11_Genes_Genomes.pdf

Lecture 11: Evolution of Genes and Genomes BIO 4083: Evolution Today’s Lecture Phylogenetic trees with alleles Lineage sorting and introgression Molecular phylogenies Evolution across genomes Phylogenies and phylogenetic trees Phylogeny: © 2020 W.H. Freeman and Company 3 Phylogenies and phylogenetic...

Lecture 11: Evolution of Genes and Genomes BIO 4083: Evolution Today’s Lecture Phylogenetic trees with alleles Lineage sorting and introgression Molecular phylogenies Evolution across genomes Phylogenies and phylogenetic trees Phylogeny: © 2020 W.H. Freeman and Company 3 Phylogenies and phylogenetic trees Phylogeny: Hypothesis of the evolutionary relationships among different taxa © 2020 W.H. Freeman and Company 4 Genetic loci have their own genealogies Trait: Genetic loci have their own genealogies Trait: Nucleotides (bases) Genetic loci have their own genealogies Trait: Nucleotides (bases) What kind of trait is the G à T? Genetic loci have their own genealogies Trait: Nucleotides (bases) What kind of trait is the G à T? Synapomorphy Sweet and Johnson 2015 Genetic loci have their own genealogy What are the Gs in Ts in genetic terms? Trait: Nucleotides (bases) What kind of trait is the G à T? Synapomorphy Genetic loci have their own genealogy What are the Gs in Ts in genetic terms? Alleles Homologous Trait: Nucleotides (bases) What kind of trait is the G à T? Synapomorphy Phylogenies can be studied at the allele level Paths of descent of 10 different alleles of BRCA1 over eight generations Note: (1) not all alleles are continuously transmitted to the next generation; (2) black and red lines show the phylogeny that includes the mutation from G g T at a locus of interest Alleles from different populations or species are used to construct phylogenies Tracking phylogenies back in time leads to nodes in gene trees that represent coalescence, or common ancestry Can also predict population bottlenecks or population expansions Positive selection can cause shallow coalescence Ideal locus? Neutral Gene trees vs. Species Trees Species Tree Phylogeny of a species Branching diagram depicting ancestor-descendent relationships of species Gene Tree Phylogeny of DNA sequence at a particular locus Branching diagram depicts geneology of alleles Gene Trees are often used to represent species trees, but they can be truly different Gene trees do not always match species trees Hebert et al. 2004. Jarvis et al. 2014 1 gene (cox1) Thousands of genes Jarvis bird tree: Not a single gene tree matched the species tree Erich Jarvis Thousands of genes Jarvis et al. 2014 Why don’t gene trees and species trees always match? Incomplete Lineage Sorting (ILS): when lineages of alleles do not “sort” consistent with lineages of species Allelic lineages are sorted into descendent species Species trees are more reliable when based on several unlinked genes Introgression Movement of alleles from one species or population to another Gante et al. 2016 Correct species trees are (sometimes) more likely to be generated by evaluating entire genomes Many genes/loci Concatenation Gene trees Multiple methods are generally used to estimate phylogenies Maximum parsimony Maximum likelihood Bayesian Distance Coalescent Networks Case study: Sponges or comb jellies the earliest diverging lineage in Metazoa? Nosenko et al. 2013 Sometimes it’s difficult to reconstruct relationships no matter what you throw at it Evolution across genomes Mutations may have different effects on fitness Synonymous (silent) mutation: does not alter the amino acid sequence of the protein Often selectively neutral Nonsynonymous mutation: alters the amino acid sequence of the protein More likely to be subject to selection Selection acts on the phenotype A substitution is a mutation that becomes fixed in a lineage Neutral theory of molecular evolution Motoo Kimura (1968): most evolution at the molecular level is neutral (due to drift) Neutral mutations become fixed (i.e., substitutions) in lineages at a regular, clocklike rate Neutral theory of molecular evolution Motoo Kimura (1968): most evolution at the molecular level is neutral (due to drift) Neutral mutations become fixed in lineages at a regular, clocklike rate Rate of molecular evolution: not necessarily the same as mutation rate Different types of DNA segments evolve at different rates Different types of DNA segments evolve at different rates in different types of organisms 4-fold degenerate sites m = mitochondrial n = nuclear c = chloroplast Lynch and Blanchard. 1998. We’ve been mostly talking about neutral mutations. What about selection? Detecting selection on DNA sequences Synonymous substitutions: do not change protein Should evolve at a neutral rate Nonsynonymous substitutions: change protein Faster evolution than synonymous sites indicates positive selection Slower evolution than synonymous sites indicates purifying selection dN/dS ratio (also known as Ka/Ks ratio) Signature of positive selection ACT ACC GCC Nonsynonymous vs. synonymous substitutions in the BRCA1 gene More similar ratios to immune genes Why? Host-virus ”arms race” Could BRCA genes be involved with viruses? Footprints of selection across a genome Alleles can spread quickly through populations when subjected to strong natural selection Selective sweep: adaptive allele spreads through a population more quickly than recombination acts to separate it from neighboring alleles Genetic hitchhiking: strongly selected alleles are frequently found in a population surrounded by the same set of alleles at neighboring locations Strong natural selection leaves a signature in neighboring alleles Selective sweeps and genetic hitchhiking in maize Tian et al. 2009 Selective sweeps and genetic hitchhiking in African malaria vector Barnes et al. 2017 James Gathany Evolution of genome size Genome size varies tremendously Bacterial genome size dependent mainly on number of genes Eukaryotic genomes vary more in size due to noncoding DNA Genome size varies tremendously Lynch 2010 Evolution of genome size seems connected to mutation rate Opposite directions in viruses/prokaryotes compared to eukaryotes Lynch 2010 In turn, mutation rate seems related to effective population size Why? Does genetic drift limit lower mutation rates? Remember, evolution does not perfect organisms (or genes!) What is another explanation? Adaptive potential Lynch et al. 2016 Bacterial symbionts often experience a reduction in genome size Muller’s Ratchet: accumulation of deleterious mutations due to lack of recombination Mitochondrial genomes in animals are usually highly conserved Mitochondrial genomes in animals are usually highly conserved But some are very different! Assignments Paper Reflection and Discussion on Friday