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.

研究重组如何在进化过程中改变基因顺序已成为线粒体基因组分析的常规部分。描述了一种基于形式逻辑的基因组图谱分析新方法。该方法的目的是：1）使用当前分类单元的线粒体基因顺序作为数据集2）计算所有线粒体基因顺序之间的重排，以及3）在最大简约性的假设下，根据这些计算的重排在树中重建系统发生关系。与主要基于概率方法的现有方法不同，此新方法的主要优势在于它可以完整地计算所有精确的树解，并提供逻辑结果作为高度可靠的结果。而且，该方法可以推断所有可能的假想祖先，并为树的所有内部节点重建字符状态。我们首先以氘化口罩作为研究案例来测试我们的方法。然后，以海绵为外群，我们调查了47个双侧门的线粒体基因组的进化历史，并着重介绍了棘齿动物的特殊情况。这项前期工作表明，在系统发育等假设假设演绎的背景下使用形式逻辑（不可能进行假设的实验检验）在氘化口罩中探索线粒体基因顺序非常有前途，应将其应用于许多其他双侧进化枝。我们调查了47个双边门的线粒体基因组的进化历史，并着重介绍了e嘴蛇的特殊情况。这项前期工作表明，在系统发育等假设假设演绎的背景下使用形式逻辑（不可能进行假设的实验检验）在氘化口罩中探索线粒体基因顺序非常有前途，应将其应用于许多其他双侧进化枝。我们调查了47个双边门的线粒体基因组的进化历史，并着重介绍了e嘴蛇的特殊情况。这项前期工作表明，在系统发育等假设假设演绎的背景下使用形式逻辑（不可能进行假设的实验检验）在氘化口罩中探索线粒体基因顺序非常有前途，应将其应用于许多其他双侧进化枝。