Download Evolutionary Physiology

Evolutionary
Physiology
Y v e s
D e s d e v i s e s
O b s e rv a t o i r e
O c é a n o l o g i q u e d e B a n y u l s
0 4 6 8 8 8 7 3 1 3
d e s d e v i s e s @ o b s - b a n y u l s . f r
h t t p : / / d e s d e v i s e s . f r e e . f r
1
2
Physiology
Physiology: how organisms work
Lot of diversity of living organisms and the different
ways they function
Multiple solutions to a given problem (such as living
in arid environment)
3
Animals possess different physiological ways to cope
with their environment
Some (but not all!) are adaptations
How did animal physiological traits came the way they
are? "Why" organisms are designed to work in particular
ways?
Need to put that in an evolutionary context
Investigation in an hypothetico-deductive framework
(≠ inductive, although preliminary obervations are
necessary)
➡Evolutionary physiology
4
Outline
Definition of adaptation
Some methods to investigate physiological adaptations
Examples
5
Adaptation
Adaptation = trait, or set of traits, increasing
fitness, then leading individuals to produce more
descendants than those without this trait
Trait which origin (and maintenance) is associated to an
increase of functional efficiciency favoured by natural
selection
Product of natural selection
Difficult to reveal: must be tested
6
Test of adaptation: correlation of the putative
adaptative trait with an environmental variable it is
supposed to adapted for
Test of the appearance of the trait in the new
environment (not only its presence in a given
environment)
7
Adaptation acts on design, and/or reproduction
Must be investigated in an evolutionary context
Adaptation “appears” (and is maintained) in a
lineage
≠ inherited from an ancestor
8
Example: adaptation = hydrodynamic shape
9
Adaptation/
Acclimatization/
Phenotypic plasticity
Adaptation: evolution via natural selection, in a species,
many generations. Modification of the genotype. Often
not reversible
Acclimatization: physiological, biochemical, anatomical
change, in an individual, due to the exposure to a new
environment. Often reversible
Phenotypic plasticity: ability of a genotype to produce
different phenotypes related to an environmental change,
in an individual. Plasticity can be adaptive.
10
Acclimatization
Adaptation
Time
Phenotypic plasticity
11
A component of evolution
Evolution ≠ adaptation. Evolution is:
Adaptation (selection)
Genetic drift
Structure (physics)
By-product of another trait (linkage)
Phylogenetic inertia (traits from ancestor)
Vestigial structure
Constraints (everything is not possible)
Organism = trade-offs
12
Gradual (Darwin) or punctuational changes
Gradual: many transitional steps
Punctuational changes
Rapid evolution in small localized populations
Regulatory genes: small genetic modification = big
phenotypic change
Polypoïdy (plants)
Combination of several elements: different
structures, genes, organisms (endosymbiosis)
13
Adaptation ≠ perfection
Time lag between adaptation and environmental change:
“imperfections”, maladaptation
Constraints
Genetic: e.g. persistence of deleterious homozygous if
heterozygous have a superior fitness
Development: development influences the possibility
of variations
14
Historical
Adaptation arises on existing state: the possible
solution may not be optimal
Do not infer abusive adapative interpretations!!
“Spandrelism”
15
Study of adaptation
Theoretical approach: models, predictions
Observational approach: in the field
Experimental approach: alteration of potentially
adaptive structure
Comparative approach: correlation between
structures or structure/function in several lineages
(usually species), taking phylogeny into account.
Comparative method/analysis
16
Comparative analysis
Study of character correlated evolution
Search for adaptations via a cross-species correlative
approach
Link: trait/trait or trait/environment
Size / longevity
Metabolism / temperature
BMR / altitude
17
Example
Chlorophylle b vs depth in Ostreococcus
Picoalgae (< 1 µm), several strains, found at different
depths
1,4
1,3
1,2
1,1
1
,9
,8
,7
,6
➡ Chloropyll b = adaptation to depth?
