Discriminating between population and speciation patterns, under single-threshold analyses, GMYC identified all MOTUs as separate species, regardless whether based on COI, 16S rRNA or the concatenated three-marker dataset including nuclear 28S rRNA.
The incorporation of nuclear markers to a combined dataset including plastid and ribosomal DNA markers should improve the robustness of phylogenetic reconstructions at all taxonomic levels by increasing the total number of informative characters (i.e. increasing phylogenetic signal) [ 30].
Subsequently, a linkage map was reconstructed using the error corrected dataset, including markers genotyped in at least 88 of 92 (>95%) individuals.
106,524 single nucleotide polymorphisms were detected in our dataset, including potential markers that are putatively fixed across drainages.
Analyses of additional markers for global datasets, including ASY, are therefore necessary to test if mtDNA phylogeography reflects the actual dog history and not merely stochastic events or selection.
E. coli strains have previously been divided into five distinct ECOR phylogenetic groups (A, B1, B2, D and E) based on genetic markers [ 26], and our dataset includes representative from each of these five groups.
Quality control for this dataset included assessment of marker genotype frequency, allelic frequency, and departure from Hardy-Weinberg equilibrium.
The dataset included 647 genetic markers (388 microsatellite, or simple sequence repeat (SSR), and 259 SNP markers) scored on the individuals.
After removing samples and markers with >25% missing data, our dataset included 87 individuals.
Quality control for this dataset included sample genotyping efficiency, assessment of marker heterozygosity and allelic frequency, departure from Hardy Weinberg equilibrium, gender consistency, reproducibility and population genetic structure.
