Molecular evolution, four class of chromosomal mutation, Negative Selection and Positive Selection, Mutations in DNA and protein, Neutral Theory of Molecular Evolution, Evidence supporting neutral evolution, Phylogenetic trees, Methods of Tree reconstruction
Cell cell hybridization or somatic cell hybridizationSubhradeep sarkar
What is Cell-Cell Hybridization?
History
More about Somatic cell Hybridization
Mapping of genes by somatic cell Hybridization
Hybridoma technology
Other Applications of Somatic Cell Hybridization
Cell cell hybridization or somatic cell hybridizationSubhradeep sarkar
What is Cell-Cell Hybridization?
History
More about Somatic cell Hybridization
Mapping of genes by somatic cell Hybridization
Hybridoma technology
Other Applications of Somatic Cell Hybridization
This presentation entitled 'Molecular phylogenetics and its application' deals with all the developmental ideas and basics in the field of bioinformatics.
To determine the variation and the limitation between species, many concepts have been proposed.
When a taxonomist study a particular taxa, he/she must adopted a species concept and provide a species limitation to define this taxa.
Plant kingdom as other living kingdoms has a hierarchy structure ends mostly with species rank.
Species are one of the basic units to compare in almost all fields of biology.
A species is defined as the largest group of organisms in which two individuals are capable of reproducing fertile offspring, typically using sexual reproduction.
Definition of a species as a group of interbreeding individuals cannot be easily applied to organisms that reproduce only or mainly asexually.
If two lineages of oak look quite different, but occasionally form hybrids with each other, should we count them as different species?
Idea of a species is something that we humans invented for our own convenience.
‘‘No matter what variations occur in the individuals or the species, if they spring from the seed of one and the same plant, they are accidental variations and not such as distinguish a species permanently; one species never springs from the seed of another nor vice versa” - JOHN RAY.
Used a sexual system ‘‘natural system” for defining species - LINNAEUS.
‘‘A species is a collection of all the individuals which resemble each other more than they resemble anything else, which can by natural fecundation produce fertile individuals, and which reproduce themselves by generation, in such a manner that we may from analogy suppose them all to have sprung from one single individual” - DE CANDOLLE.
A brief description on Molecular Evolution, Kimura's theory of Molecular evolution, Neutral theory vs. Natural Selection, Neutral theory: The Null Hypothesis of Molecular Evolution
Changes in the nucleotide sequence of DNA
May occur in somatic cells (aren’t passed to offspring)
May occur in gametes (eggs & sperm) and be passed to offspring
Changes in the nucleotide sequence of DNA
May occur in somatic cells (aren’t passed to offspring)
May occur in gametes (eggs & sperm) and be passed to offspring
Changes in the nucleotide sequence of DNA
May occur in somatic cells (aren’t passed to offspring)
May occur in gametes (eggs & sperm) and be passed to offspring
Mutations happen regularly
Almost all mutations are neutral
Chemicals & UV radiation cause mutations
Many mutations are repaired by enzymes
Some type of skin cancers and leukemia result from somatic mutations
Some mutations may improve an organism’s survival (beneficial)
chromosome mutations=
Five types exist:
Deletion
Inversion
Translocation
Nondisjunction
Duplication
This presentation entitled 'Molecular phylogenetics and its application' deals with all the developmental ideas and basics in the field of bioinformatics.
To determine the variation and the limitation between species, many concepts have been proposed.
When a taxonomist study a particular taxa, he/she must adopted a species concept and provide a species limitation to define this taxa.
Plant kingdom as other living kingdoms has a hierarchy structure ends mostly with species rank.
Species are one of the basic units to compare in almost all fields of biology.
A species is defined as the largest group of organisms in which two individuals are capable of reproducing fertile offspring, typically using sexual reproduction.
Definition of a species as a group of interbreeding individuals cannot be easily applied to organisms that reproduce only or mainly asexually.
If two lineages of oak look quite different, but occasionally form hybrids with each other, should we count them as different species?
Idea of a species is something that we humans invented for our own convenience.