P = 0,0007
-20
0 20 40 60 80 100 120 140
Depth
Y = 0,719 + 0,004 * X; R^2 = 0,779
18
Some key dates
1985: Felsenstein
1991: Harvey & Pagel; Brooks & McLennan
Closely related species tend to be similar, and are
not independent observations (pseudoreplication)
Phylogenetic constraints (morphology, physiology,
genetic, development, ...): inertia
Phylogeny = confounding variable
19
Example
Hypothesis: Hb affinity is an adaptation to altitude
Species
Altitude
Hb aff.
A
B
C
D
E
F
G
H
I
J
5
6
8
12
14
24
25
28
29
30
2
6
6
7
12
13
14
14
16
17
Hb aff.
Chl b
Strains contain different concentrations in Chloropyll b
Altitude
correlation: adaptation?
20
Problem
Species
Altitude
Size
A
B
C
D
E
F
G
H
I
J
5
6
8
12
14
24
25
28
29
30
2
6
6
7
12
13
14
14
16
17
Hb aff.
Phylogeny makes data non independent
Altitude
21
Solution
Hb aff. (corrected)
Control phylogenetic constraints
Altitude (corrected)
no correlation
Comparative analysis
22
Classical statistics requires independance of observation,
then assume a "star" phylogeny, which is not true
Take phylogenetic relationships into account in the
analysis (at least use taxonomy)
23
Is preferred body temperature positively correlated to
optimal temperature for sprint running speed in 12
species of lizards?
Computation of
observed correlation
Test against random
data simulated along
the species tree
Observed value:
r = 0.585
S
NS
NS
24
Several methods exist to take phylogeny into account in
analyses
Most known: independent contrasts (Felsenstein, 1985),
first fully phylogenetic method
Trait variation partitionning:
Environment
Phylogeny
?
100 % of trait variation
Westoby et al. (1995)
25
Models of character
evolution
Two basic models
Brownian motion (BM): variance is a linear
function of (proportional to) time = branch lengths
on tree
26
Brownian motion
.
Time
Character variance
increases with time
Trait (x)
27
Addition of constraints (adaptive, ...) and
estimation of corresponding parameters:
different relationships between branch lengths
and character variances (e.g. OrnsteinUhlenbeck model: OU)
Divergence
genetic drift (BM)
BM + stabilizing selection
Time
28
Methods
Methods based on evolutionary models
Independent contrasts (FIC; Felsenstein 1985)
Phylogenetic generalized least squares (PGLS;
Martins 1994)
Phylogenetic mixed model (PMM; Lynch et al. 2004)
29
Methods with statistical bases
Autoregressive method (ARM; Cheverud et al.
1985)
Phylogenetic eigenvector regression (PVR;
Diniz-Filho et al. 1998)
30
Independent contrasts
FIC; PIC
Most used method
Evolutionary model = Brownian motion: genetic drift,
some selective regimes
Time = branch length = variance
Supposes well known phylogeny, that is fully used
Ideally for quantitative variables but a variable can be
qualitative
31
Correlation among traits
Time
.
ρ = 0.9
ρ = 0.0
Traits (x, y)
32
Estimation of
ancestral character
values
(weighted means)
8 22
9 24
X Y
Contrasts
7 20
X Y
2 4
9 24
2
10 25
8 11
3
14 30
42,5
12
40
37,5
27,5
20 40
25
22,5
10
9
IC Y
Y
30
11
6 10
17 35
35
32,5
20
8
7
6
5
4
3
17,5
2
6
8
10
12
14
X
16
18
20
22
1
2
3
4
5
IC X
6
7
8
Contrasts must be standardised: divided by their
standard deviation (√variance)
9
33
Contrasts can be used in various kinds of analyses:
regressions, ANOVA, ANCOVA, PCA, ...
Regressions (through the origin, because contrasts
computation eliminates the constant term)
Multivariate analyses
Powerful because few parameters to estimate
Model testing: contrasts vs SD
Slope = 0 if BM
Else: transformation of branch lengths or different
model (PGLS, ...)
