AP Bio: Population Genetics

The Evolution of Populations: Population Genetics and Microevolution

from population genetics perspective, interested in the alleles assessed by population = collection of
alleles possessed by organisms that can interbreed with one another and produce fertile offspring
gene pool concept: all alleles of all loci of all individuals in the population at any moment
Review of Natural Selection:
resources are limited, more individuals are born that the resources can support struggle for existence
and to reproduce
heritable variation exists among the individuals of a population
ultimate source of this variation = mutation and sexual recombination
individuals that have heritable traits that allow them to survive and reproduce better than others
contribute a greater proportion of offspring to the next generation
these offspring inherit the favorable traits of their parents
frequencies of traits change in the population over the course of generations: favorable traits become
more common
a population evolves, individuals do not
Evolution from the Standpoint of Population Genetics:
back in 40s/50s modern knowledge of genetics being formed
had modern knowledge of genetics
had darwins pre-genetics ideas
merging of modern knowledge with classic Darwinian natural selection stuff = modern synthesis
evolution:
1) changes in the gene pool over time
2) change in the frequencies of alleles (in all the loci we possess) and genotypes of one or more loci in a
population of organisms
change in allele frequencies can occur quickly: 1 generation but evolution itself
evolution from this perspective = microevolution: change in the genetic makeup of a population from
generation to generation
distinction drawn between changes in allele frequencies (can occur as quickly as one generation)
classic view from paleontology= changing overtime, longer process
macroevolution = paleontology idea of large scale changes over a while vs. population genetics idea of
it happening in one generation
microevolution involves change over relatively short time scales, as opposed to macroevolution, which
involves changes in populations over geological time frames (paleontological perspective)
microevolution acting over long time frames results in macroevolution
microevolution occurring over long time changes can result in physical changes seen in macroevolution
not only natural selection that can change the allele frequencies of loci of a population microevolution
can occur as a result of other processes
in order to understand microevolution: How does a gene pool behave when there is no microevolution
occurring/what conditions have to exist to result in no microevolution?
Hardy-Weinberg Equilibrium: describes a population that is not evolving
in order for a population to not evolve has to have the following characteristics/conditions:
1) no natural selection
no difference in the ability of an organism to reproduce/survive based on the alleles it possesses
2) infinite population size
3) no migration/no gene flow into or out of population
no alleles coming into/out of population no organisms moving in or out of a population: organisms
represent alleles
4) no mutations
no alleles changing from one kind to another
5) random mating
not mating on preferential basis based on genotypes
only focus on a single locus, starting with the simplest possible case of only two alleles present in the
population
if only a single allele present, population is said to be fixed for that allele all individuals are
homozygous: no variation in the population for that locus

 trivial situation from the standpoint of the H-W equilibrium at this point
once you get to fixation, population wont evolve
ex: consider a single locus that determines flower color with two alleles with incomplete dominance: C R
(red) and CW (white); heterozygote has pink flowers
assume conditions for H-W equilibrium apply
if p represents the relative frequency of CR in the parental population, and q represents the relative
frequency of CW, then p and q remain unchanged in the next generation
if only 2 alleles in a population, one of the relevant equations: p + q = 1, in both the parental and
offspring generations
p = frequency of A (dominant allele)
p2 = AA homozygotes
q = frequency of a (recessive allele)
q2 = aa homozygotes
2pq = Aa heterozygotes
if HW conditions apply:
1) p and q will remain constant
2) regardless of starting genotype frequencies after one generation of mating, will remain constant
thereafter no evolution occurs

same for other genotypes^

Example:
Genotype

Genotype
Frequency

CRCR

p2

CRCW

2pq

CWCW

q2

^ as long as HW conditions apply regardless of genotype frequency, after one generation of mating
imagine the populations producing gametes in this proportion that reflects the gametes they produce
gametes combined at random

 a violation to any one of the rules will lead to a change in allele frequency natural selection isnt the
only change that starts evolution: non-adaptive evolution
in real populations, allele and genotype frequencies usually do change over time
the neutral theory: most evolution occurs without the involvement of natural selection
natural selection producing changes in organisms
changes happening regardless of natural selection
both producing evolution simultaneously, but natural selection is still the primary mechanism by which
adaptive changes occur
Finite Population Size: effect of finite population size on evolution
3 contexts in nature in which this can occur:

