A complete logical approach to resolve the evolution and dynamics of mitochondrial genome in bilaterians

Abstract

Investigating how recombination might modify gene order during the evolution has become a routine part of mitochondrial genome analysis. A new method of genomic maps analysis based on formal logic is described. The purpose of this method is to 1) use mitochondrial gene order of current taxa as datasets 2) calculate rearrangements between all mitochondrial gene orders and 3) reconstruct phylogenetic relationships according to these calculated rearrangements within a tree under the assumption of maximum parsimony. Unlike existing methods mainly based on the probabilistic approach, the main strength of this new approach is that it calculates all the exact tree solutions with completeness and provides logical consequences as highly robust results. Moreover, this method infers all possible hypothetical ancestors and reconstructs character states for all internal nodes of the trees. We started by testing our method using the deuterostomes as a study case. Then, with sponges as an outgroup, we investigated the evolutionary history of mitochondrial genomes of 47 bilaterian phyla and emphasised the peculiar case of chaetognaths. This pilot work showed that the use of formal logic in a hypothetico-deductive background such as phylogeny (where experimental testing of hypotheses is impossible) is very promising to explore mitochondrial gene order in deuterostomes and should be applied to many other bilaterian clades.

Architectural instability, inverted skews and mitochondrial phylogenomics of Isopoda: outgroup choice affects the long-branch attraction artefacts

“…Therefore, we can conclude that the use of a single outgroup exacerbated the LBA, whereas the use of a large number of outgroups and complete exclusion of outgroups ameliorated it. Intriguingly, some mitochondrial phylogenomics studies of datasets expected to exhibit compositional heterogeneity found that the outgroup choice does not affect the topology at all [66]. We hypothesize that these effects might be comparatively strongly pronounced in isopods due to exceptionally high compositional heterogeneity of their mitogenomes.…”

Mitogenomes Reveal Alternative Initiation Codons and Lineage-Specific Gene Order Conservation in Echinoderms

“…2020 ; Poliseno et al 2020 ). Apart from homologous gene sequences isolated from mitogenomes, gene order can also be useful for elucidating phylogenetic relationships, particularly for ancient divergences as mitochondrial DNA sequences are likely to be substitution saturated due to the rapid evolutionary rates ( Boore and Brown 1998 ; Oxusoff et al. 2018 ).…”