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So…. Evolutionary Stuff
Wooo We’re Almost Done!
Some Things that need to be
Mentioned a Bit
New alleles usually enter gene pool in a
An Allele that is linked with a beneficial
allele is called a Hitchhiker
Drift is intensified as genetic pressures
increase because selection lowers
population size which lowers the
number of alleles in a gene pool
Going Over Lamark
His Muscular Baby theory is called
orthogenesis. Another example of this
are the Giraffes.
Thought that a mechanism for evolution
was the inheritance of acquired
characteristics and that species never
All of this is WRONG
At Darwin’s Time There Was
Blending inheritance is the theory of
evolution before Darwin did his thing.
This said that all offspring were a
middle ground of the parents. So if the
parents were tall and short then the
offspring would be medium height.
This is also WRONG and proved wrong
Showed that offspring aren’t the blending of
parents through his pea plant experiments.
Interesting fact: Gregor sent Darwin his
paper on genetics but Darwin never opened
Mendel’s theory was thought to be crazy for a
long time and only a few people kind of
accepted it. Biometricians thought that
Mendel’s theory worked only on certain genes
that they considered aberrations.
Biologists wondered how allele frequencies
changed in a population.
Hardy and Weinberg independently found
that allele frequencies don’t change just
because an allele is rare or common.
R.A. Fisher showed that Mendel’s laws could
explain continuous traits if these traits were
due to many genes.
From this basis Fisher, Wright, and Haldane
founded the field of Population Genetics.
R.A. Fisher and Natural
Studied the effect of natural selection on large
Saw that very small changes in selective alleles could
have major changes in their allelic frequencies.
Showed the rate of adaptive change is proportional to
the amount of genetic variation present. This is called
Fisher’s Fundamental Theorem of Natural
Selection even though it doesn’t work all the time.
Weird thing: Sometimes natural selection can cause
a decline in the mean of relative fitness of a
Wright and Genetic Drift
Said that large populations subdivided into
Said that drift was more important than Selection.
Because of this there was differentiation between
subpopulations and if there was migration among
them there would be adaptations amongst the
Came up with the idea of adaptive landscape
which is really influential today even though P.A.P.
Morgan proved that these didn’t work as Wright
thought they did.
J.B.S. Haldane Liked Math
So he developed mathematical equations for
natural and artificial selection.
With his math he proved that natural selection
and mutation combated with each other
(deleterious alleles remaining in population)
He also proved that natural selection placed a
limit on the amount of adaptive substitutions a
population can undergo in a given time frame.
Lewontin and Hubby find Genetic
Variation in Natural Populations
Protein electrophoresis showed that
30% of the loci in Drosophila
pseudoobscura were polymorphic.
This technique is also said to have
missed a lot of genetic variants.
This means that there is a lot more
genetic variation than anyone thought
The Japanese Always Have a
Motoo Kimura said that most genetic variation was
neutral and used only Mutation and Drift to explain it.
His theory also said that the majority of genetic variation
was transient polymorphisms of neutral alleles.
This Neutral Theory was first thought to be true but then
people said nay because: there is less variation than the
Neutral Theory predicts, too much variance between
species to be explained by mutation and drift alone,
Selection was proven to have an impact on nucleotide
Now there is no comprehensive mathematical theory of
evolution that works.
Macroevolution is hard to
Evidence of macroevolution comes
through other fields of study which are:
comparative biochemical and genetic
studies, comparative developmental
biology, patterns of biogeography
(explaining ecological and historical
reasons of species distribution),
comparative morphology and anatomy,
and the fossil record.
DNA Review (Sorry)
4 types of nucleotides: A, G, C, T
Genes are sequences of DNA that code for proteins
Codons are three letter groupings of nucleotides that
code for an amino acid. The sequences that code for
each amino acid are the same between all organisms
Genes are transcribed into mRNA for use (What does
m stand for and what is the nucleotide that replaces
Ribosomes make proteins
Proteins do everything
Pseudogenes are Random
Things that do Nothing
Pseudogenes- genes that have been
inactivated because of mutation
They can be transcribed and translated
but the proteins won’t do anything
because it is shaped weirdly.
