What is interference?
Evolutionary Bio Test 3 Week 5 This set of notes includes everything Dr. Sears covered in class plus all of the vocabulary and major notes from the textbook from this week. 4/5 Next Tuesday is the last lecture with new material; next Thursday will be review for the exam What to know from chapter 19 How flu evolves in response to the human immune systems. Note how the comparative method is used Evolution of antibiotic resistance How virulence evolves How tissues can evolve as populations of cells Examples of selective thinking applied to humans (myopia, breast cancer, obesity) Example of fever Make sure that you have read through these examples and Eric can go over questions regarding these in the review session Understand the concepts more than the details. You should be able to reason through an answer to any questions on an exam Genome evolution and the molecular basis of adaptation Why so big Genome architecture can be viewed as a phenotype that is shaped by evolution How big or small in terms of DNA bases Mobile genetic elements mobile genetic elements are genomic parasites. They spread with genomes, sometimes with deleterious consequences for their host Evolutionary impact of mobile genetic elements Nematode example some mutant lineages had excessive transposon activity because – their innate RNA interference mechanism was broken. The evolutionary origin of defenses against mobile elements when traits are evolutionarily conserved, meaning the rate and its molecular machinery are broadly similar among organisms that are distantly related, we can infer that they were likely present in their common ancestor Mobile elements can affect phenotypes tomato example The evolution of mutation rates Can mutation rate evolve to become higher or lower Bacteria example bacteria evolve higher mutation rates in the presence of a harmful bacteriophage virus Quiz vocab Senescence/aging Rate of living theory of senescence Evolution theory of senescence Antagonistic pleiotropy Ecological mortality Beneficial pleiotropy Good chance there will be a quiz on Thursday as well…. 4/7 Gene duplication and gene families duplication is the primary source of new genes Can occur as a consequence of wholegenome duplication (polyploidization) Or in much smaller sections of the genome, by a process called segmental duplication Cone snail example Garter snake example sodium channel gene Stickleback example marine fish have spines and armor, freshwater fish have none; if a population from the ocean is suddenly dropped in a lake, after ~50 years the population will no longer have spines and armor Mechanisms of speciation How many species are there What is a species organisms who will breed when they encounter each other in nature, can exchange genes“independently evolving metapopulation lines” Dr. Sears Species consist of interbreeding populations that evolve independently of other populations Morphospecies (phonetic) species concept: species based on morphological similarities and differences (you can tell the difference a lot of the time) Phylogenetic species concept: monophyletic groups define species Biological species concept: reproductive isolation defines species Morphospecies easy to apply, also easy to misapply problems when 1 species mimics another Biological species concept easy to apply, reproductive isolation confirms lack of gene flow problems with asexual species hybrids, etc. (ligers, etc.) Reliable criteria for identifying species are essential for preserving biodiversity Tuesday talk about isolating mechanisms, chapters for exam on syllabus understand the first three chapters, last two only have smaller parts Textbook Vocab Ch. 14 Antigenic sites the specific parts of a foreign protein that the immune system recognizes and remembers Clade (context: nucleoprotein phylogeny) a set of strains derived from a particular common ancestor Antibiotics chemicals that kill bacteria by disrupting biochemical processes 3 general models of to explain the evolution of virulence 1 the coincidental evolution hypothesis the virulence of many pathogens in humans may not be a target of selection itself, but rather an accidental byproduct of selection on other traits. 2 the shortsighted evolution process because pathogens g through so many generations in an individual host, traits that enhance the withinhost fitness of pathogen strains may rise to high frequency even if they are detrimental to the pathogens ability to transmit to new hosts 3 the tradeoff hypothesis biologists traditionally believed that all pathogen populations would evolve toward everlower virulence Ch. 15 Genome architecture the structure and organization of the information encoded within Cvalue paradox the CValue of a cell is the total amount of DNA found inside. The puzzle of some less complicated organisms having significantly more basepairs than more complicated ones (ex: Japanese canopy plant has 180 million bp, humans have 3.2 million bp). Explained by 2 phenomena whole genome duplications resulting in polyploidy, and the existence of large portions of an organism’s genome that are largely functionless from the cell’s viewpoint Mobile genetic elements replicate and insert themselves in an organism’s genome by hijacking the same cellular machinery that replicates and transcribes proteincoding sequence of DNA Intergenic the space between protein coding genes Transposons mobile elements that require only the sequences needed to move from one location to another Retrotransposonstransposons that leave behind a copy of themselves Posttranscriptional sequencing after mobile elements are transcribed into RNA, the RNA molecules are targeted and destroyed Pretranscriptional silencing the attached methyl groups prevent DNA from being transcribed into RNA in the first place Evolutionarily conserved the trait and its molecular machinery are broadly similar among organisms that are distantly related Segmental duplication this can copy a single complete gene, a piece of a gene, or a stretch of DNA that contains several genes Neofunctionalization a model in which the gene copy that mutates from the original acquires an entirely new function that by chance benefits the organism Subfunctionalization a model in which the ancestral gene has two different functions Adaptive constraint multiple functions or phenotypes cannot both be optimized at the same time: A gene cannot get any better at performing action A without getting worse at performing action B Escape from adaptive conflict when an adaptive constraint is present for a gene that performs multiple functions , this gene model says gene duplication provides a pathway by which each of two genes can become specialized to a single function, and in the end both functions are performed better Adaptation from new mutation if the alleles that encode a novel adaptive phenotype appear after a new selective challenge arises Adaptation from standing genetic variation when the alleles that encode a novel adaptive phenotype were present in the population before the novel selection challenge arose