‘‘No matter what variations occur in the individuals or the species, if they spring from the seed of one and the same plant, they are accidental variations and not such as distinguish a species permanently; one species never springs from the seed of another nor vice versa” - JOHN RAY.
Used a sexual system ‘‘natural system” for defining species - LINNAEUS.
‘‘A species is a collection of all the individuals which resemble each other more than they resemble anything else, which can by natural fecundation produce fertile individuals, and which reproduce themselves by generation, in such a manner that we may from analogy suppose them all to have sprung from one single individual” - DE CANDOLLE.
A brief description on Molecular Evolution, Kimura's theory of Molecular evolution, Neutral theory vs. Natural Selection, Neutral theory: The Null Hypothesis of Molecular Evolution
Changes in the nucleotide sequence of DNA
May occur in somatic cells (aren’t passed to offspring)
May occur in gametes (eggs & sperm) and be passed to offspring
Changes in the nucleotide sequence of DNA
May occur in somatic cells (aren’t passed to offspring)
May occur in gametes (eggs & sperm) and be passed to offspring
Changes in the nucleotide sequence of DNA
May occur in somatic cells (aren’t passed to offspring)
May occur in gametes (eggs & sperm) and be passed to offspring
Mutations happen regularly
Almost all mutations are neutral
Chemicals & UV radiation cause mutations
Many mutations are repaired by enzymes
Some type of skin cancers and leukemia result from somatic mutations
Some mutations may improve an organism’s survival (beneficial)
chromosome mutations=
Five types exist:
Deletion
Inversion
Translocation
Nondisjunction
Duplication
Trends in evolution :- synopsis :- 1. INTRODUCTION
( DEFINITION OF EVOLUTION)
2.TRENDS IN EVOLUTION
3. DEFINITION OF MOLECULAR EVOLUTION
4.GENE EVOLUTION
*Mutation
*Horizontal gene transfer
*Sexual reproduction
5.EVOLUTION OF GENE FAMILIES
(Kind of gene families)
For more you can refer to www.faunafondness.com
Long-lasting alterations to DNA methylation and ncRNAs could underlie the eff...Ben Laufer
Fetal alcohol spectrum disorders (FASDs) are characterized by life-long changes in gene expression, neurodevelopment and behavior. What mechanisms initiate and maintain these changes are not known, but current research suggests a role for alcohol-induced epigenetic changes. We assessed alterations to adult mouse brain tissue by assaying DNA cytosine methylation and small noncoding RNA (ncRNA) expression, specifically the microRNA (miRNA) and small nucleolar RNA (snoRNA) subtypes. We found long-lasting alterations in DNA methylation as a result of fetal alcohol exposure, specifically in the imprinted regions of the genome harboring ncRNAs and sequences interacting with regulatory proteins. The findings of this study help to expand on the mechanisms behind the long-lasting changes in the brain transcriptome of FASD individuals.
Webinar Link: http://www.youtube.com/watch?v=fzdc0GIdCnA
Introduction to Modern Biosystemaics for Fungal ClassificationMrinal Vashisth
This is a more specific version of the slide-set "Major Characteristics Used in Microbial Classification". A presentation I could not deliver for some reasons yet turned out to be pretty nice. I hope to deliver it some day, but for the time being I am making it public. I hope it would be of some use. :)
Mutation Repair and DNA Replication.pptxhamzalatif40
In this Presentation Chapter 7 & 8 from the book Advanced Molecular Biology are discussed. Focus has been given to the mutation, its types, mutation repair, Different Repairing mechanisms and DNA Replication is explained with details.
Pharmacogenomics is new science about how the systematic identification of all the human genes, their products, interindividual variation, intraindividual variation in expression and function over time affects drug response/metabolism, etc.
Improve drug safety and reduce ADRs. The presentation explained the advantages of pharmacogenomics. Explained Goals of Pharmacogen(etics)omics.
