Limiting the number of DNA molecules per well greatly reduces or eliminates chances of having a repeated or duplicate sequence within a defined partition.
The observed differences in nucleotide frequency among secondary structure defined partitions suggest separate models of molecular evolution; irrespective of modeling covarying sites in stem regions (see the Methods and Discussion sections below).
Our analysis suggests that none of the secondary structure defined partitions are saturated – Iss, Iss.C Sym, and Iss C Asym were as follows (ambiguous positions excluded): Loops 0.159, 0.700, and 0.395; Stems 0.218, 0.686, and 0.366; and RAA after filtered using Aliscore 0.640, 11.936, 19.025.
In this study, we develop a new algorithm that automatically defines partitioning schemes by clustering similar sites together into subsets.
Thus, defining partitioning schemes and models that can accurately reflect the true processes of molecular evolution while not over-parameterizing the analysis remains critically important for phylogenetic analyses of large plastid data sets.
The proposed DSS, developed in close collaboration with the Spanish National Police Corps SNPCC), defines partitions of the territory under the jurisdiction of a district that are efficient and balanced at the same time, according to the preferences of a decision maker.
It uses an ultrametric input tree to define partitions according to transitional points between speciation and coalescence within species rates.
A spatial analysis of molecular variance, as implemented in the program SAMOVA 1.0 [ 117], was used to define partitions of sampling sites that are maximally differentiated from each other without any a priori assumption about population structure.
Because the software required the user to pre-define partitions and specify them in the configuration file, we created an input configuration file that contained four partitions corresponding to individual codon positions in the COI gene fragment and the 16S rRNA gene fragment, which was the most finely partitioned scheme possible in our mitochondrial dataset.
Finally, a spatial analysis of molecular variance, (SAMOVA 1.0, [ 81], was used to define partitions of sampling sites that are maximally differentiated from each other without any a priori assumption about population structure. This method identifies k genetically differentiated populations, where the proportion of total genetic variance (FCT) is maximized.
Categories were defined by partitioning the ranks of the 32,480 areas into quintiles (0-20th percentiles, 20-40th percentiles, etc).
