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BIO SCI 94 Study Guide - Final Guide: Dusky Seaside Sparrow, Phylogenetic Tree, Species Complex


Department
Biological Sciences
Course Code
BIO SCI 94
Professor
Robin Bush
Study Guide
Final

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BIO FINAL
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1.5 DOING BIOLOGY
-Biology is a hypothesis-driven, experimental science.
-Scientific processes:
-Make observations
-Propose a hypothesis
-Design and perform an experiment to test the hypothesis
-Analyze your data
-Results: accept or reject hypothesis (null hypothesis)
-If necessary, propose and test a new hypothesis
-Relationship between a hypothesis and a prediction:
-A hypothesis is an explanation of how the world works.
-A prediction is an outcome you should observe if the hypothesis is correct.
-Why experiments are convincing ways to test predictions?
-Because they measure predictions from two opposing hypotheses. Both predicted actions cannot occur, so one
hypothesis will be supported while the other one will not.
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25.3 HOW DOES NATURAL SELECTION WORK?
-Different definitions of “fitness” in biology and everyday English?
-Biology: the ability of an individual to produce viable, fertile offspring, relative to that ability in other individuals
in the population.
-Everyday English: a physical attribute that is acquired as a result of practice or exercise.
-Different definition of “adaptation” in biology and everyday English?
-Biology: a trait that leads to higher fitness relative to individuals without the trait.
-Everyday English: suitable requirements or conditions.
-Different definition of “selection” in biology and everyday English?
-Biology: heritable variation leads to differential reproductive success.
-Everyday English: the action or fact of carefully choosing someone or something as being the best or most
suitable.
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26.1 ANALYZING CHANGE IN ALLELE FREQUENCIES: THE HARDY-WEINBERG PRINCIPLE
-Five assumptions of Hardy-Weinberg Model:
-Random mating: individuals were not allowed to choose a mate.
-No natural selection: all members of parental generation survived and contributed equal numbers of gametes to
the gene pool, no matter what their genotype.
-No genetic drift: no random allele frequency changes.
-No gene flow: no new alleles were added by immigration or lost through immigration.
-No mutation.
-Equation:
-Allele frequencies: p + q = 1
-Genotype frequencies: p2 + 2pq + q2 = 1
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36.3 WHAT THEMES OCCUR IN THE DIVERSIFICATION OF VIRUSES?
-Darwin’s four postulates on natural selection:
-The individual organisms that make up a population vary in the traits they possess (size and shape).
-Some of the trait differences are heritable.
-In each generation, many more offspring are produced than can possibly survive.
-Individuals with certain characteristics produce more offspring than others (natural selection).
-How is it possible for viruses to evolve even thought they are not alive?
-Because most viral polymerases have high error rates and viruses lack error repair enzymes, mutation rates are
extremely high, giving them the potential to evolve rapidly.
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27.1 HOW ARE SPECIES DEFINED AND IDENTIFIED?
-prezygotic: prevents individuals of different species from mating.
-temporal, habitat, behavioral, gametic barrier, mechanical isolation.
-postzygotic: offspring of matings between members of different species do not survive or reproduce.
-hybrid viability, hybrid sterility.

