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This type of analysis has been used in reconstructing relationships among domesticated rice and its relatives, for example (Cheng et al. 2002; Xu et al. 2007).
On the other hand, the use of ITS locus in phylogenetics has proven powerful in reconstructing relationships on lower taxonomic levels (groups and subgroups).
Arbitrarily amplified DNA markers are used extensively for reconstructing relationships among various species (Bussel et al. 2005).
Furthermore, amphinomids are a morphologically plesiomorphic group of annelids, considered as a highly important taxon for reconstructing relationships at the base of the annelid tree [ 18].
Moreover, our workflow also proved successful in reconstructing relationships within the Heliantheae tribe, demonstrating that this method is useful for both broader- and finer-scaled phylogenetic reconstruction.
Reconstructing relationships among spidroins based on their repetitive regions is problematic because their extreme variability in length and sequence identity make them difficult to align [ 6, 7, 12].
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For this reason, the phylogenetic method we used to reconstruct relationships was based primarily on the Bayesian method implemented by MrBayes, Ver. 3.1 [ 79, 80].
LeDuc et al. [ 3] and May-Collado et al. [ 24] used mtDNA cytochrome b sequences to reconstruct relationships among the taxa within the family Delphinidae.
To address these major outstanding issues of annelid inclusiveness and phylogeny, we reconstruct relationships of major annelid and lophotrochozoan taxa using two data sets.
We inferred orthologous relationships by reconstructing phylogenetic relationships among the α- and β-globin genes using Bayesian and maximum likelihood approaches, as implemented in Mr.Bayes v.3.1.2 (Ronquist and Huelsenbeck 2003) and Treefinder version October 2008 (Jobb et al. 2004).
The usual approach of using 16S rRNA and protein-coding genes has been applied to reconstructing the relationships within Prochlorococcus.
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