4 Flashcards
define genotype
the genetic constitution of an organism
- defined in relation to a particular gene or gene combinations
- eg Aa, Bb
define phenotype
feature of the organism as observed
- used when discussing a trait of an organism that varies
- eg size, fur colour, mRNA expression level
define genome
the entirety of an organism’s DNA
- includes genes and non-coding regions
state 3 sources of genetic variation
- mutation
- independent assortment
- recombination
define a mutation
a stable change in the DNA sequence
how often do mutations occur?
at a low rate
- mutation rate varies in ways that are partially predictable
what are the different possible effects of mutations on fitness?
- neutral (won’t matter for the fitness of the organism)
- deleterious (weakly detrimental up to lethal)
- beneficial
state the 4 main characteristics of mutation
- mutation is an inevitable phenomenon, despite cellular mechanisms to correct errors during DNA replication
- mutation is not directed toward an outcome by the organism or by the environment
- it is random with respect to effects on fitness
- it is not ‘summoned’ to make things better - rate depends on the type of mutation, and can also vary among genes
- the environment can affect the mutation rate (eg mutagens, high temp)
what are the 4 types of mutation?
- point mutations (a simple substitution of a nucleotide)
- insertions/deletions (‘indels’) - adding/removing a nucleotide
- changes in repeat number
- chromosomal rearrangements (eg inversions)
describe a mutation involving a change in repeat number
- when there is a repeated motif (eg ATG) within the gene, the motif may accidentally be added/removed an extra time
- the repeated motif makes it harder for the replicative machinery to replicate
describe an example of a chromosomal rearrangement
inversions:
- flipping of the nucleotide sequence
- occurs when there is a double break in DNA strand; when enzymes try to put the two strands back together, it is hard to know which one was forward and which one was backwards
give an example of a method that can be used to identify a new mutation?
a trio study:
- two parents (reproducing organisms) are selected
- their genome and the genome of their offspring is sequenced
what is the rate of new mutation in humans?
per base pair of DNA: 16 in every billion nucleotides each generation
per individual genome (two copies of our 3 billion base pair genome): approx. 96 new mutations per zygote
for the entire human population (8 billion): every base pair in the genome mutated about 126 times over per generation
why do some mutations not lead to amino acid changes?
we have more codons than amino acids - so sometimes mutations don’t make a difference to the amino acid sequence (= silent substitution)
give an animal example of how single mutations can cause profound effects on traits
- Antp Hox gene mutations in Drosophila
- results in an extra pair of wings, for example, or a set of legs, instead of antennae, growing from the fly’s head
describe G6DP deficiency in humans?
Glucose-6-phosphate dehydrogenase
most common enzyme deficiency in humans
- causes severe anemia
- also protects against malaria
- 2 amino acid replacement mutations in the coding sequence of G6PD are associated with disease allele (A-)
what are polymorphisms?
- A gene is said to be polymorphic if more than one allele occupies that gene’s locus within a population.
- each allele must also occur in the population at a rate of at least 1% to generally be considered polymorphic.
what are allozymes?
Alloenzymes are variant forms of an enzyme which differ structurally but not functionally from other allozymes coded for by different alleles at the same locus.
give a flow chart for how mutations in G6PD lead to genetic variation
DNA (polymorphisms) -> proteins (allozymes) -> phenotype (polyphenisms)
define independent assortment
the alleles of two (or more) different genes get sorted into gametes independently of one another.
how does independent assortment in segregation during meiosis generate diversity?
- allows different combinations of parental chromosomes
- 2^n, where n=sets of chromosomes
how can we tell if a mutation has increased or decreased fitness from a fitness distribution bar chart?
if the mutation leads to a fitness less than 1 (which is the fitness of the ancestor) then they are detrimental
describe how recombination during meiosis (metaphase) further contributes to variation
there is synapsis of bivalents, leading to crossing over at chiasmata and recombinant chromosomes.
how did scientists believe that heredity worked before Mendel?
performatifs (1700s):
- spermists/ovists believed only one parent contributed to inheritance
theory of blending inheritance (1800s)
- postulated that factors from both parents mix together irreversibly
what is the problem with blending inheritance for evolution by natural selection?
there would be no way for a beneficial mutation to increase in frequency across generations
describe Mendel’s experiment with diagrams
- hybrid cross of pure-breeding lines (yellow and green)
- self fertilised (all yellow)
- offspring were 3/4 yellow and 1/4 green
state the key conclusions from Mendel’s pea experiments
- inheritance is determined by discrete particles, genes
- each diploid organism carries two copies (alleles) of each gene.
