Organismal Biology

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  1. Discovery Science
    Observations and descriptions
  2. Hypothesis Driven Science
    • Scientific method
    • Observations -> Questions -> Hypothesis -> Prediction -> test
    • Requires verifiable observations, repeatable experimental results
  3. Evolution
    • Definition ala Darwin: Descent with modification
    • individuals don't adapt but a population does
    • change on a generational basis
    • evolution of a species is driven by Natural Selection
    • It is not directed
    • does not create new traits but works with traits already in the population
    • need heritable traits
    • the environment can play a big role in evolution
  4. Natural Selection
    • The process in which individuals inherited traits allows it to reproduce at a higher rate (greater fitness) in a given environment relative to other members of its species.
    • Maximization of reproductive output
  5. Homology
    • Similarity resulting from common ancestry reflects the evolutionary history of the species (Example: nucleic acids as genetic information)
    • Sometimes vestigial structures exist because of common ancestry but are no longer in use (pelvic girdles in whales, appendix in humans)
  6. Evolutionary Trees
    given ancestry we can create trees, we group on similar homologous structure
  7. Convergent Evolution
    • Populations adapt to the specific environmental conditions in which they reside. Unrelated species residing in similar environments can evolve superficially similar adaptions
    • Example wings on birds and bats
  8. Gene
    a segment of DNA. can have multiple alleles
  9. Allele
    Small differences at the DNA level can be as small as 1 nucleotide
  10. locus
    the physical location of the gene on the genome
  11. character
    heritable feature that varies between individuals
  12. traits
    a varient for a character
  13. Complete Dominance
    • Mendel's model of inheritance
    • If 2 alleles differ, the dominant allele is fully expressed while the recessive allele has no noticeable effect
  14. Incomplete Dominance
    • Mendel's model of inheritance
    • If 2 alleles differ, the trait is a mixture of the two alleles
  15. Law of Segregation
    • Mendel's model of inheritance
    • the 2 alleles for each character segregate during gamete production
  16. Genotype
    the combination of alleles an individual has (PP,pp,Pp)
  17. Phenotype
    What you can see, i.e. the expressed trait
  18. Polygenic Inheritance
    the additive effect of two or more genes
  19. Hardy Weinberg
    • given allele frequency p(A) and q(a)
    • 1=p^2 + 2pq + q^2
    • p^2 = frequency of homozygous AA
    • q^2 = frequency of homozygous aa
    • 2pq = frequency of heterozygous Aa
    • Assume optimal model
    • Deviations from Hardy-Weinberg equilibrium can be easily assessed using a χ2 (Chi-square) test
  20. Average Heterozygosity
    • measure of Gene variability
    • the average number of loci that are heterzygous
    • AA, Bb, Cc, dd, EE => 2/5 = 0.4
  21. Nucleotide Variability
    • measure of gene variability
    • the average number of of heterozygous nucleotide starts
  22. Mutations
    • Mutations are always occurring.
    • Mutations can be deleterious, neutral or advantageous. – deleterious >> neutral >> advantageous
    • single base pair mutations
    • insertion and deletions (indels).
    • Chromosomal – Inversions – Translocations – Duplications/deletions – Nondisjunction
  23. Changes in the level of variation for Gene Pools
    • In addition to new mutations, a population’s gene pool will also change do to:
    • Migration (gene flow)
    • Random genetic drift
    • Natural selection
    • Non-random mating
  24. Gene flow
    • Gene flow via the migration can introduce new variants into a population. – Eg. Insecticide (DDT) resistance in mosquito (Culex pipiens).
    • Gene flow across individuals from different populations continually mixes gene pools
    • – Homogenizes the variation across populations.
    • – Prevents genetic divergence across populations.
  25. Random Genetic Drift
    • the variation across the geographic range of a species. Could be either due to natural selection (adaption) or by chance
    • Key Points:
    • • Most significant in small populations.
    • • Responsible for fluctuations in allele frequency.
    • • Eventually lead to the loss of variation.
    • • Can cause deleterious alleles to become fixed.
  26. Founder Effect
    • When species move into new areas, only a few individuals actually colonize (i.e. little variation).
    • Genetic Drift
  27. Modes of Natural Selection
    • • Directional – selection for one extreme phenotype
    • • Disruptive – selection for both extreme phenotypes
    • • Stabilizing – selection against both extreme phenotypes
  28. Heterozygote advantage
    • Heterozygote has higher fitness
    • Sickle-cell anemia is a recessive disorder that transforms red blood cells into a “sickle”.
    • --– Heterozygotes are protected again some malaria symptoms.
  29. Frequency-dependent selection
    • Fitness of a genotype dependent on its frequency in the population.
    • Relative fitness is higher at lower frequencies.
  30. Biological species concept
    • A species is a group of individuals that can successfully interbreed in nature and produce viable and fertile offspring.
    • According to this definition you would expect:
    • – gene flow (mating) within a species
    • – no gene flow (mating) between species
    • Reproductive isolation is the barrier that keeps species apart.
    • Prevents the formation of species hybrids in nature (ie. Gene flow).
  31. Reproductive barriers
    • BEFORE fertilization: Prezygotic barrier (or Prezygotic isolation)
    • AFTER fertilization: Postzygotic barrier (or Postzygotic isolation)
  32. Habitat isolation
    • Prezygotic barrier
    • Species occupy different habitats, therefore they do not have even the opportunity to mate.
    • eg. insects using different plants in the same area.
  33. Temporal isolation
    • Prezygotic barrier
    • If species are reproductively active at different times, then they can’t hybridize.
    • eg. flowering time
  34. Behavioral isolation
    • Prezygotic barrier
    • Differences in courtship rituals will prevent hybridization.
    • – eg. Blue-footed boobies
  35. Mechanical isolation
    • Prezygotic barrier
    • Mechanical differences prevent the successful mating.
    • – eg. Bradybaena snails
  36. Gametic isolation
    • Prezygotic barrier
    • Differences in egg and/or sperm prevent fertilization.
    • – eg. sea urchins
  37. Reduced hybrid viability
    • Postzygotic barrier
    • Fertilization occurs, but hybrid dies (in development or in the environment).
    • – eg. Ensatina salamanders
  38. Reduced hybrid fertility
    • Postzygotic barrier
    • Hybrid individual are sterile.
    • – eg. Drosophila mojavensis & D. arizonae.
  39. Hybrid breakdown
    • Postzygotic barrier
    • Hybrids are viable and fertile, but have a reduced or no mating success.
    • – eg. Rice strains
    • – eg. Lake white fish (Coregonus clupeaformis)
  40. Morphological species concept
    • Individuals with a similar morphology are a single species.
    • Works on sexual and asexual species, but it can be a subjective.
    • – Which morphological character is most important?
  41. Ecological species concept
    • The ecology of individuals defines the species.
    • – eg. food, shelter, physiology, etc...
    • Works on sexual and asexual species, but need to have a very clear understanding of the ecology of organisms.
  42. Phylogenetic species concept
    • Differences at the genetic level defines a species.
    • Works on sexual and asexual species, but need to define the degree of difference allowed and still be a single species.
  43. Speciation
    • Speciation ultimately occurs when two gene pools become isolated.
    • Isolating mechanism describes how two species are
    • prevented from coming back together.
    • The initial separation can occur in:
    • – allopatry
    • – sympatry
  44. Allopatric speciation
    • Gene flow is prevented do to geographic features.
    • – eg. river, mountain, island . . .
    • After the initial isolation of the two gene pools, divergence can occur via:
    • – Random genetic drift can occur via:
    • – Natural selection (adaptation, sexual, ....)
    • – Random genetic drift – Both
  45. Sympatric speciation
    • Speciation occurring between population living in the same geographic area.
    • How can you have divergence in gene pools if individuals have the possibility to mate?
    • – The force(s) splitting gene pools must be stronger than of the homogenizing effect of gene flow.
  46. Sympatric speciation: Habitat differentiation
    • Shifts in resource utilization could be a strong.
    • Apple maggot (Rhagoletis pomonella)
  47. Sympatric speciation: Sexual selection
    • Mate preference can also drive gene pools apart.
    • Given variation in morphological or behavior characters and variation in mate choice, disruptive selection could occur.
    • Lake Victoria Fish
  48. Sympatric speciation: Polyploidy
    • Polyploidy is the occurrence of extra chromosome do to an error in cell division.
    • Not very common in animals, but very common in plants (over 80% of extant species).
    • In plants you can have: – autopolyploids – allopolyploids
  49. Autopolyploids
    is when the extra set(s) of chromosomes originate from a single species.
  50. Allopolyploids
    • is when the extra set(s) of chromosomes originate from different species.
    • common in crop plants
  51. Hybrid Zones
    • Hybrid zones are regions were contact between two different species produces hybrid individuals.
    • Within a hybrid zone alleles from both species can be found in individuals sampled
    • There are 3 possible scenarios for a hybrid zone
    • 1) Reinforcement (gets narrow or goes away)
    • 2) Fusion (the two species become one)
    • 3) Stability (Persists over time)
  52. Origins of life on Earth
    • The hypothesis for the origins of life on Earth states that life came about through the following steps:
    • 1. Abiotic synthesis of small organic molecules
    • 2. Joining of these small molecules into macromolecules
    • 3. Packaging of molecules into protocells
    • 4. Origin of self-replicating molecules (RNA was likely the first genetic material.)
  53. Protocells
    Protocells are membrane structures that can isolate its content from the external environment.
  54. Endosymbiont
    are cells that lives within another cell
  55. The endosymbiont theory
    • proposes that mitochondria and living within larger host cells
    • plastids (eg. chloroplasts) were formerly small prokaryotes living within larger host cells
  56. Cambrian explosion
    • The beginning of the Cambrian (535-525 mya) is marked by the sudden appearance of fossils resembling modern animal phyla.
    • A few animal phyla appear even earlier: sponges, cnidarians, and molluscs.
    • The Cambrian explosion provides the first evidence of predator-prey interactions.
  57. Permian extinction
    • The largest of all extinctions.
    • 251 mya
    • 96% of all marine species extinct!!!
    • Caused by extremely high volcanic activity that caused global climate change.
    • – Temperature increase by 6 °C. – Ocean anoxia
  58. Cretaceous extinction
    • 65.5 mya
    • Extinction of almost all dinosaurs.
    • Likely caused by a large asteroid (10 km diameter)
  59. Adaptive radiations
    • occur when a large number of species evolve in a relative short period of time.
    • – Following mass extinctions – Colonization events – Evolution of key innovations
  60. Cladistics
    • Cladistics groups organisms by common descent.
    • A clade is a group of species that includes an ancestral species and all its descendants.
    • Clades can be nested into larger clades.
  61. monophyletic clade
    consists of the ancestor species and all its descendants
  62. paraphyletic clade
    consists of an ancestral species and some, but not all, of the descendants.
  63. polyphyletic clade
    consists of various species with different ancestors
  64. Maximum parsimony
    assumes that the tree that requires the fewest evolutionary events (appearances of shared derived characters) is the most likely.
  65. Molecular clocks
    • Mutations have a probability of occurring every generation.
    • As long as the rate of mutation is constant, mutations will accumulate at a constant rate.
    • We can use this clock-like manner of molecular evolution as a molecular clock.
  66. Neutral theory
    • The majority of mutations are deleterious, therefore will be removed from the population
    • Advantageous mutations will quickly fixed therefore will not be seen.
    • Hence the majority of mutations (variation) in a population will be neutral
  67. Higher order classification
    • Five kingdoms were recognized: Monera (prokaryotes), Protista, Plantae, Fungi, and Animalia.
    • Three-domain system has been adopted: Bacteria, Archaea, and Eukarya
  68. Horizontal gene transfer
    • is the movement of genes from one genome to another.
    • – transposable elements – virus – hybridization
