7, 8, 9, 10, 11, 12 Flashcards
3 types of selection
positive (directional) selection
negative (purifying) selection
selection to maintain variation (balancing selection)
describe the distribution of polygenic traits
- continuous distribution
- typical of size/number traits
- example of quantitative inheritance
draw and describe 3 different modes of selection on quantitative traits
stabilising selection favours average traits
directional selection favours one extreme
disruptive selection favours both extremes
what may be the effects of disruptive selection?
- trait divergence
- speciation, if trait divergence causes a reduction in gene flow
how can we study adaptation?
- test for correlation of alleles or traits with environment over space and time and analyse genomic diversity (genes targeted by selection ought to show distinctive patterns)
- experimental manipulations in field/lab
describe the struggle to determine the agents of selection
- research through today shows thousands of measurements of selection
- demonstrates fitness differences & evolutionary change in traits
and yet: - many fewer convincing cases document the mechanisms (agents) of selection in natural populations
- linking evolution to ecology is difficult
describe the peppered moth (biston betularia) and industrial melanism
- light and dark forms of species that rest on trees
- in the UK, before 1850, dark moths were rare
- dark form caused by a single dominant allele of Cortex gene
- industrial pollution blackened tree trunks near cities and resulted in an increase in the dark form
- dark variant replaced light form in polluted areas, light form predominated in rural unpolluted areas
- mechanism of selection due to predation by birds
- differences in moth crypsis (camouflage) depend on trunk coloration
what happened to the darker melanic variant of the peppered moth after the introduction of the UK ‘clean air act’ in 1956?
there was a decline,
what does the lag in evolutionary response to changes in air pollution levels reflect for peppered moths?
the time required for forests to return to a more natural (unpolluted) state as well as a low initial frequency of the recessive allele for a typical coloration
describe the evolution of heavy metal tolerance in plants
- mine waste is heavily polluted with heavy chemicals such as lead, copper, nickel, cadmium
- heavy metal tolerant genotypes can occur at very low frequency in nearby uncontaminated pastures
- tolerant genotypes invade mine tailings from nearby pastures
- gene flow between pasture and mine is restricted because of flowering time differences between them
- alleles enabling tolerance maintained on mines but not pastures
define a selective sweep
when selection causes a new mutation to increase in frequency so quickly that nearby alleles ‘hitchhike’ and also increase in frequency
describe DNA Variation at glucose-6-phosphate dehydrogenase deficiency in humans
recent natural selection has caused
- low diversity
- high frequency of derived (new) allele
- G6PD gene shows evidence of the recent, rapid spread of resistance allele (consistent with hypothesis of selection for malaria resistance)
describe the long term experimental evolution study of adaptation by E.Coli
- 36 years if propagating 12 population flasks
- > 75000 generations of evolution
- propagated in minimal glucose/citrate medium
results of long term experimental evolution study of adaptation by E.Coli
- all populations rapidly increased in fitness
- similar adaptations across populations (eg larger cell sizes, higher max growth rates on glucose)
- parallel mutations in same genes
- some unique adaptations and distinct genetic changes
- only one strain evolved ability to grow on citrate
define a population
a group of individuals of a single species occupying a given area at the same time
define migration
the movement of individuals from one population to another
define gene flow
the movement of alleles from one population to another
how can we measure gene flow?
use experimental approaches
use neutral genetic markers:
- polymorphic genetic variants that aren’t direct targets of selection
experiment to answer the question: how much gene flow occurs between geographically separated populations?
- establish two populations, fixed for alternative alleles, separated by a given distance
- score FS heterozygotes in offspring
- frequency of heterozygotes = an estimate of gene flow
formally define genetic drift
stochastic changes in allele frequency due to random variation in fecundity and mortality
what does random mean in evolution?
stochastic (unpredictable or random) evolutionary forces:
- mutation
- recombination
- genetic drift
deterministic (predictable or non-random) evolutionary forces:
- natural selection
define population bottlenecks
- a single sharp reduction in abundance, usually followed by a rebound
- causes a loss of diversity
define a founder event
- colonisation by a few individuals that start a new population
- colonising group contains only limited diversity compared to the source population
why is genetic drift more pronounced in small populations?
