Evolutionary Biology Term Test 2

AChE1

Acetylcholinesterase

An enzyme that was inhibited, esterase breaks down a wide range of toxins, including organophosphate insecticides. A high level will kill them. Ester allele thus gets pass down to offspring, shift to animals with shorter lifespans.

Ester⁴

Has less protection against insecticides, mitigates fitness consequence of the primary version which is usually found inland.

Natural selection

There is a variation in the phenotypes of individuals in a population, this variation causes some individuals to perform better than others (survival and reproductions)

Gene flow

Individuals leave one population, join another, and breed

Migration

Moving and bring alleles into a new area, changing the genetic frequency

Population

Groups of interacting and potentially interbreeding individuals of a species. Made up of individuals who carry alleles, typically varying from individual to individual

Individual genotype

Contains alleles for millions of genetic loci carried in its chromosome

Genetic locus

Use the term genotype to refer to the combination of alleles carried by an individual at a particular this.

Prediction of new genotype

1 = p² + 2pq + q²

Estimate of old genotype

1 = p + q

Hardy-Weinberg Principle

1. Population is infinitely large

2. All of the genotypes at a locus are equally likely to survive and reproduce

3. No alleles enter or leave due to migration, genetic drift, bottleneck, none of it.

4. Organisms are diploid

5. No overlapping generations

6. No mutations

Genetic drift

How alleles frequencies “drift” randomly away from starting value. Has eliminated alleles in small populations. Pulling only a few things does not represent a sample and can greatly affect the population makeup.

Fixed alleles

You lose diversity in alleles and can only pass down one type of allele. Small populations see huge changes in frequency over time, alleles become fixed or lost quickly.

Genetic bottlenecks

Affect populations that are only temporarily reduced to low numbers. Probability of an allele being lost each generation is a function of the severity of this.

Founder effect

Kind of bottleneck, where a small number of individuals leave a larger population and colonize a new habitat. Plant seeds sometimes stick the feet of migratory birds and are carried thousands of miles away

Fitness

The reproductive success of a particular phenotype. It is hard to actually study and measuring is preferably done through tallying the lifetime reproductive contribution of an individual. Fecundity, mating success, survival to reproductive age.

Relative fitness (w)

Consistently contributing more offspring than other variations makes this to be greater than 1. Fitness of individuals with one genotype compared with population average or most fit genotype.

Average excess of fitness

We must weigh how many individuals with each genotype are actually present in the population and contributing offspring to the next generation, shows how the net fitness contributes to the allele.

Pleiotropy

A single regulatory gene can influence the expression of many other genes.

Antagonistic pleiotropy

The effects of a mutation have opposite effects on fitness. Conditions that occurs when a mutation that causes beneficial effects for one trait also causes detrimental effects on other traits.

Negative selection

Common phenotypes selected against, rare phenotypes are favoured. Negative frequency-dependent selection (NFDS)

Rovers and sitters

Rovers survive best with more sitters, sitters survive best when there are more rovers. This was tested by putting them under threat in different ratios.

Epistasis

Beneficial mutations are only beneficial when they follow certain other mutations. Alleles at two loci interact together.

Additive alleles

Alleles that code for the same thing, and so having multiple copies will increase what you have and how much is present. Allelic effects can be predicted by summing number of copies present. One allele genetically dominant to another allele.

Heterozygous advantage

Occurs when selection favours heterozygous individuals over either the dominant homozygote or the recessive homozygote. Heterozygosity confers greater fitness than homozygosity.

Cystic fibrosis

Autosomal recessive, chromosome 7, CFTR gene. Excessive mucous production causes damage (pancreas, liver, kidneys, and especially lungs). Pancreatic issues leads to poor nutrient absorption. TTT coding for phenylalanine means people lose it when they delete it our - proteins is less effective.

Interbreeding

Decrease in heterozygosity. Cannot change allele frequency, but can change the distribution and decrease heterozygosity. Goes hand in hand with genetic bottlenecks.

Interbreeding depression

High degree of homozygosity exposes deleterious alleles. Increases in individuals with cystic fibrosis.

Inbreeding coefficient (F)

Probability that two alleles at any locus are identified by descent

Population structure

Also known as population subdivisions. When the constraints of landscape and distance restrict the movement of individuals from place to place, this is the result.

Subdivision

Pocket with different variation, maybe entering an extreme subdivision where they’re whole new populations

Genetically distant

Subpopulations are separated and become more different. Measure of how different populations are from each other genetically. Informs population geneticists about levels of inbreeding within a population or about the historical relationship.

F_ST (Measure of genetic distance)

The values increase as the local subpopulations diverge from each other. Measures extent of subdivisions among subpopulations. Influenced by population size and time since divergence.

= (H_T - H_S)/H_T

Polygenic

Expression is influenced by many genetic loci. Many traits are important for survival.