  69. Cell walls of prokaryotes
    • Bacterial cell walls contain peptidoglycan.
    • – sugar polymers cross-linked by polypeptides.
  70. Testing for peptidoglycan
    • The Gram stain is used to classify bacteria by cell wall
    • composition.
    • For Bacteria: – Gram-positive bacteria have simpler walls with a large amount of peptidoglycan.
    • – Gram-negative bacteria have less peptidoglycan and an outer membrane that can be toxic.
  71. What so important about Gram stain?
    • • Identification of bacterial species.
    • • In medicine, it can help direct a treatment plan.
    • • Many antibiotics target peptidoglycan and damage bacterial cell walls.
    • • Gram-negative bacteria are more likely to be antibiotic resistant.
  72. Motility
    • • Many bacteria have the ability to move toward or away from a stimulus (taxis).
    • • Chemotaxis is the movement toward or away from a chemical stimulus.
    • • Most motile bacteria propel themselves by flagella.
  73. Chemotaxis
    is the movement toward or away from a chemical stimulus.
  74. Prokayotes Genetic diversity
    • Prokaryotes have a great amount of genetic variation.
    • Three factors contribute to this genetic diversity: – Rapid reproduction – Mutation – Genetic recombination
  75. Genetic recombination / Horizontal Gene Transfer
    • Combining of DNA from two sources.
    • Contributes to bacterial diversity.
    • DNA from different individuals can be brought together by different processes.
    • When the exchange is between different species is called horizontal gene transfer.
  76. Transformation
    The uptake of DNA from the environment.
  77. Transduction
    The movement of genes between bacteria by phages (viruses that infect bacteria).
  78. Conjugation
    • The transfer of genetic material between prokaryotic cells.
    • The DNA transfer is one way.
    • A donor cell attaches to a recipient by a pilus, pulls it closer, and transfers DNA.
    • A piece of DNA called the (Fertility Factor) F factor is required for the production of pili.
  79. Prokaryotic metabolism & O2
    • Obligate aerobes require O2 for cellular respiration.
    • Obligate anaerobes are poisoned by O2 and use fermentation or anaerobic respiration.
    • Facultative anaerobes can survive with or without O2.
  80. Prokaryotic metabolism & N2
    • Prokaryotes can metabolize nitrogen in a variety of ways.
    • – Nitrogen is essential for amino acids and nucleic acids.
    • In nitrogen fixation, some prokaryotes convert atmospheric nitrogen (N2) to ammonia (NH3)
  81. Biofilms
    Surface-coating colonies
  82. Extreme halophiles
    • Archaea
    • live in highly saline environments.
  83. Extreme thermophiles
    • Archaea
    • thrive in very hot environments.
  84. Methanogens
    • Archaea
    • live in swamps and marshes and produce methane as a waste product.
    • Methanogens are strict anaerobes and are poisoned by O2.
    • Very important for sewage treatment.
  85. Bacteria
    • Diverse nutritional types.
    • – Pathogens to beneficial types.
    • • Proteobacteria
    • • Chlamydias
    • • Spirochetes
    • • Cyanobacteria
    • • Gram-positive bacteria
  86. Proteobacteria
    • [Bacteria]
    • These gram-negative bacteria include photoautotrophs, chemoautotrophs, and heterotrophs.
    • Some are anaerobic, and others aerobic.
  87. Chlamydias
    • [Bacteria]
    • These bacteria are parasites that live within animal cells.
    • Chlamydia trachomatis causes blindness and nongonococcal urethritis by sexual transmission
  88. Spirochetes
    • [Bacteria]
    • These bacteria are helical heterotrophs.
    • Some are parasites, including Treponema pallidum, which causes syphilis, and Borrelia burgdorferi, which causes Lyme disease.
  89. Cyanobacteria
    • [Bacteria]
    • These are photoautotrophs that generate O2.
    • Plant chloroplasts likely evolved from cyanobacteria by the process of endosymbiosis.
  90. Gram-positive bacteria
    • [Bacteria]
    • • Gram-positive bacteria include
    • – Actinomycetes, which decompose soil
    • – Bacillus anthracis, the cause of anthrax
    • – Clostridium botulinum, the cause of botulism
    • – Some Staphylococcus and Streptococcus, which can be pathogenic
    • – Mycoplasms, the smallest known cells
  91. Chemoheterotrophic prokaryotes
    function as decomposers, breaking down dead organisms and waste products.
  92. parasitism
    harms but does not kill its host.
  93. pathogens
    Parasites that cause disease
  94. General features of protists
    • Eukaryotes – cells have organelles and are more complex than prokaryotic cells.
    • Most protists are unicellular, but there are some colonial and multicellular species.
    • Some reproduce asexually while others sexually.
    • Vast amounts of structural and functional diversity
    • – more than other group of eukaryotes (plants, fungi & animals).
    • Very complex cells – organelles can perform multiple biological functions
  95. Photoautotrophs
    contain chloroplasts
  96. Heterotrophs
    absorb organic molecules or ingest larger food particles
  97. Mixotrophs
    photosynthesis and heterotrophic nutrition
  98. Endosymbiosis
    • One organism engulfing another and creating a stable and dependent relationship
    • Mitochondria evolved by endosymbiosis of an aerobic prokaryote (alpha proteobacteria).
    • Plastids evolved by endosymbiosis of a photosynthetic cyanobacterium
  99. Endosymbiosis in protists
    • The plastid-bearing lineage of protists evolved into red and green algae
    • The DNA of plastid genes in red algae and green algae closely resemble the DNA of cyanobacteria
    • On several occasions during eukaryotic evolution, red and green algae where themselves engulfed by another heterotrophic eukaryote (secondary endosymbiosis)
  100. Excavata
    • Protists
    • The clade Excavata is characterized by its cytoskeleton
    • Some members have a feeding groove.
    • • Diplomonads
    • • Parabasalids
    • • Euglenozoans
    • --– Kinetoplastids
    • • Trypanosomes
    • --– Euglenids
  101. Diplomonads & Parabasalids
    • [Excavata] protists
    • Lack plastids
    • Have modified mitochondria
    • Diplomonads – Derive energy from anaerobic biochemical pathways. Have two equal-sized nuclei and multiple flagella Are often parasites, for example, Giardia intestinalis
    • Parabasalids – Include Trichomonas vaginalis, the pathogen that causes “yeast” infections in human females.
  102. Kinetoplastids
    • [Excavata: Euglenozoans] protists
    • A single mitochondrion
    • This group includes Trypanosoma, which causes sleeping sickness and Chagas in humans.
  103. Trypanosomes
    • [Excavata] protists
    • Trypanosomes evade immune responses by switching
    • surface proteins.
    • A cell produces millions of copies of a single protein.
    • The new generation produces millions of copies of a different protein.
    • These frequent changes prevent the host from developing immunity.
  104. Euglenids
    • [Excavata] protists
    • Have one or two flagella that emerge from a pocket at one end of the cell.
    • Mixotrophs
  105. Chromalveolata
    • Data suggest that the clade Chromalveolata is monophyletic and originated by a secondary endosymbiosis event.
    • The proposed endosymbiont is a red algae.
    • • Alveolates
    • –-- Dinoflagellates
    • --– Apicomplexans
    • • Plasmodium
    • --– Ciliates
    • • Stramenopiles
    • --– Diatoms
    • --– Brown Algae
    • --– Oomycetes
  106. Alveolata
    • [Chromalveolata] protists
    • Alveolata have membrane-bounded sacs (alveoli) just under the plasma membrane. – function unknown
    • The alveolates include:
    • • Dinoflagellates
    • • Apicomplexans
    • • Ciliates
  107. Dinoflagellates
    • [[Chromalveolata] Alveolata]
    • Two flagella and each cell is reinforced by cellulose plates.
    • They are abundant components of both marine and freshwater phytoplankton.
    • Toxic “red tides” are caused by dinoflagellate blooms
  108. Apicomplexans
    • [[Chromalveolata] Alveolata]
    • Parasites of animals, and some cause serious human
    • diseases.
    • One end, the apex, contains a complex of organelles specialized for penetrating host cells and tissues.
    • Most have sexual and asexual stages that require two or more different host species for completion.
    • An apicomplexan Plasmodium is one of the parasite that causes malaria.
  109. Ciliates
    • [[Chromalveolata] Alveolata]
    • Use of cilia to move and feed.
    • They have large macronuclei and small micronuclei.
    • Genetic variation results from conjugation, in which two individuals exchange haploid micronuclei
    • – separate from reproduction (binary fission).
  110. Stramenopiles
    • [Chromalveolata]
    • Most have a “hairy” flagellum paired with a “smooth”
    • flagellum
    • Include important phototrophs as well as several clades of heterotrophs.
    • Diatoms, Brown Algae, Oomycetes
  111. Diatoms
    • [[Chromalveolata] Stramenopiles]
    • Diatoms are unicellular algae with a unique two-part, glass-like wall of hydrated silica.
    • Diatoms usually reproduce asexually, and occasionally sexually
    • Major component of phytoplankton and are highly diverse.
    • After population bloom, dead individuals fall to the ocean floor undecomposed. – carbon sink
  112. Brown Algae
    • [[Chromalveolata] Stramenopiles]
    • Brown algae are the largest and most complex algae. All are multicellular, and most are marine.– eg. kelp
    • Complex multicellular anatomy. – The algal body is plantlike but lacks true roots, stems, and leaves and is called a thallus.
    • Brown algae reproduce through a process of alternation of generations. – alternation of multicellular haploid and diploid forms.
    • Heteromorphic generations are structurally different, while isomorphic generations look similar.
  113. Oomycetes
    • [[Chromalveolata] Stramenopiles]
    • Water molds, white rusts, and downy mildews.
    • Most oomycetes are decomposers or parasites.
    • Their ecological impact can be great, as in potato blight caused by Phytophthora infestans.
  114. Rhizaria
    • Many move using pseudopodia – extensions of the cytoplasm that anchor itself and is used to pull the organism.
    • Many amoebas are included in this group.
    • Radiolarians, Foraminiferans, Cercozoans
  115. Radiolarians
    • [Rhizaria]
    • Mostly marine
    • Symmetrical internal skeleton usually made of silica
    • Use pseudopodia to engulf microorganisms
    • The pseudopodia of radiolarians radiate from the central body
  116. Foraminiferans
    • [Rhizaria]
    • Porous multichambered shells called tests
    • Pseudopodia extend through the pores in the test
    • Many forams have endosymbiotic algae.
  117. Cercozoans
    • [Rhizaria]
    • Most amoeboid and flagellated protists with threadlike
    • pseudopodia.
    • They are common in marine, freshwater, and soil ecosystems
    • Most are heteroptrophs, including parasites and predators
  118. Archaeplastida
    • Plastid derived from a cyanobacterial endosymbiont.
    • This supergroup that includes red algae, green algae, and land plants
    • • Red algae
    • • Green algae – Charophytes – Chlorophytes
  119. Red Algae
    • [Archaeplastida]
    • Reddish in color due to an accessory pigment
    • (phycoerythrin).
    • Red algae are usually multicellular; the largest are seaweeds
  120. Green Algae
    • [Archaeplastida]
    • Contain green chloroplasts.
    • The two main groups are chlorophytes and charophytes
  121. Chlorophytes
    • [[Archaeplastida] Green Algae]
    • Fresh water and marine.
    • Symbionts in lichens
    • Large size achieved by:
    • 1. Colonies of individual cells.
    • 2. Formation of true multicellular bodies by cell division and differentiation.
    • 3. Repeated division of nuclei with no cytoplasmic division.
  122. Charophytes
    • [[Archaeplastida] Green Algae]
    • Charophytes are most closely related to land plants.
  123. Unikonta
    • Amoebozoans include: – Slime molds – Gymnamoebas – Entamoebas
    • Opisthokonts: Fungi, animals & other protists
  124. Slime molds
    • [[Unikonta] Amoebozoans]
    • Plasmodial slime molds form large multinucleated masses and webs called plasmodium.
    • Cytoplasm streams within the plasmodium.
    • Cellular slime molds form multicellular aggregates in which cells are separated by their membranes.
    • Cells feed individually, but can aggregate to form a fruiting body
  125. Plants general
    • Land plants evolved around 500 MYA from ancestors of green algae.
    • Very diverse (290,000 species).
    • Ecologically very important.– 50% of global photosynthesis
    • Charophytes are the closest relatives of land plants.
  126. Plants: Colonization of land
    • Sporopollenin, a layer of a durable polymer, prevents exposed zygotes from drying out (also found in charophytes).
    • Many benefits in moving onto land: – unfiltered sun – more plentiful CO2 – nutrient-rich soil – few herbivores or pathogens.
    • Also several problems to deal with during the colonization of land:– desiccation – structural support
  127. Four Key traits of land plants
    • 1) Alternation of generations and multicellular, dependent embryos.
    • 2) Walled spores produced in sporangia.
    • 3) Multicellular gametangia.
