Biology Reference
In-Depth Information
5.2. Advanced Phylogenetic Analyses
and New Directions
In this chapter, we have considered each nucleotide to be a separate char-
acter and each changed nucleotide to be the result of at least one inde-
pendent evolutionary event. In reality, however, large portions of genes
may be deleted, inserted, or moved in a single event, and this can occur
across the boundaries of a gene. Advanced methods of phylogenetic
inference can detect such events and situate them within a tree.
Furthermore, there are some areas of biology where the standard
tree model for evolution does not hold true. This is especially true for
viruses. Specific techniques such as split decomposition analyses have
been developed to analyze such cases. Epidemiologists can learn a great
deal about the origin of new diseases by applying these tools. As an exam-
ple, the SARS epidemic is thought to be the result of a past recombina-
tion of mammalian and avian viruses.
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Other advanced methods of tree analysis allow more information to
be gleaned from an evolutionary scenario. Protein domain shuffling, evo-
lutionary diversification of gene families, and prediction of structure-
function relationships are just some of the possibilities.
The diminishing cost of sequencing and the ever-greater availability
of molecular sequence data are leading to a number of novel approaches
in phylogenetics. Here are some of the new directions being explored:
•
Methods have been developed to allow the construction of a plau-
sible tree from thousands of homologous sequences, explicitly
taking into account homoplasy and lineage-dependent rate
heterogeneity.
12,20,21
•
With the sequencing of complete genomes, evolution of complete
genomes can be studied and phylogenetics can take a totally new
direction. The presence or absence of complete (orthologous)
genes can be considered a phylogenetic character. Matrices of the
presence/absence of genes can be used as input for phylogenetic
analysis.
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•
Studies have attempted to reconstruct large portions of ancestral
genomes.
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