Evo Devo Flashcards
Nucleotide =
sugar + phosphate + base
Pyrimidines
Cytosine and thymine
Purines
Adenine and guanine
Transcription
mRNA is transcribed from the DNA in the nucleus
Translation
Amino acid sequence is read off the mRNA sequence in the ribosomes
what percentage of DNA codes for genes?
5%
Uses of HWE
Simple conceptual model; estimation of variables; null hypothesis
what would cause a deviation from HWE
Non-random mating (assortative, disassortative or no mating)
Assortative mating
like genotypes preferentially mate; result is a deficit of heterozygotes
Disassortative mating
different genotypes preferentially mate; result is excess of heterozygotes
Forces of genetic change
natural selection, genetic drift, mutation and migration
response to natural selection is determined by variation in…
fitness
Fitness (w)
relative survival and reproductive success of a genotype
selection coefficient (s)
relative selective intensity against a genotype/reduction in fitness relative to the best genotype (1-w)
Balance of selection and mutation
selection can never eliminate deleterious alleles because they keep re-appearing by mutation
why do chromosome heterozygotes have higher fitness
Dominance: Chromosomal heterozygotes mask deleterious recessives at many loci
example of single locus heterozygote advantage
Sickle cell anemia polymorphism in humans (anemia selects against SS, malaria selects against AA)
Why are there not many examples of single locus heterozygote advantage
not common; hard to detect; theoretical problem of genetic load
positive frequency dependence
fitness increases with frequency, results in monomorphism
negative frequency dependence
fitness decreases with frequency, result is polymorphism
examples of negative frequency dependence
predation, mate choice, niche variation
causes of genetic drift
mendelian segregation, finite population size
principles of genetic drift
- The direction of genetic drift in unpredictable
- The magnitude of genetic drift depends on population size
- The long-term effect is to reduce variation within a population
- Genetic drift causes populations to diverge from one another
- causes heterozygosity to decrease over time
factors that affect effective population size
unequal sex ratio; variation in population size; variation in family size; mitochondrial DNA
founder effect
Establishment of a new population by a few original founders
population bottleneck
population is suddenly reduced in size
identical by state
functionally equivalent alleles
identical by descent
pairs of alleles that trace to the same copy
inbreeding coefficient (F)
probability that two copies of a gene are identical by descent
effective population size (Ne)
the number that when substituted for N in equations based on ideal populations, describes the drift experienced by the actual population
what is mutation
any heritable change in genetic material
types of mutation
chromosomal; point; indels; gene duplications
chromosomal mutations
- Change in the number or structure of chromosomes
- Aneuploidy – extra or missing chromosomes
- Polyploidy – entire sets of chromosomes duplicates
- Inversions – chromosome breaks and is flipped 180 degrees
- Translocations – chromosome breaks and attaches to a non-homologous chromosome
point mutations
A change in a single nucleotide in a DNA sequence
Indels
Insertions or deletions in the DNA sequence caused by errors in DNA replication
Gene duplication
New copies of a gene or groups of genes
why does sexual reproduction exist
theories
- genetic constraint
- sex can accelerate evolution
- coevolution of hosts and parasites
- mutational theory
genetic constraint
Mutations to produce asexual reproduction have not occurred so we are ‘stuck with it’ (unlikely because mutation for asexual reproduction is not difficult, it has arisen many times)
coevolution of hosts and parasites
- Sex likely to be advantageous in changing environments
- Coevolution between hosts and parasites can generate rapid ‘environmental’ change
- Arms race between hosts resistance mechanism and parasites method of penetrating defences
sex can accelerate evolution
Beneficial mutation, at separate loci, can be combined in a single individual faster with sex
mutational theory
Sex exists because it enhances the power of selection against deleterious mutation
inbreeding
positive assortative mating for relatedness; mating between related individuals
how does inbreeding differ from assortative mating
it affects all genes, not just those controlling that trait which mating preference is based
what does inbreeding result in
excess of homozygotes and deficiency of heterozygotes
autozygous
Alleles that are ibd are derived by replication from a single allele
allozygous
Alleles that are not ibd are called
Inbreeding depression
increased appearance of lethal and deleterious traits with inbreeding
Does inbreeding ‘purge’ deleterious recessive alleles?
