Compiled as a final-year zoology student at the University of Edinburgh, based on the information given in lectures.
Adaptations are traits favoured by evolution because they serve a
How to test if a trait is an adaptation: Is it complex? Is it the optimal solution to a
problem? Analyse on first principles. Determine fate of deviants (thought
experiments, correlation studies, genetic manipulation, historical analysis,
comparison of species).
Why a trait might not be an adaptation: chance, consequence of laws of
chemistry/physics, by-product of an adaptation, result
of trade-offs, evolutionary time lag, result of adaptation by others,
historical constraints, environmental variation.
Criticism of adaptationism: it is untested storytelling, and forgets that
organisms are integrated wholes.
Is malarial fever an adaptation? Good for host? (It kills parasites.) Good for
parasites? (It immobilises host. It prevents parasites killing host - unlikely,
this is group selectionist.) Incidental consequence of stimulating immune
system? Drug trials suggest recovery from malaria is slower if fever is too
high, but result is uncertain.
Parasitic adaptations? Use of intermediate hosts; huge egg output;
making intermediate host more susceptible to predation. These could, however,
be accidental or 'unintentional' consequences of parasitism.
(Ridley 2003, Evolution; Dawkins, The Blind Watchmaker)
Selection acts if there is: variation, fitness differences, inheritance.
Selection coefficient for a genotype, s = 1 - w (where w is fitness).
Selection differential is difference in mean phenotype between
selected (breeders) and unselected.
Response to selection is change in trait value after selection: R = s
× h² (where h² is heritability).
population is not at equilibrium, trait frequency distribution of offspring
will differ predictably from parents'. Trait frequency distribution will also
differ among age classes or life-history stages.
show that guppies are selected for
crypsis where there is predation, and sexually selected for conspicuous colour
spots in the absence of predators (Endler 1980).
(Elena & Lenski 2003)
evolution uses natural selection rather than artificial selection - organisms
How rugged are fitness landscapes? Lenski et al (1991) bred test tubes of E. coli over thousands of generations. Fitness
(compared with ancestral population) increased over time, although rate of
increased slowed. All populations followed a similar trajectory of fitness
increase, but there was some variation. An increase in cell size occurred,
paralleling the increase in fitness. More extreme divergence between
populations was seen when novel environments (different sugars) were used -
underlying genetics of adaptation here may be different.
Contingency - how important is evolutionary
history? Populations of E. coli transferred from glucose to
maltose medium evolve to a similar fitness irrespective of starting point, but
this masks variation in other traits such as cell size (Travisano
et al 1995). Populations of Phi6 bacteriophage may evolve to different
endpoints. Conclusion: populations starting from different points may evolve to
different peaks, which may or may not differ in fitness.
Selection in different environments - there may be a 'cost of adaptation' due to
antagonistic pleiotropy (genes good in one environment are bad in another) or
mutation accumulation (genes neutral in selected environment deteriorate). Chlamydomonas evolved in light
conditions fare worse in dark conditions and vice versa, but it is possible to
evolve generalists that thrive in light or dark - mutation accumulation is
important (Bell & Reboud 1997). In E. coli, deterioration of ability to
survive in one environment mirrors improvement in another, and 'mutator lines'
(with an unnaturally high mutation rate) deteriorate at a similar rate to
non-mutator lines - antagonistic pleiotropy is important.
What limits adaptation? The supply of new mutations, or the efficiency
of selection? Mutator lines of E. coli
adapt faster with small populations where the supply of mutations is limiting,
but not with larger ones where the rate of spread of mutations is limiting (De Visser et al 1999). Larger populations of asexual Chlamydomonas adapt faster, but there
are diminishing returns as population size is increased. Sex increases
efficiency of selection in larger Chlamydomonas
populations, but has less effect on small populations (Colegrave 2002).
Evolution of development
(Carroll et al 2001, From DNA to Diversity)
of an organism depends on selective gene
typically have many enhancers, which can act independently - modular control.
in Drosophila grow in thousands of
precise positions, driven by different enhancers of the achaete/scute gene. Knocking out particular enhancers removes
homologous gene: orthologs
(in different species), paralogs
(in same species).
There is a
limited number of major chemical signalling
pathways (around 16-25). They are highly conserved, and used for multiple
genes do not necessarily encode homologous structures and homologous structures
need not be encoded by homologous genes" (de Beer 1971).
Pax6 gene controls eye development in different phyla that
evolved complex eyes independently, but may have had a common ancestor with
primitive photoreceptors that expressed this gene (Gehring
& Ikeo 1999).
structure and expressed genes on the ventral side of protostomes corresponds to
those on the dorsal side of chordates. There may have been a dorsal/ventral
inversion in the evolution of chordates, or the two body plans may derive from a
common ancestor with diffuse dorsoventral organisation (Gerhart
(Gould 1989, Wonderful Life; Conway Morris 1998, The Crucible of Creation)
What caused the Cambrian explosion? Advances in developmental genes? Environmental
changes (e.g. higher atmospheric oxygen)? Ecological innovation (e.g. hard body
parts for defence) and adaptive radiation?
