Biology 1020 Fall 2005 - Lectures 1 -10
Ch. 1; Ch. 22: 414-417, 414-426. Ch. 23 428-430, 432-438
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Introduction, Biodiversity, Taxonomy
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Biodiversity is a broad and very popular term these days. It can
mean a number of things
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species diversity within an area
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genetic diversity within a species or population
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it is an important measure of the genetic resources available
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in order to understand biodiversity and its implications we have to
have some understanding of what is out there. That is in part what this
course is about. It is intended as an introduction
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To appreciate diversity at the broadest level, we need some
understanding of structure, which requires learning some morphology and
terminology. That too is what this course is about.
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As it happens, most of the structures that distinguish groups of
organisms perform particular functions for the organisms, so a knowledge
of structure also necessitates or allows a knowledge of function.
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estimates of known species- 1.6 million - there may be as many as
5 to 100 million species total, indicating that we only know a fraction of
what exists
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history of the view of diversity
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even the first "scientific" classification systems are
hierarchical, with mutually exclusive categories
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Aristotle (384-322 BC)
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recognized an overall similarity among the major groups
• divided higher animals into two main groups (blood vs no
blood) that are very similar to vertebrates and invertebrates
today
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Linnaeus (1707-1778)
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pioneered binomial nomenclature
• constructed extensive hierarchical system of living
organisms
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Darwin (1809-1882)
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naturalist on the Beagle (1831-1836)
His theory of evolution
• Descent with modification - From Chapter 13 of the Origin of
Species (Darwin, 1859)
"Such expressions as that famous one of Linnaeus, .... that the
characters do not make the genus, but that the genus gives the
characters, seem to imply that something more is included in our
classification, than mere resemblance. I believe that something more is
included; and that propinquity of descent, the only known cause of
the similarity of organic beings, is the bond, hidden as it is by various
degrees of modification, which is partially revealed to us by our
classifications."
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Propinquity = nearness of relationship; kinship;
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Why are species similar to each other? - propinquity of descent
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Why are they different from one another? - Natural Selection
Natural selection
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differential reproductive success
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overproduction - i.e. the "Malthusian struggle" - results in
differential survival - think of cottonwood trees - produce more
seeds than ever survive
• selection occurs through interaction between the environment and
genetic variability among individuals within the population
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artificial selection provided some evidence that natural
selection could play a role in shaping the structures of individuals
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natural selection may take longer but the process is
essentially the same, except that the environment is applying the
selection pressure, not humans.
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The product of natural selection is adaptation
• although heritability was important in Darwin’s theory of natural selection
he had no clear idea of how genetics worked - he knew about propinquity of
descent (likeness due to kinship); but he didn’t know how it happened
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he considered inheritance to occur via ‘blending’
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he also knew that variation had to be being continually manufactured - but
did not know about mutation
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Neo-Darwinism - is the incorporation of genetics into the theory (1930s)
• at this same time, there were a number of mathematical biologists who
developed basic models for how evolution worked
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re-examine Darwin’s finches
• mutation would have to occur to allow the emergence of the new
‘traits’ such as seed eating, stick use etc.
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selection would occur to make those traits more common
• isolation would have to have occurred to allow the divergence of
the populations
• drift may have played a role also since a small number of migrants
arriving on the island may not be a representative sample
•Speciation & Phylogeny (Ch. 25)
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reproductive isolation leads to divergence
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the lack of migration among islands means that changes that occur
in one population via selection, drift or whatever means, cannot be passed
on to another population
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when this occurs the populations diverge
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as time passes and more differences accumulate, speciation may
occur; i.e. even if the two populations were in contact again, they would
not interbreed
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divergence in the tree is then thought to represent a speciation
event.
• if there is one true evolutionary history experienced by organisms on
earth, there is one true evolutionary tree that reflects that history. How can we
determine what that tree is?
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Phylogenetic (Cladistic) methods.
