Ozzie VilhelmssonZoology Building, Room 213Tel.: (01224 27) 2867Email: o.vilhelmsson@abdn.ac.uk

Estimating and using phylogenies

• 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

Fossils

• Incompleteness of fossil record

• Fossilization an unlikely event

• Only found in sedimentary rocks

• Habitat bias

• Age known

• Intermediates observed

• Can access extinct lines

PHYLOGENETIC TREES

• Pedigree of a lineage

• Evidence of dates of separation

Time Time

(trees)

• Morphology

• Development

• Metabolic

• Biochemical

• Genetic

• Anything, really

Tree constructionTree construction

Similarity matrix(numerical taxonomy)

Tree

Gather data:

Simple, right?

But, ....

... Different data can yield different trees!

Turtle/birds/crocodile picture

CLADISTICSCLADISTICS

Aims to distinguish reliable from unreliable characters:

Homologies vs. Homoplasies

Derived vs. ancestral homologies

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

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

Why the fuss?

Only this one is useful!

To reiterate:

• Derived homologous traits order TIME of separation

• Ancestral homologous traits no use for this -all members of lineage have them

• Divergence = traits unrecognizable– eg. plant leaves

Identifying non-useful traits

(fig. 23.4 in textbook)

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

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

What about wings?Homoplaseous? Ancestral? Derived?

Homoplasy/homology depends on reference/outgroup

Fig. 23.2 in textbook

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)

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

(Panda example)

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!

PARSIMONY

(“counting changes” picture)

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.)

Drawing a cladogram

• 8 vertebrates

• traits +/-

• hagfish = outgroup

• derived traits = acquired since hagfish

• cladistics minimizes branching - ie. assumes minimal homoplasy

Drawing a cladogramDerived trait

TaxonJaws Lungs Claws or

nailsFeathers Fur Mammary

glandsFour-chambered

heartHagfish - - - - - - -Perch + - - - - - -Salamander + + - - - - -Lizard + + + - - - -Crocodile + + + - - - +Pigeon + + + + - - +Mouse + + + - + + +Chimpanzee + + + - + + +

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

Properties of cladogams

• Temporal order of splits

• Horizontal axis NOT correlated with similarity

• 8 vertibrates cladogram = perfect because traits arose & not lost - BUT SNAKES???

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??

Defining clades

• Monophyletic - share common ancestor

• Polyphyletic - NO common ancestor

• Paraphyletic - some, but not all, from common ancestor

(mon/para/polyphyletic picture; similar to 23.12 in textbook)

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

Systematicists

• Still many polyphylectic groups

• Detect convergent evol. ==> change classification

• BUT favour retaining paraphyletic groups to underscore rapid evolution

• STABILITY of taxonomic system

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