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While comparisons at the individual level were not well-correlated across marker types, this was not the case for population-level comparisons: the correlation between allele-sharing distance among populations was >0.99 (Mantel test).
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The main marker types in this integrated consensus map were SSRs and transposons.
These distances are comparable to the average genetic distances between the same marker types in this investigation (data not shown) and thus we conclude that, given the diverse pedigrees of these two mapping progenies, the IRSC array should be an invaluable tool for linkage map development and saturation in any given M. pumila mapping progeny.
A second explanation is that these discordances arise from the contrasting modes of transmission, evolution, and resolution of these marker-types; this could plausibly explain a lack of isolation-by-distance in the mtDNA, but isolation-by-distance in the allozymes.
In the case of hundreds of individuals, each with mostly different markers typed, this will lead to a large proportion of imputed markers for the population.
Marker: marker type 1.f.
Given high enough sequence coverage to accurately identify all relevant alleles and loci, the sstacks algorithm implemented by Stacks assigns an aa/bb marker type in this situation (Scenario 1).
No other marker types are capable of enabling this.
Data sets included in this investigation varied in size, sampling effort, and marker types.
This difference might be explained by the examined marker types.
This could be explained by the differences in marker types.
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