Evolutionary quantitative genetics

Study of the evolution of complex phenotypic traits. Build models, view genetic and environmental variation, and environmental interaction

Variance

Estimate of the amount of the variation in a trait in a populations - larger variance = practically identical in every individuals

Broad sense heritability (H²)

Proportion of total phenotypic variance of a trait that is attributable to genetic variance (differences among individuals). Relationships between parent and offspring. Variance in genetics divided by variance in phenotypes means they are in a ratio.

Narrow sense heritability (h²)

Proportion of the total phenotypic variance of a trait attributable to the additive effects of alleles. Looking for small increments that contribute to a trait. Variance in additive effect of the allele.

Directional selection

When a species on a far end has selective success. Most of this variation of assembling all the individuals together. Corn oil driven up.

Stabilizing selection

Species in the mean of a trait has a selective advantage

Disruptive slection

A species on either far end has selective advantage. Can lead to a bimodal distribution (two means).

Selection differential (S)

Difference in mean of a trait in reproducing individuals and mean of trait for general population. How strong individuals are. Higher S means stronger selection.

= X_B - X_P

Recombination rate (r)

Probability of recombination occurs between a given pair of loci.

0.5 comes down to how close they are on the chromosome, independent assortment. 3% is very far.

Linkage equilibrium (LE)

Allele on one locus is independent of presence or absence of allele at second locus. No linkage. Relationship between loci on different chromosomes are mixed and matched so readily that the chances of maternal and paternal alleles being inherited together.

Linkage disequilibrium (LD)

Allele at one locus is nonrandomly associated with the presence or absence of allele at second locus. Physical linkage. Like beads on a string passed down. More likely to be inherited together.

Supergenes

Group of functionally related genes located close enough together that they segregate as a single unit.

Quantitative trait locus (QTL)

Stretch of DNA with variation for phenotypic trait, the regions contain genes or are linked to genes. Is there an association, we can see heritability. Can map numerous traits. Most regions found on more than one trait.

Agouti and Mc1r

interacts together and affect fur colour. Peak of colour difference occurs at the Agouti allele. Active receptor of Mc1r is brown at active receptor (eumelanin) and repressed receptor (pheomelanin). Expression during development influences area.

Genome-wide association (GWA) mapping

Detailed maps on entire genomes of a species as well as genotype information for very large numbers of individuals. Mapping different traits in diseases. Does not require a complete map of the genome, whereas GWAS mapping does.

Polyphenism

Extreme form of plasticity. Multiple discrete phenotypes from single genotype. In response to environmental cues. (Temperature affects age of maturity)

Reaction norm

Visualize the responses of organisms to the environment. Allow individuals across an entire population to produce phenotypes that match a wide range of environmental conditions

Extra variability

We can add V_GXE which shows the precise interaction of genes and their environments abbreviated. If greater than 0, the plastic responses of organisms to their environment can evolve.

Synapomorphy

Derived form of a trait that is shared by a group of related species - one that evolved in the immediate common ancestor of the group and was inherited by all its descendants.

Morphological synapomorphies

Help determine relationship of a species and a clade

Nodes

Points at which two lineages converge or coalescence into a single ancestral lineage

Coalescence

Genealogy of any pair of homologous alleles merges in a common ancestor. Tracking history of allele through time, move back through time to determine when/where alleles arose, nodes in gene trees are events (common ancestry).

Alternative alleles

Can persist in populations for long time periods. Such alleles may be passed down to daughter species in ways the do not reflect actual branching history.

Positive selection

Can accelerate the rise in frequency in an allele, shortening time to fixation and to a short coalescence.

Orthologous gene

one of two or more homologous genes spearated by a speciation event (as opposed to paralogs - homologous genes, produced by gene duplication, that are both possessed by the same species).

Introgression

Hybrid offspring survives and mates with either original species, you can introduce gene from other species to another. They may be favoured or eliminated.

Incomplete lineage sorting

Gene tree does not equal species tree. When a genetic polymorphism persists through several speciation events. Fixation of alternative alleles occurs in descendent species. Retention of alleles may yield a gene tree that differs from the true phylogeny of species.

Purifying selection

Changes that occur in exon regions typically evolve very slowly

Negative selection

Removes deleterious alleles from population, common form of stabilizing selection

Bootstrapping

Random sample of characters from their full dataset, much like drawing a character from a hat. Keep samling until get same amount as in the original set. Evaluate reliability of each branching event.

Distance-matrix methods

Convert DNA or protein sequences from different taxa into a pairwise matrix of the evolutionary distance (dissimilarities).

Maximum likelihood

Determines probability of the data, given an evolutionary model and a hypothetical tree (starts with parsimony tree).

Bayesian methods

Determines probability of a tree topology (shape), given an evolutionary model and data set.

Neighbour joining

Distance matrix method. Scientists pair together two least-distant species (join at node). Protein sequence alliance. Listing different allele sequences, seeing amount of difference.

Molecular clock

Estimating how long ago ancestors branched off based on amount of genes that differ between closely related species.

