Systematic error and the contours of a theory of macroevolution
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Transcript of Systematic error and the contours of a theory of macroevolution
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Systematic Error and the Contours of a Theory of Macroevolution
!Liliana M. DávalosAssociate Professor, Department of Ecology & EvolutionSUNY, Stony Brook!Field Museum of Natural History17 December 2014
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Our research mission
Biological diversityDiversification Human
impact
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Two kinds of questions
Biological diversity
Diversification, speciation decrease Habitat lossincrease
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Sampling error vs. systematic errorFelsenstein 1978 Syst Zool
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Thinking about errors
• Let’s say we want to answer a question:• In a finite
population, what is the frequency of an allele?
Sampling vs. systematic
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How to answer this question
• We go out, get samples, genotype different individuals
• Then we count the alleles
• What is the main source of error?
Sampling vs. systematic
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This is sampling error
• We want to get a better estimate of the allele frequency• => Sample more
• We could sample the entire population• => Best possible
estimate of allele frequency
Sampling vs. systematic
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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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pathogenic Mycobacterium complex(avium-bovis-tuberculosis)
non-pathogenic Mycobacterium smegmatis complex
Phylogenetics
• Testing relatedness• All of comparative
biology• Historical
biogeography• Evolutionary aspects
of community ecology• Diagnostics and
similar applications
Corthals et al. 2012 PLoS One
Sampling vs. systematic
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Now let’s ask a different question
• We want to find out how these 3000 microbial lineages relate to one another
• We get their genomes, map out each of the single-copy genes, estimate a phylogeny
Lang, Darling, Eisen 2013 PLoS One
Sampling vs. systematic
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But our results don’t make sense
• Is it sampling error?• Can we sample
more than the whole genome?
• We discover the model of gene evolution we are using was wrong• What kind of error is
this?
Lang, Darling, Eisen 2013 PLoS One
Sampling vs. systematic
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This is systematic error
• Even sampling whole genomes won’t fix the problem• Having more data
can make the problem worse!
• As long as we don’t change the model, we will keep obtaining the wrong answer
Lang, Darling, Eisen 2013 PLoS One
Sampling vs. systematic
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Systematic error in molecular evolutionSullivan & Swofford 1997 J Mamm EvolD’Erchia et al. 1996 Nature
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Systematic error = homoplasy that is not modeled
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q
p
Homoplasy I: inconsistency!
q
pp
Felsenstein 1978 Syst Biol
Phenotypic evolution
consistent
Non consistent
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A B
Background selection
Pe
rcen
t cod
ons
of C
YTB
in e
ach
codo
n ty
pe
0
20
40
60
Background selection Selection shift
Significantly support
Significantly rejectRejectSupport
Type of codon
Amino acid position in alignment
Sup
port
for n
ecta
r-fe
edin
g cl
ade-3
-2
-1
0
1
2
3
100 200 300 400 500
Significant supportor rejection
Selection shiftSelection shift inGlossophaginae
Type of codon
CYTB COX1
Figure 12
Homoplasy II: ecological convergence
• Phenotype exposed to selection
• Selection from similar ecology produces similar phenotypes
Dávalos, Cirranello et al. 2012 Biol Rev
Phenotypic evolution
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Homoplasy III: correlated evolution
• Expected in protein-coding genes
• Models in use for codons, aminoacids, ribosomal RNA secondary structure
Dávalos & Perkins 2008 Genomics
Phenotypic evolution
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Example with favorite gene: mt cytb Agnarsson et al. 2011 PLoS
Currents ToL
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Dávalos 2010 Island Bats Evolution, Ecology, and Conservation
Agnarsson et al. 2011 PLoS Currents ToL
Molecular evolution
© M. Tuttle© N. Simmons
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One of these is evolving fast, very fast Dávalos, Gutiérrez & Velazco
unpublishedMolecular evolution
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Speed cannot be the whole story
• High rates of change randomize shared changes
• Expect no resolution instead of actual conflict
