By Jon C. Herron and Scott Freeman
- 1 A Case for Evolutionary Thinking: Understanding HIV
- 2 The Pattern of Evolution
- 3 Evolution by Natural Selection
- 3.1 Artificial Selection: Domestic Animals and Plants
- 3.2 Evolution by Natural Selection
- 3.3 The Evolution of Flower Color in an Experimental Snapdragon Population
- 3.4 The Evolution of Beak Shape in Galápagos Finches
- 3.5 The Nature of Natural Selection
- 3.6 The Evolution of Evolutionary Biology
- 3.7 Intelligent Design Creationism
- 4 Estimating Evolutionary Trees
- 5 Variation Among Individuals
- 6 Mendelian Genetics in Populations I: Selection and Mutation
- 7 Mendelian Genetics in Populations II: Migration, Drift, and Nonrandom Mating
- 8 Evolution at Multiple Loci: Linkage and Sex
- 9 Evolution at Multiple Loci: Quantitative Genetics
- 10 Studying Adaptation: Evolutionary Analysis of Form and Function
- 11 Sexual Selection
- 12 The Evolution of Social Behavior
- 13 Aging and Other Life-History Characters
- 14 Evolution and Human Health
- 15 Genome Evolution and the Molecular Basis of Adaptation
- 16 Mechanisms of Speciation
- 17 The Origins of Life and Precambrian Evolution
- 18 Evolution and the Fossil Record
- 19 Development and Evolution
- 20 Human Evolution
A Case for Evolutionary Thinking: Understanding HIV
Evolution is important to study for a number of reasons. It is a matter of LIFE AND DEATH. HIV is an excellent example of evolution in action.
The Natural History of the HIV Epidemic
AIDS was first discovered in 1981 and everyone thought it would be easy to eradicate. 40 years later, around 30 million people have died, mostly in subsaharan Africa.
HIV spreads via bodily fluids, when they come into contact with a mucous membrane or blood stream of another person. (Anal sex makes it more readily transmitted). Antivirals can decrease transmission slightly.
HIV has two strands of RNA. After fusing with a cell, the RNA is transcribed back into DNA by the virus' reverse transcriptase. The DNA is then added to the cell's genome (via integrase), causing more viral mRNA to be produced, creating more virions that can infect other cells. HIV's use of cellular machinery makes it difficult to find drugs that are not too harmful.
Dendritic cells patrol tissues and capture viruses, which it brings to Naive helper T cells. If the virus binds, the T cell rapidly grows and divides, producing Effector helper T cells. These cause B cells to mature into plasma cells and produce antibodies, as well as recruit macrophages. After the virus is dealt with, a few T cells remain as memory T cells.
The HIV strain that binds to CD4 and CCR5 receptors attacks the immune cells. In the acute phase (~4 weeks), many virions are produced. The chronic phase, lasting many years, has steady virion counts. Finally, AIDS means the CD4 T count is super low and the patient will probably die of an opportunistic disease.
HIV attacks the gut lining, causing bacteria to enter the body and triggering a massive immune response, which HIV can leverage to produce more of itself.
Why Does HIV Therapy Using Just One Drug Ultimately Fail?
AZT (azidothymidine) replaces thymidine, but prevents further reverse transcription. It worked at first, but then started to fail. Why? It's not that the cells become resistant. Rather, the HIV virions evolved to resist AZT.
The HIV reverse transcriptase changed over time genetically to be more likely to remove AZT. Evolution happened at such a rapid rate because reverse transcriptase makes so many errors.
Evolution by Natural Selection
- Replication errors lead to variability in AZT resistance
- AZT resistance is inherited by offspring
- There is variable reproductive success
- The virions that persist are ones with resistance
Evolution just happens under these conditions. It's not a conscious decision of the viruses.
