Interpreting Phylogenetic Trees o Phylogenetic analysis inference of patterns of evolutionary relationships shared ancestors based on distributions of character states in the organisms being studied o How to infer create a tree Variation in generations is due to mutations which are chosen by natural DNA sequencing errors are mutations that are sometimes passed on to the selection when favorable next generation o How to read a tree visual display of relationships among organisms share a most recent common ancestor at closet node Sister lineages Branches can be rotated without changing relationships Outgroup can vary depending on focus of tree Trees can be chronological but usually all groups at the tips of the tree have had the same amount of evolutionary history Longest branch is not first in history Trees are relative and do not show all species A living species cannot be primitive but it can have primitive characteristics character states which are relative to which group of species is being studied Living organisms are mosaics of primitive and derived traits Derived traits first original common ancestor of group being studied newly arisen character states that were not present in o Ex platypus egg laying is primitive trait bill is derived trait Character mapping helps to trace evolution of traits overtime so that we can see where traits first arose in evolutionary time o Ex wings in insects and in flightless birds due to continental drift for some species but for others this trait arose three separate times based on DNA evidence Applications of Phylogeny o Conservation Biology Which groups we should protect translocate and replenish Application of de extinction must piece together ancient DNA find a close relative and re create genome o Epidemiology Tracing pathogen pathways Ex HIV sex or drug use Ex MRSA infections in neonatal babies from nurses o Phylomemetics phylogenetic analysis of non genetic elements that replicate with errors Similar languages and folktales around the world show common ancestry Ex little red riding hood o Forensics crime investigations Genetic Code o DNA and RNA are responsible for structure and function of organisms Nucleotide sequence amino acid sequence proteins Proteins make up and do most things in an organism DNA goes through transcription RNA goes through translation Polypeptides make up proteins o Information is heritable Using DNA RNA and amino acid sequences to infer phylogeny o Genetic code is universal to all domains of life which is evidence of common Two codes more similar more recent common ancestor ancestry o DNA confirms morphology o Rate of change depends on random Mutation rate Some sequences mutate quickly o Repetitive sequences STRs DNA polymerase slips as it replicates transcribes these regions o Mitochondrial DNA mtDNA mtDNA is haploid so there is a smaller effective population size weaker stabilizing selection faster evolution of mtDNA sequences Also is copied faster with less proof reading Natural selection non random Stronger in large populations Acts on protein sequences Some sequences are not strongly selected for o Introns do not code for protein and are usually removed during splicing so are not highly selected o 3 rd position of DNA codon usually do not change amino acid created so are not highly selected Some sequences are strongly selected to stay the same o DNA that specifies different amino acids 1st or 2nd position in codon o Critical sensitive proteins Histones and rRNA Genetic drift random due to sampling Stronger in small populations Result of balance between mutation and selection is that different sequences change at different rates Repeated sequences fastest change mtDNA nuclear DNA Introns coding sequence 3rd position of codon 1st or 2nd position of codon highly constrained genes slowest change In relation to phylogeny When comparing closely related species you need enough changes so that there are differences to compare need fast changing molecule When comparing distantly related species you need to make sure relationships are not random need slow changing molecule because sequences that change too quickly can cause random relationships DNA only has 4 bases so by chance sequences are likely to become more similar overtime Three Domains of Life o There are not many morphological characters that distinguish species o Woese study Goals of study Identify the eukaryote ancestor Understand prokaryotic evolution Determine the ancestral gene families Investigated 16 18S rRNA because It has many subunits It has a high constraint rate so the mutation rate is slow It is critical for translating mRNA into proteins It provided long sequences to compare sites Conclusions 16 18S rRNA has characteristic secondary structure for all three domains Discovered Archaea domain o Archaea Extremophiles environments salt ponds live in extreme environments scalding water acidic o How did they root the tree for all three domains Root of a phylogenetic tree is determined by the outgroup Studied species are considered the ingroup The branch where the outgroup connects to the ingroup becomes the root of the ingroup tree Iwabe et al study Used duplicated genes to establish tree of life o If gene duplicated before the three domains of life arose you can use one copy of gene to serve as the root for the other copy Genome sequencing of co habiting archaeal and bacterial thermophiles There are large sequence differences in rRNA genes between these two There are small differences in common thermotolerance genes between groups these two groups Conclusion o There are different means of gene transfer that account for the rRNA differences Vertical gene transfer parent to progeny heredity unrelated organisms viruses Lateral gene transfer the transmission of DNA from the transmission of DNA between o Archaea are more closely related to Eukarya than Bacteria After all of this research there are two proposed models for a universal tree of life 1 2 Whole genome model assumes vertical gene transfer predicts last rRNA sequence model universal common ancestor LUCA closest to true phylogeny operate through history of life Lateral gene transfer involves physiological and metabolic genes assumes vertical and lateral gene transfer that have a selective advantage Pre LUCA community interacting community of self replicating organisms with a lot of lateral gene transfer rapid evolution Post LUCA community divergence of distinct lineages with differing levels of
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