1) genetic drift: statistical phenomenon; the smaller the population the greater the effect; effect of
small sample size leading to a higher statistical likelihood of changes occurring
gene pool with a certain frequency of alleles when gene pool reproduces, high statistical likelihood
that the next generation will not have the same allele frequency as the previous generation (evolution!)

^ex: repeated instances might cause one allele to be lost, or the population = fixed
cant predict if a population will be fixed or what allele may be fixed
once a population is fixed, the lost allele will not come back
2) The Bottleneck Effect: effect of small population size, but in a particular context: involves a large
population of organisms with a certain amount of genetic diversity then, population size gets reduced
to a small number of individuals then, population is allowed to re-expand but as a result of the
restriction in population size, the population experiences a loss of genetic diversity, rare alleles are lost:
more likely to disappear
ex: sea otters, seals due to hunting
evolutionary effect of a loss of variation: increased likelihood of an extinction event because in the face
of a new selective challenge (ex: disease, environmental change), lower likelihood that there will be
variants that will be able to survive and reproduce well in these circumstances

3) The Founder Effect: occurs when a few individuals become isolated from a larger population
ex: birds blown off the mainland to an island
essentially an isolation bottleneck with similar results
Migration/Gene Flow:
causes a population to gain or lose alleles

results from the movement of fertile individuals or gametes

overall effect of migration tends to homogenize populations; populations become like on another
degree of homogenization is dependent on the migration rate
p = 0.5, q = 0.5 in all populations if really high migration rate
if low migration rate, differences will be lessened, but populations will still be different
Natural Selection:

 certain alleles passed to the next generation with greater success than others; over time natural
selection will maintain favorable genotypes that lead to effective survival, but more importantly
reproduction

natural selection acts upon phenotypes: expressed conditions selected from

both discrete and quantitative characters contribute to variation within a population:
1) discrete characters: can be easily categorized, limited number of states of the character
ex: eye color: blue = one condition, alternative condition = brown; hair color
2) quantitative characters: members exhibit different character states that continually vary along a
continuum
ex: height, melanism
molecular basis for a quantitative character/why does it vary along a continuum? multiple loci contribute
to the character: polygenic character
polymorphism = presence of genetic variation within a population, upon which natural selection can
operate; multiple types:
1) phenotypic polymorphism: refers to something that varies phenotypically within a population
2) genetic polymorphism: a particular locus in a population has more than one allele, not fixed;
polymorphism of multiple loci contribute to a quantitative character: phenotypic characters that vary
along a continuum
relative fitness: way of quantifying the relative success of one genotype producing offspring into the
next generation; reproductive success
quantitatively, is a proportion: varies from 0 to 1.0
0 = organism that has no success in passing offspring onto the next generation
1.0 = maximum relative fitness
allele that is lethal dominant goes to zero, other/alternative allele goes to one; both happen in just one
generation
genotype frequencies: in one generation, beginning in HW expectations: go from homozygotes with A1
allele goes to 1; alternative homozygotes and heterozygotes go to 0
recessive deleterious allele is not eliminated in nearly as quick a fashion, able to persist at really low
frequencies over a long time frame: as A1 allele frequency increases, number of individuals increase;
because alternative allele going down, heterozygotes and the recessive allele go down but not
eliminated in one generation, instead the homozygotes asymptotically approach 0; heterozygotes not
affected by allele because danger is held in the recessive allele
recessive deleterious allele decreases in frequency because natural selection selects against it but hides
in the heterozygous condition because it is not selected against in a heterozygous genotype found
most frequently in heterozygotes; when the frequency of the deleterious allele becomes really low, it
persists because there is a very low likelihood: 1) rare to find a heterozygote that has it because already
rare in the population; 2) rare for heterozygote to mate with another heterozygote because
heterozygotes = rare and even then there is only a 25% chance their offspring will have the double
recessive genotype
ex: this is the way you would expect sickle cell anemia to behave in a place where malaria is not
common; in places where there is malaria, heterozygous genotype is advantageous because you are
resistant to malaria and dont suffer the effects of the anemia; dominant: susceptible to malaria;
recessive: suffers effects of sickle cell anemia

