L22 Genome Evolution 15 (1)

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<ul><li><p>rDNA structure </p><p> The role of the IGS in the rDNA is mostly unknown"</p></li><li><p>Phylogenetic footprinting identi!ed noncoding promoter </p></li><li><p>Characterisation of the noncoding promoter </p><p>Kobayashi &amp; Ganley, 2005 Science 309: 1581-1584</p><p>rDNA copy number usually recovers if some are deleted </p><p>The noncoding IGS promoter is required </p><p>for this rDNA amplification </p></li><li><p>Detecting positive selection We will look at three methods for detecting </p><p>positive selection:" More non-synonymous than synonymous </p><p>mutations (Dn/Ds ratio)" Phylogenetic Dn/Ds ratio" Selective sweeps"</p></li><li><p>dN/dS ratio redux The reverse logic for the dN/dS ratio can be </p><p>used to find evidence for positive selection" Under positive selection, you expect more </p><p>non-synonymous mutations than synonymous mutations!</p><p> Therefore a dN/dS ratio of greater than 1 suggests positive selection"</p></li><li><p>Example: heterochromatin protein 1 variant </p><p> Looking at a protein called heterochromatin protein 1 (HP1), which functions in specifying heterochromatin"</p><p> In Drosophila melanogaster there there are five HP1 paralogs"</p><p> Found that one (HP1-rhino) showed evidence of evolving via positive selective"</p><p> Suggests its involved in some aspect of adaptation"</p></li><li><p>Example: HP1_rhino protein </p><p>Other HP1 paralogs are evolving under negative selection, but the HP1-rhino shows a high dN/dS ratio"</p><p>Vermaack et al, 2005. PLoS Genetics 1: e9</p></li><li><p>Limitations of dN/dS for positive selection </p><p> Similar to those for the dN/dS ratio with negative selection"</p><p> Only works on protein-coding regions of the genome"</p><p> Has limited sensitivity typically only a few sites are undergoing positive selection"</p><p> Need to take bias in mutations into account"</p></li><li><p>Phylogenetic dN/dS ratio The dN/dS ratio averages over all evolution </p><p>that has occurred between species" However, the positive selection may have </p><p>only occurred during one part of the evolutionary history difficult to detect"</p><p> Therefore, phylogenetic approaches are used to estimate the dN/dS ratios on each branch of a phylogenetic tree"</p></li><li><p>Lineage-speci!c dN/dS Maybe positive selection only occurred in this gene at this point in time?"</p></li><li><p>Ancestral state reconstruction </p><p>By recreating the ancestral sequences, we can now compare dN/dS at each point in the phylogeny"</p></li><li><p>Limitations of phylogenetic dN/dS for positive selection </p><p> Similar to those for the simple dN/dS ratio " In addition, ancestral state reconstruction is </p><p>not simple, and the dN/dS relies on it being accurate, which it might not be"</p></li><li><p>Selective sweeps When a mutation is selected, it will take </p><p>along neighbouring SNPs that are linked" This is called a selective sweep, and the </p><p>the neighbouring SNPs are said to hitchhike along with the positively selected mutation"</p><p> The extent of DNA that hitchhikes along with the selected mutation is governed by meiotic recombination"</p></li><li><p> Involves the adaptive allele sweeping to fixation in the population"</p><p> Normally, this happens on an ongoing basis"</p></li><li><p>Selective sweeps Positive selection for green mutation </p><p>Neutral evolution and selection against red mutations </p></li><li><p>Selective sweeps Results in a signature of decreased genetic variation around the positively-selected mutation </p></li><li><p>Detecting selective sweeps Selective sweeps can be detected by </p><p>scanning the genome in a population for regions of low polymorphism/high linkage disequilibrium"</p><p> However, limitations arise because other factors can also result in this pattern"</p><p> In particular, variation in the rate of meiotic recombination across the genome can cause dramatic differences in the level of linkage disequilibrium "</p></li><li><p>Horizontal gene transfer One unusual way a genome can evolve is </p><p>by picking up bits from other species genomes"</p><p> Known as horizontal gene transfer (HGT) exchange of genetic material between non parent-offspring individuals"</p><p> HGT is very common in bacteria they seem to swap parts of their genome with abandon but is much more controversial in eukaryote evolution "</p></li><li><p>Horizontal gene transfer </p></li><li><p>Horizontal gene transfer Soucy et al, 2015 Nature Reviews Genetics 16: 472-482</p></li><li><p>Mitochondria/chloroplasts Mitochondria and chloroplasts are examples </p><p>of HGT" They are bacterial endosymbionts of </p><p>eukaryote cells" In both cases many genes have been </p><p>horizontally transferred from mitochondria and chloroplasts into the nuclear genome"</p><p> Because of the endosymbiotic relationship, these are considered special cases"</p></li><li><p>Detecting HGT The gold standard for detecting HGT is </p><p>phylogenetic incongruence" When the phylogenetic tree for a region of </p><p>the genome disagrees with the established species phylogeny"</p><p> Such incongruence is consistent with that region having been horizontally transferred"</p><p> However, other explanations are possible: e.g. frequent gene gains/losses, or rapid evolution of a gene in one lineage"</p></li><li><p> Urochordates (tunicates) are marine invertebrates with notochords (sea squirts, etc)"</p><p> Only animals known to have cellulose"</p><p> The gene encoding cellulose synthase in Ciona (a model urochordate) groups with bacteria cellulose synthases, and not with eukaryote enzymes"</p><p> Suggests the gene was horizontally transferred from bacteria into urochordates"</p></li><li><p>Care is needed The original paper describing the human </p><p>genome in 2001 found 113 genes that are likely to have been horizontally transferred to vertebrates from bacteria"</p><p> Based on BLAST searches where the closest match outside of vertebrates was a bacterial gene"</p></li><li><p>A more careful phylogenetic analysis showed a variety of eukaryotes orthologs, thus none of these are HGT examples"</p></li><li><p> A gene that is evolving quickly in one lineage but not others will show up as a long branch in a phylogenetic tree"</p><p>Long branch problems </p><p>http://mesquiteproject.org/mesquite1.0/Mesquite_Folder/docs/mesquite/studies/study002/index.html</p></li><li><p> These often falsely group together in phylogenetic trees, or otherwise end up in weird places"</p><p>Long branch problems </p></li><li><p> Problems like long branches mean simple phylogenetic incongruence can be misleading"</p><p> Therefore, convincing evidence for HGT: the HGT recipient lineages nest within the donor lineages, to the exclusion of other lineages related to the recipient lineages"</p><p>Nested phylogenetic incongruence: gold standard! </p></li><li><p> This pattern could result from a variety of causes, including, but not limited to, HGT"</p><p>Simple incongruence is not enough </p><p>Gene X species phylogeny</p></li><li><p>Chou</p><p> et al, 20</p><p>15 </p><p>Nature 5</p><p>18: 98</p><p>- Shows transfers of antimicrobial genes from bacteria into water fleas and ticks"</p><p> Genes are functional in their eukaryotic hosts, protecting against bacterial infection"</p><p>HGT from bacteria to eukaryotes </p></li><li><p> HGT of genes involved in breakdown of seaweed cell walls from algal parasites to human gut microbes"</p><p> So far, only found in Japanese people, giving them a unique ability to use seaweed as a food source!"</p><p> Placental syncytin genes came from HGT of viral genes into mammals"</p><p>Final cool examples </p></li></ul>