View source for Chapter !5 - Evolution and Genomic Change Code: KSI0014

<p style="text-align:center"><span style="font-size:36px"><strong>&lt;Index of Chapter 5&gt;</strong></span></p>

<p><span style="color:#0000CD"><strong>Evolution is exploration</strong></span></p>

<p>Industrial melanism and its reversal. (Moth example)</p>

<p>The two elements of exploration - variation from the current state of the system and change to a new one - occur at many levels from individual genomes to proteins to cells to ecosystems</p>

<p>A long-standing challenge of biology is to understand the relationships among these different levels of evolution.</p>

<p>&nbsp;</p>

<p><span style="color:#0000CD"><strong>Biological systematics</strong></span></p>

<p>Study of the vast variety of living organisms requires that we organize what we observe and measure.&nbsp;</p>

<p>We have to agree on what we call things. Biological taxonomy encompaseses identifying new life forms, deciding where they fit in, and assigning them a name</p>

<p>Biological nomenclature</p>

<p>Measurement of biological similarities and differences&nbsp;</p>

<p>-In order ti develop a clear picture of the relationships between species, it&#39;s necessary to pick &nbsp;a molecule that is changing at a reasonable rate. There must e enough change such that the signal does not sink below the noise level, but not too much change as to obscure common features.&nbsp;</p>

<p>&nbsp;</p>

<p><span style="color:#0000CD"><strong>Homogoues and families</strong></span></p>

<p>Products of evolution retain similarities. The similarities appear at many levels- related people, recently diverged species, tissues within an organism containing related cell types but varying protein expression patterns, amino acid sequences and structures of proteins and DNA sequences.&nbsp;</p>

<p>To trace the course of evolution, we must quantitatively measure such similarities. There are many possible objects of such analysis -sequences of individual genes, full-genome sequences, sequences and structures of proteins , anatomical features, apatterns of development and any other phenotypic character one might choose.</p>

<p>&nbsp;</p>

<p><span style="color:#0000CD"><strong>Pattern matching - the basic tool of bioinformatics</strong></span></p>

<p>To measure similarity between two sequences, find their optimal alignment - the best matching up of the individual characters and produce a cumulative score of the similarites between the characters at each position.&nbsp;</p>

<p>&nbsp;</p>

<p>Sequence alignment</p>

<p>- Given two or more sequences, we wish to</p>

<p>1. Measure their similarity</p>

<p>2. Understand how the residues match up</p>

<p>3. Observe patterns of conservation and variability&nbsp;</p>

<p>4. infer evolutionary relationships.&nbsp;</p>

<p>&nbsp;</p>

<p>The dot plot is a simple picture that gives an overview of pairwise sequence similairity.&nbsp;</p>

<p>Dot plots and alignments&nbsp;</p>

<p>A dot plot shows perspicuously the quality and distribution of the pattern of similarity between two sequences. Each possible alignment of the two sequences corresponds to a path through the dotplot, from upper left to lower &nbsp;right.</p>

<p>Global alignment assigns correspondences to all residues in the sequences. If one sequence is shorter than the other, the difference in length must be made up by insertions/ deletions.&nbsp;</p>

<p>Local alignment is a pattern - matching technique for identifying a match for a short probe sequence within a much longer text.&nbsp;</p>

<p>A very &nbsp;important extension of pairwise sequence alignment is multiple sequence alignment, the mutal alignment of three or more sequences.&nbsp;</p>

<p>&nbsp;</p>

<p>Definining the optimum alignment</p>

<p>Hamming / transition / transversion / The BLOSUM matrices / gap weighting /&nbsp;</p>

<p>To define optimal alignment, we must assign scores for each possible substitution and corresponding scores for gap initiation and extension .</p>

<p>&nbsp;</p>

<p>&nbsp;</p>

<p>Approximate methods for quick screening of databases</p>

<p>Multiple sequence alignments and pattern detection.&nbsp;</p>

<p>Profile</p>

<p>hidden markov models&nbsp;</p>

<p>BLAST search different databases</p>

<p>- BLASTN / BLASTX ./ BLASTP / TBLASTN / TBLASTX&nbsp;</p>

<p>A multiple matching in 3D structures&nbsp;</p>

<p>&nbsp;</p>

<p>Pattern matching in three-dimensional structures</p>

<p>Extraction of the maximum common substructure induces an alignment of the sequences. This is called a structural alignment.&nbsp;</p>

<p>A srructural alignment is nevertheless an alignment = an assignment of residue-residue &nbsp;correspondences. Instead of assigning the correspondence by matching the chracters in two or more sequences, a structural alignment assigns the correspondence to residues that occupy similar positions in space, relative to the molecular framework.&nbsp;</p>

<p>&nbsp;</p>

<p><span style="color:#0000CD"><strong>E</strong></span><span style="color:#0000CD"><strong>volution of protein sequences, structures, and functions</strong></span></p>

<p>The effects of single-site mutations</p>

<p>- A sequence that so lacked robsutness that nay mutation would destroy it, could not exist. It could have no neighboring precursor and processes of evolution could never find its sequence.&nbsp;</p>

<p>Evolution of protein structure and function</p>

<p>&nbsp;</p>

<p><span style="color:#0000CD"><strong>Phylogeny</strong></span></p>

<p>A phylogenetic tree is a diagram showing ancestor- descendant relationships, that captures a pattern of similarities, in that individuals or species closely linked in the tree have high similarity.&nbsp;</p>

<p>Homology/ Similiarity/ similarity and dissimilarity &nbsp;/ Clustering / Groupers / splitters/ Hierarchical clustering / classification / phylogeny/&nbsp;</p>

<p>&nbsp;</p>

<p>Phylogenetic trees</p>

<p>Evolutionary tree // root&nbsp;</p>

<p>Clustering methods</p>

<p>Cladistic methods</p>

<p>The problem of varying rates of evolution</p>

<p>Batesiian methods</p>

<p>&nbsp;</p>

<p>The idea of phylogeny is to observe different degrees of similarity among species or higher taxa, assume that the species are related by descent from a common ancestor and that higher degress of similarity correspond to closer relationships, and to try to capture the relationships in a tree diagram showing ancestor - descendant relationships such that species more closely related according to the tree do have higher degrees of similarity.&nbsp;</p>

<p>&nbsp;</p>

<p>Maximum parsimony and maximum likelihood.&nbsp;</p>

<p>&nbsp;</p>

<p><span style="color:#0000CD"><strong>Short-circuiting evolution : Genetic engineering</strong></span></p>

<p>&nbsp;</p>