Abstract
Methods based on genetic distance matrices usually lose information during the process of tree-building by converting a multi-dimensional matrix into a phylogenetic tree. We applied a heuristic method of two-dimensional presentation to achieve a better resolution of the relationship between breeds and individuals investigated. Four hundred and nine individuals from nine German dog breed populations and one free-living wolf population were analysed with a marker set of 23 microsatellites. The result of the two-dimensional presentation was partly comparable with and complemented a model-based analysis that uses genotype patterns. The assignment test and the neighbour-joining tree based on allele sharing estimate allocated 99% and 97% of the individuals according to their breed, respectively. The application of the two-dimensional presentation to distances on the basis of the proportion of shared alleles resulted in comparable and further complementary insight into inferred population structure by multilocus genotype data. We expect that the inference of population structure in domesticated species with complex breeding histories can be strongly supported by the two-dimensional presentation based on the described heuristic method.
Highlights
By using nP jackknife replicates, we showed that the average cophenetic correlation for the phylogenetic tree (0.604) is significantly lower (P < 0.00001) than the average cophenetic correlation for 2D illustration (2DI) (0.695)
The population differentiation found in this study (GS T being 0.23) was similar to that found by other authors using different microsatellite marker sets in dog breeds: 0.233 in Koskinen and Bredbacka [15], 0.23 in Irion et al [12], 0.27 in Parker et al [21]
One reason to estimate Nm is that this combination of parameters indicates the relative strengths of gene flow and genetic drift
Summary
While genetic distance methods based on a sum over loci such as the Nei DA-distance [19] provide valuable insight into the phylogenetic relationship between breeds of several domestic species, they have often failed to support. We used the cophenetic correlation coefficient [27] to analyse to which extent a tree or a 2D illustration (2DI) represents the multi-dimensional relationships within genetic distance data. The comparison of 2DI based on allele sharing distances with the results of the methods implemented in the Structure programme should give an appropriate insight into the usefulness of the heuristic algorithms developed in this work.
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