Is it an
artefact of the fossil record? Unlikely. Knowledge of the Cambrian is based on
several fossil deposits. If animals were diverse in the Precambrian their
tracks should have fossilised even if their soft bodies didn't.
explosion may have been preceded by a 'Precambrian slow-burn' during which body
diversity of phyla higher in Cambrian than today? It depends on your
interpretation of Cambrian animals.
fuelled debate over contingency vs.
determinism. Convergent evolution is evidence for determinism, e.g. Anolis lizards
have radiated independently into the same set of niches on four different
islands (Losos et al 1998).
Hox genes all share a distinctive 'homeobox' region. They
code for transcription factors.
Hox genes are side-by-side along a chromosome. Position of Hox genes along a chromosome corresponds
to the physical position of expression along the anterior-posterior axis (colinearity). None are expressed in the
anterior-most part of an animal. They are turned on early in development and remain
genes have been found, in some form, in all advanced animal phyla...
Drosophila has 8 Hox
genes (other arthropods have additional ones, some of which appear to have
evolved into non-Hox genes in Drosophila). ‘Ultrabithorax’ mutation is
due to failed expression of a Hox
gene, causing third thoracic segment to develop like second one (with proper
wings instead of halteres).
Annelids have a similar Hox
Chordates have an extended 13-gene Hox family, duplicated into four sets.
Echinoderms have Hox genes
but their expression in the non-bilaterally symmetrical adults is hard to
elegans has only 4
recognisable Hox genes, and their
function is relatively trivial, but this may not be true in other nematodes.
Molluscs have Hox genes,
and there is some colinearity in their expression (most evident in nerve
ganglia). Squid arms express different combinations of Hox genes, but not colinearly (Hox genes adopting new functions?).
Sexual arms races
Bean weevils: male has spiky penis to damage female, increasing time
she takes to mate again; female fights back by trying to throw off male early
during copulation (Crudgington & Siva-Jothy 2000).
Drosophila: males inject toxins during mating that kill previous males' sperm, but
also selfishly harm females. Exposure to a particular Accessory Gland Protein
(AGP) in seminal fluid reduces female life expectancy: mating with castrated
males doesn't harm female, but mating with sperm-less males does (Chapman et al
1995). AGP genes appear to be under strong selection - high proportion of
non-synonymous mutations (Swanson et al 2001). Males become less 'nasty' if
evolved under artificially monogamous conditions (Holland & Rice 1999).
(Griffiths et al 1996,
An Introduction to Genetic Analysis)
Southern blotting is used to locate a known sequence of DNA on a gel. It
involves electrophoresis, blotting of DNA onto filter paper, denaturing to
produce single-stranded DNA, and combining with a radioactive probe.
Polymerase Chain Reaction (PCR) makes many copies of a DNA strand. DNA is
heated to separate strands, two primers (at either end of the DNA region of
interest) are added, solution is annealed by cooling, bases and enzyme
(thermostable Taq polymerase from
thermophilic bacteria) are added, and cycle is repeated many times.
Dideoxy (Sanger) sequencing uses modified bases that halt replication when
they become incorporated into a growing DNA strand. The bases can be linked to fluorescent
dyes that show up as coloured bands on gel.
Restriction Fragment Length Polymorphisms (RFLPs),
used in DNA fingerprinting, can be identified by cutting with restriction
enzymes and Southern blotting. Only detects insertions/deletions or mutations at
DNA fingerprinting analyses variation in multi-locus mini-satellite DNA.
Relatedness is measured by the band-sharing
coefficient (similarity index); the average BSC of unrelated individuals
equals the frequency of each band in population. Satellite DNA consists of
highly repeated regions believed to function-less and selectively neutral.
DNA profiling, which uses single-locus micro-satellite DNA regions
amplified by PCR, has largely superseded DNA fingerprinting. Probability of
random match at one locus is 1 - (1-q)² where q is
frequency of alleles (rarer ones are thus more diagnostic). Exclusion probability for multiple loci
is product of individual probabilities.
techniques have discovered that: extra-pair fertilisations but not egg dumping
occur in indigo buntings (Westneat 1987), the contribution
that a beta male dunnock makes to rearing chicks depends on his chances of
paternity (Burke et al 1989), dominant meerkats father most of a group's
offspring but subordinate immigrants also father a few (Griffin et al 2003),
polar bears have genetically-distinct populations (Paetkau
et al 1999).
et al 1996, Molecular Systematics)
Cladograms simply show relationships; phylograms also show distance. Trees may be rooted or unrooted.
Unresolved trees have nodes giving rise to more than two branches
be monophyletic, paraphyletic or polyphyletic.
Characteristics of phylogenetic methods: efficiency ("doability" given
computer limitations), power (amount of data needed), consistency (will it converge
on the "right" solution given sufficient data?), robustness,
Measuring phylogenetic difference: nucleotide substitution models (taking into
account different probabilities of different types of substitution - transition
vs. transversion, base composition bias), distance correction (taking into
account multiple substitutions), aligning sequences (may involve a scoring
Clustering methods of constructing trees: neighbour joining (link closest individuals
first, then next closest, etc).
