  Large scale databases are available that contain homologous gene families
constructed from hundreds of complete genome sequences from across the three
domains of Life. Here we discuss approches of increasing complexity aimed at
extracting information on the pattern and process of gene family evolution from
such datasets. In particular, we consider models that invoke processes of gene
birth (duplication and transfer) and death (loss) to explain the evolution of
gene families. First, we review birth-and-death models of family size evolution
and their implications in light of the universal features of family size
distribution observed across different species and the three domains of life.
Subsequently, we proceed to recent developments on models capable of more
completely considering information in the sequences of homologous gene families
through the probabilistic reconciliation of the phylogenetic histories of
individual genes with the phylogenetic history of the genomes in which they
have resided. To illustrate the methods and results presented, we use data from
the HOGENOM database, demonstrating that the distribution of homologous gene
family sizes in the genomes of the Eukaryota, Archaea and Bacteria exhibit
remarkably similar shapes. We shown that these distributions are best described
by models of gene family size evolution where for individual genes the death
(loss) rate is larger than the birth (duplication and transfer) rate, but new
families are continually supplied to the genome by a process of origination.
Finally, we use probabilistic reconciliation methods to take into consideration
additional information from gene phylogenies, and find that, for prokaryotes,
the majority of birth events are the result of transfer.
