Topic1 BIOL1030NR
Topic1 BIOL1030NR
Topic1 BIOL1030NR
A. Scientific Method
1. observations
2. scientific model
explains observations
makes testable predictions
3. test predictions (can confirm predictions)
4. reject, revise, or tentatively accept scientific model
5. caveats:
Scientific models can only be proven false, never proven true.
Correlation does not equal causation.
Testable predictions cannot include the supernatural (the supernatural cannot, by definition, be tested
scientifically); thus, the supernatural is outside the realm of science.
The term “theory” has a very different meaning in science than in most everyday conversations.
6. terms:
hypothesis – model that has not been tested or has only been tested some
theory – model that has been tested extensively and is accepted by most scientists in that field
law – usually a very well-established theory that explains a wide body of observations
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II. Classification of organisms
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2. asexual species – definition based on biochemical (think DNA sequence) and morphological differences; no solid rules
also includes use of “race,” “subspecies,” and “strain” designations
in asexual species, microevolution over time directly leads to macroevolution (speciation)
3. evolutionary species concept – a single line of descent (lineage) that maintains its distinctive identity from other
lineages; works for all species, but it can be hard to clearly define “distinctive identity”
D. So how many species are there?
1. no one knows for sure, best guess is about 10 million, but only about 1.8 million have been described by humans
2. most are tropical
3. human activities (particularly in the tropics) are certainly destroying many species before they can even be described; we
are undergoing the sixth mass extinction event in the history of life on earth (and the first one driven by the activities of
man)
A. classification is largely based on inferred evolutionary relationships between organisms; the two major approaches to this are
cladistics and traditional taxonomy
1. phylogeny – evolutionary tree; explanation of evolutionary relationships among groups (what evolved from what, in
what order, and when)
2. systematics – study and reconstruction of phylogenies
3. groups of organisms may be:
monophyletic (includes most recent common ancestor and all descendants)
paraphyletic (includes most recent common ancestor BUT not all descendants)
polyphyletic (does not include most recent common ancestor)
4. both cladistics and traditional taxonomy avoid polyphyletic groups; cladistics also avoids paraphyletic groups
EXPLANATION
What do terms monophyletic, paraphyletic and polyphyletic mean?
These terms are used to describe groupings of organisms, and indicate the extent to which they can be considered as ``natural
groups''. They are best explained using examples, so consider the following family-tree diagram:
Aves
/
/
Crocodilia /
Mammalia \ Dinosauria
\ \ /
\ \ /
\ \ /
Synapsida Reptilia
\ /
\ /
\ /
Amniota
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Consider the group consisting of all the animals in this diagram - that is, Amniota. This group is monophyletic because it
consists of a single animal together with all of its descendants. The Dinosauria, including the modern birds, is another
monophyletic group, sometimes defined as the most recent common ancestor of Igunanodon and Megalosaurus together with
all its descendants.
Monophyletic groups are also called clades, and are generally considered as the only ``natural'' kind of group. They are very
important in phylogenetic classification.
Now consider the group consisting of the non-avian dinosaurs (which is what people usually mean by the informal term
``dinosaurs''). This is a paraphyletic group, because it can't be defined simply as ``this animal plus all its descendants'', but
must be described as one clade minus another: in this case, Dinosauria minus Aves.
The ``non-avian dinosaurs'' make up a singly paraphyletic group because only one clade need be omitted from its base
definition. Groups may also be doubly paraphyletic, thrice paraphyletic, etc., depending on how many sub-clades they omit.
Finally, consider the group of ``warm-blooded animals'', which consists of Mammalia and Aves. This is a polyphyletic group - a
totally unnatural assemblage - because it can't even be expressed as a paraphyletic group, that is, a clade minus one or more
of its subclades. Such groups are not used at all in phylogenetic work since they are a purely artificial construct. In terms of
common descent, a ``warm-blooded animals'' grouping makes no more sense than a Synapsida-plus-Crocodilia group -
though this is not to say the notion of a warm-blooded group may not be useful in some informal discussions.
So far, so straightforward. The only wrinkle in this scheme is that some workers use the word ``monophyletic'' in a sense that includes
what we have described here as paraphyletic groups. These people then use ``holophyletic'' to describe what are usually called
monophyletic groups. It's tempting in the face of this ambiguity just to abandon the word ``monophyletic'' and use a
holophyletic/paraphyletic dichotomy, but this terminological abuse is probably not widespread enough to merit such extreme measures.
It's just something to be on the watch for.
Exercise: Determine which of these groupings are mono, para and polyphyletic (Refer Textbook for more details).
