ozzie vilhelmsson zoology building, room 213 tel.: (01224 27) 2867 email: [email protected]...
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Ozzie VilhelmssonZoology Building, Room 213Tel.: (01224 27) 2867Email: [email protected]
Estimating and using phylogenies
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• What fossils tell us
• What living organisms tell us
• Cladistics
• Constructing phylogenies
• Classification & Evolutionary Relationships
• Molecular Analyses - the way ahead!
Taxonomy and PhylogenyTaxonomy and Phylogeny
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Fossils
• Incompleteness of fossil record
• Fossilization an unlikely event
• Only found in sedimentary rocks
• Habitat bias
• Age known
• Intermediates observed
• Can access extinct lines
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PHYLOGENETIC TREES
• Pedigree of a lineage
• Evidence of dates of separation
Time Time
(trees)
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• Morphology
• Development
• Metabolic
• Biochemical
• Genetic
• Anything, really
Tree constructionTree construction
Similarity matrix(numerical taxonomy)
Tree
Gather data:
Simple, right?
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But, ....
... Different data can yield different trees!
Turtle/birds/crocodile picture
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CLADISTICSCLADISTICS
Aims to distinguish reliable from unreliable characters:
Homologies vs. Homoplasies
Derived vs. ancestral homologies
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Method of determining evolutionary histories - displayed as trees
Clade: entire portion of phylogeny from a common ancestor = Monophyletic group
Cladogram: unrooted evolutionary tree (no ancestors but points where lineages diverged)
CLADISTICSCLADISTICS
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HOMOLOGIES
• A trait shared between species and inherited from their common ancestor = homologous
• Ancestral (general) homologies: shared by all species in lineage - eg. vertebrae in vertebrates
• Derived (special) homologies: shared by few species in lineage - eg. indeterminate incisors in vertebrates
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Why the fuss?
Only this one is useful!
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To reiterate:
• Derived homologous traits order TIME of separation
• Ancestral homologous traits no use for this -all members of lineage have them
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• Divergence = traits unrecognizable– eg. plant leaves
Identifying non-useful traits
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(fig. 23.4 in textbook)
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Identifying non-useful traits
• Divergence = traits unrecognizable– eg. plant leaves
• Homoplasy = trait evolves more than once– different structures resemble each other by
convergent evolution eg. bat/bird/insect wings
• Both cases = analogous traits
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Hennig’s Method
• Same trait in 2 species = provisionally homologous ie. innocent, until proven guilty
• Ancestral homology = found in group and outside in species = outgroup
• Outgroup = branched off from below base of lineage
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What about wings?Homoplaseous? Ancestral? Derived?
Homoplasy/homology depends on reference/outgroup
Fig. 23.2 in textbook
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Rooting the treeHaving figured out which traits are important, we can draw a cladogram. But, where does it root?
• Distance• Parsimony• Maximum likelihood
Three methods:
(Possible roots picture)
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Distance
• Simple principle: How similar are the species? (similarity matrix/measurement)
• Works well for simple molecular methods, such as DNA:DNA hybridization data
• “Molecular clock” assumption
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(Panda example)
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PARSIMONY
• Simple distance rooting assumes:
–trait evolution irreversible, ie. ancestral to derived
–trait can change only once per lineage UNREALISTIC
• But, cladogram requiring fewest reversals/changes most likely to be correct
• PARSIMONY = simplest is correct!
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PARSIMONY
(“counting changes” picture)
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Maximum likelihood
• Requires a lot of data, massive computing power
• Need model of evolutionary change to calculate probabilities
• Probably the most widely used method today (sequence homologies, etc.)
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Drawing a cladogram
• 8 vertebrates
• traits +/-
• hagfish = outgroup
• derived traits = acquired since hagfish
• cladistics minimizes branching - ie. assumes minimal homoplasy
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Drawing a cladogramDerived trait
TaxonJaws Lungs Claws or
nailsFeathers Fur Mammary
glandsFour-chambered
heartHagfish - - - - - - -Perch + - - - - - -Salamander + + - - - - -Lizard + + + - - - -Crocodile + + + - - - +Pigeon + + + + - - +Mouse + + + - + + +Chimpanzee + + + - + + +
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Hagfish
Perch
Salamander
Lizard
Crocodile
Pigeon
Mouse
Chimpanzee
Jaws
Lungs
Claws ornails
Four-chamberedheart
Fur, mammaryglands
Feathers
A phylogenetic tree
Relative evolutionary time
Ancient events Recent events
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Properties of cladogams
• Temporal order of splits
• Horizontal axis NOT correlated with similarity
• 8 vertibrates cladogram = perfect because traits arose & not lost - BUT SNAKES???
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Classification & Evolutionary Relationships
• Linnaeus - predated evolution as central concept of biology– but what features natural? important?
• Modern taxonomists - classification reflects evolutionary relationships– BUT should classification reflect time or rate
of evolution??
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Defining clades
• Monophyletic - share common ancestor
• Polyphyletic - NO common ancestor
• Paraphyletic - some, but not all, from common ancestor
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(mon/para/polyphyletic picture; similar to 23.12 in textbook)
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The problem of paraphyly
• Birds and crocodiles - more recent ancestor than crocs. and snakes/lizards
• Crocs. evolved more slowly than birds since lineages separated
• Birds as separate class recognizes their rapid evolution = major unique derived traits
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Systematicists
• Still many polyphylectic groups
• Detect convergent evol. ==> change classification
• BUT favour retaining paraphyletic groups to underscore rapid evolution
• STABILITY of taxonomic system
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Future of Systematics
• Molecular genetics & powerful computers
• Fossil history - dating and derived vs ancestral traits
• Molecular = more traits than ever before
• Combining two lines of evidence produces accurate dated phylogenies