• For conflict, must reflect other forces• E.g., base
composition Dávalos, Gutiérrez & Velazco unpublished
Molecular evolution
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Dávalos, Gutiérrez & Velazco unpublished
Agnarsson et al. 2011 PLoS Currents ToL
Molecular evolution
© M. Tuttle© N. Simmons
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MacrotusLampronycterisMicronycteris minutaMicronycteris schmidtorumMicronycteris hirsutaMicroncyteris megalotisDiphyllaDiaemusDesmodusLonchorhinaMacrophyllumTrachopsChrotopterusVampyrumLophostomaTonatiaPhyllodermaPhyllostomusMimon
AnouraHylonycterisChoeroniscusMusonycterisChoeronycteris
ErophyllaBrachyphyllaMonophyllusGlossophagaLeptonycteris
LonchophyllaLionycterisCarolliaTrinycterisGlyphonycteris daviesiGlyphonycteris sylvestrisRhinophyllaSturnira
MesophyllaVampyressaPlatyrrhinusVampyrodes
Uroderma
Vampyressa bidensVampyressa brocki
Chiroderma
EnchisthenesEctophyllaArtibeusDermanuraAriteusArdopsStenodermaCenturioPygodermaAmetridaSphaeronycteris
< 0.97������
BYS posterior probability
Dumont, Dávalos et al. 2012 P R Soc B
Molecular evolution
Baker et al. 2003 Occas Pap Mus TTU Dávalos, Cirranello et al. 2012 Biol Rev
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A B
Background selection
Pe
rcen
t cod
ons
of C
YTB
in e
ach
codo
n ty
pe
0
20
40
60
Background selection Selection shift
Significantly support
Significantly rejectRejectSupport
Type of codon
Amino acid position in alignment
Sup
port
for n
ecta
r-fe
edin
g cl
ade
-3
-2
-1
0
1
2
3
100 200 300 400 500
Significant supportor rejection
Selection shiftSelection shift inGlossophaginae
Type of codon
CYTB COX1
Figure 12
Turns out: ecological convergence!
• Brings together ecologically similar lineages• Mt cytochrome b
gene of nectar-feeding bats
• Link between molecular adaptation and support for node
Dávalos, Cirranello et al. 2012 Biol Rev
Molecular evolution
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The genome is littered with such genes Parker et al. 2013 Nature
© N. Simmons
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Diphylla Diaemus Desmodus Brachyphylla Erophylla Phyllonycteris Platalina Lonchophylla Lionycteris Monophyllus Glossophaga Leptonycteris Anoura Hylonycteris Lichonycteris Scleronycteris Choeroniscus Musonycteris Choeronycteris Phylloderma Phyllostomus Macrophyllum Lonchorhina Mimon crenulatum Mimon bennettii Trachops Tonatia Chrotopterus Vampyrum Trinycteris Glyphonycteris Lampronycteris Macrotus Micronycteris minutaMicronycteris hirsutaMicronycteris megalotisRhinophylla Carollia Sturnira Enchisthenes hartiiArtibeus concolorArtibeus jamaicensisArtibeus cinereusUroderma Platyrrhinus Vampyrodes Chiroderma Vampyressa bidensVampyressa nymphaeaVampyressa pusillaEctophylla Mesophylla Ametrida Centurio Sphaeronycteris Pygoderma Phyllops Stenoderma Ariteus Ardops
�����
�����
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MP bootstrap
MacrotusLampronycterisMicronycteris minutaMicronycteris schmidtorumMicronycteris hirsutaMicroncyteris megalotisDiphyllaDiaemusDesmodusLonchorhinaMacrophyllumTrachopsChrotopterusVampyrumLophostomaTonatiaPhyllodermaPhyllostomusMimon
AnouraHylonycterisChoeroniscusMusonycterisChoeronycteris
ErophyllaBrachyphyllaMonophyllusGlossophagaLeptonycteris
LonchophyllaLionycterisCarolliaTrinycterisGlyphonycteris daviesiGlyphonycteris sylvestrisRhinophyllaSturnira
MesophyllaVampyressaPlatyrrhinusVampyrodes
Uroderma
Vampyressa bidensVampyressa brocki
Chiroderma
EnchisthenesEctophyllaArtibeusDermanuraAriteusArdopsStenodermaCenturioPygodermaAmetridaSphaeronycteris
< 0.97������
BYS posterior probability
Baker et al. 2003 Occas Pap Mus TTU Dávalos, Cirranello et al. 2012 Biol Rev
Wetterer et al. 2000 B Am Mus Nat HistSystematic error in phenotype
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Dated trees more important than ever
• Dated trees need fossils
• Why use dated trees?• Trait evolution• History of
assemblages in time and space
• Key innovations
Dumont, Dávalos et al. 2012 P R Soc B
Phenotypic evolution
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• We use morphological characters
• How do phenotypes evolve?• Characteristics of
the data• Compare to models
molecular evolution
Fossils without genomes
Dávalos & Russell 2012 Ecol Evol
Phenotypic evolution
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Species CharactersThese are morphological characters
• They look like this —>• Discontinuous
between species• Factors, not
numbers• Difficult to model
Phenotypic evolution
© N. Simmons
© M. Tuttle
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The trouble with morphological characters
• At first, only model was parsimony
• Neutral Jukes-Cantor 1969 model implemented 2001• Current model varies
rates across characters
• Applying this model does not solve conflict
Dávalos, Cirranello et al. 2012 Biol Rev
Phenotypic evolution
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Could conflict arise from systematic error?