These also mutate more quickly
because mutations don’t change the
fitness of the organism
Introns and Exons (You would think
that their Names would mean the
Introns- sequences inside a gene that don’t
code for anything.
Exons- sequences of genes that do code for
Introns are spliced out of mRNA before it
goes to the ribosome.
Introns are sometimes used in the regulation
of a gene and generally mutate more quickly
Silent Sites and Replacement
Silent sites- places where nucleotide
sequence can change without affecting the
Replacement sites- places where changes
result in changes of amino acid sequence.
Silent sites are generally the sites that show
the most difference between populations and
are usually used for this because
replacement sites are constrained from
mutation through Natural Selection.
Kreitman is the Master of
Demonstrated that Silent sites are more viable than
replacement sites by sequencing 11 alleles for
alcohol dehydogenase. He found 43 polymorphic
nucleotides and only one changed the amino acid
But silent sites are not always selectively neutral
because there are regulatory sites for the gene, so
if there is a change here it may be deleterious.
Also several codons code for the same amino acid
but an organism may prefer one codon over
another, this is a codon bias
Li and Graur use Math to find
They found that silent sites evolve at an
average of 4.61 nucleotide substitutions
per 1,000,000,000 years
Replacement sites evolve at an
average of .85 nucleotide substitutions
per 1,000,000,000 years.
Organisms that are Related
have the Same Types of Things
Take mammals for example: bones of a
human hand grow the same way as the wing
of a bat or the fin of a whale. They also share
the same muscle insertion points.
The only difference is that they are scaled
differently; this suggests that all mammals
evolved from the same ancestor and thus all
mammals have the same type of bones.
We also share the same beginnings of our
developmental pathways and all look the
same while we’re fetuses.
Natural Selection Modifies
There are differences in early vertebrate
Amphibians form a ball of cells because their
eggs aren’t heavily yolked
Birds and Reptiles have heavily yolked eggs,
making their embryos form disks by having
them stretch out over the yolk.
Humans also form disks because all
mammals evolved from reptiles
Vestigial Structures help us
Delve into Evolutionary Past
Vestigial structures are structures that
have not entirely disappeared from our
Vestigial structures are not always
useless; they usually acquire a new
Example: the Human appendix is not
useless, it houses some immune cells.
Organisms that are close
Geographically are usually
Evolutionary close too.
Australian Marsupials are usually used
for this example.
Marsupials fill all the ecological niches
on Australia that placentals usually fill.
This means that the physical distance
between placentals and marsupials
means that the potential niches were
filled by marsupial radiation.
Selection Chose Lizards that
can Reproduce by
ThemselvesIn lizards of the Genus Cnemodophorus, the
females can reproduce parthenogenetically
These lizards evolved from sexual lizards
whose hormones were aroused by sexual
behavior. Now these lizards can’t reproduce
sexually but they still need to get aroused to
Fossils show Similarities between
Species and explain
Examples: South America was once populated by
lots of marsupials but when the Americas collided
placentals took the marsupials’ places as they left
and most marsupials died.
Then there are transitional fossils that show a stage
in between two evolutionary lineages.
Example is a transitional skull between mammals and
reptiles. A big difference is that mammal jaws only
have one big dentary bone while reptiles have four.
Also, mammals have differentiated teeth and nasal
passage ways while reptiles don’t. We also have
more muscles in our jaw.