Non-synonymous substitutions

Much more subject to selection than synonymous substitutions. This changes an allele while synonymous switches a codon that keeps allele the same. Most evolutionary change is neutral, not this though.

Selective sweep

The elimination of polymorphism near a beneficial mutation that has spread to fixation. Allele experiences strong natural selection and quickly spreads through a population.

Genetic hitchhiking

Selected for an allele cuz it was close to the selected allele

dN/dS ratio

Rate of nonsynonymous to synonymous substitutions

• <1 - most N mutations are deleterious andare removed (purifying selection)

• =1 - neutrally evolving both

• >1 - many N differences between species are fixed by positive selection

Gene control region

Upstream of DNA has promoter region and other regulatory sequences. Influences transcription.

Repressor

Protein that binds to DNA or RNA sequence, and inhibits expression of one or more genes

Transcription factor

Protein that binds to a specific DNA sequences, like a light switch turning things on or off.

Complex adaptation

Suite of coexpressed traits. Experience selection for a common function. Multiple components must be expressed together for the trait to function.

Gene recruitment

Co-option of a particular gene or network for a totally different function as a result of a mutation. The reorganization of pre-existing regulatory network - major evolutionary event.

Promiscuous proteins

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

Antennapedia

Usually in thorax, mutation of Hox genes (expression time and location) you get legs where antenna is supposed to be

Pleiotropic genes

Capable of carrying out more than 1 function, especially likely to take on new functions if duplicated

Paralog

Homologous gene arising from gene duplication

Ortholog

Homologous gene in different species that originate in common ancestor

Snake venome

1. Duplication of defensin gene in pancreas

2. change in regulation, duplicate of copy in mouth venom gland

3. Additional duplications and losses as venom diversify in different lineages

Hox genes

Participate in regulatory networks that demarcate the geography of developing animals, determining the relative locations and sizes of body parts.

Flies and mice

homologous genes for Dorsal-Ventral patterning, but expression differs in “mirror images”

Leg genes

Derivation from a common ancestor. Blocking Shh expression stops limb patterning. It does the dorsal cells, proximal-distal axis, and ventral cells.

Hoxd13

Expression in zebrafish and mouse embryos do basically the same things. Also shows evolution of tetrapod limbs from fins, an example of subtle changes of developmental genes having a dramatic alteration of phenotypes.

Endemic animals

Animals found here and nowhere else, evolving in those locations.

Isla Daphne Major

Small, no introduced animals (eg. goats), not appealing to people, low vegetation, undisturbed, trek to get there. Vegetation is knee height. Variety and choices went down after drought, only big and tough seeds left, little to no mating, lots of eating. Seed abundance went down. Forced to eat Tribulus.

Medium ground finches

generalist feeders, variation in beak size influences efficiency at eating different types of seeds. G. fortis likes spurs (easy to find and eat), while tribulus are hard to eat, but they can in a pinch. G. magniostris prefers tribulus because of its big beak.

Tribulus

Each is a schizocarp. Within 3-5 seeds, but it is a pain to get open. High effort, low payload if beak is not strong enough to crack open.

Parent offspring regression

R = h² S, average beak size = additive genetic effect * selection coefficient

• 0.3 is average heritability in nature. 0.9 is very congruent of parent and offspring, responds relatively high to genetic responses.

• S is the selection coefficient, if selection is strong, heritability will be strong.

Requirements for evolution by natural selection

1. Phenotypic variation in population (variation)

2. Variation is heritable (heritability)

3. Differential survival or reproductive success of variants (fitness)

Non-cryptic environment

Prey are more at risk in these environments. Being cryptic increases survival and is favoured in these environments, explained by multiple origin of light colour hypothesis.

Mice colouration

Thousands of years ago - amino acid switch in melanocortin-1 receptor (Mc1r), decreasing dark pigmentation added to by another gene called the Agouti gene, which resulted in two genetic changes → reduced levels of melanin synthesis and lighter overall coat colour. Dark mice mainland, white mice coastal.

Extended phenotype

A trait that is controlled by another species

Gall fly

female has an ovipositor, pincher at the back end that gets inserted into goldenrod and lays their eggs. Reaction forms a gull around the larvae. Our body would wrap stuff in mucus. The goldenrod pumps food and is protected.

You can see galls on goldenrod, you can see a fly maggot. Gull becomes woody in winter, and you can find a pupae waiting for spring to emerge.

Three spined stickleback

Dorsal fins and small little spine, erects spine to avoid being eaten by predator. The armour length of marine (ancestral) form is long and armour plates are protective. Freshwater (derived) form are shorter and don’t have as much protection (individual sections are bigger).

Eda

Is associated with divergence between marine and freshwater fish. They did genomic mapping and one peak forward one peak down, the gene is the most important for water conditions. Specific alleles form spines and armour and varies with degree of it. Relatively shorter spines compared to marine.