Reduced median network analyses, based on nucleotide variation on the complete sequences, were carried out by Network 4.5.1.0 (http://fluxus-engineering.com) [53] with an e default value of zero.
An ML tree based on nucleotide variation of the cpDNA atpB- rbcL intergenic spacer identifies six chlorotypes I-VI (Fig. 2B).
A second ITS typing scheme was developed by Tsolaki et al. (24 – 26 ) and is based on nucleotide variation at four positions in the ITS1 and at six positions in the ITS2.
SUB1A is recognized in two allele forms in submergence tolerant and intolerant indica and aus accessions, based on nucleotide variations in the protein-coding region (Xu et al. 2006).
In-depth analysis of the available sequence data on SARS-CoV also revealed that the viral isolates could be readily subclassified into several major genotypes based on nucleotide variations at specific genomic positions [ 8, 12].
Strain analysis of P. jirovecii had been conducted by molecular genotyping based on nucleotide sequence variations because of the inability to culture.
Our findings of lower levels of diversity in males and on the Z-chromosome relative to the autosomes are concordant with results of previous studies based on nucleotide sequences or microsatellite variation in a wide range of species including the collared flycatcher [ 22], chicken [ 23], human [ 24, 25], house mice [ 26] and Drosophila [ 27, 28].
The number in italics below the value for each test is the upper limit of the 95% confidence interval, calculated by coalescence simulation based on θπ and free-recombination, n = number of sequences compared, S = number of segregating sites, π = nucleotide polymorphism and θπ = theta (an estimator of genetic variation) based on nucleotide polymorphism.
For phylogenetic analyses based on nucleotide sequences, GTR+G+I (general time reversible model + among site rate variation + invariable sites) was selected as the best-fitting model.
First, the read coverage across a single genome will be highly consistent, excepting for variation due to statistical sampling error and known biases based on nucleotide content (Lander and Waterman 1988; Aird et al. 2011).
In conclusion, our approach to Neanderthal variability, based on nucleotide sequences analysis, confirms from a genetic point of view the morphological variations between western and eastern Neanderthals and the existence of a southern group (fig. 2).