There are many HIV drugs that act on different levels. HIV needs mutations to resist all of these at the same time, which is much less likely if many drugs are being used in combination. When patients skip their drugs, it gives HIV the chance to evolve resistance to multiple drugs. Patients who picked up most but not all prescriptions were most vulnerable.
Are Human Populations Evolving as a Result of the HIV Pandemic?
Humans might evolve too, if there are traits that confer HIV resistance.
One example is a mutant CCR5 receptor called Δ32 [delta 32]. Homozygosity was found to confer strong resistance to infection. Δ32 is only found in Europeans (especially Finns/Baltics).
African populations have alternate CD4 receptors. People with the C868T version of the receptor are infected much more readily. Since this sort of heritable variation leads to differential reproductive success, it can be predicted (and seen) that evolution in response to HIV is occurring in human populations.
~8% of human DNA has been inserted by retroviruses. Retrocyclin suppresses retroviruses, but has been deactivated by the substitution of just two bases. If it mutated back, a functional gene might confer advantages.
Understanding the adaptations humans have that fight HIV can help us develop drugs.
If you're sharp, you're asking what happened in the baltics that made them all resistant to HIV.
Where Did HIV Come From?
A doctor was accused of injecting his mistress with HIV infected blood from another of his patients. On a tree, the things with the most recent common ancestor are most related.
Trees are constructed for patients, with the start being one of the virions from a previous host.
The virus of the mistress was found to share a closer common ancestor with the patient's viruses than with any outgroups. The doctor was convicted and is now serving 50 years hard labor.
HIV-1 (the virulent kind) came across from chimps (or gorillas?) a number of times. In simians, it is called SIV.
The most likely human transmission was in 1930, based on the earliest HIV samples. SIV[chimpanzee] (SIV[cpz]) and HIV cause overt disease, whereas monkey SIV doesn't really.
The starting point was predicted by finding the x intercept of the best fit line for a plot of viral divergence from the average by year the sample was collected.
Why is HIV Lethal?
Viruses are selected by survivability in the host and by how readily they are transmitted. Causing damage to the host appears to be more common, meaning transmission is higher. Why?
Intermediate viral load is best for transmission.
Some HIV variants are less susceptible to immune defense. For example, HIV in patients with HLA-B antigens, the HIV epitope (cell surface viral identity protein) p24 had a mutation that the immune cells react much less strongly to.
HIV contributes to death in 3 ways:
- Evolution of new epitopes helps avoid elimination
- Viruses evolve towards more aggressive replication
- Viruses evolve the ability to bind to more receptors than just CCR5. X4 viruses targeting CXCR4, on naive T cells, develops and makes HIV more lethal.
The evolution eventually kills the host. It isn't planned for maximum efficacy, it just happens.
HIV that accumulates synonymous mutations actually causes a faster progression to AIDS than those with high non-synonymous rates, since it keeps the immune system activated for longer (providing more targets to infect) rather than hiding.
HIV-1 group M has vpu, which inhibits tetherin, a suppressor of virion release. This means that higher immune activation actually helps since more virions can be released.
TRIM5a blocks retroviruses. In primates, the binding region has evolved incredibly rapidly. Human TRIM5a is just not as good. A glutamine substitution at pos. 332 confers high HIV-1 resistance in mice, but at the same time makes the mice very vulnerable to the ancient PtERV virus. Humans evolved resistance to PtERV long ago and haven't caught up with HIV yet.
The Pattern of Evolution
There are lots of stupid people, mostly in Turkey and low-tier EU countries. Jon Herron is sad that he even needs to give evidence for evolution because it's so fucking obvious.
There are two competing models: the special creation "model," where species are immutable creations of a divine entity and are unrelated, and the earth is ~6000 years old; then there's Darwin's correct theory: species come from a common ancestor through descent with modification.
