| What is fitness? | Variants that are more fit left greater number of progeny |
| Relative fitness | W = 1 - s
W = Proportion of gametes which are successful
1 = no selection against the phenotype
s = amount of selection against the phenotype (selection coefficient) |
| Prediction of allele frequency | - Small selection advantage rapidly affects allele frequency
- Recessive advantageous alleles take a long time to become fixed
- Ignores effect of drift
- Used to estimate fitness differences |
| Mutation load | The death of individuals due to double recessive genotype. The No. of new mutations = the No. of eliminated (Haldane) |
| Haldane-Müller Principle | The reduction of fitness of a population due to the generation of harmful mutations is dependent on the mutation rate alone. Severity is irrelevant. |
| The shifting balancing theory | Adaptive landscapes and the effect of genetic drift. Pop. descends to a point for a better ascending point. If pop. too small then the peak will go far down leading to extinction. If pop. too large, the genetic drift will not contribute. |
| Adaptive peaks | Random drift and selection can antagonise or enhance. Random drift prevents pop to ascend smoothly |
| Modern Synthesis | Variation is stable. Mutations have selective value. NS comes at a cost, which limits the pace of evolution |
| Motoo Kimura Argument | 28 x 10^6 years for a new nucleotide substitution in 100. 1 allele is substituted every 2 years for humans. Species have coped with many subs. Our mutations have selective value |
| Haldane | 1 allele is subbed every 6k years. Species cannot cope with many subs. New subs are determined by mutations rate. Cannot have too many subs. |
| Neutral Theory | Vast majority of mutations have no selective value. Therefore they will be subjected to stochastic processes and associate with genetic drift. Evolution is driven by genetic drift. |
| Neutral Theory and rate of evolution | K = 1/2N x 2Nμ
K = Sub rate
1/2N = Prob of fixation of a new mutation
2Nμ = number of mutations in new gen
K= μ rate of evolution is the mutation rate
Neutral mutation becomes fixed = proportion of pop
Large pops, have more mutations that take longer to fix. Small pops have fewer mutations and are easier to fix,
Evolution proceeds at a constant rate |
| Consequences of Neutral theory | Neural mutation occur in unpredictable and uniform way. Genomic region will evolve more quickly (not under selection). Large pops carry more variations than smaller ones. Species with high divergence show polymorphism within a species. Molecular characters are good for phylogenetic reconstruction. |
| Molecular Phylogenetics Methods | Distance based trees, Parsimony based trees, Maximum Likelihood trees, Bayesian trees using the coalescen |
| Distance based trees | Count the number of subs between species. Correction factor for when the same AA is mutated. Computationally quickly. Methods that use distances: UPGMA, Neighbor-Joining |
| Parsimony based trees | Chooses a tree topology that is associated with the fewest subs. Computationally difficult |
| Orthologs and paralogs | New genes evolve by duplication from old ones. Orthologs are genes which are separated by speciation events. paralogs are genes which are separated by gene duplication events.
-Inparalogs duplications subsequent to speciation
-Outparalogs duplications prior to speciation |
| Molecular clock reliability | Different genes evolve at different rates. Functional constraints can change over time. Different nucleotides evolve at different rates. |
| Coalescence | All genes descended from one gene. Extrapolates from modern diversity backwards. t = 4N(1-1/k) most recent common ancestor. |
| Neutral gene evolution test | Test if there is a significant deviation (NS) from neutral expectation. An allele may be associated with an extended area of linkage disequilibrium around it. We can compare interspecies and intraspecies variation. The tips and nodes of a tree should balance with the extent of allele sharing in the tree. Compare the ratio of synonymous to non-synonymous substitutions, under neutral conditions 20% of mutations should be synonymous |
| Tajima’s D | Works on the balance of sites supporting nodes and tips in a tree, and the extent to which alleles are shared among individuals. Sites which define nodes are segregating sites |
| Hamilton's rule | rB > C
r = coefficient of relatedness
B = benefit to the recipient
C = cost of the actor |
| r = S (0.5)^L | The sum of all possible paths to a common ancestor to the power of the generational links. |
| Inclusive fitness concept | Inclusive fitness: Direct fitness, indirect fitness.
NS favours alleles that increase indirect fitness. |
