Mitochondrial genetic material (mtDNA) is widely used for phylogenetic reconstruction and as a barcode for species identification. The utility of mtDNA in these contexts derives from its particular molecular properties, including its high evolutionary rate, uniparental inheritance, and small size. But mtDNA may also play a fundamental role in speciation - as suggested by recent observations of coevolution with the nuclear DNA, along with the fact that respiration depends on coordination of genes from both sources. Here we study how mito-nuclear interactions affect the accuracy of species identification by mtDNA, as well as the speciation process itself. We simulate the evolution of a population of individuals who carry a recombining nuclear genome and a mitochondrial genome inherited maternally. We compare a null model fitness landscape that lacks any mito-nuclear interaction against a scenario in which interactions influence fitness. Fitness is assigned to individuals according to their mito-nuclear compatibility, which drives the coevolution of the nuclear and mitochondrial genomes. Depending on the model parameters, the population breaks into distinct species and the model output then allows us to analyze the accuracy of mtDNA barcode for species identification. Remarkably, we find that species identification by mtDNA is equally accurate in the presence or absence of mito-nuclear coupling and that the success of the DNA barcode derives mainly from population geographical isolation during speciation. Nevertheless, selection imposed by mito-nuclear compatibility influences the diversification process and leaves signatures in the genetic content and spatial distribution of the populations, in three ways. First, speciation is delayed and the resulting phylogenetic trees are more balanced. Second, clades in the resulting phylogenetic tree correlate more strongly with the spatial distribution of species and clusters of more similar mtDNA's. Third, there is a substantial increase in the intraspecies mtDNA similarity, decreasing the number of alleles substitutions per locus and promoting the conservation of genetic information. We compare the evolutionary patterns observed in our model to empirical data from copepods (T. californicus). We find good qualitative agreement in the geographic patterns and the topology of the phylogenetic tree, provided the model includes selection based on mito-nuclear interactions. These results highlight the role of mito-nuclear compatibility in the speciation process and its reconstruction from genetic data.

中文翻译：

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模拟有丝分裂核相容性及其在物种鉴定中的作用

线粒体遗传物质 (mtDNA) 广泛用于系统发育重建和作为物种识别的条形码。mtDNA 在这些情况下的效用源于其特殊的分子特性，包括其高进化率、单亲遗传和小尺寸。但 mtDNA 也可能在物种形成中发挥基本作用——正如最近对与核 DNA 共同进化的观察所表明的那样，以及呼吸依赖于两种来源基因的协调这一事实。在这里，我们研究了线粒体-核相互作用如何影响 mtDNA 物种鉴定的准确性，以及物种形成过程本身。我们模拟了携带重组核基因组和母系遗传的线粒体基因组的个体群体的进化。我们将缺乏任何有丝分裂核相互作用的空模型适应度景观与相互作用影响适应度的场景进行比较。健康是根据个体的线粒体核相容性分配给个体的，这推动了核基因组和线粒体基因组的共同进化。根据模型参数，种群分为不同的物种，然后模型输出允许我们分析 mtDNA 条形码用于物种识别的准确性。值得注意的是，我们发现通过 mtDNA 进行的物种识别在存在或不存在有丝分裂核耦合的情况下同样准确，并且 DNA 条形码的成功主要源于物种形成过程中的种群地理隔离。尽管如此，由有丝分裂-核相容性强加的选择以三种方式影响多样化过程并在种群的遗传内容和空间分布中留下特征。首先，物种形成被延迟，由此产生的系统发育树更加平衡。其次，由此产生的系统发育树中的进化枝与物种的空间分布和更相似的 mtDNA 簇的相关性更强。第三，种内 mtDNA 相似性显着增加，减少了每个基因座的等位基因替换数量，促进了遗传信息的保存。我们将我们模型中观察到的进化模式与桡足类（T. californicus）的经验数据进行比较。我们在地理模式和系统发育树的拓扑结构中发现了很好的定性一致性，假设该模型包括基于有丝分裂 - 核相互作用的选择。这些结果突出了有丝分裂核相容性在物种形成过程中的作用及其从遗传数据中的重建。