34
Improvements to take polytomies into account
Recent improvement to consider data variance
(Felsenstein 2008)
FIC method “removes phylogeny” (without
explicitly quantifying it) in correlation among traits
Paradox to study adaptation because supposes
selection (≠ BM)
35
Phylogenetic generalized
least square regression
PGLS
Generalization of FIC to other models
Consider phylogenetic structure of the error term (non
independent observations, heteroscedasticity)
Estimation of a constraint parameter α (adaptation,
stabilizing selection...) adding to BM
36
Consider data variances
The number of parameters to estimate reduces power
Allows to reconstruct ancestral character states (like IC)
37
Phylogenetic eigenvector
regression
PVR
Statistical basis (no explicit model)
Transforms phylogenetic distance matrix in principal
coordinates (PCs)
Versatility of distance matrices: trees, reticulograms
(networks), raw distances, ...
Allows variation partitionning and quantification of
“phylogenetic niche conservatism”
38
Phylogenetically structured
environmental variation
“Phylogenetic” fraction (inertia)
“Non historical” fraction, specific
(adaptation, ...)
We can quantify the common
fraction (phylogenetic niche
conservatism)
Environment
Phylogeny
?
39
100 % of trait variation
Environment E = R21 = a+b
Phylogeny P = R22 = b+c
a
b
c
d
100 % of the variation of Y
Environment and Phylogeny = R21,2 = a+b+c
Unexplained variation = d
b: phylogenetically-structured physiological variation
40
Example
Variation of resting metabolic rate due to body mass,
bone growth rate, and phylogeny
41
Recent development for 3 components partitioning
42
1,4
1,3
1,2
1,1
1
,9
,8
,7
,6
Chl b
Chl b
Chlorophylle b vs depth in Ostreococcus
P = 0,0007
,3
,25
,2
,15
,1
,05
0
-,05
-,1
-20
0 20 40 60 80 100 120 140
Depth
Y = 0,719 + 0,004 * X; R^2 = 0,779
P = 0,0147
-5 0
5 10 15 20 25 30 35 40 45 50
Depth
Y = 0 + 0,003 * X; R^2 = 0,546
Raw data
Independent contrasts
Variation partitioning of Chl b
28%
51%
5%
16%
Phylogenetic variation Phylogeny
structured by depth
Depth
Unexplained
43
Micromonas
OT95
RCC501
RCC371
100
RCC343
64
55
RCC420
Surface (0 - 65 m)
32
RCC356
37
62
RCC344
OS1
96
RCC410
65
RCC141
Deep (90 - 120 m)
37
RCC393
39
RCC143
0.1
44
Concentration in Chl b is linked to depth even after
controlling for phylogeny: adaptation
Phylogenetic nich conservatism very important: one or
a few evolutionary events followed by a radiation
under the same ecological pressure
45
Design of experiments
Use phylogenetic information when choosing species
Do not compare only 2 distant species, because too
many uncontrolled differences
Avoid comparison between very contrasted clades
Ideal: several pairs of closely related species with
differences for the trait under study
Do not a priori exclude unusual species (e.g. snake from
lizards)
46
Examples
Low metabolism in desert
Mouse-to-elephant curve: basal metabolic rate vs body
size
Environmental determinants of metabolic rate
Herbivory and body size in lizards
47
Low metabolic rates, low body temperatures, and
ability to become torpid would be beneficial to
endotherms in hot, arid environments (minimization of
energetic demands), such as deserts
Test in desert caprimulgid birds (Lane et al. 2004)
Test in Procyonidae (Garland and Adolph, 1994)
48
Birds
Ability to low metabolism not restricted to desert
species, but widely dispersed across the phylogeny
➡Not an adaptation in this species
49
Racoons
Species with low metabolism falls
outside the confident intervall
computed from other species, only
in phylogenetically-corrected
analysis
➡Adaptation in this species
50
Basal metabolic rate vs body size
Slope of the log-log relationship: constant for all
animals (value is controversial)
51
Test in bird species
52
Environment and metabolism in rodents
53
Herbivory and body size in
lizards
Hypothesis (from
observations): strict
herbivory in lizards requires
large body size and high
temperature, interpreted as
constraints on thermal
requirement for digestion
However, most known
large-bodied herbivorous
lizards from a single clade,
the iguanidae
54
Need to consider phylogeny: test in
Liolaemidae
Phylogeny: multiple origin of
herbivory, very "easy" appearance
of herbivory in Liolaemidae
Independent contrasts: herbivory
associated with low temperature!
55