Lecture notes for lecture 4.
This lecture covers chapters 6 and 7 in the textbook.
What is evolution?
- The book emphasizes that evolution can be seen as two things: a) a process of descent with
modification (a pattern over a long time period), and b) genetic change in a population over time
(generally looked at a smaller time scale).
- Let’s think about the “process of descent with modification”. A misconception is that this is an idea
that Charles Darwin came up with. But actually, the idea of evolution in this sense was floating around a
lot even in the time of Darwin’s grandfather (who was a famous scientist of his day).
- Evolution contrasts with religious theories of the creation of life. For example, creationism (closely
associated with Christianity) postulates that species were created independently of each other, that
they are fixed entities that do not change, and that creation itself was not long ago (~ 6000 yrs).
- Charles Darwin himself took a worldwide trip as a young man on a ship called the H.M.S. Beagle (see
his great book “Voyage of the Beagle” (1840s), in which he saw a lot of evidence that was inconsistent
with creationism.
- For example, he found many fossils, including fossils resembling, but different from animals currently
living in the same area.
- He noticed that many animals have “vestigial” features, attributes that don’t currently have a function.
For example, humans have a tail bone; salamanders that live in caves still have eyes, although they do
not work. These characters can be understood as “homologous” (similar to) working characters in other
animals that are related (in the case of our tailbone, primates with tails).
- He saw that many species appear to be related to each other. A particularly famous observation of his
was that on the island chain of the Galapagos each different island had slightly different species of birds.
A group of finches on these islands are names after him and we will use them later to explain the
process of natural selection.
- Darwin was also a geologist, and read with great interest many of the geologists’ writings of that age
who argued that the earth was quite ancient.
- In summary then, there is a lot of evidence that species are related to each other (those in nearby
areas, especially those slightly separated from each other, are relatively similar), that they have changed
over time (fossils, vestigial features), and that the earth is in fact ancient.
- At a smaller time scale, evolution is just a change in the frequencies of genes in a population over time.
We often talk about “allelic changes” – an allele is an alternative form of a gene (one famous example
controls coat color in leopards), and over time the frequencies which with alleles are found in a
population can change. This is a simple fact that has been shown in many populations over time.
- Why do these genetic changes occur in a population over time? Darwin proposed a “mechanism of
evolution”, natural selection, that drives these changes. This, rather than simply arguing for the
existence of evolution, is Darwin’s signature accomplishment.
Natural selection.
- The central ideas of natural selection are listed in Slide 10. Basically, there is variation among
individuals in their traits that is hereditable (offspring resemble their parents), and individuals that have
traits that fit the environment best will survive and reproduce, with their genes making up a larger
percentage of the population in the next generation (hence the phrase “survival of the fittest”).
- Before continuing I want to emphasize that while some of the variation between individuals is
heretitable, some is not. That is because individuals with the same genotype (genetic information) can
have different phenotypes (appear differently). Think of human identical twins.
- Or think of how a tree can adjust to where it is planted. If you plant it in the middle of a garden with
lots of sun, it will grow wide with many side branches. But plant it in the middle of the forest where
there is not much light and it will grow straight upwards without much side branching.
- The ability for living things to have different phenotypes in different environments is called
“phenotypic plasticity” and is a hot topic in evolutionary biology.
- In class, we then go through the example of Darwin’s Finches as evidence for evolution and natural
selection in the wild.
- Darwin’s finches have been studied for a very longtime by two remarkable (husband and wife)
biologists by the name of Peter and Rosemary Grant (Princeton University). Their research has become
the basis of the popular and easy-reading book called “The Beak of the Finch”.
- The Grants worked on a small island in the Galapagos called “Daphne Major”. They captured and
banded every single finch on that island, concentrating on one species called the “Medium Ground
finch”.
- They then demonstrated that: 1) there is variation in beak size in this species and 2) it is heritable (note
the axis on slide 15 says “mid-parent” beak depth. How do you think this is calculated and why do they
do such a calculation?
- Between 1975 and 1979 then then experienced a remarkable thing. Daphne Major experienced a
major drought (probably associated with an El Nino event). The number of seeds on the island was
dramatically reduced and consequently the number of Medium Ground finches declined dramatically,
form over 1400 to 200.
