Genome Evolution

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4. Gene Duplication & Pseudogene formation	Pseudogenes are genes which have lost their function or it has not been maintained by NS, but they're still present in the genome. E.g GLOBIN GENES (used to find common ancestors) have been through duplication resulting in multiple copies of globin genes - often only 1 remains active.
5. Hox Genes	Very important in body plan development. Their evolution has involved gene duplication & deletion. E.g. SCORPION has 12 or 13 segments & which is determined by their hox genes. Similarly, arachnid ancestors, but hox genes had differences
6. Silk Genes	These are double stranded fibres with varied AA sequences & proteins. Spiders also have vared methods of spinning the web and their morphology varies too (E.g. Orbweaver Vs. Tarantula). the proportions of proline, serine, glycine & alanine determine the physical properties of the silk. But a change in silk gene AAs does not guarantee a change in the silk morphology. This has allowed spiders to occupy a wide range of niches.
7.Duplication of Entire Genomes	E.g. AFRICAN TOAD is a tetraploid (4 gametes) which is thought to have arisen after a duplication of the entire genome. The extra pair is thought to be beneficial perhaps it is tolerant to wider conditions? It's also massive.
How do changes occur?	Germ cell DNA can be driven to variation by external factors (mtagens etc.). Natural error during replication. Or natural part of recombination.
Natural Error in DNA Replication	Polymerase enzymes have a natural error rate. This is minimised by proof reading enzymes, but is never 0. Insertions/deletions occur during replication and are particulaly common in repetitive regions. E.g. DNA fingerprinting markers are repetitive & differ between people because the error rate is high.
Recombination & Error	Recombination is a natural part of meiosis & is the crossing over of chromosomes. This jumbles up allele combinations. Having regions of very similar DNA sequences on different chromosomes increases the chances of non-homologous recombination events (ectopic events). Unequal recombination results in different genomic content of each gamete.
Changes as a Result of the Outcome of Repair	Gene conversion is when an allele on 1 chromosome is repaired by copying a homologous gene. This is biased in the direction of repair & so 1 allele can end up domination - this is responsible for concerted evolution. E.e the switching of mating types in Saccharomyces.
Homogenisation Through Gene Conversion	Gene conversion through repair is not always random. If it is biased then all alleles will eventually look the same.
More Changes	Changes can also occur as a result of the intro. of exogenes (i.e. non-host) DNA. this is HORIZONTAL GENE TRANSFER. E.g. plasmid up take (antibiotic resistance) or mobilisation of transposable elements.
Hybridisation	Can cause genome changes as alleles from 1 spp move into another. Often this is in closely related spp. E.g. Mus musculus & Mus domesticus. This relies on recombination & synapse formation during chromosome pairing.
Transposable Elements	These are gene elements capable of moving from 1 loci to another. Often a copy is left behind, thus increasing their overall no. They also usually encode their own transposase enzyme. 2 Types: Retrotransposons & P-elements
Transposable Elements Type 1	RETROTRANSPOSONS - they leave a copy of themselves behind when they transpose. E.g. line elements in humans.
Transposable Elements Type 2	Some leave a copy behind, others don't. This is the most common type in bacteria. E.g. P-elements in Drosophila & IS-elements in E. coli.
Effects of Transposition	They can 'knock out' genes if a transposon lands in the middle & disrupts its function. E.g WHITE EYE MUTATION IN DROSOPHILA. Inversions/deletions/translocations can be caused by recombination on different chromosomes or different loci of same chromosomes or transposons. Recombination relies on the pairing of matching gene regions - if transposons provide these matches then they can interrupt the gene's function
Horizontal Gene Transfer	Virogenes are a strain thought to transfer horizontallu. There is a strain found in baboons which is very similar to cats.The 2 spp are very distantly related, so this is thought to have been caused by horizontal gene transfer. They are originally thought to have developed in viruses but are now incorporated in to 'host' genomes.
How Fast do Genomes Change?	The underlying rate of mutation is SLOW - few errors are inherited as most mutations are REPAIRED. Mutations that are not repaired are usually SELECTED AGAINST. But some evolution can occur over ecological (short) timeframes -> these are usually alterations in allele freq. rather than new alleles generated. This can = alterations in heterozygosity or allele loss.