This presentation represents the Genetic use restriction technology (GURT), also known as terminator technology. This presentation explain the advantages and impact of terminator technology.
it helps to known about ELISA ,it is one of the technique,, its type , its benefits & disadvantages , it also help to known about antigen,antidody, immunity etc
IT HELPS TO KNOWN ABOUT DIFFERENT TYPES OF TRANSPLANTATION AND ALSO ABOUT DONOR TYPES , THIS PPT HELPS TO UNDERSTAND BRIEFLY ABOUT TRANSPLANTATION IN HUMAN OR ANY OTHER LIVING ORGANISMS.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
This pdf is about the Schizophrenia.
For more details visit on YouTube; @SELF-EXPLANATORY;
https://www.youtube.com/channel/UCAiarMZDNhe1A3Rnpr_WkzA/videos
Thanks...!
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...Scintica Instrumentation
Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
Multi-source connectivity as the driver of solar wind variability in the heli...Sérgio Sacani
The ambient solar wind that flls the heliosphere originates from multiple
sources in the solar corona and is highly structured. It is often described
as high-speed, relatively homogeneous, plasma streams from coronal
holes and slow-speed, highly variable, streams whose source regions are
under debate. A key goal of ESA/NASA’s Solar Orbiter mission is to identify
solar wind sources and understand what drives the complexity seen in the
heliosphere. By combining magnetic feld modelling and spectroscopic
techniques with high-resolution observations and measurements, we show
that the solar wind variability detected in situ by Solar Orbiter in March
2022 is driven by spatio-temporal changes in the magnetic connectivity to
multiple sources in the solar atmosphere. The magnetic feld footpoints
connected to the spacecraft moved from the boundaries of a coronal hole
to one active region (12961) and then across to another region (12957). This
is refected in the in situ measurements, which show the transition from fast
to highly Alfvénic then to slow solar wind that is disrupted by the arrival of
a coronal mass ejection. Our results describe solar wind variability at 0.5 au
but are applicable to near-Earth observatories.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
2. What is Molecular Evolution ?
Molecular evolution address two broad range of
questions:
• 1. Use DNA to study the evolution of organisms,
e.g. population structure, geographic variation
and phylogeny
• 2. Use different organisms to study the evolution
process of DNA
3. •The increasing available completely sequenced
organisms and the importance of evolutionary
processes that affect the species history, have stressed
the interest in studying the molecular evolution events
at the sequence level.
Molecular evolution
4. Molecular evolution
GACGACCATAGACCAGCATAG
GACTACCATAGA-CTGCAAAG
•Mutations arise due to inheritable changes in
genomic DNA sequence;
•Mechanisms which govern changes at the
protein level are most likely due to nucleotide
substitution or insertions/deletions;
•Changes may give rise to new genes which
become fixed if they give the organism an
advantage in selection;
5. A brief historical perspective
• Darwin first came up with the idea that
living organisms are evolutionarily related
• Molecular evolution became a science
following discovery of DNA and crack of
genetic code
• Insulin: first protein sequenced (Sanger,
1955), and sequence compared across
species.
• Neutral theory: Motoo Kimura, Thomas
Jukes (1968,69)
• Effect of population size: Michael Lynch
(2000s)
6.
7. • In 1961, Ernst Mayr argued for a clear distinction
between two “distinct and complementary” pillars of
biology:
• Functional biology, which considered proximate causes
and asked "how" questions;
• Evolutionary biology, which considered ultimate
causes and asked "why" questions;
• This reflects a “culture change” in biology after the
emergence of molecular biology and biochemistry. It
was in that context that Dobzhansky first wrote in 1964,
"nothing in biology makes sense except in the light of
evolution”.