 allele frequencies stay at 0.5; heterozygotes stay at 0.5 in the population and the two alternative
homozygotes are at the same place at 0.25 means that selection for the heterozygote maintains both
alleles in the population and tends to keep them around at roughly equal frequencies would preserve
the sickle cell allele in the population at a higher frequency: another example in which genetic variation
is preserved
natural selection tends to reduce genetic variation
selection for heterozygotes means higher frequency for sickle cell anemia staying around
modeling discrete characters: one or the other phenotype

Directional, Disruptive, and Stabilizing Selection: in a quantitative character

selection favors certain genotypes by acting on the phenotypes of certain organisms
3 modes of selection:
1) directional selection: favors one of the phenotypic extremes other extreme and all other
phenotypes in the phenotypic range are selected against
2) disruptive selection: selection for both extremes and selection against the middle
3) stabilizing selection: selection for the middle and against the extremes

^top graph: how a typical quantitative character is normally distributed; in the normal distribution:
illustrated by the top graph bell curve
frequency of individuals that have a particular phenotype on y-axis; phenotypic range on x-axis
the majority of the kangaroo rats have an intermediate fur color: medium brown is most frequent
most frequent because the rats live in a desert environment so most surroundings are medium brown
the rats of this color as least visible to predators
as you move to either extreme, the number of individuals that possess that particular character state
drops off; very few
darker and lighter colors stand out more against the medium brown background easier for a predator
to detect
bottom right graph: stabilizing selection extremes selected against so the shape of the distribution
narrows around the peak; narrower bell curve
bottom middle: disruptive selection creates a bimodal distribution: two peaks with a valley in the
middle
ex: dark colors would be favored if habitat changed to be more dark and light, selection against the
medium brown
bottom left: directional selection curve remains the same, but curve shifts in the favored direction
ex: soil background changes to darker brown darker rats blend in better compared to anything lighter

The Preservation of Genetic Variation:

Diploidy and dominance maintains genetic variation in the form of hidden recessive alleles in
heterozygotes; still tends to preserve the allele being selected against though it is rare
balancing selection occurs when natural selection maintains stable frequencies of two or more
phenotypic forms in a population; leads to a state called balanced polymorphism
heterozygote advantage: individuals who are heterozygous at a particular locus have greater fitness
than homozygotes; natural selection will tend to maintain two or more alleles at that locus
Sexual Selection:
situation where selection for reproductive success has wound up selecting for characteristics that
compromise the survival of the individual to a certain degree; makes something really good at
reproducing, but not as good at surviving but the improved reproductive success more than makes up for
the compromised ability of the organism to survive
often seen in mating systems of animals that have evolved where females have a choice of males to
mate with males compete lots of males are left out
evidence is in species that have sexual dimorphism: organisms of different sexes in a species differ in
secondary sexual characteristics
primary sexual characteristics: involve reproductive organisms always there by necessity
secondary sexual characteristics: those that males or females possess but that are not directly a
result of different sex organisms; allow one to distinguish male vs. female
ex: female breast development, facial hair in males, greater shoulder and narrower hip width in malesreverse in females
classic example of sexual selection: elaborate plumage of male peacocks that females find attractive
males compete for access to a female the bigger the tail feathers, the higher likelihood of reproductive
success (bigger plumage attracts females)
offspring will then inherit the plumage of their parents, so if large they will also experience greater
reproductive success
males with large plumage are much more likely to fall victim to a predator:
1) stand out
2) compromises ability to fly even though they arent too heavy, but tail feathers still cause drag
ex: bowerbirds build nests to attract females
Online Program: http://radford.edu/~rsheehy/Gen_flash/popgen/

