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Slides from my phyloseminar on phylogenetic paleobiology, given 12-10-2013. Watch the seminar at http://www.youtube.com/watch?v=RDe2wbkSv5Q
Citation preview
Phylogenetic Paleobiology: What do we stand to gain from integrating fossils and
phylogenies in macroevolutionary analyses?
SmithsonianNational Museum of Natural History
Graham SlaterDepartment of Paleobiology, National Museum of Natural History
SmithsonianNational Museum of Natural Historywww.fourdimensionalbiology.com
@grahamjslater
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get a time-calibrated phylogeny
gather some trait data
40 30 20 10 0
fit some models
“insert_model” explains the evolution of “insert_trait” in
“insert_clade” !
LETTERdoi:10.1038/nature10516
Multiple routes to mammalian diversityChris Venditti1, Andrew Meade2 & Mark Pagel2,3
The radiation of themammals provides a 165-million-year test casefor evolutionary theories of how species occupy and then fill eco-logical niches. It is widely assumed that species often divergerapidly early in their evolution, and that this is followed by alonger, drawn-out period of slower evolutionary fine-tuning asnatural selection fits organisms into an increasingly occupiedniche space1,2. But recent studies have hinted that the processmay not be so simple3–5. Here we apply statistical methods thatautomatically detect temporal shifts in the rate of evolutionthrough time to a comprehensive mammalian phylogeny6 and dataset7 of body sizes of 3,185 extant species. Unexpectedly, themajorityof mammal species, including two of the most speciose orders(Rodentia and Chiroptera), have no history of substantial and sus-tained increases in the rates of evolution. Instead, a subset of themammals has experienced an explosive increase (between 10- and52-fold) in the rate of evolution along the single branch leading tothe common ancestor of their monophyletic group (for exampleChiroptera), followed by a quick return to lower or backgroundlevels. The remaining species are a taxonomically diverse assem-blage showing a significant, sustained increase or decrease in theirrates of evolution.These results necessarily decouplemorphologicaldiversification from speciation and suggest that the processes thatgive rise to the morphological diversity of a class of animals are farmore free to vary than previously considered. Niches do not seem tofill up, and diversity seems to arise whenever, wherever and at what-ever rate it is advantageous.Our approach uses a generalized least-squares model8,9 of trait
evolution in a Bayesian reversible-jump10 framework that allows ratesof evolution to vary in individual branches or entire monophyleticsubgroups of a phylogeny (Supplementary Information). This allowsus to trace the evolutionary history of shifts in the rate and timing ofevolutionwithout specifying in advancewhere these events are located,and to derive posterior probability density estimates of their magni-tudes and probability of occurrence (Supplementary Information).The null model states that evolution has proceeded at a constant ratethroughout the classMammalia. Applied to log-transformed body sizedata (n5 3,185 species) arrayed on the mammalian tree6 , this modelreturns a Bayesian posterior density of log-likelihoods with a mean of2939.346 0.99 (Fig. 1a), and a mean instantaneous rate of body sizeevolution of 1.02 g per million years. If rates are allowed to varythroughout the tree, the posterior density improves to a mean log-likelihood of 2364.136 23.01 (log(Bayes factor)5 993.51; values.10 considered ‘very strong’ support11; Fig. 1a). We detect evidencefor a shift or change in the rate of evolution in approximately one-third, or 1,494 branches, of the tree, where to be included in this countbranches had to either experience a change in rate in that branch orinherit that change from its immediate ancestral lineage, in at least 95%of the trees in the posterior sample. These shifts range from a 3-folddecrease to a 52-fold increase in the rate of evolution along a branch(Fig. 1b).It has long been believed that the radiation of extant mammals
underwent a burst of body-size evolution that occurred early in itshistory and coincided with the appearance of the mammalian orders,
and that this was followed by a gradual slowdown towards the pre-sent4,12–14. Explanations for this pattern suppose that mammals movedinto a largely unoccupied niche and geographical space as they came tobe the dominant vertebrate group on Earth. Then, as time went on,niche space and unexplored geographical regions became scarce,reducing opportunities for diversification4. In striking contrast to thispicture, we do not find any evidence for either a generalized burst ofevolution early inmammalian evolution or for the rates of evolution todecrease as time moves towards the present (Fig. 2a). Instead, rates ofevolution were low and stable for about the first 60 million years, onlystarting to increase around 90million years ago and then showing onlyabout a twofold increase over the previous ‘baseline’ rate. This increaseoccurred before the origin of the present-daymammalian orders and is
1Department of Biological Sciences, University of Hull, Hull HU6 7RX, UK. 2School of Biological Sciences, University of Reading, Reading RG6 6BX, UK. 3Santa Fe Institute, 1399 Hyde Park Road, Santa Fe,New Mexico 87501, USA.
