spring 2014: mondays 10:15am – 12:05pm (fox hall, room 204)
TRANSCRIPT
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LECTURE 07
Spring 2014: Mondays 10:15am – 12:05pm (Fox Hall, Room 204)
Instructor: D. Magdalena SorgerWebsite: theantlife.com/teaching/bio295-islands-evolution
Today:
Quiz
Follow‐up on minute papers
Sexual selection (cont.)
Evolutionary trees• Interpret a phylogenetic tree
• Explain how to infer phylogenies
• Describe different methods to infer phylogenies
• Discuss difficulties in phylogenetic analysis
• Give an example how phylogenetic tree is used to test a hypothesis
Guest speaker: Dr. Brian Wiegmann
Summary
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FOLLOW-UP MINUTE PAPERS
Follow‐up on minute papers
• What defines a subspecies?
• How do small arthropods get to islands?
• Birds of paradise – how did they evolve such crazy features? beneficial for survival?
• More on cichlids
• Sperm competition in a monogamous system?
• Any cases with significant investment by males?
• Answers from Dr. Fergus posted online
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EVOLUTIONARY TREES
0.005 changes
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L. hapapa
L. hualalai
L. pruna
L. kohalensis
L. kona
L. paranigra
L. makaio
L. orientalis
L. vespertina
L. molokaiensis
L. tantalis
L. wailua
L. kokeensis
L. prosea
L. nigra
L. koloa
P. kukui
L. cerasina
L. fugax
L. eukolea
L. melewiki
L. spisa
L. neospisa
L. oahuensis
L. pacifica
L. kanaele
What can you tell me about this
phylogenetic tree?
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Phylogenetic tree (phylogeny)
• graphical summary of evolutionary history of a group
• pattern (and timing) of events that occurred as species diversified
• records sequence in which lineages appeared
• documents which organisms are more closely related
Reconstructing evolutionary history is like solving a crime…
We cannot directly observe it, we must infer using deductive logic.
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Phylogenetics= the study of evolutionary relationships among organisms
Taxonomy= classification and naming of organisms
Systematics= Phylogenetics & Taxonomy
Traditionally: Morphology.
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Classification (Taxonomic categories)KingdomPhylumClassOrderFamilyGenusSpecies
ClassificationKingdomPhylumClassOrderFamilyGenusSpecies
AnimaliaArthropoda
InsectaHymenoptera
FormicidaeOdontomachus
relictus
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Taxon (pl. Taxa)= particular group of organisms assigned to a categorical rank
Most recent common ancestor (MRCA)
Family tree
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Most recent common ancestor
1st cousins
1st cousins
Grandfather
Most recent common ancestor
3rd cousins
3rd cousins
Great‐great‐grandmother
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What a tree represents
“REAL” EVOLUTIONARY HISTORY
SUMMARY OF “REAL” EVOLUTIONARY HISTORY
4 alternative trees: same evolutionary history
don’t be distracted by shape or proximity of tips to each other
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Who is more closely related?
MRCA
Who is more closely related?
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Who is more closely related?
Who is more closely related?
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Who is more closely related?
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3 alternative trees: same evolutionary history
order of taxa on tree does not matter, phylogeny grows by lineage splitting
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Ancestral character state= found in common ancestor (plesiomorphic)
Derived character state= state has evolved from ancestral state (apomorphic)
Synapomorphy= shared, derived character state
Autapomorphy= derived character state unique to particular taxon
Homology= shared character state due to common ancestry
Homoplasy= parallel/convergent evolution
Monophyletic group= common ancestor and all descendants of that ancestor (CLADE), identified by synapomorphies
Polyphyletic/Paraphyletic
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HOW TO INFER PHYOGENIES
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When did legs evolve?
origin of legs
When did legs evolve?
origin of legs
secondary loss of legssecondary loss of legssecondary loss of legs
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When did legs evolve?
independent origins of legsindependent origins of legsindependent origins of legsindependent origins of legs
When did legs evolve?
Most “parsimonious” option!
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Main methods of inferring phylogenies
• Parsimony methods: minimize number of evolutionary changes needed to explain traits of tips, fewest homoplasiouschanges, bootstrapping
• Distance methods: tree on which difference between each pair of tips is most similar to evolutionary distance between those two tips, algorithmic method, single tree estimated (distance matrix, neighbor‐joining)
• Likelihood methods: tree that most likely generated observed data (given statistical model on how traits evolve)
• Bayesian methods: tree that most likely is true given data, model of evolution and prior beliefs about evolutionary process
Bootstrapping
• Many random subsamples of characters are used for repeated phylogenetic analyses
• Confidence in reliability of particular grouping greater if grouping is consistently found by using different data sets (bootstrap samples)
35 characters total:1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35
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Bootstrapping
• Many random subsamples of characters are used for repeated phylogenetic analyses
• Confidence in reliability of particular grouping greater if grouping is consistently found by using different data sets (bootstrap samples)
35 characters total:1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35
?
