Exam 2: Gene flow - Neutral Theory

Gene flow and migration

movement of individuals between populations

continent - island model

1 way migration from mainland to an island

• Initially and island may have allele frequnies unique to that of the mainland, becuase of a small subset of colonizers

• But over time, if it’s still a one way migration from the mainland, the island will resemble the mainlaind allele freqnces and homogonize

Gene flow does what…

• It homogonizes, and by itself will cause all populations to have the same allele frequncies

Gene flow alone VS Gene flow with Selection

Gene flow alone:
Alleles move between populations and tend to homogenize allele frequencies, making populations more genetically similar.

Gene flow + selection:
Selection can favor or remove certain alleles, so the final allele frequencies depend on the balance between migration introducing alleles and selection removing or favoring them. If selection is strong, it can maintain differences between populations despite gene flow.

Genetic Drift definition

is the random change in allele frequencies in a population due to chance events, especially in small populations.

Genetic drift characterisitics

• “sampling error” - random change in alleles not due to selection

• Random change in allele frequency

• Binary choice: Fixation (1) or Allele loss (0)

  • Drunkards walk

consequences of drift

• random fixation of alleles

• loss of heterozygosity / loss of alleles

Example of drift: Pingelap island

• Massive typhoon hits island and kills a bunch of people

• The king was one of few to survive. But he had a recessive allele for complete colorblindness

• Now 1/20 people on the island are color blind

Effects of population size on drift

• Small populations: drift is strong, so allele frequencies change quickly by chance, leading to faster fixation or loss.

• Large populations: drift is weak, so allele frequencies change more slowly and are more stable.

Wright fisher model

• Like HW but with a small population

• 1/2N

• N = population size

Founder affect

new populations founded by a subgroup of the population

• ex.) of ant colonizers all came from the same original population, so they don’t war will each other, and make them very affective unified colonizers of native ant species.

Motoo Kimura

• BOOK: Neutral theory of molecular evolution

  • How does drift and mutation interact

Neutral

• no affect on fitness

Neutral theory equation

Neutral Theory

• Most molecular variation is neutral

• Most charges in DNA or amino acid sequences are due to drift

  • even differences between species

• Advantageous mutations are very rare, and most evolution is neautral mutation

Selectionist theory

• Advantageous mutations commonly contribute to evolutionary change

• Counter argument to neutral theory

Observations of Neautral Theory

• When looking at sequences differnces in proteins across species and the estimated substitution rate based on fossil records:

  • Replacement mutation rate requaled one every 2 years

  • This is VERY high rate

Molecular Clock

The molecular clock is the idea that genetic mutations accumulate at a roughly constant rate over time, so the number of DNA differences between species can be used to estimate how long ago they diverged.

Key idea:
Because many mutations are neutral (from neutral theory) and spread by genetic drift, they accumulate at a predictable average rate, allowing scientists to estimate evolutionary timelines.

A claim of neutral theory

• Positive natural selection

  • leads to changedchanges

  • But is irrelevant for DNA differences

• Supported by Psuedogenes as evidence

• Supported by Sunomonous mutations

Major claims of neautral theory

• Most molecular mutations are neutral — they do not affect an organism’s fitness.

• Genetic drift is the main force changing allele frequencies at the molecular level, rather than natural selection.

• The rate of molecular evolution equals the neutral mutation rate, producing a roughly constant molecular clock.

• Most genetic variation within populations is due to the accumulation of neutral alleles maintained by mutation and drift.

Pseudogenes

Pseudogenes are nonfunctional copies of genes that no longer produce a working protein. Because they do not affect fitness, mutations in them are not removed by natural selection.

As a result:

• Mutations in pseudogenes accumulate freely through genetic drift.

• They evolve at a rate close to the neutral mutation rate.

Why this matters:
Since pseudogenes show rapid accumulation of neutral mutations, they provide clear evidence that many DNA changes occur without selection, which is a key prediction of neutral theory.

Synomonous mutations

Synonymous mutations are DNA mutations that do not change the amino acid produced because multiple codons code for the same amino acid.

In the context of neutral theory:

• They are usually neutral because the protein sequence stays the same.