Log-likelihood
Fold rate increase or decrease
500
1,000
1,500
2,000
2,500
12,000
–970 –870 –770 –670 –570 –470 –370 –270
0 5 10 15 20 25 30 35 40 45 50 55
Variable-rates model
Equal-rates modela
Freq
uenc
y
100
200
300
400
2,250b
Figure 1 | Log-likelihood of trait models when rates are allowed to vary.a, Posterior distribution of log-likelihoods from a model with equal rates ofevolution (red), compared with the posterior distribution of log-likelihoodsfrom the model in which evolutionary rates are allowed to vary (green):log(Bayes factor)5 993.51 (calculated from the log-harmonic means of thelikelihoods); values.10 considered ‘very strong’ support. b, The coloured barsshow distributions of rates for the one-third of the branches (1,494) for whichthe posterior probability of having a rate shift was greater than 0.95. Blue barssignify x-fold rate increases and yellow bars indicate x-fold rate decreases. Greybars show the distribution of the mean fold rates for all the branches in themammal phylogeny, independent of the level of posterior support.
0 0 M O N T H 2 0 1 1 | V O L 0 0 0 | N A T U R E | 1
Macmillan Publishers Limited. All rights reserved©2011
phylogenies don’t really look like this
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they look like this
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Finarelli and Flynn 2006 Sys. Biol.
adding fossils improves ancestral state estimates
do those extinct things matter for testing macroevolutionary
hypotheses?
do those extinct things matter for testing macroevolutionary hypotheses?
do those extinct things matter for testing macroevolutionary hypotheses?
• how much macroevolutionary information do fossils hold relative to extant taxa?
do those extinct things matter for testing macroevolutionary hypotheses?
• how much macroevolutionary information do fossils hold relative to extant taxa?
• does a paleontological perspective change the way we formulate our hypotheses?
do those extinct things matter for testing macroevolutionary hypotheses?
• how much macroevolutionary information do fossils hold relative to extant taxa?
• does a paleontological perspective change the way we formulate our hypotheses?
• can we use fossil information when we have no phylogeny including extinct species?
do those extinct things matter for testing macroevolutionary hypotheses?
• how much macroevolutionary information do fossils hold relative to extant taxa?
• does a paleontological perspective change the way we formulate our hypotheses?
• can we use fossil information when we have no phylogeny including extinct species?
simulate trait evolution
prune to extant taxa only
simulate trait evolution
prune to extant taxa only
fit models
simulate trait evolution
prune to extant taxa only
replace a proportion of extant taxa for fossils
simulate trait evolution
prune to extant taxa only
fit models
simulate trait evolution
replace a proportion of extant taxa for fossils
TimeTime
Phen
otyp
eBrownian motion
Time
0.0 0.2 0.4 0.6 0.8 1.00.0
0.2
0.4
0.6
0.8
1.0
swapping fossils for extant taxa has no effect if BM is the true model of evolution
Akaik
e Weig
hts
proportion of taxa that are extinct
0.0 0.2 0.4 0.6 0.8 1.00.0
0.2
0.4
0.6
0.8
1.0
swapping fossils for extant taxa has no effect if BM is the true model of evolution
Akaik
e Weig
hts
proportion of taxa that are extinct
BM is a special case of most current models
AIC = 2k - 2ln(L)
BM is a special case of most current models
# parameters Likelihood
trend
Time
Phen
otyp
e
trend
Time
Phen
otyp
e
Benson et al. 2013 PLoS ONE
Cope’s rule -- an evolutionary trend
no trends can be detected from extant taxa only
0 1 2 3 4 5 60.0
0.2
0.4
0.6
0.8
1.0
Akaik
e Weig
hts
root - tip increase in mean
0/100 fossils
