1. What are the basic processes that drive evolution of populations and species?
    • 4 testable predictions...
    • Individuals are variable within populations
    • Variation among individuals can be inherited
    • More successful individuals are selected
    • Over time variations accumulate to form divergent populations and eventually new species
  2. Ancient Greeks (570-480BC) on biodiversity
    • Recognized fossils as ancient organisms (but not ancestors)
    • Recognized that H2O previously covered the earth
  3. Leclerc (1707-1788)  on biodiversity
    • Species evolved after dispersing from "centers of creation"
    • Considered possibility of human/ape shared ancestry
  4. What contribution did Lineaus make to understanding biodiversity?
    • "father of modern taxonomy"
    • Created classification system for all living things (DKPCOFGS) based on physical traits
  5. What contribution did Erasmus Darwin make to understanding biodiversity?
    • Reactions of plants/animals to environment responsible for adaptive modifications
    • Offspring inherited these changes
  6. What contribution did Jean Lamarck make to understanding biodiversity?
    • "Inheritance of acquired traits"
    • Giraffes acquiring longer and longer necks and passing them down
    • Traits acquired throughout life therefore older=more complex
    • ("epistasis"?)
  7. What contribution did Thomas Malthus make to understanding biodiversity?
    • (not a scientist)
    • Wrote "An Essay on the Principles of Population"
    • Idea: no population can grow w/o limits, there is a "population cap"
    • The earth has limited resources
  8. What contribution did Georges Cuvier make to understanding biodiversity?
    • Used comparative anatomy (w/ meticulous attention to detail) to develop classification system.
    • Founder of paleontology
    • Demonstrated extinction (while not necessarily ancestral)
    • Showed catastrophism (a succession of catastrophic events)
  9. What contribution did Charles Lyell make to understanding biodiversity?
    • Wrote "Principles of Geography"
    • Showed earth (not animals) as constantly changed
    • stated "present is the key to the past"
    • Uniformitarianism: earth shaped by steady accumulation of minute changes over millions of years
  10. What contribution did Alfred Wallace make to understanding biodiversity?Where did he gain the data?
    • Extensive fieldwork (Amazon river, SE Asia)
    • Expert on geographical distribution of animals
    • Transmutation: independently proposed how natural selection could produce new species
    • Exchanged ideas w/ Darwin and suggested joint publication
    • First time the idea of NS/evo unified ALL species (very controversial)
    • Theory had a testable mechanism that did not require deity, miracles, or an arbitrary purpose
  11. What contribution did Charles Darwin make to understanding biodiversity?Where did he gain the data?
    • Proposed all species evolved from common ancestors over time through NS
    • Spent 5 years aboard HMS Beagle accumulating evidence on geology, fossils, living organisms, etc
    • Spent 20 years accumulating evidence for theory after initial idea
    • contact by Wallace provoked him to finish book
    • Theory had a testable mechanism that did not require deity, miracles, or an arbitrary purpose
  12. What contribution did Herbert Spencer make to our understanding of Darwin's theory?
    • Rephrased idea as "survival of the fittest" which is a bit of a misnomer, and confused many about Darwin's true idea
    • the truth: Fitness is always relative
    • the truth: Survival of the fit enough
  13. Very brief summary of Drawin's theory of evolution by NS
    • All organisms share a common ancestor
    • Variations among individuals are passed from parent to offspring
    • Some of these variations may increase an individuals fitness in a given environment
    • Over time, variations accumulate to form divergent populations which eventually form new species
    • "descent w/ modification"
  14. How did Mendel's work on heredity in pea plants add to our understanding of Darwin's theory?  What did Hardy and Weinberg contribute?
    • Menedel's particulate theory of genetics showed that genes do not blend, but are passed intact from parents to offspring
    • Hardy and Weinberg showed that genes have a low tendency to disappear from populations (except by NS) thanks to heterozygosity
  15. What is meant by "new synthesis"
    • Merger of genetics, mathematics, population biology, systematics, paleontology, and Darwinian evolution 
    • Used to explain that adaptive evolution is caused by NS acting on genetic variation
  16. define: clade, anagenesis
    • clade: a group of species derived from a common ancestor (can be large or small)
    • anagenesis: evolutionary change of features of a single lineage
  17. what is a pleisiomorphy, apomorphy, synapomorphy. What is the use of an outgroup?
    • pleisiomorphy: ancestral, primitive, or less specialized trait
    • apomorphy: derived, specialized, or adv trait
    • synapomorphy: apomorphy occuring in >1 taxa
    • Outgroups, defined as pleisiomorphic, are used to determine apomorphies of a lineage (in group)
  18. Monophyletic vs paraphyletic vs polyphyletic
    • Monophyletic: includes all descendants of a single ancestor
    • Paraphyletic: includes some, but not all descendants of a single ancestor
    • Polyphyletic: includes descendants of 2+ ancestors
  19. What basic steps must be taken to use nucleotide sequence data from several species as characters for phylogenetic reconstruction?