The Fossils that show the Changes
between Mammals and Reptiles
Fossil species that have these differences are:
Procynosuchus has an increase in the size of the
Thrinaxodon has fewer incisors and more tooth
Cynognathus has a gigantic dentary jaw, the other
three bones are in the back of the skull, and some
teeth are multi cusped and most are differentiated
Diademodon has close fitting teeth
Probelesodon has a double jointed jaw which
helped more muscles to come forward, attach, and
Morgonucudon was the first true mammal that had
all of these characteristics
Strongest Evidence of
Taxonomy! All biological entities can be
classified into specific categories that are in a
Example: plants are either non-vascular or
vascular, seedless or seeded, gymnosperms
Each type has its own specific collection of
traits that are not mixed with organisms of
Speciation is a mechanism of
Speciation is when one species becomes 2
Paleontologists generally think that certain
evolutionary phenomena only occur at
speciation and thus macroevolution can’t
happen without it
Geneticists, on the other hand, generally
believe that major evolutionary change can
occur without speciation and that changes
between lineages are an extension of
changes within each lineage.
Two Types of Speciation
Allopatric and Sympatric speciation
Allopatric is the most common and occurs in
distinctly separate locations. The resulting
species rarely interbreed because of the
Sympatric speciation is when subpopulations
become reproductively isolated before they
are geographically isolated
Weird Example of Sympatric
A type of apple maggot fly (Rhagolettis pomenella)
began infesting apples in the 1860s. It was previously
infesting hawthorn fruit. Now the flies on both types of
fruit will not mate with each other because they are
on different fruit. Now the two fly races are diverging
in their alleles at six loci. This was shown by Feder,
Chilcote, and especially by Bush who is really
important and one of the major proponents of
Some biologists call sympatric speciation
microallopatric speciation to emphasize the fact
that the two species are separated geographically at
Biologists have no idea how
Speciation works so there is a lot
Ernst Mayr thinks that the founder effect
may set the stage for rapid speciation.
Alan Templeton says a few key genes
could change and confer reproductive
isolation. This is called genetic transilience.
Lynn Margulis thinks speciation events are
caused by internal symbionts.
It is possible that all of these hypotheses are
Speciation is Happening Even
Under the plant genus Tragopogon two new
species (T. mirus and T. miscellus)have
emerged in the past 50-60 years!!!!!
They evolved by one diploid plant fertilizing
another diploid plant, forming a tetraploid
offspring that could not mate with the diploid
plants around it, thus it is reproductively
isolated and is a new species by definition.
Every single organism in a species DIES!!!!!!
This can happen for many reasons:
A species is completely excluded from another
close related species
The organism’s habitat disappears
The organisms an organism exploits could rise
against the exploiting organism
Some biologists think that species are
supposed to go extinct but most believe that if
the conditions stay favorable a species can
These shape the over all patterns of
When lots of organisms die, the living organisms
go through rapid speciation and fill all the niches.
The largest Mass Extinction happened when the
world’s continents collided forming Pangaea II
The most well known is when the Dinosaurs
died. This most likely occurred because an
asteroid hit the earth, forming the K/T Boundary.
Currently Humans are causing a global mass
extinction right now!!!
Hierarchical Theory of Evolution
Proponents link speciation to mutation and
species replacement (species Selection) to
They also say that Evolutionary trends among
a group would result of selection among
species, not within the individual species.
This last part is really controversial
Punctuated Equilibrium is
Supported with Transitional Fossils
A transition from one species to another
is usually quite abrupt and only
happens in a specific place usually.
This led Eldredge and Gould to propose
that most morphological changes
happen relatively quickly in small,
specific places. Thus the transition from
one species to another is abrupt.
Critics of Punctuated
These people say that species selection isn’t similar
to natural selection and thus it doesn’t work.
They back this up with the fact that there are a lot
more alleles in a gene pool than there are species in
a species pool. So the amount of adaptive evolution
produced by species selection would have to be a
LOT less than the amount of adaptive evolution within
a species through natural selection
Also there can be major polymorphisms within a
species. An example is the bluegill sunfish. One
morph is big, long living, and protective of its mate.
The other is small, short living, and a creep that
sneaks matings from unprotected mates.
