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Midterm II Lecture Summary.docx

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BIOL 359
Jonathan Witt

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BIOL359 – Evolution Winter 2013 Topic 7: Phylogeny - Phylogenetics: The study of ancestor descendent relationships, goal of studying is to construct phylogenies o Phylogenetic tree: A graphical summary of a phylogeny - Phylogeny: A hypothesis of ancestor descendent relationships o Based on morphological, physiological, molecular data or all three o Today: DNA sequence data (Rapid evolving genes - Recent vs. Slower evolving genes - Overall) o Phylogeny is constructed based on phylogenetic characters  Phylogenetic characters: Attribute of an organism that can provide us with insights to history  E.g. Nucleotide positions in molecular phylogenies o Each position possess 4 character states: A, C, G, or T  Cladistic character state  Plesiomorphy: The ancestral character state  Apomorphy: Derived state, a character state different than the ancestral state o Synapomorphy: Derived character state SHARED by 2+ taxa due to inheritance from a common ancestor  Phylogenetically informative, identifies monophyletic groups (Homology)  E.g. Fur & lactations by mammals o Autapomorphy: Uniquely derived character state possessed by one lineage only  No insight - Phylogeny and Taxonomy: o Monophyletic/Clades: Group with ALL of the descendent of a single common ancestor o Non-Monophyletic:  Paraphyletic: Group contains some but NOT ALL of the descendent of a common ancestor (e.g. Reptiles, fish, prokaryotes, dicots)  Polyphyletic: Taxa that have been erroneously grouped on the basis of homoplasious characters (E.g. vultures)  Homoplasy: 3 methods of independent evolution of a shared character (different ancestor) o Parallel evolution: Same features evolved from the same ancestral condition independently  3 spine stickle back, different ancestor stickle backs colonized each individual lake after the ice glacier retreated, the fish inside the lakes diverged into 2 different forms of 3 spine stickle backs as a result of positive assortative mating and disruptive selection.  Large stickle backs feeds on insects & small stickle backs feeds on planktons  They are sibling species  Even though the large ones from every lake looks the same, they are however more closely related to the small ones from the same lake than from each other o Convergent evolution: Same features evolved from different ancestral condition independently  Vultures (Old world vs. New world)  Eyes @ top of their head (Crocodile vs. Hippopotamuses)  Fins of whale vs. Fins of shark  Camera eye of mollusks & vertebrates o Secondary loss/Reversal: Reversion back to the ancestral state - Goal of cladistic taxonomy  Want to recognize strictly monophyletic taxa o E.g. Reptiles  Sauropsdia o E.g. Artiodactyla  Cetartiodactyla o Cladistics: The use of parsimony to construct evolutionary relationships BIOL359 – Evolution Winter 2013 o Cladistic taxonomy = evolutionary taxonomy - 3 Domains of Life: Archaea, Bacteria, Eukarya o Eukarya: Super group  Kingdom  Phylum  Class  Order  Family  Genus  Species o E.g. The amniotic egg: several membranes to protect the developing embryo, important evolutionary innovation & adaptation for life on land “The Amniota – Turtle, Kangaroo, Mouse, & Human” - The principle of parsimony: Simple explanations are preferred over more complicated ones (less evolutionary steps = most parsimonious) o Ingroup: The group of interest o Outgroup: Not a part of the ingroup but not too distantly related to it either, the character state possessed by the outgroup is a priori as ancestral (pleisiomorphic)  Used to polarize the character states or infer change  Need to employ an outgroup when constructing a phylogeny for a group of organisms o E.g. The Evolution of Whales  Are whales members of the artiodactyla?  Artiodactyla: Even toed hoofed mammals (e.g. camels, pigs, peccaries, deer, hippos, cattles & giraffes)  Perissodactyla: Odd toes hoofed mammals  Whales Early Hypothesis: Whales is an outgroup to the artiodactyla group  Whales Late Hypothesis: Whales is an ingroup of the artiodactyla, they are closely associated with the hippo o Parsimony using morphology (Single character - astrogala)  Whales Early: 1 Evolutionary step, one gain for the artiodactyla group  Whales Late: 2 Evolutionary steps, initial gain for the artiodactyla group & subsequence loss in whales o Parsimony using molecular characters (Multiple characters – gene for the milk protein)  Only use synapomorphies, they indicate shared derived character states different from the outgroup  Conflict resolution  Real synapomorphies will swamp out the homoplasies when the entire gene is examined  Whales early require more nt changes than whales late  Whales late is the most parsimonious explanation  