- It happened that during the drought, one variety of plants with large seeds continued to do well and
make many seeds. Thus, the average seed size was larger during this time (slide 17). At the same time
the average bill size in the population increased; documenting evolution (slide 18). Since larger bills are
able to crush larger seeds, the data strongly suggests that this evolution occurred due to natural
selection.
- In class we also talk about another example of natural selection: the horn size of bighorn sheep that
are hunted. Be able to walk through the entire process of natural selection, telling how each step applies
for the bighorn sheep example.
Other mechanisms of evolution
- It should be remembered that Darwin understood little about genetics. Gregor Mendel, who
discovered the basic genetic principles of heredity, was a contemporary of Darwin, but Mendel’s results
were not about widely until the early 1900s. And it was only in 1953 that the genetic material was
shown to be DNA by Watson and Crick.
- So Darwin didn’t really understand why individuals differed from each other. Today we know that
much of such variation is produced by mutation, the process of making mistakes in the reproduction of
genetic material.
- Mutations can be of many kinds and on many scales. For example, one of the simplest kinds of
mutations is a “point mutation” in which one of the 4 DNA nucleotides is substituted for another. In the
process of transcription – when DNA is used as a template to produce a protein – this mistake could
mean that a different amino acid (subcomponent of a protein) is attached to the growing peptide chain.
- If this part of the protein is not essential to the protein’s function, then there may be no detectable
change in the new organism’s phenotype compared to its parents. But the mutation could be in the
active site of the protein, and then could change the function of the protein. Or the nucleotide
substitution could lead to the DNA replication machinery reading a “Stop codon” (a nucleotide code that
tells replication to end), and the protein could not be even made. Or one nucleotide could be removed,
changing everything that follows it (a “nonsense mutation”).
- Beyond these different kinds of mutations in the nucleotide sequence, there are even larger types of
mutations that can occur. For example, whole pieces of the chromosome can be missing (this is the case
for Down’s syndrome, for example). Or the entire chromosome can be doubled in number (polyploidy).
I’m not worried about you understanding the details here, just the general idea that mutations can
range from the very minor to the radically different.
- Another source of variation in sexual organisms is recombination. This occurs in meosis when the two
copies of the same chromosome (one from each parent) come together and exchange pieces, forming
new combinations of genes.
- Mutation can be considered a mechanism of evolution because it introduces new genes into a
population, hence changing gene frequencies.
- Another mechanism of evolution is called “genetic drift”. Gene drift is the change in gene frequencies
over time due to random events. For example, think you have a population of 5 individuals, only one of
which has a gene for red hair. Then a volcano erupts and just by chance that one red haired individual is
killed. Now there are no genes for red hair in the population.
- As the example above suggests, genetic drift is most important in small populations. Another example
when this can happen is if there is a sudden drop in the population (like the finches during the drought),
which is called a “bottleneck event”, or if a small number of colonists establish a new colony (the
“founder event”). You have a simulation about genetic drift for homework, that we will start in class.
- A final mechanism of evolution is called “gene flow”. Gene flow is simply the movement of genes from
one population to another because some individuals move between the populations. While natural
selection and genetic drift will over time make two populations different from each other, gene flow
makes them more similar to each other, and hence slows the pace of evolution.
- in reviewing the different mechanisms of evolution that we discussed (natural selection, mutation,
genetic drift, gene flow) it’s important to recognize that only natural selections leads to organisms
having adaptations to their environment.
- An adaptation is a trait of an organism that fits the environment well. In class, we discuss the case of
the soapberry bugs which switched hosts to an invasive tree. That tree had a thinner fruit, and the
population of bugs that live on this fruit have shorter beaks, which can be viewed as an adaptation.
- Remember that adaptation is not a perfect process for a number of reasons: 1) there needs to be
genetic variation on which natural selection can act. If there is no gene for, say, resistance to a pesticide
in a mosquito, it can’t magically appear (it requires either mutation or introduction via gene flow from
another population).
- 2) Because of this, the evolutionary history of an organism limits what is possible. A mammal, because
it descends from animals that lived on land, is unlikely to evolve a way of breathing under water.
- 3) Gene flow tends to decrease the match between organism and environment, because organisms are
moving from some other place, where the environment might be different.