- more drastic fluctuations in each generation
- more rapid loss of genetic diversity (i.e. faster time to allele fixation or loss)
- less consistency across replicate populations
as distance increases, gene flow
decreases
define isolation by distance
accumulation of local genetic variation due to geographically limited dispersal
phenotypic variation may be:
- adaptive (‘local adaptation’
- due to genetic drift
- phenotypic plasticity
how do we test for local adaptation and plasticity?
reciprocal transplant studies
Genomic analyses
define phenotypic plasticity
the ability of a genotype to modify its phenotype in response to a particular environment
draw 3 graphs for no plasticity, plasticity, and highly variable plasticity
how does phenotypic plasticity occur?
through modifications to development, growth, and/or behaviours under genetic control
in what organisms is phenotypic plasticity common?
in sedentary organisms like plants and corals, but also in animal behaviour
phenotypic plasticity often is an adaptation to…
unpredictable environments
does all phenotypic plasticity result from adaptation?
no
describe reciprocal transplant studies
Growth of equivalent genotypes in contrasting environments and comparisons of their relative
performance
why are reciprocal transplant studies useful?
- Can separate phenotypic variation into genetic and environmental components
- Enables measurement of selection against non‐local genotypes
- Can provide evidence for/against local adaptation
Clausen‐Keck‐Hiesey Transplant Conclusions
- Differences between populations due to BOTH plasticity and genetics
- Evidence for widespread local adaptation
– Local populations had highest fitness
How do we test for plasticity and adaptation in species that we can’t manipulate experimentally?
genomic studies
Tradeoffs Associated With Skin Pigmentation
High UV radiation:
– Degrades folate, critical in highly dividing tissues (e.g. embryos, testes)
– May have selected for increased pigmentation
- Strong purifying selection on MC1R in equatorial
regions
Low UV radiation:
– Reduced vitamin D synthesis
- VitD critical for bone development, immunity, etc.
– May have selected for reduced pigmentation
was there a history of local adaptation in skin pigmentation?
Numerous genes known to affect skin pigmentation
* These genes show higher between‐population differentiation than most others
–> Evidence supporting a history of local adaptation
* Pigmentation genes show evidence for positive selection in regions with distinctive skin
colouration
what was the confusion about the link between micro and macroevolution?
can processes of microevolution lead to macroevolution?
taxonomic (morphological) species concept
based primarily on distinct measurable differences
biological species concept
based on inter-fertility among individuals
why is it so hard to define a species?
concepts vary among groups of organisms and among scientists. There is no universal species concept.
- geographic isolation alone is NOT sufficient
- isolation does NOT have to be absolute (what cutoff?)
Darwin’s definition of a species
groups of organisms that are sufficiently similar in phenotype
Ernst Meyer’s view on distinguishing species
reproductive isolation as key to distinguishing species
what species does the BSC not apply to?
does not apply well for bacteria, asexuals, highly self-fertilising species…or fossils
allopatric speciation
often called geographic speciation
- due to involvement of geographical isolation
- much more common and easier to evolve
stages where reproductive isolation can occur
pre-zygotic:
- finding a compatible mate and mating
- fertilisation
post-zygotic:
- development and growth of zygote (F1)
- adult survival & reproduction
- growth, survival, reproduction of offspring (F2)
pre-zygotic barriers
prevent mating or fertilisation so no zygote is formed:
- geographical, ecological
- temporal, behavioural (mate recognition)
- mechanical (genital stricture compatibility)
- cellular (sperm-egg compatibility)
use Rhagoletis pomonella (Apple Maggot Flies) as an example of pre-zygotic isolation
- host shift after arrival of domesticated applies in 1800s
- differences in timing of host planting fruiting (apple vs hawthorn)
- different timing of fly mating on preferred host plant)
- reduces fly gene flow by 94% in sympatry (same region)
describe pre-zygotic isolation in abalone
binding of sperm lysin protein to egg vitelline envelope receptor (VERL) required for fertilization (molecular lock and key)
Lysin/VERL interaction has coevolved
– Different evolutionary changes in different species
– Causes reproductive isolation due to fertilization
incompatibility
post-zygotic barriers
prevent proper functioning of zygotes
once they are formed
* Caused by combinations of genes with low fitness in the
hybrid
* Arise as an indirect byproduct of evolution acting
separately in different populations (cannot be directly
favored by natural selection)
intrinsic post-zygotic barriers vs extrinsic post-zygotic barriers
Intrinsic Post‐zygotic Barriers:
* Inviability, sterility, or abnormal development of hybrids
Extrinsic Post‐zygotic Barriers:
* Ecological mismatch of hybrid phenotype to environment
example of intrinsic post-zygotic isolation
Mule is a sterile hybrid cross of:
* Male donkey (62 chromosomes)
* Female horse (64 chromosomes)
Hinny is a sterile hybrid of:
* Male horse (64 chromosomes)
* Female donkey (62 chromosomes)
relation between genetic distance and post-zygotic isolation in fruit flies
- The more that fly pairs are genetically differentiated,
the more likely they are to be reproductively isolated
example of extrinsic post-zygotic isolation
aposematic helicons butterflies
Hybrids have aberrant colour patterns
* Higher predation risk
* Lower mating success
local adaptation by different populations can lead to
reproductive isolation and speciation
distinct evolutionary responses happen due to
different selective pressures
is local adaptation necessary for speciation?
