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When models mislead

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Page 1: When models mislead

When models mislead

Liliana M. DávalosAssistant Professor, Department of Ecology & EvolutionSUNY, Stony Brook

SUNY Stony Brook25 September 2013

Page 2: When models mislead

My lab’s research mission

Biological diversity

Diversification

Human impact

Page 3: When models mislead

Two kinds of questions

Biological diversity

Diversification, decrease Habitat lossincrease

Page 4: When models mislead

The limits of models

• In phylogenetics• Models missing key biology• Improving phylogenetic models• How phenotypes evolve!

• In environmental change• Drivers of forest loss

Page 5: When models mislead

The limits of models

• In phylogenetics• Models missing key biology• Improving phylogenetic models• How phenotypes evolve!

• In environmental change• Drivers of forest loss

Page 6: When models mislead

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

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10063

63

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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

Page 7: When models mislead

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

Page 8: When models mislead

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

Page 9: When models mislead

• 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

Page 10: When models mislead

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

Page 11: When models mislead

The organisms in question Phyllostomidae and relatives

Models missing key bio

Page 12: When models mislead

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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

Page 13: When models mislead

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

Page 14: When models mislead

If the Jukes-Cantor model is not enough, then what else could be going on?

Page 15: When models mislead

q

p

Homoplasy I: inconsistency!

q

pp

Felsenstein 1978 Syst Biol

Models missing key bio

consistent

Non consistent

Page 16: When models mislead

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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

Page 17: When models mislead

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

Page 18: When models mislead

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

Page 19: When models mislead

Dávalos, Cirranello et al. 2012 Biol Rev

Inconsistency!

Models missing key bio

Page 20: When models mislead

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Dávalos, Cirranello et al. 2012 Biol Rev Dávalos et al. Accepted Syst Biol

Convergent evolution!

Models missing key bio

Page 21: When models mislead

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Dávalos et al. Accepted Syst Biol

Correlated evolution!

Models missing key bio

Dissimilarity between characters ->

Page 22: When models mislead

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

Page 23: When models mislead

Morphology...

AminoacidsCodons

Why we aren’t there yet

Neutral genotype

Model complexity

Models missing key bio

Page 24: When models mislead

The limits of models

• In phylogenetics• Models missing key biology• Improving phylogenetic models• How phenotypes evolve!

• In environmental change• Drivers of forest loss

Page 25: When models mislead

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

Page 26: When models mislead

The limits of models

• In phylogenetics• Models missing key biology• Improving phylogenetic models• How phenotypes evolve!

• In environmental change• Drivers of forest loss

Page 27: When models mislead

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

Page 28: When models mislead

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

Page 29: When models mislead

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

Page 30: When models mislead

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

Page 31: When models mislead

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

Page 32: When models mislead

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●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●

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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

●●●

●●●●

●●●●

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

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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

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The limits of models

• In phylogenetics• Models missing key biology• Improving phylogenetic models• How phenotypes evolve!

• In environmental change• Drivers of forest loss

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My lab’s research mission

Biological diversity

Diversification

Human impact

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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

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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

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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

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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

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• 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!