Chapter 5: Evolutionary Biology

What are the three sources of variation?

1. genetic

2. environmental

3. genotype-by-environment interaction

Phenythiocarbamide (PTC)

Bitter flavor taste receptor - TAS2R38 gene on chromosome 7 with two alleles PAV and AVI they may be associated with the ability to detect toxins

Genetic variation

Differences among individuals in the composition of their genes or other DNA segments

environmental variation

Traits that are not genetically controlled and are not heritable

Phenotypic plasticity

The ability of an organism to change its phenotype in response to changes in the environment.

Inducible defenses in Daphnia

Juveniles that smell phantom midge larvae grow neck teeth and other defense mechanisms so they will be prepared this is an example of environmental variation and phenotypic plasticity

Aversion to cilantro

Linked to several genes only 4% higher chance of hating cilantro with two copies of this gene vs people with zero copies

Conclusion of cilantro gene

Aversion is only partially genetic and could also be driven by environment or interactions with environment

Reaction norm

phenotypic expression of a single genotype across a range of environments

Genotype by environment interaction

Ability to display phenotypic plasticity may be genetically controlled, with no phenotypic plasticity or genotype by environment interaction the phenotype is the same in different environments

What indicates the amount of plasticity on a reaction norm graph?

The steepness of slope on the graph indicates the amount of plasticity, more steep is more plasticity, plasticity many vary among genotypes in different environments

Environmental sex determination

Both genotype and temperature influence sex in leopard geckos, incubation at higher temperatures is more likely to be male

What is mutation?

A raw material of evolution caused by a change in DNA sequence

Why is mutation important in evolution?

Without mutation no new alleles, new genes, and no evolution

DNA

Made up of deoxyribose sugar, phosphate group, and nitrogenous base

Purines

Adenine and Guanine

Pyrimidines

Cytosine and Thymine

DNA replication

DNA replicates with the help of DNA polymerase through complementary base pairing

How does a point mutation occur?

Sometimes wrong base pairs will be paired, sometimes they are corrected but if they are not corrected it results in a point mutation

Point mutation

gene mutation in which a single base pair in DNA has been changed

Normal DNA pathway

DNA -> mRNA -> protein

Can mutation affect amino acid sequence (protein)?

Yes

Redundancy in genetic code

a particular amino acid can be coded for by more than a single codon because of this not all point mutations cause changes in proteins

Transitions

Change from purine to purine or pyrimidine to pyrimidine (same type swap) These are at least twice as common in nature as Transversions

Transversions

Change from purine to pyrimidine or pyrimidine to purine

(different type swap)

Synonymous mutation

A silent mutation that does not change the amino acid sequence

Nonsynonymous mutation

A replacement mutation that changes the amino acid sequence

Exons

DNA sequences that code for proteins

DNA mutations within coding regions are either...

synonymous or nonsynonymous

Frameshift mutation

Where nucleotides in the DNA sequence are added or deleted ,creating a change in the reading frame for the protein encoded by the gene

Nonsense mutation

Mutation caused by point mutation to stop codon, premature stop

Gene duplications

Result from unequal crossing over, extra copy is free to accumulate mutations and is not under natural selection

Where do new genes come from?

Gene duplication

Gene duplication in globin family

Humans have two globin clusters of loci alpha-like and Beta-like, we need two subunits from each cluster to from the hemoglobin molecule, during embryonic, fetal, and adult stagers different chains are made

Globin gene switching

Adult: Alpha and Beta

Embryonic: Zeta and epsilon

Fetal: Alpha and gamma

Why do globin genes switch?

Different globin family loci produced by past gene duplication events and took on new functions over time

Gene duplication and pseudogenes

One gene in duplication because a pseudogene and can evolve a new trait

Paralogous

Genes that duplicated and diverge in a species (ex alpha and beta in humans) may have a different function

Orthologous

Genes that are homologous and evolve from a common ancestral gene by speciation ( beta in humans and in mouse)

Retrotransposition

An element's RNA is used as a template to synthesize DNA molecules, which are inserted into new chromosomal sites

(processed mRNA is inserted into genome)

Chondrodysplasia

Collagen chains are asymmetric and too wide, causing stunted growth and deformed joints in dogs caused by genetic mutations/ retrogene genotypes

Inversions

Segment of DNA is cleaved in two places the excised segment flips and re-anneals in the opposite direction

What are the issues with inversions?

They can disrupt the linked of genes that are near each other and inherited in groups, also cannot align properly with homologs and results in dysfunctional gametes

Polymorphic

having many forms

Drosophila inversions

5 of 6 Drosophila chromosomes are polymorphic for inversions ex: chromosome inversion polymorphism in Drosophila pseudoobscura, Inversion frequencies vary along a cline that is linked to temperature and body size

Polyploidy

Entire extra sets of chromosomes, Tetraploid, octoploid, etc, common in plants but rare in animals, common in hermaphroditic species that can self fertilize

How does polyploidy occur?

