Exploring Biomedicine 2024: Wk 3-4

Evolution

cumulative change in a population or species over tim

Natural Selection

mechanisms leading to evolution where phenotypic differences among a population cause some to survive and reproduce more effectively than others

Adaptation

inherited aspect of an individual that allows it to outcompete other members of the same population- traits that have evolved through mechanism of natural selection

Macroevolution

major evolutionary changes among large taxonomic groups over long periods of time

Species

An interbreeding natural population that is reproductively isolated from other groups which are exchanging genes as a fundamental unit of evolution

Microevolution

• changes in allele frequency in species/small organism groups

• subtle and over short periods of time

• agents of change

What are the agents of change?

• natural selection

• mutation

• sexual reproduction

• genetic drift

• gene flow

Natural selection

survival and reproduction of the fittest

mutation

ultimate source of genetic variation which can be large or small changes

sexual reproduction

recombination of genes and mate’s choice

Genetic drift

changes to allele frequencies based on random chance. This has a large impact on small populations

Gene flow

migration, movement and hybirdisation

What are the assumptions hardy-weinberg functions under?

1. no migration

2. no mutation

3. equal fitness

4. infinite population size

5. random mating

How does reproduction impact population size, distribution, and structure?

• sex

• age

• societal systems

all affect random mating

How is population distribution affected by mutation?

• small mutation: no immediate affect

• large mutation: greater distribution positively impacts population as there are more immediate and noticable impacts

How did natural selection act on the galapagos ground finch?

The lack of intermingling birds allowed for speciation due to the differing environmental pressures from food source and the drought

How does size impact a population in relation to mutation and reproduction?

• smaller population are more greatly affected and undergo genetic drift

• larger population less effected and undergo natural selection

How did natural selection act on rock pocket mice?

The envrionmental pressure of habitat colour and avian attacks impacted the coat colour of the mice.

Black coat - dark volcanic rock & light coat - pale sandstone

Variation

individuals within a population differ in appearance, behaviour or physiology

heredity

offspring resemble their parents more than unrelated individuals

selection

some forms are more successful at reproducing in particular environments

selection differential

difference between population mean and selected mean

directional selection

• a.k.a positive selection

• favour individuals on one end of the distribution of phenotypes

  • e.g. small fish over big fish

stabilising selection

• favours individuals in the middle of the distribution of phenotypes

• acts against individuals at the extreme

• population approaches a mean value

• e.g. birth weight

disruptive selection

favours individuals at either end of the distribution

• e.g. specialist feeding

why does selection act faster on dominant alleles than recessive alleles?

• sleection not likely to drive a dominant allele to fixation

• recessive alleles can hide in heterozygous state

• favoured recessive alleles are not exposed to selection initially becuase they are more likely to occur only in heterogenous genotypes

• once recessive homozygotes begin to appear they quickly fix in the population

Artificial selection

natural selection resulting from human activity breeding organisms for favourable traits

Describe the heterozygote advantage

when selection favours heterozygous individuals over homozygotes

e.g. sickle-cell haemoglobin and malaria

fitness

success of an organism at surviving and reproducing thus contributing offspring to future generations

relative fitness

• describes the success of genotype at producing new individuals

• standardised by the success of other genotypes in the population

  • ranges from 0-1

Germline mutations

• affects gamets

• mutations transmitted via sexual reproduction

  • mutation in the germline create new variation and can be heritable

somatic mutation

• affects all the daughter cells of the single cell

  • non heritable

Point mutation

single base change (substitution)

Indel

insertion/deletion of middle of an existing sequence

Frameshift

if indel is not a multiple of 3 then this leads to frameshift

inversion

DNA is copied a second time and/or flipped around

chromosome fusion

chromosomes joined together or gained/lost (aneuploidy = speciation driver)

genome duplication

entire genome is duplicated

What do mutations in regulatory genes do?

• affect expression

• increase/decrease mRNA abundance

  • presence or absence in tussues/cells

What are the 6 key principals of gene flow?