    • 4) Apical meristems
  128. Plants: Alternation of generations
    • Plants alternate between two multicellular stages, a
    • reproductive cycle called alternation of generations.
    • The gametophyte is haploid and produces haploid gametes by mitosis.
    • Fusion of the gametes gives rise to the diploid sporophyte,which produces haploid spores by meiosis.
  129. Plants: Multicellular dependent embryos
    • The diploid embryo is retained within the tissue of the female gametophyte.
    • Nutrients are transferred from parent to embryo through placental transfer cells.
    • Land plants are called embryophytes.
  130. Walled spores produced in sporangia
    • The sporophyte produces spores in organs called sporangia
    • Diploid cells called sporocytes undergo meiosis to generate haploid spores.
    • Spore walls contain sporopollenin, which makes them resistant to harsh environments.
  131. Multicellular gametagia
    Gametes are produced within organs called gametangia
  132. Apical meristems
    • Plants sustain continual growth in their apical meristems.
    • Cells from the apical meristems differentiate into various tissues.
  133. Bryophytes
    • Non vascular land plants
    • Bryophytes are represented today by three phyla of small herbaceous (nonwoody) plants.
    • – Liverworts, phylum Hepatophyta
    • – Hornworts, phylum Anthocerophyta
    • – Mosses, phylum Bryophyta
    • Gametophytes are larger and longer-living than sporophytes
    • A spore germinates into a gametophyte composed of a protonema and gamete-producing gametophore.
  134. Bryophyte Gametophyte Generation
    • Mature gametophytes produce flagellated sperm in antheridia and an egg in each archegonium
    • Sperm swim through a film of water to reach and fertilize the egg
  135. Bryophyte Sporophyte Generation
    • Sporophytes grow out of archegonia, and are the smallest and simplest sporophytes of all extant plant groups.
    • A sporophyte consists of a foot, a seta (stalk), and a through a peristome. sporangium, also called a capsule, which discharges spores through a peristome.
  136. Protonema
    are branched filaments that absorbs nutrients.
  137. Gametophore
    is the gamete-producing structures stemming from the protonema.
  138. Rhizoids
    anchor gametophytes to substrate
  139. Origins of vascular plants
    • Vascular plants began to diversify during the Devonian and Carboniferous periods (425 MYA).
    • Vascular tissue allowed these plants to grow tall
  140. Vascular plant traits
    • Life cycles with dominant sporophytes
    • Vascular tissues called xylem and phloem.
    • Well-developed roots and leaves.
  141. Life cycle of a seedless vascular plant
    • Seedless vascular plants have flagellated sperm.
    • Sporophytes are the larger generation.
    • The gametophytes are tiny plants that grow on or below the soil surface
  142. Xylem
    • conducts most of the water and minerals and includes dead cells called tracheids.
    • – strengthened by lignin and provide structural support.
  143. Phloem
    consists of living cells and distributes sugars, amino acids, and other organic products
  144. Roots
    • are organs that anchor vascular plants.
    • They enable vascular plants to absorb water and nutrients from the soil.
    • Roots may have evolved from subterranean stems
  145. Leaves
    • are organs that increase the surface area of vascular plants
    • – Increase the amount of solar energy that is used for photosynthesis.
  146. Spores
    • Most seedless vascular plants are homosporous, producing one type of spore that develops into a bisexual gametophyte
    • All seed plants and some seedless vascular plants are heterosporous
    • – megaspores ⎝ female gametophytes
    • – microspores ⎝ male gametophytes
  147. Plants Benefits of seeds
    • The evolution of seeds allowed for the further colonization of terrestrial habitats.
    • Seeds consists of an embryo and nutrients surrounded by a protective coat.
    • Can remain dormant for days to years, until conditions are favorable for germination.
    • Can be transported long distances by wind or animals
  148. Characteristics of Seed Plants
    • • Seeds
    • • Reduced gametophytes
    • • Heterospory
    • • Ovules
    • • Pollen
  149. Seed plant gametophyte
    • Develop within the walls of spores.
    • Greatly reduced, microscopic.
    • Protected, housed within tissues of the parent sporophyte.
    • Dependent on sporophyte for nutrition and protection
  150. Heterospory
    • Megasporangia produce megaspores that give rise to female gametophytes.
    • Microsporangia produce microspores that give rise to male gametophytes.
  151. Ovule
    • An ovule consists of:
    • – megasporangium – megaspore – one or more protective integuments
  152. Pollen
    develops from the microspore housed within the microsporangium
  153. Gymnosperms
    • Gymnosperms means “naked seeds”.
    • Vascular seed plants
    • appear about 350 MYA. Extant gymnosperms appear about 300 MYA.
    • Dominated Mesozoic (251–65 MYA) forest.
    • Adapter to drier conditions.
    • Dominated by sporophyte.
    • Seeds develop from fertilized ovules
    • Sperm transferred via pollen
    • Four extant phyla:
    • – Cycadophyta
    • – Gingkophyta
    • – Gnetophyta
    • – Coniferophyta
  154. Cycadophyta
    • Gymnosperms
    • Vascular seed plants
    • Large cones and palmlike leaves.
    • Very abundant during Mesozoic.
    • Flagellated sperm.
  155. Ginkgophyta
    • Gymnosperms
    • Vascular seed plants
    • This phylum consists of a single living species, Ginkgo
    • biloba.
    • Flagellated sperm
  156. Gnetophyta
    • Gymnosperms
    • Vascular seed plants
    • Tropical to desert species
  157. Coniferophyta
    • Gymnosperms
    • Vascular seed plants
    • ~600 species
    • Evergreens
  158. Lycophytes
    • Vascular seedless plants
    • Club mosses, spike mosses & quilworts
  159. Pterophytes
    • Vascular seedless plants
    • Ferns and horsetails
  160. Angiosperms
    • Vascular seed plants
    • Flowering plants
    • Have Flowers, Fruit
    • The most widespread and diverse of all extant plants
    • A single phylum, Anthophyta
  161. Flowers
    • Specialized for sexual reproduction.
    • Pollinated by insects, mammals or wind.
    • A flower is a specialized shoot with up to four types of modified leaves.
    • • Stamens = produce pollen
    • --– filament (stalk)
    • --– anther is the site of pollen production
    • • Carpels = produce ovules
    • --- stigma is where pollen attache
    • --- style
    • --- ovary where ovules are housed
    • • Petals = brightly colored and attract pollinators
    • • Sepals = enclose the flower.
  162. Fruit
    • A fruit typically consists of a mature ovary.
    • Fruits protect seeds and aid in their dispersal.
    • Mature fruits can be either fleshy or dry.
  163. Angiosperm life cycle
    • The flower is the sporophyte.
    • Male gametophytes are within pollen grains produced by the microsporangia of anthers.
    • The female gametophyte, or embryo sac, develops within an ovule.
  164. Basal angiosperms
    • Less derived and include the flowering plants belonging to the oldest lineages
    • • Amborella (egg formation resembles gymnosperms)
    • • Water lilies
    • • Star anise
  165. Magnoliids
    Magnoliids include magnolias, laurels, and black pepper plants
  166. Unikonta
    • Amoebozoans
    • – Plasmodial slime molds
    • – Cellular slime molds
    • Opisthokonts
    • – Fungi, animals & other protists
  167. Fungal ecology
    • Fungi are heterotrophs.
    • Use enzymes to break down complex molecules into smaller organic compounds.
    • These digestive enzymes are very versatile, which contributes to fungi’s ecological success.
  168. General structure of a fungus
    • The most common body structures are multicellular filaments and single cells (yeasts).
    • Some species grow as either filaments or yeasts; others grow as both.
    • The morphology of multicellular fungi enhances their ability to absorb nutrients
    • Fungi consist of mycelia, networks of branched hyphae adapted for absorption
    • A mycelium’s structure maximizes its surface area-to-volume ratio
    • Fungal cell walls contain chitin.
  169. Septate hyphae
    Most fungi have hyphae divided into cells by septa, with pores allowing cell-to-cell movement of organelles.
  170. Mycorrhizal fungi
    • have a mutualistic relationship with plants
    • These fungi have specialized hyphae called haustoria that allow them to penetrate the tissues of their host
  171. Coenocytic fungi
    • lack septa
    • Have a continuous cytoplasmic mass with hundreds or thousands of nuclei
  172. Ectomycorrhizal fungi
    form sheaths of hyphae over a root and also grow into the extracellular spaces of the root cortex.
  173. Arbuscular mycorrhizal fungi
    extend hyphae through the cell walls of root cells and into tubes formed by invagination of the root cell membrane
  174. Fungi Sexual reproduction
    • Fungal nuclei are normally haploid, with the exception of transient diploid stages formed during the sexual life cycles.
    • Sexual reproduction requires the fusion of hyphae from different mating types.
    • Fungi use sexual signaling molecules (pheromones) to communicate their mating type.
    • Under the appropriate conditions when cells from different mating types meet they will fuse
  175. Plasmogamy
    • is the union of cytoplasm from two parent mycelia.
    • – NOT the fusion of the nuclei.
  176. Fungi Sexual reproduction: heterokaryon
    In most fungi, the haploid nuclei from each parent do not fuse right away; they coexist in the mycelium, called a heterokaryon.
  177. Fungi Sexual reproduction: dikaryon
    In some fungi, the haploid nuclei pair off two to a cell; such a mycelium is said to be dikaryotic.
  178. Fungi Sexual reproduction: karyogamy
    • During karyogamy, the haploid nuclei fuse, producing diploid cells. – a long time can pass until fusion occurs.
    • The diploid phase is short-lived and undergoes meiosis, producing haploid spores.
    • The paired processes of karyogamy and meiosis produce genetic variation.
  179. Fungal evolution
    • Fungi, animals, and their protistan relatives form the opisthokonts clade.
    • Fungi are most closely related to unicellular nucleariids.
    • Oldest fossils of fungi are only about 460 million years old.
    • Molecular analyses suggests the fungal/animal split occurred 1 BYA
  180. Chytrids
    • Fungi
    • (phylum Chytridiomycota) are found in freshwater
    • and terrestrial habitats.
    • They can be decomposers, parasites, or mutualists.
    • Molecular evidence supports the hypothesis that chytrids diverged early in fungal evolution.
    • Chytrids are unique among fungi in having flagellated spores, called zoospores
    • The chytrid Batrachochytrium dendrobatidis might be the cause of the recent decline in amphibians worldwide
  181. zygomycetes
    • Fungi
    • (phylum Zygomycota) exhibit great diversity of life histories.
    • They include fast-growing molds, parasites, and commensal symbionts.
    • The zygomycetes are named for their sexually produced zygosporangia.
    • Zygosporangia are the site of karyogamy and then meiosis.
    • Zygosporangia, which are resistant to freezing and drying, can survive unfavorable conditions.
    • Some zygomycetes, such as Pilobolus, can aim their sporangia toward conditions associated with good food source
  182. Glomeromycetes
    • Fungi
    • (phylum Glomeromycota)
    • Glomeromycetes form arbuscular mycorrhizae
  183. Ascomycetes
    • Fungi
    • Ascomycetes (phylum Ascomycota) live in marine, freshwater, and terrestrial habitats
    • Produce sexual spores in saclike asci contained in fruiting bodies called ascocarps.
    • – sometimes called sac fungi
    • From unicellular yeasts to elaborate cup fungi and morels
    • Plant pathogens, decomposers, symbionts and predators
    • Arthrobotrys is one of several species of fungi that are predatory.
    • Ascomycetes reproduce asexually by enormous numbers of asexual spores called conidia.
    • Conidia are not formed inside sporangia; they are produced asexually at the tips of specialized hyphae called conidiophores.
  184. Basidomycetes
    • Fungi
    • (phylum Basidiomycota) include mushrooms,
    • puffballs, and shelf fungi, mycorrhizae, and plant parasites.
    • The phylum is defined by a clublike structure called a basidium, a transient diploid stage in the life cycle.
    • – sometimes called club fungi
    • Usually includes a long-lived dikaryotic mycelium.
    • The mycelium reproduces sexually by producing elaborate fruiting bodies call basidiocarps.
    • The numerous basidia in a basidiocarp are sources of sexual spores called basidiospores
  185. Lichens
    • A lichen is a symbiotic association between a photosynthetic microorganism and a fungus.
    • Millions of photosynthetic cells are held in a mass of fungal hyphae.
    • The photosynthetic component is green algae or cyanobacteria.
  186. Heterotrophs
    Obtain energy from consuming organic matter
  187. Tissues
    Groups of cells that have a common structure and/or function
  188. Clevage
    The rapid cell division without cell growth that occurs after fertilization