Local adaptation not absolutely necessary, but accelerates population divergence and
evolution of RI
describe sticklebacks in marine and freshwater environments
In marine environment:
– Bony armor protects against large fish predation
In freshwater:
– Loss of armor increases growth rate
– Greater winter survival
– Earlier breeding
so, can microevolution lead to macroevolution?
yes - as populations diverge genetically as a result of evolutionary forces
(mutation, natural selection, genetic drift), they become reproductively
isolate
define and describe adaptive radiation
The evolution of ecological and phenotypic diversity within a rapidly multiplying lineage
– Originates from a single common ancestor
– The process results in an array of many species
– The species differ in traits allowing exploitation of a range of habitats and resources
Four features commonly identify an adaptive radiation
1) Recent common ancestry from a single species
2) Phenotype‐environment correlation
3) Trait utility
4) Rapid speciation
define ecological opportunity
the absence (or reduction) of competition for resources
two things that cause adaptive radiation
ecological opportunity and high propensity for speciation
how does ecological opportunity come about?
Colonization of competition‐free regions (e.g., islands, lakes, or continents)
Extinction (which can eliminate competitors)
Key innovation (evolution of a trait that provides access to new resources)
high propensity for speciation
RI evolves more readily in some clades than others
define hybridisation
The exchange of genes between species as a result of occasional inter‐species mating
– Sometimes can reverse speciation process to merge two groups into one
how does hybridisation vary across the tree of life?
common in plants and fish, rare in mammals
how can hybridisation result in complex patterns of variation?
Can be evolutionarily significant for speciation, especially by polyploidy
define polyploidy
Describes an organism, tissue, or cell with more than
two complete sets of homologous chromosomes
define and describe allopolyploidy
Allopolyploidy (e.g. AA x AA -> AA AA)
– Arises from duplicated karyotype following
hybridization between species
– Commonest type of polyploidy
define and describe autopolyploidy
Autopolyploidy (e.g. AA -> AA AA)
– Arises from duplicated karyotype within a species
(e.g. non‐disjunction)
describe how allopolyploid hybridisation comes about
- Two species mate and produce an F1 hybrid
offspring (genotype AA*) - F1 hybrid offspring produces unreduced diploid
gametes (genotype AA*) due to meiotic
nondisjunction - Diploid gametes combine to produce tetraploid
F2 offspring - Tetraploid is fertile, but is reproductively
isolated from parental species
evolutionary significance of polyploidy
Polyploids are reproductively isolated from their
diploid parents
– Hence a form of sympatric speciation
* Polyploids exhibit novel phenotypes
– Allows exploitation of new habitats
* Polyploids often show hybrid vigor due to
heterozygosity, particularly in allopolyploids
* Polyploid origin for ~50% of flowering plants
– Many crop plants & invasive species
draw the speciation continuum
Define taxonomy
the theory and practice of classification and naming
define systematics
the study of biodiversity and the evolutionary relationships among organisms
Carolus Linnaeus
1707-1778
- father of taxonomy
- binomial nomenclature
- hierarchical system of classification
define a taxon
a single named taxonomic unit at any level (plural = taxa)
7 taxa
kingdom (kingdoms)
phylum (phyla)
class (classes)
order (orders)
family (families)
genus (genera)
species (species)
what is the purpose of a biological classification?
