Lecture 1: Introduction to Human Evolution
Evolution is the change in the heritable characteristics of biological
populations over successive generations
Evolutionary biology is used to explain the diversity of life (variety of
species, variation within populations, specific characteristics etc)
and how it changes over time. Also to elucidate the evolutionary
processes that are responsible for (mal)adaptation to environmental
conditions.
The inventor of the concept of evolution is Jean-Baptiste Lamarck,
who stated that organs that are not being used will disappear, while
organs with a function will develop further. He also said that
characteristics are acquired during the lifetime of an organism and
are passed onto offspring [called Lamarckism]. E.g. giraffes and
their long necks.
Charles Darwin proposed the theory of Natural Selection, where the
organisms better adapted to their environment tend to survive more
and produce more offspring. Alfred Russel Wallace independently
came to the same conclusion. The “ingredients” for evolution are
reproductive ability, environmental restrictions, competition,
heritable variations, natural selection and environmental changes,
all of which lead to evolution. Genetic/heritable variation is the fuel
for evolution.
The two main theories for evolution are:
1. Variationism: evolution is driven by survival, and the favorable
traits are passed onto offspring; aka natural selection/Darwinism
2. Transformationalism: all individuals in a population
simultaneously acquire the same structures and adaptations; aka
Lamarckism
Modern synthesis/neo-Darwinism arose from Darwinism, and it
discusses gene mutations, mendelian inheritance, epigenetics etc
Does evolution have a purpose/direction? Evolution is a random
process with no predetermined outcomes, plan or design. Natural
selection provides direction based on reproductive success, and
fitness advantages. These higher fitness advantages, however, do
not ensure longevity or health.
Is evolution adaptive? No everything; there are tradeoffs, random
processes, and evolutionary constraints. Claims of adaptation need
experimental validation
What is the speed of evolution? It takes place over successive
generations, and is fueled by genetic variation and selective
pressure.
Can evolution explain diseases? In many cases, yes it can
,Lecture 2: Population Genetics Part 1
Population genetics is the study of genetic changes in a population. You
can study genetic ancestry using this (study of the Netherlands where
they compared genetics between the Netherlands and neighboring
countries).
Genetic Analysis: An important factor in genetic analysis is scale.
The same data can be subsampled using varying numbers of loci
(specific positions in the genome). To see small changes in a
population, you need to use a higher loci. So, when we use lower
loci, the small changes go away (so differences between continents
will still be visible, but the smaller changes disappear).
Principle Component Analysis = a common way to reduce
complexity in data by condensing it to fewer dimensions, but
retaining as much original variation as possible. This is what is done
when you cannot visualize 100,000 loci at once, so you get the data
in less dimension but can still see the biggest differences. The
percent variation explained tends to increase as the number of loci
decreases, because with fewer loci, a larger proportion of the total
variation can be captured.
Genetic cluster = different genetic groups/entities
The geographic/phylogenetic scale matters
Geographic structure of populations is one of the most fundamental
topics, called isolation genetics, which is true in humans and most
animals.
Hardy-Weinberg Populations
The Hardy-Weinberg principle important since there are mutations,
genetic leakage, migration, genetic drift and selection pressures
that can cause genetic variation. Without all these, we will have an
idealize population! An ideal population is one with:
- no migration
- no mutation
- no selection
- have a large population size
- panmixis (=when there is random mating in the population [the
likelihood that any individuals breed with another is the same for
all])
, Hardy-Weinberg rule describes the equilibrium between allele and
genotype frequencies. The two alleles would be “p” and “q”.
The formulas are p + q = 1 p2 + 2pq + q2 = 1
To see if a population is in the Hardy-Weinberg population, you can
see if the alleles’ expected frequency matches the actual frequency
using the second formula.
When a population deviates from the Hardy-Weinberg, we start to
wonder what went wrong.
In the image below, the computer tries to assign individuals into
clusters/groups to minimize deviations from the equilibrium. The
deviations can occur often since the assumptions made are
extreme, so SNPs or tandem repeats are used to identify these
clusters. When populations deviate, we want to find out why is
happening with the population (hence research may begin).
What could be causes of deviations from equilibrium?
- Population declines
- Migration [fragmentation occurs, which is where the population
gets fragmented into smaller isolated populations; and human-
mediated dispersals, which is where the larger the human
footprint is, the more or less animals can move around. E.g.
jungle animals cannot move around as freely anymore v.s. lizards
that are brought by German tourists]
- Panmixis (some lizards prefer mating with a partner of the same
color phenotype)
- Selection (SNP change in gene for taking up cholesterol exhibits
selective pressure)
How is DNA organized?
Some species have more, some have less chromosomes.
A locus = a position in the genome [is a loose concept, can be a
broad region, gene, or a SNP].
Allele = variants at a locus [diploids have two alleles at each locus].
A genotype = combination of the alleles at a locus; calculated at the
individual level. Can also be the allelic variants across the genome
Genotype frequency is calculated at the population level; how many
individuals with that specific genotype appear in a population.
Allele frequency is the frequency of a specific allele in a population.
If we have 2 alleles GC, the allele frequency is 0.5 (goes from 0-1).
