PAPER 4:-EVOLUTIONARY BIOLOGY

COURSE CODE-23PSIMBMJ4EVB

MODULE 2
Population Genetics And Experimental
Evolution
-SD Maam
2.1 BIOLOGICAL SPECIES:

• Concept
• Mendelian Population
• Models of Population growth and Variation
• A population is a group of organisms of the same species that are found in the same area and can interbreed.

• Population genetics –It is the study of genetic variation within populations, and involves the examination
and modelling of changes in the frequencies of genes and alleles in populations over space and time.

• The study of change of :-

1) Allele frequencies
2) Genotype frequencies
3) Phenotype frequencies

• Benefits- Allows prediction of gene frequencies in future generations.

Defines how or why genetic variation is maintained or lost in populations.
Is critical to understanding the evolutionary process.

• The gene pool of a population consists of all the copies of all the genes in that population.

• Genetic equilibrium is the condition of an allele or genotype in a gene pool where the frequency does not
change from generation to generation.
If we look at the two gene copies in each plant and count up how many W copies are present, we find there are 13. If we count up how many w
copies are present, we find that there are five. The total number of gene copies in the whole population is
[13 + 5 = 18].
We can divide the number of copies of each allele by the total number of copies to get the allele frequency. By convention, when there are just
two alleles for a gene in a population, their frequencies are given the symbols
p = frequency of W=13/18=0.72 or 72%
q = frequency of w=5/18=0.28 or 28%
The frequencies of all the alleles of a gene must add up to one, or 100%.
Allele frequency is different from genotype frequency or phenotype frequency. Genotype and phenotype frequencies can also be calculated and
are important for understanding how populations evolve, but they are not the same thing as allele frequency.
Calculating Allele Frequencies
Allele frequencies can be calculated using the Hardy-Weinberg equilibrium, a principle that stipulates that in a large,
randomly mating population with no mutation, migration, or selection, the allele and genotype frequencies will remain
constant from one generation to the next. This provides a baseline expectation for allele frequencies in a Mendelian
population.
The Hardy-Weinberg equilibrium is represented by the equation p^2 + 2pq + q^2 = 1, where:
p^2 is the frequency of homozygotes for one allele (AA)
2pq is the frequency of heterozygotes (Aa)
q^2 is the frequency of homozygotes for the other allele (aa)
p is the frequency of one allele (A)
q is the frequency of the other allele (a)
These frequencies can be easily calculated given the genotypic distribution in the population
•Sources of Genetic
Variation • New genes and alleles can arise by mutation or gene duplication.

• Formation of New Alleles

• A mutation is a change in the nucleotide sequence of DNA.
• Only mutations in cells that produce gametes can be passed to offspring.
• A “point mutation” is a change in one base in a gene.

• The effects of point mutations can vary –

Mutations in noncoding regions of DNA are often harmless – Mutations to genes can be neutral
because of redundancy in the genetic code.

• The effects of point mutations can vary –

Mutations that alter the phenotype are often harmful – Mutations that result in a change in protein
production can sometimes be beneficial
•Altering Gene Number or Position
• Chromosomal mutations that delete, disrupt, or rearrange many loci are typically harmful •
Duplication of small pieces of DNA increases genome size and is usually less harmful • Duplicated genes can
take on new functions by further mutation • An ancestral odor-detecting gene has been duplicated many times:
Humans have 350 functional copies of the gene; mice have 1,000

• Rapid Reproduction
• • Mutation rates are low in animals and plants • The average is about one mutation in every
100,000 genes per generation • Mutation rates are often lower in prokaryotes and higher in viruses • Short
generation times allow mutations to accumulate rapidly in prokaryotes and viruses

• Sexual Reproduction
In organisms that reproduce sexually, most genetic variation results from recombination of alleles
• Sexual reproduction can shuffle existing alleles into new combinations through three mechanisms: crossing
over, independent assortment, and fertilization
•Variation in heritable traits is a prerequisite for evolution • Mendel’s work on pea plants provided evidence
of discrete heritable units (genes). Genetic variation makes evolution possible