    Leads to formation of a multicellular blastule
  189. Blastula
    A multicellular hollow formed after cleavage.  Will undergo gastrulation, and form a gastrula with different layers of embryonic tissue
  190. Larva
    Sexually immature and morphologically distinct from adult.

    Larva undergoes metamorphosis, the reorganization of larval tissues into a juvenile.
  191. Hox Genes
    Only animals have these (mostly).

    • Regulate the development of body form.  Master regulators that give orientation to the embryo.  The genes are ordered in the
    • order they are expressed from anterior to posterior
  192. Animal Characteristics
    Multicellular Eukaryotes

    • Multicellular bodies held together by structural
    • proteins

    Nervous and muscle tissue are a unique characteristic of animals

    Most reproduce sexually.

    Diploid stage is dominant.
  193. Animal Sister group
    • Choanoflagellates
    • Sponges collar cell in coaocyte
  194. Animal Evolution: Cambrian Era
    Cambrian explosion (535-525mya) marks the early radiation of species.  

    • Contributing Factors:
    • ·     Evolution of predator/prey relationship
    • ·     Evolution of defensive and offensive structures
    • ·     Evolution of Hox genes
    • ·     Changes in atmosphere composition
  195. Animal Evolution: Paleozoic Era
    Diversity continues to increase.

    Several mass extinction events

    Transition to terrestrial habitats (460mya)

