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When models mislead
Liliana M. DávalosAssistant Professor, Department of Ecology & EvolutionSUNY, Stony Brook
SUNY Stony Brook25 September 2013
My lab’s research mission
Biological diversity
Diversification
Human impact
Two kinds of questions
Biological diversity
Diversification, decrease Habitat lossincrease
The limits of models
• In phylogenetics• Models missing key biology• Improving phylogenetic models• How phenotypes evolve!
• In environmental change• Drivers of forest loss
The limits of models
• In phylogenetics• Models missing key biology• Improving phylogenetic models• How phenotypes evolve!
• In environmental change• Drivers of forest loss
0.1 substitutions/site
Mycobacterium bovis BCG str. Pasteur 1173P2M. tuberculosis H37RaM. bovis BCG str. Tokyo 172M. bovis AF212297M. tuberculosis CDC1551M. tuberculosis F11M. tuberculosis KZN 1435M. tuberculosis H37Rv
M. avium subsp. paratuberculosis K10M. avium 104
M. vanbaalenii PYR1M. sp. Spyr1
M. smegmatis str. MC2 155M. sp. KMSM. sp. MCSM. sp JLS
Mycobacterium sp. *Nocardia farcinica IFM 10152
Gordonia bronchialis DSM 43247Rhodococcus opacus B4
R. equi ATCC 33707R. equi 103S
Segniliparus rotundus DSM 44985Bifidobacterium longum NCC2705 B. longum DJO10A B. longum subsp. infantis 157FB. longum subsp. longum JCM 1217B. longum subsp. longum BBMN68 B. longum subsp. infantis ATCC 55813B. longum subsp. longum JDM301 B. longum subsp. infantis ATCC 15697B. breve DSM 20213
B. dentium Bd1B. dentium ATCC 27679
B. adolescentis ATCC 15703 B. bifidum PRL2010B. bifidum S17Bifidobacterium sp. *
Corynebacterium matruchotii ATCC 14266C. efficiens YS314
C. genitalium ATCC 33030 Sca01C. glucuronolyticum ATCC 51866
C. urealyticum DSM 7109Arthrobacter sp. FB24
A. chlorophenolicus A6Kocuria rhizophila DC2201
Micrococcus luteus NCTC 2665Clavibacter michiganensis subsp. michiganensis NCP
C. michiganensis subsp. sepedonicus Cellulomonas flavigena DSM 20109
Kineococcus radiotolerans SRS30216Nakamurella multipartita DSM 44233
Saccharopolyspora erythraea NRRL 2338 Geodermatophilus obscurus DSM 43160
Amycolatopsis mediterranei U32Intrasporangium calvum DSM 43043
Kytococcus sedentarius DSM 20547Nocardioides sp. JS614
Streptomyces avermitilis MA4680S. scabiei 87 22
S. coelicolor A3 2Catenulispora acidiphila DSM 44928
Thermobifida fusca YXThermobispora bispora DSM 43833
Thermomonospora curvata DSM 43183Streptosporangium roseum DSM 43021
Micromonospora aurantiaca ATCC 27029M. sp. L5 Salinispora tropica CNB440
Salinispora arenicola CNS205Acidothermus cellulolyticus 11B
Rhodococcus jostii RHA1Mycobacterium gilvum PYRGCK
Frankia alni ACN14a
100
10084
9642
10063
63
65
55
84
10074
51
70
98
9299
74
100100
10075
99
100
78
4378
100
49
20
100
9992
32
10092
50
26
5618
14
6
37
32
11
66100
51
5
463878
15
100
100
10077
99
84
88
pathogenic Mycobacterium complex(avium-bovis-tuberculosis)
non-pathogenic Mycobacterium smegmatis complex
Phylogenetics
• All of comparative biology
• Historical biogeography
• Evolutionary aspects of community ecology
• Diagnostics and similar applications
Corthals...Dávalos 2012 PLoS One
Models missing key bio
0.1 substitutions/site
Mycobacterium bovis BCG str. Pasteur 1173P2M. tuberculosis H37RaM. bovis BCG str. Tokyo 172M. bovis AF212297M. tuberculosis CDC1551M. tuberculosis F11M. tuberculosis KZN 1435M. tuberculosis H37Rv
M. avium subsp. paratuberculosis K10M. avium 104
M. vanbaalenii PYR1M. sp. Spyr1
M. smegmatis str. MC2 155M. sp. KMSM. sp. MCSM. sp JLS
Mycobacterium sp. *Nocardia farcinica IFM 10152
Gordonia bronchialis DSM 43247Rhodococcus opacus B4
R. equi ATCC 33707R. equi 103S
