Download Some types of evolutionary change seem to occur repeatedly

Some types of evolutionary change seem to occur repeatedly
Phylogenetic patterns
Are genes leaders or followers
Conversion of mechanisms
Regulatory mechanism with switches seem to evolve
easily, at least the cue type provoking switching
Are there examples wit little evolutionary change over long periods?
Evolutionary Constraints
Evolutionary Constraints
No evolutionary response – why?
Mechanisms causing constraints
Trade-offs – Coupling
No Evolutionary Constraints
Conover et al. 2009
Cold adaptation
Trophy hunting
Genetic Variation and Short-Term Evolution
Trait two
Evolutionarily
Convergence Stable
Traits
Response
Selective
advantage
Selection
Genetic Variation
Initial Population
Selective
disadvantage
Trait one
No response in the short term
The breeders equation for selection response R = Gβ
Two possibilities:
Some variation cannot be produced
(genetic variance - covariance G is degenerate)
(Stabilizing) selection prevents change
(selection gradient β = 0)
(consensus paper Maynard Smith et al. 1985)
Allen, C., Beldade, P., Zwaan, B.J., Brakefield, P.M. (2008) Differences in the selection
response of serially repeated color pattern characters: Standing variation,
development, and evolution. BMC Evolutionary Biology 2008, 8:94
What are causes of constraints in the more long term?
Mechanical/Physical constraints
produce allometric patterns
Any organism has to obey the laws of physics
and chemistry
• Gravity pulls everything down
Meganeura moryi
Gigantic proto-Odonata
because of
different composition
atmosphere during Carboniferous
(Dudley 1998)
• E.g. limits on body size in organisms that
have access to oxygen through trachea
Ecological Constraints
β(E)
Available options depend on the
environment
High (Unavoidable?) Cost of
Reproduction when
1) Carrying eggs
2) Predators are present
3) Visibility is high
Not structure, but cost is constrained
Daphnia pulex
Levels of organization
Environment
Genes
Developmental
Constraints
Phenotype
Performance
Ecological Constraints
Physical Constraints
Fitness
Historical or Phylogenetic Constraints
Some traits evolved already in the past and not recently
Organisms resemble their ancestors
Species are not independent samples
Problem of generalization: contingency of actual species traits
Primates cannot occupy all herbivore niches
Muller et al. 2011
Waved albatross
Phoebastria irrorata
All Procellariiformes lay a single egg per clutch
Physiological constraints :
The properties of physiologies are not allowing to perform certain
tasks or produce some phenotypes
Genetic constraints :
genotypic variation cannot produce some phenotypes
Classifications of Constraints: What a Mess
Physical Constraints
Genetic Constraints
Phylogenetic
Constraints
Physiological
Ecological
Constraints (Roff 1992)
Trade- Offs (Roff 2002)
No response – the short term perspective does not always
relate easily to the categories of constraints
Species
Variation
Selection
Albatross
Absent
Foraging
efficiency
Daphnia
Absent
Reproduction
Dragonfly
Aquatic larva
known from
Permian
Performance
Large Meganeuridae exist from the Permian with lower oxygen
There are other large insects still present (stick insects)
Maybe they were just selected for large size
No response – the short term perspective does not always
relate easily to the categories of constraints
Species
Variation
Selection
Albatross
Absent
Foraging mode
Daphnia
Absent
Reproduction
Dragonfly
Aquatic larva
known from
Permian
Performance
-> Estimate both variation and selection on larger
timescales
Phylogenetic patterns
One often models evolution along a tree assuming
responses R = Gβ
Species traits will change or not, but also the genetic variance-covariance G
Steppan et al. 2002
Phylogenetic patterns
One often models evolution along a tree assuming R = Gβ
Species traits will change or not, but also the genetic variance-covariance G
We are aware that phylogenetic patterns are there,
and need models of how they appeared!
→ Try to reconstruct the emergence of the constraint
→ Try to reconstruct the patterns of selection
http://cran.r-project.org/web/views/Phylogenetics.html
What is the phenotype exactly which is constrained?
Switches
Morphologies
When multiple traits are considered,
beta and G can be non-zero and non-degenerate
Does it matter for the detection of patterns of natural selection?
Internal selection: interactions between
developmental modules constrain
evolution
Galis et al. 2006
Phylotypic stage
Developmental hourglass Prud’homme and Gompel 2010
Germband
Aminoserosa
Head region minus
gnathal segments
Fig. 1. Extended (a) and segmented (b) germband
stages in Drosophila.
The germband (blue) refers to the part of the embryo
that will give rise to the metameric regions: gnathal
segments of the head region (Md, mandible; Mx,
maxilla; Lb, labium), thoracic segments (T1–3) and
abdominal segments (A1–8). The amnioserosa (red) is
an extra-embryonic membrane. The extended
germband stage starts ~.6.5 h after fertilization
and the segmented germband stage ends at ~10.5 h
after fertilization.