Optimality methods: maximum likelihood, maximum parsimony (minimising putative
sites evolve at different rates, providing a variety of molecular clocks
suitable for different purpose.
Search strategies: algorithmic (stepwise addition, star decomposition),
exhaustive (not computationally feasible for large trees), heuristic (branch
swapping and binary evaluation, "walking in tree space").
Problems: long branches attract (the chance of homoplasy - parallel
or convergent substitution - increases with genetic distance), evolutionary
noise may obscure phylogenetic signal.
Assessing support for trees: bootstrap (resample dataset to produce another
with same number of characters and reassess), jack-knife (sub-sample dataset
using fewer taxa - quicker but less meaningful).
the use of trees: discovery that African forest and savannah elephants are
The history of life
strata give an order of events but no absolute timescale; radioisotopes give
'molecular clock' dates divergence between extant species. A neutral sequence
evolves at the mutation rate (around 10-8 bases per year). Over very
long timescales, 'saturation' will occur (sequences will no longer be
recognisably similar at all), but conserved sequences (e.g. rRNA) provide an
of related genes (e.g. catalytic and non-catalytic subunits of ATPase) allows
rooting of the tree of life.
Events in the history of life: fossil stromatolites (~3500 Ma), cyanobacterial markers (~2800 Ma, diversifying ~2100 Ma),
increase in oxygen (~2000 Ma), eukaryote fossils (>1200 Mya), 'Cambrian
explosion' (~550 Ma).
Major transitions: replicating molecules to populations of molecules in
compartments; unlinked replicators to chromosomes; RNA to DNA and proteins;
prokaryotes to eukaryotes; asexual to sexual populations; unicellular to
multicellular organisms; solitary individuals to social colonies; primate
societies to human societies with language. These events changed the way
hereditary information is encoded and involved the coming together of
components into an interdependent whole. (Maynard Smith & Szathmáry 1995, Major
transitions in evolution)
benefited from an increasing division of labour: DNA and protein as well as
RNA, evolution of specialised enzymes following gene duplication, organelles in
eukaryotic cells, separate sexes.
selfish selection on individuals not disrupt the whole? Kin selection,
and ‘contingent irreversibility’.
The RNA world
Universal Common Ancestor of life on Earth (LUCA) had DNA making RNA making protein,
metabolism involving glycolysis and ATP, and lipid-based cell membranes.
that, there may have been an RNA world
in which RNA acted as both gene and enzyme.
RNA is still
an essential part of ribosomes, mRNA processing, DNA replication, etc.
are used as signals (e.g. cAMP), energy carriers (ATP), cofactors (NAD), etc.
Ribozymes - RNA-based enzymes (Cech 1982)
- include self-splicing ribosomal RNA in the protist Tetrahymena, the enzyme RNase P (in which the catalytic centre is
Efficient ribozymes can be selected for in vitro...
& Joyce (1993) evolved a version of the Tetrahymena
ribozyme that uses Ca2+ rather than Mg2+ as a cofactor.
This ribozyme becomes attached to a part of its substrate, allowing molecules
that work as catalysts to be separated from those that don't. RNA was
multiplied by converting it to DNA and using PCR.
al (1989) evolved an RNA sequence de novo
that replicates efficiently in the presence of Q-beta
replicase (a viral enzyme). The spread of these RNA
molecules through a gel follows population genetics equations developed by
Fisher. Their spread occasionally accelerated when a new beneficial mutation
al (2001) evolved an RNA polymerase ribozyme, which originally added a few
bases to itself, into one that could add up to 14 bases to an external RNA
template with 97% accuracy.
the simple RNA-copying ribozymes known cannot handle large enough sequences,
and are not accurate enough, to allow reliable coding for long RNA molecules.
Maybe an even simpler system predated the RNA world?
Evolution of the genetic code
size of the genetic alphabet, there is a trade-off between simplicity and
versatility - the present 4-base alphabet represents an optimum (Szathmáry 2003).
translated into protein using a fairly arbitrary genetic code. This may have
arisen from an ancestral code that underwent "codon shuffling" or
that gradually became less ambiguous.
been occasional slight modifications to
the genetic code (e.g. in mitochondria). How did these occur without
messing up an organism? 'Stop' codons can be reassigned to amino acids without
badly affecting protein functionality. If there is biased codon usage (e.g. pressure
to use G/C rather than A/T because the former is more thermostable), some
codons might be rarely used and could then be reassigned.
present code does have some regularities: the 1st codon position is associated
with four 'biosynthetic families' of amino acids; the 2nd with polarity of
amino acids; the 3rd is usually redundant (this minimises translation errors
since there is a 'wobble' in the translation machinery that can cause the final
base in a codon to be misread).
acids may originally have been cofactors for ribozymes in the RNA world. A
system might have developed in which amino acids were 'tagged' with short RNA
molecules (the ancestors of transfer RNAs) for easy attachment to other RNAs.
Enzymes linking amino acids together may then have developed to stabilise
ribozyme/amino acid complexes; these enzymes later evolved into protein-manufacturing
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