The Right Answers to the Wrong Questions

44

Transcript of The Right Answers to the Wrong Questions

Page 1: The Right Answers to the Wrong Questions

The Right Answers to the Wrong Questions

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

University of Miami8 April 2013

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Who am I?

• Evolutionary biologist• Focus on biodiversity,

including:• Speciation• Diversification• Conservation

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Two kinds of questions

Biological diversity

Diversification, decrease Habitat lossincrease

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The Right Answers to the Wrong Questions

• Evolution of Diversity• What to do when models fail• Right answers, wrong questions

• Understanding habitat loss• A lot of cattle without much beef

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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

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10063

63

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55

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10074

51

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pathogenic Mycobacterium complex(avium-bovis-tuberculosis)

non-pathogenic Mycobacterium smegmatis complex

Evolutionary framework Corthals et al. 2012 PLoS One

0.1 substitution/site

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The organisms in question Phyllostomidae and relatives

When models fail

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Baker et al. 2003 Occas Pap Mus TTU Datzmann et al. 2010 BMC Evol Biol

Wetterer et al. 2000 B Am Mus Nat Hist

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• Majority of species are extinct• Fossils are all that

remain• Phylogenies must use

morphology• Can morphology be

trusted?

Genome not always available

Morgan & Czaplewski 2012 Evolutionary History of Bats

When models fail

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When models fail

Springer et al. 2007 Syst BiolHermsen & Hendricks 2008 Ann Missouri Bot Gard

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• Homology: character changes reflect common descent

• IID: Independent and Identically Distributed

Assumptions of phylogeny

When models fail

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Dávalos, Cirranello et al. 2012 Biol Rev

When models fail

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• If rates of evolution are high, then signal erased over time• Results in

unresolved phylogeny

• Other signal must emerge to resolve phylogeny

Saturation is not everything

When models fail

Dávalos & Perkins 2008 Genomics

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Page 14: The Right Answers to the Wrong Questions

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• >10Kb from 7 chromosomes & mt + <300 dental traits

• = signal from dental traits

• What makes this signal so strong?

Morphology has a strong signal

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When models fail

Page 15: The Right Answers to the Wrong Questions

0

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• Measured dissimilarity between pairs of characters

• Most sequence characters are completely dissimilar• Despite protein-

coding loci• This is not the case for

dental charactersDávalos et al. In Review Syst Biol

When models fail

Page 16: The Right Answers to the Wrong Questions

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Page 17: The Right Answers to the Wrong Questions

• Less is more when collecting certain kinds of characters

• Dental data violate key assumptions of phylogenetic models

• Saturation, convergence, and non-independence• = model failure

• New models needed

Models failed

Czaplewski et al. 2003 Caldasia

When models fail

Page 18: The Right Answers to the Wrong Questions

The Right Answers to the Wrong Questions

• Evolution of Diversity• What to do when models fail• Right answer, wrong question

• Understanding habitat loss• A lot of cattle without much beef

Page 19: The Right Answers to the Wrong Questions

Cracraft 1983 Syst BiolMacArthur & Wilson 1963 Evolution

Right answer, wrong question

Page 20: The Right Answers to the Wrong Questions

Preston 1962 EcologyMacArthur & Wilson 1963 Evolution

Right answer, wrong question

Equilibrium Null Model

Page 21: The Right Answers to the Wrong Questions

Recent disequilibrium Dávalos & Turvey 2012 Bones, Clones & Biomes

Right answer, wrong question

Page 22: The Right Answers to the Wrong Questions

Buckets of Caribbean fossils

Right answer, wrong question

Page 23: The Right Answers to the Wrong Questions

Why they went extinct

• Competition by other invasive bats – Koopman & Williams 1951

• Cave flooding – Morgan 2001

• Interglacial floods – McFarlane & Lundberg 2004

• Anthropogenic habitat destruction – Gannon et al. 2005

Right answer, wrong question

Page 24: The Right Answers to the Wrong Questions

Area change and species lossRight answer, wrong question

Dávalos & Russell 2012 Ecology & Evolution

Page 25: The Right Answers to the Wrong Questions

Log of present/LGM area in the Greater Antilles

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Dávalos & Russell 2012 Ecology & Evolution