Bootstrapping
• Many random subsamples of characters are used for repeated phylogenetic analyses
• Confidence in reliability of particular grouping greater if grouping is consistently found by using different data sets (bootstrap samples)
35 characters total:1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35
?
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TA C C C A C C G C G T TA C T T T C A A C C G C G T TA C T T C A A C C C G C G T TA C TAT C GTA C T C A C C G C G T TA C T T T C A A C C G C G T TA C T T C A ‐ ‐ ‐ C C G C G T TA C TAT C GTA C T C ‐ C C A C G T TA C T T T C A A C C G C T T TA C T T C A A A C C G ‐ G T TA C TAT C GTA C T C A C C G C G G TA C T T T C A ‐ C C G C G T TA C T T C A A A C C G C G T TA C TAT C GTA C T C A C C G C G T TA C T T T C A A C C G C G T T T C T ‐ C A A A C C G C G T TA C TAT C GTA C T C A C C G C G T TA C T T T C A A C C G C G T TA C T T C A A A C C G C G T TA C TAT C GTA C C A C C C G T TA C ‐ ‐ ‐ T T T T C C A A G C G T T TATA A C G T C TA C C T T G C A C C C C
Sequence alignment: 7 taxa
Bootstrap
ping
T A C C C A C C G C G T TA C T T T C A A C C G C G T TA C T T C A A C C C G C G T TA C TAT C GTA C T C A C C G C G T TA C T T T C A A C C G C G T TA C T T C A ‐ ‐ ‐ C C G C G T TA C TAT C GTA C T C ‐ C C A C G T TA C T T T C A A C C G C T T TA C T T C A A A C C G ‐ G T TA C TAT C GTA C T C A C C G C G G TA C T T T C A ‐ C C G C G T TA C T T C A A A C C G C G T TA C TAT C GTA C T C A C C G C G T TA C T T T C A A C C G C G T T T C T ‐ C A A A C C G C G T TA C TAT C GTA C T C A C C G C G T TA C T T T C A A C C G C G T TA C T T C A A A C C G C G T TA C TAT C GTA C C A C C C G T TA C ‐ ‐ ‐ T T T T C C A A G C G T T TATA A C G T C TA C C T T G C A C C C C
Sequence alignment: 7 taxaBootstrap
ping
?
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TA C C C A C C G C G T TA C T T T C A A C C G C G T TA C T T C A A C C C G C G T TA C TAT C GTA C T C A C C G C G T TA C T T T C A A C C G C G T TA C T T C A ‐ ‐ ‐ C C G C G T TA C TAT C GTA C T C ‐ C C A C G T TA C T T T C A A C C G C T T TA C T T C A A A C C G ‐ G T TA C TAT C GTA C T C A C C G C G G TA C T T T C A ‐ C C G C G T TA C T T C A A A C C G C G T TA C TAT C GTA C T C A C C G C G T TA C T T T C A A C C G C G T T T C T ‐ C A A A C C G C G T TA C TAT C GTA C T C A C C G C G T TA C T T T C A A C C G C G T TA C T T C A A A C C G C G T TA C TAT C GTA C C A C C C G T TA C ‐ ‐ ‐ T T T T C C A A G C G T T TATA A C G T C TA C C T T G C A C C C C
Sequence alignment: 7 taxa
Bootstrap
ping
?
TA C C C A C C G C G T TA C T T T C A A C C G C G T TA C T T C A A C C C G C G T TA C TAT C GTA C T C A C C G C G T TA C T T T C A A C C G C G T TA C T T C A ‐ ‐ ‐ C C G C G T TA C TAT C GTA C T C ‐ C C A C G T TA C T T T C A A C C G C T T TA C T T C A A A C C G ‐ G T TA C TAT C GTA C T C A C C G C G G TA C T T T C A ‐ C C G C G T TA C T T C A A A C C G C G T TA C TAT C GTA C T C A C C G C G T TA C T T T C A A C C G C G T T T C T ‐ C A A A C C G C G T TA C TAT C GTA C T C A C C G C G T TA C T T T C A A C C G C G T TA C T T C A A A C C G C G T TA C TAT C GTA C C A C C C G T TA C ‐ ‐ ‐ T T T T C C A A G C G T T TATA A C G T C TA C C T T G C A C C C C
Sequence alignment: 7 taxaBootstrap
ping
?
