spring 2014: mondays 10:15am – 12:05pm (fox hall, room 204) · lizards in an evolutionary tree:...
TRANSCRIPT
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LECTURE 09
Spring 2014: Mondays 10:15am – 12:05pm (Fox Hall, Room 204)
Instructor: D. Magdalena SorgerWebsite: theantlife.com/teaching/bio295-islands-evolution
Today:
Mini feedback
Follow‐up on minute papers
Evolutionary trees follow‐up
Species concepts• Define “species”• Discuss three of the most common species concepts• Give an example for how to deal with cryptic species
diversity
Independent project: draft presentations
Summary
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FEEDBACK
FOLLOW-UP MINUTE PAPERS
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Follow‐up on minute papers
• Predict analogy/homology in traits?
• How to eliminate discrepancies in molecular clock (rate of base pair changes)?
• How to determine how closely related two species are if look similar but not in same area?
• How to increase confidence, when consider different configuration of tree?
• What’s the point of an unrooted tree?
• Synapomorphy vs. autapomorphy – differences?
EVOLUTIONARY TREES
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Follow‐up: Evolutionary trees
• What is a phylogenetic tree
• Bootstrapping
• Rooted vs. unrooted tree
• Outgroup
• How to use a phylogenetic tree
• Synapomorphy vs. autapomorphy
• Sister species
What is a phylogenetic tree: revisited
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A phylogenetic tree is a HYPOTHESISabout species relationships.
1 gene (CO1, mtDNA):
1 gene (Wg, nDNA):1 gene (Wg, nDNA):
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D
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F
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B
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1 gene (CO1, mtDNA):
1 gene (Wg, nDNA):1 gene (Wg, nDNA):
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B
C
D
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F
A
B
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D
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POLYTOMY: unresolved relationship!POLYTOMY: unresolved relationship!
5 genes (mtDNA & nDNA) – CONSENSUS TREE:
mtDNA
nDNA
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D
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F
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BOOTSTRAPPING: revisited
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
“characters” could be combination of character traits, could be DNA sequences
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94
Bootstrap
ping
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9494 % of trees:
Bootstrap
ping
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94 % of trees:
6 % of trees:
Bootstrap
ping
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94 % of trees:
6 % of trees:
POLYTOMY: unresolved relationship!
Bootstrap
ping
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Bootstrap
ping
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Bootstrap
ping
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Each node is viewed independently!
Each node is viewed independently!
Each node is viewed independently!
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Bootstrap
ping
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HIGH SUPPORT FOR THIS RELATIONSHIP
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Bootstrap
ping
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LOW SUPPORT FOR THIS RELATIONSHIP
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Bootstrap
ping
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ADD MORE GENES: A
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ROOTED vs. UNROOTED TREE: revisited
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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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OUTGROUP: revisited
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OUTGROUP
Same genus!
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Outgroup
Day et al. 2006
More closely related taxa as outgroup
More distantly related taxon for
outgoup
How to use a phylogenetic tree: revisited
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What can be at the tips of branches?
• Individuals/populations (below species level)
• Species/genera/families/orders/phyla/kingdoms (above species level)
• Morphology
It depends on the hypothesis you’re testing!
0.005 changes
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0.43 my
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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
BRANCH TIPS?
individuals/populations
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BRANCH TIPS?
species
Day et al. 2006
BRANCH TIPS?
genera
Moreau et al. 2006
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BRANCH TIPS?
morphology
Losos, J.B. 2009. Lizards in an Evolutionary Tree: Ecology and Adaptive Radiation of Anoles. University of California Press: Berkeley, CA.
BRANCH TIPS?
species
Alföldi et al. (2011)
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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 groupRed hair: autapomorphyBig nose: apomorphy
Ancestral state
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Monophyletic groupNo tail: synapomorphy
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WHAT ARE SISTER SPECIES?
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WHAT ARE SISTER SPECIES?
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WHAT ARE SISTER SPECIES?
SISTER SPECIES
SISTER SPECIES
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A
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WHAT ARE SISTER SPECIES?