Phylogeny confidence: Bootstrap method – computational technique for estimating the confidence level of a phylogenetic hypothesis o Random generation of new data set (1000 replications), compute the number of times a particular grouping appears in the tree (0 to 100% confidence that certain lineage falls below particular node) o Stimulate sequence data, know the real phylogeny & use the data for reconstruction to see if we come up with the same result  Frequency Probability Methods: Better than the method of parsimony o Maximum likelihood & Bayesian methods of phylogenetic inference - Biogeography: Seeks explanations for why organisms are found in some regions but not others o E.g. Chameleons  Distributions of chameleons are not based on the sequence of breakup of Pangaea  The dispersal hypothesis: Supported by DNA analysis, chameleons rode on small pieces of vegetation from one location to another - Coevolution: Process where evolutionary changes in the traits of one species drives evolutionary changes in the traits of another species (Predator & prey, host & parasites, mutualisms). Coevolution can result in co- speciation o Evolutionary Arms Race: Aphids vs. Plants vs. Bacteria o Symbiotic bacteria living in the guts of aphids digests the plant sap BIOL359 – Evolution Winter 2013 o Remarkable similarities between phylogeny of aphids & phylogeny of bacteria, lots of co-speciation, but the potential differences can be due to wasps, which transfers bacteria from aphids to aphids Topic 8: Adaptation - Adaptation: Trait that increases the fitness of the individual relative to individuals that do not possess the trait o Primarily occurs as a consequence of natural selection, but process can be hindered by genetic drift or migration o Differences among populations are NOT ALWAYS ADAPTATIONS o NOT every trait an organism possesses is adaptive o NOT every adaptation is perfect o Just-so story: Something that has never been tested in any kind of detail, wish to avoid because all scientific hypothesis must be tested o 3 methods to study adaptations:  Experimental (Most powerful), observational, & comparative studies o Correlation between 2 variables DOES NOT indicate causation  E.g. Oxpeckers & mammalian hosts:  Assumed to eat ticks, eat off dead skin, earwax of the mammal, and lick clean wounds (Experimental approach)  Exclusion experiments: Took a herd of mammals, divided them into 2 groups (1 with exposure and 1 without exposure), repeated the experiment 3 times o When oxpeckers were excluded, tick load did increase/decrease, but not statistically significant  No association between oxpecker exposure & tick loads o When oxpeckers were excluded, there are fewer wounds & is statistically significant  Oxpeckers are not cleaning the wounds but are inflicting them o When oxpeckers were excluded, the amount of earwax increased, is statistically significant  Oxpeckers are eating the earwax in hosts  Oxpeckers & mammalian hosts are not in a mutualistic relationship  E.g. Tephritid fly & jumping spider (Experimental approach)  Assumed the tephritid fly got their territorial threat display from their predator – jumping spiders “mimicking the behaviour of their own predator”  Experiment: Create flies with different properties by removing their wrings & reattaching them o Control: Untreated tephritid fly & Untreated housefly o Tephritid fly with own wings reattached, tephritid fly with Drosophila wings & Drosophila with tephritid fly wings attached o Results  Untreated tephritid fly & tephritid fly with own wings reattached  Predators retreated majority of the time  Tephritid fly with own wings reattached, tephritid fly with Drosophila wings & Drosophila with tephritid fly wings attached  Predators attacked & killed prey majority of the time o Tephritid fly imitate their own predator in order to deter them  E.g. Garter snakes (Observational approach)  Assumes they thermoregulate behaviorally because they don’t have the ability to physiologically regulate internal temperature (or do they chose rock retreat at random) BIOL359 – Evolution Winter 2013  Experiment: Tested temperatures under different size of rocks and different depth where snakes stay at during the day o Ctmax Critical maximum temperature – Death if temperature rises above o CtminCritical minimum temperature – Death if temperature falls below o Tp Range: Optimum body temperature, close to 30C o Thin rock: Out of max o Thick rock: Below the Tp Range throughout o Burrow & surface: Temperature range depends on depth o Medium rock: Able to stay very close/within the preferred temperature range o Results  Thick, thin, & medium rocks are about equally available to the snakes  Majority of snakes choose medium rocks (statistically significant) - Comparative studies: Evaluates the strength of hypotheses by testing for patterns across species or lineages o Comparative studies require knowledge of the evolutionary relationships “phylogenies” o E.g. Why do some bats have larger testes than others?  