    Vertebrates transition to land ~360mya
  196. Animal Evolution: Mesazoic Era

    Coral reefs

    Dinosaurs dominated terrestrial habitats

    Mammals evolve

    Angiosperms and insects diversify
  197. Body Plan
    A set of morphological and developmental traits used to categorize animals.  Involves symmetry, tissue development, and order of developmental steps.
  198. Cephalization
    Development of a central nervous system in the head.  A central location that controls body function.   Result is more active animals.
  199. Ectoderm
    The Germ layer covering the embryo's surface
  200. Mesoderm
    An intervening layer of tissues between Ectoderm and endoderm
  201. Endoderm
    Inner most germ layer, lines the developing digestive tube called the archentron
  202. Acoelomates
    triploblastic animals that lack a body cavity (Flat worms)
  203. Pseudocoelomates
    Body cavity is derived from the mesoderm and endoderm.
  204. Coelomates
    Triploblastic animals that have a true coelom (earth worms)
  205. Radial Symmetry
    • Animals have no front, back, left or right.
    • Often sessile or planktonic animals
  206. Bilateral symmetry
    2 sided symmetry.  Have a dorsal (top), ventral (bottom), anterior (head), and posterior (tail).
  207. Protosome
    • Cleavage is spiral and determinate (ultimate fate of cells is established early on).
    • The splitting of solid masses of mesoderm forms a true coelom.
    • The blastophore forms during gastrulation and connect the archentron to the exterior of the gastrula.  
    • The blastophore will become the mouth.
  208. Deuterosome
    • Cleavage is radial and indeterminate 
    • The mesoderm buds from the wall of the archentron to form the coelom.  
    • The blastophore will become the Anus.
  209. Grade
    A group whose members share key features
  210. Porifera
    • Group metazoa
    • Sponges
    • Heterotrophic
    • Sedentary
    • Water is drawn through pores into a cavity called a spongocoel and out through the osculum.  
    • Most are hermaphrodites
  211. Cnidarians
    • One of the oldest phyla
    • Both sessisle poly p and motile forms (free-swimming medusa)
    • Simple diploblastic radial body plan
    • Gastrovascular Cavity
    • Classes: Hydrozoans, Scyphozoans, Cubozoans, Anthozoans
    • Carnivores that use tentacles to capture prey that are armed with cnidocytes with a nematocyte "harpoon"
  212. Gastrovascular Cavity
    A sac with a central digestive compartment that functions as both mouth and anus
  213. Hydrazoans
    • Phylum: Cnidarian
    • Mostly marine
    • alternate between polyp and medussa forms
  214. Scyphozoans
    • Phylum: Cnidarian
    • Jellies are most prevalent
    • Medussa form is prevalent
  215. Cubazoa
    • Phylum: Cnidarian
    • Box Jellies and sea wasps
    • highly toxic cnidocytes
  216. Anthozoans
    • Phylum: Cnidarian
    • Corals and sea anemones
    • only polyp
  217. Ctenophora
    • A clade
    • Includes comb jellies
    • diploblastic
    • radial symmetry
    • use cilia for locomotion
  218. Lophotrocochozoa
    • Grade
    • Some have feeding structures called lophophores
    • others have a distinct developmental stage called the trophophore larva
    • others have lost one or the other during evolution
    • Phylums: Platyhelminthes, Rotifera, Ectoprocta, Braciopoda, Mollusca, Annelida
  219. Platyhelminthes
    • Phylum
    • Flatworms
    • Triploblastic Acoelomates
    • Are flattened dorsoventrally and have a gastrovascular cavity with 1 opening
    • gas exchange occurs across the body surface
    • Classes: Catenulida (chain worms) & Rhabditophans
  220. Rhabditophans
    • Phylum: Platyhelminthes
    • Free living and parasitic
    • Planarians: live in fresh water and prey on small animals.  Have light sensitive eye spots (not true eyes)
    • Subgroups: Trematodes, and Tapeworms
  221. Rotifera
    • phylum
    • Tiny animals that inhabit fresh water and ocean, and damp soil.
    • Have an alimentary canal with a separate mouth and anus that lies within a fluid filled pseudocoelom
    • Triploblastic
  222. Brachiopoda
    • phylum
    • Like clams but with different shell orientation
    • have a lophophore
    • coelomates
  223. Ectoprocta
    • phylum
    • Filter feeders
    • sieve food out of water using lophophore lined with cilia
    • marie species
    • colonial
  224. Mollusca
    • phylum
    • Includes snails, slugs, oysters, clams, squid, octopi etc
    • most are marine, some terrestrial
    • Coelomates
    • Contain a muscular foot, visceral mass and mantle
    • feed with rasp like radula
    • separate sexes
    • Classes: Polyplacophora, Gastropoda, Bivalvia, Cephalopoda
  225. Polyplacophora
    • phylum: Mollusca
    • Chitins are oval shapped marine animals encased in an armor of 8 dorsal plates.  Use a foot like suction to hold on to the rock, and radula to scrape algae off it.
  226. Gastropoda
    • phylum: Mollusca
    • Majority 
    • Snails and slugs
    • Torsion which causes the animals anus to end up above its head
  227. Bivalvia
    • phylum: Mollusca
    • Marine
    • clams, oysters, mussels, and scallops
    • A shell divided into 2 halves drawn together by abductor muscles.
    • Some have eyes and sensory tentacles along the edge of their mantle
  228. Cephalopoda
    • phylum: Mollusca
    • Carnivores with beak-like jaws surrounded by tentacles
    • closed circulatory system, well developed sense organs and complex brains.
    • Squid, Octopi and nautiluses
  229. Annelida
    • Phylum
    • Bodies composed of fused rings
    • Classes: Polychaeta, Olgiochaeta
  230. Polychaeta
    • Phylum Annelida
    • "many bristles"
    • Have padlike parapodia that work as gills and aid in locomotion
  231. Olgiochaeta
    • Phylum Annelida
    • "few bristles"
  232. Ecdysozoa
    • grade
    • covered by a tough coat called a cuticle which is shed or molded through the process called ecdysis
    • Phylums: Anthropoda and Nematoda
  233. Nematoda
    • grade Ecdysozoa
    • Round worms found in everywhere
    • Have an alimentary canal, pseudocoelom, no circulatory system, no segmented body
    • C. Elgans
  234. Anthropoda
    • grade Ecdysozoa
    • 2/3 of extant species
    • segmented hard exoskeleton and jointed appendages  little variation between segments
    • Generally 3 sections: head, thorax and abdomen
    • Have eyes, olfactory receptors and antennae that function in touch and smell
    • Open circulatory system with hemolymph
    • Evolution characterized by a decrease in the number of segments and increase in specialization
    • Sub phyla: Chielicereta, Myriapoda, Hexapoda, Crustacea
  235. Chielicereta
    • Major Phylum Anthoropoda
    • Named for clawlike feeding appendages called chelicerae.  
    • Horseshoe crabs, arachanids, ticks, mites and scorpions
    • Cephalothorax with 6 pairs of appendages (Chelicerae, pedipalps, 4 walking leg sets)
    • Gas exchange occurs via book lungs
  236. Myriapoda
    • Major Phylum Anthoropoda
    • Millipedes: eat leaves, 2 leg pairs per segment
    • centipedes: eat decaying animals, 1 leg pair per segment
  237. Hexapods
    • Major Phylum Anthoropoda
    • six legs
    • Includes insects and relatives
    • Tracheal tubes are used for gas exchange
    • many undergo metamorphosis
    • some undergo incomplete metamorphosis
    • Key Innovations for success: Flight, gymnosperm adaption, angiosperm adaption
    • Over 30 orders!
  238. Coleoptera
    • phylum Heapods
    • Beetles
    • 2 pairs of wings (1 thick and strong, 1 for flying)
    • Complete metamorphosis
  239. Diptera
    • phylum Heapods
    • Flies and mosquitoes
    • 1 pair of wings and halteres (reduced second pair for balance)
    • Complete metamorphosis
  240. Hymenoptera
    • phylum Heapods
    • Bees, ants and wasps
    • Social
    • 2 pairs of wings
    • Complete metamorphosis
  241. Lepidoptera
    • phylum Heapods
    • Moths and butterflies
    • 2 pairs of wings covered in scales
    • Complete metamorphosis
  242. Hemiptera
    • phylum Heapods
    • Assassin bugs, kissing bugs (true bugs)
    • 2 pairs of wings (1 leathery)
    • Incomplete metamorphosis
  243. Orthoptera
    • phylum Heapods
    • grasshoppers and crickets
    • 2 pairs of wings (1 leathery)
    • large hind legs (hoppers)
    • Incomplete metamorphosis
  244. Crustacea
    • Phylum
    • Typically have branched appendages that are extensively specialized for feeding and locomotion
    • smaller exchange gas through cuticle, others have gills
    • Marine
    • Classes: Isopods (6 legs), Decapods (5 pairs of appendages), Barnacles (mostly sessile), Copepods (food source for many filter feeders)
  245. Fungi clade?
  246. Fungi
    • Heterotrophs
    • structures are muticellular filaments and single cells
    • Consist of mycellia, and hyphae, and septa
  247. Mycellium
    • Fungi
    • A collection of hyphae in a net like structure.
    • Most of a fungus's life cycle is spent in this structure.
  248. Hyphae
    • Fungi
    • Funcale cell walls containe chitin, divided into cells by septa
  249. Septa
    • Fungi
    • pores allowing cell to cell movement of organelles
  250. Coenocytic Fungi
    Have a continuous cytoplasmic mass with hundreds or thousands of nuclei
  251. Mycorrhizal Fungi
    • Have a mutalistic relationship with plants
    • Have specialized hyphae call haustoria that allow them to penetrate the tissues (cell walls not membranes) of their host.  resulting in an increase in surface to area which they interact and exchange nutrients.
  252. Ectomycorrhizal Fungi
    Form sheaths of hyphae over a root and grow into the extracellular spaces of the root cortex
  253. Arbuscular Mycorrhizal Fungi
    extend hyphae through cell walls of root cells and into tubes...
  254. General Fungus Life cycle
    Image Upload 1
  255. Plasmogamy
    • Fungi
    • The union of the cytoplasm from two parent mycellia.
    • Fusion of two haploid cells to make an heterokaryotic cell (n+n)
  256. Karyogamy
    • Fungi
    • Fusion of haplois nuclei to make a zygote (2n).
    • This step can take awhile to occur
  257. Heterokaryon
    • Fungi
    • A cell where the haploid nuclei from each parent does not fuse right away they coexist in the mycellium
    • Organism is technically diploid (n+n)
  258. Dikaryotic
    • In some fungi the haplois nuclei pair off two to a cell. 
    • 1 cell with 2 haploid nuclei still unfused
  259. Meiosis in Fungi
    After karyogaomy, the diploid zygote stage is short lived and undergoes meiosis producing haploid spores.
  260. Fungi Evolution
    • Oldest fossils are ~460MYA
    • Molecular analysis suggests that fungal animal split occured ~1BYA
    • Fungi are among the earliest colonizers of land
  261. Fungal Phylogeny
    Image Upload 2
  262. Chytrids
    • Fungi kingdom
    • Fresh water and terrestrial habitats
