We observed many independent gene losses frequently involving one of two ancestral paralogs, for example, Cdc6/Orc1 and GINS.
Both, positive selection between paralogs for altered C2H2 zinc finger DNA binding domains [ 59, 6] as well as diversification of the expression patterns between paralogs [ 51] has been shown for the (KRAB) ZNF family.
However, the numbers of paralogs is lower; for example, in the channel catfish, if exclude alternative spliced transcripts which concern only the S3 family, paralogs have been found for only two types of RPs (S26 and S27) and one paralog pair has a high percentage of amino acid similarity with 94.8% identity, whereas the other paralog pair only differs by one amino acid [ 44, 45].
In the medium paralog specificity analysis for example, 62% of the paralogous pairs had a Pearson correlation coefficient that was below 0.866, a value below which were 95% of the correlation coefficients between non-paralogous genes.
We compiled a database of Hox genes with 4 5 species for each gene (155 sequences in total) and compared conserved and variable sites between paralog group members to identify if there are characteristic residues that distinguish which cluster a paralog belongs to (for example, see Figure 1).
Because even a single point mutation in the binding site of an OR can alter the ligand specificity thereby increasing or decreasing the affinity of the OR for certain odorant molecules [ 44], a large number of paralogs could be advantageous, for example in evolutionary arms races between predator and prey.
When we re-examined the linked essential genes in the network, we found paralogs or isozymes in every case in which a series of linked essential genes was interrupted by a "non-essential" gene in the same pathway (Figure 2; for example, paralogs SSA_0791/SSA_1494 involved in peptidoglycan biosynthesis, isozymes SSA_0578/SSA_2195 involved in NAD+/NADP+ biosynthesis).
This showed that the paralogs were associated with for example energy production, cell motility, ion transport, and defence mechanisms.
For example, paralogs of hba in tiger salamander showed both increasing (SRV_00496_s_at) and decreasing (SRV_02508_x_at) patterns of mRNA abundance, while all axolotl hba paralogs showed flat or increasing patterns (Additional File 1).
The majority of false positive mutation calls are generated from mismapped reads, for example, paralogs were mistakenly mapped to a single locus.