    • ID and acquire sequences to include int he tree (must use "like" sequences, apples to apples)
    • Align the sequences (easier w/ increased similarity, take ins/del into acct)
    • Estimate tree by one of several methods
    • Draw tree and present it to intended audience
    • *Whole genome data >> morph. data
    • **Generate multiple trees?
    • ***problems - who is outgroup? A single site may have undergone numerous mutations? Reverse mutations?
  20. What multiple sources of data can be used to build trees and infer relationships
    • Anatomy (only way for extinct organisms)
    • Behavior (may be possible for extinct organisms)
    • Genetic similarities (incl pseudogenes)
  21. What does the molecular clock theory describe? Is there evidence to support it? What interesting exceptions to the clock have been discovered?
    • DNA sequences evolve and diverge at a constant rate
    • Yes - sequence of evolution of birds and fruit flies from geological events of known age (Hawaii)
    • Degree of relatedness affects rate (rodents are faster than primates)
    • Some genes evolve slowly, and others are mutational "hotspots"
  22. Difficulties when building trees
    • Extinct organisms make comparison difficult (only anatomical, MAYBE behavioral)
    • Evolution may ERASE traces of history (multiple substitutions over time)
    • *we see mutation RETENTION not actual mutation rate (3rd codon mutation vs 2nd)
    • *Fast evolution may now allow time for distinct formation of synapomorphies
    • Hybridization may obscure relationships
  23. How can phylogenetics be used to address co-evolution?
    • Compare phylogenies of 2 closely-related organisms (host/parasites, plants/obligate pollinators, predator/obligate prey)
    • Diverges may be identical
    • Often the result of evolutionary arms races  (eg toxin production/resistance, floral tube & proboscus length)
  24. How can phylogenetics be used to address species biogeography?
    • Can resolve geographic origin and spread of species
    • eg independent sites of pig domestication (pigs were seen to have evolved w/ humans in civilization)
  25. How can phylogenetics be used to address epidemiology/medical forensics?
    • Trace origins of disease
    • link diseases resistance mechanisms in other hosts to new therapies/treaments
    • (eg multiple origins of HIV from SIV, tracking SARS to source)

    Med forensics - tracing HIV spread back to dentist due to genetic sequence
  26. What is homoplasy? Convergence? Parallelism? Evolutionary reversal? (w/ examples)
    • Homoplasy: independent evolution of trait (character state) in different taxa
    • Convergence: evolution of similar features occurring independently in different lineages (eye of vertebrates and cephalopods)
    • Parallelism: evolution of similar features occuring independently in related lineages (transformation of crustacean legs into feeding structures)
    • Evolutionary reversal: return from derived state to ancestral state (salamanders produce aquatic larva [ancestral], but certain clade is fully terrestrial [derived].  Dusky salamanders have since regained ancestral trait)
  27. Define heterochrony, allometry.  How can you explain them?
    • Heterchrony: evolutionary change in traits caused by alteratin of timing of development events (eg paedomorphosis in axolotls [retain gills as adults])
    • *earlier during development a mutated gene is activated the more profounce the alteration will be
    • Allometry: differential rate of growth in diff body parts during development (eg human head)
    • *Allometric traits are usually important
  28. Broad patterns that have been observed across clades w/ respect to genes/genomes? Which approaches are useful and which would generate false signal of complexity?
    • Physiologically and behaviorally complex organisms have larger genomes than simpler organisms
    • Eukaryotes tend to have large amt of non-coding repetitive DNA
    • # of f(x) genes among eukaryotes is better method of comparison
    • multicellular organisms w/ tissue organisation >multicell. w/o > single-celled organisms
    • endosymbionts < free living
  29. What lines of evolution reveal history of techtonic plate movement?
    • Comparing age of mountains or volcanoes in different locations
    • Looking within layers of rock laid down sequentially over time
    • Same fossils occur in sedimentary rock on both sides of Atlantic
  30. What is the K-T boundary layer? When was it deposited? What hypothesis has been proposed for its formation and with what evidence?
    • Unique rock layer that formed WORLDWIDE 65 MYA
    • Marks abrupt transition in fossil record
    • Proposed to be a meteor
    • Layer has significant amount of Iridium (rare on Earth)
    • Barringer crater is consistent w/ a meteorite impact
  31. Explain the geological times scale, what are era and period changes are usually associated with?
    • Provides a system of measurement relating stratigraphy (identifiable layers of rock) to the passage of time
    • Allows us to describe the timing of major events that have occurred during Earth's history
    • Usually associated w/ appearance/disappearances of major lineages NOT divergence events
  32. What important things happened in the Paleozoic era (245-570mya)? Mesozoic era (66.4-245mya)? Cenozoic era (present-66.4mya)?