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the branches of the tree show two aspects of evolution
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anagenesis - change without branching - a single species
changes over time
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cladogenesis - divergence events
determining the branching points
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we use the concept of derived characters and parsimony to
construct a tree
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derived characters are recognized by outgroup comparison;
the closest relative to the group under study is the outgroup
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from each branching point there has to be a derived
character that occupies one branch while the ancestral character
may remain and occupy the other branch
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the correct tree is thought to be the one that incorporates the
fewest steps (fewest changes from ancestral to derived characters the idea that evolution is parsimonious)
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symplesiomorphies (shared ancestral characters) versus
synapomorphies (shared derived characters)
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symplesiomorphies show no evidence of relationship
• the presence of ‘more than two’ digits on the forearm would
be a symplesiomorphy shared by most four legged organisms
(e.g. frogs and gorillas); the shared presence of two digits
(cloven hooves) on ungulates is a synapomorphy that unites
cattle, deer, moose etc.; yet ungulates are more related to
gorillas than frogs are (both are mammals)
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homology and analogy
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shared derived characters are homologies; they are present
in the common ancestor; ancestral characters are also homologies
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parallelisms or convergences are analogies; they are not
similar due to common descent
• for example - the wings of insects, birds, and bats parallelisms
• the similarities of whales and fish are due to convergence or
a reversal, not due to common ancestry
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organisms can be similar for three reasons
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synapomorphies
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symplesiomorphies
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homoplasy or analogies (Convergences/parallelisms)
we then can therefore think of three different kinds of groups
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monophyletic - based on synapomorphies
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paraphyletic - based on symplesiomorphies
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polyphyletic - based on analogies
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only monophyletic groups reflect the branching pattern of the tree.
They are therefore considered the most useful.
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some of our system is still based on overall similarity (or difference)
rather than strict cladistic methodology, so paraphyletic groups still exist.
• Origin of Life (Chapter 26) and Prokaryotes (Chapter 27)
• Origin of Life
• the age of the earth is estimated at 4.5 billion years
• 3.5-1.7 billion years ago - prokaryotes and aqueous environments
• evidence for life
• how did life originate?
• properties of life
• Heredity - reproduction
• Metabolism - controlled reactions and growth
• cellular structure - membranes
• all three of these properties depend on long chain molecules - polymers
(made up of monomers)
• DNA/RNA (bases)
• Proteins (amino acids)
• Membrane (phospholipids)
• Miller’s studies were the first to show the formation of monomers
• anaerobic conditions (like in the primitive atmosphere) promote polymer
formation - some perhaps requiring a clay surface
• the formation of short RNA strands can also occur spontaneously
• replication using existing RNA as a template has been demonstrated (for
short strands)
• RNA can also act as an enzyme and therefore promote its own
replication (Fig. 26.5) - if protected within a membrane then the enzyme
produced will benefit only the RNA that produced it
• Prokaryotes (Chapter 27)
• Characteristics of prokaryotes
• no true nucleus - no nuclear membrane and the DNA is not
associated with protein (not a chromosome like in eukaryotes)
• 1 - 5 um
• shape varies, most are unicellular, for some its not too clear
(Cyanobacteria)
• cell wall of peptidoglycan for Eubacteria - gram positive - lots of
peptidoglycan; gram negative - less and more complex structure
• motility
• reproduction via binary fission
• metabolic diversity is greater among prokaryotes than eukaryotes
(Table 27.1)
• nitrogen metabolism is in prokaryotes
• the origins of metabolism
• Table 27.2 compares Archaea, Bacteria, Eukarya
• Endosymbiosis & Origin of Eukaryotes (Ch. 28); Origin of Diploidy & Life
Cycles (Ch. 13)
• Ecology of Prokaryotes
• decomposers
• nitrogen fixers, photosynthesis,
• can metobolize a range of inorganic molecules that other organisms
cannot
• many bacteria are symbiotic
• disease bacteria
• research and technology
• Origins of Eukaryotes
• compartmentalization of processes within cells
• could have arisen in 1 of 2 ways
• invagination of the plasma membranes
• endosymbiosis of other prokaryotes
• structures that needed to arise
• membrane bound nucleus
• mitochondria, chloroplasts, endomembrane system
• cytoskeleton
• 9+2 flagella
• chromosomes with linear (not circular) DNA associated with proteins
• meiotic life cycles
• Endosymbiotic Theory (Fig. 28.3)
• mainly chloroplasts and mitochondria
• chloroplasts are descended from cyanobacteria
• mitochondria from aerobic heterotrophs
• perhaps either parasites or undigested prey of larger prokaryotes
• the association progressed to one of mutualism
• as it became more stable the two organisms melded into one
• endosymbiotic relationships still exist today
• evidence for the hypothesis
• molecular systematic evidence also supports theory (rRNA sequence
data)
• the 9+2 flagella may also have arisen via endosymbiosis (a spirochete)
• the spindle apparatus that facilitates mitosis/meiosis may be of the
same origin as the flagellum
• Implications for Phylogeny
• the possibility of continued endosymbioses means that there is
continued “leakage” across wide branches of the tree
• Sexual Reproduction
• the ancestral eukaryotic cell was haploid (outgroup comparison)
• how did diploidy arise
• fusion of two haploid cells
• temporary co-existence of the two cells may have had an advantage
under some circumstances
• cell would be larger; cell division is slower; genetic base may be
broader
• cell division may be the “regurgitation” of the original nucleus
• or it may be triggered by normal ‘mitotic division’ including chromosome
doubling beforehand
• or it could be a combination of the two like modern meiosis
•Lecture #6 - Photosynthetic Protista (Chapter 28 and the following
web sites are useful)
http://www.ucmp.berkeley.edu/chromista/chromista.html
http://www.ucmp.berkeley.edu/protista/dinoflagellata.html
http://tolweb.org/tree?group=Eukaryotes&contgroup=Life
• Introduction
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the aqueous environment provides a stratified light environment
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different depths have different light quantity and quality
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eukaryotic PHS organisms all have chloroplasts
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if endosymbiosis happened more than once, there is the possibility
that chloroplast may differ (derived from different organisms; they also
may have differentiated after endosymbiosis
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they do differ in the kinds of chlorophyll they have!
