Genetics and Evolution Final

Evolutionary Biology

study of life; specifically, of changes that occur in populations of organisms over time

stromatolites

mushroom-shaped globs built from sequential layers of sheets of cyanobacteria that secreted a sticky film to protect them from ultraviolet light. Dramatically changed the ecosystem with their excessive release of oxygen.

multicellularity

key innovation which permitted organisms to grow larger than a single cell and to compartmentalize function, with subsets of cells becoming specialized for particular tasks

sexual reproduction

key innovation which permitted individuals to combine genetic material from multiple individuals, including things like independent assortment and recombination, resulting in a spectacular increase in the rate at which new genetic variation arise within populations

genetic variation

raw material for evolution

Rigid skeletal structure

key innovation that caused the explosion of body forms appearing in the oceans during the Cambrian Period, providing structure and attachment points for muscles, and permitted controlled propulsion, clasping jaws, swimming, and walking legs, etc.

amniotic eggs

key innovation that permitted moisture to be retained inside egg shells and for embryos to develop in a protected case that could survive outside of water.

convergent evolution

separate lineages of organisms that evolved independently but converged on astonishingly similar solutions to ecological situations

topology

a sequence of pairwise branching events that connects the included taxa

monophyletic

connect back to a single, shared common ancestor

paraphyletic

Groups that contain species sampled from different clades (e.g., convergent species that independently converged on similar morphologies, and which were grouped together based on those superficial similarities)

homology

"shared derived" nature of traits--due to the fact that they all inherited the trait from the same common ancestor

homoplasy

Similar traits that arise independently

ecologist

-focus on populations

-focus on interactions between species

-focus on ecosystems

evolutionary biologist

-focus on individuals within a population

-focus on how/why the genetic composition of a population changes over time

molecular evolution

Change (turnover) in allele frequencies from one generation to the next

alternate splicing

For many genes, not all exons are utilized at any one time, and different combinations of exons may be spliced together to form related, but distinct proteins

coding region

-mutations to this region of the gene may alter the amino acid sequence of the resulting protein, possibly leading to altered function

-highly pleiotropic

cis-regulatory regions

-mutations to this region affect gene expression only in the specific developmental context that that region regulates

-where, when, how much is expressed

-do NOT alter the amino acid sequence of the gene product

-not very pleiotropic

pleiotropy

when a mutation affects more than one trait

Epi-genetic

factors bind to the outside of DNA and can cause regions of DNA to remain coiled

diploid

organisms carry 2 copies of each chromosome (with the exception of the sex determining chromosomes, XY or ZW)

meiosis

-special form of cell division that only occurs in the gonads, ovaries and testes

-generates haploid gametes

haploid

-eggs/sperm inherit only a single copy of each chromosome

independent assortment

-during meiosis

-when the maternal and paternal copies of each chromosome separate, one goes into each daughter cell

-which one goes into each cell is random

-2^N=number of combinations in an organism

recombination

-occurs during meiosis

-arms of chromosome pairs break and re-attach to the opposite strand

-mixing and matching segments of maternal and paternal DNA

locus

location on a chromosome

allele

alternative versions of a particular locus

genotype

result from the particular pair of alleles that are inherited

homozygous

individuals have two identical copies of an allele

heterozygous

individuals that have two different alleles

population genetics

success and failure of alleles within populations, as they change in relative frequency from generation to generation

dominant

allele mutations that manifest in the phenotype regardless of genotype of the individual

recessive

allele mutations that do not affect the phenotype unless they are combined with another copy in a homozygous individual

Somatic

body cell

germ line mutations

-mutations that arrise in the gonads

-may be passed into eggs and sperm

-permanently heritable

dominant

-characteristic of a mutation that will affect the phenotype immediately

-selection can act on it to increase or decrease its frequency

recessive

-characteristic of a mutation that will not affect the phenotype

-will be sheltered/hidden form action of selection

genetic drift

gradual changes in gene frequencies in a population due to random events

random mating

-mating with respect to a particular allele

Hardy Weinberg theorem

If several key assumptions are met, the allele frequencies of a population will not change from generation to generation

