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of duplicated genes. Comparative genomics therefore provides an
insight into the dynamics of gene family evolution, guiding the forma-
tion of hypotheses that can be tested experimentally to dissect the roles
of different protein classes in core processes as well as in lineage-specific
biology.
4. Orthologs and Paralogs
In comparative genomics, it is important to distinguish between two
types of homologous genes: orthologs and paralogs. 24,25 Orthologs are
genes in different species separated by the speciation event (vertical
descent) from a single gene of the last common ancestor. It is therefore
likely that orthologs retain the functions of the ancestral gene. Paralogs
are related by gene duplication events in one lineage, and some of these
additional copies may be more flexible to change their molecular func-
tions. If duplication occurs after the speciation event, however, the aris-
ing paralogs are still also orthologous to the genes in the other species
and are therefore co-orthologs (Fig. 2). In practice, such pairwise defini-
tions are frequently expressed as one-to-one, one-to-many, or many-to-
many relationships with respect to the copy number of the co-orthologs
in each species. When several species are examined, all co-orthologs are
considered together as one orthologous group. The explicit reference in
definition relative to the last common ancestor of the considered species
defines the hierarchical nature of orthologous classifications along the
phylogenetic species tree. Examining closely related species produces
many fine-grained orthologous groups of mostly one-to-one relations;
while, inversely, considering more distantly related species results in
fewer, more general (inclusive) orthologous groups containing all of the
descendants of the ancestral gene. Although conservation of ortholog
functions is not part of the definition, it is the most likely evolutionary
scenario and provides a strong working hypothesis, particularly when the
orthologs are preserved over a long period of time in single copy.
Paralogs, however, are generally believed to perform distinct (though
often related) functions. 26 The accurate detection of orthologous and
paralogous relations among homologous genes is therefore particularly
important for confident functional interpretations.
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