• Since they typically do not affect fitness, they are mainly influenced by genetic drift.

• Because of this, synonymous sites are often used to estimate neutral mutation rates and molecular clocks.

Why they matter:
Their high rate of accumulation compared to non-synonymous mutations supports the idea that many DNA changes occur neutrally, consistent with neutral theory.

Challenges to neautral theory

• Saturation - mutations can only get so different from each other

• Holes in molecular clock

  • Uses a concept of years, and not generations,

  • Substituion rates were the same in species with very different generation timelines

Ohta’s solution to Neutral theory challenges

• Bad mutations behave like neutral mutations when

Effective population Size (Ne)

Ne < N ; It is always less than the normal population size because:

• sex ratio is not always 1:1

• variation in offpsring #

• natural selection

• overlapping genernations

• Population sizes (N) flucuate over time.

Short lived creatures have:

• Large populatoins

• And slight bad mutations get selected against

Long lived creatures have:

• small populations

• small, bad mutations are neutral

The neuatral model…

is treated as a null hypothesis because it assumes DNA changes occur due to mutation and genetic drift, not natural selection.

Scientists first test whether observed genetic patterns fit what we would expect under neutrality. If the data match the neutral prediction, the null hypothesis is not rejected. If the data significantly deviate (e.g., too many advantageous mutations), it suggests natural selection is acting.

Detecting selection equation

• Ka = rate of nonsynomonous substitions

• Ks = rate of synomonous substitutions

• Ka / Ks = ratio tells you if selection is present

McDonald - Kreitman (MK) Test

is used to test whether natural selection or neutral drift explains DNA evolution.

Idea:
It compares two types of mutations in a gene:

1. Synonymous (silent) — do not change the amino acid → usually neutral.

2. Nonsynonymous — change the amino acid → may affect fitness.

Then it compares these mutations in two contexts:

• Within a species (polymorphisms)

• Between species (fixed differences)

Prediction under neutral theory:
The ratio of nonsynonymous to synonymous mutations should be the same within and between species.

Interpretation:

• More nonsynonymous fixed differences between species → evidence of positive selection.

• Fewer nonsynonymous changes than expected → purifying selection removing harmful mutations.

Neautral theory breif summary

• Most molecular variation is neutral

• Most changes in DNA or amino acid sequence are due to drift

  • Even species differences

Modern ideas related to neautral theory

• silent sites may not be complete nuetral =

• Codon bias may exist

  • All codons may not be used equally

• Hitchiking

Genetic Hitchhiking

(selective sweep) occurs when a neutral or even slightly harmful allele increases in frequency because it is physically linked to a beneficial allele under positive selection.

Key idea:
As the beneficial mutation spreads, nearby alleles on the same chromosome are “carried along”, reducing genetic variation in that region. Can become a fixated allele even if it’s not being selected for

Codon bias

preferential use of some codons by an amino acid

• seemingly very common

• ex.) E-Coli uses CUG codon combination far more frequently, even though other synomonous combinations exist.

• In yeast, the UUG is favored

  • Indication variation in codon preferenes across speices

Neutral theory in light of today’s ideas:

• It helps us explain the molecular clock

• Helps explain the role of psuedogenes

• However, differences across species seem to be more of a result of selection

• So neutral theory serves as a good Null model

Biological speices concept

defines species based on reproductive isolation.

Criteria:

1. Can interbreed — individuals mate and produce offspring.

2. Produce viable, fertile offspring — offspring can survive and reproduce.

3. Reproductively isolated from other groups — no gene flow with other populations (due to prezygotic or postzygotic barriers).

Key idea:
A species is a group of populations that actually or potentially interbreed and are isolated from others.

• Note this concept is only used for sexually reproducing organisms

Morphospecies concept

• Original species concept

• Based on appearance

• Useful for fossils

• Not good for sexual dimorphisms, mimicry, etc

Phenetic species concept

Species are defined based on overall similarity in observable traits (morphology, appearance, measurable characteristics).

Criteria:

1. Individuals are grouped by quantitative similarity in traits.

2. Uses many characteristics at once (not just one trait).

3. Species are clusters that are most similar to each other and distinct from other groups.

Key idea:
Species are identified by how similar they look/measure, not by reproductive isolation or evolutionary history.