Hardy Weinberg Assumptions

-No genetic drift

-Random mating

-no migration

-no mutation

genetic bottleneck

When a small sample is plucked from a large population, most of the alleles will be lost, and the resulting frequencies of the new population will be very different from what they were before

panmixia

situation where individuals are equally likely to encounter and mate with all other individuals in the population, irrespective of actual geographic distance

natural selection

Some individuals, by virtue of the traits that they possess (i.e., because of their PHENOTYPES) perform better than others - grow faster, forage more effectively, compete more effectively, reproduce more effectively - and as a result, these individuals contribute disproportionately to the production of offspring

adaptations

traits that arose through the mechanism of evolution

critical ingredients of selection

-variation

-heredity

-differential reproduction

HOX genes

"master regulators" in the sense that they tell cells which body region they are in, and as such, they influence/direct all subsequent development that occurs in those regions

Law of the Additivity of Variances

Vtotal = Vgenetic + Venvironmental

heritability

proportion of the total variation attributable to heritable/genetic/allelic differences among individuals

H^2 = Vgenetic/Vgenetic + Venvironmental

breeders equation

relates the strength of selection and heritability with the speed of evolution

R = h^2 * s

stabilizing selection

selection that favors individuals with trait values that are intermediate

directional selection

selection that favors individuals with trait values at one extreme or the other

artificial selection

occurs when humans preferentially breed individuals with desired characteristics

sexual selection

selection that arises from competition for access to reproduction

Female Choice; male-male competition

type of sexual selection in which the female chooses a male and the males compete for reproduction

Male Choice; female-female competition

-very unlikely but does exist

-type of sexual selection in which the male chooses a female and the females compete for reproduction

pre-mating

type of barrier that occurs before two organisms mate

pre-zygotic

type of barrier that occurs after mating but before fertilization

post-zygotic

type of barrier that occurs after fertilization

post mating

type of barrier that occurs after mating

coevolution

ituation where two (or more) populations of organisms evolve in response to each other

species

biological species concept: considers species to be groups of actually or potentially interbreeding populations that are reproductively isolated from other such groups

allopatry

occurs when a physical barrier separates populations, restricting gene flow between them

sympatry

occurs when populations begin to divide without physical/geographic separation

parapatry

occurs when populations are spread out across a sufficiently large geographic range (a cline) that they begin to diverge at their endpoints

ex:ring species

ring species

-special form of parapatry

-occurs when the range of a species wraps around a physical barrier in such a way that the most extreme "end point" populations come back into physical contact on the far side of the barrier

The S allele at the Beta-Globin locus was described in class as being unusual primarily because:

a. A single base pair substitution leads to disease

b. Allele frequencies differed strikingly from region to region (e.g., areas with and without malaria)

c. Individuals with heterozygote genotypes performed better than either of the homozygotes (overdominance, or heterozygote advantage)

d. Selection favored an intermediate frequency for the allele (balancing selection)

e. Selection acting on the allele changed through time

c. Individuals with heterozygote genotypes performed better than either of the homozygotes (overdominance, or heterozygote advantage)

Why are mosquitoes especially prone to serving as vectors for mammalian diseases?

a. They are unusually abundant in tropical regions where most of these diseases occur

b. They are poikilotherms ("cold blooded") exposing pathogens to extreme temperatures that these microbes do not encounter inside mammalian hosts

c. They have coevolved with humans and pathogens for longer than other insects

d. Their gut linings are unusually conducive to colonization by pathogens

e. Their straw-like mouthparts require mosquitoes to inject anticoagulants into the wound when they bite.

e. Their straw-like mouthparts require mosquitoes to inject anticoagulants into the wound when they bite.

