BIO 370 1st EditionExam # 3 Study Guide Lectures: 15 - 19Molecular Evolution I: Mutations & Selection (Lecture #15)- Informational macromolecules led to the understanding of what?o Relationships among lifeformso Fate of alleles in populationso Genetic basis of phenotypic variationo How new traits/species originate- What encompasses the informational macromolecules?o Proteinso Nucleic acid- Is it generally correct to assume that organisms with more phenotypic similarity are more genetically similar?o Yeso Assumption that morphological variation has genetic basis.o DNA sequences of similar looking organisms similar because of divergence from amore recent common ancestor.o Organisms accumulate genetic mutations over time.- What is the ultimate source of all genetic variation?o Mutations Also one of the fundamental forces of evolution Only those that are heritable Germline (sperm and eggs) not somatic mutationso Definition A change in nucleotide sequence of a genomeo Characteristics of mutation Random Undirected Not equal likeliness- Know the types of mutations.o Point Substitutions Insertions Deletions Transitions and transversionso Chromosomal alterations Inversions Duplications Translocations Deletions Polyploidy Aneuploidyo Whole genome duplicationso New DNA obtained Transposable elements Foreign sequences- Significance of Hermann Joseph Mullero Won Nobel prize in physiology/medicineo University of Texas graduateo Discovered X-ray induction of mutations Gave early evidence for nature of hereditary materialo Also researched: Evolutionary importance of mutations  Evolutionary advantages of genetic recombination Model for genetic isolation during speciation Public awareness of the danger of radiation- What is a homolog?o Genes in a common ancestor that have been passed down- Know when and how mutations occur.o DNA damageo Replication errorso Recombination processes- Review all about point mutations/base substitutions.Molecular Evolution II: Divergence & Rates (Lecture #16)- Be able to answer these questions:o How frequent are mutations?o What is the rate of mutations?o How often are errors made during replication of DNA?o What is the chance that a nucleotide will mutate?o How can you measure mutation rates?- If mutations occur randomly, why would mutation rates vary over genes?o Target sizeo Paternityo Penetranceo Phenocopies- What is the overall average mutation rate?o 10^-5 per gene copy per generation- How do you measure mutation rates today?o Determine full genome sequence of parent and offspringo Count the number of new point mutation in the offspring- When using sequences to study evolutionary processes what are the issues that need to be considered?o Rates and patterns of molecular evolution within geneso Multiple hits and saturationo Molecular clocks- What occurs when a new mutation arises?o Most removed by natural selection because most are bad.o Rare beneficial mutations provide for evolutionary changeo Unusual kinds of selection maintain variation/polymorphism- Know about the selectionist view- Know about the neutralist view.- Be able to determine how often different kinds of substitutions occur.- Be extra sure to know the difference between a mutation and a substitution.- Know the definition of:o Synonymous substitutiono Nonsynonymous substitutiono Be able to recognize all details from these topics.- Identify the Ka/Ks relationship of the following:o Purifying selectiono Positive selectiono Neutral evolution- Differentiate positive from negative selection.- What are way to detect adaptive evolution?o Test based on linkage disequilibriumo Examine genome for region of depressed polymorphism- What does the MacDonald-Kreitman Test examine?o Detection of positive selection acting on protein-coding regionso Compares the number of nonsynonymous and synonymous substitutions within species to its divergent changes between species- Answer these questions:o Can evolution occur if there is no genetic variation? No.o Can selection occur without evolution? Sure.o Can evolution occur without natural selection? Sure.- Know all about random genetic drift.- At what percent difference do sites reach saturation?o Variable- At what percentage of sites would random DNA sequences match?o 25%- Which genomic sites or regions would be expected to reach saturation first?o Coding DNA befire non-coding DNAo Introns before exonso Synonymous sites before nonsynonymous oneso Transitions before transversions- What does the molecular clock assume?o That evolutionary rates are: Constant over time Constant in different groups of organisms- Know about the relative rate test.Phylogenetics I: Estimation & Inference (Lecture #17)- What is phylogenetics?o Tree-like depiction of evolutionary relationship of specieso Framework for testing of biological hypotheses- How do Darwin realize it could be possible to place organisms into groups?o Based on Relationship to one another Common ancestor- Know micro vs. macroevolutionary processes.- Know that classification schemes are subjective.- What is the classification of humans?o Kingdom – Animaliao Phylum – Chordatao Class – Mammaliao Order – Primateso Family – Hominidaeo Genus – Homoo Species – sapiens- All organisms are a mosaic of what?o Ancestralo Derived characters- Know definitions of:o Tree/phylogeny/cladogramo Clade/monophyletic groupo Paraphyletic o Topologyo Rooto Sister group o Polytomyo Synapomorphyo Symplesiomorphyo Parsimony Phylogenetics II: Applications (Lecture #18)- Be informed of the phylogenetic approaches.o Including distance approaches- Be able to deduce how to measure tree length.- Know about Woese and his molecular phylogenetic approach.o 16S ribosomal RNA- Characteristics of molecule to be used.o Universally conservedo Slow evolutiono Heritabilityo Easy isolation- How to prove which taxa is correct?o Look at which taxon I most distantly relatedo Use and outgoup- What can serve as an outgroup for all lifeforms?o Gene phylogeny not an organismal one- Know about the rooting phylogenies using a duplicate gene as the outgroup.- Which were the first cellular organisms?o Bacteria- Study the latest view of classification at the highest taxonomic level.- Know the definition of:o Long branch attractiono Homoplasyo Homology o Convergenceo Parallelismo Incomplete lineage sortingGenome Evolution (Lecture #19)- What is a genome?o The totality of