• Genetic Variation
• Phenotypic variation often reflects genetic variation • Genetic variation among individuals is
caused by differences in genes or other DNA sequences
• Some phenotypic differences are due to differences in a single gene and can be classified on an
“either-or” basis • Other phenotypic differences are due to the influence of many genes and vary in
gradations along a continuum

•Genetic variation can be measured at the whole gene level as gene variability • Gene variability can be
quantified as the average percent of loci that are heterozygous

• Genetic variation can be measured at the molecular level of DNA as nucleotide variability • Nucleotide
variation rarely results in phenotypic variation.

• Phenotype is the product of inherited genotype and environmental influences • Natural selection can only
act on phenotypic variation that has a genetic component
• Mutation: Among the individuals of a population, heritable differences are generated by gene
mutations .Gene mutation is also called point mutation. It occurs at random and is not directed wards
a goal. The effect of mutation on an individual within a population, is manifold and include change in
form and structure (morphology).

• Reombination: Genetic variations are also caused by reshuffling of genes.New genotypes arise in the
gene pool from already existings and this is termed recombination. It occurs by an exchange of
segments between chromosomal pairs called crossing over.
• Evolution

• The Smallest Unit of Evolution:-

1) One common misconception is that organisms evolve during their lifetimes.
2) Natural selection acts on individuals, but only populations evolve.
3) Consider, for example, a population of medium ground finches on Daphne Major Island – During a
drought, large-beaked birds were more likely to crack large seeds and survive – The finch population
evolved by natural selection

• Microevolution is a change in allele frequencies in a population over generations

Three mechanisms cause allele frequency change – Natural selection – Genetic drift – Gene flow
Only natural selection causes adaptive evolution

• It is the process of heritable changes in the population of organisms over several generations. The
inherited traits are the expression of genes that are copied and passed on to the offspring during
reproduction. The heritable traits that are helpful for survival and reproduction become more common,
while the harmful traits become rare.
Mechanism of Genome Evolution
• Gene Duplication
This is the duplication of a particular region of DNA. It occurs by recombination, aneuploidy,
transposition, polyploidy and error in DNA replication.

• Transposable elements
This refers to a region of DNA that can be inserted anywhere in the genome. For eg., Ty elements in
Drosophila. Alu sequence is the most common transposable element found in humans.

• Mutation
Spontaneous mutations are responsible for changes in the genome. The nucleotide sequences change
resulting in a frameshift mutation that alters the genome. This is more common in prokaryotes.

• Exon Shuffling
During this, two exons from different genes come together. New genes are formed by this mechanism.
Thus, a new gene is introduced into the genome.
• During 1977 there was a major drought on Daphne Major and many of the plants on the island produced few or no
seeds. The medium ground finch population, which depends on seeds for food, declined drastically from about 1400
individuals to a few hundred in just over two years.

• What the Grants' research group observed was that following the drought the population of finches had recovered; but
now, the average size of the beaks was larger. The underlying reason for this was that during the drought, small seeds
were exceedingly rare but large seeds with thick husks were still available. Only the large birds with large beaks were
able to crack open the husks and eat the contents of the seeds. Smaller birds with smaller beaks were unable to do so and
therefore starved. From this differential pattern of death, there was a rapid change in the finch population.
• Mendelian populations were first introduced in the early 20th century, named after Gregor Mendel, the father
of modern genetics, and have since played a pivotal role in our understanding of the genetic makeup of species.

• Mendelian population is a breeding group where random mating occurs, and Mendel’s principles of
inheritance can be applied (Hartl & Clark, 1997). These populations are indispensable to the study of genetic
variation and evolution within a species. Each member of a Mendelian population shares a common gene pool
and exchanges genetic material freely.

• The Principle of Mendelian Inheritance

Before we delve into the specifics of Mendelian populations, it is important to comprehend the
underpinning principle of Mendelian inheritance. Gregor Mendel’s genetic experiments with pea plants, performed
in the mid-19th century, led to the elucidation of the fundamental laws of inheritance. These laws encapsulate the
mechanics of heredity and form the basis of modern genetics (Bateson, 1909).