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B. cladistics groups organisms on the basis of unique shared characters inherited from common ancestor, or derived character
1. clade – group of organisms related by descent
2. synapomorphy – a derived character that is unique to and thus defines a particular clade
3. cladogram – branching diagram based on cladistic analysis that represents a phylogeny
cladograms are based on comparative analysis, so each cladogram must have an outgroup and ingroup
outgroup – organism that is different from all others in the cladogram (but not too different); it is expected to have
split with the others from a common ancestor before any of the rest (the ingroup) split from each other
4. often different cladograms can be produced for a given set of organisms depending on how the analysis is done; usually a
choice has to be made for which cladogram is the most likely reflection of evolutionary history (usually the most
parsimonious one, the one that requires the simplest explanation)
5. cladograms are always open to refinement as more date become available
6. naming based on cladograms only allows for monophyletic groups
C. traditional taxonomy weighs characters according to presumed biological or evolutionary significance
1. line of descent is considered as well (and may incorporate cladograms), but naming allows for some paraphyletic groups
2. example: classifying birds.
traditional taxonomists view feathers as being so important that birds are placed in own Class (thus making Reptilia
paraphyletic in their taxonomies)
cladists put birds with reptiles to make Reptilia monophyletic
D. So who is right? How the heck do we classify birds?
1. right is in the eye of the beholder, and is an area of much debate – both ways are still used
2. if you are after phylogeny, cladistics is clearly the way to go – any traditional taxonomy that is at majors odds with
phylogeny is likely to lose out
3. most biologists use traditional taxonomy informed (and often revised by) cladistics; that is what we will use in this
course
4. traditional taxonomy is the old way and is being replaced in many cases with cladistics
E. characters useful for classification
1. morphology (form, such as unicellular or multicellular, etc.)
2. nutrition mode (autotroph or heterotroph, etc.)
3. cell structure (presence or absence of a nucleus; presence or absence of a cell wall, etc.)
4. chemistry (cell wall makeup, protein sequences, DNA sequences, etc.)
5. reproductive traits (sexual, asexual, etc.)
6. many others
V. The most widely accepted classification system today includes three domains and six kingdoms
A. Two domains consist of prokaryotes, organisms with no internal membrane-bound organelles (and thus no true cellular
nucleus)
1. Domain Archaea – Kingdom Archaebacteria
bacteria typically found in extreme environments;
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distinguished from other bacteria mainly by ribosomal RNA sequence and lack of peptidoglycan in their cell walls
include methanogens, extreme halophiles, and extreme thermophiles
some nonextreme archaebacteria exist – distinguished from eubacteria by signature sequences in their DNA
2. Domain Bacteria – Kingdom Eubacteria
very diverse group of bacteria; defined best as prokaryotes that are not archaebacteria
examples: blue-green algae, Escherichia coli
3. prokaryotes are abundant and important organisms
more in your mouth than mammals on Earth!
5 million per square cm of your skin
1 gram of soil has 2.5 billion bacteria
more biomass than rest of life on Earth combined!
Play important roles in life:
Some are photosynthetic (vital for putting energy into ecosystems)
Some are decomposers (vital for recycling matter in ecosystems)
Some cause disease
B. One domain, Eukarya, consists of eukaryotes, organisms with a discrete cellular nucleus (and other internal membrane-
bound organelles); it is divided into four kingdoms
1. Kingdom Protista - protists
single celled and simple multicellular organisms having nuclei
includes protozoa, algae, water molds, and slime molds
where everything that doesn’t fit another eukaryotic kingdom is put
2. Kingdom Fungi - fungi
organisms with cell walls consisting of chitin
most are multicellular
includes molds and yeasts
3. Kingdom Plantae – plants
complex multicellular organisms having tissues and organs
plant cells have walls containing cellulose
most (but not all) contain chlorophyll in chloroplasts, and carry on the process of photosynthesis.
4. Kingdom Animalia – animals
complex multicellular organisms that must eat other organisms for nourishment
typically contain cells lacking walls, and have organs and organ systems
most (but not all) forms are motile
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C. a phylogeny from rRNA analysis indicates that Eubacteria are the most ancient group or an outgroup to the domains Archaea
and Eukarya – but some analyses of complete genome sequences give cladograms that contradict this
D. in this course we will focus on eukaryotes; key characteristics of eukaryotes include:
1. evolution of eukaryotes involved endosymbiosis, incorporation of Eubacteria cells into eukaryotes as mitochondria and
chloroplasts
2. true multicellularity (a body formed of cells which are in contact and coordinate activities) is a trait not found in any
prokaryotes, but found in many eukaryotes
3. sexual reproduction by syngamy is a trait not found in any prokaryotes, but found in many eukaryotes
E. a major consideration will be eukaryotic life cycles for sexually reproducing species
1. these life cycles always involve:
meiosis (reduction division)
diploid (2N) cell produces one or more haploid (1N) cells
chromosome number halved
gametes: cells that must join to another cell before a new organism is produced
fertilization (syngamy): fusion of gametes to form a zygote, first diploid cell for a diploid organism
2. the three major types of life cycles are zygotic meiosis, gametic meiosis, and alternation of generations with sporic
meiosis
zygotic meiosis
zygote immediately undergoes meiosis
diploid zygote never undergoes mitosis; mitosis only in haploid cells, making haploid individuals
found in many protists
gametic meiosis
meiosis produces gametes that never undergo mitosis
zygote undergoes mitosis, making diploid individuals
found in most animals
alternation of generations with sporic meiosis
zygote undergoes mitosis, making diploid individuals
some diploid cells undergo meiosis to make haploid spores (sporic meiosis)
mitosis in haploid spores, making haploid individuals
some spores develop into gametes, which undergo syngamy to make a diploid zygote
thus, two bodies in one life cycle – two instances of mitosis in one life cycle
found in plants and some algae
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