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Experiment one tested the effects of varying substrates on survival. In each of the three
tanks, 20 random guppies, 5 Rivulus and 5 Blue Acara were added. Each tank represents a
different substrate, the three substrates are sandy, muddy and vegetative. Spot brightness was
measured after 1000 days.

Experiment two tested the effects of varying levels of predation on survival. Only tank 1
was used, representing a constant sandy substrate. Five various levels of predation were tested
separately in this tank. For each trial 20 random guppies were added. Then 0, 4, 8, 12, or 16
predators were added. An equal number of Blue Acara and Rivulus were added, so with eight
predators, there were four Blue Acara and four Rivulus. Spot brightness was measured after 500
days.

There are numerous intricate processes involved in the determination and evolution of

male guppy coloration. Since guppies exhibit sexual dimorphism, sexual selection is likely a

prominent factor in varying levels of male showiness. The more ornate a guppy is, the more

likely it is to obtain a mate, reproduce, and pass on its genes. However, theses elaborate colors

also pose a threat to survival, as they attract predators. Therefore, the varying environments and

substrates will affect survival, because certain environments will provide more protection and

hiding spots from predators. Several hypotheses for varying levels of male showiness are:

1. When predators are present, the type of substrate will affect survival, resulting in a

change in spot brightness over time.

2. As predation increases, male guppy spot brightness will decrease, because higher spot

brightness attracts predators.

3. In the absence of predation, and at low predations levels, spot brightness will increase

due to sexual selection.

There are numerous intricate processes involved in the determination and evolution of
male guppy coloration. Since guppies exhibit sexual dimorphism, sexual selection is likely a
prominent factor in varying levels of male showiness. The more ornate a guppy is, the more
likely it is to obtain a mate, reproduce, and pass on its genes. However, theses elaborate colors
also pose a threat to survival, as they attract predators. Therefore, the varying environments and
substrates will affect survival, because certain environments will provide more protection and
hiding spots from predators. Several hypotheses for varying levels of male showiness are:
1. When predators are present, the type of substrate will affect survival, resulting in a
change in spot brightness over time.
2. As predation increases, male guppy spot brightness will decrease, because higher spot
brightness attracts predators.
3. In the absence of predation, and at low predations levels, spot brightness will increase
due to sexual selection.

Chapter 1 - The Natural History of the HIV Epidemic

• HIV has infected over 65 million people, 30 million deaths, spreads via bodily fluids

• Antiviral drugs reduce risk of transmission

• HIV is an intracellular parasite incapable of reproducing on its own, afflicts immune system

• HIV virions enter host cells by binding to proteins on surface, then use host machinery to make new virions

• Dendritic cells patrol vulnerable tissues, take viruses to lymph nodes, present bits of its protein to naive helper T cells, these cells divide to produce helper T cells

• Effector helper T cells stimulate B cells to mature into plasma cells, which make antibodies

• Killer T cells destroy infected host cells

• HIV infection depletes CD4+ T cells in gut, impaired gut defenses allow translocation of bacteria into bloodstream, activates immune response, effector T cell proliferation, gives HIV more target cells, chronic infection and inflammation, damaged lymph nodes

Why Does HIV Therapy Using Just One Drug Ultimately Fail?

• Drugs inhibit enzymes that are special to the virus

• AZT blocks reverse transcription, loses effectiveness, population of virions become resistant to disruption by AZT

• Categories of drugs used: Coreceptor inhibitors, fusion inhibitors, reverse transcriptase inhibitors, integrase inhibitors, protease inhibitors

• Multiple drugs that target different point in HIV life cycle is much more effective, reduces the genetic variation for resistance, HIV can be resistant to multidrug cocktails

Ancient DNA and Human Evolution

• Started with Egyptian mummies, looking at tissues

• Cloned DNA from mummies, PCR made this possible

• Ancient DNA carries modifications, degraded to short sections, can be contaminated and polluted with other DNA