0 1 2 3 4 5 60.0
0.2
0.4
0.6
0.8
1.0
but a few fossils have a substantial effectAk
aike W
eight
s
0/100 fossils
5/100
root - tip increase in mean
0 1 2 3 4 5 60.0
0.2
0.4
0.6
0.8
1.0
and more fossils improves ability to detect weaker trends
Akaik
e Weig
hts
0/100 fossils
5/100
50 /100
95 /100
root - tip increase in mean
Early Burst - Declining rates
Time
Phen
otyp
e
Early Burst - Declining rates
Time
Phen
otyp
e
ORIGINAL ARTICLE
doi:10.1111/j.1558-5646.2010.01025.x
EARLY BURSTS OF BODY SIZE AND SHAPEEVOLUTION ARE RARE IN COMPARATIVEDATALuke J. Harmon,1,2,3 Jonathan B. Losos,4 T. Jonathan Davies,5 Rosemary G. Gillespie,6 John L. Gittleman,7
W. Bryan Jennings,8 Kenneth H. Kozak,9 Mark A. McPeek,10 Franck Moreno-Roark,11 Thomas J. Near,12
Andy Purvis,13 Robert E. Ricklefs,14 Dolph Schluter,2 James A. Schulte II,11 Ole Seehausen,15,16
Brian L. Sidlauskas,17,18 Omar Torres-Carvajal,19 Jason T. Weir,2 and Arne Ø. Mooers20
1Department of Biological Sciences, University of Idaho, Moscow, Idaho 838442Biodiversity Centre, University of British Columbia, Vancouver, BC V6T1Z4, Canada
3E-mail: [email protected] of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 021385National Center for Ecological Analysis and Synthesis, University of California, Santa Barbara, 735 State Street, Suite 300,
Santa Barbara, California 931016Department of Environmental Science, Policy and Management, University of California, Berkeley, California 947207Odum School of Ecology, University of Georgia, Athens, Georgia 306028Department of Biological Sciences, Humboldt State University, Arcata, California 955219Department of Fisheries, Wildlife, and Conservation Biology, University of Minnesota, St. Paul, Minnesota 5510810Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 0375511Department of Biology, Clarkson University, Potsdam, New York 1369912Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 0652013Division of Biology, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY United Kingdom14Department of Biology, University of Missouri—St. Louis, St. Louis, Missouri 6312115Institute of Ecology & Evolution, Division of Aquatic Ecology & Macroevolution, University of Bern, CH-3012 Bern,
Switzerland16Eawag Centre of Ecology, Evolution and Biogeochemistry, Department of Fish Ecology & Evolution, Seestrasse 79,
CH-6047 Kastanienbaum, Switzerland17National Evolutionary Synthesis Center, Durham, North Carolina 2770518Oregon State University, Department of Fisheries and Wildlife, 104 Nash Hall, Corvallis, Oregon, 9733119Escuela de Biologıa, Pontificia Universidad Catolica del Ecuador, Apartado 17-01-2184, Quito, Ecuador20Department of Biological Sciences, Simon Fraser University, Burnaby, BC V5A1S6, Canada
Received May 11, 2009
Accepted February 21, 2010
2 3 8 5C⃝ 2010 The Author(s). Journal compilation C⃝ 2010 The Society for the Study of Evolution.Evolution 64-8: 2385–2396
Slater and Pennell (in press) Syst. Biol
early bursts need lots of taxa and big changes in rate
Slater and Pennell (in press) Syst. Biol
Akaike Weight
0.2
0.4
0.6
0.8
1.0
weight
50 100 150 200
0
2
4
6
8
10
number of taxa
# of
hal
f liv
es
0
2
4
6
8
10
0.2
0.4
0.6
0.8
# elapsedrate half lives
50 100 150 200
# taxa
1.0
early bursts need lots of taxa and big changes in rate
Slater and Pennell (in press) Syst. Biol
Akaike Weight
0.2
0.4
0.6
0.8
1.0
weight
50 100 150 200
0
2
4
6
8
10
number of taxa
# of
hal
f liv
es
0
2
4
6
8
10
0.2
0.4
0.6
0.8
# elapsedrate half lives
50 100 150 200
# taxa
1.0
early bursts need lots of taxa and big changes in rate
Slater and Pennell (in press) Syst. Biol
Akaike Weight
0.2
0.4
0.6
0.8
1.0
weight
50 100 150 200
0
2
4
6
8
10
number of taxa
# of
hal
f liv
es
0
2
4
6
8
10
0.2
0.4
0.6
0.8
# elapsedrate half lives
50 100 150 200