• Mendelian Populations:
In the simplest of terms, a Mendelian population is a breeding group where random mating occurs,
and Mendel’s principles of inheritance can be applied (Hartl & Clark, 1997). These populations are indispensable
to the study of genetic variation and evolution within a species. Each member of a Mendelian population shares a
common gene pool and exchanges genetic material freely.
• Characteristics of Mendelian Populations

1. Mendelian populations possess certain defining characteristics. Here are the key features:
2. Random mating: The mating within a Mendelian population is random, i.e., there are no restrictions or
preferences based on genotype or phenotype.
3. Large population size: Mendelian populations are generally large in size to ensure genetic diversity and
reduce the effects of genetic drift.
4. Absence of selection, migration, and mutation: These populations ideally exhibit no selection, migration, or
mutation pressures, enabling gene frequencies to remain constant over generations.
5. Shared gene pool: All individuals within the population have the ability to contribute to the gene pool.
6. The Gene Pool and Allele Frequencies
7. In a Mendelian population, the collective sum of all the genes and their different forms, or alleles,
constitutes the gene pool. The relative proportion of each allele in the population is referred to as the allele
frequency. Understanding these frequencies is crucial to the study of genetic variation and evolution
(Futuyma & Kirkpatrick, 2017).
8. The proportion of variation in a population trait that can be attributed to inherited genetic factors.
Heritability estimates range from 0 to 1 and are often expressed as a percentage. A number close to 1 may
be indicative of a highly heritable trait within a population.
Genetic Variation in Mendelian Populations
• Genetic variation is the bedrock of evolution, and Mendelian populations serve as the stage upon which this
play of variation and selection unfolds. This variation primarily occurs due to mutations, gene flow, genetic
drift, and selection.

• Mutations
Mutations are changes in the DNA sequence and are the primary source of new genetic material. They
introduce novel alleles into the gene pool and increase genetic variation.

• Gene Flow
Gene flow, or migration, involves the movement of individuals and their genetic material from one
population to another. This transfer can introduce new alleles into the population and change allele frequencies.

• Genetic Drift
Genetic drift is a random process that changes allele frequencies over generations. It can lead to the loss
or fixation of alleles and plays a significant role in shaping genetic variation in small populations.

• Selection
Selection, both natural and artificial, influences allele frequencies by favoring individuals with certain
genotypes that enhance survival and reproduction. Over generations, selection can lead to significant shifts in
allele frequencies.
• The concept of a Mendelian population helps geneticists model inheritance patterns. Comparing real groups to this
ideal shows how reproduction is more complex. Ways real populations diverge from the Mendelian model include:

• Small population size

• Nonrandom mating
• Subpopulations and genetic drift
• Mutations
• Natural selection and fitness differences
• External gene flow
• These factors disrupt Hardy-Weinberg equilibrium. The Mendelian population concept simplifies genetics for its
analysis.

• Non-Mendelian inheritance is any pattern in which traits do not segregate in accordance with Mendel's laws. These
laws describe the inheritance of traits linked to single genes on chromosomes in the nucleus.
 Models of Population Growth

• A particularly important feature that is studied by ecologists is the rate at which a population grows or declines.

• Growth model shows the specific and predictable pattern of growth of population with time.

• Growth of population takes place according to availability of food, habit condition and presence of other biotic
and abiotic factors.

• There are two main types of models:

(a) Exponential Growth: This kind of growth occurs when food and space is available in sufficient amount.
When resources in the habitat are unlimited, each species has the ability to realise fully its innate potential to grow in
number .
The population grows in an exponential or geometric fashion.

(b)Logistic Growth:When resources are limited, populations exhibit logistic growth. In logistic growth, population
expansion decreases as resources become scarce, leveling off when the carrying capacity of the environment is
reached, resulting in an S-shaped curve.
• In exponential growth, a population's per individual growth rate stays the same regardless of population size, making the
population grow faster and faster as it gets larger.
• In nature, populations may grow exponentially for some period, but they will ultimately be limited by resource availability.