Segniliparus rotundus DSM 44985Bifidobacterium longum NCC2705 B. longum DJO10A B. longum subsp. infantis 157FB. longum subsp. longum JCM 1217B. longum subsp. longum BBMN68 B. longum subsp. infantis ATCC 55813B. longum subsp. longum JDM301 B. longum subsp. infantis ATCC 15697B. breve DSM 20213
B. dentium Bd1B. dentium ATCC 27679
B. adolescentis ATCC 15703 B. bifidum PRL2010B. bifidum S17Bifidobacterium sp. *
Corynebacterium matruchotii ATCC 14266C. efficiens YS314
C. genitalium ATCC 33030 Sca01C. glucuronolyticum ATCC 51866
C. urealyticum DSM 7109Arthrobacter sp. FB24
A. chlorophenolicus A6Kocuria rhizophila DC2201
Micrococcus luteus NCTC 2665Clavibacter michiganensis subsp. michiganensis NCP
C. michiganensis subsp. sepedonicus Cellulomonas flavigena DSM 20109
Kineococcus radiotolerans SRS30216Nakamurella multipartita DSM 44233
Saccharopolyspora erythraea NRRL 2338 Geodermatophilus obscurus DSM 43160
Amycolatopsis mediterranei U32Intrasporangium calvum DSM 43043
Kytococcus sedentarius DSM 20547Nocardioides sp. JS614
Streptomyces avermitilis MA4680S. scabiei 87 22
S. coelicolor A3 2Catenulispora acidiphila DSM 44928
Thermobifida fusca YXThermobispora bispora DSM 43833
Thermomonospora curvata DSM 43183Streptosporangium roseum DSM 43021
Micromonospora aurantiaca ATCC 27029M. sp. L5 Salinispora tropica CNB440
Salinispora arenicola CNS205Acidothermus cellulolyticus 11B
Rhodococcus jostii RHA1Mycobacterium gilvum PYRGCK
Frankia alni ACN14a
100
10084
9642
10063
63
65
55
84
10074
51
70
98
9299
74
100100
10075
99
100
78
4378
100
49
20
100
9992
32
10092
50
26
5618
14
6
37
32
11
66100
51
5
463878
15
100
100
10077
99
84
88
pathogenic Mycobacterium complex(avium-bovis-tuberculosis)
non-pathogenic Mycobacterium smegmatis complex
Phylogenetics
• Diagnostics and similar applications
• Phylogenetics enables testing relatedness
Models missing key bio
Corthals...Dávalos 2012 PLoS One
Dated trees more important than ever
• (We need fossils)• Testing models of trait
evolution• Understanding history
of assemblages in time and space
• Testing key innovations
Dumont, Dávalos et al. 2012 P R Soc B
Models missing key bio
• How good are existing models for morphology?• Characteristics of
the data• Compare to models
molecular evolution
Questions
Dávalos & Russell 2012 Ecol Evol
Models missing key bio
Species CharactersWhat do I mean by morphological characters?
• They look like this —>• Discontinuous
between species• Factors, not
numbers• Difficult to model
Models missing key bio
The organisms in question Phyllostomidae and relatives
Models missing key bio
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Baker et al. 2003 Occas Pap Mus TTU Dávalos, Cirranello et al. 2012 Biol Rev
Wetterer et al. 2000 B Am Mus Nat Hist
Models missing key bio
The trouble with morphological characters
• At first, only model was parsimony
• Neutral Jukes-Cantor 1969 model implemented 2001
• Applying this model does not solve conflict
Dávalos, Cirranello et al. 2012 Biol Rev
Models missing key bio
If the Jukes-Cantor model is not enough, then what else could be going on?
q
p
Homoplasy I: inconsistency!
q
pp
Felsenstein 1978 Syst Biol
Models missing key bio
consistent
Non consistent
A B
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Figure 12
Homoplasy II: convergent adaptation
• Can bring together unrelated ecologically similar lineages• This example: mt
cytochrome b gene of nectar-feeding bats
• Association adaptive molecular evolution and supporting wrong node Dávalos, Cirranello et al. 2012 Biol Rev
Models missing key bio
Homoplasy III: correlated evolution
• Expected in protein-coding genes
• Models in use for codons, aminoacids, ribosomal RNA secondary structure
Dávalos & Perkins 2008 Genomics
Models missing key bio
Might these affect morphological characters?