Functional versus Evolutionary biology:
“The molecular war”
8. Similar statements …
• “Nothing in Evolution Makes Sense Except in the
Light of Biology”
• “Nothing in Evolution Makes Sense Except in the
Light of Domestication”
• “Nothing in Evolution Makes Sense Except in the
Light of Population Genetics (in relation to
population size)” – Michael Lynch
9. Mutations in DNA and protein
• Synonymous mutation -> do not change amino acid
• Nonsynonymous mutation -> change amino acid
• Nonsense mutation: point mutation resulting in a pre-mature stop
codon
• Missense mutation: resulting in a different amino acid
• Frameshift mutation: insertion / deletion of 1 or 2 nucleotides
• Silent mutation: the same as nonsynonymous mutation
• Neutral mutation: mutation has no fitness effects, invisible to
evolution (neutrality usually hard to confirm)
• Deleterious mutation: has detrimental fitness effect
• Beneficial mutation:
Fitness = ability to survive and reproduce
10. Consider molecular evolutionary changes
at two levels
• Changes in DNA;
– Point mutation; mutations of single genes; small alterations
in sequence or number of nucleotides
– Chromsomal mutations; alterations that are more extensive
than point mutations; four types – deletions duplications,
inversions, translocations
– scope extends from point mutations in introns or exons, to
changes in the size and composition of genomes
• Changes in gene products;
– RNA
– Proteins…polypeptide chains…amino acid sequences
12. Degeneracy of genetic code
•Because there are only 20 amino acids, but 64 possible codons, the same amino
acid is often encoded by a number of different codons, which usually differ in the
third base of the triplet.
•Because of this repetition the genetic code is said to be degenerate and codons
which produce the same amino acid are called synonymous codons.
13.
14. Negative Selection and Positive Selection
• Negative selection (purifying selection)
– Selective removal of deleterious mutations (alleles)
– Result in conservation of functionally important amino acids
– Examples: ribosomal proteins, RNA polymerase, histones
• Positive selection (adaptive selection, Darwinian selection)
– Increase the frequency of beneficial mutations (alleles) that
increase fitness (success in reproduction)
– Examples: male seminal proteins involved in sperm competition,
membrane receptors on the surface of innate immune system
– Classic examples: Darwin’s finch, rock pocket mice in Arizona
(however the expression level of these genes instead of their
protein sequence are targeted by selection)
15. Nature 2006
“They show that calmodulin
(CaM), a molecule involved in
mediating Ca2+ signalling, is
expressed at higher levels in the
long and pointed beaks of cactus
finches than in more robust beak
types of other species.”
17. Purifying (negative) Selection
Ka / Ks
= Non-synonymous / Synonymous substitutions
= 0
Seq1
Seq2
AAG
AAA
ACT
ACA
GCC
GCA
GGG
GGA
CGT
CGA
ATT
ATC
Seq1 K T A G R I
Seq2 K T A G R I
# Synonymous substitutions = 6
# Non-synonymous substitutions = 0
18. Neutral Selection
Ka / Ks
= Non-synonymous/Synonymous substitutions
= 1
# Synonymous substitutions = 3
# Non-synonymous substitutions = 3
Seq1
Seq2
AAG
AAA
ACT
ACA
GCC
GAC
GGG
GGA
CGT
CAT
ATT
ATG
Seq1 K T A G R I
Seq2 K T D G H M
19. Positive Selection
Ka / Ks
= Non-synonymous/Synonymous substitutions
=5
# Synonymous substitutions = 1
# Non-synonymous substitutions = 5
Seq1
Seq2
AAG
AAA
ACT
ATT
GCC
GAC
GGG
GAG
CGT
CAT
ATT
ATG
Seq1 K T A G R I
Seq2 K I D E H M
20. Synonymous substitutions are NOT
always neutral
Different codons for the same amino acid may have different
functional constraints and fitness effects
• Translational efficiency: codon usage bias
• RNA stability and correct folding of secondary structures
• RNA editing
• Protein folding
• Exon splicing regulatory motifs
• Binding sites for microRNA and RNA binding proteins (RBP)
24. The Neutral Theory of Molecular Evolution
• Motoo Kimura advanced the Neutral Theory of Molecular Evolution
in 1968. Two observations underlie the theory
• 1. Most natural populations harbor high levels of genetic variation
higher than would be expected if natural selection were the
evolutionary force primarily responsible for influencing the level of
genetic variation in populations
• 2. Many mutations in sequences of genes do not alter the proteins
encoded by those genes
• virtually always true for synonomous substitutions
• sometimes true for non-synonomous substitutions
• If protein function is not altered by a mutation, the allelic variant
that results from that mutation is unlikely to be influenced by
natural selection…
25. The Neutral Theory of Molecular Evolution
The Neutral Theory holds that, because most mutations are selectively
neutral at the molecular level..