• In logistic growth, a population's per capita growth rate gets smaller and smaller as population size approaches a maximum
imposed by limited resources in the environment, known as the carrying capacity (K)

• Exponential growth produces a J-shaped curve, while logistic growth produces an S-shaped curve.
• If in a population of size N, the birth rates as represented as .b. and death rate as .d..
Then increase and decrease in N during unit period time .t. will be
dN/dt=(b−d)×N
Let (b−d)=r, then
dN/dt=rN.
• Then, the r in this equation is called .intrinsic rate of natural increase. and is a very important parameter
chosen for assessing impacts of any biotic or abiotic factor on population growth.
References:-

• https://anthroholic.com/mendelian-population
• https://geneticeducation.co.in/gene-flow-vs-genetic-drift/

• Books: Molecular Evolution and Phylogenetics.

• IGenetics.
• Principal of population genetics.
• Research Article-Population genetics and Demography unite Ecology and Evolution.
2.2 Population Genetics

• Natural selection, Mutation

• Hardy Weinberg equilibrium
• Genetic drift, Gene flow
• Non random mating
• Fitness landscape(Sewall wright- RA Fisher controversy)
Factors causing genotype frequency changes or evolutionary principles
• Selection = variation in fitness; heritable
• Mutation = change in DNA of genes
• Migration/ Gene flow = movement of genes across populations
– Vectors = Pollen, Spores
• Recombination = exchange of gene segments
• Non-random Mating = mating between neighbors rather than by chance
• Random Genetic Drift = if populations are small enough, by chance,
sampling will result in a different allele frequency from one generation to the
next.
 Natural Selection
• Selection occurs because different genotypes exhibit differential survivorship and/or
reproduction.

• If we consider a continuously distributed trait (e.g., wing length, weight) with a strong
genetic basis, the response to selection can be characterized by where in the
distribution the "most fit" (greatest survivorship & reproduction) individuals lie.

• If after selection one extreme is most fit this is directional selection; if the intermediate
phenotypes are the most fit this is stabilizing selection; if both extremes are the most fit
this is disruptive selection.
• Differential success in reproduction based on variation in a population.

• Fitness-Better suited organisms in an environment tend to produce more offspring than

less suited organisms.

• Types
– Directional(One extreme phenotype only is favored)
– Disruptive(extreme phenotypes are favored and the average is selected against)
– Stabilizing (Average individuals are selected for and extremes are selected against.)
– Sexual (Intersexual and Intrasexual)
– Artificial(Modification of species due to selective breeding to produce organisms with
desired traits Ex: pets)
 Mutations
• Change in DNA’s nucleotide sequence.
• Raw source for new genes and alleles
• Most mutations are somatic cell mutations and do not affect offspring
• Only gametic mutations affect a gene pool.

• Mutation rates
– Lower in organisms with a longer generation span
• Plants and animals – 1/100000 genes
– Higher in organisms with a shorter generation span
• Bacteria and viruses
• Point Mutations – alter one nucleotide base only
– Usually neutral
– Sickle cell anemia
• Chromosomal Mutations – alter many regions or
loci of the entire chromosome
– Gene duplication
• Usually harmful, but when beneficial act as
an important source of variation in a
population
 Nonrandom Mating – sexual selection
• A mating system in which at least some individuals are more or less likely to mate with
individuals of a particular genotype than with individuals of other genotypes.

• Creates sexual recombination – joining of different alleles in a gene pool

– Huge source of variation in a population

• Gametes from different organisms contribute different alleles to the next generation.
 Genetic Drift Bottleneck effect

• Sudden environmental change can drastically reduce the size of a population – only some survive

• Fire, flood, human influence etc.

