Molecular Evolution And Softwares for Phylogenetic Construction

1. Molecular basis of evolution and
software used in phylogenetic tree
contruction
Udaykumar Pankajkumar Bhanushali
Exam no. 21807241

2. What is molecular evolution ?
At molecular level , evolution is a process of
mutation with selection.
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. 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

4. • 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

5. 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

6. • • Changes in gene products;
• – RNA
• – Proteins…polypeptide chains…amino acid
sequences

7. Studies began in 1950s with the first sequencing of protiens and
in 1967 first phylogenetic tree was developed by Fitch and
Margolish on the basis of molecular data .
Molecular Taxonomy: The classification of organisms on the
basis of distribution and composition of chemical substances in
them.
Molecular Phylogenetics: Study of evolutionary relationships
among biological entities ( individuals, population, species,
higher taxon) by using combition of molecular data and stastical
techniques.
• Phylogenetic studies assess historical processes which affects
relationship and phylogeographic studies assess the
geographical distributions.

8. Molecular Markers
Type 1
Markers are associated
with the gene of known
function.
Example: Alloenzyme
Type 2
Markers are associated
with the gene of unknown
function.
Example: Microsatellites

9. Alloenzyme
• Alloenzymes are varient forms of an enzyme which differ
structurally but not functionally from other alloenzymes
coded for different alleles at the same locus.
•These are common biological enzymes that exibit high levels
of functional evolutionary conservation throughout specific
phla and kingdoms.
• These are type 1 marker as the proteins , they encodes are
associated with some function.
• Alloenzyme electrophoresis is a method which can identify
genetic variation at the level of enzymes that can directly be
encoded by DNA.
• They are codominant markers have been expressed in a
heterozygous individual in a Mendelian ruler.

10. Microsatellites
• Microsatellites also known as Single sequence repeats.
• Microsatellites (1 to 10 nucleotides) are predominant
transposable elements, make up genomic repetitive regions.
• They are widely distributed throughout the genome, in
coding and non coding nuclear and organeller DNA.
• These are most widely used as markers for over past 20
years because they are highly informative , codominant ,
multi-allelic and are experimentally reproducible and
transferable among related species.
• These markers are enormously useful in studies of
population structure , genetic mapping , evolutionary
processes , core repeats of 3 to 5 nucleotides are preffered in
forensics and parentage analysis.

11. Objectives
1. Reconstruct the correct genealogical ties among
biological entities.
2. Estimate the time of divergence between biological
entities.
3. Chronicle the sequence of events along evolutionary
lineages.

12. • Due to molecular evolution we can construct
phylogenetic trees to know the evolutionary
distance and relationship between different
organisms.

13. Software used for Tree Construction
NAME BRIF DISCRIPTION METHODS
Ez Editor It allows manipulation of
both DNA and protein
sequence alingnment for
Phylogenetic analysis
• Neighbour-Joining
Method
BAli-Phy Simultaneous Bayesian
inference of alignment and
phylogeniy
• Bayesin infrance
alingnment
• Tree search
Clustal ω Peograssive multiple
sequence alingnment
• Distance matrix
• Nearest neighbor
Bayes Traits Analyses traits evolution
among group of species
• Trait analysis
fastDNAml Optimized maximum
likehood. (nucleotides
only)
• Maximum likelihood

14. Ez Editor
• EzEditor is a Java-based molecular sequence editor
allowing manipulation of both DNA and protein
sequence alignments for phylogenetic analysis.
• It provides various functionalities for editing rRNA
alignments using secondary structure information.
• In addition, it supports simultaneous editing of
both DNA sequences and their translated protein
sequences for protein-coding genes.

15. • EzEditor is the first sequence editing software
designed for both rRNA- and protein-coding
genes with the visualization of biologically
relevant information and should be useful in
molecular phylogenetic studies.
• EzEditor is based on Java, can be run on all
major computer operating systems and is
freely available from
• http://sw.ezbiocloud.net/ezeditor/

17. • EzEditor uses external software, such as
CLUSTAL W, for computer-assisted multiple
alignment.
• The edited alignment can be exported to
various types of phylogenetic software,
including MEGA , PHYLIP and PAUP.
• Various types of sequence data can be
imported into
• EzEditor, including data in the FASTA and
GenBank formats.

18. BAli-Phy
• BAli-Phy simultaneously estimates the alignment and
phylogenetic tree that relate molecular sequences.
• BAli-Phy employs a Metropoliswithin-Gibbs approach.
• BAli-Phy also contains a number of tools to summarize
the joint
• posterior samples. The most important among these is
Alignmentgild that produces alignment uncertainty plots.

19. • We distribute BAli-Phy as C++ source code and
precompiled binaries.
• BAli-Phy should run on all hardware with a
modern operating system such as Linux,
Windows or Mac OS X.

21. • The model employs standard continuous-time
Markov chain (CTMC) processes to describe
residue substitution along the branches of an
unknown tree relating the sequences.

22. Clustal ω
• Multiple alignments of protein sequences are important
tools in studying sequences.
• Sequences can be aligned across their entire length
(global alignment) or only in certain regions (local
alignment). This is true for pairwise and multiple
alignments.
• Global alignments need to use gaps (representing
insertions/deletions) while local alignments can avoid
them, aligning regions between gaps.

23. • ClustalW is a fully automatic program for
global multiple alignment of DNA and protein
sequences.
• 'Trees can also be calculated from multiple
alignments.' The program has some adjustable
parameters with reasonable defaults.
• https://www.ebi.ac.uk/Tools/msa/clustalo/

25. Bayes Traits
• BayesTraits is a computer package for
performing analyses of trait evolution among
groups of species for which a phylogeny or
sample of phylogenies is available.
• BayesTraits can be applied to the analysis of
traits that adopt a finite number of discrete
states, or to the analysis of continuously
varying traits.

26. • Hypotheses can be tested about models of
evolution, about ancestral states and about
correlations among pairs of traits.

28. fastDNAml
• fastDNAml estimates maximum likelihood
phylogenetic trees from nucleotide
sequences.
• fastDNAml uses a maximum likelihood
approach and is based on Felsenstein's dnaml
program.
• It has been used to develop an initial version
of the phylogenetic tree of prokaryotic
microorganisms based on the rRNA alignment.

29. • The tool provides a rapid estimate of the
location at which to insert a new sequence
into the growing tree.
• Link:-
https://www.gnu.msn.by/directory/science/Bi
ology/fastDNAml.html

30. Applications of Molecular evolution
• 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...)

31. REFERENCES
• Bioinformatics and Molecular Evolution Paul G. Higgs and
Teresa K. Attword
• Bioinformatics for Beginners:- Genes, Molecular Evolution,
Dadabases and Analytical Tools by Supratim Choudhuri.
• Cunningham, C. 1999. Some limitations of ancestral character-
state reconstruction when testing evolutionary hypotheses.
Syst. Biol. 48:665–674.
• BoyleJ., Butler.R., Disz.T., Glickfeld.B., Lusk.E.L., Overbeek.R.A.,

32. • Bininda-Emonds, O. R. (2005). transAlign: using amino acids to
facilitate the multiple alignment of protein-coding DNA
sequences. BMC Bioinformatics 6, 156.
• Brown,J. and Doolittle,W. (1997) Archaea and the prokaryote-to-
eukaryote transition. Microbiol. Mol. Biol. Rev., 61, 456–502.
• PattersonJ. and Stevens, R. (1987) Portable Programs for Parallel
Processors. Holt, Rinehart, and Winston, New York.
• https://www.ebi.ac.uk/seqdb/confluence/pages/viewpage.actio
n?pageId=54646458

33. THANK YOU