|
BIOL
4160
Evolution
Phil Ganter
301 Harned Hall
963-5782 |
A dense
"biocovering" of intertidal rocks, including algae, snails, mussels,
and barnacles. The barnacles surround the open patch in the
center, where the underlying rock has been exposed. Each
barnacle (the long, white, tooth-like structures with attached
algae making
their tops look green) is the product of a long developmental process
in which eggs and the initial stages are brooded by the parent,
passed through two different larval stages in the open ocean
and
became
rooted
when
the second
larval
stage,
called
a
cyprid
larvae, settled
on its head on the
rock
and
metamorphosed
into a small version of what you see here. Why such a complicated
set of changes in an already complex process of turning a single
cell into an organism of many millions of cells? |
Evolution and Development
Email me
Link
to a list of Specific
Objectives for lectures
Back
to:
Developmental biology was once called embryology
Important area in biology, no just for it intrinsic
value but for the influence it had on other areas of biology
- In the late 1800's, some European biologists
began to promote "Entwicklungsmechanik" (developmental mechanics) as a
way of investigating zoology
- Prior to this, most zoologists were naturalists,
who collected observational data and interpreted patterns found in the
data
- This approach, known under the general
title of "Naturphilosophie", a philosophical
movement to develop a set of ideas from which all of reality, including
nature, can
be explained
- The mechanics (Wilhelm Roux, Hans Driesch,
Jacques Loeb - who came to America and became influential in both scientific
and
wider circles) focused less on large principles and more on specific
mechanisms of change, on
experimental evidence and less on observational data
- Their guiding principles came from chemistry
and physics, not philosophy
- Their first successful applications of this approach
were in embryology
- So embryology becomes experimental and the success
of experimentation there inspired adoption of the experimental approach
in other areas
- Most famous example was Thomas Hunt Morgan's
adoption of the approach (in the 1890's) which, along with his adoption
of Drosophila as a model organism, began modern genetics in the US (Morgan
worked with
both
Driesch and Loeb, who were influential in his change to experimentation)
It would be wrong to think that embryology was
estranged from Naturphilosophie in the sense that there was always a search
for general principles
- An example of this is the influence of constraint
in development
- Constraint means that the attainable phenotypes
in the adult are a subset of all possible phenotypes and developmental
constraints are those that arise from the mechanics of the developmental
system
- This is a very hot topic today but is not a new
topic
- C. H. Waddington proposed (as early as 1942)
that canalization was an outcome of developmental constraint
- Canalization (literally,
a metaphor in which the developing organism is moving down a canal,
with walls
to either side that constrain its trajectory,
so that it will end up in the proper place - a viable, fertile
adult phenotype)
- Waddington felt that and genetic change that
took the developing organism out of the proper canal (I think I would have
used Channel rather than canal) would be countered by changes to other
genes that would bring the organism into the proper trajectory
- Here, only some of the possible adult phenotypes
are likely to be successful and, once a developmental system produces a
successful outcome, then change is likely to produce a less successful
outcome and should be resisted
- Did experiments with Ultrabithorax mutants in
Drosophila that demonstrated the phenomenon
The modern era in embryology opened with discovery
of homeobox genes in the 1980's - a discovery so exciting that it led to
a change in name (from embryology to developmental biology)
- Evolutionary biology has long included ideas
about the importance of evolution in explaining similarities among developmental
systems (Waddington's canalization has long been influential in this area)
- Development offered some of the most compelling
instances of adaptation, especially adaptation as gradual modification
of pre-existing structures
- With the advent of molecular biology and the
explosion of developmental genetics that resulted, the evolution of developmental
systems has advanced
- This area is often called Evo-Devo
- Some evo-devo researchers have stressed the importance
of constraint and history in the evolution of the phenotype
- They see natural selection (and its outcome,
adaptation) as less important than do other evolutionists
Hox and MADS-box genes
and development
Metamerism - the construction of an animal from
a set of repeating units (metameres), each of which can be subsequently
modified for specific tasks
- Metamerism is an example of Modularity in development
- the construction of complex organisms from a set of similar modules (the
similarity of the modules may be confined to early development and much
modification of individual modules is possible)
- In plants, the basic above-ground module
is the node, leaf, lateral bud, and internode (stem between nodes)
- The basic module can be heavily modified : leaves
may be greatly modified (lead to such things as flowers or spines), the
internode can be
very short
(so no
stem
is
readily visible), etc
Homeobox - a conserved region in a set of genes that affect the fate of
metameres (the homeobox is about 180 base pairs long and codes for a portion
of the protein called the homeodomain that is, of course, about 60 amino
acids long
- Homeodomain forms three a-helices that bind to DNA (one fits into the major
groove) - this structure is called a leucine zipper