There are 5 key elements:
- Species change over time, like birds getting bigger beaks (microevolution)
- Lineages diverge, creating new species (speciation)
- Over long periods of time, major modifications can occur, like fish getting legs (macroevolution)
- Species come from shared ancestors (and perhaps the same primordial form)
- Earth is more than 6000 years old
Evidence of Microevolution: Change through Time
Species obviously change in small ways over time. All you need is to select animals with certain traits and have them breed with each other. Mice that run farther, can be selected to breed and their offspring will run faster than controls. A subgroup of the species has changed clearly. This can also be seen in literally all agriculture.
The micro changes are also clearly linked to genes. Microevolution can be seen in mustard greens in response to drought.
Vestigial structures are another example. Tailbones, snake stubby feet, flightless bird wings are all pointless if they weren't inherited from earlier beings. In genes, some coding regions are disabled in humans but active in apes.
Freshwater sticklebacks are lightly armored, whereas their marine counterparts have heavy armor. When marine sticklebacks were introduced into fresh water, they lost their armor over time.
Evidence of Speciation: New Lineages from Old
We are to use the biological species concept, where only those organisms which can interbreed are within the same species.
Scientists studying a bacteriophage found that after growing them in separate populations, the population-specific phages could not interbreed, making them separate species. In drosophila, bugs growing on different food sources are disinclined to mate.
Speciation progresses as such in natural populations:
- Variation exists (Vancouver Island sticklebacks)
- Interbreeding yet distinguishable subpopulations emerge (Robert's Lake sticklebacks)
- Interbreeding becomes rarer (Paxton Lake sticklebacks)
- The populations cease to interbreed and become reproductively isolated (new species!) (Japanese sticklebacks)
Sometimes all four stages are visible in a "geographically continuous loop." These are ring species, e.g. the Siberian greenish warbler. These interbreed with those close by, but as distance increases, so does genetic divergence. There is a zone where they are too different to interbreed.
Evidence of Macroevolution: New Forms from Old
A fossil is a trace of a past organism. The fossil record is every fossil found so far.
Fossils exist for organisms no longer surviving. In fact, the vast majority of organisms are extinct.
Moreover, fossils found in specific regions tend to have similarities to the organisms living there. This is the law of succession. The fossil record is consistent with descent with modification.
Transitional forms must exist between ancient species and modern ones. There are things called leaping blennys. These exist in aquatic, amphibious, and terrestrial forms. There is a gradient of terrestrial leaping coordination between the three forms. The amphibious one is transitional.
Make note, transitional means it has a blend of traits. All three are still evolving, but the amphibious and terrestrial share a closer common ancestor.
Transitional species can be found in the fossil record as well. One example is Archaeopteryx (Arc’teryx). It has lizard qualities but could glide like a bird. It is the link between dinos and birds. Transitional forms have predictive ability, because a continuous chain likely exists—the fossils only need to be found.
Turtle fossils also show a predictable transition.
Study of macroevolution is cool because it helps explain otherwise puzzling human traits.
Evidence of Common Ancestry: All Life-Forms Are Related
The previous info heavily implies a single primordial ancestor of all life on Earth. The evidence is homology.
All vertebrate forelimbs have the same bones in the same patterns, despite the wide range of uses (dolphins vs moles vs horses vs bats). The similarities between marine mammals and fish are not homologous, since the underlying structures are not the same—they have simply arrived at the same relatively ideal place. Orchid flowers, likewise, although appearing in astonishing variety, have the same general arrangements of organs. Descent from a common ancestor is the most logical explanation.
One example testing Darwin's common ancestry theory is Jon Herron's famous imaginary snails. There is a common ancestor and numerous branches, with one branch terminating further evolution. (in a nested kinda way). This initiates the prediction that traits should be nested. Indeed this is true in nature—see apes. There is generally a strong correlation between the time fossils are from and their position in a nested tree of trait acquisition.
Shared flaws suggest common ancestry (like many shared correct answers vs many shared wrong answers on an exam!!). On chromosome 17 there is a gene setup where heterozygosity equals disease. Chimps and bonobos have the same flaw, indicating that they're closer to us than gorillas.
