BIOB 272 1st Edition Lecture 25Outline of Last Lecture Molecular Evolution and Genealogies I. DNA Sequence VariationII. Neutral Theory of Molecular Evolution- Rate of Genetic Change- Applications of the neutral theory- Molecular Clocks RequireIII. Mammalian Diversification ExampleIV. Coalescent and Gene TreeOutline of Current Lecture Coalescent and GenealogiesI. Coalescence and Gene TreeII. Mitochondrial DNAIII. Effects Differing Coalescence Time For Different Genesa. On Selectioni. Directional Selectionii. Balancing Selectionb. Gene Trees don’t Always match Species TreesCurrent LectureThese notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.Coalescent and GenealogiesI. Coalescence and Gene Tree– Individual genetic loci (genes) have their own phylogeny =genealogy that dates back to a MRCA (most recent common ancestor)– Coalescent: is a stochasticprocess that relates theprobability of shared ancestryin a collection of individuals (orgenes, or alleles) sampledfrom agiven population.– Gene Tree: the branched genealogical lineage of homologous alleles that traces their evolution back to a single ancestral allele.– **allels in population coalesce to a common ancestor– Eventually all lineages coalesce to a single lineage=MRCA of the sample– Rate in which lineages coalesce depends on the size of the populationo Larger the population (more parents to choose from) the slower the rate= big population (Ne) have deep coalescent timeso The coalescent times to MRCA vary across the geneomeo Average time to MRCA is 4Ne generation = much of this variation is stochastic and essentially due to the same random sampling process that leads to genetic drifClicker Question:What is the average time to MRCA across genes in human populations?A) 5,000 years B) 100,000 years C) 800,000 years D) 3,000,000 yearsanswer: C) 800,000 = 4*10,000*20-20 years per generation-Long term Ne in humans is about 10,000 -4 is from average time to MRCA is 4Ne– Average coalescence time also varies for different subsets of the genome- mtDNA, chromosomal DNA, higher for autosomal DNA, X and Y genes, 3 X chromosomes per 4 autosomes, 1 Y chromosome per 1 autosomeII. Mitochondrial DNA– In humans is about 16 kb and encodes just 13 genes- all necessary for oxidative phosphorylation– Haploid: circular DNA molecule derived from bacterial endosymbiont– Maternally inherited– Little or no recombination– Used to help determine out-of-Africa migration (talked about later in semester)- Africa has deepest MRCA to about 136Ko Does not imply that all humansdescend from a single individual inAfrica 136K ago – just that all mtDNAdescend from an ancestral copy thatexisted at this time.III. Effects Differing Coalescence Time For Different Genesa. On Selection– Directional Selection- reduces diversity, leading to shallow genealogies and rapid calescence– Balancing Selection (maintains diversity) : long term balancing selection can lead to maintenance of genetic diversity over deep evolutionary timescaleso More common at genes involved in aspects of immunity and defense against pathogens i.e. MHC-class II = diversity is SUPER old=helps in preventing disease- inbreeding decreases this diversity so one reason why disease more prevalent in breeding casesb. Gene Trees don’t Always match Species Trees– Gene trees don not always match evolutionary history of populations orthe species treeo Lots of independent (unlinked) genes needed to infer the evolutionary history of populations/species.o Only about 70% genome suggest that humans and chimps are each other’s closest
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