Von Dassow et al. (2000)
Are phenotypes constrained because they are robust,
perturbations are dampened?
Not in this case.
WT
Null
Df(2)DE
NE2
Null (wg−/−), reduced [Df(2)DE] and partial (NE2) function mutations of the wg
gene lead to abnormalities in the larval ectoderm. Expression of wg in the
ectoderm (A–D), and cuticular pattern in the ventral (E–H) and dorsal (I–L)
larval epidermis (W.T. denotes wild type). In Df(2)DE mutants, wg expression
is reduced, and in NE2 mutants, wg transport is hampered (reproduced, with
permission, from Ref. [27]).
Galis et al. 2002
Are phenotypes constrained because they are robust?
Not in this case.
Hypomorphic Wg-1 mutant
showing a failure in the
development of antennae, wings,
halteres and thorax
Galis et al. 2002
Germband
Aminoserosa
Head region minus
gnathal segments
Fig. 1. Extended (a) and segmented (b)
germband stages in Drosophila.
The germband (blue) refers to the part of the
embryo that will give rise
to the metameric regions: gnathal segments of
the head region (Md,
mandible; Mx, maxilla; Lb, labium), thoracic
segments (T1–3) and
abdominal segments (A1–8). The
amnioserosa (red) is an extra-embryonic
membrane. The extended germband stage
starts ~.6.5 h after fertilization
and the segmented germband stage ends at
~10.5 h after fertilization.
Internal selection due to
interactions causing
effects on many
phenotypes
Internal selection is selection due to shapes of genotypephenotype maps
I will show
the genotype phenotype map is both
• A component of variation
• A component of the selection gradient
Assume smooth genotype-phenotype maps
Apparent phenotype Y - Underlying trait X
Barbara Stadler has worked the ingredients to do this analysis
for discrete genotype spaces
Apparent phenotype Y - Underlying trait X
Phenotypic trait vector Y
underlying traits X of a haplotype
Y depends on X
Y (X )
Apparent phenotype Y - Underlying trait X
Phenotypic trait vector Y
underlying traits X
Y
X
Apparent phenotype Y - Underlying trait X
allelic traits → organismal traits → fitness
devo
eco
evo
The map Y(X) is locally approximately linear
Phenotypic trait vector Y
underlying traits X of a haplotype
Y
.
.
.
.
X
Invasion fitness
fitness of the phenotype of a mutant heterozygote Y in a
population with phenotype Z of the resident allele (genotype)
r (Y , Z )
fitness of a mutant X' in a population of alleles with trait X
ρ ( X ' , X ) = r (Y ( X '), Y ( X ))
Invasion fitness gradient
∇' ρ ( X ) =
∂
r (Y ( X '), Y ( X ))
∂X '
X '= X
∇' ρ ( X ) = ∇Y ( X )∇' r (Y ( X ))
devo
∇' r ( Z ) =
eco
fitness gradient =
phenotypic effects of allele × ecological effects of phenotype
∂
r (Y , Z )
∂Y
Y =Z
Evolutionary Dynamics
Gradual directional evolution by new mutations occurring
d
1
X (t ) = G X ( t )∇Y ( X (t ))∇' r (Y ( X (t ) ))
dt
2
scaling for
devo
available variation
d
Y (t ) =
dt
d
Y (t ) =
dt
eco
1
∇Y ( X (t ))T G X ( t )∇Y ( X (t ))∇' r (Y ( X (t ) ))
2
1
GY (t )∇' r (Y ( X (t ) ))
2
Evolutionary Dynamics
d
1
X (t ) = G X ( t )∇Y ( X (t ))∇' r (Y ( X (t ) ))
dt
2
selection
d
1
Z (t ) = ∇Y ( X (t ))T G X (t )∇Y ( X (t ))∇' r (Y ( X (t ) ))
dt
2
variation
Evolutionarily Stable Configuration
• evolves in the same way in any environment, independent
of ecology
• evolution driven by internal coherence and system
performance
• performance is for a proper function (raison d'être)
Example: iguanians use their tongue as a prehensile organ
(Wagner and Schwenk 2000)
One type of internal selection
Evolutionarily Stable Configuration
∇Y(X*) = 0 for all loci involved
performance is for a proper function (raison d'être)
→ Y is one-dimensional = e.g. capture rate
∇'r(y) > 0
performance y
x*
tongue traits
Some antidote against all this smoothness
Genotype network spaces
The viewpoint of the underlying level is essential to
understand constraints
“All complex macroscopic traits comprise microscopic, submicroscopic
and molecular traits, down to the level of DNA.
Likewise, DNA change can percolate all the way up to macroscopic
traits. Although an understanding of the full complexity of this
hierarchical organization is beyond current means, important systems
can be studied that are necessary to form complex traits and changes
therein.”