• transfer of genetic information from one population to another can alter allele frequencies

• introduce new genetic variation

• reintroduce existing genetic variation

• homogenise more connected populations

• lack of gene flow promotes interpopulation differentiation

• dependent on the level of migration, movement, or hybridistation

What are the benefits of sexual reproduction?

• combinging beneficial alleles

• generation of novel genotypes

• faster evolution

• clearance of deleterious mutations

Assortative-mating

• positive assortment

• mate with individuals that share allele

• look the same

• common

• increase homozygous genotypes

• with selection can be a driver of speciation

• inbreeding

• less genotype diversity

Disassortative mating

• Negative assortment

• Mate with individuals that do not share alleles

• Look different

• Uncommon

• Maintenance in genotypic variation in population

• More heterozygotes

• Obligate outcrossing

Promiscuity

multiple males with multiple females

monogamy

one male pairs with multiple females

polyandry

one female mates with multiple males

polygyny

one male mates with multiple females

adaptive introgression

inheritance of beneficial variation from related species that accelerate adaptation to and survival in new environments

• net movement of alleles from one species or population to another

• interbredding between lineages shown with dotted arrow

Incomplete linear sortage

• allele is lost overtime

• genetic signals from DNA does not match past lineage

molecular genetics

study of DNA sequences encoding specific genes to understand function

Genomics

• Study of the DNA sequences in all of the organisms' genes

• Large scale

• Fragment and make sequencing library

• Find out which ones overlap

• Collect samples/record phenotypes

• Create libraries and sequence

• Investigate one locus/gene or entire genome

• Identify SNPs and other genetic variation

What are the benefits of molecular genetics and genomics?

• look across phenotype distribution

• look at evolutionary relationships

• compare specific situation

What are GWAS (genome wide associtation studies)

• associating genotypes with measurable phenotypes

• medical research

• evolutionary biology

• agriculture

How are molecular genetics/genomics used to investigate phylogenetics?

• Study of evolutionary relationships among biological organisms based of similarities and diff in DNA

• Knowledge of molecular clocks (rate mutations occur)

• Phenotypes: behaviour, anatomy

• Fossil record can be used for calibration

How are molecular genetics/genomics used to investigate phylogeographics?

• a.k.a landscape genetics

• Considers geographic distributions through fossil records and other evidence

• Interprets at landscape level

• e.g. mitochondrial genome

  • Inherited maternally and represent clonal lineages

  • Circular double stranded DNA molecule

  • Mutations occur

  • Haploid genome

  • Easy to isolate

  • Used mitogenome, locational information, and molecular clock

• Single rapid migration along the east or west coasts in the first 10,000 years

• Regional patternign developed post continent wide settlement where little movement occurred across the landscape for the next 40,000 years

Cladogram

• analysis of relationships between the nucleic acid sequences to create a tree of relatedness

• allows for comparison of transmission and epidemiological information with the established evolutionary relationships

Genetic drift

• Random changes in allele frequencies

• Alleles become more or less common by chance

• Element of randomness

• Directionless

• Allele frequencies change with each successive generation

• One allele can reach a frequency of 1

• Cannot predict which allele will be lost/fixed

• More pronounced in small populations

  • Stronger evolutionary agent of change

  • Outcomes more unpredictable

  • Probability of change is greater

• Less pronounced in large populations

  • Buffer genetic drift making it less significant agent of change

  • Need to be large enough random sampling effects don't impact allele frequencies significantly

Genetic Bottleneck

Cuased by events that reduce the size and genetic diversity of a population significantly

Founder Effect

smaller group from a larger population creates a new distinct population

selective sweep

• Rapid increase in the frequency of favourable allele beffore recombination disrupts the region of DNA

  • Mutation arises with adaptive advantage

  • Mutation lost be chance or sweep through population

• Can decrease diversity

• Originated from convergent evolution allowing for same traits to be expressed but with different genotypes

• Alleles increased over tie