Why phylogenetic reconstruction of molecular evolution?
e.g.: Who were the first angiosperms? (i.e. where are the first angiosperms
to present day angiosperms?)
Where in the tree of life is the last common ancestor located?
e.g.: domain shuffling, reassignment of function, gene duplications, horizontal gene transfer, drug targets, detection of genes that drive evolution of a species/population (e.g. influenca virus, see here for more examples)
1) Obtain sequences
Databank Searches -> ncbi a) entrez, b) BLAST, c) blast of pre-release data
2) Determine homology (see notes for homology assessment for practical implementation)
Homology: Two sequences are homologous, if there existed an ancestral molecule in the past that is ancestral to both of the sequences
Types of homology:
Orthology: bifurcation in molecular tree reflects speciation
Paralogy: bifurcation in molecular tree reflects gene duplication
Xenology: gene was obtained by organism through horizontal transfer
Synology: genes ended up in one organism through fusion of lineages.
Orthologues: bifurcation in molecular tree reflects speciation. These are the molecules people interested in the taxonomic classification of organisms want to study.
Paralogues: bifurcation in molecular tree reflects gene duplication. The study of paralogues and their distribution in genomes provides clues on the way genomes evolved.
Gen and genome duplication have emerged as the most important pathway to molecular innovation, including the evolution of developmental pathways.
Xenologues: gene was obtained by organism through horizontal transfer. The classic example for Xenologs are antibiotic resistance genes, but the history of many other molecules also fits into this category: inteins, selfsplicing introns, transposable elements, ion pumps, other transporters,
Synologues: genes ended up in one organism through fusion of lineages. The paradigm are genes that were transferred into the eukaryotic cell together with the endosymbionts that evolved into mitochondria and plastids
3) Align sequences
(most algorithms used for phylogenetic reconstruction require a global alignment. An exception is statalign
from Thorne JL, and Kishino H, 1992, Freeing phylogenies from artifacts of alignment. Mol Bio Evol 9:1148-1162)
Select part of the alignment that is reliable! Modify alignment, if necessary.
4) Reconstruct evolutionary history
i) using optimality criterion
(e.g.: smallest error between distance matrix
and distances in tree, or use
ii) algorithmic approaches (UPGMA or neighbor joining)
find that tree that explains sequence data with minimum number of substitutions
(tree includes hypothesis of sequence at each of the nodes)
given a model for sequence evolution, find the tree that has the highest probability under this model.
This approach can also be used to successively refine the model.
Bayesian statistics use ML analyses to calculate posterior probabilities for trees, clades and evolutionary parameters. Especially MCMC approaches have become very popular in the last year, because they allow to estimate evolutionary parameters (e.g., which site in a virus protein is under positive selection), without assuming that one actually knows the "true" phylogeny.
spectral analyses, evolutionary parsimony, i.e., look only at patterns of substitutions,
Another way to categorize methods of phylogenetic reconstruction is to ask if they are using
- an optimality criterion (e.g.: smallest error between distance matrix and distances in tree, least number of steps), or
- algorithmic approaches (UPGMA or neighbor joining)
5) Interpret the result.
It is especially important to consider artifacts that might originate in phylogenetic reconstruction, and to asses the reliability of your results.