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However, the limited number of available whole chloroplast genome sequences can result in misleading estimates of relationship [ 27, 30].
To what extend do tetra-nucleotides affect previous estimates of relationship between within-population heterozygosity and distance from sub-Saharan Africa?
It could be that a higher marker density reduces errors in the estimates of relationship between distant relatives, which may improve the contribution of ancient relationships to the accuracy of GW-EBV.
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Pooling sequences from multiple mitochondrial protein-coding genes should result in statistically more powerful estimates of relationships among species that diverged sufficiently recently that most nucleotide substitutions are synonymous.
Our estimates of relationships among squamates were different based on the phylogeny estimates from the two datasets described above.
Our data show that intraspecific inversions can lead to an overestimate of divergence among conspecific sequences and misleading estimates of relationships among closely related species.
While all SNPs are relatively infrequent among B. anthracis isolates, the use of whole genome analysis has identified many sSNPs (Table 1) and resulted in highly robust estimates of relationships among isolates [5].
In general, our estimates of relationships among these species are consistent with previous reconstructions [ 57, 64].
Estimates of relationships are always relative to an arbitrary base population in which the average relationship is zero.
A simple explanation could be a low level of diversity and consequently of resolution in estimates of relationships.
In the present study, this selection may have affected estimates of relationships between variables of interest through restricted variance.
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