Reviewer 1:
I don't see the point. If the characters are good characters (meaning that they have some phylogenetic signal at some level), then there is nothing especially wrong with the fact that they are weighted a little more than other characters.
Models missing key bio
Dávalos, Cirranello et al. 2012 Biol Rev
Inconsistency!
Models missing key bio
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Dávalos, Cirranello et al. 2012 Biol Rev Dávalos et al. Accepted Syst Biol
Convergent evolution!
Models missing key bio
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Dávalos et al. Accepted Syst Biol
Correlated evolution!
Models missing key bio
Dissimilarity between characters ->
Models missing key biology
• Morphology = phenotype• Neutrality and
independence wrong assumptions• Not neutral• Not independent
Skelly et al. 2013 Genome Res
Models missing key bio
Morphology...
AminoacidsCodons
Why we aren’t there yet
Neutral genotype
Model complexity
Models missing key bio
The limits of models
• In phylogenetics• Models missing key biology• Improving phylogenetic models• How phenotypes evolve!
• In environmental change• Drivers of forest loss
Analytical innovations
• Statistical scaffolds• Condition
morphological resolution on molecular posterior
• Morphological simulations• Uncover significantly
conflicting characters
Dávalos et al. Accepted Syst Biol
Photos: M. Tschaptka & E. Kalko
The limits of models
• In phylogenetics• Models missing key biology• Improving phylogenetic models• How phenotypes evolve!
• In environmental change• Drivers of forest loss
How does morphology evolve?
• Ordering: each character state gives rise to a finite range of states
• Evidence of limits to states driven by• Development• Natural selection
Dávalos, Cirranello et al. 2012 Biol Rev
How phenotypes evolve
Modeling selection in morphology
• Brownian motion vs. Ornstein-Uhlenbeck models
• Continuous phenotypic traits
• Might selection for performance explain homoplasy in morphological data?
How phenotypes evolve
Butler & King 2004 Am Nat
A BB C D
nectarivorous
other
OU2a
frugivorous (figs)
other
OU2b
frugivorous (figs)
other
nectarivorous
OU3
frugivorous (figs)
other
nectarivorous
strictly frugivorous (figs, Short-faced bats)
OU4
Figure 5
Ardops
Ariteus
Carollia
Diphylla
MimonTonatia
Sturnira
Ametrida
Centurio
PygodermaSphaeronycteris
Stenoderma
Lonchophylla
Chrotopterus
DesmodusDiaemus
Lampronycteris
Lophostoma
Macrotus
Micronycteris
Phylloderma
Phyllostomus
Rhinophylla
Trachops
Vampyrum
Artibeus
Chiroderma
EctophyllaEnchisthenes
Mesophylla
Platyrrhinus
Uroderma
Vampyressa
Vampyrodes
Metavampyressa
LonchophyllaPlatalina
Anoura
Choeroniscus
Choeronycteris
Hylonycteris
Erophylla
Glossophaga
LeptonycterisMonophyllus
PhyllonycterisBrachyphylla
Dumont ... Dávalos In Review Evolution
Engineering model of performance
How phenotypes evolve
0
100
200
300
400
500
0.0 0.4 0.8 1.2MA
count
dietfigs
figs only
nectar
other
• Performance related to diet• Low MA in nectar-
feeding bats• Convergence on
this phenotype• Analyzing function and
integrating selection better than ignoring
Three performance peaks
Dumont ... Dávalos In Review Evolution
How phenotypes evolve
Mechanical advantage
Freq
uenc
y
Function just as important in genome
• What drives diversity of olfactory receptors (OR)?• OR largest gene family
in mammals• Prior: variation ~ sensory
modes• Echolocation• Development of
vomeronasal organ• Alternative: Feeding
