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Lecture and slides notes Evolutionary Development Biology (AB_1141)

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Instelling
Vrije Universiteit Amsterdam (VU)

Boek
Human Evolution and Development

33 Lectures are fit in one nice document that summarises all the necessary information from the slides and the book to prepare for all three exams of Evolutionary Developmental Biology.

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Geupload op 9 juli 2023
Aantal pagina's 28
Geschreven in 2022/2023
Type College aantekeningen
Docent(en) K.m.h
Bevat Alle colleges

evolution
charles dawin
natural selection
mutation
linkage equilibrium
selection
drift
migration
snp
genotype
phenotype
panmixis
haplotype
genetic map
selection drift
microe
hardy weinberg equilibrium

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EVOLUTIONARY DEVELOPMENTAL BIOLOGY
Lecture 1
Introduction
Evolution – the change in the heritable characteristics of biological populations over successive
generations.

To explain the diversity of life:
● The variety of species
● Variation within populations
● Specific characteristics
● How they change over time

Charles Dawin (1859) is known for his natural selection theory, “survival of the fittest” – the
process whereby organisms that are better adapted to their environment tend to survive and
produce more offspring.

In 1920-1950, “Modern Evolutionary Synthesis” – merging natural selection with genetics.

Not everything is adaptive, for example, trade-offs, random processes, mismatches, evolutionary
constraints. Therefore, claims of adaptation need experimental validation. Evolution is a random
process so there is no pre-ordained plan/purpose or design. Natural selection provides direction:
selection on higlher Darwinian fitness (= reproductive success). But higher fitness does not mean
health or longevity. And reproductive success does not mean the number of offspring.

Speed of evolution is a concept that evolution takes place over successive generations and is
fueled by genetic variation and selective pressure. Phylogenetic trees demonstrate the
relationship among organisms and their evolutionary history.

Lecture 2-3
Genetic Variation Linkage

,Natural selection acts upon the phenotypes, however, genetic variation is the fuel for evolution.
Changes in allele frequencies in populations:
- Mutation → new alleles arise by changes in the DNA
- Linkage equilibrium → change in frequency due to genetic linkage
- Selection → Natural selection on alleles with a disadvantage
- Drift → change due to random effects (neutral evolution)
- Migration → new alleles enter the population from another population

Human genomes are 99.9% similar, so we differ from eo at 3.3 million nucleotides. It is a source
of phenotypic variation and genetic diseases.

❖ Mutations
They are spontaneous changes in the DNA. They are caused by errors during DNA
replication and recombination. UV radiation and reactive chemicals and transposable
elements that make up 44.7% of the human genome.

Structural characteristics of mutations:
➢ Point mutations (SNPs 1bp) – where a single nucleotide ATC or G is altered. If
SNP then single DNA base variation is found in the population. Major allele is the
most frequent variant.
➢ Insertions/deletions (1-49bp)
➢ Repeats – Variable Number Tandem Repeats
➢ Structural variations (>50bp)
■ Inversions, translocations, duplications, deletions, insertions

SNP is the most common form of genetic variation >35’000’000 in humans; typically bi-allelic;
mostly neutral meaning they do not have a measurable phenotypic effect but some have positive
or negative effects; often used in genome-wide association studies. Example: a single nucleotide
change in the LDL receptor which can alter the amino acid sequence and the function of a
protein and therefore, the mutation results in hypercholesterolemia in patients. Non-coding SNPs
may change regulatory units and regulate expression of genes (rapid evolution takes place by
regulatory changes). Example: LCT encodes lactase and an intronic SNP disables
downregulation of lactose.

Evolution of lactose tolerance in human populations that have a tradition of drinking milk from
animals opened up a valuable new source of nutrients and different mutations in different geo
locations.

, VNTRs are sequences in which a shorter or longer core sequence is repeated a variable number
of times. Microsatellite is a short core sequence while minisatellite is a long sequence >100bp.
VNTRs are often located in non-coding regions and the number of repeats is highly variable,
indicating neutral evolution; used to quantify genetic variation between individuals. Example:
Long variants of DRD4 emerged 30000 years ago coinciding with the cultural explosion and
might have had an evolutionary advantage.

Structural variations are the chromosomal mutations that often have large phenotypic effects
with medical relevance like Trisomy 21 or Robertsonian translocation. Gene duplication is an
important source of new genes. Different numbers of chromosomes prevent the production of
fertile hybrid offspring, due to problems with synaptic pairing during meiosis.

❖ Hardy-Weinberg equilibrium
Locus is the position in the genome where a trait is encoded.

Allele is one of several variants of a locus – in diploid organisms every individual has two alleles
of a locus.
Allele frequency is the number of alleles of a particular variety in a population, relative to the
total number of alleles present in the population at that locus.

Genotype is an individual’s collection of allelic variants across the genome, and also it refers to
the two alleles inherited for a particular gene.
Genotype frequency is the number of individuals with a given genotype, relative to the total
number of individuals in the population.

Hardy-Weinberg rule describes the equilibrium between allele and genotype frequencies. If the
allele frequencies for a locus with two alleles are equal to p and q then the frequencies of the
three genotypes are equal to p2, 2pq and q2, if five conditions are met:
➢ Large population
➢ Panmixis
➢ No migration
➢ No mutation
➢ No selection

Panmixis is the likelihood that any individual breeds with another individual is the same for all
individuals.
After one generation of random mating the genotype frequencies are in H-W equilibrium and
constant in the next generations
When in H-W equilibrium, the allele frequencies remain constant across generations,
independent of genotype frequencies.

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