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At the subfamilial level, the single difference between mt genome tree and combined nuclear gene tree is the phylogenetic position of Helictidinae.
As regards the mt gene analyses, we observed that the ND5 and CYTB genes recovered all 9 nodes of the mt genome tree.
In mt genome tree, Helictidinae is closer to the clade uniting Lutrinae and Mustelinae than to Martinae (MP = 60%; ML BS = 95%; PP = 1.00).
When using nuclear data, the mt genome tree topology was rejected by the AU and SH tests (P < 0.05), and vice versa.
When using nuclear data, the mt genome tree topology, in which Helictidinae is closer to the clade uniting Lutrinae and Mustelinae, was rejected by the AU and SH tests (P < 0.05).
Similar(54)
When using mt genome data, the nuclear tree topology, in which Helictidinae and Martinae are grouped together, was rejected by the AU and SH tests (P < 0.05).
A pt (and mt) genome based reference phylogenetic tree was first constructed based on the concatenated nucleotide sequences of all protein-coding genes on the pt (and mt) genomes of the seven Nannochloropsis strains.
To further illustrate the relationship of the mt genome haplotypes, a maximum likelihood phylogenetic tree based on the complete genome sequences was constructed (Additional file 3).
However, the processes involved in mitochondrial (mt) genome evolution differ considerably across the eukaryotic tree of life.
The phylogenetic tree reconstructed from the combined nuclear and mt genome data set by using the BCA analysis [ 45] produced a tree topology (Additional file 2) identical to that from the combined nuclear gene analysis.
Although the BCA analysis of the combined nuclear intron and mt genome sequences, which is an approach that allows for gene tree discordance, retrieved an identical tree topology to that of the nuclear intron gene, the position of Helictidinae received week support.
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