Another flaw is processed pseudogenes. Retrotransposons, viral DNA left in the genome, can code for reverse transcriptase. When this creates DNA and the DNA is inserted into an exon (introns are ok since they're spliced out in eukaryotes), the gene is nonfunctional ("processed pseudogenes") because it lacks introns and promoters. Mutations accumulate in pseudogenes because selection doesn't remove them. By comparing the numbers of mutations in pseudogenes with the parent gene, the relative age of the pseudogene can be estimated. Processed pseudogenes in common represent homologies.
Other homologies exist. The genetic code (DNA -> amino acids), for example, is generally universal. It would be beneficial to use a different code, since it would decrease susceptibility to viruses, among other things like efficiency. However, everything uses the same code. Why? Common ancestry. Common ancestry is useful in medicine/science because discoveries in yeast, for example, often imply something similar occurs in mice.
The Age of Earth
Uniformitarianism is the claim that geological processes worked the same before as they did now (as opposed to catastrophic events like floods happening only in the past). This suggests that Earth is super old, since processes that form modern geology take so frickin long.
(Ma = million years ago)
For example, the Atlantic expands at a rate of 2.5 cm per year. To get where it is today, it would've taken 148,000,000 years.
A relative geologic time scale was established by applying geological concepts (lava flow orientation, etc.). A more accurate scale was established with radiometric dating, using unstable isotope decay to date things. A rate of decay is found for a substance, then the ratio of parent to child isotopes is determined and used to extrapolate the age. The starting ratio must be known—this can be challenging. For example, argon-40 leaves molten rock, which means lava has 100% potassium-40 at first.
Meteorites and moon rocks imply that Earth is 4.6 billion years old. The earliest fossils are at most 3.4 billion years old!!! This makes evolution easily plausible.
Evolution by Natural Selection
The process of evolution is natural selection.
Artificial Selection: Domestic Animals and Plants
Darwin studied breeding of ornamental pigeons. Pigeons with specific traits are selected to breed and their offspring have those traits as well.
Tomatoes are small in the wild, but over centuries the largest have been re-planted, making tomatoes startlingly huge! Mutations changing size alleles were selected for. Wild cabbage was bred to be cabbage, Brussels sprouts, kohlrabi, and broccoli! Wow! Wild plants don't evolve like humans want them to—"imagine a chihuahua among wolves." Often wild types are more successful in nature.
Evolution by Natural Selection
Darwin has got four postulates:
- Individuals within a population vary
- The variation is heritable
- Some varieties are more successful at reproduction
- That success is affected by their variations
Natural selection just happens, as a statistical/mathematical result of the postulates. Over time, populations change (the individuals don't).
Fitness describes an individual's ability to survive and reproduce. It has nothing to do with muscle tone. Fitness is relative. A trait that increases relative fitness is an adaptation.
Each postulate can be tested independently.
The Evolution of Flower Color in an Experimental Snapdragon Population
In a meadow, there were varied populations of snapdragons that inherited color. They had varying levels of pollination. Pollination was correlated with color, and so the successful-colored flowers became more common in the population.
The Evolution of Beak Shape in Galápagos Finches
Galápagos finches exhibit lots of variation in beak size. The variation reflects their various food sources. Daphne Major is a small island where all the finches are tracked.
The birds eat seeds. Large beaks help crack bigger seeds.
Variation was found to exist. High correlation between parent beak size and child beak size was found. Further genetic analysis confirmed things. BMP4 factor is likely responsible.
There was a major drought and many birds died. The beak size average changed as the number of seeds changed. A type of hard seed became necessary, and only the big beaked birds could access it.
Later populations had big beaks, confirming evolution.
The Nature of Natural Selection
- Evolution is a statistical process. Watch out kids!
- It occurs generation by generation, based on who reproduces.
- Natural selection acts on phenotypes, but evolution depends on genotype changes.
