Mitochondrial gene rearrangements as phylogenetic characters in the invertebrates: the examination of genome 'morphology'

Abstract

Mitochondrial gene rearrangements are the latest tool in the arsenal of phylogeneticists for investigating historical relationships. They are complex molecular characters that may provide more reliable evidence of ancestry than comparative molecular data. Here we review the phylogenetic utility of mitochondrial gene rearrangements, and find that despite isolated incidences of convergence, derived gene order appears highly congruent with phylogenies produced from other sources of data. We calculate that the chance of two mitochondrial genomes sharing the same derived genome organisation is only 1/2664, but caution that this ignores the possibility that the (as yet uncharacterised) gene rearrangement mechanism may greatly increase the chance of convergence. Broader taxonomic surveys of mitochondrial genome organisation will lead to a more realistic indication of the historical incidence of convergence in genome organisation.

Two nearly complete mitogenomes of wheat stem borers, Cephus pygmeus (L.) and Cephus sareptanus Dovnar-Zapolskij (Hymenoptera: Cephidae): An unusual elongation of rrnS gene

“…The analysed partial mitogenomes of the C. pygmeus, C. sareptanus and C. cinctus comprised 15221, 15212, and 15220 bp in size, respectively, including 13 PCGs, 20 tRNAs, and 2 rRNAs ( Table 1). The mitogenomes of Cephus species are mostly arranged in the same order and direction of the inferred insect ancestral mitogenome (Dowton et al, 2002) consistent with all previously determined sawfly mitogenomes, P. condei (Castro and Dowton, 2005), O. occidentalis (Dowton et al, 2009), Monocellicampa pruni (Wei et al, 2013) and Allantus luctifer . The only exception is the location of several tRNAs (Table 1, Fig.…”

“…Mitochondrial genome (mitogenome) information can be utilized in two ways as the total nucleotide sequences and the structural features of genome such as gene content, genome size, compositional features, secondary structure of RNAs and motifs of replication and transcription processes (Cameron, 2014;Dowton et al, 2002;Gissi et al, 2008). These genomic features generally reflect differences in function and evolutionary limitations and are also evolved by various mechanisms and at different evolutionary rates.…”

Changing identities: tRNA duplication and remolding within animal mitochondrial genomes

“…These models help us to determine the likelihood of homopla-sious arrangements, and consequently, the reliability of specific markers. While, in theory, the probability that two mitochondrial genomes share the same derived genome organization by chance alone is low (38), functional constraints may make some tRNA arrangements more likely than others (39), resulting in convergence in gene order within portions of the mitochondrial genome (40,41). Whereas four mechanisms have been invoked to explain mtDNA rearrangements [duplication͞random loss, illicit priming by tRNA genes, recombination, and duplication͞nonrandom loss (39)], a fifth involving duplication͞anticodon mutation (3) has not been considered important, given the paucity of evidence for this within particularly well-studied taxonomic groups (41).…”

A comparison of the mitochondrial genomes from two families of Solifugae (Arthropoda: Chelicerata): Eremobatidae and Ammotrechidae

“…Mt genome data have also been used for phylogeny reconstruction. In addition to sequence-based analyses, gene order and secondary structure of RNA sequences have been used as comparative characters in phylogenetic inference (reviewed in Dowton et al, 2002;Boore, 2006). In metazoans, a typical mitochondrial genome contains 37 genes -13 coding for protein subunits, two coding for ribosomal RNAs, and 22 coding for transfer RNAs.…”