^effect of genetic drift, not infinite population, over time allele frequencies are changing

^smaller population size, greater variation, none are fixed

 ^all became fixed, in a small population size, the degree of genetic drift is such that theres a higher
likelihood one or other alleles will be lost, fixation
along same plane with minimal variation: genetic drift reduce population 10-fold: greater genetic drift
50 individuals: fixation
ever-decreasing size of population: the smaller the population, the greater amount/degree of genetic
drift: a random process that does not involve evolution

^bottleneck effect: two-fold:

1) individuals going through bottleneck are not representative of previous population
2) while the population is small in size, genetic drift will be greater once back to a population of
greater size, will wind up with a slower amount of genetic drift but the overall effect is to change the
allele frequencies and lower the amount of genetic diversity (observed with different initial allele
frequencies)

^Relative fitness: infinite population size, lethal dominant allele allele wont reproduce, will be fixed
and go away in one generation
allele that is lethal dominant goes to zero, other/alternative allele goes to one; both happen in just one
generation
genotype frequencies: in one generation, beginning in HW expectations: go from homozygotes with A1
allele goes to 1; alternative homozygotes and heterozygotes go to 0

 ^recessive deleterious allele is not eliminated in nearly as quick a fashion, able to persist at really low
frequencies over a long time frame: as A1 allele frequency increases, number of individuals increase;
because alternative allele going down, heterozygotes and the recessive allele go down but not
eliminated in one generation, instead the homozygotes asymptotically approach 0; heterozygotes not
affected by allele because danger is held in the recessive allele

^allele frequencies stay at 0.5; genotypes: heterozygotes stay at 0.5 and 0.25 respectively
selection for heterozygotes maintains both alleles, keeping them around and at equal frequencies
preserves sickle cell allele at higher frequency
normal hemoglobin allele also maintained at high frequency; both at 0.5
another way genetic variation is preserved
natural selection tends to reduce genetic variation
selection for heterozygotes means higher frequency for sickle cell anemia staying around
Speciation:
speciation: process/mechanism by which new species arise/evolve into more than one species
involves the evolution of reproductive isolating mechanisms between populations of organisms
life started with a prokaryote and the millions of species today = result of that one species undergoing
speciation all life is related at some level
to have species form, have to evolve reproductive isolating mechanisms
species names are Latin binomials (two words/names): first name = genus, second = species epithet:
never used alone because a lot of species share this term
first letter of genus is capitalized, others are lower case
ex: American Alligator = Alligator mississippiensis; Chinese Alligator = Alligator sinensis; humans =
homo sapiens
on computers, latin words in english are designated by italics but when writing, underlined
domain kingdom phylum class order family genus species: taxonomic system that
expresses evolutionary relationships
several different definitions/concepts of what a species is, all have advantages and disadvantages:
morphological species concept: used in species descriptions, especially for larger organisms;
members of a species are those who possess a unique combination of characteristics that is possessed
by no other collections of organisms
ex: turtles

 phylogenetic species concept: defines a species as the smallest group of individuals that share a
common ancestor, forming one branch on the tree of life
ecological species concept: emphasizes a species as occupying a niche
evolutionary species concept: species is a single lineage of ancestor-descendant populations which
maintains its identity from other such lineages and which has it own evolutionary tendencies and
historical fate
biological species concept: standard theory; a species is one or more populations of individuals that
interbreed under natural conditions and produce fertile offspring and are reproductively isolated from
other such populations
barrier that prevents two populations from mating: reproductive isolating mechanisms:
Prezygotic Isolation: comes into play before formation of the zygote and prevent the formation of the
zygote something prevents fertilization
habitat isolation: potential mates occupy different habitats within the same area

