BIOB 272 1st EditionLecture 15 Outline of Last Lecture Genome Sequencing and Physical MapsI. PolyploidyII. Diploid and Tetraploid HylaIII. Chromosome Structural Differencesa. Deletionb. Duplicationc. Inversionsi. Pericentric Inversionii. Paracentric Inversiond. TranslocationsIV. Chromosomal Variation Key Points:V. Genome Mapsi. Cytological Mapii. Genetic/linkage mapiii. Physical (sequence) Mapiv. Cytological MapsVI. Sequencing DNAa. Sanger SequencingThese notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.Outline of Current Lecture Phylogenies and Tree of LifeI. Comparison of Genetic Linkage and Physical MapsII. Complete Genome MapsIII. Genome Annotationa. Compare to Known Genesb. Predict GenesIV. Phylogenies and Tree of LifeV. Reconstructing PhylogenyVI. Monophyletic Group vs. Paraphyletic GroupVII. Reading a Phylogenetic Treea. Types of Trees:i. Unrootedii. Rootedb. Extant Speciesc. Taxonomic Units VIII. Phylogenetic Reconstructiona. Choosing Characters:b. Homologousc. Convergent Evolution- Analogous Characterd. How to Choose the Correct Phlylogenyi. Principle of Parsimony: Occam’s Razore. Other Phylogenetic Methodsi. Distance-Based Methodsii. Model-Based MethodsCurrent LecturePhylogenies and Tree of LifeI. Comparison of Genetic Linkage and Physical Mapso Genetic or Linkage map: linear arrangement of genes based on the analysis ofrecombination (crossing over) in crosses or pedigrees.o Physical (sequence) map: Genome map based on determining the linear sequence of DNA.o Linkage maps can be lined up with cytological maps of chromosome features and physical maps of the DNA sequence.o Recombination rate may vary across the genomeo A comparison of genetic and physical maps can be used to quantify variation in the average recombination rate between genomic regionso cM/MbII. Complete Genome Maps: Include info from genetic linkage, cytological, and physical sequence mapsIII. Genome Annotation: identifying what part of DNA corresponds to genes, etco Compare to Known Geneso Gene already described and sequenceo Expressed Sequence Tags (EST)- essentially randomly sequenced mRNAo Predict Geneso Computer predictionsIV. Phylogenies and Tree of Lifeo Darwin viewed evolution as a branching processo Phylogeny similar to family tree, except over a much deeper timelineo Phylogeny: branching diagram that represents a HYPOTHESIS on the evolutionary relationships among groups of organismsV. Reconstructing Phylogenyo Example using synapomorphies to group different mammals:o Give birth to live young? yes or noo Complex placenta?-Group accordinglyVI. Monophyletic Group vs. Paraphyletic Groupo Monophyletic group: all descendants share an exclusive common ancestor(synapomorphy)-all come from the most recent node. Share one of more derived characterso Paraphyletic group: contains some, but NOT all, descendants of the most recent common ancestor, and its definition is based on a derived character state that arose only onceVII. Reading a Phylogenetic Tree- can draw the same trees in multiple ways by rotating them on their nodeso Types of Trees:o Unrooted: can’t tell how closely species are related because they don’t have a rooto Rootedo Extant Species: no currently existing species is ancestral to any other- life is organized in a nested hierarchyo Taxonomic Units: only ok if they represent a MONOPHYLETIC clade **However some familiar groups and Linnean classifications are not monophyleticVIII. Phylogenetic Reconstructiono Choosing Characters: should be homologouso Homologous: similar because of shared ancestryo Convergent Evolution- Analogous Character- convergent evolution can cause apparent similarity of characters which are not homolous- i.e flyingo How to Choose the Correct Phlylogeny- tough because convergence is common?o Principle of Parsimony: Occam’s Razor: the simplest explanation is the best explanation- in the absence of other data, the optimal tree minimized the total number of evolutionary steps- relies on synapomorphies or shared-derived characterso Other Phylogenetic Methodso Distance-Based Methods: reconstrut phylogeny based on overall similarity (no emphasis on shared-derived characters)o Model-Based Methods: max likelihood and Bayesian inference, usually for DNA sequences-Genealogy: phylogeny estimated from an alignment of DNA sequences to establish homology-Substitutions in DNA sequences can create synapomorphies-Reversals (back mutations) can remove synapomorphies from genealogy -Parallel substitutions lead to convergent evolution in DNA
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