evolution exam 3

polygenic traits: traits influenced by multiple genetic loci rather than just one

quantitative genetics: study of genetic mechanisms and evolution of continuous genotypic traits

What are polygenic traits and quantitative genetics?

an interaction between the products of genes in which one of the genes modify the phenotypic expression produced by the other

What is epistasis?

effects of alleles add up independently to influence a trait

What are additive genetic effects?

environmental factors play a bigger role in phenotypic variations than alleles:

• Ve> Vg 

environmental factors are negligible:

• Vp ≈ Vg

What are the main components of phenotypic variation (Vp=Vg+Ve)?

Broad sense heritability (H²): the proportion of the total phenotypic variation of a trait that is attributable to genetic differences among individuals

H² = Vg/Vp = Vg/Vg+Ve

Narrow-sense heritability: the fraction of the total variance due to additive genetic variation; predicts evolution

H² = Va/Vp = Va/Vg+Ve

What is the difference between broad and narrow-sense heritability?

H² can be estimated as the slope of a linear regression between the average phenotype of the two parents and the phenotype of the offspring; x is average parent & y is offspring & slope is h²

What might happen if slope > than 0?

• Offspring tend to resent their parents & genetic variation is contributing to the trait

• H² = 0 → no genetic influence (all variation is environmental)

• 0 < H² < 1 → both genetics and environment influence the trait

• H² = 1 → trait is almost entirely determined by genetics

How do we estimate narrow-sense heritability (h²)?

Directional selection  

• Favors one extreme phenotype  

• The population mean shifts in one direction

Stabilizing 

• Favors intermediate phenotype  

• Reduces variation, keeps the mean the same  

Disruptive 

• Favors both extremes over the average

• Increases variation, may create two peaks  

• Intermediate phenotype is selected against

What are the main modes of selection on quantitative traits?

It predicts how much a trait will change from one generation to the next due to selection  

What is the breeder's equation (R=h² x S)?

(often called hidden genetic variation): genetic differences in a population that does not show up in the phenotype under normal conditions, but can become visible until selection/drift draw them out

What is latent variation?

• Linkage disequilibrium: exists if the occurrence of an allele at one locus is non randomly associated with the presence or absence of an allele at a second locus; non-random or statistical associations between alleles at multiple loci

• put me near my grave

  • physical linkage

  • mutation

  • natural selection

  • migration

  • genetic drift

What is linkage disequilibrium, and what causes it?

Gene trees: represents the genealogy of a particular locus; history of a specific gene

Species tree: represents the diversification history of a lineage; evolutionary history of species

What is a gene tree and a species tree?

No

i hate hells gala

• Incomplete lineage sorting

• Hybridization

• Horizontal Gene Transfer

• Gene Duplication

Are gene trees and species trees always concordant? What might drive phylogenetic discordance between them?

History of a gene doesn’t match the history of the species it’s in

When species split from a common ancestor, you’d expect their genes to follow the same branching pattern. But sometimes, older genetic variation sticks around and gets passed down in a mixed way

What is incomplete lineage sorting?

Neutral theory provides a mathematical model that we can use to make predictions about the variation we expect in a population, the rates of synonymous subs., the rates of non-synonymous subs, and several other population genetic parameters in populations operating outside of selective pressure. 

describes patterns of nucleotide substitution predicted under drift alone

What is the neutral theory of evolution?

Motoo Kimura

Who proposed it?

1. Most molecular variation present in a population is selectively neutral 

2. Most of the changes to DNA over time are also selectively neutral 

What does the neutral theory of evolution predict?

so not very effective

1. Synonymous substitutions 

2. Non-synonymous substitutions may have little effect 

3. Variation is in untranslated regions 

4. Effective neutrality

How can mutations across the genome be neutral?

A method that uses the rate of DNA (or protein) mutations to estimate how long ago two species or populations shared a common ancestor; can estimate evolutionary changes

Neutral theory can be used to support the idea that selectivity neutral mutations arise at similar rates in different taxa and are fixed at similar rates and all of this is independent of demographic parameters

As a result, these substitution rates give us a way to measure time using genetic data

What is the molecular clock?

Polymorphisms (within populations)

• Different alleles exist at the same locus in the same population

• Different variations exist at the same time

  • Ex. some people have A, some have a

Substitutions (between populations)

• A change where one allele has become fixed (replaced another allele)

• One version replaced the other over time

  • Ex. everyone used to have A, now everyone has a

What is the difference between polymorphisms within populations and substitutions between populations?

dN/dS

>1 - amino acid changes are often beneficial

~1 - amino acid changes are on average neutral

<1 - amino acid changes are usually deleterious

What does the rate of non-synonymous/synonymous mutations tell us about the effects of natural selection across a phylogeny?

Groups of actually or potentially interbreeding populations which are reproductively isolated from other such groups

What is a species?

REM

Reproductive isolation 

Evolutionary history / ancestry

Morphology 

In what aspect different species concepts differ?

Biological Species Concept 

• Based on reproductive isolation 

• Species = groups of actually or potentially interbreeding populations which are reproductively isolated from other such groups 

• Gene flow is the main predictor here of whether or not to call something a species

Phylogenetic Species Concept 

• Smallest group worth shared common ancestor (monophyletic group) 

• Species are identified by shared derived traits (synapomorphies)  

• Uses gene trees/evolutionary history to define species

Describe two alternative species concepts and their differences.

Formation of new species via reproductive isolation

The process where one species splits into two (or more) different species over time

What is speciation?

Allopatric  

• Geographic separation; speciation due to geographic isolation 

• A population is split by a physical barrier (mountain, river, ocean)  

• No gene flow between groups  

• Each group evolves independently  

Parapatric  

• Speciation in adjacent populations with limited gene flow 

• Populations live next to each other  

• Some gene flow, but selection differs across environments 

• Partial isolation + different selection pressures 

Sympatric

• No geographic barrier 

  • Divergence due to: 

  • Depth, diet, inland/open water, and sexual selection

• Speciation without geographic barrier  

• Populations live in the same location  

How does speciation occur (allopatric, parapatric and sympatric)?

Prezygotic (before fertilization) 

• Prevents mating or fertilization from happening  

• No zygote is formed  

Postzygotic (after fertilization) 

• Occurs after zygote is formed  

• Dobzhansky-Muller incompatibility: genetic incompatibility in hybrid offspring arising from epistatic interactions at two or more loci

What are reproductive isolating mechanisms?

Temporal isolation

• Species or populations are prevented from interbreeding b/c they reproduce at different time   

Mechanical isolation (incompatible structures) 

• Physical, anatomical, or structural differences prevent mating or fertilization between species

Mention two prezygotic mechanisms.

1. Hybrid inviability

• The offspring (hybrid) does not develop properly or dies early

2. Hybrid sterility

• The offspring (hybrid) survives but is unable to reproduce (infertile)

Mention two postzygotic mechanisms.

process where natural selection increases reproductive isolation because hybrids are less fit 

What is reinforcement in the context of a hybrid zone?

diss

Dispersal 

• Populations don’t move much

• Less gene flow -> differences build up faster

Isolation 

• Geographic barriers separate populations

• Prevents interbreeding 

Selection 

• Favors certain traits or mating preferences

• Leads to assortative mating

• Populations stop recognizing each other as mates

Specialization 

• Populations adapt to different niches/environments

• Become more different over time

• Less likely to interbreed

How quickly reproductive isolation arises?

Rapid speciation in a single lineage is followed by divergence into many different adaptive forms

What is adaptive radiation?