Traits and phylogeny

Burns and Strauss 2012

Traits and phylogeny
• Traits are a product of evolution
• Traits of similar species are also similar
As the species of the same
genus usually have …
much similarity in habits
and constitution, and
always in structure, …
 Many approaches rely
on the assumption that
phylogenies represent
functional aspects
Evolutionary time
Traits and phylogeny
• Traits of similar species are also similar
– Is that really so?
• How to statistically model trait evolution
– Brownian motion model (random walk)
Brownian motion
Brownian motion
Phylogenetic signal
• How well do the values of a trait agree with a
Brownian model of evolution, given a
phylogeny of the species
– Pagel’s lambda (Pagel 1999)
– Bloomberg’s K (Bloomberg et al. 2003)
– Mantel tests (Debastiani and Duarte 2016)
Phylogenetic data in R
• Testing for phylogenetic signal
– Lambda: how well are observed trait values
“correlated” with trait values from Brownian
motion model? (0 < lambda < 1)
– K: Is variation of a trait within or across clades
Phylogenetic signal: Pagel’s λ
Traitgrams
Phylogenetic signal: Pagel’s λ
Data imputation
Databases
• Missing data
– Data imputation: replacing missing data with
substituted values
Databases

Bruggemann et al. 2009

Most of the methods rely on the assumptions

that traits are conserved (i.e. closely related
species are similar) and/or correlated
Traits and phylogeny
• Phylogenetic constraint and adaptive capacity
• Phylogeney as a “nuisance” (dependency of
data points)
• Phylogeny as a proxy for function
Species level analyses
 Species level analyses
• Phylogenetic constraint and adaptive capacity
Lack of lipogenesis in insects

Software: Mesquite & MacClade 4.0

Lack of lipogenesis is phylogenetically constrained

Visser et al.1:(2010).
Visser etPNAS 107: 8677-8682
al., submitted
Adaptation vs phylogenetic conservatism

• Lack of lipogenesis in insects

– most species have ability to assimilate fat after
resource uptake
– some species have lost this ability
– it seems that lack of lipogenesis is accompanied by a
parasitic life style
– what is cause and consequence here?
 Species level analyses
• Phylogeny as a “nuisance” that we need to
“correct” for (dependency of data points)
Felsenstein 1985
Felsenstein 1985
Independent contrasts
Log(pollen ovule ratio) ~ Log(pollen size)

Götzenberger et al. 2007

“Correcting” or modeling the
evolution of correlated traits
 Bigger and harder leaves Smaller and softer leaves

No grazing Grazing
Combining Functional & Phylogenetic Diversity
 Community level analyses
• Phylogeny as a proxy for function
 Distance based indices of diversity

Species’ traits Pairwise distance Community

matrix data Functional
Species Diversity
Species’ traits

Samples

Samples
Species

Species
 Distance based indices of diversity
Species’ traits Pairwise distance Community
matrix data Functional
Species Diversity
Species’ traits

Samples

Samples
Species

Species

Functional
Species Diversity
Species’ traits

Samples

Samples
Species

Species

Randomization x 1000 x 1000

 Phylogeny

Regional
species pool

Filter 1

Habitat
species pool

Filter 2

Local community 1 Local community 2

Distance based indices of diversity
Phylogenetic Pairwise distance Community
tree matrix data Phylogenetic
Species Diversity

Samples

Samples
Species

Species

Phylogenetic
Species Diversity

Samples

Samples
Species

Species

Randomization x 1000 x 1000

A
A 0
B B 1 0
C 3 3 0
C D 3 3 1 0

D A B C D
Distance based indices of diversity
Observed
Functional Species more similar in their traits
Diversity
than expected by random assembly
expected
SES =
Samples

standardized
difference
between
Random observed
Functional observed and
Diversity
expected
diversity
Samples

x 1000
A

D
A A
B
B

C
C
D
D
A A
D
B

C
C

D B
A

D
A A
C
B

C
B
D
D
A A
C
B

C
B
D
D
 Post-fire succession in Australian heathlands

Letten et al. 2014

Mayfield and Levine 2010, Ecology Letters
Mayfield and Levine 2010, Ecology Letters
Functional & Phylogenetic Diversity

LHS traits
Phylogenetic Functional
Diversity Diversity

Unknown Known Known

conserved conserved labile
traits traits traits
Combining Functional & Phylogenetic Diversity