• Reduces the genetic variation in a population

• Ex: An example of a bottleneck: Northern elephant seals have reduced genetic variation probably because of a
population bottleneck humans inflicted on them in the 1890s. Hunting reduced their population size to as few as 20
individuals at the end of the 19th century. Their population has since rebounded to over 30,000—but their genes still
carry the marks of this bottleneck: they have much less genetic variation than a population of southern elephant seals
that was not so intensely hunted.
 Genetic Drift Founder effect

• Occurs when a few individuals become isolated from the original

population
• The smaller population may not have the same gene pool as the
original and speciation is likely
 Migration – Gene Flow

• Addition or loss of alleles to or from a gene pool.

• Caused by the movement of fertile individuals to or from a population – migration, a
deer goes to live with another population
• Scientists are studying the effects of cultivated crop’s (artificially selected crops) gene
flow on wild populations

Genetic Variation
• Differences in phenotypes between members of a population
• Inherited in genotype
• The raw source for natural selection within a population
• Relative Fitness:
• The of offspring
• An individual passes
• To the next generation
 Hardy-Weinberg Principle

• Its all about frequencies

• “Frequencies of alleles and genotype in a population will remain constant

over time in absence of other evolutionary influences”

• The Hardy-Weinberg equilibrium is a principle stating that the genetic variation

in a population will remain constant from one generation to the next in the
absence of disturbing factors.

• Example-Diseases causing alleles in a population.(cyctic fibrosis)

 Hardy-Weinberg assumptions

• There are five basic Hardy-Weinberg assumptions:

no mutation, random mating, no gene flow, infinite population size, and no selection.

• If the assumptions are not met for a gene, the population may evolve for that gene (the gene's allele
frequencies may change).

• Mechanisms of evolution correspond to violations of different Hardy-Weinberg assumptions. They

are: mutation, non-random mating, gene flow, finite population size (genetic drift), and natural
selection.
 Hardy-Weinberg Equilibrium

• Evolution does NOT occur if the gene pool

remains constant from one generation to the
next.

• Outside forces must act on a population for

there to be change.

• Evolution is a change in allele frequencies in

a population over time, so a population in
Hardy-Weinberg equilibrium is not evolving
Equation - Hardy-Weinberg Equilibrium

• p2 + 2pq + q2 = 1
• p+q=1
• p = dominant allele
• q = recessive allele
• p2 = homozygous dominant
• 2pq = heterozygous
• q2 = homozygous recessive
 Conditions

NO Evolution = genetic equilibrium Evolution = no genetic equilibrium

• No Mutations • Mutations
• Extremely Large population size – no • Small populations – genetic drift
genetic drift • Gene flow – migration
• No gene flow – no migration • Non Random mating
• Random Mating • Natural Selection
• No Natural selection
 Violations to H-W Equilibrium – cause evolution

• Mutations
• Small populations – genetic drift
• Non random mating
• Natural Selection
• Migration – gene flow

• 23_08EvolutionaryChanges_A.swf
In our population, let's say that the A allele has a frequency of 0.3,
while the a allele has a frequency of 0.7.
If a population is in Hardy-Weinberg equilibrium, allele frequencies will be related to genotype
frequencies by a specific mathematical relationship, the Hardy-Weinberg equation.
• In the simplest case of a single locus with two
alleles denoted A and a with frequencies f(A)
= p and f(a) = q, respectively, the expected
genotype frequencies under random mating
are f(AA) = p2 for the AA homozygotes,
f(aa) = q2 for the aa homozygotes, and f(Aa)
= 2pq for the heterozygotes. In the absence of
selection, mutation, genetic drift, or other
forces, allele frequencies p and q are constant
between generations, so equilibrium is
reached.
 Fitness landscape (Sewall wright- RA Fisher controversy)
• In evolutionary biology, fitness landscapes or adaptive landscapes are used to visualize the
relationship between genotypes and reproductive success.

● The intense controversy between R. A. Fisher and Sewall Wright, which lasted from 1929
until Fisher's death in 1962.

• Wright's adaptive landscape and shifting balance theory of evolution versus Fisher's
fundamental theorem of natural selection

• Wright's theory is a detailed dynamical model of evolutionary change in actual

populations.

