation
Morphology versus molecules
Ideal taxonomic characters
Multigene tree of Aspidochirotida
Gervais 1871
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Simple model of character evolution
Phylogenetic estimation
Morphology versus molecules
Ideal taxonomic characters
Multigene tree of the Aspidochirotida
Gervais 1871
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(No Transcript)
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Principle of parsimony
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Simple model of character evolution
Phylogenetic estimation
Morphology versus molecules
Ideal taxonomic characters
Multigene tree of the Aspidochirotida
Gervais 1871
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Length 11
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Length 9
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Maximum parsimony
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Maximum parsimony
Best when rates of evolution are slow
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Maximum parsimony Maximum likelihood
Best when rates of evolution are slow
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Maximum parsimony Maximum likelihood
Best when rates of evolution are slow Works over
larger range of rates
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Maximum parsimony Maximum likelihood Bayesian
analysis
Best when rates of evolution are slow Works over
larger range of rates
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Maximum parsimony Maximum likelihood Bayesian
analysis
Best when rates of evolution are slow Works over
larger range of rates Computationally more
efficient than ML
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Maximum parsimony Maximum likelihood Bayesian
analysis Minimum evolution Neighbour-joining UPG
MA Divide and conquer
Best when rates of evolution are slow Works over
larger range of rates Computationally more
efficient than ML
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Simple model of character evolution
Phylogenetic estimation
Morphology versus molecules
Ideal taxonomic characters
Multigene tree of the Aspidochirotida
Gervais 1871
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MORPHOLOGY
MOLECULES
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MORPHOLOGY Easily documented
MOLECULES
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MORPHOLOGY Easily documented
MOLECULES Expensive to document
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MORPHOLOGY Easily documented 150 characters
known for Holothuroidea
MOLECULES Expensive to document
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MORPHOLOGY Easily documented 150 characters
known for Holothuroidea
MOLECULES Expensive to document gt7000 sequenced
to date
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MORPHOLOGY Easily documented 150 characters
known for Holothuroidea Rate of evolution
unknown for most
MOLECULES Expensive to document gt7000 sequenced
to date
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MORPHOLOGY Easily documented 150 characters
known for Holothuroidea Rate of evolution
unknown for most
MOLECULES Expensive to document gt7000 sequenced
to date Well corroborated models of evolution
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MORPHOLOGY Easily documented 150 characters
known for Holothuroidea Rate of evolution
unknown for most Few small independently
evolving sets of characters
MOLECULES Expensive to document gt7000 sequenced
to date Well corroborated models of evolution
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MORPHOLOGY Easily documented 150 characters
known for Holothuroidea Rate of evolution
unknown for most Few small independently
evolving sets of characters
MOLECULES Expensive to document gt7000 sequenced
to date Well corroborated models of
evolution Unlimited sets of independently
evolving characters
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Simple model of character evolution
Phylogenetic estimation
Morphology versus molecules
Ideal taxonomic characters
Multigene tree of the Aspidochirotida
Gervais 1871
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Monophyletic
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Clades
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Non-monophyletic
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Homoplasy
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IDEAL TAXONOMIC FEATURES
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IDEAL TAXONOMIC FEATURES
Taxa descended from a common ancestor
Monophyletic
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IDEAL TAXONOMIC FEATURES
Taxa descended from a common ancestor Taxa
consist of all members of a lineage
Monophyletic Clades
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IDEAL TAXONOMIC FEATURES
Taxa descended from a common ancestor Taxa
consist of all members of a lineage No reversals
in characters states of diagnostic criteria
Monophyletic Clades No homoplasy
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Simple model of character evolution
Phylogenetic estimation
Morphology versus molecules
The hegemony of spicules
Multigene tree of the Aspidochirotida
Gervais 1871
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Marker 18S 28S Histone 3 12S 16S
Length (nt) 1900 3500 400 350 550
Type Nuclear rDNA Nuclear rDNA Nuclear protein
coding Mitochondrial rDNA Mitochondrial rDNA
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Holothuriidae is monophyletic
Holothuriidae
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Holothuriidae is monophyletic Holothuria is not
monophyletic
Holothuriidae
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Holothuriidae is monophyletic Holothuria is not
monophyletic Many subgenera in Holothuria are
not monophyletic
Holothuriidae
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Holothuriidae is monophyletic Holothuria is not
monophyletic Many subgenera in Holothuria are
not monophyletic
Holothuriidae
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Holothuriidae is monophyletic Holothuria is not
monophyletic Many subgenera in Holothuria are
not monophyletic
Holothuriidae
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Holothuriidae is monophyletic Holothuria is not
monophyletic Many subgenera in Holothuria are
not monophyletic
Holothuriidae
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Holothuriidae is monophyletic Holothuria is not
monophyletic Many subgenera in Holothuria are
not monophyletic Stichopodidae may not be
monophyletic
Holothuriidae
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Holothuriidae is monophyletic Holothuria is not
monophyletic Many subgenera in Holothuria are
not monophyletic Stichopodidae may not be
monophyletic Synallactidae is probably not
monophyletic
Holothuriidae
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Holothuriidae is monophyletic Holothuria is not
monophyletic Many subgenera in Holothuria are
not monophyletic Stichopodidae may not be
monophyletic Synallactidae is probably not
monophyletic Holothuriidae appears to consist of
two large clades
Holothuriidae
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Holothuriidae is monophyletic Holothuria is not
monophyletic Many subgenera in Holothuria are
not monophyletic Stichopodidae may not be
monophyletic Synallactidae is probably not
monophyletic Holothuriidae appears to consist of
two large clades
Holothuriinae
Bohadschiinae
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Holothuriidae is monophyletic Holothuria is not
monophyletic Many subgenera in Holothuria are
not monophyletic Stichopodidae may not be
monophyletic Synallactidae is probably not
monophyletic Holothuriidae appears to consist of
two large clades
Holothuriinae
Bohadschiinae
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Holothuriidae is monophyletic Holothuria is not
monophyletic Many subgenera in Holothuria are
not monophyletic Stichopodidae may not be
monophyletic Synallactidae is probably not
monophyletic Holothuriidae appears to consist of
two large clades Only Holothuriinae needs
substantial revision
Holothuriinae
Bohadschiinae
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Holothuriidae is monophyletic Holothuria is not
monophyletic Many subgenera in Holothuria are
not monophyletic Stichopodidae may not be
monophyletic Synallactidae is probably not
monophyletic Holothuriidae appears to consist of
two large clades Only Holothuriinae needs
substantial revision Numerous non-traditional
characters diagnose aspidochirote clades
Holothuriinae
Bohadschiinae
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Holothuriidae is monophyletic Holothuria is not
monophyletic Many subgenera in Holothuria are
not monophyletic Stichopodidae may not be
monophyletic Synallactidae is probably not
monophyletic Holothuriidae appears to consist of
two large clades Only Holothuriinae needs
substantial revision Numerous non-traditional
characters diagnose aspidochirote clades
Holothuriinae
Bohadschiinae
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Holothuriidae is monophyletic Holothuria is not
monophyletic Many subgenera in Holothuria are
not monophyletic Stichopodidae may not be
monophyletic Synallactidae is probably not
monophyletic Holothuriidae appears to consist of
two large clades Only Holothuriinae needs
substantial revision Numerous non-traditional
characters diagnose aspidochirote clades
Holothuriinae
Bohadschiinae
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Forbes 1841