Why do we care about Phylogenies? – Flashcards
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Why do we care about phylogenies?
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-All biological relationships can be defined by constructing phylogenies.
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Phylogenies
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show genetic and evolutionary relationships among groups and individuals
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Sister taxa
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groups that share an immediate common ancestor
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pedigree
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depiction of relations within a population
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Parts of phylogeny: taxon
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The ends of each branch
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Parts of phylogeny: root
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beginning of phylogenetic tree
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Parts of phylogeny: node
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speciation event has occurred: where a new branch is created
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Parts of phylogeny: internal branch (internode)
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space in between different speciation events
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monophyletic
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clade consisting of ancestral taxa and ALL descendents
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Molecular clock
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phylogenies rely on the molecular clock--mutations (on average) occur at a given rate.
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If more mutational differences?
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species branched a long time ago
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If fewer mutational differences?
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species branched more recently
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Problems with molecular clock
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mutation rate can vary among species
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Parsimony
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uses discrete characters (like mutations or some trait)
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How to choose which tree is most parsimonious?
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Draw multiple trees, one with fewest character-state transition is most parsimonious
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Pros of Parsimony:
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-fastest and simplest method of phylogenetic reconstruction
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Cons of Parsimony:
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-May give misleading results if rates of evolution (mutation rate) differ in dif. lineages. -Beomes less accurate as genetic distance increases (only 4 nucleotides so will get same mutations occurring repeatedly)
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Distance Matrix
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calculate pairwise distances between taxa, chose tree that minimizes overall distances between taxa
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Distance Matrix in relation to parsimony
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Generally more accurate than parsimony, but is also very quick like parsimony
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Maximum Likelihood
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probability of data given a tree -has one true answer and one true tree (no drawing multiple and choosing the best one)
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Maximum likelihood and other methods
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More accurate than parsimony and distance matrix but requires much more computation -relies on accuracy of which mutations are more probable
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Bayesian inference
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probability of tree given data (opposite of maximum likelihood) -uses prior information, doesn't assume there is only one correct tree
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Bayesian inference and other methods
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more accurate than parsimony or distance (similar to likelihood) -more computationally intensive than parsimony or distance but less than maximum likelihood.
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Problems of phylogenetic reconstruction
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-Insufficient data: yields tree lacking resolution (lacks statistical power) -Evolutionary history of individual genes aren't necessarily the same (try to get data from many genes or whole genome)
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Sometimes the Molecular Clock (based on genetic data) conflicts with the Geological Record. Why would this happen? a) Sometimes there are gaps in the geological record, because fossils do not form everywhere, and mutation rate might vary between different species b) Radiometric dating relies on chance events in the preservation of isotopes, making the timing events in the geological time scale less accurate than the molecular clock c) Mutation rates slow down as you go back in time, making estimation of timing of events less accurate as you go back in time d) The molecular clock is calculated from radioisotopes, while the geological record is obtained from fossil data. The two can conflict when fossils end up displaced from their original sedimentary layer 52
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a) Sometimes there are gaps in the geological record, because fossils do not form everywhere, and mutation rate might vary between different species
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Which of the following is most TRUE regarding phylogenetic reconstructions? a) Phylogenetic reconstruction based on any gene would yield the same tree b) Parsimony is the most accurate method for reconstructing phylogenies c) Some DNA sequence data is better for phylogenetic reconstruction than others, such as those that tend to be less subjected to selection (3rd codon, introns) d) Maximum likelihood relies on maximizing distances among taxa
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c) Some DNA sequence data is better for phylogenetic reconstruction than others, such as those that tend to be less subjected to selection (3rd codon, introns)
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Which of the following types of data would be most optimal for constructing a phylogeny? a) Amino acid sequences b) Intron sequences within rapidly evolving genes c) Non-coding (and non-regulatory) sequences, or even better, whole genome sequences d) Genes that were introduced to the genome through horizontal gene transfer e) Genes that have undergone natural selection due to adaptation to different environments
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c) Non-coding (and non-regulatory) sequences, or even better, whole genome sequences
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Why would the type of data chosen in the question above be optimal for constructing phylogeny? a) Because we want the phylogeny to most accurately reflect patterns of adaptation to the environment b) Because we want the phylogeny to most accurately reflect patterns of protein evolution c) Because we want the phylogeny to most accurately reflect patterns of rapid genome evolution d) Because we want the phylogeny to most accurately reflect information from the pan genome e) Because we want the phylogeny to most accurately reflect neutral genetic relationships (based on the molecular clock) among organisms
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e) Because we want the phylogeny to most accurately reflect neutral genetic relationships (based on the molecular clock) among organisms