Meiosis error creates diploid gametes those organisms self or fuse with other diploid gametes and make tetraploid offspring, if two tetraploids mate a new species is created (ex: triploid watermelon and octoploid strawberry)

Triploidy

If a diploid gamete fuses with a haploid one triploidy results, triploids have low fertility unless they are parthenogenetic, polyploid organisms have whole chromosomes of genes that are free from natural selection, creation rate of polyploid plant species is as common as point mutation rate

Parthenogenetic

population exists entirely of females that produce more females from unfertilized eggs

Ambystoma salamanders

All female population of triploids they maintain triploidy by using sperm from a male of another species to activate their eggs after which the sperm nucleus is eliminated, unisexual salamanders steal sperm from donors of normally bisexual species, and their reproductive mode is described as kleptogenesis

Kleptogenesis

female "steals" sperm from the male, used for energy or to stimulate parthenogenesis, but not fertilization

Fitness effects of mutations

Usually neutral but can sometimes benefit or be deleterious

(sickle cell anemia caused by single transversion in hemoglobin gene)

Mutation rates

Best data on mutation rates are from loss of function mutations, mutation deactivates gene and causes a protein to not be made not always easy to identify the genes causing problems

Loss of function mutations

A mutation that results in the loss of a functional protein. Some known human examples are hemophilia and achondroplasia, dominant conditions so you can assess spontaneous mutation rate, nine out of ten dwarf children have normal parents

Hemophilia

A hereditary disease where blood does not coagulate to stop bleeding

Achondroplasia

A form of human dwarfism caused by a single dominant allele; the homozygous condition is lethal (ex: game of thrones tyrion)

How do loss of function mutations happen?

Point mutations, insertions, deletions, transposable genetic elements, 10% of all human gametes carry a phenotypically detectable mutation, genes within a species vary in mutation rate

Why are mutation rates variable?

- DNA polymerase varies in error rate

- mismatch repair systems vary in effectiveness

- some species have higher or lower mutation rates overall

- coding regions have fewer mutations than noncoding regions (natural selection specifically purifying selection)

Species with higher or lower mutation rates

Viruses (high) Drosophila (low)

Determining genotypes

We can know genotypes by examining phenotypes or in some cases need to look directly at proteins or DNA sequences using gel electrophoresis

Gel electrophoresis

DNA and proteins have charge, apply electric current to samples and they migrate toward oppositely charged pole, migrate according to size and mass, differently sized alleles go different distances

What does the human gene CC-CKR-5 encode?

CCR5 cell surface protein receptor on helper T cells.

How does the CCR5 receptor function in the immune response?

It senses pathogens and informs killer T cells to attack.

Which virus uses CCR5 as a coreceptor to bind with CD4 T cells?

HIV-1.

What is the infection status of individuals who are homozygous dominant for the delta 32 mutation?

They can be infected with HIV-1.

What is the infection status of individuals who are homozygous recessive for the delta 32 mutation?

They cannot be infected with HIV-1.

What is the infection status of heterozygous individuals (+/delta 32) regarding HIV-1?

They can be infected but progress to AIDS more slowly.

How is allele frequency calculated?

the number of specific alleles divided by the total number of alleles, each allele has two copies (ex: 43 individuals is 83 allelic copies) frequencies of the two alleles always add to 1

Calculating allele frequency

Add up all A's and a's divide each by the total number of alleles (A+a) which gives the frequency of that allele

Calculating genotype frequencies

Add up all the AA's, Aa's, and aa's divide by the number of genotypes (-AA/total number genotypes) = frequency of AA

Calculating frequencies from genotypes

(delta 32 homozygotes) + 1/2 (delta 32 heterozygote) = frequency of delta 32

How much genetic diversity if typical?

Gel electrophoresis of many organisms shows that between 15 and 33% of all enzyme loci are polymorphic and more than one allele exists, avg individuals are heterozygotes for 4-15% of loci

% of polymorphic loci

Fraction of loci in a population that have multiple alleles

Loci

Location of a gene on a chromosome

Selectionist Theory

Genetic diversity persists because natural selection favors allelic diversity

Neutral theory

Polymorphic alleles are functionally equivalent so they are not selected against which could be why genetic variation persists

Mutation is..

A random process and not all conceivable mutations are equally likely to occur not all loci or regions within a locus are mutable, environmental factors may influence mutation rate

Why is mutation random?

We can only predict the probability of a mutation occurring but not with mutation will occur or when, chance is not influenced by whether or not the organism is in an environment where the mutation would be advantageous, natural selection does not see, think, plan, or feel, it just acts on whatever variation exists