- Natural selection is not aware of the future. See: finches.
- New traits can evolve through mutation! Death of small-beak finches doesn't mean new big-beak finches suddenly appear.
- A trait that becomes repurposed is an exaptation. Additional modifications are "secondary adaptations." butterworts had sticky hairs, which over time became a tool of capture rather than defense.
- Natural selection does not lead to perfection. Selection can act in contradictory ways.
- "survival of the fittest" is not circular. Fitness can be measured.
- Selection is not for the good of the species. (unless it improves fitness for the altruistic individuals).
The Evolution of Evolutionary Biology
The theory of evolution had some problems:
Variation was unexplained until mutation was discovered.
Inheritance was not explained for a while. Blending inheritance would make the kind of inheritance necessary for evolution impossible (without random mutation).
Time was misunderstood too, since radioactive decay as an energy source was unknown.
The modern four postulates are as follows: (direct quote from book)
- Individuals vary as a result of mutation creating new alleles, and segregation and independent assortment shuffling alleles into new combinations.
- Individuals pass their alleles on to their offspring intact.
- In every generation, some individuals are more successful at surviving and reproducing than others.
- The individuals most successful at surviving and reproducing are those with the alleles and allelic combinations that best adapt them to their environment.
Intelligent Design Creationism
Religious nuts are trying to call creationism an alternate theory to get it allowed in public schools.
Intelligent design asks how life is so perfect if a god didn't create it. The answer is time, dipshits.
An irreducibly complex structure would conflict with evolution, since stepwise advancements could not have led to it. A creationist thinks a cilium is an example. He's wrong.
Irreducibly complex systems CAN arise, since other things can be repurposed.
Crystallins (eye lens proteins) are mostly repurposed enzymes and proteins from other sources.
For all you losers out there:
- Evolution is falsifiable and makes testable predictions.
- Evolution does not violate the second law of thermodynamics because Earth is not a closed system. The no free lunch theorem is not applicable because changes in biology often produce only small deviations.
- Speciation has definitely been observed. Even if it hadn't, you are an idiot if you can't use logical reasoning to figure out the implications of evolution.
Estimating Evolutionary Trees
Some guys went to Japan and analyzed whale (food) samples. They created a phylogenetic tree and placed the samples as humpback from the North Pacific, an illegal place to hunt humpbacks.
How to Read an Evolutionary Tree
An evolutionary tree shows the history of change for a single lineage.
The root node represents the most recent common ancestor of all shown descendants. The end nodes represent existing organisms found.
The nodes represent transitions where populations diverged.
Evolutionary relationships are determined by the most recent common ancestor: the more recent the shared ancestor, the greater relation. Pairs of taxa with no other closer recent ancestors are "sister species."
Evolutionary trees do not show everything, since only a small set of species are shown. Other relationships can exist. They can be drawn in different styles as long as time flows from the root. They are only hypotheses, made using limited methods.
The Logic of Inferring Evolutionary Trees
Shared derived characters can be used to make trees. These trees imply the evolutionary history of the taxa.
A derived character is an apomorphy. An ancestral character is a plesiomorphy. These are context-dependent. A derived character shared by two or more lineages is a synapomorphy.
A monophyletic group/clade is a lineage with a common ancestor. A paraphyletic group has the ancestor and some (but not all) descendants. A polyphyletic group has some (but not all) descendents and no ancestor. syanpomorphies identify monophyletic groups.
Synapomorphies that split into three represent polytomy, as opposed to bifurcation.
Non-ideal cases make estimation necessary. This is when similar traits evolve separately, or traits are lost, or the ancestor is unknown.
Phylogenies can be estimated by counting the number of steps it would have taken to get to the current situation (relative to an outgroup). The path with fewest steps is selected. This is parsimony analysis.
Convergent evolution is when a similar trait arises independently. Reversal is when a trait is lost. Similar characters due to these things is called homoplasy.