# taxa
1.0
0.2
0.4
0.6
0.8
1.0
weight
50 100 150 200
0
2
4
6
8
10
number of taxa
# of
hal
f liv
es
early bursts need lots of taxa and big changes in rate
0 2 4 6 80.0
0.2
0.4
0.6
0.8
1.0
we need a lot of fossils to detect weaker early bursts
Akaik
e Weig
hts
# elapsed rate half-lives
0/100
5/100
50 /10
095
/100
Time
Phen
otyp
eLate Burst - Accelerating rates
Time
Phen
otyp
eLate Burst - Accelerating rates
0 2 4 6 80.0
0.2
0.4
0.6
0.8
1.0
Akaik
e Weig
hts
# elapsed rate doubling times
no ability to detect accelerating rates from ultrametric trees
0/100 fossils
0 2 4 6 80.0
0.2
0.4
0.6
0.8
1.0
Akaik
e Weig
hts
# elapsed rate doubling times
no ability to detect accelerating rates from ultrametric trees
0/100 fossils
0 2 4 6 80.0
0.2
0.4
0.6
0.8
1.0
Akaik
e Weig
hts
# elapsed rate doubling times
and may be mistaken for other “low-signal” processes like Ornstein-Uhlenbeck
0/100 fossils
0 2 4 6 80.0
0.2
0.4
0.6
0.8
1.0
Akaik
e Weig
hts
# elapsed rate doubling times
swapping extant tips for fossils increases support for accelerating rates over OU
5/100 fossils
0 2 4 6 80.0
0.2
0.4
0.6
0.8
1.0
Akaik
e Weig
hts
# elapsed rate doubling times
swapping extant tips for fossils increases support for accelerating rates over OU
50/100 fossils
0 2 4 6 80.0
0.2
0.4
0.6
0.8
1.0
Akaik
e Weig
hts
# elapsed rate doubling times
swapping extant tips for fossils increases support for accelerating rates over OU
95/100 fossils
how much macroevolutionary information do fossils hold relative to extant taxa?
how much macroevolutionary information do fossils hold relative to extant taxa?
on a “per-taxon” basis, fossils contribute more macroevolutionary
information than extant taxa
how much macroevolutionary information do fossils hold relative to extant taxa?
on a “per-taxon” basis, fossils contribute more macroevolutionary
information than extant taxa
impact of fossils depends on the underlying evolutionary process
do those extinct things matter for testing macroevolutionary hypotheses?
• how much macroevolutionary information do fossils hold relative to extant taxa?
• does a paleontological perspective change the way we formulate our hypotheses?
• can we use fossil information when we have no phylogeny including extinct species?
do we test the right models?
How fast...do animals evolve...? That is one of
the fundamental questions regarding
evolution
Photo: Florida Museum of Natural HistorySimpson (1944, 1953)
Illustration by Mark Hallet
Eoce
neO
ligoc
ene
Mio
cene
Alroy (1999) Systematic Biology
fossils suggest an increase in mean and variance of body size after the K-Pg
K Pg Ng K Pg Ng
standard deviation massmean mass
Venditti et al. (2011) Nature
K Pg NgJ
relative rate
Phylogenetic approaches find no rate increase in the Cenozoic
do we really think mammals changed their rate of body
size evolution?
From Simpson (1953)
Simpson’s adaptive zones
Mesozoic CenozoicT J PgK Ng
body sizethe mammalian adaptive zone
Mesozoic CenozoicT J PgK Ng
body sizethe mammalian adaptive zone
variation in tempo
Mesozoic CenozoicT J PgK Ng
body size
variation in tempo
evolution slow
Mesozoic CenozoicT J PgK Ng
body size
variation in tempo
evolution slow
evolution fast
Mesozoic CenozoicT J PgK Ng
body size
images from http://dinosaurs.about.com
Mesozoic CenozoicT J PgK Ng
body size
variation in mode
images from http://dinosaurs.about.com
Mesozoic CenozoicT J PgK Ng
body size
variation in mode
images from http://dinosaurs.about.com
evolution constrained
Mesozoic CenozoicT J PgK Ng
body size
variation in mode
images from http://dinosaurs.about.com
evolution constrained
evolution unconstrained
Mesozoic CenozoicT J PgK Ng
body size
3 paleo-motivated models for mammalian body size evolution
Slater (2013) Methods Ecol. Evol.
