Models of sequence evolution Chap. 4 Higgs and Attwood.

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Presentation transcript:

Models of sequence evolution Chap. 4 Higgs and Attwood

Nothing in biology makes sense except in the light of evolution (T. Dobzhansky) Evolution at the molecular level means mutations Mutations in the genetic material that are passed to the progeny (offspring) Divergent and convergent evolution… TERMINOLOGY 1.Locus (gene) 2.Alleles: variants at a locus 3.Polimorphisms: number of alleles in a population 4.Haploid(prokaryotic organisms)/Diploid (eukaryotic organisms) 5.Diploids have two copies of each locus (paired chromosomes) 6.Diploid individuals may be homozygous or eterozygous at a certain locus

TYPES OF MUTATIONS (A and G purines; C and T/U are pyrimidines) Causes of mutations: DNA damage, errors in the replication Transitions/ transversions

Part of the alignment of the DNA sequencees of the BRAC1 gene (fig.3.1)

Alignment of the Brca1 protein sequences from the same region of the gene as in fig. 3.1

BASIC CONCEPTS UP TO THIS POINT: HOMOLOGY, ORTHOLOGY, PARALOGY

“Family tree” of a gene over a population and its generations: time is the background elusive concept behind evolution

The accumulation of substitutions in two sequences descending from a common ancestor Q. Why evolutionary models? A.To infer d(A,B) from D(A,B) B.Through an evolutionary (probabilistic model) Note: D is not linear in time (see above) and is not Additive D 12  D 01 +D 02