If deleterious recessives are responsible for inbreeding depression, then populations that habitually inbred should have higher frequencies of fitter wild-type alleles
population subdivision
Most populations are grouped into smaller subpopulations where random mating usually occurs (genetic neighbourhood)
reduction in heterozygosity due to population subdivision
wahlund effect
why is it important to know F statistic for conserving genetic variation
- When a population has no population structure (FST close or equal to 0), there is no variation in allele frequencies between subpopulations, therefore genetic resources can be conserved by protecting one or two large populations
- If FST is large, there is a high population structure and most genetic variation exists between subpopulations rather than within subpopulations, in these species it is necessary to protect as many subpopulations as possible to conserve genetic diversity
gene flow
The movement of genes between subpopulations within a species
Homogenising force
holds the gene pools of subpopulations together and limits how much genetic divergence takes place
genetic variation has two impacts on island populations:
- Reduces genetic variation within populations
- Increases genetic variation between populations
stepping stone model
Recognizes that gene flow is likely to be greater among demes (populations) closer together
polygenic
traits that are controlled by multiple genes (e.g. height)
coadaptation
allele favoured by selection if it is in the same individual as a particular allele at another locus
haplotype
combinations of alleles at different loci
linkage equilibrium
When alleles at different loci combine independently
linkage disequilibrium
when haplotype frequencies deviate from linkage equilibrium
recombination frequency
the frequency of recombination between two loci (range 0-0.5)
significance of linkage equilibrium
- Simplest model for 2 loci (HWE for single locus)
- Deviations can indicate that something interesting is happening (i.e. one of the assumptions is not met)
- Lets us know if more complex two-locus theory is needed
causes of linkage disequilibrium
linkage; genetic drift; non-random mating; mutation; natural selection
linkage disequilibrium mapping
Associations between traits and molecular markers are used to identify genes controlling traits
species concepts
biological; recognition; ecological; phenetic; phylogenetic
biological species concept
Groups of interbreeding natural populations that are reproductively isolated from other groups (no gene flow)
recognition species concept
Group of individuals with shared specific mate recognition systems
ecological species concept
Defines a species as a set of individuals with shared ecological attributes
phenetic species concept
Defines a species as a set of individuals with shared morphological attributes
phylogenetic species concept
Species are identified by estimating the phylogeny of closely related populations and finding the smallest monophyletic group
what stops species interbreeding
Reproductive isolating barrier (pre or post zygotic) are evolved characters that prevent interbreeding between species
how does reproductive isolation evolve?
- allopatric speciation model (geographical isolation)
- sympatric speciation model
genetic correlation can exist for two reasons:
- Pleiotrophy – one gene influences more than one trait
- Hitch-hiking – natural selection favours one locus, genes at other loci also increase
qualitative vs quantitative traits
- qualitative: discrete categories
- quantitative: needs to be measured
quantitative traits
Depend on genes whose individual effects are small in relation to variation attributed to other causes
common property of quantitative traits
sibling resemblance (generally, the closer the relationship, the closer the resemblance)
breeder’s equation
- Proportion of total phenotypic variance that is due to genetic causes
method for quantifying resemblance between parents and offspring
parent-offspring regression
paternal half siblings
A powerful method for testing for additive genetic effects based on the covariance among paternal half siblings
basic principle of paternal half siblings
where males provide no resources at reproduction other than genes, and phenotypic similarity among his offspring from different females must be due to those offspring sharing the same paternal genes
the fitness function
Describes the strength and form of selection acting on the phenotype
direct selection
causal relationship between relative fitness and phenotype
indirect selection
when there is a correlation between the focal trait and another one that experiences direct selection
correlational selection
When two traits interact to determine fitness
applications of quantitative genetics in the wild
medicine; conservation; selective breeding; disease resistance
additive genetic variation
the variation that causes offspring to resemble their parents
allelic diversity
the variation discernable through molecular genetic techniques
fisher’s fundamental theorem
- at each generation, only a subset of fitness related alleles pass on to the next generation
- There should be very little genetic variation for traits that are closely related to fitness
mutation:selection balance
Selection and drift must be balanced by mutation and other mechanisms that maintain genetic variation
whether mutations can supply enough genetic variation depends on:
- the genomic mutation rate
- the intensity of selection
- the number of genes involved
how can variation be maintained in variable environments
When generations overlap or environmental heterogeneity is spatial, genetic variation can be maintained by migration between the ‘patches’
disruptive selection
- Short term increases in heritability
- Practice: natural selection
theory of selection for heterozygotes
- where the optimum phenotype is the heterozygote
- Practice: mate choice in Antarctic fur seals
theory of frequency dependent selection
- rare genotypes have higher fitness than common ones, creating ‘negative’ frequency dependent selection
- Practice: frequency dependent selection on male phenotype in a species of guppy
theory of antagonistic pleiotrophy
- Genes that enhance the fitness pay-off from one aspect of life-history reduce the pay-off from another
- Practice: attractiveness and male survival in the guppy