SISTER CLADES
SPECIES CONCEPTS
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SPECIES= smallest evolutionarily independent unit
evolutionarily independent…mechanisms of evolution operate on populations separately…species form boundary for spread of alleles…different species follow different evolutionary trajectories
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SPECIES CONCEPTS
• Morphospecies Concept
• Phylogenetic Species Concept
• Biological Species Concept
• Many others…
MORPHOSPECIES CONCEPTPhenotypic differences as basis for identification of morphospecies
BIOLOGICAL SPECIES CONCEPTEvolutionary independence based on reproductive isolation
PHYLOGENETIC SPECIES CONCEPTSmallest monophyletic group (lineages that contain all of known descendants of common ancestor)
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MORPHOSPECIES CONCEPT
widely applicable
extinct/living
sexual/asexual reproduction
species IDs can be arbitrary
IDs not comparable
difficult to apply in certain groups (bacteria, archaea, fungi)
CRYPTIC SPECIES
+ –MORPHOSPECIES CONCEPTPhenotypic differences as basis for identification of morphospecies
BIOLOGICAL SPECIES CONCEPTEvolutionary independence based on reproductive isolation
PHYLOGENETIC SPECIES CONCEPTSmallest monophyletic group (lineages that contain all of known descendants of common ancestor)
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BIOLOGICAL SPECIES CONCEPT (BSC)
Ernst Mayr (1942)
Legal definition employed by Endangered Species Act
BIOLOGICAL SPECIES CONCEPT (BSC)
most commonly used
confirms lack of gene flow
can be difficult to apply (e.g., populations don’t overlap, fossils, irrelevant to asexual populations, hybridization in plants)
+ –
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MORPHOSPECIES CONCEPTPhenotypic differences as basis for identification of morphospecies
BIOLOGICAL SPECIES CONCEPTEvolutionary independence based on reproductive isolation
PHYLOGENETIC SPECIES CONCEPTSmallest monophyletic group (lineages that contain all of known descendants of common ancestor)
PHYLOGENETIC SPECIES CONCEPT (PSC)
traits can only distinguish population on phylogeny if populations have been isolated in terms of gene flow
populations must have been evolutionary independent long enough for diagnostic traits to evolve
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PHYLOGENETIC SPECIES CONCEPT (PSC)
applicable to any organism (sexual/asexual reproduction, fossil)
testable (statistically significant differences)
resources necessary to put it into practice (time, money, skills)
only done for handful of groups
could double # of named species…
+ –
CASE STUDY
Amazonian frogs
Photo: Dr. Santiago Ron
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Background
• 2 independent frog clades
• Engystomops toadlets (terrestrial)
• Hypsiboas treefrogs
• 8 % of global amphibian species richness in Amazon basin
Amazonian frogs
Funk et al. 2011
Research questions
Is species richness in Engystomops and Hypsiboasunderestimated?
And if yes, by how much?
CRYPTIC SPECIES DIVERSITY?
Amazonian frogs
Funk et al. 2011
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Methods
• Delimitation of candidate species– CCS (Confirmed candidate species): differing by morphological and bioacoustic characters, high genetic differentiation, hypothesized to be undescribed species
– UCS (Unconfirmed candidate species): deep genealogical lineages, bioacoustically and morphologically unstudied, derived from geographically distant populations, general indication that they are undescribed species
• Sampling in 6 countries (focus on Ecuador)• 252 individuals from 36 localities (Engystomops)• 208 individuals from 65 localities (Hypsiboas)
Amazonian frogs
Funk et al. 2011
Methods
• Mitochondrial & nuclear DNA – For Engystomops: gene region: 12S, 16S, tRNA genes (mtDNA),
portions of a2ab, CXCR4, NTF3, tyrosinase (nDNA)– For Hypsiboas: portions of 12S, 16S, COI (mtDNA), POMC
(nDNA)– Maximum likelihood & Bayesian methods for tree
reconstruction
• Morphological data– 9 morphometric variables– Principal Components Analysis (PCA), Discriminant Function
Analysis (DFA)
• Bioacoustic data– Call recordings – variables measured: frequency, note duration, number of notes,
rise time
Amazonian frogs
Funk et al. 2011
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Results: Enystomops
Amazonian frogs
Funk et al. 2011
Results: Enystomops
• previously 2 recognized species actually 5‐7 species
• significant but subtle morphometric differences among clades
• striking differences in bioacoustics
Amazonian frogs
Funk et al. 2011
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Results: Hypsiboas
Amazonian frogs
Funk et al. 2011
Results: Hypsiboas
• previously 2 recognized species actually 6‐9 species
• Subtle but significant morphometric differences
• Bioacoustically highly differentiated
Amazonian frogs
Funk et al. 2011
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Discussion
• High levels of undescribed cryptic diversity
• Species richness increased by 150‐250 % (Engystomops), 200‐350 % (Hypsiboas)
• May still be underestimate due to limited sampling
Amazonian frogs
Funk et al. 2011
Discussion
• Phylogenetic species concept
• Biological species concept (female choice experiments) A
mazonian frogs
Funk et al. 2011
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Morphological differences less pronounced than bioacoustics differences – WHY?
Calls evolve faster than morphology – WHY?– strong selection on species recognition & sexual selection
OR
– strong stabilizing selection on morphology
Amazonian frogs
Funk et al. 2011
Cryptic species ID
Li et al. 2013
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Li et al. 2013
Cryptic species ID
INDEPENDENT PROJECTS
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A few notes
• Draft script: max. 50 points
• Full citation: always include author/s, year, title, journal title, journal issue, page numbers
• Always back up statements with references!
Recap
Evolutionary trees follow‐up
Species concepts• Define “species”• Discuss three of the most common species concepts
• Give an example for how to deal with cryptic species diversity
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SUMMARY
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 2/25/2014
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For next week:
The Beak of the Finch: Read Chapter 14
Read paper (will be posted)
Homework due Friday 5pm (21‐Mar)