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The analysis of systems involving several variables is of great importance in population and quantitative genetics, for example, in multi-trait prediction of breeding values or in the study of networks using multi-locus data.
Although species-tree methods have been widely adopted for multi-locus data, little consideration has been given to the source and character of the loci used in these approaches.
We used available EST (expressed sequence tags) and whole genome databases in order to obtain multi-locus data matrices for phylogenetic inferences (see Table S1).
STRUCTURE version 2.2 [34], which implements a Bayesian approach for deducing population structure from multi-locus data, was used to analyze the population clustering of an isolate, assuming that each isolate has derived all of its ancestry from only one population.
We constructed two multi-locus data sets using from data collected from different sequencing methods.
The method is useful because it is computationally tractable with large multi-locus data sets.
We present hapConstructor, software to construct and test multi-locus data, allowing for non-contiguous SNP subsets.
Recent studies emphasize the need of multi-locus data for accurate estimation of various population parameters [ 3, 61].
Nonetheless, analyses of 660 fragments from 350 individual loci echo the results of the analyses of combined multi-locus data.
Using multi-locus data gathered from 124 individuals, we show that lowland and montane birds form two distinct genetic lineages.
We found UCEs to be far superior to the multi-locus data set in estimating formicine relationships.
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