Exam 1 Material- Lecture 2~Tree Thinkingo Tree of Life Trees show ancestral relationships and provide context for evolution Kingdom, phylum, class, order, family, genus, species Darwin’s tree of life—taxa change along the branches Allow us to compare patterns across 3.8 BY history of life- Patterns reveal how organisms diverge, where/when new species evolvedo Anatomy of a Phylogeny Shows relationships through time Tips are the taxa being studied Internal nodes are inferred speciation events Clade is a group that shares a common ancestor F is the outgroup- Has the oldest common ancestor with otherso Cladistics—methods to estimate phylogenies Group organisms into clades Clade- includes an ancestral species and all of its descendants Shared traits result from shared ancestry which define the clade Descent with modificationevolution- Need to find shared derived characters Monophyletic- includes all of the descendants of its ancestors Paraphyletic- does not include all of the descendants of its ancestorso Building phylogenies using traits Originally used phenotypic traits to build traits- Number of bones, presence/absence of morphology But, these traits may have evolved through convergence, so not useful This is still used for fossilso Homoplasy- analogous structures that arose independently Wings of bat and bird use different bones, but similar structures Arose through separate processes which recruited different bones to support wing structure NOT HOMOLOGOUS BECAUSE NOT SIMILAR BY DESCENT Homologous- similarity due to shares descent/ancestry- Same ratio/proportions, so joins related organisms Homoplasy- similar but arose independently- “to mold in the same way”- does NOT inform us about relatednesso Builiding phylogenies using molecules (DNA, RNA, proteins) Genetic data may provide more unbiased means of building trees LATERAL GENE TRANSFER WILL FUCK THIS UP- Fucks up molecular phylogenies because genes are shared BECAUSE OF TRANSFER AND NOT ANCESTRY- Not similar by descent Molecules cannot provide trees representative of the species because genes can duplicate, evolve convergently and use same AA to do particular jobo Phylogenies are hypotheses Shows the evolutionary history of a species Display relationships as a branching phylogenetic tree Ideally, it can be determined if we have enough data A hypothesis based off of existing data o Cladograms vs. phylograms Cladogram shows branching order—no information from branch lengths Phylogram branch lengths are proportionate to similarity- Shows time that has passed- Horizontal lines show time that has passed- Vertical lines are for spacingo Tree misconceptions Reading the tips- Order of tips do not correlate with closeness of taxa- ****test question****- The further down the common ancestor between the taxa, themore distantly related they are Higher and lower organisms- NO higher and lower taxa Main and side tracks on tree- NO mainline and side tracks on a tree- Cannot draw straight line from bottom to top to show a progression or a pinnacle of evolution Relatedness vs. similarity- Similarity is not the same as relatedness- Example: crocodiles appear to be more similar to lizards, but are more closely related to birds Siblings vs. ancestors- Your sibling is your closest relative but you do not descend from your sibling, you share a common ancestor—your parento Trees need to be rooted to infer direction Assume change happens linearly across the tree- Root comes in the middle of the tree=midpoint root- Use fossil evidence to determine which common ancestors appeared first to help locate root Lecture 3~Information, codes and molecular treeso How do we determine the tree of life? Why do organisms need to store information?- Store information on how to interact/survive in their environmento Code for set of enzymes- Pass information from one generation/cell to another (improve their survival)o DNA/RNA- Need a genetic code to interpret information and convert it to enzymes- Information flow similar in most present day organismso Central dogma: DNARNAProteino DNA is a stable way to store information. It is carried byRNA and converted into proteins. Proteins do the enzymatic work in the system.- Genetic code is common to nearly all organisms w/only a few exceptionso Code is the universal common ancestoro We can use DNA sequences as a trait to build phylogenetic trees- Can use many kinds of molecular data such as DNA, RNA and amino acidso DNA mutates slowly and steadilyo The more similar two sequences, the more recently the two taxa had a common ancestoro mtDNA mutates easily because it is single stranded for along period of time during replication- Some sequences are not strongly selectedo Introns do not code for protein and so are not highly selected- Some sequences are very strongly selected to stay the sameo DNA that specifies amino acidso Certain proteins that are critical to organismal function Histones Ribosomal RNA- Because of this, difference sequences change at different rates- If a sequence changes too slowly, we can’t use it to compare closely related species- If comparing distantly related species, sequences that change too quickly will become randomly relatedo Three domains of life—Carl Woese Chose rRNA as his molecule of choice- Many critical domains that must fit together with other rRNA subunits and 50 different ribosomal proteinso High constraint so slow mutation rateo Good molecular clock for long evolutionary times- Critical for translating mRNA into proteino All organisms have it so no lateral gene transfer- Slow “tick” rate of rRNA molecular clock- 16/18S has characteristic secondary structure for three domains- Woese determined that there are two domains in prokaryotes, the bacteria and the archaea—these are just as different from each other as they are from eukaryotes- The root of the tree comes from using genes that duplicated before the three domains diverged where one of the duplicates serves as an outgroup for the other- Thermophiles- Vertical gene transer- the transmission of DNA from parent to progeny- Lateral gene transfer- the transmission of DNA between unrelated organisms Lecture 4~RNA Worldo Prebiotic Earth Chemicals formed in the ocean Increasing chemical complexity Oldest evidence of life is about 2.6 BY ago Microbial organisms as
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