The breadth and comprehensiveness of RiTE-db was deliberately conceived to help develop Hidden Markov Models of repeated sequences, since scanning genomes with these profiles allows for the identification more ancient or diverged repetitive sequences [ 28].
A simpler explanation is that the PAML algorithm has a bias toward reconstructing shorter sequences and FastML to reconstructing longer sequences the more ancient the ancestor becomes.
In contrast, there is little evidence of co-clustering of family members in the genome of filamentous Ascomycetes, suggesting they are more ancient as evidenced by sequence divergence and that they have become widely distributed about the genome predominantly through translocation events [ 19].
"We need the sequencing of more ancient genomes to address this question," Dr. Willerslev said.
It should be emphasized that the methods used will not detect some GIs – such as those that have been acquired from genomes with similar sequence composition, or more ancient GI acquisition events that may have ameliorated to the host genome sequence composition over time.
To look for common coding domains relevant to the evolution of the Msx family, comparisons were deliberately made between Msx sequences from taxa more ancient than that utilized in the engrailed comparisons, since current evidence suggests that the Msx family is more ancient than the engrailed family [ 61].
In other words, if a sample is taken from a genomic database that selects short, highly similar sequences, the gene it is in is more ancient if an intron is also shared between these sequences.
Conversely, other genes subject to LGT have less nucleotide-level sequence similarity, suggesting more ancient transfers (Table 1).
It appears that one of these ancient sequences has been duplicated more recently, after the separation of Teleostei from Archausauria and Mammals.
Modern chromosomes are thought to represent mosaics of genomic segments laid in sequence and drawn from more ancient chromosomes [ 1, 7].