Lecture 3: Population Genetics Part 2
Neutral evolution & Selection
Evolution is the change in the heritable characteristics of biological
populations over successive generations
Evolutionary biology is used to explain the diversity of life (variety of
species, variation within populations, specific characteristics etc)
and how it changes over time. Also to elucidate the evolutionary
processes that are responsible for (mal)adaptation to environmental
conditions.
The inventor of the concept of evolution is Jean-Baptiste Lamarck,
who stated that organs that are not being used will disappear, while
organs with a function will develop further. He also said that
characteristics are acquired during the lifetime of an organism and
are passed onto offspring [called Lamarckism]. E.g. giraffes and
their long necks.
Charles Darwin proposed the theory of Natural Selection, where the
organisms better adapted to their environment tend to survive more
and produce more offspring. Alfred Russel Wallace independently
came to the same conclusion. The “ingredients” for evolution are
reproductive ability, environmental restrictions, competition,
heritable variations, natural selection and environmental changes,
all of which lead to evolution. Genetic/heritable variation is the fuel
for evolution.
The two main theories for evolution are:
1. Variationism: evolution is driven by survival, and the favorable
traits are passed onto offspring; aka natural selection/Darwinism
2. Transformationalism: all individuals in a population
simultaneously acquire the same structures and adaptations; aka
Lamarckism
Modern synthesis/neo-Darwinism arose from Darwinism, and it
discusses gene mutations, mendelian inheritance, epigenetics etc
Does evolution have a purpose/direction? Evolution is a random
process with no predetermined outcomes, plan or design. Natural
selection provides direction based on reproductive success, and
fitness advantages. These higher fitness advantages, however, do
not ensure longevity or health.
Is evolution adaptive? No everything; there are tradeoffs, random
processes, and evolutionary constraints. Claims of adaptation need
experimental validation
What is the speed of evolution? It takes place over successive
generations, and is fueled by genetic variation and selective
pressure.
Can evolution explain diseases? In many cases, yes it can
,Lecture 2: Population Genetics Part 1
Population genetics is the study of genetic changes in a population. You
can study genetic ancestry using this (study of the Netherlands where
they compared genetics between the Netherlands and neighboring
countries).
Genetic Analysis: An important factor in genetic analysis is scale.
The same data can be subsampled using varying numbers of loci
(specific positions in the genome). To see small changes in a
population, you need to use a higher loci. So, when we use lower
loci, the small changes go away (so differences between continents
will still be visible, but the smaller changes disappear).
Principle Component Analysis = a common way to reduce
complexity in data by condensing it to fewer dimensions, but
retaining as much original variation as possible. This is what is done
when you cannot visualize 100,000 loci at once, so you get the data
in less dimension but can still see the biggest differences. The
percent variation explained tends to increase as the number of loci
decreases, because with fewer loci, a larger proportion of the total
variation can be captured.
Genetic cluster = different genetic groups/entities
The geographic/phylogenetic scale matters
Geographic structure of populations is one of the most fundamental
topics, called isolation genetics, which is true in humans and most
animals.
Hardy-Weinberg Populations
The Hardy-Weinberg principle important since there are mutations,
genetic leakage, migration, genetic drift and selection pressures
that can cause genetic variation. Without all these, we will have an
idealize population! An ideal population is one with:
- no migration
- no mutation
- no selection
- have a large population size
- panmixis (=when there is random mating in the population [the
likelihood that any individuals breed with another is the same for
all])
, Hardy-Weinberg rule describes the equilibrium between allele and
genotype frequencies. The two alleles would be “p” and “q”.
The formulas are p + q = 1 p2 + 2pq + q2 = 1
To see if a population is in the Hardy-Weinberg population, you can
see if the alleles’ expected frequency matches the actual frequency
using the second formula.
When a population deviates from the Hardy-Weinberg, we start to
wonder what went wrong.
In the image below, the computer tries to assign individuals into
clusters/groups to minimize deviations from the equilibrium. The
deviations can occur often since the assumptions made are
extreme, so SNPs or tandem repeats are used to identify these
clusters. When populations deviate, we want to find out why is
happening with the population (hence research may begin).
What could be causes of deviations from equilibrium?
- Population declines
- Migration [fragmentation occurs, which is where the population
gets fragmented into smaller isolated populations; and human-
mediated dispersals, which is where the larger the human
footprint is, the more or less animals can move around. E.g.
jungle animals cannot move around as freely anymore v.s. lizards
that are brought by German tourists]
- Panmixis (some lizards prefer mating with a partner of the same
color phenotype)
- Selection (SNP change in gene for taking up cholesterol exhibits
selective pressure)
How is DNA organized?
Some species have more, some have less chromosomes.
A locus = a position in the genome [is a loose concept, can be a
broad region, gene, or a SNP].
Allele = variants at a locus [diploids have two alleles at each locus].
A genotype = combination of the alleles at a locus; calculated at the
individual level. Can also be the allelic variants across the genome
Genotype frequency is calculated at the population level; how many
individuals with that specific genotype appear in a population.
Allele frequency is the frequency of a specific allele in a population.
If we have 2 alleles GC, the allele frequency is 0.5 (goes from 0-1).
Lecture 3: Population Genetics Part 2
Neutral evolution & Selection