• Fisher's theory is an abstract invariance and conservation law that, like all physical laws,
captures essential features of a system but does not account for all aspects of dynamics in
real examples.
• American biologist Sewall Wright (1889–1988) was an influential pioneer in the field of
evolutionary genetics.

• Like his British counterparts Sir Ronald Fisher and J. B. S. Haldane, Wright formulated a
mathematical theory of evolution, thereby showing how frequencies of alleles and
genotypes could change in response to evolutionary pressures such as natural selection,
mutation, and migration.

• Wright also examined the effects of inbreeding and random genetic drift in evolution, and
he was influential in the development of various statistical methods used in evolutionary
analysis.

• Indeed, Wright drew from his research in each of these areas in his development of a
new, comprehensive theory of evolution that he termed the "shifting balance" theory.
Although Wright initially proposed this theory in the 1930s, it remains a source of great
interest and controversy among evolutionary geneticists today.
• Fisher's fundamental theorem of natural selection shows that the part of the rate of
change of mean fitness that is due to natural selection equals the additive genetic variance
in fitness.

• Fisher embedded this result in a model of total fitness, adding terms for deterioration of
the environment and density dependence.

• The rate of increase in fitness of any organism at any time is equal to its genetic variance
in fitness at that time.
● Fisher and Wright theory. -Their differences were in interpretation, not in the mathematics.

● Although their techniques were different, for any particular problem their theoretical conclusions were
the same.

● The issue was inbreeding vs. random gene frequency drift. Random drift is especially important in
small populations where random mates may be related and share a fraction of their genes. Nonrandom
consanguineous matings of course can occur in populations of any size.

● After Fisher’s death in 1962, and until his own in 1988, Wright continued to write, repeatedly
supporting his views and especially his shifting-balance theory.

● Counterarguments made by others were that his preferred population structure with subdivisions and
appropriate balance of selection, mutation, random drift, and migration is very rare and that while his
mechanism is at work the population fitness is substantially reduced.
• Two giants of evolutionary theory, Sewall Wright and R. A. Fisher, fought bitterly
for over thirty years.

• Wright emphasized stochastic fluctuations of gene combinations in small,

isolated populations. By contrast, Fisher believed that fluctuating selection in
large populations was the main cause of fluctuation in nonadditive gene
combinations.
 References:-

• https://www.khanacademy.org/science/ap-biology/natural-selection/hardy-weinberg-equilibrium

• https://www.youtube.com/watch?v=oG7ob-MtO8c

• https://link.springer.com/chapter/10.1007/978-94-011-2856-8_8

• Books: Molecular Evolution and Phylogenetics.

• iGenetics (3rd evolution)

• Principal of population genetics (4th edition)

• Evolution (2004) Ridley Mark

• Research Article-Hardy–Weinberg Equilibrium and Random Mating

2.3 Experimental Evolution

• Long term evolution experiment –E.coli (Richard Lenski).

• Multicellularity experiments-Will Ratcliff.
• Designing evolution experiments.
 Richard Lenski’s Long Term Evolution Experiment (LTEE).
• The E. coli long-term evolution experiment (LTEE) is an ongoing study in experimental evolution begun
by Richard Lenski at the University of California, Irvine, carried on by Lenski and colleagues at Michigan
State University, and currently overseen by Jeffrey E. Barrick at the University of Texas at Austin.

• Model Organism: E coli

• Medium of evolution: Glucose-limited medium called DM25
• Number of replicates: 12, maintained at 37 degree Celsius.

• The core idea is to observe and quantify the process of evolution in action.

• The LTEE involves daily transfers of 12 E. coli populations, and it has been running for over one third of a
century.

• Survival of the fittest.

• The long-term evolution experiment was designed as an open-ended means of empirical examination of
central features of evolution. The experiment was begun with three principal goals:
• To examine the dynamics of evolution, including the rate of evolutionary change.
• To examine the repeatability of evolution.
• To better understand the relationship between change on the phenotypic and genotypic levels.