- 4) The environment itself is changing, and hence provides a “moving target” so there can be no perfect
fit.
Diversification over time
- Natural selection leads over time to tree kinds of outcomes. The most common is “directional”
selection. This is when the mean value of a trait changes in one direction or another. For example, bill
size in the finches increased.
- Another outcome is called “stabilizing selection”. Stabilizing selection is when extremes (both larger
and smaller) are selected against. Stabilizing selection often occurs because there are some trade-offs at
work. For example, children who are born at very low weights have poor immunity. But children who
are very heavy risk problems at childbirth getting through the birth channel. The trade-off here is that
size helps the general health of the baby but too big is also dangerous. Stabilizing section here
eliminates the extremes, with the mean (average) staying the same.
- A final outcome (“disruptive selection”) is that both extremes are selected for. Imagine, for example,
that during the drought on Daphne Minor there were plants with either extremely small seeds or very
large ones. Then we might expect birds with small bills and with large bills to do well, but intermediate
birds to do poorly. This may lead to two populations with different characteristics … and possible
speciation.
- Speciation is the breaking of one species into two or more species.
- We believe that most speciation occurs through the physical isolation of populations. For example a
species of bird reaches a group of islands, and forms separate populations on different islands (like the
Galapagos), which are reproductively isolated (they don’t interbreed).
- Over time, natural selection, mutation and genetic drift act to make the populations different from
each other, so much so that if the populations ever meet again in the future they do not successfully
interbreed. This model is called “allopatric (different place) speciation”.
- Speciation can occur, however, in the same place (“sympatric”) if somehow two groups of the same
species live separately and interbreed only within the group. Remember the example of small-beaked
and large-beaked birds above (disruptive selection)? Speciation could occur if small-beaked birds
preferred to mate with other small beaked birds. We discuss in class how something similar might have
occurred in the crossbill system described by Benkman (2003).
- We then look at examples of “Cladograms” which means literally “tree diagrams”. These represent the
evolutionary history(“phylogeny”) of organisms. A split in the tree is a speciation event, and when one
branch doesn’t reach the present, that’s extinction (no more individuals of that species). See Darwin’s
famous written cladogram from his notebooks as he started to think about evolutionary diversification
(slide 35).
- Two kinds of large scale patterns can be seen in evolutionary history of many organisms. First are
events of mass extinction, when many species went extinct at one time. An example is the well-known
extinction 65 mya when dinosaurs died off, probably because the earth was hit by an asteroid that
raised so much dirt into the air that all the plants died.
- Another pattern is called “adaptive radiations”. This is the rapid evolution of many species from one
ancestor. This can occur when an organism colonizes a new environment (like the islands of Hawaii,
raised from the sea by volcanos), or when mass extinction has removed competitors (a radiation of
mammals and birds followed the extinction of the dinosaurs).
- In class, we end this section by talking about ways in which ecology and evolution are completely
linked together.
Life histories
- This material fills a whole chapter of the textbook, but I have not covered it in the lecture so
extensively.
- A life history summarizes for a species summarizes the major events in the lives of individuals: growth,
development, reproduction, survival (and death). Questions we can ask are: does it go through a stage
of metamorphosis, when does the species first reproduce, how many offspring does it have per
reproductive event, what are the size of those offspring, how long will it continue to reproduce and
survive? See slide 45.
- In class we go through two examples of very complex life histories. One is a coral… it goes through
metamorphosis, changing from a free-moving small fishlike organism to a non-moving polyp that lives in
colonies. The other is a fern. Whereas in most organisms such as humans our haploid stage (sperm and
eggs) is only one cell, in ferns the haploid stage itself is a separate multicellular organism. I don’t want
you to memorize details here; just get a sense of how radically life histories can vary one from another.
- We next ask the question why should animals be sexual or asexual.
- There actually is a big disadvantage for sex: for every two offspring, one is male (and can’t make its
own offspring without mating with a female). So the number of offspring one can have is much less
than in asexual reproduction (slide 43).
- At the same time there are advantages to sex, primarily in making a lot of genetic variation through an
individual receiving two sets of genes, and then having some recombination. If a population has a lot of
variation, at least some individuals may fit a difficult or rapidly changing environment.