Phenotypic evolution
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Might systematic error 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.
Phenotypic evolution
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Dávalos, Cirranello et al. 2012 Biol Rev
Inconsistency!
Phenotypic evolution
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Dental characters ●
●
MandibularMaxillary
● CanineIncisors
MolarsPremolars
● Significant
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0
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Supp
ort fRU�QHFWDUï
feed
ing
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●
●
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●
●
●
●
●●
●
●
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●●
●
●
●
A B
Background selection
Pe
rcen
t cod
ons
of C
YTB
in e
ach
codo
n ty
pe
0
20
40
60
Background selection Selection shift
Significantly support
Significantly rejectRejectSupport
Type of codon
Amino acid position in alignment
Sup
port
for n
ecta
r-fe
edin
g cl
ade
-3
-2
-1
0
1
2
3
100 200 300 400 500
Significant supportor rejection
Selection shiftSelection shift inGlossophaginae
Type of codon
CYTB COX1
Figure 12
Dávalos, Cirranello et al. 2012 Biol Rev
Convergent evolution!
Phenotypic evolution
Dávalos, Velazco et al. 2014 Syst Biol
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Correlated evolution!
Phenotypic evolution
Dissimilarity between characters ->
‘
Dávalos, Velazco et al. 2014 Syst Biol unpublished
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Systematic error in phenotypes
• Morphology = phenotype• Neutrality and
independence wrong assumptions• Not neutral• Not independent
Skelly et al. 2013 Genome Res
Phenotypic evolution
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The trouble with systematic error
• In sampling error mode• More is more• More characters• = thousands of
correlated phenotypes• This will fail, we have
systematic error• Improve model• Improve data• Understand data
Phenotypic evolution
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The contours of a theory of macroevolution
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Modern synthesis is about populations
• Features of populations become important• Population size• Migration
• Generations• Time
• Mutation rate
Dávalos & Russell 2014 J Mammal
Contours of macroevolution
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From micro to macro: successful example
• Coalescent stochasticity• Genes may represent
different histories by chance
• No selective force, only population characteristics
• Solution• Account for pop size
(Ne), # generations (t), mutation rate (mu) Neigel & Avise 1986 Evolutionary
Processes and TheoryContours of macroevolution
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Another example
• Phenotypic traits• Often expected to
be under selection• Solution• Extend quantitative
genetics• Compare Brownian
motion to Ornstein-Uhlenbeck process
• Model t, s, and optima Martins & Hansen 1997 Am Nat
Butler & King 2004 Am NatContours of macroevolution
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Dávalos, Velazco et al. 2014 Syst Biol unpublishedContours of macroevolution
There is a limit to modeling these, though
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The chasm genetics-phenotype
• Biochemistry defines units and processes of genetics
• Genetics defines units and processes of genotype evolution in population
• What is there for (morphological) phenotypes?
Contours of macroevolutionLöytynoja & Goldman 2008 Science
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Units and process
• How to define units of morphological evolution?
• Can using functional and developmental processes help?• Aren’t these also
unknown?• Are such processes
generalizable?• I.e., the way Ne, T and
mu areContours of macroevolution
Rieppel & Kearney 2007 Biol Philos
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Morphology...
AminoacidsCodons
The challenge ahead
Neutral genotype
Model complexity
Contours of macroevolution
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Thank you for inviting me!