Molecular Phylogeny Inference and the Origin of Whales
Cetaceans are identified by skull characteristics (some of which improve underwater hearing).
Morphologically, they are similar to artiodactyles, like cows sheep and pigs. But some traits are hard to analyze, giving an imprecise picture.
DNA is problematic because homoplasy is not readily detected (bases can only be 4 things).
Phylogenies can be inferred with a number of methods:
- Sequence alignment: Sequences are aligned so that matching bases line up, smoothing over additions/deletions. The number of differences can help indicate lineage.
- Parsimony analysis where each base is treated as a step.
- Likelihood analysis: branch length is included. We know rates of various substitutions, so the probabilities of evolving can be determined. The probability of the data given the tree is found.
Various search methods can accelerate things, instead of brute-forcing every possible tree.
Bootstrapping is a technique that uses a computer to sample small bits of sequence data and reconstructs trees. Confidence is based on how often the same relations are found.
Bayesian phylogeny inference finds the probability of the tree given the data (opposite of likelihood analysis).
Presence of SINEs and LINEs (short/long interspersed elements) can be used as homology. With these, whales are most similar to hippos. Whales show lots of homoplasy with their kin.
Using Phylogenies to Answer Questions
Dog herpes: caused by virus? or direct cell transfer? The tumors cells were closer to each other than the dogs. Therefore, cell transfer.
Neutral mutations occur at a somewhat predictable. This can be used as a molecular clock. Humans started wearing clothing about 100k years ago, since that's when head and body lice diverged.
How did the seychelles chameleon get there? Biogeographers/phylogeographers have the answer! By vicariance, they would have stayed there as continents drifted apart. By dispersal, they would've rode a vegetable raft. The most recent common ancestor with madagascar and india is in line with vicariance. On the other hand, the chameleons in comoros and Reunion islands rode rafts, since the islands are volcanic. Wow!
Variation Among Individuals
Humans seem to vary tremendously, but analysis shows that animals exhibit greater variation in many ways, such as height/length.
Heritable variation is the raw material for evolution.
Three Kinds of Variation
- Genetic variation: people have different skin colors
- Environmental variation: people get tan in the sun
- Genotype-by-environment interaction: some people get more tan than others.
Most functions in cells are carried out by proteins. Red blood cells carry oxygen in hemoglobin, goblet cells make mucigen, and rod cells have the light-absorbing rhodopsin. Proteins are made of amino acids, which determine its structure and chemical function.
DNA codes for proteins with its sequence of AGTC bases. There are many genes per chromosome. Loci of genes is shared within species. The collection of chromosomes represents an organism's genome.
Genetic variation results from differences in sequence. Environmental variation results from changes in protein expression. Genotype-by-environment results from sequence and modified changes in expression due to different sequence.
phenylthiocarbamide (PTC) tastes bitter only to some humans. This is a result of having different alleles for the taste receptor. The combination of alleles people have is called genotype. The exhibited character is the phenotype. Low bitterness sensitivity is homozygous. PTC detection favors veggie eating and protects against toxins.
An inducible defense is an example of environmental variation. It changes gene expression. Environmental variation does not itself supply material for evolution.
The pattern of response an individual has to conditions is its reaction norm. Leopard geckos have sex determination based on reactions to incubation temperature, and the sensitivity to temperature is heritable. Ability to change in different environments is called phenotypic plasticity. Using tobacco hornworms, Japanese scientists showed that the temperature sensitivity (at high temperature they would turn green) of the caterpillars was heritable by selective breeding.
Clearly, genotype-by-environment can work as raw material for evolution.
Where New Alleles Come From
New alleles come from mutations to the genome.
DNA is double stranded, and is replicated by pairing complementary bases. Mutations occur during replication. For example, cytosine can have CH4 added and turn into thymine. Alternatively, sequences can be misaligned and have a base pair inserted or deleted.