- alleles can exhibit dominance/recessivity
- gametes contain only one allele per gene - gametes fuse to make offspring
- sperm/pollen fuses with egg/ovule - offspring inherit one gamete from each parent at random
- one allele per gene at random from each parent
describe phenotypic polymorphisms with simple mendelian genetic causes
- common in nature
- direct correspondence between trait and its genetic basis
- easy to track selection and evolution
what are the two types of genetic variation?
discrete variation:
- mendelian genetics
- genes of major effect, dominance, and recessiveness
- involves a spread of alleles and a change in allele frequency
continuous variation
- quantitative genetics
- many genes each with alleles of small effect, important environmental effects
- selection response as change in average trait value
define discrete variation
Discrete variation refers to traits with a finite number of phenotypes, often controlled by single genes
define continuous variation
Continuous variation, on the other hand, displays an infinite number of phenotypes across a continuum and is usually polygenic.
how is the phenotype of a quantitative trait established?
- often affected by many factors
- complex polygenic inheritance
AND - environmental factors
define partial dominance
a form of Gene interaction in which both alleles of a gene at a locus are partially expressed, often resulting in an intermediate or different phenotype.
define a polygenic trait
a characteristic that is influenced by two or more genes.
locus
the location of the gene on a region of a chromosome
What happened between the 1920s and the 1950s?
- the creation of the mathematical evolutionary theory for population genetic change
- initiated by Fisher, Haldane, and Wright
- provided the foundations for Neo Darwinism and the New Synthesis
- showed that continuous variation and Darwinian natural selection are entirely consistent with Mendel’s Laws
- demonstrated the evolutionary significance of genetic variation
state the 5 forces that influence patterns of genetic diversity and evolution and what effect they tend to have
- mutation - increases diversity
- recombination - increases diversity
- genetic drift - decreases diversity
- natural selection - increases/decreases diversity
- migration - increases diversity
how does mutation influence patterns of genetic diversity?
- increases genetic variation in populations
- caused by errors during replication
how does recombination influence patterns of genetic diversity?
- increases genetic variation in populations
- creates new combinations of alleles and mutations
how does genetic drift influence patterns of genetic diversity?
defined as the change in the frequency of an existing gene variant (allele) due to random chance
- acts to decrease genetic variation in populations
- random sampling affects every generation
- more important for populations that are smaller
three types of natural selection
- negative (purifying) selection
- positive (directional) selection
- selection favouring diversity
negative (purifying) selection
- decreases genetic variation in populations
- mutations that reduce fitness are removed by natural selection
positive (directional) selection
- decreases genetic variation in populations
- mutations that increase fitness will eventually become fixed in a population
selection favouring diversity
- increases or retains genetic variation in populations
- natural selection can act to maintain diversity over the long term (eg heterozygote advantage)
how does migration (gene flow) influence patterns of genetic diversity?
- increases genetic diversity in populations
- migration influences the structuring of diversity over a large spatial scale
describe the two metrics of genetic variation
Heterozygosity (H)
- fraction of individuals that are heterozygous, averaged across gene loci
Polymorphism (P)
- proportion of gene loci that have 2 or more alleles in the population
- a locus can be polymorphic without being heterozygous
what maintains genetic variation?
- mutation-selection balance
- selection maintaining variation
define fixation
occurs when a polymorphic locus becomes monomorphic due to the loss of all but one allele (can occur due to natural selection or genetic drift)
decreases differences between populations.
mutation-selection balance
- less fit types reintroduced by mutation
- followed by selection acting to remove them
selection maintaining variation
- the maintenance of genetic variants at intermediate frequencies over long periods of time
what are the two models of population genetic variation?
- the “classical” theory asserted that most genetic variation within species is maintained by mutation-selection balance
- the “balance” theory proposed that genetic variation is maintained primarily by overdominant selection or some other type of balancing selection.
classical model
- Morgan, muller
- low heterozygosity
- low polymorphism
- wild type is ‘normal’ genotype
- selection typically negative
balance model
- Dobzhansky, Ford
- heterozygote advantage
- high heterozygosity
- high polymorphism
- selection favours diversity
define gene flow
movement of genetic material from one population to another
how was genetic diversity studied before 1966?
morphological
- eg snail colour polymorphism
cytological
- eg chromosome inversions
what was the early quantitative evidence for the existence of genetic variation?