    • Paleozoic: Early multicellular organisms gave rise to living lineages of animals or became extinct (none alive today) (~535mya)
    • Cambrian- animals w/ recognizable body plans (heads, legs, etc) (~500mya)
    • Plants established larger ecosystems on land
    • Arthropod animals lived on land (~400mya)
    • Evolution of tetrapods (4 legged land-animals evolved from lobe-finned fishes) (~380mya)
    • Lobe-finned fishes and reptillian tetrpods (dinosaur ancestors) (~350mya)
    • Donimant land vertebrates were synapsids (reptile-like vertebrates that eventually gave rise to mammals) (~280mya)
    • Most fish belong to teleost group (~250mya)
  33. What important things happened in the Mesozoic era (66.4-245mya)?
    • True mammals evolved from Therocephalian synapsids (~150mya)
    • -most were very small insectivores
    • Did not increase in size or diversity until dinos went extint (~65mya)
    • Oldest fossils of flowering plants (~132mya)
    • Brinds branched from Saurichian Theropod dinos (~150mya)
  34. What sequence events must occur for a dead organism to fossilize?  What are the different general types of fossils?
    • Must be buried BEFORE decomposition
    • Burial site must escape damage from geological events
    • Fossil must be discovered
    • Mineralized bones, teeth, shells, seeds, other hard body parts OR footprints, impressions, nests, eggshells, feces
  35. How can phylogenetic analyses be used to predict the appearance of a clade in the fossil record? Be specific re: how the data are analyzed and presented in a graph
    • Correlations between clade rank and age rank in equid lineage are strong
    • Each node is gene-based phylogenetic tree predeicted a new lineage appearing in fossil record
    • (not as powerful in the dinosaur phylogenetic tree)
    • this is why multiple genes and consensus tree should be used to create a phylogeny
  36. Compare/contrast phyletic gradualism, punctuated equilibrium, and punctuated gradualism.  Draw a graph depicting change in a character state over time.
    • Phyletic gradualism: evolutionary change is gradual and is not necessarily associated with speciation
    • graph appears as mostly diagonal w/ slight curves
    • Punctuated equilibrium: daughter spp diverges rapidly then continues w/o change
    • graph appears as straight vertical line then nearly straight horizontal line then straight vertical line (repeat).  2 lineages a result each time
    • Punctuated gradualism: a lineage evolves in rapid spurts from one equilibrium to another, but specialization does not necessarily occur
    • graph is similar to phyletic gradualism, but more distinct vertical/horizontal lines
  37. What is the significance of former supercontinents in our current understanding of biogeographical processes?
    • Continents that once formed Gondwanaland may be fitted together to form a single landmass (identical rock formations/composition, etc)
    • Past climates and fossil distribution can be reconstructed using a combination of continental drift and evolution
    • eg- seed from Glossopeteris too big and heavy for overseas dispersal but found on multiple continents
  38. Summarize Darwin's 4 arguments for how current global dist. of organisms came about
    • Convergence is evidence of evolution by NS: similar climates and habitats exist in old and new world, yet their organisms may not be related
    • However these climates can make distantly related groups look similar to eachother
    • Island biogeography is evidence of evolution by NS: most spp on islands are related to spp on closest mainland
    • colonists usually come from nearby continents, distribution refelcts blend of chance (winds, currents, storms, kelp beds) and outcome (colonization, adapting to fill niches, speciation events)
    • Vicariance is evidence of evolution by NS: regions separated by barries such as unfavorable habitat have a different set of spp
    • What happens if barriers are removed?
    • Our similarity to African apes is evidence of evolution by NS:
  39. What patterns must occur for species to colonize an island, and how do these events influence biogeographical patterns?
    • Colonists must come from nearby continents 
    • Long distance dispersal events are rare
    • Distribution reflects blend of chance (winds, currents, storms, kelp beds) and outcome (colonization, adapting to fill niches, speciation events)
    • Oceanic islands are missing many types of native spp (eg mammals) found on neighboring continents
  40. What are the three rules that seem to govern the number of spp on an island?
    • As # spp increases immigration decreases and extinction increases
    • Smaller island results in an increased extinction rate
    • Farther away island results in less likely to be colonized
  41. What are the 3 major processes that influence biogeographical patterns?
    • Extinction: decreased dist of spp, higher taxa may lost constituent spp
    • Dispersal: movement of individuals allowing spp to expand their ranges
    • Vicariance: fragmentation of a continuous distr by emergence of a barrier
  42. Compare the two competing hypotheses for the evolution and diaspora of the homo lineage across the globe.  Which is most parsimonious?  Is there genetic data?  Fossil data?
    • Multiregional: single lineage, not truly separated by vicariance, genese exchanged within all populations of Africa Asia and Europe
    • Replacement: All modern homosapiens were derived from African origin ("eve") THEN dispersed replacing all other human populations
    • Genetic evidence (mtDNA) shows heritage to a single woman (eve) and shows oldest lineage to be African and youngest to be Native American
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