^dont interbreed because though they live in the same location, they live in two different habitats
temporal isolation: different timing of breeding/mating; organisms that have different breeding
seasons
ex: locusts: have breeding years, not seasons; egg that hatches makes larvae in soil and eats, etc. stays
there underground for years when it is time to mate, undergo metamorphosis and mate for weeks
species of locusts have different mating years: some 5 year, some 4 year
behavioral isolation: species (not plants) with unique behaviors regarding mating that are not shared
with other species
ex: 3-spined sticklebacks have own unique mating dance as well as blue footed boobies
mechanical isolation: physical/mechanical barrier exists that prevents sperm from meeting the egg,
e.g.parts dont fit
ex: elephant and mouse
gametic isolation: egg puts up chemical barrier so only a sperm of the same species with proper
chemical signature can gain entry into the egg
important for organisms who release sperm in water (ex: sea urchins)

Postzygotic Isolation: will get zygote and might get a fully intact and functioning organism (though
not sexually functioning)
reduced hybrid viability: the fertilized egg fails to develop into a viable organism; zygote formed, but
fails developmentally, ability to survive is severely compromised
reduced hybrid fertility: get a viable organism that may be quite good at surviving but is
sterile/infertile
ex: mules: result of mating of horse and donkey; very strong, desirable for work but sterile
heterozygous at many loci
hybrid breakdown:
hybrid = result of two species interbreeding
members of two species interbreed and produce fertile offspring but either:
1) mate back into one or the other species, dont maintain genetic identity; dilution effect
rate of exchange of alleles is not high enough to compromise the identity of each species

 2) hybrid formed from two species interbreeding are fertile and are able to interbreed with one another
but after several generations, start to see certain genetic defects in the offspring that ultimately
compromises their ability to survive/become inviable and die off
two views of evolutionary change:
anagenic change: change within a lineage over time
question: Can you then recognize two or more different species within one lineage over time?
cladogenic change: speciation; lineage splitting
historical events and relationships represented by cladograms or phylogenetic trees

^earlier at bottom, most recent at top: over time the species has changed
left: species has evolved, hasnt split into two species not speciation: anagenic change
right: has evolved into two species speciation: cladogenic event
this cladogenic event involves anagenic change because it requires some evolution for the two species
to become different enough to officially become species
above is called a cladogram/evolutionary tree

^cladogenic change also involves anagenic change

left: population able to exchange alleles with each other; certain degree of gene flow holds it together
as one species
anagenic change
as long as theres enough gene flow, will remain one species
if something interrupts flow among populations top splits, need anagenic change in one set of
populations
if there are one or more reproductive isolating mechanisms that have evolved, now have descendants
in order for cladogenic change to occur (right) have to have anagenic change in one or both of the
lineages, have to evolve to become different from one another which involves anagenic change from
time C time D
types of cladogenic speciation:
1) allopatric speciation: involves some sort of physical separation of the populations of what was one
species into temporarily, at least, two sets of populations that cannot interbreed; physical/geographic
isolation has interrupted gene flow populations counteracts evolutionary divergence among populations
and therefore speciation
isnt the case that geographic isolation will lead to speciation, it might
if the two or more different sets of populations evolve reproductive isolations/become different enough
that they can no longer interbreed, speciation has occurred
if these things are brought back into contact and reproductive isolating mechanisms are different but can
still evolve, no speciation: still members of the same species
migration/flow of alleles among
better understood and much more common
organisms not isolated from one another will interbreed
interbreeding among organisms tends to reduce differences among them
geographic isolation leads to independent evolutionary directions (divergence of characteristics)

 ^Isthmus of Panama: 3 million years ago

land barrier for oceanic creatures
allowed animals to go from the Atlantic pacific and vice versa closure of the isthmus of Panama =
geographic isolation led to the evolution of different species

^ex: shrimp and other species closely related on either side after the closure of the isthmus

^founder effect combined with natural selection new species evolving fairly rapidly to reproductive
isolation
underwent numerous cladogenic events
if part of archipelago: island hopping migration events where locally adapts to conditions
local adaption + founder effect leads to relatively rapid speciation of many species starting from a single
ancestor adaptive radiation