    • Unique among fungi in having flagellated spores called zoospores
  263. Zogomycetes
    • Fungi kingdom
    • Include molds, parasites etc
    • Named for their sexually produced zygosporangia (site of karyogamy and meiosis).
    • Resistant to drying and freezing and can survive unfavorable conditions
  264. Glomeromycetes
    • Fungi kingdom
    • Form arbuscular mycorhizae
  265. Ascomycetes
    • Fungi kingdom
    • All habitats
    • PRoduce spores in sac like asci contained in fruiting bodies called ascocarps - sometimes called sac fungi
    • From unicellular yeasts to elaborate cup fungi and morels
    • Reproduce asexually by enormous numbers of asexual spores called condia which are not formed inside the sporangia
  266. Basidiomycetes
    • Fungi kingdom
    • Mushrooms, puff balls, shelf fungi, mycorrhizae and plant parasites
    • many are decomposers
    • Defined by a cubelike structure called the basidium, a transient diploid stage.
    • Reproduces sexually by producing elaborate fruiting bodies called basidiocarps (mushrooms)
  267. Echinodermata
    • Vertebrates, Deuterostomia
    • Slow moving sessile marine animals
    • Have a thin epideris that is calcified
    • Water vascular system (network of hydrolic canals branching into tube feet that function in locomotion and feeding)
    • Seperate sexes, external fertilization
    • Radial like symmetery with multiples of 5 (starfish)
    • Larvae have bilateral symmetry
    • Classes: Asteroidea, Ohiuroidea, Echinoidea, Crinoidea, Holothuroidea
  268. Asteroidea
    • Phylum: Echinodermata
    • Sea Stars
    • Multiple arms radiating from a central disk
    • Feed on bivalves by prying them open with their tube feet
  269. Ohiuroidea
    • Phylum: Echinodermata
    • Brittle Stars
    • Distinct disk with long flexible arms which they use for movement
    • Some are suspension feeders, some are predators
  270. Echinoidea
    • Phylum: Echinodermata
    • Sea Urchins and sand dollars
    • Have no arms but 5 rows of tube feet
    • Spines are used for locomotion and protection
    • Mostly feed on seaweed
  271. Crinoidea
    • Phylum: Echinodermata
    • Sea lillies and feather stars
    • Suspesion feeders can live attached to the substrate stalk.
    • Feather stars can crawl using long flexible arms
  272. Holothuroidea
    • Phylum: Echinodermata
    • Sea cucumbers
    • lack spines, reduced endoskeleton
    • have 5 rows of tube feet, some are modified feeding tubes
  273. Chordata
    • Major phylum
    • 2 clades of invertebrates, rest are vertebrates
    • Body plan: Notochord, Dorsal hollow nerve cord, pharyngeal slits or clefts, and muscular post anal tail
  274. Notochord
    • found in chordata
    • a longitudinal flexible rod between digestive tube and nerve cord.  Provides skeletal support throughout most of the chordate.
    • In most a more complex exoskeleton develops
  275. Dorsal Hollow nerve cord
    The nerve cord of a chordate embryo develops from a plate of ectoderm that rolls into a tube dorsal to the notochord
  276. Pharyngeal Slits and Clefts
    • Clefts: in most chordates grooves in the pharynx called pharangeal clefts develop into clits that open to the outside of the body
    • Slits:
    • suspension feeding structures in many invertebrate chordates,
    • gas exchange in vertebrates (not tetrapods)
    • develop into parts of the ear, head, and neck in tetrapods
  277. Muscular post anal tail
    • chordates have a tail posterior to the anus
    • in many species its greatly reduced
  278. Cephalochordata
    • Chordata
    • Include lancelets
    • Are marine suspension feeders that retain characteristics of the chordate body plan as adults
    • Invertebrates
    • most basic chordate
  279. Urochordata
    • Chordata
    • Tunicates
    • resemble chordates in their larval stage
    • sea squirts
  280. Craniates
    • Group
    • Have a skull brain, eys, and other sensory organs
    • Have a neural crest: gives rise to bones, cartlidge or a skull
    • Have higher metabolism and are more muscular than invertebrates, lancelets and tunicates
    • Have: Heart with at least 2 chambers, red blood cells, kidneys
    • ~530 mya we see origin of skulls
  281. Myxini
    • Most basic craniates
    • Hag fishes
    • lack jaws and vertebrae
    • marine, bottom dwelling scavengers
  282. Vertebrates
    • Group
    • Characteristics:
    •  Vertebrae enclosing a spinal cord
    •  An elaborate skull
    •  Fin rays in the aquatic forms
  283. Conodonts
    The first vertebrates with mineralized skeletal elements in their mouth and pharynx
  284. Petromyzontida
    • Vertebrates
    • Lampreys
    • Oldest living lineage of vertebrates
    • jawless maring and freshwater
    • feed by clamping their mouth onto the side of a fish
    • have cartilaginous segments surrounding the notochord and arching partly over the nerve cord
  285. Gnathostomes
    • group
    • Evolution of jaws and mineralized skeleton
    • Includes sharks, ray-finned fishes through mammalia
    • Jaws are believed to be derived from skeletal supports of the pharyngeal slits
    • large forebrain
    • 3 lineages left today:
    •  Chondrichtyes
    •  Ray Finned fishes
    •  lobe fins (us)
  286. Chondrichtheys
    • most basal phylum of vertebrates
    • Have a skeleton composed primarily of cartlidge
    • sharks, rays and skates
  287. Oviporous
    • Embryo development from eggs
    • eggs hatch outside the mother's body
  288. Ovoviviparous
    • Embryo development from eggs
    • Embryo develops within the uterus and is nourished by the egg yolk
  289. Viviparous
    • Embryo development from eggs
    • Embryo develops within the uterus and is nourished through the yolk sac placenta from the mother's blood
  290. Osterichthyes
    • group
    • Evolution of lungs
    • nearly all have an endoskeleton
    • includes bony fish and tetrapods
  291. Fish
    • defines the phylums Actinistia, Diponi and Actinpterygii
    • Control buoyancy with an air sac known as a swim bladder (a modified lung)
    • most are ovipoarous
  292. Actinpterygii
    • group Osterichthyes
    • Ray-fnned or bony fish
    • Originated during Silurian period
    • Have fins supported by long flexible rays used for locomotion and defense
    • Include seahorses
  293. Lobe-Fin Fish
    • group
    • us included in lobe fins
    • have rod shaped bones surrounded by muscles in their pelvic and pectoral fins
  294. Tetrapods
    • groups
    • Have specific adaptations
    • 1) Four limbs and feet with digits
    • 2) have a neck which allows for separate movement of head
    • 3) fusion of pelvic bone and girdle to backbone
    • 4) the absence of gills
    • 5) ears for detecting airborne sounds
  295. Tiktaalik
    • Evolution of the tetrapod
    • "fish a pod"
    • ~375 MYA
  296. Amphibia
    • Clade
    • Body plan: undergo metamorphosis from an aquatic larva into a terrestrial adult
    • most have moist skin that complements the lungs in gas exchange
    • Fertilization is external and requires a moist enviroment
    • contains:
    • 1) Urodela, ie salamanders
    • 2) Anura, frogs and toads
    • 3) Apoda, legless salamanders
  297. Urodela
  298. Anura
    Frogs and toads
  299. Apoda
    Caecilians (legless salamanders not snakes)
  300. Aminotes
    • group
    • All reptiles, birds and mammals
    • major derived character is amniotic egg
    • relatively impermeable sking and ability to use ribcage to ventilate the lungs
    • split from common ancestor ~350MYA
  301. Amniotic Egg
    • contains 4 extraembryonic membranes
    • 1) Amnion (protection)
    • 2) Allatois (wastes and gas exchange)
    • 3) Chorion (gas exchange)
    • 4) Yolk sac (storage of nutrients for embryo)
  302. Reptiles
    • Includes: Tuataras, lizards, snakes, turtles, aves, crocodilia, and extinct dinosaurs
    • Have scales that create a waterproof barrier.  Lay shelled eggs on land
    • most are ectothermic - aves are endothermic
    • ~359-299 MYA
  303. Testudines
    • Turtles
    • have a boxlike shell made of upper and lower shields that are fused to the vertebrae, clavicles and ribs
    • Phylogenetic placement not yet determined
  304. Aves
    • Birds or archosaurs adapted for flight
    • HAve:
    • 1) Wings with keratin feathers
    • 2) lack a urinary bladder
    • 3) females with 1 ovary
    • 4) small gonads
    • 5) loss of teeth
    • May have evolved from theropods
    • Early feathers may have helped dinosaurs gain lift when they jumped, gain traction running up hills, or helped glide from trees
  305. Squamates
    Lizards and snakes
  306. Mammalia
    • "Milk"
    • +/- 5000 species
    • Have:
    • 1) Mammary glands
    • 2) Hair
    • 3) A high metabolic rate due to endothermy
    • 4) larger brain than vertebrates of equivalent size
    • 5) differentiated teeth
    • Evolved from synapdids (a characteristic of which is the fenestra - a hold behind the eye socked to support muscles).
    • By ~140MYA 3 living lineages of mammals emerged
    • Lineages: Monetremes, Marsupials, Eutherians
  307. Monotremes
    • Mammals
    • Small group of egg laying mammals consists of echidnas and platypus. 
    • No nipples instead have an area of skin that sweats milk
  308. Marsupials
    • Mammals
    • Opossums, kangaroos, and kooalas.
    • Embryo develops within a placenta in the mother's uterus.  Born very early and finishes development in mother's pouch called a marsupium
  309. Eutherians
    • Mammals
    • More complex placenta
    • Complete embryonic development inside a uterus joined to the mother by the placenta
  310. Fixed Action Pattern
    • A sequence of unlearned, innate behaviors that is unchangeable.
    • Once initiated it is usually carried to completion
    • Triggered by an external cue, known as stimulus
    • Example: Male stickleback fish see the red underside of an intruder and attack
  311. Migrating Behavior
    • Migration is regular, long-distance change of location
    • Environmental cues can trigger movement in a particular direction
  312. Courtship: Chemical Communication
    • He smells a female's chemicals in the air
    • (step 1 in drosophila melanogaster courtship)
  313. Courtship: Visual Communication
    • He sees the female and orients his body toward her
    • (step 1 in drosophila melanogaster courtship)
  314. Courtship: Tactile Communication
    • He taps the female with a foreleg
    • (step 2 in drosophila melanogaster courtship)
  315. Courtship: Chemical Communication
    • He chemically confirms the female's identity
    • (step 2 in drosophila melanogaster courtship)
  316. Courtship: Auditory Communication
    • The male produces a courtship song to inform the female of his species
    • (step 3 in drosophila melanogaster courtship)
  317. Honeybee Communication
    Honeybees show complex communication with symbolic language

