Estimating and using phylogenies Ozzie Vilhelmsson Zoology Building, Room 213 Tel.: (01224 27) 2867 Email: o.vilhelmsson@abdn.ac.uk Estimating and using phylogenies

Taxonomy and Phylogeny What fossils tell us What living organisms tell us Cladistics Constructing phylogenies Classification & Evolutionary Relationships Molecular Analyses - the way ahead!

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 (trees) Time Time

Tree construction Similarity matrix Tree Simple, right? Gather data: Morphology Development Metabolic Biochemical Genetic Anything, really Similarity matrix (numerical taxonomy) Tree Simple, right?

But, .... Turtle/birds/crocodile picture ... Different data can yield different trees!

CLADISTICS Aims to distinguish reliable from unreliable characters: Homologies vs. Homoplasies Derived vs. ancestral homologies

CLADISTICS 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)

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

Identifying non-useful traits Divergence = traits unrecognizable eg. plant leaves

(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? Homoplasy/homology depends on reference/outgroup Homoplaseous? Ancestral? Derived? Fig. 23.2 in textbook Homoplasy/homology depends on reference/outgroup

Rooting the tree Having figured out which traits are important, we can draw a cladogram. But, where does it root? (Possible roots picture) Distance Parsimony Maximum likelihood Three methods:

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 cladogram

A phylogenetic tree Relative evolutionary time Ancient events Hagfish Perch Salamander Lizard Crocodile Pigeon Mouse Chimpanzee Lungs Jaws Claws or nails Four-chambered heart Feathers Fur, mammary glands 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