Chapter !5 - Evolution and Genomic Change Code: KSI0014

<Index of Chapter 5>

Evolution is exploration

Industrial melanism and its reversal. (Moth example)

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

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

 

Biological systematics

Study of the vast variety of living organisms requires that we organize what we observe and measure. 

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

Biological nomenclature

Measurement of biological similarities and differences 

-In order ti develop a clear picture of the relationships between species, it's necessary to pick  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. 

 

Homogoues and families

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. 

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.

 

Pattern matching - the basic tool of bioinformatics

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. 

 

Sequence alignment

- Given two or more sequences, we wish to

1. Measure their similarity

2. Understand how the residues match up

3. Observe patterns of conservation and variability 

4. infer evolutionary relationships. 

 

The dot plot is a simple picture that gives an overview of pairwise sequence similairity. 

Dot plots and alignments 

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  right.

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. 

Local alignment is a pattern - matching technique for identifying a match for a short probe sequence within a much longer text. 

A very  important extension of pairwise sequence alignment is multiple sequence alignment, the mutal alignment of three or more sequences. 

 

Definining the optimum alignment

Hamming / transition / transversion / The BLOSUM matrices / gap weighting / 

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

 

 

Approximate methods for quick screening of databases

Multiple sequence alignments and pattern detection. 

Profile

hidden markov models 

BLAST search different databases

- BLASTN / BLASTX ./ BLASTP / TBLASTN / TBLASTX 

A multiple matching in 3D structures 

 

Pattern matching in three-dimensional structures

Extraction of the maximum common substructure induces an alignment of the sequences. This is called a structural alignment. 

A srructural alignment is nevertheless an alignment = an assignment of residue-residue  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. 

 

Evolution of protein sequences, structures, and functions

The effects of single-site mutations

- 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. 

Evolution of protein structure and function

 

Phylogeny

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. 

Homology/ Similiarity/ similarity and dissimilarity  / Clustering / Groupers / splitters/ Hierarchical clustering / classification / phylogeny/ 

 

Phylogenetic trees

Evolutionary tree // root 

Clustering methods

Cladistic methods

The problem of varying rates of evolution

Batesiian methods

 

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. 

 

Maximum parsimony and maximum likelihood. 

 

Short-circuiting evolution : Genetic engineering