Coding and non-coding sites were separated into unlinked partitions for the analysis.
The data were separated into two partitions, one containing all chloroplast gene regions and the second containing nrITS.
In the former case individual strands of the duplex can become separated into different partitions and be amplified, resulting in a 'double-count' which could lead to overestimation of template concentration under the assumption of double-stranded conformation [ 38].
When separated into similar partitions, the high RIG group (most efficient) had both the lowest (P < 0.001) feed intake (18.86 vs. 19.57 and 20.41 kg) and the highest (P < 0.001) body weight gain (7.41 vs. 7.03 and 6.43 kg) relative to the medium and low groups, respectively.
Additionally, msp1 alignment columns were separated into a partition composed of first and second codon position sites (partition of nonsynonymous sites; codon 1 + 2) and another partition comprised of third codon position sites (partition of synonymous sites; codon 3), with trees constructed independently for the two distinct partitions.
21 After manual inspection of the alignments, the data were separated into three partition sets that corresponded to the first, second and third positions of each codon.
A total of 31 binary characters were coded for gaps according to Simmons and Ochoterena [ 42] and separated into independent partition in all analyses.
While phylogenetic incongruence may be caused by real differences in evolutionary history, it can also be the result of evolutionary model misspecification [ 17], high levels of homoplasy [ 18], long branch attraction [ 19], inadequate sampling [ 20] or separating data into partitions [ 21].
In amphibians, only the atrium is separated into two halves, by a partition starting from the posterior end.
In the light dark box adaptation (Crawley and Goodwin 1980; Malmberg-Aiello et al. 2002), the test apparatus described above is separated into two equal compartments by a partition with an opening in the middle; a black plastic roof covers one compartment.