Mutations susceptible to repair are permutations. Most permutations are fixed before becoming actual mutations. Without repair enzymes, we would be cancerous blobs of tumors.
Mutations result in changes in protein sequence.
A point mutation is the substitution of one base for another. Purine to pyrimidine or vice verse is called transversion. Purine to purine or pyrimidine to pyrimidine is transition. If the mutation does not change the amino acid coded for, it is silent/synonymous. If it does change the amino acid, it is replacement/nonsynonymous. Nonsense mutations are when a stop codon is added prematurely. Changing intron or exon splicing sites can also cause significant mutations.
Insertions and deletions (indels) of anything other than multiples of 3 cause a shift in reading frame that leads to all downstream codons being changed.
Allele frequency is homozygote frequency + 1/2 * heterozygote frequency.
Where New Genes Come From
New genes come from many places as well.
Gene duplication can happen due to unequal crossing over or retrotransposition, i.e. RNA is reverse transcribed and inserted.
The douc langur has an extra RNASE1 gene, with modifications that reduce its virus-fighting potential. Instead, it is used for digesting RNA for nitrogen. Duplicated genes with different functions are paralogous. Genes similar but separated by speciation are orthologous.
The gene for short corgi legs came from retrotransposition, indicated by its lack of introns (since it went from RNA to DNA again).
Gene duplication accounts for a great deal of new variation. Sometimes noncoding sequences can become genes.
Chromosomes can be mutated as well, having much larger effects.
Inversion occurs when two breaks occur in the chromosome, and the section between the breaks flips arround before reattaching. This makes crossing over fail to occur since homologs cannot align, causing the inverted section to be inherited as a supergene.
In drosophila, different inversions are found at different climates (a cline for the inversions exists). When an old-world drosophila was introduced to the new world, flies with the same inversions were found at similar latitudes, indicating that selection plays a role. Inversions result in selection on groups of alleles.
Genome duplication can occur due to chromosomes failing to separate in meiosis. If this duplication takes in the population, descendants with duplicated genomes can result. Organisms with more than two chromosome sets are polyploid. Polyploidy is more common in plants. Duplication often leads to speciation, since offspring of parents with different numbers of chromosomes are often infertile, leading to isolation. Changes in ploidy can themselves alter fitness in different environments.
Rates and Fitness Effects of Mutations
Mutation rates can be found by mutation accumulation experiments.
In rapidly changing environments, high mutation rates are more favorable because the likelihood of survival increases with more options available. On the other hand, the deleterious mutations might outweight the benefits in a static environment.
Most mutations are deleterious. Over time, populations without selection will become less fit. Under selection, the population will show increasing average fitness.
Mendelian Genetics in Populations I: Selection and Mutation
Mendelian Genetics in Populations II: Migration, Drift, and Nonrandom Mating
Evolution at Multiple Loci: Linkage and Sex
Evolution at Multiple Loci: Quantitative Genetics
Studying Adaptation: Evolutionary Analysis of Form and Function
A trait that increases fitness is called an adaptation. To show that a trait is adaptive, its function must be known and it must be determined whether or not it increases reproductive success.
All Hypotheses Must Be Tested: Oxpeckers Reconsidered
It was believed that oxpeckers had a mutualistic relationship with mammals, eating ticks and cleaning wounds. In reality, the animals hate them because they aggravate wounds and eat dead skin and earwax.
Not every trait needs to be an adaptation. Not every adaptation needs to be perfect.
Experiments are powerful because they let us isolate the effects of a single factor.
The zonosemata fly was found to mimic a predator not to fool other species, but the predator itself (into thinking that zonosemata was one of its own).
Experiments are strengthened by responding to competing hypotheses.
Control groups are critical. All treatments must be handled alike. Randomization is key. Repetition is essential.
Statistical hypothesis testing starts with a null hypothesis, which is attempted to rule out (in favor of alternative explanations).
Sometimes observation can work almost as well as experimentation.