    A bee returning from the field performs a dance to communicate information about the distance and direction of a food source
  318. Fixed Behavior
    • Innate behavior is developmentally fixed and does not vary among individuals
    • Some behavior is influenced by the environment
    • A cross-fostering study places the young from one species in the care of adults from another species
    • – e.g California mice and white-footed mice
  319. Learning
    Learning is the modification of behavior based on specific experiences
  320. Imprinting
    • Imprinting is a behavior that includes learning and innate components and is generally irreversible.
    • It is distinguished from other learning by a sensitive period.
    • A sensitive period is a limited developmental phase that is the only time when certain behaviors can be learned
  321. Spatial Learning
    • Spatial learning based on experience with the spatial structure of the environment.
    • Animals build cognitive maps – a representation of spatial relationships between objects in it’s surroundings.
  322. Associative Learning
    • In associative learning, animals associate one feature of their environment with another.
    • – operant conditioning
    • – classical conditioning
  323. Cognition
    Cognition is a process of knowing that may include awareness, reasoning, recollection, and judgment
  324. Problem Solving
    Problem solving is the process of devising a strategy to overcome an obstacle.
  325. Social Learning
    Social learning is learning through the observation of others and forms the roots of culture.
  326. Culture
    Culture is a system of information transfer through observation or teaching that influences behavior. – can alter behavior and fitness of individuals.
  327. Promiscuous Mating Behavior
    No strong pair-bonds or lasting relationships
  328. Monogamous Mating Behavior
    • One female with one male
    • Monogamous species tend to be less sexually dimorphic
    • If the offspring required lots of resources A male maximizes his reproductive success by staying with his mate, and caring for his checks (monogamy).
  329. Polygamous Mating Behavior
    • individual of one sex mates with several individuals of the other sex
    • Polygamous species tend to be more sexually dimorphic.
    • polygynous: male more showy,one male mates with many females
    • polyandrous :female more showy, one female mates with many males
    • If the offspring required few resources A male maximizes his reproductive success by seeking additional mates (polygyny).
  330. Parental care behavior
    • Certainty of paternity influences paternal care and mating behavior.
    • Paternal certainty is relatively low in species with internal fertilization. – more paternal care
    • Paternal certainty is high in species with external fertilization. – little paternal care
  331. Sexual selection
    • Sexual dimorphism results from sexual selection, a form of natural selection.
    • In intersexual selection, members of one sex choose mates on the basis of certain traits.
    • Intrasexual selection involves competition between members of the same sex for mates.
  332. Alturism
    Sometimes animals behave in ways that reduce their individual fitness but increase the fitness of others