• The use of E. coli as the experimental organism has allowed many generations and large populations
to be studied in a relatively short period of time.
All populations showed a pattern of rapid increase in relative fitness during early
generations, with this increase decelerating over time.

How a 30-Year Experiment Has Fundamentally Changed Our View of How Evolution Works | Discover Magazine
Developed defects in their ability to repair DNA, greatly increasing the rate of
mutation in those strains.

Legendary bacterial evolution experiment enters new era (nature.com)

Evolution of aerobic citrate usage in one population.
• Due to the long use of E. coli as a principle model organism in molecular biology, a wide array of tools,
protocols, and procedures were available for studying changes at the genetic, phenotypic, and
physiological levels.

• The bacteria can also be frozen and preserved while remaining viable. This has permitted the creation of
what Lenski describes as a "frozen fossil record" of samples of evolving populations that can be revived
at any time. This frozen fossil record allows populations to be restarted in cases of contamination or
other disruption in the experiment, and permits the isolation and comparison of living exemplars of
ancestral and evolved clones.

• Lenski chose an E. coli strain that reproduces only asexually, lacks any plasmids that could permit
bacterial conjugation, and has no viable prophage.

• As a consequence, evolution in the experiment occurs only by the core evolutionary processes of
mutation, genetic drift, and natural selection.

• This strict asexuality also means that genetic markers persist in lineages and clades by common
descent, but cannot otherwise spread in the populations.
● The genetic bases of adaptation are being investigated in 12 populations of Escherichia coli,
founded from a common ancestor and serially propagated for 20,000 generations, during which time
they achieved substantial fitness gains. Each day, populations alternated between active growth and
nutrient exhaustion.
● DNA supercoiling in bacteria is influenced by nutritional state, and DNA topology helps coordinate
the overall pattern of gene expression in response to environmental changes. We therefore examined
whether the genetic controls over supercoiling might have changed during the evolution experiment.
● Parallel changes in topology occurred in most populations, with the level of DNA supercoiling
increasing, usually in the first 2000 generations.
● Two mutations in the topA and fis genes that control supercoiling were discovered in a population
that served as the focus for further investigation. Moving the mutations, alone and in combination,
into the ancestral background had an additive effect on supercoiling, and together they reproduced
the net change in DNA topology observed in this population.
● Moreover, both mutations were beneficial in competition experiments.
● Clonal interference involving other beneficial DNA topology mutations was also detected. These
findings define a new class of fitness-enhancing mutations and indicate that the control of DNA
supercoiling can be a key target of selection in evolving bacterial populations.
 Multicellularity evolution experiment-Will Ratcliff

• William Ratcliff, an evolutionary biologist at the Georgia Institute of Technology, and his
colleagues have conducted multiple experiments to study the evolution of multicellularity.

• Combining theory and experiments, scientists have now been able to evolve
multicellularity in laboratories from unicellular microbes.

• One remarkable example of multicellular yeast, normally a unicellular organism, evolved

in the lab.

• Model Organism: Saccharomyces cerevisiae

• Multicellularity was one of the most significant innovations in the history of life, but its initial evolution
remains poorly understood

• Using experimental evolution, it shows key steps in this transition could have occurred quickly.

• The unicellular yeast Saccharomyces cerevisiae to an environment in which we expected multicellularity to

be adaptive.

• Observed the rapid evolution of clustering genotypes that display a novel multicellular life history
characterized by reproduction via multicellular propagules, a juvenile phase, and determinate growth.

• The multicellular clusters are uniclonal, minimizing within-cluster genetic conflicts of interest.

• Simple among-cell division of labor rapidly evolved.

• Early multicellular strains were composed of physiologically similar cells, but these subsequently evolved
higher rates of programmed cell death (apoptosis), an adaptation that increases propagule production.