^ex: Darwins finches, underwent adaptive radiation: burst of divergence from a single lineage that
gave rise to many new species

1) immigrants from the mainland colonize the Galapagos

2) birds disperse to other islands and become adapted to local food supplies
3) populations of birds recolonize an island on which their ancestors lived
if you have species that only reproduce asexually (ex: bacteria), cant use the biological species
definition: disadvantage/failure of this definition
2) sympatric speciation: species form within the home range of an existing species in the absence of a
physical barrier; have populations that are still in a large degree of contact with one another
poorly understood and not primary set of circumstances that lead to cladogenic speciation
polyploidy = extra sets of chromosomes; has
2 subtypes:
autopolyploidy: occurs within a species
ex: cell fails to divide during meiosis could have a plant, that instead of producing haploid gametes,
produces diploid gametes 4n zygote when this 4n plant produces 2n gametes by meiosis that are
not able to unite with 1n gamete produced by parent species
offspring reproductively isolated from parents by doubling the amount of DNA in the cell isolated
genetic entity that can mate with itself and others that have the same conditions, but not with one from
the parent species
plants have higher tolerance for this can have viable offspring
allopolyploidy: involves two different species
species that form hybrids and a mistake like from above occurs wind up with a polyploidization event
(ex: 2n 4n) but in this case its the gametes of two different species that happen to be compatible and
produce a new species
Gradualism vs. Punctuated Equilibrium: terms to describe relative tempo of evolutionary changes
gradualism: change (anagenic change) occurs very slowly and gradually in a lineage over time
punctuated equilibrium: spurts of anagenic change that probably coincide with cladogenic events:
short periods of rapid change followed by relatively long periods of relative stasis
new forms change, then stay the same for awhile
paleontologists champion this model

^left: gradualism: species gradually divides into two different ones

right: morphological change: one species, rapid anagenesis within right lineage and then a little later left
Systematics:
systematics = the study of phylogenetic (evolutionary) relationships
all organisms are (probably) related at some level
Darwin suggested that life had a single origin all living organisms descended from a single ancestor
predominant view that there is one tree of life that expresses how all organisms are related
evidence for relationship: suggests original ancestor had all of these:

 1) DNA
although a bacterium that has possibly replaced phosphorus with arsenic in its DNA and other molecules
has been found wasnt an independent organism of life
2) universal genetic code: turning codons into amino acid sequences = universal process
3) ribosomes: all cells have ribosomes
4) cell membrane: universal boundary between the inside of the cell and the outside environment
taxonomy = the science of naming things

highest group = Kingdom

nexus between systematics and taxonomy use the hierarchical taxonomic system to express the
phylogenetic relationships among organisms
Phylogenetic Trees:
phylogenetic tree/evolutionary tree = branching diagram that hypothesizes cladogenic events that
gave rise to the diversity of organisms within any particular group
2 ways of making them:

time goes from left right or bottom top: either way, base tips
taxa = entities we are trying to determine the relationships of
^taxa that have a related ancestor = sister taxa
branching points = node: each one represents a hypothesis of cladogenesis/speciation events
very base = common ancestor of all taxa
polytomy: reflects an inability to distinguish a relationship; no basis to further establish a relationship

^all four trees depict the same phylogenetic relationships

 ^The branch leading to Node 1 represents the common ancestor of ABCDE, the branch leading to Node 2
is the common ancestor of BCDE (but excluding A)
B, C, D, and E share a more recent common ancestor not shared with A, they are more closely related to
one another

^All three of these trees are equivalent: trees can be swiveled/rotated about their nodes without
changing the expressed relationships; the important thing to look at is the pattern of common ancestry
Phylogenetic Reconstruction and Subsequent Taxonomic Considerations:
to determine relationships:
1) collect data: if trying to compare organisms to establish a relationship between/tree, not confined to
living things can refer to paleontological record (fossils) but also not confined to physical
characteristics of the body (morphology/anatomy) can collect behavioral data, molecular data (DNA
sequences)
2) analyze data to produce trees; many methods of analysis
3) taxonomic classification: based on those trees, can rearrange taxonomy if necessary