- a name is key to shared information on an organism (eg scientific literature, field guides)
- therefore has predictive power
- enables interpretation of origins and evolutionary history
systematics research requires
a robust and stable system for classifying organisms (i.e. taxonomy)
describe how phylogenies arise/what they are made up of
- individual organisms within a population
- parents produce offspring
- lines of descent persist across generations
- a population is an aggregation of the genetic lineages of the individuals they contain
- a species is made of many populations, linked by gene flow
- individual species split to give rise to multiple species
- a phylogeny shows the relationships and evolutionary histories of species
node
corresponds to historical lineage splitting events, when one lineage splits into two
branches/ edges
correspond to single ancestor-descendant lineages. All branches are connected by nodes
tips/leaves/terminals/OTUs
tips do not have represented descendants. can be individuals, species, clades
internal vs external branches
external branches (aka terminal branches) connect a tip and a node. internal branches connect two nodes
root
- a node representing earliest time point in the diagram
- often represented by an unlabelled branch
sister groups/taxa
those that are immediate descendants of the same ancestor, eg sister species, sister branches, sister clades
parents and daughters
parent branches give rise to daughter branches
ingroup
consists of the focal species in a phylogenetic study
outgroup
a more distant relative of the in-group taxa; can help to root the phylogeny and determine what character states are ancestral
MRCA
most recent common ancestor; the youngest node that is ancestral to all lineages in a given group of taxa
clade
- any piece of a phylogeny that includes a MRCA and all of its descendants
- i.e. any piece of a phylogeny that exhibits monophyly
monophyly
- describes a group made up of an ancestor and all its descendants
- ie a monophyletic group or clade
paraphyly
- describes a group made up of an ancestor and some (but not all) of its descendants
- ie a paraphyletic group or grade
polyphyly
- describes a group that does not contain the most recent common ancestor of all members
- ie. a polyphyletic group
for the species in a clade a trait is ancestral if
it was inherited in its present form from the MRCA of the clade
for the species in a clade, a trait is derived if
it originated within the clade, ie in a descendant of the clade’s MRCA
relationship between ancestral and derived clades
the same trait can be ancestral for a clade, but derived within a larger clade
define a synapomorphy
a shared, derived trait for a clade. it is a trait that all species in the clade share, and that evolved on the branch leading to the clade (ie its derived within the context of more inclusive clades)
homology
when structures observed in different taxa can be traced to a single structure present in a shared evolutionary ancestor
homoplasy
when a character or character state arises more than once on a phylogenetic tree (convergence is one kind)
why conduct a phylogenetic analysis?
- understand history of life
- understand large scale patterns of evolution
- understand how many times traits have evolved how fast, under what conditions
- practical: where/when did parasites spread? which fly strain is most successful? what are the driver mutations as covid evolves?
why is phylogenetic relatedness inferred from homologous traits and not homoplasy?
homoplasy (eg convergent trait evolution) can mislead phylogenetic inference
2 principal sources of macroevolutionary insights?
palaeontology
- provides a direct record of past evolutionary change
- inference is strongest for groups that fossilise well
phylogenetics
- provides an indirect record of past evolutionary change
- inference is strongest for groups that have living representatives
mass extinction
extinction of >75% of earth’s species in a geologically short period
uses of fossil record
- provides only evidence for completely extinct clades
- documents long-term patterns of biodiversity
- provides evidence for catastrophic extinctions during earth’s history
diversification rate
speciation rate minus extinction rate
what happens after mass extinctions and how do we know?
explosive diversification; phylogenetic provides evidence for this
features associated with increased diversification
- herbivory
- species with more sexual selection
- animal pollination in plants
- increased dispersal
- increased range size
give a broad description of the tree of life
- has both simple and complex organisms
- bacteria, archaea, and eukaryotes are main 3 groups
- eukaryotes typically more complex in cell number, tissue types, physiology…
major transitions in evolution
- origin of cells
- origin of chromosomes
- origin of genetic code
- origin of eukaryotes
- origin of sexual reproduction
- origin of multicellularity
- origin of colonies (eg non-productive castes)
what is the ultimate target of selection and why?
genes because they are the unit of inheritance
what are the units competing?
- DNA/gene
- cells
- individual organisms
- species
- larger clades
why does multi-level selection pose a problem for complexity
- selection at a given level of organisation means that units compete to maximise fitness
- competition among lower-level units of organisation may reduce fitness at higher levels
what is the solution to the multi-level selection problem?
if lower-level units of organisation cooperate rather than competing, higher-level fitness costs can be avoided
how do biological subunits stay so cooperative?
many features of individual organisms prevent competition within an individual:
- prevents evolution within individuals
- align fitness interests across levels of organisation
- this ensures that many genes succeed by enhancing the fitness of the individual
two ways in which biological subunits stay cooperative
- meiosis and mitosis:
- ensures that alleles don’t compete within an individual
- fair representation of gene variants among daughter cells - development and multicellularity
- starting from a single cell prevents initial competition among cell lineages
what is fair meiosis?
meiosis provides a fair representation of an allele’s fitness effects on individuals
define and describe meiotic drive
- if an allele can bias its own transmission then it can spread to higher frequency even while reducing individual fitness
- selfish genetic element relative to organism’s fitness interests
give an example of meiotic drive and cheating Mendel’s law of segregation
drosophila segregation distorter locus (SD)
- almost all (95-99%) of offspring are Ss
- S allele prevents proper ‘s’ sperm formation
- counteracting restorer alleles are favoured at other genes in the genome to silence the S allele
what is the evolutionary response to meiotic drive?
when cheating alleles spread, there is strong selection on rest of genome for suppression of cheating
define and describe over-replication
transposable elements are self-replicating segments of DNA (transposons)
- TE replication is separated from cellular replication
- ensure their own over-representation in offspring
two ways to cheat a fair meiosis
- meiotic drive
- over-replication
how do genomes not explode from transposition?