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NODE LABELS
Liu et al. 2012
Bootstrap values
Day et al. 2006
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Bayesian methods: posterior probability
Moreira & Brochier‐Armanet 2008
# of estimated changes per position for a unit of
branch length
Both
Liu et al. 2012
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Unrooted tree: no implication of ancestral state
Parmakelis et al. 2008
Rooted tree: reflect most basal ancestor
Day et al. 2006
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4 distinct morphospecies of monkeys
OUTGROUP
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Monophyletic groupRed hair: autapomorphyBig nose: apomorphy
Ancestral state
Monophyletic groupNo tail: synapomorphy
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Monophyletic group
Monophyletic group
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Derived state
Ancestral state
IDENTICAL
Homplasy (Convergent evolution)Also: polyphyletic group
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Molecular clock
• Goal: estimate time since different taxa diverged
• Calculate # of differences (in bp) that have accumulated since common ancestor
• If there is an estimate for absolute time of divergence (fossil), calculate average rate of bpsubstitution
• Problem: what if rate is not constant?!
Difficulties in Phylogenetic Analysis
• Scoring characters is difficult (same character state or not (morphology), base pair changes independent or not (DNA))
• Homoplasy is common (several trees that are equally good, need more data!)
• Evolution often erases traces of prior evolutionary history
• Some lineages diverge rapidly, ancestors of each monophyletic group may not evolve distinctive synapomorphies (adaptive radiations)
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For recently diverged taxa use rapidly evolving DNA sequences
Use slowly evolving sequences to assess relationships among taxa that diverged in distant past
0.005 changes
100
82
100
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100
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88
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100
95
0.43 my
94
100
71
97
73
65
94100
100
100
100
100
98
91
69
L. hapapa
L. hualalai
L. pruna
L. kohalensis
L. kona
L. paranigra
L. makaio
L. orientalis
L. vespertina
L. molokaiensis
L. tantalis
L. wailua
L. kokeensis
L. prosea
L. nigra
L. koloa
P. kukui
L. cerasina
L. fugax
L. eukolea
L. melewiki
L. spisa
L. neospisa
L. oahuensis
L. pacifica
L. kanaele
What can you tell me about this
phylogenetic tree?
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Testing hypothesis using a phylogeny
• Classification & nomenclature
• Timing of evolutionary events using molecular clock
• Phylogeography (= historical processes responsible for current geographic distribution of taxa)
• Cospeciation (coevolution)
• Ancestral state
Classification & nomenclature
assign species names to monophyletic groups only!
0.005 changes
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L. hapapa
L. hualalai
L. pruna
L. kohalensis
L. kona
L. paranigra
L. makaio
L. orientalis
L. vespertina
L. molokaiensis
L. tantalis
L. wailua
L. kokeensis
L. prosea
L. nigra
L. koloa
P. kukui
L. cerasina
L. fugax
L. eukolea
L. melewiki
L. spisa
L. neospisa
L. oahuensis
L. pacifica
L. kanaele
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Timing of evolutionary events using molecular clock
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CASE STUDY EVOLU
TION OF SEXUAL SW
ELLINGS
Natural history
• In some species of old‐world monkeys: Females advertise sexual receptivity
• Tend to live in multi‐male groups
• Sexual swellings don’t occur in apes that live in smaller, single‐male groups (monogamy or harem)
EVOLU
TION OF SEXUAL SW
ELLINGS
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Multi‐maleSingle‐ and multi‐maleSingle‐male
EVOLU
TION OF SEXUAL SW
ELLINGS
Is there a relationship between multimaleness and exaggerated swellings?Swellings evolved 3 times independently, every time associated with evolution of multimalegroups from single‐male ancestral state
EVOLU
TION OF SEXUAL SW
ELLINGS
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What is the ancestral state?No swellings, single‐male
EVOLU
TION OF SEXUAL SW
ELLINGS
Multi‐maleSingle‐ and multi‐maleSingle‐male
2 losses
3 gains
EVOLU
TION OF SEXUAL SW
ELLINGS
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Is there a relationship between multimaleness and exaggerated swellings?Swellings evolved 3 times independently, every time associated with evolution of multimalegroups from single‐male ancestral state
EVOLU
TION OF SEXUAL SW
ELLINGS
What is the ancestral state?No swellings, single‐male
EVOLU
TION OF SEXUAL SW
ELLINGS
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GUEST SPEAKER
Dr. Brian Wiegmann
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Recap
• Sexual selection (cont.)
• Evolutionary trees• Interpret a phylogenetic tree
• Explain how to infer phylogenies
• Describe different methods to infer phylogenies
• Discuss difficulties in phylogenetic analysis
• Give an example how phylogenetic tree is used to test a hypothesis
• Flies
SUMMARY
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SUMMARY
1. What was the most important thing you learned during this class?
2. What important question regarding what you learned remains unanswered for you? (What would you like to know about next?)
NAME & DATE 2/24/2014
For next week:
The Beak of the Finch: Read Chapter 10 & 11
Read paper (will be posted)
Homework due Friday 5pm (28‐Feb)
Draft script due next week! (3‐Mar)