Evolution - Exam III

Kimura-2-Parameter Model

• K2P

• Model of nucleotide substitution with separate rates for transitions and transversions.

Jukes Cantor Model

Model of nucleotide substitution with equal rates for all substitutions.

Transitions

• Interchange of purines (A-G) or pyrimidines (C-T)

• bases of similar shapes.

Transversions

• Interchange between purine and pyrimidine bases

• Exchanges of one-ring and two-ring bases

Saturation

• Once substitutional differences become common between the two species.

• Many new substitutions occur at previously substituted sites.

Prob (D|H)

• The likelihood function: Pr[R1, R2 | Biased]

• Priors for the data:

  • Pr[R1, R2 | Biased]

  • Pr [R1, R2 | Fair]

Orthologous Genes

genes in different species that evolved from a common ancestral gene by speciation.

Paralogous Genes

genes that are related by gene duplication in a genome.

Coalescent

Point in their history that two alleles in a population merge to one (i.e., the origin of two alleles)

Positive Selection

Darwinian selection: natural selection that increases the frequency of a favorable allele.

Purifying Selection

Selection that lowers the frequency of or even eliminates deleterious alleles.

dN/dS

• Ratio of non-synonymous to synonymous substitutions

  • >1 = positive selection

  • <1 = purifying selection

  • = 1 = neutral selection

McDonald-Kreitman Test

• A test for selection at a locus by comparing DNA sequence variation within species with the variation among species.

  • dN/dS: the ratio of nonsynonymous to synonymous substitutions between species.

  • pN/pS: the ratio of nonsynonymous to synonymous substitutions within species.

Distance Matrix

Procedures for constructing phylogenetic trees by clustering taxa based on the distance between the taxa based on a comparison of traits which yields a coefficient of distance.

Maximum Parsimony

• Simplest explanation favors.

• The tree with the fewest and hoc (extra assumptions of change is the preferred tree).

Bayesian Inference

• Phylogenetic method that utilizes Bayes theorem to generate posterior probabilities for branches on a tree.

• Prob Tree | Data

Maximum Likelihood

• The tree with the greatest likelihood is the one in which the data are the most probably (likely) given the topology

• Prob Data | Tree

Genome Size Variability

• Bacterial genome size depends mainly on the number of genes.

• Eukaryotic genomes vary more in size due to noncoding DNA.

Molecular Clock

Model that uses DNA comparisons to estimate the length of time that two species have been evolving independently.

Synonymous Substitution

• a mutation that does not result in a different amino acid

• does not change protein

Non-synonymous Substitution

• a nucleotide mutation that alters the amino acid sequence of a protein.

• does change a protein.

What indicates positive selection?

A faster evolution than synonymous sites

What indicates a purifying selection?

Slower evolution than synonymous sites.

Incomplete Lineage Sorting

Described the case when the history of a gene differs from the history of the species carrying the gene.

What is LTEE?

Long-Term Evolution Experiment (LTEE) is a study that began in 1988.

• Involves 12 populations of Escherichia coli that live in a medium where glucose is the limiting resource.

• Quantified the dynamics of adaptation by natural selection.

Homeobox

Genes are a group of genes that regulate development in multicellular organisms.

Homeotic Genes

Hox genes are transcription factors that control the development of body parts in animals, such as their head to tail axis.

Convergent Evolution

Independent evolution of similar traits in different lineages due to similar selection pressures.

Parallel Evolution

Independent evolution of similar traits starting from a similar ance

Gene Duplication

A process that creates two identical copies of a gene or part of a gene.

Defensin

a family of antimicrobial peptides that are part of the innate immune system.

Defensins in skin

beta-defensins produced in skin and other parts of the body for fighting bacteria.

Defensins in pancreas

Beta-defensins for fighting bacteria are expressed in snake pancreas and other organs (but not venom glands).

Defensins in mouth

Beta-defensins evolve into crotamine venom that is expressed only in glands in snakes.

Crotamine

Venom produced in venom glands duplicated beta-defensin gene.

Crystallins

Refractive proteins in the lens that are responsible for the clarity and focusing power of the lens.

Co-opted Genes

• Co-option occurs when natural selection finds new uses for existing traits.

• Including genes, organs, and other body structures.

Exaptation

The process in which existing structures take on new functions through descent with modification: co-option.

Opsins

• Photosensitive pigments in the photoreceptors.

• Originated by a gene duplication of melatonin gene (and additional subsequent duplications).

Promiscuous Protein

Proteins capable of carrying out more than one function, such as catalyzing reactions of different substrates.

Deep Homology

Traits in different lineages arise from the same fundamental, regulatory network(s).

Mate Guarding

A strategy evolved to prevent a mate from defecting and to fend off potential mate poachers.