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those with similar chlorophylls have other similar traits, and are
not clearly related to the other lineages, aside from being eukaryotes
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besides chloroplast characters, we look at cell wall structure,
storage products and motility to determine relationships among the
photosynthetic protists
• The Chlorophyll A+C lineage - (Bacillariophyta, Phaeophyta,
Dinoflagellates, some heterotrophs) - spans two different major clades (Table
28.1)
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Alveolata
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Dinoflagellates (Fig. 28.10 - photo)
• both colourless and chlorophyllous forms
• marine or fresh -common marine phytoplankton
• cell wall of cellulose plates inside the plasma membrane
• storage of starch
• flagella
• symbionts in animals = zooxanthellae - coral
• nucleus is unusual
• red tides (paralytic shellfish poisoning and other toxins)
• bioluminescence
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Stramenopila
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Bacillariophyta (diatoms) - (Fig. 28.16 - photo)
• wide distribution
• silica shells (cell walls)
• chrysolaminarin - storage product
• chiefly vegetative reproduction
• important member of the food chain
• useful paleoecologically
• important for filters, as abrasives (polishers),
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Oomycota (water molds) - Fig. 28.14 - know the life cycle
(gametic meiosis)
• large aquatic group with some terrestrial pathogens
• cellulose cell wall, not chitin like the fungi
• mycolaminarin storage product
• coenocytic (multinucleate) filaments
• vegetative reproduction -motile zoospores 1 tinsel; 1
whiplash
• sexual reproduction is oogamous
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Phaeophyta - brown algae
• cell wall cellulose and alginic acids
• storage - laminarin/mannitol (sugar alcohol) but no starch
• characteristic zoospores
• mostly marine north temperate rocky shore dwellers
• structural complexity
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reproduction (Fig. 28.21) - know the life cycle (sporic meiosis)
Photosynthetic Protista 2 - the algae (Ch. 28)
• The Chlorophyll A lineage
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Rhodophyta
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accessory pigments (phycobilins) impart red colour
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floridean starch as a storage product
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cell wall of cellulose and sulfated polysaccharides
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no flagellated types
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mostly marine -tropical and sub-tropical
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mostly filamentous (even parenchymatous types)
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pit connections exist between cells
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many parasitic types
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complex life cycles are characteristic
• The chlorophyll A+B lineage - Greens, Euglenoids, stoneworts
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Chlorophyta
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chl A+B; other accessory pigments
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starch for storage
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cell wall -cellulose or other polysaccharides
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flagella -whiplash; different numbers
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widespread
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unicellular to large multicellular
• Class Chlorophyceae-zygotic meiosis
• Class Ulvophyceae -sporic meiosis
• Class Charophyceae -zygotic meiosis
2. - Heterotrophic Protista
• Archaezoa
• ancient animals - maybe (because they lack mitochondria)
• DIplomonads have two nuclei (Giardia is an example)
• it is possible they once had mitochondria, based on their ability to
encode mitochondrial proteins
• either way they are basal on the tree
• mitochondrial loss may not be a homology
• Euglenozoa (flagellates)
• Euglenoids
• paramylum (storage)
• cell wall of protein
• autotrophic, mixotrophic and/or heterotrophic
• Kinetoplastids
• several parasites like African sleeping sickness
• kinetoplast organelle that houses extra nuclear DNA
• Alveolata
• Dinoflagellates
• Apicomplexans
• all are parasites of animals
• the apex of the sporozoite is specialized for penetration of host cells
• many have intricate life cycles with different hosts
• Plasmodium causes malaria
• every year up to 300 million infected; 2 million die
• the parasite hides in the red blood cells and the liver
• Ciliates (e.g. Paramecium)
• cilia are shorter than flagella
• coordinated by microtubules
• very complex and often large cells
• two types of nuclei (macro and micro) (Fig. 28.9)
• macro
• contains many copies of the genome packaged in units of a
few genes (but many copies)
• RNA synthesis and asexual reproduction
• micro - sex - see Fig. 28.9
• Amoebae (Table 28.1)
• pseudopodia - feeding and locomotion
• Rhizopods (Amoebae)
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• Actinopods (Heliozoans, Radiolarians)
• ray foot
• radiating pseudopodia
• silica shells like the Diatoms
• Foraminiferans
• mostly marine
• calcium carbonate shells
• extensive fossil record
• Plasmodial Slime Molds
• Cellular Slime Molds
Fungi - - Introduction to the Fungi (Ch. 31)
1. people used to think fungi were plants or related to plants- why?