    Three key variables involved in an altruistic act – Benefit to the recipient (B) – Cost to the altruistic (C) – Coefficient of relatedness (r)
  333. Inclusive fitness
    Inclusive fitness is the total effect an individual has on proliferating its genes by producing offspring and helping close relatives produce offspring
  334. Coefficient of Relatedness
    • Fraction of genes that, on average, are shared
    • – parent-offspring = 0.5 
    • – full-sibs = 0.5
    • – uncle = 0.25
    • – cousins = 0.125
  335. Hamilton’s rule
    • Natural selection favors altruism when
    • rB > C

    • Benefit to the recipient (B)
    • Cost to the altruistic (C)
    • Coefficient of relatedness (r)
  336. Ecology
    • Ecology is the scientific study of the interactions between organisms and the environment.
    • These interactions determine distribution of organisms and their abundance
  337. Organismal ecology
    • Organismal ecology studies how an organism’s structure, physiology, and (for animals) behavior meet environmental challenges.
    • Organismal ecology includes physiological, evolutionary, and behavioral ecology
  338. Population ecology
    • A population is a group of individuals of the same species living in an area.
    • Population ecology focuses on factors affecting population size over time.
  339. Community ecology
    • A community is a group of populations of different species in an area.
    • Community ecology deals with the whole array of interacting species in a community
  340. Ecosystem ecology
    • An ecosystem is the community of organisms in an area and the physical factors with which they interact.
    • Ecosystem ecology emphasizes energy flow and chemical cycling among the various biotic and abiotic components.
  341. Landscape ecology
    • A landscape or seascape is a mosaic of connected ecosystems.
    • Landscape ecology focuses on the exchanges of energy, materials, and organisms across multiple ecosystems.
  342. Global ecology
    • The biosphere is the global ecosystem, the sum of all the planet’s ecosystems.
    • Global ecology examines the influence of energy and materials on organisms across the biosphere.
  343. Climate
    • The long-term prevailing weather conditions in an area constitute its climate.
    • Climate is shaped by four major abiotic components:
    • – temperature
    • – precipitation
    • – sunlight
    • – wind
  344. Anthropogenic climate change
    • Global climate change caused by humans. – Emission of greenhouse gasses
    • • Fossil fuels
    • • Agriculture
    • • Land use change
  345. Microclimate
    • Microclimate is determined by fine-scale differences in the environment that affect light and wind patterns
    • Every environment is characterized by differences in:
    • – Abiotic factors, including nonliving attributes such as temperature, light, water, and nutrients.
    • – Biotic factors, including other organisms that are part of an individual’s environment.
  346. Biomes
    • Biomes are major life zones characterized by vegetation type (terrestrial biomes) or physical environment (aquatic biomes).
    • Climate affects the latitudinal patterns of terrestrial bones
    • Biomes are affected by the mean and variance in temperature and precipitation.
  347. Population Density
    • Density is the number of individuals per unit area or volume.
    • Sampling techniques can be used to estimate densities and total population sizes.
    • Population size can be estimated by: – extrapolation from small samples – an index of population size – mark-recapture method
    • Density is the result of an interplay between processes that add individuals to a population and those that remove individuals
  348. Dispersion
    • Dispersion is the pattern of spacing among individuals within the boundaries of the population
    • Environmental and social factors influence the spacing of individuals in a population
    • Clumped Dispersion: In a clumped dispersion, individuals aggregate in patches. A clumped dispersion may be influenced by resource availability and behavior
    • Uniform Dispersion: A uniform dispersion is one in which individuals are evenly distributed. It may be influenced by social interactions such as territoriality.
    • Random Dispersion: In a random dispersion, the position of each individual is independent of other individuals.  It occurs in the absence of strong attractions or repulsions
  349. Demographics
    Demography is the study of the vital statistics of a population and how they change over time.
  350. Survivorship Curves
    • Type I: low death rates during early and middle life and an increase in death rates among older age groups
    • Type II: a constant death rate over the organism’s life span
    • Type III: high death rates for the young and a lower death rate
    • for survivors
  351. Exponential population growth
    • Exponential population growth is population increase under idealized conditions
    • Under these conditions, the rate of increase is at its maximum, denoted as rmax
    • Exponential growth cannot be sustained for long in any population
  352. Carrying Capacity
    • Carrying capacity (K) is the maximum population size the environment can support.
    • Carrying capacity varies with the abundance of limiting resources
  353. Logistic population growth
    • In the logistic population growth model, the per capita rate of increase declines as carrying capacity is reached
    • Exponential model + an expression that reduces per capita rate of increase as N approaches K
  354. Life history traits
    • An organism’s life history comprises the traits that affect its reproduction and survival
    • – Age at which reproduction begins
    • – How often the organism reproduces cycle
    • – How many offspring are produced during each reproductive cycle
    • Species that exhibit semelparity reproduce once and die
    • Species that exhibit iteroparity produce offspring repeatedly
Card Set
Organismal Biology
For Organismal Biology class
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