Honest Signaling

Individuals honestly signal their quality because the signaling is costly and therefore low-quality individuals cannot afford to produce dishonest signals.

• Costly ornaments can do this

Ornaments

Attractive traits that increase mating success.

Armaments

Weaponry used to outcompete other individuals.

Anisogamy

Differential investment in gametes.

Two-Fold Cost of Sex

Asexual lineages multiply faster than sexual lineages because all progenies can produce offspring.

• In sexual lineages half of the offspring are males who cannot themselves produce offspring.

Sexual Conflict

Traits that confer a fitness benefit on one sex but cost to the other.

What are characteristics of sexual conflict?

• Traits coevolve antagonistically.

• Leads to antagonistic coevolution between males and females.

Antagonistic Coevolution

• the relationship between males and females where sexual morphology changes over time to counteract the opposite’s sex traits to achieve the maximum reproductive success.

• Has been compared to an arms race between sexes.

Monogamy

One male pair with one female

Polygamy

One or both sexes mate with multiple partners

Polyandry

Females mate with multiple males

Polygyny

Males mate with multiple females.

Red Queen Hypothesis

• Coevolving populations, to maintain relative fitness, must constantly adapt to each other.

• This term was borrowed from Lewis Carrol’s Through the Looking-Glass by Leigh Van Valen to refer to biological arms races, such as those between parasites and their hosts.

Nuptial Gift

Direct benefit (e.g., good) offered by one sex (usually the male) to enhance or prolong sexual reproduction with the other sex (usually the female).

Fecundity

• a measure of the reproductive capacity of an individual or population, typically restricted to the reproductive individuals.

• Can be equally applied

Muller’s Ratchet

Process by which the genome of an asexual population irreversibly accumulate deleterious mutations.

Uncertain Paternity

Explains why male parental care is rare.

• Females (mostly) have certain paternity.

• Males have uncertain paternity.

• Parental care could be be directed towards offspring not their own.

Sexual Dimorphism

• Manifest as a size difference

• The presence of ornaments used to attract mates and/or armaments used to out-compete others for access to a mate.

Intrasexual Selection

• occurs between two sexes

• usually involved members of one sex choosing members of opposite sex

• mostly seen in male-male competition

Intersexual Selection

• occurs between two sexes

• usually involved members of one sex choosing members of opposite sex

Direct Benefits of Female Choice

Benefit the female directly.

• e.g., food, nest sites, protection, help raising young, reduced risk.

Indirect Benefits of Female Choice

benefits that affect the genetic quality of female’s offspring.

Sperm Competition

• Traits that confer a fitness benefit on one sex but represent a cost to the other.

• Drives evolution of larger tests.

Intrinsic Mortality

the rate at which internal events (aging, disease, mutations) lead to death in a population.

Extrinsic Mortality

the rate at which external events (predation, starvation) lead to death in a population.

Sapelo Island & O’Possum

• Austad’s prediction: O’Possum on Sapelo Island would mature later and have fewer offspring per season than O’Possum on the mainland.

• Tradeoff between survival and reproduction: O’Possum on the island live longer, so they produce less offspring.

Survival vs. Reproduction

The longer an organism survives, the lower offspring count per year.

Antagonistic Pleiotropy

Selection may favor alleles that are beneficial early in life, even if they are deleterious late in life.

Pipefish & Sex role reversal

• Female are more likely than make to have more than one mate.

• Shorter females mate more often than longer ones.

• Longer females have a higher egg transfer.

• Longer females have a higher number of viable offspring per egg.

Balanced Sex Ratios

Generally due to frequency-dependent selection

Frequency Dependent Selection

a situation where fitness is dependent upon the frequency of a phenotype or genotype in a population

Haplodiploid

• sex differentiation in which haploid males are produced from unfertilized eggs and diploid females from fertilized eggs.

• Exhibited in fig wasps.

Trivers-Willard Hypothesis

if the mother’s conditions are good, she’ll be biased to invest in favor of competitive offspring (male); if mother’s conditions are poor, she’ll be biased to invest in favor of non-competitive offspring (female)

Sequential Hermaphrodism

a reproductive pattern in which an individual reverses its sex during its lifetime.

Senescence

The natural physical decline brought about by aging.

Calorie Restriction

• slows aging process

• Genes involved in repair switched on under stress

• may involve trade-offs

Menopause

• The natural cessation of menstruation

• refers to the biological changes a woman experiences as her ability to reproduce declines

• not observed in other great apes

Mother Hypothesis of menopause

The risk of reproduction at an older age leads to selection for reduced fertility coupled with investment in current offspring

Grandmother Hypothesis of menopause

The loss of fertility is associated with a shift in investment to grandchildren