• Kinda quantifies the morphological species concept

Bacteria and Archea dilemma

• Asexual species

• Can’t use the Biological species concept

• Horizontal gene transfer, gene flow

  • Gene flow may trigger speciation

Phylogenetic species concept

• Can be applied to all organisms

• Testable, quantifiable

• Uses genetics

• Can be difficult

• And as a result, it drastically increases the number of defined, unique species

Classic view of speciation

• Isolation of populations

• divergence of traits

• reproductive isolation

• This is very simplified

Allopatric speciation

speciation is happening when populations are physically separated

• Dispersal (moving to isloation)

• Vicarance (barrier forms between groups)

Dispersal vs Vicariance

• Allopatric speciation

Panamanin isthmus

• example of vicariance

• land mass formed, separating two oceans and the species in them.

• Allopatric speciation

Hawaii / islands

examples of dispersal from the mainland to an island

• allopatric speciation

Founder affect

• small group with a unique genetic makeup disperses to a new area

• Type of genetic drift

• allopatric speciation

Sympatric speciation

• Same place speciation

  • physical separation isn’t required for speciation to occur

• ex.) Insects, and plants (if a human brings a new plant into an environment, insects may shift their niche to fit that plant)

Rhagelois Fly example of sympatric speciation

• Hawthorwn was original food source

• Apples got introduced

• They have different growing seasons, and some flys began specializing for one or the other

• because of different temporal seasons, they no longer interact with each other naturally

• example of disruptive speciation

• Parasites within the flyes have also speciated

Incipient speciation

• speciation in progress but not yet complete

Cichlids

• fish that are like the post child for diverse speciation

• variatoin in size, color, and food

• Lake Tanganika

• Lake Apayo

Hybridization

two species come back into contact and still interbreed in a geographic area called the hybrid zone

• Fire bellied toads

Reinforcement

if hybrids are selected against

• If both parents and unique specialist, a hybrid may not be equipped for that unique environment

• If the hybrid is selected against, selection should eventually act to prevent mating between the two speices

Prezygotic isolation:

Barriers that prevent mating or fertilization before a zygote forms (e.g., temporal, behavioral, mechanical isolation).

Postzygotic isolation:

Barriers that occur after fertilization, where offspring are inviable, sterile, or have reduced fitness (e.g., hybrid sterility like mules).

examples of prezygotic isolation

• different sexual organs

• different mating seasons

• different mating signals and behaviors

• Physical isolation

• Temporal isolation

• No fertilization / no gamete recognition

examples of postzygotic isolation

• sertilization of offpsring

• zygote forms, but development doesn’t occur

• hybrids aren’t viable

sterility

• Differences in numbers of chromosomes across species

  • If you don’t have a matching number, more than lilkey the offspring will be streile

How does sexual selection preferences influence speciation?

ex.) Brids of paradise (very colorful)

• Have more speciation, and different sexual selection preferences

ex.) Manudces (muted, normal coloring)

• minimal speciation

Polyploidy

• a condition where an organism has more than two complete sets of chromosomes (e.g., 3n, 4n instead of 2n).

• changes in chromosome # = instant isolation

• very common in plants

Three spine stickleback example

• lots of speciation and specialization

• Marine species - more armor

• Freshwater species - less armor, different food source

• EDA gene mutation - removes plated armor protection

• Pit x1 locus - gene that produces hind limb, is detached in freshwater fish

structural change

change in strucutre / form of a protein usually through change in amino acid sequence

Regulatory

change in WHEN + WHERE proteins are expressed usually change in promoter or transcription factors

monophyletic group

common ancestor and all of its descendants

synapomorphy

is a shared derived trait that is present in a group of organisms and inherited from their most recent common ancestor, used to define evolutionary relationships.

parsimony

• simplest solution is more likely to be correct

• Fewest changes in a phylogeny will probably be right

Two things essential for Phylogenys

• DNA data

• Fast computers

Character data

• phylogeny term that quantifies confidence in accuracy

Bootstrap replicates

• phylogeny term that describes % of time you get a replication of a branch.