• Studying cave bears provided insights to neanderthals

• Total replacement vs assimilation theories

• First mitochondrial dna share dabout 0.5 mya

• There is no mtDNA remaining from neanderthals today in humans

• Library based techniques can be amplified and immortalized to construct genome

• Found neanderthals bones in Vindija Cave, Croatia

• DNA extract is a mixture of microbial DNA deanimated DNA and contamination

• Focused on C-T changes, Deanimated DNA

• Europeans should share more variants with Neanderthals than Africans

• About half of the Neanderthal genome is available in people that live today

• Denisovans contribute DNA in mainland Asia

• “Leaky Replacement” Genetic replacement and some contribution

• People that live in Europe today share more with the genome from Croatia

• Direct evidence of Neanderthal mixing in Europe with mandible

• A risk variant for type 2 Diabetes came from Neanderthals, possible adaptation to starvation

• High altitude adaptation in Tibet came from Neanderthals

• DNA can be obtained from archaeological sediments

• There are some functions that are unique to modern humans

• There are about 30,000 single nucleotide changes that are fixed in present day humans

• Humans have less GMP, AMP, Guanine and Adenine in brain

• Humanized mice have decreased ADSL activity

   The authors found that “ Scandinavian wolves are highly differentiated both from the neighbouring eastern population and from historical Scandinavian wolves.” All of the wolf populations were found to be significantly differentiated. The genetic variability was significantly lower in the Scandinavian wolf population than other populations. A sharp decline in heterozygosity was observed. The decrease in heterozygosity was measured at 30 % per generation which matches the estimate. The addition of a new immigrant to the population increased mean heterozygosity from 0.49 to 0.62. The sharp decline in heterozygosity was thought to be due to inbreeding, The expected loss of heterozygosity for a population of two individuals would be 25% per year. The observed value was 30%, which is relatively close. However the formula is likely not accurate in such small populations. As expected, the addition of the new immigrant and new alleles increased heterozygosity.

What were the authors trying to test, and what predictions did they make?

    The authors were studying the geographically isolated Scandinavian population of grey wolves. This population was founded by only two individuals and recovered by the arrival by addition of a single immigrant. The original population suffered from inbreeding depression. The addition of an immigrant granted new genetic variation and allowed the population to thrive.

What, exactly, did the authors do?

    The authors collected tissue and blood samples from Scandinavian wolves and wolves from Finland and northwest Russia. DNA was extracted and analyzed. Twelve microsatellite markers were chosen to examine. The relationships between individuals was analyzed using Kinship.

What did the authors find (i.e, what were their data)?

    The authors found that “ Scandinavian wolves are highly differentiated both from the neighbouring eastern population and from historical Scandinavian wolves.” All of the wolf populations were found to be significantly differentiated. The genetic variability was significantly lower in the Scandinavian wolf population than other populations. A sharp decline in heterozygosity was observed. The decrease in heterozygosity was measured at 30 % per generation which matches the estimate. The addition of a new immigrant to the population increased mean heterozygosity from 0.49 to 0.62.

How did the authors interpret their findings?

    The sharp decline in heterozygosity was thought to be due to inbreeding, The expected loss of heterozygosity for a population of two individuals would be 25% per year. The observed value was 30%, which is relatively close. However the formula is likely not accurate in such small populations. As expected, the addition of the new immigrant and new alleles increased heterozygosity.

What were the authors trying to test, and what predictions did they make?

    The authors were assessing the genetic diversity and relatedness in the critically endangered species hawk Buteu ridgwayi. The island population of birds is expected to exhibit a lower genetic variation than mainland populations. This is because there is reduced gene flow, smaller population sizes and increased genetic drift due to isolation. The island birds also likely suffer from inbreeding depression.

What, exactly, did the authors do?