In the worked example of selection acting on the S (sickle cell) allele of the Beta-Globin gene in class, three different time points were explored and the average excesses of fitness for the S allele (aS) in Africa were calculated. The strength - and even the direction - of selection acting on the S allele changed over these time points. Why?

a. The frequency of the S allele (q) was different at each of the three time points

b. The average fitness of the population (ŵ) was different at each of the time points

c. The background level of malaria was different at the different time points

e. Gene flow between areas with (tropical) and without (temperate) malaria influenced the speed of evolution in response to selection.

a. The frequency of the S allele (q) was different at each of the three time points

Alternate splicing refers to which of these statements?

a. . Different cis-regulatory regions that initiate transcription of the same gene in different developmental/functional contexts

b. Different third-codon base pairs that code for the same amino acid

c. Different regions of a chromosome that are recombined during meiosis

d. Different sequences of exons that are combined to make proteins from the same gene.

e. Different forms of gene silencing resulting from binding of methyl groups to the "backbone" of DNA of a gene

d. Different sequences of exons that are combined to make proteins from the same gene

Which of the following is true of the Ediacaran fauna fossils?

a. They represented the next big diversification of animals after the Cambrian Period

b. They included fan-like organisms that lived on the floors of shallow seas

c. They included fossils of the first terrestrial animals

d. They are largely comprised of layered cyanobacterial mats called stromatolites

e. They included the first recognizable flowering plants

b. They included fan-like organisms that lived on the floors of shallow seas

The Burgess Shale fossils discovered by Charles Doolittle Walcott in 1909 were especially important because they

• Contained examples of body plans unlike anything alive today

• Were an example of aLagerstätte fossil bed

• Preserved soft tissues of a variety of marine organisms

• Captured a snapshot of an ecosystem during the "Cambrian Explosion"

When population sizes are very small, which is NOT likely to be true?

Heterozygous genotypes become more common

When populations of organisms are panmictic, they….

Have no barriers to gene flow and individuals mating randomly

Some strict religious sects are particularly prone to genetic diseases because

-Their traditions prohibit marriage outside of the faith

-A history of persecution forced them to disperse to distant locations

-Their populations experienced a genetic bottleneck

A new allele arises in a population that is associated with a phenotypic change in the coat colors of squirrels. The wild-type allele, designated B, is associated with a brown phenotype and is dominant to the new allele. The new allele, designated b, is associated with a black coat phenotype and is recessive to the wild-type. If a homozygous dominant and heterozygous individual were to mate (BB x Bb), what proportion of their offspring would be expected to exhibit the black coloration phenotype and what are the phenotypes of the parents?

0% of the offspring will have black coats; Both parents have brown coats

A new allele arises in a population that is associated with a phenotypic change in the coat colors of squirrels. The wild-type allele, designated B, is associated with a brown phenotype and is dominant to the new allele. The new allele, designated b, is associated with a black coat phenotype and is recessive to the wild-type. f a heterozygous and homozygous recessive individual were to mate (Bb x bb), what proportion of their offspring would be expected to exhibit the black coloration phenotype and what are the phenotypes of the parents?

50% of the offspring will have black coats; One parent has a brown coat and one parent has a black coat

If a new mutation were to arise in the coding region of a transcription factor and it affected the amino acid sequence of the transcription factor, which of the following qualities would you expect to be associated with this new mutation in regards to pleiotropic effects?

High chance of pleiotropic effects because transcription factors are trans-acting elements that may affect the expression of many different target genes

Rooted phylogenetic trees take many different forms and orientations, but they all connect the past with the present. How is evolutionary time inferred on these trees?

Past to present is inferred as the direction from the root to the leaves/tips

The crossing of a red flowered Hibiscus with a white flowered Hibiscus resulted in offspring with all pink flowers. This demonstrates the principle of:

Incomplete dominance

Which of the following is NOT an Hardy-Weinberg assumption?

a. Infinite population size

b. No mutation

c. No migration

d. Non-random mating

d. Non-random mating

Which of the following is true of the inheritance of autosomal-dominant traits?

a. Males are more often affected than females

b. The trait occurs in every generation

c. The trait is usually common in a pedigree

d. A, B, and C are true