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Estimating and using phylogenies

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Presentation on theme: "Estimating and using phylogenies"— Presentation transcript:

1 Estimating and using phylogenies
Ozzie Vilhelmsson Zoology Building, Room 213 Tel.: ( ) 2867 Estimating and using phylogenies

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

3 Fossils Incompleteness of fossil record
Fossilization an unlikely event Only found in sedimentary rocks Habitat bias Age known Intermediates observed Can access extinct lines

4 PHYLOGENETIC TREES Pedigree of a lineage
Evidence of dates of separation (trees) Time Time

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

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

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

8 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)

9 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

10 Why the fuss? Only this one is useful!

11 To reiterate: Derived homologous traits order TIME of separation
Ancestral homologous traits no use for this -all members of lineage have them

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

13 (fig in textbook)

14 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

15 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

16 What about wings? Homoplasy/homology depends on reference/outgroup
Homoplaseous? Ancestral? Derived? Fig in textbook Homoplasy/homology depends on reference/outgroup

17 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:

18 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

19 (Panda example)

20 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!

21 PARSIMONY (“counting changes” picture)

22 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.)

23 Drawing a cladogram 8 vertebrates traits +/- hagfish = outgroup
derived traits = acquired since hagfish cladistics minimizes branching - ie. assumes minimal homoplasy

24 Drawing a cladogram

25 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

26 Properties of cladogams
Temporal order of splits Horizontal axis NOT correlated with similarity 8 vertibrates cladogram = perfect because traits arose & not lost - BUT SNAKES???

27 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??

28 Defining clades Monophyletic - share common ancestor
Polyphyletic - NO common ancestor Paraphyletic - some, but not all, from common ancestor

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

30 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

31 Systematicists Still many polyphylectic groups
Detect convergent evol. ==> change classification BUT favour retaining paraphyletic groups to underscore rapid evolution STABILITY of taxonomic system

32 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

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