ecologyHayden, Dávalos et al. In Review Mol Biol Evol
How phenotypes evolve
OR subfamily
Spec
ies
●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●
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Diet Echolocation MorpholologyVNO
Rousettus lanatusP. giganteusPteropus rayneriCynopterus sphinxNyctimene albiventerCraseonycteris thonglongyaiR. ferrumequinumRhinolophus hipposiderosEmballonura atrataThyroptera tricolorPteronotus parnelliiMacrotus californicusDesmodus rotundusCarollia perspicillataSturnira tildaeArtibeus jamaicensisPlatyrrhinus helleriVampyrodes caraccioliAnoura geoffroyiLeptonycteris curasoaeErophylla bombifronsPhyllonycteris poeyiVampyrum spectrumLophostoma silvicolaTrachops cirrhosusMyotis lucifugusEumops auripendulus Molossidae
Vespertilionidae
Phyllostomidae
MormoopidaeThyropteridaeEmballonuridae
RhinolophidaeCraseonycteridae
Pteropodidae
YangochiropteraYinpterochiroptera
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AnimalivorousPlant-visitingFruit specialist
EcholocationNo echolocation
Has VNONo VNO
Figure 1
EauMluTciLsiVspPpoEboLcuAgeVcaPheAjaStiCpeDroMcaPpaTtrEatRhiRfeCthNalCspPraPgiRla
:
Not sensory system, but diet
• Only NW frugivores highly differentiated • Enriched for OR1/3/7• Lose OR 5/8/9
• In OW, not enough power• But same direction of
enrichment for frugivores
How phenotypes evolve
Hayden, Dávalos et al. In Review Mol Biol Evol
Where is this going?
• Whole-transcriptome survey of adaptive convergence
• Target: energy metabolism in nectar-feeding bats
• Bottleneck: low quality samples in collections
• Requires much fieldwork
How phenotypes evolve
The limits of models
• In phylogenetics• Models missing key biology• Improving phylogenetic models• How phenotypes evolve!
• In environmental change• Drivers of forest loss
My lab’s research mission
Biological diversity
Diversification
Human impact
Why do rainforests decline? Three hypotheses
Hamburger! (or steak)Kaimowitz et al. 2004 CIFOR
CocaDávalos et al. 2011 Environ
Sci Technol
Land tenure and propertyHecht 1993 BioScience
Drivers forest loss
Predictions
Hamburger! (or steak)Kaimowitz et al. 2004 CIFOR
CocaDávalos et al. 2011 Environ
Sci Technol
Land tenure and propertyHecht 1993 BioScience
Drivers forest loss
+ demand beef + beef, + cattle + cattle, + pasture + pasture, - forest
+ demand cocaine + cocaine, + coca + coca, - forest
+ demand land + pasture, + cattle + cattle, - forest
The real drivers of habitat loss
Forest, coca nothing Eradicationdecrease
Urbanization &
Development
Dávalos et al. 2009 Int J Drug Pol Dávalos et al. In Review Biol Cons
becomes
Pasture &
Cowsisproperty
Drivers forest loss
When models mislead
• Models shape the kinds of data we collect• And how we interpret
those data• Data may violate
model assumptions• Data may reveal
underlying process not captured by model
• Models and data: a dialogue
• Funding• NSF–DEB, CIDER–SBU
• Speciation & diversification: A. Cirranello, A. Russell, N. Simmons, P. Velazco
• Functional evolution: E. Dumont, S. Rossiter, E. Teeling
• Conservation & policy: D. Armenteras, A. Bejarano, A. Corthals, L. Correa, J. Holmes, N. Rodriguez, C. Romero
• Dávalos Lab• Phylogenetics: R. Dahan, S. DelSerra,
A. Goldberg, O. Warsi, L. Yohe, X. Zhang
• Land use: P. Connell, M. Hall, E. Simola, G. Tudda, Y. Shah
• Special thanks to staff: D. DiGiovanni, M. Nolan, I. Roth, A. Stanley
• Colleagues for excellent dialogue & mentoring
Thanks!