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Taxonomic groups such as the D. mojavensis species cluster provide a unique opportunity to analyze morphological evolution at multiple levels of divergence.
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Complete mtDNAs offer variation over multiple levels of organization, from gene content and gene order to variation in amino acids and nucleotides, offering opportunities to resolve both recent and ancient divergence events.
For each of the three levels of divergence and from each multiple sequence alignment (i.e. the initial one as well as those outputted by BMGE, Gblocks, Noisy and trimAl), phylogenetic trees were inferred with several approaches.
The average lengths of these multiple sequence alignments are 513, 561, and 573 for the levels of divergence ×1, ×2, and ×3, respectively.
To explain the observed levels of divergence based on HGT without an increase in evolutionary rates would require multiple phylogenetically distant donor species (i.e. outside the angiosperms).
Levels of divergence at these loci exceed observed levels of divergence observed at a mitochondrial gene region at Easter Island.
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