R2  =  0.83 R2  =  0.85

Change in area ~ change in richness

Right answer, wrong question

Page 26: The Right Answers to the Wrong Questions

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Room for additional work Dávalos & Russell 2012 Ecology

& EvolutionRight answer, wrong question

Page 27: The Right Answers to the Wrong Questions

How to answer the right question

• Equilibrium null model• Successfully

explains richness• Short-term

disequilibrium modeled• Real interest is not

richness• But composition

Drawing by A. Tejedor

Right answer, wrong question

Page 28: The Right Answers to the Wrong Questions

The Right Answers to the Wrong Questions

• Evolution of Diversity• What to do when models fail• Right answers, wrong questions

• Understanding habitat loss• A lot of cattle without much beef

Page 29: The Right Answers to the Wrong Questions

Antioquia, Colombia 2010Vaupes, Colombia 2009

Understanding habitat change

Page 30: The Right Answers to the Wrong Questions

Geist & Lambin 2002 BioScienceWhy deforestation?Understanding habitat change

Page 31: The Right Answers to the Wrong Questions

World Bank Statistics 2012Population growth over

timeUnderstanding habitat change

Page 32: The Right Answers to the Wrong Questions

An in-depth look

• Guaviare from 2001-2010

• One of two large foci of Plan Colombia (the other was Putumayo)

• Poor development indicators

• Extractive land uses

Guaviare, Colombia 2008

Understanding habitat change

Page 33: The Right Answers to the Wrong Questions

1400

1600

1800

2000

2200●

●●

3035404550

Forest

NP

1500

2000

2500

●●

28 30 32 34 36 38 40

Pasture

150200250300350400

●●

0.51.01.52.02.5

Coca

500

550

600

650

700 ●●

●●

3035404550

PA

(ha)

150

200

250

300

350

●●

●●

● ●

28 30 32 34 36 38 40

2468101214

●●●

●●

0.51.01.52.02.5

90

100

110

3035404550PLAND

EN

N (m

)

95100105110115120

● ●

28 30 32 34 36 38 40PLAND

300

400

500

600

0.51.01.52.02.5PLAND

Figure 2

BA

G

C

E FD

H I

253035404550

2001 2004 2007 201025

30

35

40

2001 2004 2007 2010

1

2

3

2001 2004 2007 2010

PLA

ND

K L M

Fate of forest

• Consistent year-to-year forest decline

• Fragmentation indices consistent with unchecked process of conversion to pasture

Understanding habitat change

Dávalos et al. In Review Global Environ Chang

Page 34: The Right Answers to the Wrong Questions

Three explanations

Understanding habitat change

Hamburger! (or steak)Kaimowitz et al. 2004 CIFOR

CocaDávalos et al. 2011 Environ

Sci Technol

Land tenure and propertyHecht 1993 BioScience

Page 35: The Right Answers to the Wrong Questions

Municipality●

CalamarEl RetornoSan Jose

Figure 6

A B

●●

●●

●●

● ●

20

30

40

30,000 60,000 90,000

Cattle

Perc

enta

ge la

nd p

astu

re

● ●

●●

2,000

4,000

6,000

30 40 50 60

Percentage population urban

Coc

a cu

ltiva

tion

(ha)

A

B

C

Figure 4

Calamar

El Retorno

San Jose

30,000

60,000

90,000

10

20

30

Year

Cat

tleP

rice

of b

eef (

peso

s/K

g)R

anch

ing

GD

P (1

09 pe

sos)

2000 2002 2004 2006 2008 2010

1,600

1,800

2,000

2,200

Pastures with few cowsUnderstanding habitat change

Dávalos et al. In Review Global Environ Chang

Page 36: The Right Answers to the Wrong Questions

If coca were the cause

• Perhaps eradication is the solution

• Great because we can solve the problem of coca

Understanding habitat change

coca decrease Eradication

Page 37: The Right Answers to the Wrong Questions

1400

1600

1800

2000

2200●

●●

3035404550

ForestN

P

1500

2000

2500

●●

28 30 32 34 36 38 40

Pasture

150200250300350400

●●

0.51.01.52.02.5

Coca

500

550

600

650

700 ●●

●●

3035404550

PA

(ha)

150

200

250

300

350

●●

●●

● ●

28 30 32 34 36 38 40

2468101214

●●●

●●

0.51.01.52.02.5

90

100

110

3035404550PLAND

EN

N (m

)

