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Semelhante a Molecular basis of evolution and softwares used in phylogenetic tree contruction
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Molecular basis of evolution and softwares used in phylogenetic tree contruction
- 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