3 paleo-motivated models for mammalian body size evolution
Mesozoic Cenozoic
BM rate 1 BM rate 2
K-Pg Shift
Slater (2013) Methods Ecol. Evol.
3 paleo-motivated models for mammalian body size evolution
Mesozoic Cenozoic
BM rate 1 BM rate 2
K-Pg Shift
Mesozoic Cenozoic
Ornstein-Uhlenbeck BM
ecological release
Slater (2013) Methods Ecol. Evol.
3 paleo-motivated models for mammalian body size evolution
Mesozoic Cenozoic
BM rate 1 BM rate 2
K-Pg Shift
Mesozoic Cenozoic
Ornstein-Uhlenbeck BM
ecological release
Mesozoic Cenozoic
BM*
release and radiate
Ornstein-Uhlenbeck
Slater (2013) Methods Ecol. Evol.
Q
Ng
Pg
K
J
T
P
02.59
23
66
145
201.3
252.2
264.94
time calibrated phylogeny of living and fossil mammals
Cenozoic
Mesozoic
Pz
Slater (2013) Methods Ecol. Evol.
Q
Ng
Pg
K
J
T
P
02.59
23
66
145
201.3
252.2
264.94
Cenozoic
Mesozoic
Pz
Slater (2013) Methods Ecol. Evol.
standard models paleo-inspired models
BrownianMotion
Directional Trend
Ornstein Uhlenbeck
AC /DC
White Noise
K-Pg shift
Ecological release
Release & radiate
0.0
0.2
0.4
0.6
0.8
1.0
Aka
ike
Wei
ghts
release & radiate fits best
standard models paleo-inspired models
BrownianMotion
Directional Trend
Ornstein Uhlenbeck
AC /DC
White Noise
K-Pg shift
Ecological release
Release & radiate
0.0
0.2
0.4
0.6
0.8
1.0
Aka
ike
Wei
ghts
Parameters Mesozoic Cenozoic
rate (σ2) 0.97 0.1
OU param (α) 0.01 -
faster rates of body size evolution in the Mesozoic?
Parameters Mesozoic Cenozoic
rate (σ2) 0.97 0.1
OU param (α) 0.01 -
faster rates of body size evolution in the Mesozoic?
Brownian motion is a diversifying process
time
phen
otyp
e
Brownian motion is a diversifying process
time
phen
otyp
e
starting state
Brownian motion is a diversifying process
time
phen
otyp
e
rate σ2
starting state
Brownian motion is a diversifying process
time
phen
otyp
e
rate σ2
starting state
Brownian motion is a diversifying process
time
phen
otyp
e
rate σ2
starting state starting state
Brownian motion is a diversifying process
time
phen
otyp
e
rate σ2
starting state starting state
σ2 * time
time
phen
otyp
e
OU is an equilibrium process
time
phen
otyp
e
OU is an equilibrium process
starting state
time
phen
otyp
e
OU is an equilibrium process
rate σ2
starting state
time
phen
otyp
e
rubber band parameter α
OU is an equilibrium process
rate σ2
starting state
time
phen
otyp
e
rubber band parameter α
OU is an equilibrium process
rate σ2
starting state
time
phen
otyp
e
rubber band parameter α
OU is an equilibrium process
rate σ2
starting state starting state
time
phen
otyp
e
σ2 / 2α
rubber band parameter α
OU is an equilibrium process
rate σ2
starting state starting state
time
phen
otyp
eBrownian motionOrnstein-Uhlenbeck
BM and OU simulated at the same rate give very different disparities
the OU process has an equilibrium disparity
250 200 150 100 50 0
variance
millions of years ago
CenozoicMesozoic
the OU process has an equilibrium disparity
250 200 150 100 50 0
variance
millions of years ago
CenozoicMesozoic
250 200 150 100 50 0
variance
millions of years ago
CenozoicMesozoic
a low BM rate increases disparity
do we really think mammals changed their rate of body
size evolution?
