Among the PIWI subfamily proteins, six (AUB-A to AUB-F) form a clade within the larger AUB/PIWI clade, indicating multiple gene duplications have occurred in the Daphnia lineage.
In addition, our results support the following evolutionary scenario of this gene family: multiple gene duplications had occurred independently before the split of Physcomitrella patens (moss) from other land plants, and since then each of orthologs experienced molecular divergence by mutations, domain acquisition and gene structure changes, resulted in different orthologous groups.
This can complicate phylogenetic reconstruction, often producing trees that appear to indicate that multiple, independent and parallel duplications have occurred [ 20, 22].
The nine TIMELESS protein homologs (TIM-C to TIM-M) form a strongly-supported clade among the arthropod copies, indicating that multiple TIMELESS/TIM-1 gene duplications have occurred in the Daphnia lineage.
In multiple plant species, whole genome duplications have been associated with drastic changes in the environment (Blanc and Wolfe 2004; Van de Peer et al. 2009), potentially enabling these species to survive.
Ancient duplications have led to multiple homologues in different lineages, with three in fish, frogs and birds and four in mammals.
The imbalance of gene family trees suggests that relatively few gene duplications have occurred as segmental duplications affecting multiple loci.
Gene duplications have also occurred in some lineages, for example, there are multiple copies of Osiris 9 in B. mori.
The analyses completed in this study reveal that, although the gene content and organization of the bovine TRB locus are broadly similar to that of humans and mice, multiple duplication events have led to a marked expansion in the number of TRB genes.
As a final step, we resolve the conflicts among the tandem duplications, which are caused by multiple distinct tandem duplications having overlapping boundaries, by applying an algorithm that relies on the maximum parsimony principle.