1. non-motile
2. similar habitat
3. cell walls
4. basically......because they looked similar
2. there are two sources of similarity among organisms
1. they either are similar because they share a common ancestor
2. or they are similar because there was strong selection pressure for the
organisms to evolve the same character and converge
3. more than 100,000 species of fungi (estimated to be about 1.5 million)
4. Fungal Characteristics
1. Habitat - most fungi are terrestrial
2. cell wall of chitin
3. glycogen is the major storage product; lipids are also used sometimes
4. cell division
1. nuclear envelope doesn’t break down as it does in other organisims constricts
2. most fungi (except the chytrids) lack centrioles
5. heterotrophs - absorptive
1. hyphae in a mycelium
2. extensive surface area and rapid growth
6. reproduction
1. spores are common
1. both sexual and asexual
2. sexual reproduction is less common
3. mostly haploid except after hyphal fusion
1. plasmogamy and karyogamy are distinct events - dikaryon can be a
long term event
2. after fusion the dikaryon may have dispersed nuclei (within hyphae) or
not
7. most fungi have no motile stages
5. There are 4 phyla, separated most easily with the help of reproductive structures,
especially sexual
6. Biology and Classification (Fig. 31.9)
1. Chytridiomycota (790 species)
1. mainly aquatic, some unicellular
2. Allomyces is the best known
7.
8.
9.
10.
3. only ones with flagellated stages
4. some saprobes, others are parasites
5. absorptive nutrition; chitin as a cell wall
1. enzymes and metabolism similar to fungi
6. ancestral position according to molecular data - flagella are therefore
ancestral in fungi
2. Zygomycota (600 species)
1. terrestrial - saprophytic
2. some are mycorrhizal
3. Rhizopus (bread mould) is a good example (Fig 31.12 - life cycle - know)
3. Ascomycota (60,000 species)
1. sac fungi - marine, fresh water, terrestrial
2. some pathogens, many saprophytes
3. about half are in association with algae growing as lichens
4. some are mycorrhizal; some mutualistic in other ways (live in leaf surfaces
and secrete toxins that protect the plant against insects)
5. ascospores in asci in or on ascocarps
6. asexual spores are naked spores or conidia
7. a more extensive dikaryon than the basidiomycota (Fig. 31.17 - life cycle know)
4. Basidiomycota (25,000 species)
1. mushrooms, shelf fungi, puffballs and rusts
2. saprophytic - wood and other plant materials - degrade lignin
3. septate hyphae with clamp connections
4. life cycle - long lived dikaryon - Fig 31.20 - know
1. asexual reproduction less common than in ascomycetes
2. basidiocarp (Basidioma)
1. formation may require light and CO2 - signals the fungus that it is
outside its environment
3. gills are about 200 sq. cm in area - about a billion spores
4. stinkhorns disperse spores via insects
5. rusts like wheat rust are also basidiomycetes, although they don’t
produce a basidiocarp
5. Deuteromycota; molds; fungi imperfecti
1. commercial uses - antibiotics; cheeses etc
2. asexual fungi - various groups
Relation to Plants - what makes them similar?
Relatin to Animals
History (Fossil Record)
1. date back to the phanerozoic (900-500 mya)
2. evidence of association with the first fossil land plants (400 mya)
3. molecular data strongly suggest an association with the choanoflagellates
Saprophytes - decomposition
1. Wood rot fungi, dung, leaf litter, dead animals
2. decompose carbon, nitrogen and other elements back into the soil
3. decomposition is important for nutrient cycling but it is also a problem for
destruction (Crops and other plant materials like wood)
11. Biotrophs
1. pathogens
1. human pathogens
2. most important plant pathogens
12. Lichens (over 25000 species)
1. long lived algal-fungal interaction
2. algae can be in distinct layer or interspersed
3. fungi absorb nutrients from the dust or the air
4. important pioneers - dissolve rock substrate, fix nitrogen
5. reproduction asexual (soredia) or sexual as distinct units
6. those with cyanobacteria can fix nitrogen, and photosynthesize
13. Mycorrhizae (Glomeromycota plus)
1. mutualism
2. endomycorrhizae - crops
1. usually zygomycota
3. ectomycorrhizae - forest trees
1. diverse basidiomycota