The Right Answers to the Wrong Questions
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Transcript of 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
Who am I?
• Evolutionary biologist• Focus on biodiversity,
including:• Speciation• Diversification• Conservation
Two kinds of questions
Biological diversity
Diversification, decrease Habitat lossincrease
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
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
Evolutionary framework Corthals et al. 2012 PLoS One
0.1 substitution/site
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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When models fail
• 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
When models fail
Springer et al. 2007 Syst BiolHermsen & Hendricks 2008 Ann Missouri Bot Gard
• Homology: character changes reflect common descent
• IID: Independent and Identically Distributed
Assumptions of phylogeny
When models fail
Dávalos, Cirranello et al. 2012 Biol Rev
When models fail
• 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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Dumont, Dávalos et al. 2012 P R Soc BDávalos, Cirranello et al. 2012 Biol Rev
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• What makes this signal so strong?
Morphology has a strong signal
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When models fail
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When models fail
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• 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
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
Cracraft 1983 Syst BiolMacArthur & Wilson 1963 Evolution
Right answer, wrong question
Preston 1962 EcologyMacArthur & Wilson 1963 Evolution
Right answer, wrong question
Equilibrium Null Model
Recent disequilibrium Dávalos & Turvey 2012 Bones, Clones & Biomes
Right answer, wrong question
Buckets of Caribbean fossils
Right answer, wrong question
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
Area change and species lossRight answer, wrong question
Dávalos & Russell 2012 Ecology & Evolution
Log of present/LGM area in the Greater Antilles
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R2 = 0.83 R2 = 0.85
Change in area ~ change in richness
Right answer, wrong question
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Room for additional work Dávalos & Russell 2012 Ecology
& EvolutionRight answer, wrong question
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
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
Antioquia, Colombia 2010Vaupes, Colombia 2009
Understanding habitat change
Geist & Lambin 2002 BioScienceWhy deforestation?Understanding habitat change
World Bank Statistics 2012Population growth over
timeUnderstanding habitat change
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
1400
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Figure 2
BA
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2001 2004 2007 2010
1
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2001 2004 2007 2010
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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
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
Municipality●
●
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CalamarEl RetornoSan Jose
Figure 6
A B
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4,000
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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
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tleP
rice
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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
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
1400
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Figure 2
BA
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1
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Coc
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Forest lost, coca declinedUnderstanding habitat change
Dávalos et al. In Review Global Environ Chang
1400
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150200250300350400
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500
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Figure 2
BA
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253035404550
2001 2004 2007 201025
30
35
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2001 2004 2007 2010
1
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2001 2004 2007 2010
PLA
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Municipality●
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CalamarEl RetornoSan Jose
Figure 6
A B
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Percentage population urban
Coc
a cu
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(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
A
B
C
Figure 5
Calamar
El RetornoSan Jose
2010
0.00
0.02
0.04
0.06
20
30
40
50
2
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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
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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
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
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
The real drivers of habitat loss
Understanding habitat change
coca nothing More Eradicationdecrease
Urbanization &
Development
becomes
Pasture &
Cowsisproperty
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
• 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!