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In summary, classical and most recent morphological and molecular studies based on nuclear data support the Mecopterida and Coleopterida hypotheses.
In comparison with the mitochondrial tree, the tree based on nuclear data resolved the more recent divergences poorly.
Nucleotide diversity estimates based on nuclear data are available for other cichlids, too, albeit based on much smaller samples of orthologous genes.
In addition, since this assignment based on nuclear data was totally congruent with the mitochondrial tree (Fig. 2), we assigned the rest of specimens using this mitochondrial tree.
The main goal of these population genetic analyses was to determine genetic structure of bigeye tuna within the Atlantic Ocean based on nuclear data, and to compare it with mitochondrial evidence.
In the bigeye tuna, the main source of disagreement largely arises from the existence in the Atlantic Ocean of two highly divergent mt clades [ 10, 26, 27], which were not recovered by AMOVA tests based on nuclear data.
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In all our analyses based on nuclear rDNA data, the three species of Plakinastrella form a monophyletic group, thus making the combination of those spicules a valid morphological character to define this genus.
A previous study on J. vulgaris, based on nuclear AFLP data, did not show a difference in the amount of variation between native and invasive individuals.
However, phylogenetic analyses based on nuclear molecular data, including rDNA [ 6, 7, 13, 28- 30] and protein-coding genes [ 8, 9, 11, 31], have recovered Hexapoda as monophyletic.
We assign individuals to populations based on nuclear genetic data to test for the genetic cohesiveness of each lake/crater lake population.
Mitogenomic analyses have challenged hexapod monophyly and suggested the reciprocal paraphyly of Hexapoda and Crustacea, whereas studies based on nuclear molecular data support the monophyletic origin of hexapods.
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