BIOL 2040 Lecture Notes - Lecture 4: Eucalyptus Pauciflora, Ultrametric Space, Genetic Drift
3 May 2018
School
Department
Course
Professor
Phylogeny Estimation
September 22 & 24, 2015
Why reconstruct phylogenies?
• Understand evolutionary relationships
• Test hypotheses about evolution
o Understand trait evolution from ordered grouping
o Study adaptation: P)Cs comparative method
o Rates of evolution
▪ Phenotypic evolution
▪ Molecular evolution
▪ Rates of speciation
Why do biological groups differ in a nested fashion?
Ex. Velvet worm, Onychophora
• A fire interrupts a population of worms and prevents gene flow between Scribbly Gum and
Snow Gum gullies
o Genetic variation occurs in this population
o *Note: Gully’s are wet environments
o One population contained a single unique organism
• In the scribbly pop a mutation occurred (pheromone)
• In the snow pop substitution by random genetic drift creates a new genetic makeup
• Forest grows back in previously burnt area
o Migration occurs but no mating can happen due to pheromones in one population
(no real gene flow)
• If another tree falls and separates the population within snow gum gully, random genetic
drift causes substitution in small population
• Therefore, result is 3 genetically isolated populations
find more resources at oneclass.com
find more resources at oneclass.com
Facts about Phylogenic Trees
• Tree terminology:
o Terminal node
o Internal node – ancestor
o Branch
o Root
• Causes of similarity:
o Homologous: inherited from a common ancestor (ex. Human and mouse eyes)
o Homoplasious: similar but not because of inheritance from a common ancestor
1. Convergent evolution in two different organisms: analogous
characters
2. Character reversals
• Types of Phylogenic Trees: *all styles (box/branch/web) are equivalent – can rotate about
any node; Always look for nested clades, not order of branch tips.
o Cladogram – branching order only
o Ultrametric – length of branch is proportional to the divergent time
o Phylogram – conveys sense of time or rate of evolution; distances apart recorded
▪ Branch lengths indicate genetic distance:
• Average number of nucleotide substitutions per site in descendant
• Number of substitutions per site under some more-or less
complicated model of evolution
• Relatedness:
o Are crocodiles more closely related to lizards or birds?
▪ Crocodiles are more closely related to birds because they share a common
ancestor more recently
o Are frogs more closely related to fishes or to human?
▪ Frogs are more closely related to humans because their last common
ancestor is also that of humans but fish were already existing
• Misconception: trait evolution only occurs at nodes
o Trait evolution can occur everywhere along branches
o Nodes are where populations became genetically isolated, permitting them to
accumulate differences independently during subsequent evolution
Logic of Building Phylogenic Trees
Ideal Case:
• Consider 4 species
o Known common ancestor
o Each new trait evolved only once (no homoplasy)
o Once evolved, trait was never lost
• Ex. 4 birds
• Discern 5 traits:
o Determine unique derived characters
o Determine shared derived characters: synapomorphies
• Unique characters must have evolved after the split from ancestors
(no reversals in this example)
• Ex. Unique: mask, wing tips, dark tail, long bill; shared: tail bar
• Plesiomorphies & apomorphies – depends on context:
o Plesiomorphies – ancestral character (within set of masked species)
o Apomorphy – derived character (mask- all 4 share)
• Monophyletic groups: include ancestor and all descendants
find more resources at oneclass.com
find more resources at oneclass.com
Document Summary
Why reconstruct phylogenies: understand evolutionary relationships, test hypotheses about evolution, understand trait evolution from ordered grouping, study adaptation: p)cs (cid:523)(cid:498)comparative method(cid:499)(cid:524, rates of evolution, phenotypic evolution, molecular evolution, rates of speciation. Velvet worm, onychophora: a fire interrupts a population of worms and prevents gene flow between scribbly gum and. Snow gum gullies: genetic variation occurs in this population. *note: gully"s are wet environments: one population contained a single unique organism. In the scribbly pop a mutation occurred (pheromone) In the snow pop substitution by random genetic drift creates a new genetic makeup: forest grows back in previously burnt area, migration occurs but no mating can happen due to pheromones in one population (no real gene flow) If another tree falls and separates the population within snow gum gully, random genetic drift causes substitution in small population: therefore, result is 3 genetically isolated populations. Facts about phylogenic trees: tree terminology, terminal node.