do we really think mammals changed their rate of body
size evolution?✗
How fast...do animals evolve...? That is one of
the fundamental questions regarding
evolution
Photo: Florida Museum of Natural HistorySimpson (1944, 1953)
How fast...do animals evolve...? That is one of
the fundamental questions regarding
evolution
Photo: Florida Museum of Natural HistorySimpson (1944, 1953)
...hang on a minute
D
A
B
C
8 6 4 2 0
D
A
B
C
8 6 4 2 0
B
C
D
A B C D
A 8.24 0.00 0.00 0.00
B 0.00 8.24 0.61 0.61
C 0.00 0.61 4.65 4.10
D 0.00 0.61 4.10 8.24
B
C D
D
A
B
C
8 6 4 2 0
B
C
D
A B C D
A 8.24 0.00 0.00 0.00
B 0.00 8.24 0.61 0.61
C 0.00 0.61 4.65 4.10
D 0.00 0.61 4.10 8.24
B
C D
D
A
B
C
8 6 4 2 0
B
C
D
A B C D
A 8.24 0.00 0.00 0.00
B 0.00 8.24 0.61 0.61
C 0.00 0.61 4.65 4.10
D 0.00 0.61 4.10 8.24
B
C D
D
A
B
C
8 6 4 2 0
B
C
D
A B C D
A 4.04 0.00 0.00 0.00
B 0.00 4.04 0.18 0.13
C 0.00 0.18 3.03 1.75
D 0.00 0.13 1.75 4.04D
A
B
C
8 6 4 2 0
OU VCV transformation DC
BB
C
D
A B C D
A 4.04 0.00 0.00 0.00
B 0.00 4.04 0.18 0.13
C 0.00 0.18 3.03 1.75
D 0.00 0.13 1.75 4.04D
A
B
C
8 6 4 2 0
OU VCV transformation DC
BB
C
D
A B C D
A 4.04 0.00 0.00 0.00
B 0.00 4.04 0.18 0.13
C 0.00 0.18 3.03 1.75
D 0.00 0.13 1.75 4.04D
A
B
C
8 6 4 2 0
OU VCV transformation DC
BB
C
D
A B C D
A 4.04 0.00 0.00 0.00
B 0.00 4.04 0.18 0.13
C 0.00 0.18 3.03 1.75
D 0.00 0.13 1.75 4.04D
A
B
C
8 6 4 2 0
OU VCV transformation DC
BB
C
D
A B C D
A 4.04 0.00 0.00 0.00
B 0.00 4.04 0.13 0.13
C 0.00 0.13 1.48 1.22
D 0.00 0.13 1.22 4.04D
A
B
C
8 6 4 2 0
OU branch length transformation DC
BB
C
D
BrownianMotion
Directional Trend
Ornstein Uhlenbeck
AC /DC
White Noise
K-Pg shift
Ecological release
Release & radiate
0.0
0.2
0.4
0.6
0.8
1.0
Aka
ike
Wei
ghts
standard models paleo-inspired models
release & radiate still fits best...
BrownianMotion
Directional Trend
Ornstein Uhlenbeck
AC /DC
White Noise
K-Pg shift
Ecological release
Release & radiate
0.0
0.2
0.4
0.6
0.8
1.0
Aka
ike
Wei
ghts
standard models paleo-inspired models
but ecological release is almost as good
Parameters Mesozoic Cenozoic
rate (σ2) 0.2 0.1
OU param (α) 0.03 -
a less pronounced rate decrease ...
250 200 150 100 50 0
variance
millions of years ago
CenozoicMesozoic
but σ2 / 2α makes more sense
250 200 150 100 50 0
variance
millions of years ago
CenozoicMesozoic
but σ2 / 2α makes more sense
Tree transformations under OU don’t work for non-ultrametric
trees!
do those extinct things matter for testing macroevolutionary hypotheses?
• how much macroevolutionary information do fossils hold relative to extant taxa?
• does a paleontological perspective change the way we formulate our hypotheses?
• can we use fossil information when we have no phylogeny including extinct species?
a touch of realism
most comparative biologists don’t have this
40 30 20 10 0
40 30 20 10 0
but have this
††
†
†
40 30 20 10 0
†
40 30 20 10 0
†
40 30 20 10 0
†
40 30 20 10 0
†
density.default(x = X)
-4 -2 0 2 4 6
0.00
0.10
0.20
0.30
ln(mass)
Density
caniform carnivores span a huge range of body sizes
caniform carnivores span a huge range of body sizes
30-250 grams
caniform carnivores span a huge range of body sizes
30-250 grams > 3, 000 Kg
Finarelli and Flynn 2006 Sys. Biol.
do caniform carnivores exhibit a trend towards large body size?