Adaptation for sperm competition (greater sperm competition for bats in larger groups, which will evolve larger testes for their body size)  There is strong correlation between the size of the group & the size of the testes  However, there are 6 species of bats, phylogeny shows that species A, B & C might’ve inherited their small testes size from their common ancestor, species D, E, & F might’ve inherited their big testes size from their common ancestor  Strength of the data deflates due to common ancestry  After applying the method of phylogenetically independent contrasts  Still a positive upward steep line, correlation still exists after correction  The more the competition the larger the testes size  The larger the testes size, the smaller the brain size “metabolically expensive – trade off?” - Factors that limit the evolution of adaptive traits o Trade-offs – Begonia involucrata (Monoecious – separate male & female flowers)  Compromise between 1 trait & another, unavoidable  Female flower looks like male flowers  H1: Female flower wants to mimic the average male flowers  Stabilizing selection  H2: Female flower wants to mimic the big male flowers  Directional selection  Experiment: Artificial flower arrays of different sizes, & recorded # of time bees approached flower of different sizes  Largest flowers  Most pollinators  Rea l life: Measure the size of female flowers, very close to the size of the average male flower  Trade-off, larger the flower, fewer flower can occur on an inflorescence o Functional/Developmental constraints – Fuschia excorticata (dioecious plants, male = female flower)  Factor that tends to retard the rate of adaptive evolution, or prevent a population from optimizing a trait  Green & red flowers, pollinated by birds, pollen grains are deposited at the stigma  When the flower initially opens, they are green for about 5 & ½ days, while they produce nectar & attract birds  After pollination, flower turns red, signals no more pollen is present  Why does abscission occurs after the flower turns red for ~3 days but not when the flower first turns red (metabolically expensive)  H1: Red flowers are maintains to attract pollinators  Experiment: Took a bunch of red flower & look for the number of birds that approaches BIOL359 – Evolution Winter 2013  No correlation  Physiological constraint, pollen must grow a pollen tube down to the ovary so sperms can swim down to fertilize the egg, takes approximately 3 days to grow that tube  Abscission cannot occur when the flower just starts to turn red o Genetic constraints – Ophraella sp. (Phytophagous beetles, closely associated with specific species of plants, specific hosts)  In order to reproduce on the plant host, they must be able to detoxify the chemical defenses produced by the plants against insects  H1: All host shifts are genetically possible  H2: Most host shifts are genetically impossible  Are host shifts possible? Can they detoxify all of the different host defenses?  4 major host shifts  There is a lack of genetic variation among Ophraella sp. So they are constrained to live on just a few species of host plants o Ecological constraints – Dove body feather lice  Less congruence for dove wing feather lice, capable of colonizing on multiple host species  More congruence for dove body feather lice, lower dispersal capability due to ecological constraints - Phenotypic plasticity: Identical genotypes can result in different phenotypes in different environments, it is a heritable trait that can be adapted o Phenotype = Genotype + Environment Topic 9: Our Closest Relatives - Hominidae: Gorilla + Chimps+ Bonobo + Human + Orangutan - Our closest relatives are 2 species of chimps: Bonobos Edge of extinction & Chimps “4 subspecies” - Common chimpanzee vs. Bonobo o Morphological differences, bonobos has a roundish nose, less robust body, with hair on the forehead o Bonobo walks similar in the way human does o Common chimpanzees are aggressive, strong, unpredictable, & bonobos are less temperamental o Different diet: Common chimpanzees eats meat & bonobos eats vegetarians o Different environment: Common chimpanzees lives in drier habitats “savannah”, and bonobos lives in wet habitats “rain forest”  Fission/Fusion societies: A constantly changing form of social organization, larger groups undergo fission into smaller units & smaller units fuse into larger units  Bonobos: Communities don’t interact with each other (1:1 sex ratio), society dominated by females, status of the male depends on the ranking of the mother  Strongest social bonds are among females  Sex is used as a method for conflict resolution  The only animal other than human that have sex face-to-face  Common chimpanzees
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