Wagner 2011
The viewpoint of the underlying level is essential to
understand constraints
Example
Variation
Selection
Gene regulation
networks
X
X
Metabolic
networks
X
X
Macromolecules
X
X
These models provide simple genotype-phenotype maps
used to investigate constraints
Wagner 2011
No response –
Genotype networks
Each colour is a
phenotype
Lines represent
possible mutational
changes
Selection on robustness
To study effects of:
Genotype space
structure
G-P mapping
Wagner 2011
Genotype Networks Novelties
Connected genotype spaces with different accessible phenotypes
promote novelties,
Below are three opposites to that:
Genotype networks Plasticity
Simplified
plasticity:
Alternative
phenotype
If present,
can mutate in
a new constitutive
phenotype
Espinosa-Soto et al. (2011)
Genotype networks and plasticity
(a) Populations find a novel genotype
network faster when plasticity is allowed.
The symbol t*, plast refers to the number of
generations that a population of circuits
needs to discover a specific genotype
network when we allow plasticity. The
symbol t*, control refers to the same number,
but for populations without plasticity.
(b) Plasticity slows the accumulation of
individuals in the new genotype network.
The symbol t0.25,plast stands for the number
of generations that a population in which
we allow plasticity needs to have at least
25 percent of its circuits in the new
genotype network (after its discovery by a
single individual); t0.25,control corresponds to
the same number but without plastic
phenotypes.
Release from constraints
Plasticity and a new environment revealing cryptic variation
Evolutionary novelty facilitated by plasticity
Exploration of genotype network spaces
Life history trade-offs and constraints
"Detailed knowledge of the genetic,
developmental, and physiological
mechanisms that affect life history
traits is of major importance for
understanding, from first principles,
how life history traits are expressed,
why they vary, and how they evolve."
But some relatively old ideas are still strong….
Love for Meccano?
Stearns chapter:
"The glass is at least half empty"
"For them life history theory provided a
general motivational structure"
Onto the boundary of a feasibility set
Fitness often increases
in this direction:
The more of survival
and reproduction, the
better
LH Trait two
Feasibility Set
LH Trait one
Rueffler et al. 2004
Options - Fitness contours
Begon et al. 2005
Classification of Environments
Sensitive to growth
InSensitive to growth
Begon et al. 2005
Begon et al. 2005
Many open questions: constraints
can arise from specialization?
Heteroecious aphids (Moran 1988)
Specialists
References
Charnov, E. L. 1993. Life History Invariants. Oxford University Press
Conover, D.O., S.B. Munch, and S.A. Arnott (2009) Reversal of evolutionary downsizing caused by
selective harvest of large fish. Proceedings of the Royal Society of London. Series B: Biological Sciences
276:2015-2020.
Dudley, R. 1998. Atmospheric oxygen, giant Paleozoic insects and the evolution o aerial locomotor
performance. Journal of Experimental Biology 201: 1043-1050.
Espinosa-Soto, C. Martin, O.C., Wagner, A. (2011) Phenotypic plasticity can facilitate adaptive evolution
in gene regulatory circuits. BMC Evolutionary Biology 11:5, doi:10.1186/1471-2148-11-5
Galis, F. , T.J.M. van Dooren and J.A.J. Metz (2002). Conservation of the segmented germband stage:
robustness or pleiotropy? Trends Genet. 18 (10), 504-509.
Galis F., T.J.M. van Dooren, Feuth, H., Ruinard, S., Witkam, A., Steigenga, M.J., Metz, J.A.J.,
Wijnaendts, L.C.D. (2006). Extreme selection against homeotic transformations of cervical vertebrae in
humans.Evolution 60 (12):2643-2654.
Maynard Smith, J., R. Burian, S. Kaufman, P. Alberch, J. Campbell et al., 1985. Developmental
constraints and evolution. Q. Rev. Biol. 60: 265–287.
Muller et al. 2011. Phylogenetic constraints on digesta separation: Variation in fluid throughput in the
digestive tract in mammalian herbivores. Comparative biochemistry and physiology. Part A, Molecular &
integrative physiology. 06/2011;
Nee S et al. The illusion of invariant quantities in life histories. Science. 2005 Aug 19; 309(5738):1236-9
Prud’homme and Gompel 2010
Roff, D.A. 1992. The Evolution of Life Histories: Theory and Analysis. Chapman and Hall, New York.
Roff, D.A. 2002. Life History Evolution. Sinauer Associates, Sunderland, MA.
G. von Dassow, E. Meir, E. M. Munro, and G. M. Odell (2000) The segment polarity network is a robust
developmental module. Nature 406: 188-92.
Wagner 2011. Genotype networks shed light on evolutionary constraints. Trends in Ecology & Evolution.
doi:10.1016/j.tree.2011.07.001
Wagner, G. P. and K. Schwenk (2000) Evolutionarily Stable Configurations: functional integration and the
evolution of phenotypic stability. Evolutionary Biology 31:155-217.