Molecular phylogenetics and evolutionary tree reconstruction

A convincing evolutionary relationship can be
established by reconstructing past events. A
phylogenetic tree may be based on different
types of evidence: on fossils, on differences in
proteins, on immunological data, on DNA–DNA
hybridization, and on DNA sequence similarity.
One determines the number of events that must
have taken place to explain the diversity observed
today. In the path from an ancestral gene
(1), different events of divergence can be distinguished
(two events are shown schematically
here). However, trees are not always as simple
as shown here. Since the term homology does
not distinguish whether the common evolutionary
origin is within or between species, the
terms paralogy and orthology are used (2).
Genes or nonallelic chromosomal segments or
DNA sequences are called paralogous if they
have evolved within a species (for example the
two !-globin loci in humans). If they evolved
between species prior to diversion, they are
called orthologous (for example the !-globin
and the "-globin genes).