Cadotte et al. 2013 ELE

Combining Functional & Phylogenetic Diversity
Combining Functional & Phylogenetic Diversity

Functional
Phylogenetic
Species Diversity

1-a

Samples

Samples
Species

a Species
Phylogenetic Functional
Diversity Diversity

Unknown Known Known

conserved conserved labile
traits traits traits
Phylogenetic Functional
Diversity Diversity

Unknown Known Known

conserved conserved labile
traits traits traits

Unknown labile traits

 Combining Functional & Phylogenetic Diversity

Phylogene)c+tree+ Phylogene)c++ PCoA+ Species+PCoA+scores+(eingevectors)+ RDA+ Phylogene)c+sp.+pairwise+

species+pairwise+ (on$squared$root$distances)$ on$ALL$axes$$ PCoA$scores$$ dissim.+decoupled+from+traits+++
explained$by$traits$++
dissimilarity++ Axis1$ Axis$n$ Weighted$dissimilarity$$

Axis2$
INPUT$ Sp$1$
Sp$1$ is$n
$ Sp$1$ Sp$1$ Sp$1$
from$scores$on$
OUTPUT$ Ax Reduced+PCoA+eingenvectors+ unconstrained$axes$
axes$significant$on$at$least$one$trait$$ Trait1$
Sp$1$ OUTPUT$
Axis1$ Sp$1$

Pdist+ Sp$n$ dcPdist+

Sp$n$ Trait$n$ Sp$n$
Sp$n$
Sp$n$
Sp$1$ Sp$n$ Sp$1$ Sp$n$

$
rs
Sp$n$

o
ct
di
Sp$n$

re
Func)onal+traits+sp.+ Func)onal+traits+sp.+pairwise+

$p
Species+traits+

Significant$

$as
Sp$1$ dissim.+decoupled+from+phylogeny+
pairwise+dissimilarity++

ts
$axes$

ai
Trait1$ Trait$n$ Stepwise$selec:on$ Weighted$dissimilarity$$

Tr
Phylo$axis$1$
Sp$1$ Sp$1$ of$PCoA$axes$on$each$trait$ Sp$n$
Sp$1$ from$scores$on$
unconstrained$axes$
OUTPUT$
+

Trait+n+~+all+axes++++ OUTPUT$

Fdist+ Traits$as$response$variables$ Phylo$axis$n$

Sp$n$ Sp$n$
dcFdist+
Sp$n$ RDA+
Sp$1$ Sp$n$ Covariance+between+traits+and+phylogeny+ All$traits$$$ Sp$1$ Sp$n$
Weighted$dissimilarity$from$scores$on$ explained$by$reduced$
INPUT$ constrained$axes$ $PCoA$axes$+
NONHDECOUPLED++ covFPdist+ OUTPUT$ DECOUPLED++
dissimilari)es+ dissimilari)es+

De Bello et al. submitted

Combining Functional & Phylogenetic Diversity
Combining Functional & Phylogenetic Diversity

• Many assumptions made when using phylogenetic diversity to

explain community assembly are not met
• Phylogenetic diversity as “result” (of evolutionary processes) vs
PD as proxy for traits
Landuse change and litter decomposition

• Community response
– SRF independent of t1 / t2
– weak phylogenetic signal

1: Ellers 2010 in: Community Diaz et al
Ecology
(Verhoef
• Ecosystem processes
– SEF depending on t1 / t2
– strong phylogenetic signal
– SRF / SEF not correlated
– species loss (45 à 16)
– SEF trait distribution
unchanged
– similar mean and range
(2013).&Ecology
Morin), &
2: Evolution
Berg & Ellers2010 Evolutionary Ecology
Hunting and long-distance seed dispersal

• Community response
– SRF depending on t1
– strong phylogenetic signal
– reduction in evolutionary
history

1: Ellers 2010 in: Community Diaz et al
Ecology
(Verhoef
• Ecosystem processes
– SEF depending on t1
– strong phylogenetic signal
– SRF / SEF neg. correlated
– species loss (> 50%)
– SEF’ strongly reduced
(2013).&Ecology
Morin), &
2: Evolution
Berg & Ellers2010 Evolutionary Ecology
Phylogenetic data in R
• Important R packages: ape, picante, phytools,
geiger
• Import and Visualization
• Testing for phylogenetic signal
• Phylogenetic independent contrasts
• Traitgrams
• Functional vs. phylogenetic diversity