95100105110115120

● ●

28 30 32 34 36 38 40PLAND

300

400

500

600

0.51.01.52.02.5PLAND

Figure 2

BA

G

C

E FD

H I

253035404550

2001 2004 2007 201025

30

35

40

2001 2004 2007 2010

1

2

3

2001 2004 2007 2010

PLA

ND

K L M

● ●

●●

2000

4000

6000

0 3000 6000 9000Eradication previous year (ha)

Coc

a cu

ltiva

tion

(ha) 5

● 5

mpio●

CalamarRetornoSan Jose

Forest lost, coca declinedUnderstanding habitat change

Dávalos et al. In Review Global Environ Chang

1400

1600

1800

2000

2200●

●●

3035404550

Forest

NP

1500

2000

2500

●●

28 30 32 34 36 38 40

Pasture

150200250300350400

●●

0.51.01.52.02.5

Coca

500

550

600

650

700 ●●

●●

3035404550

PA

(ha)

150

200

250

300

350

●●

●●

● ●

28 30 32 34 36 38 40

2468101214

●●●

●●

0.51.01.52.02.5

90

100

110

3035404550PLAND

EN

N (m

)

95100105110115120

● ●

28 30 32 34 36 38 40PLAND

300

400

500

600

0.51.01.52.02.5PLAND

Figure 2

BA

G

C

E FD

H I

253035404550

2001 2004 2007 201025

30

35

40

2001 2004 2007 2010

1

2

3

2001 2004 2007 2010

PLA

ND

K L M

Page 38: The Right Answers to the Wrong Questions

Municipality●

CalamarEl RetornoSan Jose

Figure 6

A B

●●

●●

●●

● ●

20

30

40

30,000 60,000 90,000

Cattle

Perc

enta

ge la

nd p

astu

re

● ●

●●

2,000

4,000

6,000

30 40 50 60

Percentage population urban

Coc

a cu

ltiva

tion

(ha)

Why did coca decline?

• Each municipality started out with different amounts of coca

• As the municipalities become more urban, there is less coca

• At ~50% urban population there is 0 coca in the smaller municipalities Dávalos et al. In Review Global

Environ ChangUnderstanding habitat change

Page 39: The Right Answers to the Wrong Questions

A

B

C

Figure 5

Calamar

El RetornoSan Jose

2010

0.00

0.02

0.04

0.06

20

30

40

50

2

3

4

5

2000 2002 2004 2006 2008Year

Fina

ncia

l GD

P(1

09 pe

sos)

Con

stru

ctio

n G

DP

(109

peso

s)P

rope

rty T

ax(1

06 pe

sos/

capi

ta)

What urbanization looks like

• Urban people paying more taxes that finance construction

• Finance becomes important

• Less dependence on ranching (and agriculture)

Dávalos et al. In Review Global Environ Chang

Understanding habitat change

Page 40: The Right Answers to the Wrong Questions

Urban cows!

• Cows enhance claim to the land

• The region is rapidly urbanizing

• Per capita taxes are rising => property values are rising• Clearing the land to

sell in future urban market

Dávalos et al. In Review Global Environ Chang

Understanding habitat change

Page 41: The Right Answers to the Wrong Questions

A disturbing development model

• Development excludes coca• Not eradication

• Development centered on a model of settlement that is destructive• And probably not

peaceful

Guaviare, Colombia 2008

Page 42: The Right Answers to the Wrong Questions

The real drivers of habitat loss

Understanding habitat change

coca nothing More Eradicationdecrease

Urbanization &

Development

becomes

Pasture &

Cowsisproperty

Page 43: The Right Answers to the Wrong Questions

Models and data: a dialogue

• Models shape the kinds of data we collect• And how we

interpret those data• Models may answer

the wrong question• Data may violate

model assumptions

Page 44: The Right Answers to the Wrong Questions

• Funding

• NSF–DEB

• CIDER—SBU

• Speciation & diversification: A. Cirranello, E. Dumont, A. Russell, N. Simmons, P. Velazco

• Conservation & policy: A. Bejarano, A. Corthals, L. Correa, C. Romero

• Dávalos Lab

• Phylogenetics: S. DelSerra, A. Goldberg, O. Warsi, L. Yohe

• Land use: P. Connell, M. Hall, E. Simola, G. Tudda

Thanks!