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-Why are there so many concepts? some cases are complicated => need more than one concept.
-Dusky Seaside Sparrow:
-Using morphospecies and biological species concepts, researchers had traditionally named six subspecies
-Habitats were threatened due to geographical isolation: no gene flow.
-Dusky Seaside Sparrow: only six individuals, all were males => breed with other subspecies.
-Crossbreed between dusky males from Atlantic Coast and females from Gulf coast.
=> Fail to preserve existing genetic diversity.
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28.1 PHYLOGENETIC TREES
-Parsimony: a hypothesis of relationships that requires the smallest number of character changes is most likely to be
correct.
-Read phylogenetic trees.
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29.1 WHY DO BIOLOGISTS STUDY BACTERIA AND ARCHAEA?
-Difference between a bacteria, an archaea, and a eukaryote:
-Bacteria and archaea are the most abundant organisms on Earth and are found everywhere.
-Bacteria and archaea are very small, prokaryotic cells, and most are unicellular.
-Eukaryotes have a nuclear envelope; bacteria and archaea do not.
-Bacteria have cell walls that contain peptidoglycan, and archaea have phospholipids containing isoprene subunits
in their plasma membranes. Thus, the exteriors of a bacterium and arch eon are radically different.
-Bacteria play beneficial roles in bioremediation and medicines (antibiotics) but also cause some of the most
dangerous human diseases including plague, syphilis, botulism, cholera, and tuberculosis.
-Archaea and eukaryotes also have similar machinery for processing genetic information.
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30.2 HOW DO BIOLOGISTS STUDY PROTISTS?
-Major differences between eukaryotic cells and prokaryotic cells.
-Eukaryotic cells contain many organelles, including a nucleus, endomembrane system, and an extensive
cytoskeleton.
-Most prokaryotic cells contain few or no organelles, and no nucleus or endomembrane system and lack a
complex cytoskeleton.
-Origin of nucleus:
-Infoldings of plasma membrane surround the chromosomes.
-Nucleus (eukaryotic cell) arises, with infoldings forming nuclear envelope and ER.
-Origin of mitochondria: endosymbiosis
-Archaeal cell surrounds and engulfs the cyanobacterium.
-Bacterium lives within host archaeal cell.
Criterion for
identifying species
Advantages
Disadvantages
Biological
species
reproductive
isolation between
populations (they
don’t breed and don’t
produce viable,
fertile offspring).
reproductive isolation =
evolutionary independence
- not applicable to asexual or fossil species
- difficult to assess if populations do not
overlap geographically.
Morpho-
species
Morphologically
distinct populations
- useful when biologists
have no date on gene flow
- applicable to asexual,
sexual and fossil species
- subjective (researchers often disagree
about how much or what kinds of
morphological distinction indicate
speciation).
- misidentifies polymorphic species.
- misses cryptic species.
Phylogene-
tic species
smallest
monophyletic group
on phylogenetic tree
- widely applicable.
- logical because different
species have different
synapomorphies only if
they are isolated from gene
flow and have evolved
independently.
- relatively few well-estimated phylogenies
are currently available.

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-Endosymbiosis: host cell supplies bacterium with protection and carbon compounds. Bacterium supplies host cell
with ATP => 2 membranes (1 from the cell and 1 from the bacterium).
-Origin of chloroplasts: secondary endosymbiosis.
-Predatory protist (with a nucleus) engulfs aerobic photosynthetic protist (with a nucleus and a chloroplasts with 2
membranes)
-Nucleus from the photosynthetic protist is lost, leaving the the chloroplast by itself.
-Organelle has four membranes (2 from chloroplast, 1 from photosynthetic protist, 1 from predatory protist).
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32.2 HOW DO BIOLOGIST STUDY FUNGI?
-Why fungal infections are more difficult to treat than bacterial infections?
-Like humans, fungi are composed of eukaryotic cells, so what kill them can also kill the host.
-How about non-fungal organisms that cause human disease?
-Bacteria are prokaryotic and thus have many more unique targets for antibiotics.
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31.3 TRANSITION TO LAND OF PLANTS
-Preventing water loss
-Cuticle: waxy layer that prevents water loss from stems and leaves.
-Stomata: have pores that allow gas exchange in photosynthetic tissues.
- Liverworts: have pores but no guard cells.
-Providing protection from UV irradiation:
-Flavonoids: UV-absorbing compounds that protect DNA from damage.
-The importance of upright growth:
*Vascular tissues:
-help transporting water from tissues that are in contact with wet soil to tissues that are in contact with dry air,
against the force of gravity.
-help plants becoming rigid enough to avail falling over in response to gravity and wind.
*Tracheids and vessels:
-Tracheids have a lignin-containing secondary cell wall in addition to a cellulose-based primary cell walls; pits in
the sides and ends of the cell where the secondary cell wall is absent, where water can flow efficiently from one
tracheid to the next.
-Vessel elements: found in gnetophytes and angiosperms: ends have gaps through both cell walls.
-Producing gametes in protected structures:
-Gametangia: protect gametes from drying and from mechanical damage.
-Sperm-producing gametangium: antheridium.
-Egg-producing gametangium: archegonium.
-Retaining offspring:
-Land plant embryos are nourished by their parent.
-Eggs that formed inside archegonia.
-Sperm swim to the egg, fertilization occurs, then the resulting zygote stays attached to the parent.
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34.1 TRANSITION TO LAND OF ANIMALS
-Exchanging gases:
-Worms: high surface-area-to-volume-ratio to exchanges gases across body surface.
-Avoid drying out:
-Arthropod: gills/respiratory structure inside the body.
-Insects: waxy layer on the body surface, with openings to respiratory passages that can be closed when dry.
-Insect eggs: thick membrane to keep moisture in.
-Move to moister habitats.
-Hold up their bodies under their own weight
-Great structural supports - limbs, to hold their bodies up and move.
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