- Slide 44 describes an experiment on a worm (C. elegans) that can elect to either reproduce sexually or
asexually. In normal conditions it prefers to reproduce asexually. But in a challenging environment
where the worms are exposed to pathogens, the worms prefer to reproduce sexually.
- Genetically engineered worms that can only reproduce asexually fare poorly over time when exposed
to bacteria, whereas worms genetically engineered only to reproduce sexually survive well.
- We then look at two major issues in life history studies. First, we ask how many and what size of
offspring does an organism have? There’s an obvious trade-off here: an organism can chose either to
put a lot of investment into a few large offspring or little investment into many small offspring.
- Advantages to large offspring include that the bigger you are generally the fewer predators there are
that are bigger than you. Also for seeds and eggs, the more nutrients stored in them, the better their
chances of establishing themselves and surviving the difficult early stages of life.
- But there are advantages to being small, too. Small organisms can move more easily in the wind or
through water and hence go to new environments where there may be more opportunities. And as we
talked about before, small organisms are also often able to go dormant and survive with little use of
energy until the environment is more welcoming to them.
- The next issue is at what age to reproduce. Generally, the more investment put into reproduction
early in life the less long you live. For example, we discuss male flies where the more energy the males
put into breeding, the less their survival … courting females is difficult work! Also we discuss pine trees
where the more cones produced the less the tree grows, showing again that energy is limited and that
spent on reproduction can’t be put towards growth and survival.
- We also discuss the example of animals with parental care, like birds. In birds one can do experiments
whereby you increase the number of eggs the bird has in its nest. The parents (actually the fathers, the
mothers don’t have much of an effect) have poorer survival if they are given more eggs, showing a
trade-off between reproduction now and reproduction later.
- An extreme strategy in this regard is to be semelparous: reproduce once and then die. Some plants like
bamboo or animals like salmon have this life history. Note that they have very many offspring when they
do reproduce.
- What are the advantages to having a short life, reproducing quickly and then dying? Well if one is an
organism that makes use of environments that are short-term, this life history might be beneficial.
These organisms require many offspring so that a few have the chance to find this rare and always
disappearing environment. Then they grow rapidly and reproduce while the environment is still there.
- These kind of animals (which we say have a “r” strategy; we will explain later why we use this
terminology) are not good competitors. Think of a farm field that is recently plowed. Weeds (typical r
strategists) move in, grow fast and reproduce. But after a time they are out-competed by other
organisms like trees that grow larger than and get all the light.
- the other extreme strategy (in actuality we are talking about a continuum between these extreme
strategies) is called the “K” strategy. These are the good competitors, like the tree in the plowed field.
Once they’ve started growing they live long and eventually outcompete all others.
- K strategists tend to live a long time and reproduce many times (iteroparous), with each reproductive
event having a relatively small number of offspring, so that each offspring has lots of investment (in
nutrition or parental care) to do well.
- Hence these life history traits are related the stability of the environment that the organism lives in.
- We end this section with a discussion of a life history of the clownfish. Clownfish have been
immortalized in the movie “Finding Nemo”, but the movie gets their life history wrong!
- This strange little fish lives in anemones on coral reefs, which have stingers that can kill many
organisms. But the clownfish are immune to the anemone stingers.
- Clownfish have many offspring per reproductive event and the small fry (little hatched offspring) then
disperse off the reef and live planktonically in the open ocean until they mature and look for a reef and
an anemone.
- Within one anemone, several fish can live. But interestingly they are not related, and they have a strict
hierarchy: the biggest individual is female, the next sized one is a male, and the rest are sexually inactive.
- If the female dies for some reason (like what happened in “Nemo”) something really strange happens:
the male turns into a female and the next-biggest fish turns into a male. This strategy of changing sexes
at different parts of adulthood is known as “sequential hermaphroditism”.
- Why have clownfish evolved this strange system? Two reasons probably apply: first, large animals are
better able to make eggs, since eggs require more investment than sperm. So large animals are better
off as females. But why wouldn’t fish try to leave the hierarchy and reproduce earlier? Perhaps because
survival on the reef outside of the anemone is very poor for these fish. Since competition for anemones
is strong, the best the fish can do is wait for their turn!