Evolution ~Trees 3

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Monophyletic

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– contains all the descendants of a common ancestor

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Paraphyletic

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– contains some, but not all, the descendants of a common ancestor (e.g., Reptilia)

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Polyphyletic

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– a group that consists of unrelated lineages, each more closely related to other
species not placed in the taxon

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Maximum likelihood

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– maximizes the probability of achieving the data

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Genetic distances

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– generally includes phenetic methods

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3 types of genomes

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-nuclear, mitochondrial, and chloroplast data

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nuclear genome

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-bi-parentally inherited- 30-45 thousand genes, 2 alleles, crossover mixes chromosomes which can mess up phylogenetic trees, genes that code for protein (which are under selection because they are an expressed physically), introns are not under natural selection because they are not physically expressed-may still evolve due to things like genetic drift, multiple codons code for amino acids (often condons with different 3rd position often code for the same protein-3rd codon would not be under natural selection but the first 2 would)-different parts of the genome are evolving at different rates due to different natural selection constraints

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mitochondrial and chloroplast genomes

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- from one parent- mammalian mitochondrial DNA comes from mother as a function of fertilization (meiosis produces egg that dumps chromosomes and has 23 haploid chromosomes and organelles, sperm is little more than 23 chromosomes with just a little mitochondria to power flagella)-repair mechanisms during mitosis better in nuclear dna so end up with more mutations in mitochondria and chloroplast dna (if looking at coding data-noncoding nuclear dna might have more mutations due to lack of selection)

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need to pick a gene that is right for what you are studying

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~if you want to look at real old relationships need to choose conservative gene that doesn’t evolve very fast
~if looking at recent changes a fast evolving gene would be better so it shows changes

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Molecular clocks

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work on the fact that mutations accumulate at a certain rate

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how do you set a molecular clock?

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-varies depending on taxa, mutations accumulate faster in organisms with faster metabolism
--almost always set with the fossil record- (see paper notes )

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problems with molecular clocks

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-do you even have a fossil, is your fossil actually related, and if it is how do you know at which point in evolution and time it is from
-calibration is problematic
-mutations don’t accumulate at a consistent rate-sometimes in a new environment a lot of selective pressure occurs in a short period of time
-need to calibrate each gene
-we use them, they have problems and big error bars that need to be bracketed-molecular clocks from recent past aren’t very useful but at large time scales are better-when you read about molecular clocks see how they calibrated it and take it with a grain of salt

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Synapomorphy

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– shared, derived character (e.g., fur and lactation in mammals)

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outgroup

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used to represent common ancestor (plethedon salamanders the ingroup and outgroup should be truly outside that group and a closely related organism-ideal to choose multiple outgroups)