•the majority of evolutionary change that macromolecules undergo
results from random genetic drift
•much of the variation within species results from random genetic
drift (variation in the relative frequency of different genotypes in a
small population, owing to the chance disappearance of particular
genes as individuals die or do not reproduce).
•Kimura developed a mathematical model showing that the rates at
which neutral substitutions accumulate is a function of the mutation
rate (not to selection forces)
•by this theory, levels of molecular variation in genomes are strongly
influenced by a balance between mutation, which generates variations,
and genetic drift, which can eliminate it.
26. Neutral theory of evolution
• Using sequence data of hemoglobin, insulin, cytochrome c from
many vertebrates, Motoo Kimura calculated on average sequence
evolution in mammals had been very rapid: 1 amino acid
change every 1.8 years
• Such a high mutation frequency suggest the majority of
substitutions have no fitness effects, i.e. selectively neutral, and
are created by genetic drift.
• Rate of molecular evolution is equal to the neutral mutation rate,
this gives rise to the concept of “molecular clock”
27. “The Neutralist-Selectionist debate”
• Agree:
– Most mutations are deleterious and are removed.
– Some mutations are favourable and are fixed.
• Neutral theory
– Advantageous (adaptive) mutations are very rare
– Most of the amino acid changes and polymorphisms are
neutral, and created by genetic drift.
– The concept of Molecular clock
• Selectionist theory
– Advantageous mutations are more common
– Molecular evolution will are dominated by selection
– No Molecular clock
28. Evidence supporting neutral evolution
• Pseudogenes (dead genes that have no function and no fitness
effect) evolve very fast.
• Synonymous codon positions (3-fold, 4-fold degenerate sites)
evolve faster than non-synonymous sites, and should evolve with
a constant rate. (not always true, see previous slides)
• Genes that have important functions should evolve slower.
29. Evidence for Rate Constancy
in Hemoglobin
Page and Holmes
p229
Large carniverous
marsupial
30. The
Molecular Clock
Hypothesis
• The molecular clock is figurative term for a technique
that uses the mutation rate of biomolecules to deduce
the time in prehistory when two or more life
forms diverged.
• Amount of genetic difference between sequences is a
function of time since separation.
• Rate of molecular change is constant (enough) to
predict times of divergence
• It is sometimes called a gene clock or an evolutionary
clock.
31. Outline
• Methods for estimating time under a molecular clock
– Estimating genetic distance
– Determining and using calibration points
– Sources of error
• Rate heterogeneity
– reasons for variation
– how its taken into account when estimating times
• Reliability of time estimates
• Estimating gene duplication times
32. Measuring Evolutionary time with a
molecular clock
1. Estimate genetic distance
d = number amino acid replacements
2. Use paleontological data to determine date of
common ancestor
T = time since divergence
3. Estimate calibration rate (number of genetic
changes expected per unit time)
r = d / 2T
4. Calculate time of divergence for novel sequences
T= d/ 2r
33. Five factors combine to limit the
application of molecular clock models:
• Changing generation times (If the rate of new mutations
depends at least partly on the number of generations
rather than the number of years)
• Population size (Genetic drift is stronger in small
populations, and so more mutations are effectively neutral)
• Species-specific differences (due to differing metabolism,
ecology, evolutionary history, ...)
• Change in function of the protein studied (can be avoided
in closely related species by utilizing non-coding
DNA sequences or emphasizing silent mutations)
• Changes in the intensity of natural selection.