-2.5 7.5ln(body mass)
50 40 30 20 10 0Millions of Years Ago
Canidae
UrsidaeOdobenidaeOtariidae
Phocidae
MephitidaeAiluridae
Procyonidae
Mustelidae
Slater et al. 2012 Evolution
-2.5 7.5ln(body mass)
50 40 30 20 10 0Millions of Years Ago
Canidae
UrsidaeOdobenidaeOtariidae
Phocidae
MephitidaeAiluridae
Procyonidae
Mustelidae
Slater et al. 2012 Evolution
12 node priors - 11 internal - root
0.1 1 10 100 10000.0
0.2
0.4
0.6
0.8
1.0
0.1 1 10 100 10000.0
0.2
0.4
0.6
0.8
1.0
0.1 1 10 100 10000.0
0.2
0.4
0.6
0.8
1.0
0.1 1 10 100 10000.0
0.2
0.4
0.6
0.8
1.0
BM
OU
Trend
AC/DCextant
nodes
nodes + root
mass mass
mass mass
dens
ityde
nsity
dens
ityde
nsity
ancestral size is too large based on extant taxa ...
0.1 1 10 100 10000.0
0.2
0.4
0.6
0.8
1.0
0.1 1 10 100 10000.0
0.2
0.4
0.6
0.8
1.0
0.1 1 10 100 10000.0
0.2
0.4
0.6
0.8
1.0
0.1 1 10 100 10000.0
0.2
0.4
0.6
0.8
1.0 extantfossilsfossils + root
BM
OU
Trend
AC/DCextant
nodes
nodes + root
... but is more realistic with fossil priors
mass mass
mass mass
dens
ityde
nsity
dens
ityde
nsity
Trend ACDC OU
-10
12
32*
Ln(B
ayes
Fac
tor)
extant.onlyfossilsfossils.plus.root
Trend OUAC/DC
extant
nodes
nodes + root
Trend ACDC OU
-10
12
32*
Ln(B
ayes
Fac
tor)
extant.onlyfossilsfossils.plus.root
Trend OUAC/DC
extant
nodes
nodes + rootpositive
Trend ACDC OU
-10
12
32*
Ln(B
ayes
Fac
tor)
extant.onlyfossilsfossils.plus.root
Trend OUAC/DC
extant
nodes
nodes + root
Trend ACDC OU
-10
12
32*
Ln(B
ayes
Fac
tor)
extant.onlyfossilsfossils.plus.root
Trend OUAC/DC
extant
nodes
nodes + root
root-tip increase in Ln(mass)
dens
itymode = 1.55
-1 0 1 2 3 4 5
0
5
10
15
20
25
the estimated change in mean mass is subtle
0 1 2 3 4 5 60.0
0.2
0.4
0.6
0.8
1.0
Akaik
e Weig
hts
root - tip change in mean
0/100 fossils
5/100
50 /100
95 /100
which is difficult to detect using AIC
-1012345
0.5 1 10ancestral mass (Kg)
root
-tip
incre
ase
in Ln
(mas
s)
joint marginal distribution of root state and trend parameter
-1012345
0.5 1 10ancestral mass (Kg)
joint marginal distribution of root state and trend parameter
root
-tip
incre
ase
in Ln
(mas
s)
PP(Mu> 0) = 0.97
-1012345
0.5 1 10ancestral mass (Kg)
joint marginal distribution of root state and trend parameter
root
-tip
incre
ase
in Ln
(mas
s)
no fossils with fossils
ancestral size
mode of evolution
how do fossils change our picture of caniform size evolution?
no fossils with fossils
ancestral size large (~25kg) small (~2 kg)
mode of evolution
how do fossils change our picture of caniform size evolution?
no fossils with fossils
ancestral size large (~25kg) small (~2 kg)
mode of evolution Brownian motionBrownian motion + trend to large
size
how do fossils change our picture of caniform size evolution?
can we use fossil information when we have no phylogeny including extinct species?
can we use fossil information when we have no phylogeny including extinct species?
even using fossil traits as informative node priors improves model fitting
do those extinct things matter for testing macroevolutionary
hypotheses?
today’s model systems for macroevolutionary studies
images: wikipedia
tomorrow’s model systems for macroevolutionary studies
images: www.amnh.oig., wikipedia