MSA & Phylogenetic Tree Anlysis

Tools in MSA

• similarity among individuals or species • a species is split into two or more species that do not crossbreed

● Study of evolutionary history of living organisms ● Study of speciation

• attempts to determine the rates and patterns of change occurring in DNA and proteins • reconstructs the evolutionary history of genes and organisms

Why use protein sequences or DNA in phylogenetic analysis?

• Genomes of most organisms do not have a simple origin • There is horizontal transfer of genetic material between species (through virus, DNA transformation).

tandem copies of a gene

• introduced in most sequence alignment • may represent mutational changes in the sequences

Gene and protein evolution often involve the comparison of ____

Sequences that share an arbitrary level of similarity determined by alignment of matching bases

• produced by speciation • directly derived from a common ancestral locus

• produced by gene duplication • derived from a common ancestral gene, duplicated within an organism and diverged • tend to have different functions

result from the horizontal transfer of a gene between two organisms

visual representation of evolutionary relationships among organisms or among genes

the common ancestor of all taxa

represents a taxonomic unit

defines the relationship of the taxa in terms of descent and ancestry

represents the number of changes that have occurred in the branch

branching patterns of the tree

a group or more of two or more taxa or sequences that includes both their common ancestor and all their descendants

all the sequences under study have a common ancestor from which a unique evolutionary path leads to all other nodes

does not assume knowledge of a common ancestor