    The authors collected samples, and monitored nests and breeding pairs over four years. Blood was collected from 149 Ridgway’s Hawks. Fourteen microsatellite loci were tested to examine allelic variation. The program Bottleneck was used to test for the presence of a genetic bottleneck. Alrequin was used to calculate the observed heterozygosity, expected heterozygosity, and number of alleles. The relatedness was determined used a program called Kin Group.

What did the authors find (i.e, what were their data)?

    The allele frequencies ranged from 0.0069 to 0.4960. The observed heterozygosity across loci ranged from 0.521 to 0.884. Relatedness coefficients of the seven sampled breeding

pairs ranged from -0.09 to 0.55.  There was no structure present, all of the samples came from one genetic population. A significant excess of heterozygotes was found.

How did the authors interpret their findings?

    The results from the study show that the population underwent a recent genetic bottleneck, had a high level of heterozygosity, and occurred inbreeding. The significant excess of heterozygotes indicates a recent genetic bottleneck. The relatedness analysis verified the presence of inbreeding. Island avian populations are of great concern, because they have a higher risk of extinction than mainland animals. These island birds are more susceptible to extinction primarily due to human caused habitat loss and introduced species.

What were the authors trying to test, and what predictions did they make?

The authors were testing the effects of two specific major barriers, a river and a road, on the endangered european wildcat. The two features represented both anthropogenic and natural landscape barriers that pose a threat to the wildcat. They predicted that if the dispersal of wildcat populations is limited by these two barriers, then the isolation would be reflected in the genome.

What, exactly, did the authors do?

    The authors investigated the genetic structure of wildcat populations separated by the Rhine River, and a major highway. Hair and tissue samples were collected over five years. Fourteen microsatellite loci were genotyped, and 188 individuals were studied. Questionnaires were also sent to forestry districts that queried regional distribution, habitat, sightings and tracks, roadkills, and behavior. Lure sticks were set up to obtain hair samples at varying distances from the highway and forest edge. Finally, DNA isolation, mitochondrial sequencing and microsatellite analysis were performed.

What did the authors find (i.e, what were their data)?

    Analysis from the program Structure showed that the individuals were likely configured into four clusters. One hybrid was found, and five individuals did not cluster into a group. Two genetic outliers were also found, and could not be assigned to a cluster. Both barriers were found to have consequences for dispersal of wildcats. However, the natural river was a strong barrier and had a greater effect than the highway. The river was a significant barrier to wildcats, but not a complete one. Evidence suggested that wildcats recently migrated across both the river and the highway. The isolation by distance was determined to be low, but significant.

How did the authors interpret their findings?

    The two genetic outliers were thought to be reintroduced wildcats from captivity. The data show that wildcats are capable of migrating across both the river and the highway. However, the structures are still capable of effectively isolating the populations, as migration is low. Wildcats are thought to have low dispersal, therefore increasing connectivity between their habitat is crucial for conservation of the species. The natural river served as a larger barrier to dispersal

The authors studied microsatellite loci in the Afognak population and compared them to the parent population. Microsatellites were used because they have a high degree of polymorphism. Tissue samples of elk from Afognak island and Olympic Peninsula were conducted. The Olympic Peninsula is where the elk that were introduced to Afognak island originated from. DNA extraction, amplification and genotyping took place, fifteen specific microsatellites were chosen to represent the elk genome. The authors found that the two populations of Elk differed in both allele and genotype frequencies. Specifically 10 of 15 allele frequencies differed, and 11 of 15 genotype frequencies differed.  One specific loci exhibited excess heterozygosity in Afognak. Another loci exhibited a deficit in heterozygosity in the Olympic population. The inbreeding coefficient for the Afognak population was 0.019, and -0.006 for the founder population. Surprisingly, a genetic bottleneck in the Afognak population was not found.“Despite the demographic bottleneck, no evidence of a genetic bottleneck in the Afognak population was detected using a test for heterozygosity excess or mode shift of allele frequencies.”