34. Applying a Molecular Clock: The Origin
of HIV
• Phylogenetic analysis shows that HIV is descended
from viruses that infect chimpanzees and other
primates
• HIV spread to humans more than once
• Comparison of HIV samples shows that the virus
evolved in a very clocklike way
• Application of a molecular clock to one strain of HIV
suggests that that strain spread to humans during the
1930s
35. Genome Evolution
• Orthologous genes are widespread and extend across many
widely varied species
– For example, humans and mice diverged about 65 million
years ago, and 99% of our genes are orthologous
• Gene number and the complexity of an organism are not
strongly linked
– For example, humans have only four times as many genes as
yeast, a single-celled eukaryote
• Genes in complex organisms appear to be very versatile,
and each gene can perform many functions
36. Phylogenetic trees
• Phylogeny is the evolutionary history of a
species or group of related species
• Taxonomy is the ordered division and naming
of organisms
• A taxonomic unit at any level of hierarchy is
called a taxon
• Systematists depict evolutionary relationships
in branching phylogenetic trees
• A phylogenetic tree represents a hypothesis
about evolutionary relationships
37. • Each branch point represents the divergence of
two species
• Sister taxa are groups that share an immediate
common ancestor
• A rooted tree includes a branch to represent the
last common ancestor of all taxa in the tree
• A basal taxon diverges early in the history of a
group and originates near the common ancestor
of the group
• A polytomy is a branch from which more than
two groups emerge
38. Branch point:
where lineages diverge
ANCESTRAL
LINEAGE
This branch point
represents the
common ancestor of
taxa A–G.
This branch point forms a
polytomy: an unresolved
pattern of divergence.
Sister
taxa
Basal
taxon
Taxon A
Taxon B
Taxon C
Taxon D
Taxon E
Taxon F
Taxon G
39. Phylogenetic analysis using DNA sequence
Human
Chimp
Gorilla
Orangutan
Gibbon
Traditional
Human
Chimp
Gorilla
Orangutan
Gibbon
Molecular
40. • Phylogenetic inference or “tree building”:
– To infer the branching orders and lengths between “taxa” ( or
genes, populations, species etc).
– For example, can DNA tell us giant panda more similar to
bear or to dog, and when did they diverge ?
• Character and rate analysis:
– Using phylogeny as a framework to understand the evolution
of traits or genes.
– For example, is gene X under positive or
purifying selection ?
Two Areas in Phylogenetic analysis
42. Methods of Tree reconstruction
• Maximum Parsimony methods
• Distance based methods
• Maximum Likelihood methods
• Bayesian methods
(Don’t worry, there are software programs that
are easy and fun to use)
43. Parsimony Methods
• Optimality criterion: The “most-parsimonious” tree is the one that requires
the fewest number of evolutionary events (e.g. nucleotide substitutions,
amino acid replacements) to explain the observed sequences.
• Advantages:
– Intuitive, logical and simple (can be done with pencil-and paper)
– Can be used on molecular and other (morphological, language) data.
– Can be used to infer the sequences of extinct (hypothetical) ancestors
• Disadvantages
– Can be fooled by high levels of homoplasy (“same events”)
– Can be problematic when the real tree is mixed with very short and long
branches, e.g. long-branch attraction
45. • Estimate the number of substitutions between each pair of
sequences in a group of sequences.
• Try to build a tree so that the branch lengths represent the pair-
distances.
• What are these “distances” ? Example: sequence identity
between two protein and DNA sequences
Distance based methods
46. What distance to use ?
Cat ATTTGCGGTA
Dog ATCTGCGATA
Rat ATTGCCGTTT
Cow TTCGCTGTTT
Number of
different
nucleotide
s
?
•The observed differences do not always
represent the actual evolutionary events that
occurred, e.g. multiple substitutions at the
same site.
•Substitution rates are different between
different types of nucleotides
Distance based methods
47. Applications:
Molecular evolution analysis has clarified:
•the evolutionary relationships between humans and
other primates;
•the origins of AIDS;
•the origin of modern humans and population migration;
•speciation events;
•genetic material exchange between species.
•origin of some deseases (cancer, etc...)
Molecular evolution