- This is the region responsible for binding the
protein to DNA - binding site can be upstream of the developmental gene being
regulated, within the gene, or cis-acting
- Because the proteins bind to DNA and affect the
transcription of another gene, they belong to a general class of proteins
(and their genes) called
Transcription Factors
Hox genes - these are a subset of homeobox genes that are clustered togther
along a single chromosome in all animals (in Drosophila, there are two separate
clusters)
- The position of the Hox gene within the cluster corresponds to the position
of the metamere that the gene affects (so as one goes along the chromosome,
one is going from anterior to posterior in the metamere affected)
- The number of Hox genes seems to increase
with increasing complexity (at a crude level)
- Cnidaria (diploblastic) have only 2, while
the Protostomes have up to 12 and Deuterostomes have up to 13 (both
are triploblastic)
- The close similarity of Hox genes means that duplications have produced
the paralogous loci
- Some lineages have lost particular paralogs
- Within the Chordates, there is a great expansion of Hox genes through duplication
events
- Early Chordates have a single cluster of Hox genes
- At least two duplications of the region between happened
early in the vertebrate lineage
- A third duplication occured in the Teleost lineage after it diverged from
the Tetrapod lineage (which includes the tetrapods and things like lungfish
and coelacanths)
- So there are 4 sets of Hox genes in us and up to seven sets in bony fish
(most modern fish)
- Not enough genomes have been sequences
to time the duplications very precisely but most place them soon
after the split between the vertebrate lineage and the rest of the
chordates
Controversy:
- Some argue that the duplications of the Hox
clusters due to duplications of portions of the vertebrate chromosmes
containing the hox genes
- Others propose the 2R hypothesis
- 2R means 2 rounds of whole-genome
duplication (WGD ) either through alloploidy
or autoploidy
- If the 2R hypothesis is correct, then
almost all of the duplicate genomes have been lost and the four paralogs
expected from the two events are
found only at loci where no duplicate has been lost
- The "local duplication" hypothesis does not need to postulate the secondary
loss of many loci
- However, recent comparisons of duplications
of different gene families have shown that the preservation of gene
order, expected in WGD but not
from local duplications, has greatly strengthened the 2R hypothesis
- If 2R is correct for Tetrapods, then Teleosts may be 3R
Plants also have homeobox genes, but not Hox genes
- MADS-box genes
- There is a second group of transcription factors that share a different
homeobox sequence (and different homeobox domain)
- MADS-box is found in more eukaryote lineages than Hox sequence (found in
metazoa), including plants, animals and fungi
Homology
Homology is a similarity due to shared ancestry,
a synapomorphy
- in construction of a phylogeny, syapomorphies
contain the important information but not all homologies are synapomorphies
- orthologs are clearly synapomorphies but paralogs,
which are still considered homologs, are useful only if the duplication
has been recognized (i. e. it is known that these are paralogs, not othologs)
- Some other instances of homology are not
useful as synapomorphies
- In modular development, each module has
the same basic structure but development may modify these basic parts
into
very different adult structures
- Serial Homology is the idea of homology applied
to these modified structures
- Each crustacean metamere has a pair
of biramous (two-branched) appendages which are modified into
walking legs, swimmerets,
feeding appendages (mandibles and maxillipeds), sex appendages,
and sensory appendages (antennae)
- Serial homology is the similarity of repeated
structures based on common developmental origins
- This form of homology is not a synapomorphy
Developmental Pathways
and Gene Regulation
A developmental pathway (or circuit) is a set
of events in development controlled by the products of a particular set
of genes
- The genes encode:
- Structural proteins (enzymes
and cytoskeletal proteins) that are responsible for the actual
construction of particular phenotype (these are also called Effector
loci)
- Transcriptions factors - proteins that bind to
DNA and either promote (upregulate) or discourage (downregulate) the production
of mRNAs from a locus
- the sites to which the factors bind are
often called enhancer sites (enhancers may contain
the binding sites for multiple transcription factors)
- Hox genes belong to this class of loci
- Signaling proteins - responsible
for local communication between cells - these are signals that begin
signal transduction in target cells
- Receptor proteins - responsible
for binding to incoming signaling proteins and beginning transduction pathway
in the
cell (may be transmembrane proteins (when the signal is as large as
a protein, then this is the sort of receptor), cytoplasmic receptors or
even nuclear
receptors
Evolution is a tree-like branching process, so
developmental pathways are part of the shared ancestral heritage
- Ectopic eye example illustrates this - human Pax6 ortholog, when
expressed in Drosophila segments not normally having eyes (ectopic
expression), it has the same effect as ectopic expression of Drosophila's
Pax allele
- Pax was found in the ancestor of both fly and us
- Pax was part of development of visual apparatus in ancestor
and still is part of development of eye in both fly and us
- Both are expected outcomes if Darwin's branching ancestry
- Structure of Drosophila eye (compound eye)
and ours (camera eye) radically different, but all of the genes that
build both eyes (and get them