Cant you reconstruct phylogeny by just grouping organisms by overall similarity? first glance, it would
seem you dont need to worry about all the different methods of analysis/that organisms that share a
more recent common ancestor would always be more similar to one another (compared to other
organisms that dont share the common ancestor)
Sources of error: if using overall similarity to determine relationship
1) Symplesiomorphies: shared ancestral characteristic, arose earlier than in the stage where you are
establishing relationships didnt arise late enough to be used in the analysis
ex: mouths: showed up early, doesnt help to see mouths of monkeys and humans these similarities
can swamp out the similarity trying to be made
can detect a symplesiomorphies by using a proper outgroup in your analysis
2) unequal evolutionary rates among lineages

 ^hypothesis: things like alligators and birds are more closely related than crocodiles to a lizard or snake
crocodilians and birds share a common ancestor and therefore are more closely related than crocodiles
to lizards and snakes unequal evolutionary rates produced this: in the time since crocodilians and birds
shared a common ancestor, crocodiles didnt change much but birds evolved very rapidly look very
different misleading
3) homoplasy = any phenomenon where two different lineages change in the same way independently
and wind up changing the same character state, not because they inherited it from a common ancestor,
but happened independently; 3 subtypes that cause this:
a) convergent evolution (analogous characters)

b) parallel evolution

c) reversals

no data are immune from these difficulties

synapomorphies = shared derived characters shared because they were shared in a common ancestor

 many credible methods of phylogenetic analysis attempt to identify synapomorphies that reveal
relationship/common ancestry
dont just take any tree building method available on the internet or elsewhere and apply it to your data
without knowing more about the assumptions of the method!
the method of analysis matters a lot: your tree(s) will be garbage if you dont use a correct method of
analysis
a given data set is informative for investigating relationships only within a certain range; no data set is
applicable to all levels of relationship
*overall similarity does not = relationship trees that are only based on overall symmetry are less
reliable: evolutionary rates assumed, parallel evolution
Cladistics:
cladistic analysis = best way to analyze data
many different methods of analysis, but cladistics favors methods that try to establish a tree based on
shared derived characteristics
once tree is made, cladistics favor a classification scheme that directly reflects it: accomplished by
constructing monophyletic groups
Mono-, Para-, and Polyphyletic Groups:
monophyletic group = a group that contains all of the descendants of a given ancestor
all taxonomic classification based on monophyletic groups is the only one that is completely equivalent
with the phylogenetic tree of relationships
paraphyletic group = a group that has a shared common ancestor, but omits one or more of the
descendants
polyphyletic group = a group that has no common ancestor not shared with groups
even less favored by cladistics than the paraphyletic group

^para: includes some descendents but excludes G, poly: C isnt even closely related to highlighted
organisms

^monophyletic groups allow you to make a tree from taxonomic categories: 1:1 relationship makes this
desirable
ancestor at base, includes all descendants: kingdom; first branch point: 2 phyla: 1) includes A, 2)
includes B, C, D, E, F, G phylum split into 2 classes: 1) B, 2) CDEFG; order: C, D and other = E,F,G; 2
families: one that includes E, other includes F,G
in this approach, directed correspondence between tree and taxonomy
if made tree of life: would have to have many taxonomic categories, but whatever groups we do have
should be monophyletic (express relationship)
ex: reptiles = paraphyletic group

 importance of knowing the assumptions involved in a given method of analysis when constructing
hypotheses of relationship (phylogenetic trees)
especially the reasons that trees constructed using overall similarity can be problematic I went into
detail regarding the specific reasons that overall similarity does not necessarily indicate relationship (and
what we mean by relationship in the first place), so maybe I think this is important
other important topics: HW equilibrium conditions and how violation of the conditions leads to evolution,
speciation ppt