- rather than focussing on Mendelian discrete traits, there was a focus on continuous polygenic traits
- selection experiments were done on different groups of organisms
- these involved controlled breeding of individuals with particular traits for many generations
= artificial selection
evolutionary responses of continuous traits
- demonstrates existence of heritable variation in fitness-related phenotypes
- due to many underlying genes
give a summary of the artificial selection experiments that were done on quantitative traits
- selection responses demonstrate that abundant genetic variation exists for polygenic quantitative traits
- but often no information on P & H as key population genetic parameters
- also comparative studies difficult as traits studied often are group specific
still no solution to the question: what maintains genetic variation?
describe Richard Lewontin and the Electrophoresis Revolution
- allozyme gel electrophoresis provided a way to ask
- what proportion of genes are variable (p&h)?
- addresses fundamental dispute between classical and balance schools
advantages of studies of enzyme polymorphism
- many loci can be examined
- can be used in nearly any organism
- loci co-dominant, heterozygotes can be identified
- variation examined close to DNA level
- provides genetic marker loci for other studies
describe the neutral theory by Motoo Kimura
- negative selection rapidly eliminates detrimental mutations
- positive selection rapidly fixes beneficial mutations
- the only mutations left to create genetic variation are selectively neutral
describe DNA variation in maize vs teosinte
- corn has reduced genetic diversity compared to its wild ancestor teosinte
- a consequence of population bottlenecks during domestication
describe human genetic variation
- humans show a loss of genetic variation with increasing distance from East Africa
- reflects founder events as humans migrated from source population
describe comparisons of polymorphism in Arabidopsis lyrata
- regions that were recently glaciated have lower DNA diversity
- genetic drift following recolonisation
state the 4 important elements of Darwin’s theory
- Evolution occurs primarily at the level of populations - individuals do not evolve
- Variation is not directed by the environment - individuals do not induce adaptive variation when needed
- Most fit type depends on the environment and changes from generation to generation
- ‘Survival of the fitter’ - evolution works with available variation, and will not necessarily achieve perfection
State the implications of Darwin’s theory
The concept of a changing universe; a phenomenon with no purpose
State the 4 sources of evidence for evolution:
- Geology
- Homology
- Biogeography
- Domestication
Lessons from Geology
- Earth is very old - this allows for an immense amount of time for biological evolution
- Intermediate forms - evidence for transitional fossils linking features of seemingly dissimilar relatives (eg ungulates and whales, or tetrapods and fish)
- Fossils in younger strata increasingly resemble modern species in the same region - older strata show increasing differences
Give an example of how discoveries of transitional fossils continue today
Tiktaalik roseae, discovered 2006
- has 2 legs and 2 fins
- nickname: fishapod
Define homology
Similarity of traits in two or more species that is due to inheritance from a common ancestor
Lessons from homology
Vestigial traits provide evidence of the evolutionary past:
- have no function/reduced function in extant organisms
- can only be explained by the presence of functional traits in ancestors, followed by evolutionary degredation
Homologous structures are ubiquitous across organisms:
- fundamental structural similarity reflects common ancestry
- homologous structures have evolved to serve very different functions
Define a vestigial structure
- features inherited from an ancestor, but reduced in morphology and function
- are homologous to functional structures in related species
Describe vestigial structures in Galapagos flightless cormorants compared to mainland cormorants
Mainland cormorants need to fly as they nest on trees; GF cormorants do not as they nest on rocks by the water. The wings of these two species, albeit varying in use, are homologous structures.
what is a vestigial structure in cave-dwelling morphs of Astynax Mexicanus?
they have evolved to lose their eyes as they do not need them
vestigial structures in humans
- ear muscles
- appendix
- tailbone
- goosebumps
why is the presence of vestigial structures significant?
- organismal features are consistent with modifications of pre-existing structures
- this would not be expected if each organism was individually optimally designed
describe homology in genes
- approximately 500 genes are shared across all forms of life
- there is a strong, shared constraint for genes involved in basic cellular function (eg transcription/translation)
Lessons from Biogeography
Remote islands biotas:
- have continental affinities
- are dominated by good colonists
- have locally-differentiated species
biogeographically isolated regions:
- have species adapted to niches unusual for their group
- harbor endemic radiations of species that are convergent with radiations elsewhere
3 main points of evidence from biogeography
- geographically close organisms resemble each other
- different groups of organisms adapt to similar environments in different parts of the world
- geographically isolated regions have unusual organisms
use Australia as an example of a location with an interesting Biogeography
- although a continent, Australia is also an island
- distinct flora and fauna with high endemism and many unique adaptations
- australia has endemic radiations of species that are ecologically convergent with those of other continents
what is Australia’s biological uniqueness a result of?
its long history of isolation from other land masses
give a summary of evidence from domestication
Heritable variation can be selected on, leading to dramatic changes over generations