enervated) are under the control of Pax locus in both flies an us
Regulatory genes are the reason for differences in phenotypes between modules
- Each segment uses the same basic set of genes to build the set of modular
structures
- Differences in the outcomes are mostly due to changes in regulation, not
changes in the structural genes
- Structural genes may impact more than one aspect of the phenotype (this
is pleiotropy) and it is hard to make changes in a structural
gene that would target one pleiotropic effect and leave others unchanged
- Easier to change expression of the gene in one tissue or segment and
leave its regulation unchanged in other tissues or segments
- Changes in regulation may be due to
- Trans-regulatory changes (different alleles for the transcription factor
loci)
- Changes in enhancer sites (many genes have multiple enhancer sites
and are, therefore, affected by more than one set of transcription factors)
- Changes in signal/receptor pairs
- Changes in transduction pathway
- Exaptations - new functions for pre-existing
phenotypic characters
- Corresponds to developmental terms for appearance
of novel functions from pre-existing developmental pathways (recruitment or co-option)
- if the novelty is the result of expression
of the pathway in a different place (new segment or new part of organism)
then the result is Heterotopy (introduced in Basic Patterns lecture)
- tetrapod limb differentiation due to Hox gene
expression along axis of appendage, not body axis
- lepidopteran wing patterns arise from co-option
of basic anterior-posterior patterning loci
- Heterochrony also results from changes to a
regulatory pathway
- Neoteny in salamanders due to loss of expression
of a signal protein that triggers the pituitary to begin metamorphosis
- Allometry is an obvious change in the timing
of morphological events, clearly a regulatory issues
Developmental Constraints
Mammals have five digits on their forelimbs but
frogs have four - why the different?
- might be adaptation - four favored for frogs
and five for mammals
- might be the result of a Constraint, something preventing the addition of
a fifth digit in frogs or loss of a digit in. . . etc.
There are four generally recognized types of constraint:
- Physical
Constraint - why no dinosaurs the size of whales? maybe
bone will not support such large masses without buoyancy of water to help
- Selective Constraint - when selection of an adaptation is not favored because
it is never advantageous in the particular niche occupied by the species
- Genetic Constraint - several sources here
- Lack of needed genetic variation - population size, mutation rate, migration
rate, history can all lead to variation needed for phenotype not being present
in the population or species
- Gene interactions - Pleiotropy can prevent adoption of new allele, even
when it leads to an adaptation, if its pleiotropic effects are harmful and
the harm outweighs the benefits
- Developmental Constraint - developmental system precludes building a particular
phenotype -
- Canalization may force the developmental pathway away from novel phenotype
(canalization preserves pre-existing phenotypes)
Constraints may profoundly affect the course of
evolution
- Constraints may explain the failure of some lineages
to adopt useful phenotypes, behaviors,
or life
histories
- Constraints may lead to directional
trends when comparing species if some
changes are more likely than others
- For instance, what if plants are easier to make taller than to make many-branched
- As each new lineage is produced, the novelty will be more height but not
more branches
- Parallel evolution (a form of homoplasy - see lecture on phylogenetics)
may be more likely if constraints only allow a subset of possible changes
- Canalization - the production of a standard phenotype is likely due to constraint
on variation
- Morphological Stasis - this comes from paleontology and means a species
or a particular morphology is found continuously in the fossil record for
a long period of time and constraint is a possible explanation
- Similar changes to a developing animal (the pattern is called the species
ontogeny and viewing the similarity between two currently very different
animals (shark, chicken, kangaroo) as a result of shared ontogeny lead to
the old saw: "Ontogeny recapitulates phylogeny."
- the idea that all of phylogeny is due to changes
in ontogeny is now no longer accepted but the strong connection between
similarity of developmental pattern
and closeness of ancestry is currently accepted
Human Development and Evolution
Interesting difference here is that much of the
interest in evolutionary developmental biology has been in the patterns of
shared developmental patters
- With humans, the uniquely human developmental patterns
are often the center of attention
- Given our genetic similarity with our closest
relatives and our phenotypic differences (gait, skull and brain size, opposable
thumb,
etc.), it is obvious that regulatory changes are mostly
responsible for the phenotypic divergence of humans from Pan and that we
will need to compare our genome to theirs
Aside - how similar are we to the genus Pan (2
species, the chimpanzee and the bonobo)
- Depends on how you do similarity comparison and
how you define the term "gene"
- Genome sequencing shows that about 94%
of human protein-coding loci also occur in the chimps- each lineage has specific
duplications and losses (which explains the other 6%)
- Note that this comparison does not include much
of the genome (micro-RNAs and repeated regions)
- The sequence divergence for chimp and human alleles
at a particular locus can be lower than the overall genomic difference (it
is sequence comparisons that give the higher 95% or 98% similarities normally
quoted)
Last updated February 8, 2010