• These results shows that key aspects of multicellular complexity,a subject of central importance to biology,
can readily evolve from unicellular eukaryotes.
Snowflake yeast clusters go from ~100 cells per cluster (left
tube) to nearly half a million cells per cluster (right tube)
 Designing evolution experiments.
● Scientists funded by NIH's National Cancer Institute (NCI) first developed
azidothymidine (AZT) in 1964 as a potential cancer therapy. AZT proved ineffective
against cancer and was shelved, but in the 1980s, it was included in an NCI screening
program to identify drugs to treat HIV/AIDS

● AZT interferes with an enzyme called reverse transcriptase (RT), which is used by HIV-
infected cells to make new viruses. Since AZT inhibits, or reduces the activity of this
enzyme, this drug causes HIV-infected cells to produce fewer viruses.

● Why Does HIV Therapy Using Just One Drug Ultimately Fail?

● AZT is incorporated by HIV’s reverse transcriptase into the viral DNA strand, where the
drug prevents the enzyme from adding more nucleotides. However, alterations in the
structure of reverse transcriptase can make viral replication less vulnerable to disruption.
• The Evolution of HIV Strains Resistant to Multiple Drugs Because HAART cannot eradicate HIV, the evolution
of strains resistant to multiple drugs is a constant threat for patients. Richard Harrigan and colleagues (2005)
followed 1,191 patients on HAART. By the end of three years, the HIV populations in 25% of the patients had
evolved resistance to at least one antiretroviral drug. The HIV populations in some patients were resistant to both
reverse transcriptase inhibitors and protease inhibitors.
• Highly active antiretroviral therapy (HAART) is a treatment regimen typically comprised of a combination of
three or more antiretroviral drugs. HAART may also be called antiretroviral therapy (ART) or combination
antiretroviral therapy (cART)
Evolution by Natural Selection The process we have described involves four steps:
1. Replication errors produce mutations in the reverse transcriptase gene. Virions carrying different reverse
transcriptase genes produce versions of the reverse transcriptase enzyme that vary in their resistance to AZT.
2. The mutant virions pass their reverse transcriptase genes, and thus their AZT resistance or susceptibility, to their
offspring. In other words, AZT resistance is heritable.
3. During treatment with AZT, some virions are better able to survive and reproduce than others.
4. The virions that persist in the presence of AZT are the ones with mutations in their reverse transcriptase genes
that confer resistance
Understanding Evolution Helps Researchers Design Better Therapies
Since AZT was introduced, the number of drugs approved for treatment of HIV has grown to over two dozen (De Clercq
2009). The categories of drugs in use, in order of the stage of HIV’s life cycle they are intended to disrupt, include •
Coreceptor inhibitors. These bar HIV from entering host cells in the first place by preventing them from latching onto the host
cell’s CCR5 molecules. • Fusion inhibitors. These bar HIV from entering host cells by interfering with HIV’s gp120 or gp41
proteins. • Reverse transcriptase inhibitors. Some, like AZT, inhibit reverse transcriptase by mimicking the normal building
blocks of DNA. Others inhibit reverse transcriptase by interfering with the enzyme’s active site. • Integrase inhibitors. These
block HIV’s integrase from inserting HIV’s DNA into the host genome, preventing the transcription of new viral RNAs. •
Protease inhibitors. These prevent HIV’s protease enzyme from cleaving viral precursor proteins to produce mature
components for new virions

Results like these have earned regimens including three or more drugs that block HIV in two or more different ways the
nickname highly active antiretroviral therapy, or HAART
 References:-
• LTEE
https://the-ltee.org/about/
https://lenski.mmg.msu.edu/ecoli/index.html
https://www.youtube.com/watch?v=w4sLAQvEH-M

• Multicellular experiment
The Origins Of Multicellular Life: Long-term Experimental Evolution In The Lab - Astrobiology
https://www.youtube.com/watch?v=5os_9gBV7-A

• Research Article-Experimental_Evolution_as_a_High-Throughput_Screen_for_Genetic_Adaptations.
• https://www.youtube.com/watch?v=CnWxn5y3jf0
• https://www.youtube.com/watch?v=U52g6ZlR1W0

• Books: Evolution analysis