- alleles arising elsewhere in genome that silence TES will be favoured by individual selection
- mechanisms controlling DNA & histone methylation
- piRNAs and RNA interference may have evolved as silencing mechanisms - transposition-selection balance
- transposition is a form of mutation that can disrupt a gene
- natural selection against harmful effects on the organism reduces abundance of chromosome copies with most TES
- abundance of TEs in an organism results from a balance between these opposing forces
what can lead to rampant activation of transposable elements?
mutations in genes for DNA methylation:
- mutation in DDM1 gene reduces methylation
- this reactivates silenced TEs
what experiments were done with C.Elegans and why?
- cell lineage mapped from 1 cell zygote to 959 cells of adult
- how do collections of cells maintain cooperation to make an organism?
what features may inhibit unregulated cell division?
tumour suppression
what makes it harder for collections of cells to stay cooperative?
- somatic mutation is inevitable in long-lived multicellular organisms
- some of those somatic mutations might be selectively favoured within an individual
use cancer as an example of selfish cell lineages evolving within an individual
- spreads commonly in tissue that is relatively undifferentiated
- evolves resistance to treatment and the immune system
- illustrates the short sightedness of the evolutionary process
3 main methods in which evolution may be applied
- agricultural relevance; pesticide and herbicide resistance
- evolutionary medicine; evolution of resistance to antibiotics, evolution-proof vaccination
- global change and evolution; adapt or go extinct
what is the problem with pests and evolution?
- we use chemicals to combat pests and pathogens
- we create strong selective pressure for resistance, with fitness advantage to resistant genotypes arising from mutation and gene flow
why are weeds an issue for agriculture?
- cause approx. 34% loss of crop yields annually
- compete with crops for light, nutrients, space
- usual solution is to spray with herbicides; however, weedy plants have repeatedly evolved resistance to herbicides
where does herbicide resistance come from?
- pre-existing genetic variation in the population
- new mutations - in very large populations new, simple mutations may be introduced at a high rate
- gene flow - epidemic spread of resistance from one region to the next
what type of weeds has the greater pre-existing resistance variation?
outcrossing weeds have more pre-existing resistance variation than selfing weeds
how can herbicide resistance be stopped
- multi-herbicide treatment
- makes new adaptation less likely
- requires more complex adaptation - rotation of different kinds of herbicides
- weeds regularly hit by different selection pressures
- but could select for generalised resistance
give a graph for time vs population size of endangered species and weedy plants
what is the problem with malaria and mosquitoes?
- malaria causes approximately 700,000 deaths annually
- major prevention strategy is insecticides
- strong selective pressure on mosquitoes has led to rapid evolution of resistance
what could be evolution-proof solutions to malaria?
- tailor insecticide application to knowledge of mosquito generation times and spacial distributions
- goal: minimise selection for mosquito resistance while still reducing malaria transmission
use HIV treatment as an example of evolution in medicine
- multi-drug cocktails slow evolution of HIV resistance
- single mutations unlikely to confer resistance to multiple drugs with different mechanisms of action
- lower viral loads make multiple mutations less likely
describe evolutionarily informed cancer treatment
- strong, prolonged selection pressures using the same chemotherapy drugs - may not be the best solution as it selects for resistance
- cycling drugs, multi drug cocktails, lower drugs - may be a better option but ethical considerations make tests of theory for human application challenging
describe environmental change as a problem
- loss of habitat
- habitat fragmentation
- altered abiotic conditions (temperature, precipitation, pH)
- altered biotic composition (transport of species, invasive species)
define extinction
permanent elimination of a species
genetic issues in conservation biology caused by environmental change
- loss of genetic diversity
- loss of heterozygosity
- inbreeding depression
- fixation of deleterious alleles
- inability of populations to adapt
probability of evolutionary rescue from adaptation depends on
- population size
- beneficial mutation rate
- how much fitness was reduced
