Lecture 3 Tree of Life 1 Phylogenetic trees a Monophyletic groups share derived traits b DNA RNA amino acids are molecular data used for phylogenies 2 Molecular data for phylogenies a Dna mutates slowly and steadily b Different molecules change at different rates i Strongly selected don t mutate frequently Introns 3rd position DNA sequence not strongly selected Exonic DNA for amino acids strongly selected ii Looking at a quickly mutating things short period of time Repetitive sequences mutate easily DNA polymerase slips as it replicates mtDNA single stranded for a while during replication susceptible to mutation use it to examine the differences between closely related species iii Looking at slowly mutating things long period of change Look for strongly selected for Proteins critical to organismal function mutate slowly or not at all a Exonic DNA for central proteins b Histones c Ribosomal RNA Distantly related species if use faster will seem random i As sequences mutate and change they will eventually just be similar at random at that point can t use it for determining evolutionary relatedness c Change in mtDNA faster than change in nuclear DNA d Change in introns faster than nuclear DNA e 3rd codon faster than 1st or 2nd codon f Only 4 nucleotide bases 25 similar minimum g Lengths i 150 years dog breeds CA n repeats ii Chimps humans 6my mtDNA iii Rodents primates 100my nuclear DNA amino acids iv Flies mammals 1000my ribosomal RNA 3 To study common ancestor rRNA chosen very strongly selected molecule 4 Woese studied rRNA to find tree of life a Wanted to find eukaryote ancestor understand prokaryotic evolution determine ancestral gene families b Used rRNA because its critical for translating mRNA proteins i All organisms use so no lateral gene transfer ii Slow mutation rate iii Good molecular clock for deep evolutionary times c 16 18S rRNA i Different types or rRNA that were used to create Woese s tree of life ii Has unique aspects in secondary structure for each domain d Found 2 prokaryote domains archaea and bacteria e rRNA gave no temporal info cant tell what came first need additional info to find this out f MEMORIZE THIS TREE 5 Fossil record a Finding organisms earlier in fossil record implies they are the outgroup b Archaea lipids have ether linkage branched isoprene chains bacteria Eukarya have ester linkage i Can be dissolved from rocks and analyzed with mass spec Isoprene residues found thought to be 3 8byo archaea c d Fossil evidence of cyanobacteria 3 1 bya i Cyanobacteria leave behind layers from earlier bacterial colonies called stromatolites e This info not definitive enough to determine root of tree of life 6 Gene duplication theory a Gene A split into 2 copies of the same gene which mutated and evolved from there b Allows us to root the tree of life use genes that duplicated before domains diverged c Root of tree comes from using genes that duplicated before domains diverged where one of the duplicates serves as outgroup for the other 7 PROBLEM Co habiting archaeal and bacterial thermophiles a Large differences in rRNA genes but similar thermotolerant genes b i Used rRNA to show divergence but same genes in another location from lateral gene transfer i ii Vertical gene transfer transmission of DNA from parent to progeny Lateral gene transfer transmission of DNA between unrelated organisms c LUCA last universal common ancestor d rRNA tree assumes only vertical gene transfer and predicts LUCA i probably close to phylogeny of major lineages ii misses lateral transfer of some of key genes e LUCAC last universal common ancestral community i Assumes both VGT and LGT throughout history of life ii LGT involved genes offering selective advantage iii Pre LUCAC interacting community with tons of LGT very rapid evolution iv Post LUCAC divergence of distinct lineages with differing levels of LGT 8 Merging theory a Two domains of life merged to make eukarya through ring of life
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