Long Article Thing that is Pretty
interesting and talks about
Guy Bush debuted as a major biologist in 1966
talking about sympatric speciation and now he’s
spent all these years building an argument that
proves he’s right. Did it by proving that the flies use
the apples as a stage for their courtship dance and if
they don’t dance on an apple the two flies won’t
Others who have talked about or tried to prove this
Benjamin Walsh who said this in 1862 when the
apple maggot flies first started to go to apples but
had no proof
People who opposed
Now: Dolph Schutler was against this for multiple
years but is now seeing Sympatric Speciation in his
stickleback fish which only mate with others that
share its diet and are about the same size. Eric
Taylor confirmed that sticklebacks of the same
diet and size were related through DNA
1947-Now: Mayr said that there was no proof so
it has been discarded mostly until now. He still
believes that this idea should be discarded after
seeing all the evidence we will talk about on the
Bush Publishes Paper with the
help of Colleagues
Bush, Feder (former Grad Student who found that
only 6% of the apple and hawthorn flies mated
together) and co-workers Stewart Berlocher,
Bruce McPheron, and David Courtney Smith
published paper that identified the differences in
chromosomes of the different populations.
These differences make the different fly populations
leave the fruit they are born in to go into the ground
at different times and then come out of the ground in
the summer at different times too (the apple flies do
both things earlier than the hawthorn flies.)
Bush Gets Help from Rice and
William R. Rice put Drosophila mekmogaster in a maze
and because of their different genes they separated into
their slightly different habitats throughout the maze and
they only mated in these specific areas so they were all
Cichlid species of fish have evolved reproductively
isolated from each other in their specific lakes and river
areas. This is proven through mitochondrial DNA and this
showed that all of the fish in one lake were more closely
related to others in the lake than those in the surrounding
area and through the diet of all the fish which led them to
the specific lake areas and separated the different
populations from each other. Ulrich Schliewen
Last Funny Blurb Thing:
Amazon Diversity!!!! I’m Sad.
James L. Patton went to the Amazon to study
allopatric speciation caused by Rio Jauruá (tributary
of the Amazon)
Gathered lots of gene samples from species, tested
their mitochondrial DNA
Found that there were lots of differences and that a
couple of these differences occurred because of Rio
Jauruá. But others occurred for no apparent reason
until he found out that there used to be ancient ridges
made by the movement of tectonic plates that are
now covered over because the Andes started to
erode and fill in the Amazon basin
Stupid Bird Names and More
Michael Sorenson and Robert Payne
study the Blue Indigobird (STUPID NAME).
It lays eggs in two species of finches nests:
the African Firefinch and the Black Bellied
Firefinch. Then this blue bluebird that hatches
gets raised by these finches and acts like
them, picking up signature tweets and trills.
Then when they grow up they usually mate
with those that share the same types of bird
More of the fish, some Trees
and Cool Names this time
Axel Meyer (cool name) studied the arrow
and the Midas cichlids and found the same
stuff as Ulrich found (Yay for repetition!).
Vincent Savolainen and William Baker
studied the kentia and the curly palm trees on
Lord Howe Island. They found that the curly
palm speciated from the kentia palms when
they moved to more acidic soils which
messed with their timing to flower so the
pollens couldn’t mix with the old kentia palms
and thus they are two species.
Thibaut Malausa found that some
European corn-borers prefer hop or mugwort
They types that prefer the different plants
have stopped mating because they do the
mating on the plants and if the different types
don’t go to the plants they don’t like then they
will never mate, this is what happens.
Arguments against Sympatry
There is still some geographic isolation even
on the corn or the apples and the hawthorn
trees even if it is small
The kentia and the curly palms may have
come about because pollen from far away
fertilized the kentia palm making the curly
Richard Glor studied Cuban anoles that
speciated because Cuba was flooded 5
million years ago so the anoles were
GO FORTH AND CREATE A NAME
FOR THE BLUE INDIGOBIRDS SO
THEY CAN HAVE A BETTER ONE.