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Our results indicate that CGH data can be problematic for phylogenetic analysis.
The low cpDNA substitution rate combined with possible selective effects (which can be problematic for phylogenetic reconstructions [ 31]) led us to focus on "length polymorphisms".
Polyploidy is fairly common in anurans, which can be problematic for phylogenetic analyses because polyploid taxa do not arise by ordinary cladogenesis [ 51].
HTT essentially causes introgression of TE sequences across affected species and results in incomplete lineage sorting that tends to be problematic for phylogenetic algorithms.
Because this large number of sequences would be problematic for phylogenetic analyses, we reduced the size of these alignments by clustering sequences by similarity.
In contrast, if patterns of overestimation/underestimation are differentially distributed across the tree topology then it is likely to be problematic for phylogenetic analyses.
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The protein sequences of cystatins and stefins are problematic for phylogenetic analysis, because they are quite short, highly divergent and produce low bootstrap values in the phylogenetic trees.
The high variation can, however, be problematic for inferring phylogenetic relationships due to mutation rate heterogeneity among nucleotide sites [ 3] and high rates of homoplasy [ 4, 5] that can lead to ambiguous phylogeographic patterns [ 6].
However, both can be problematic for resolving deep phylogenetic relationships.
The phylogenetic relationships between these taxa can be problematic for use in population genetic and molecular evolutionary analysis because alleles from these species are not always reciprocally monophyletic (Obbard et al. 2007, 2009).
This can be problematic for molecular systematic studies where missing data may result in misleading phylogenetic results (Lemmon et al., 2009).
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