Driving Factor of Genome Evolution	Mutation is the driving factor of genome evolution over evolutionary (long) timeframes. This can be change in genonme size and/or content. (Genome size = C-value)
Dynamism	Evolution & genome change is dynamic. E.g. snake venom can evolve back in to non-tocix compounds. Coevolution of genomes (e.g. endosymbionic bacteria) can occur too where selection acts on each independently. E.g. Bacteria in BOBTAIL SQUID gets a home in exchange for the squid getting a light source.
Pleiotropy	1 gene = many traits. This can limit the types of genetic changes that occur. E.g. MELANOCORTIN systems in OWLS is a series of genes which code for colour patterns and other traits such as immunity. Which is why often dark, wild vertebrates are often more aggressive, sexually active and more resistant to stress than other, lighter individuals.
Genome Adaptation	There is often more than 1 cause of adaptation. E.g. Lactose tolerance in humans is caused by a mutation in the lac operon gene around the same time as Dairy farming BOOMED! This was then selected for.
Why are genes relevant?	They tell us what we might expect genes to do. How fast and what. The help us interpret evolutionary patterns that we see today. We can see it by studying patterns in diversification and adaptation. BRING IN SPIDER EXAMPLES!
Spider Examples Which Illustrate the Use of Studying Genomes	1. G. cancriformis - there are 3 colour morphs in any population. Both males and females have the same dimorphisms which shows its not sexual selection, adaptation instead? 2. G. kuhli - similar spider spp but only has 2 colour morphs. Again not sexual selection. Perhaps not enough time has passed to evolve 3 dimorphisms & they are headed to convergence?
Genome Structure	DNA = highly coiled in to chromosomes. Nuclear chromosomes are linear & mitochondrial are circular. Nuclear DNA -> X&Y chromosomes determine sex in humans. In spiders they have no Y chromosomes & the no. of X chromosomes determines sex. Mitochondrial DNA is carried down the female line.
Genomic Changes	1. Single Nucleotide Polymorphisms (SNPs). 2. Chromosome Fusions & Rearrangements. 3. Chromosome inversion. 4. Gene Duplication & Pseudogene formation. 5. Hox Genes. 6. Silk Genes. 7. Duplication of Entire Genomes.
1. Single Nucleotide Polymorphisms (SNPs)	They may be synonymous & not change the protein sequence, but they may still not be equal. It leads to CODON BIAS. Overall synonymous (silent) base changes accumulate faster than non-synonymous because they are less likely to be favoured by NS. If the pop. is small NS is weak and mutations fix more easily. In larger pops. changes find it hard to persist. Mutations aren't always independent - 1 can lead to another. E.g. rRNA STEMS & LOOPS
Codon Bias	This is caused by SNPs. It is where not all codons are used equally. E.g. in C. cerevisiae, glutamic acid uses CTT rather than CTC. Selection tools tend to act against the use of the 'rare' codon (CTC) in highly expressed genes. This effect is weaker in rarely expressed genes. E.g. tRNA use is rare, not a problem and selected against in most genes, but it is not selected against in rare genes. So if these are promoted you get problems
1 Mutation -> 2nd Mutation: tRNA Example	tRNA has stems & loops, but compensatory changes only occur in stems, not loops due to the structure of the pairing of bases. So if a mutation occurs in a 'loop' the chance of fixation is greatly increased.
2. Chromosome Fusions & Rearrangements	Uncommon in mammals but common in RODENTS & v. common in plants. In shrews (SOREX spp) you can see evidence of where 2 bits of DNA have fused together. Is this a FUNCTION or a FAULT of their DNA repair system? It has been proposed that this method created the rearrangements of chromosomes in primates - this is a RARE thing though so has happened over a LONG evolutionary timescale.
3. Chromosome Inversion	E.g. The SEAWEED FLY has an inversion of a set of genes on one chromosome. The result is 2 types of male (large & small). This can't be reversed by recombination - the genes are inextricably linked. Does this lead to a change in female preference?

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