Modeling Mito-nuclear Compatibility and Its Role in Species Identification

Abstract

<jats:title>Abstract</jats:title> <jats:p>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 (Tigriopus 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.[Mito-nuclear coevolution; mtDNA barcode; parapatry; phylogeny.]</jats:p>

Population genomics of free‐ranging Great Plains white‐tailed and mule deer reflects a long history of interspecific hybridization

“…Therefore, given all the evidence, the dominant pattern from our data is likely of strong purifying selection for some functional process. For instance, this may be associated with maintaining mito‐nuclear compatibility for vital cellular processes (Hill, Linacre, et al, 2019; Hill, Havird, et al, 2019; Princepe & de Aguiar, 2021; Wolff et al, 2014). By extension, and considering the shared mitochondrial and nuclear assignments of hybrids are consistently associated with (opposite) external morphology, the process of hybridization may play a significant role in deer speciation within North America.…”

Mitochondria and their potential role in acute lung injury (Review)

“…The status of mtDNA and the associated nuclear-encoded proteins exert an influence on the health, fertility and lifetime of organisms ( 58-61 ). Furthermore, the level of compatibility between mtDNA and nuclear genes has been shown to influence the genetic divergence ( 62 , 63 ). The main function of the mitochondrion is to produce ATP via OXPHOS, and to provide energy for the cells ( 64 ).…”

Mito-nuclear selection induces a trade-off between species ecological dominance and evolutionary lifespan

“…We use an individual-based model (IBM) of speciation adapted from [5], following the same methodology of our previous work [38]. We consider a spatially distributed population evolving in the absence of geographic barriers under the influence of mutation, genetic drift, and dispersion.…”

“…Here we present an investigation of population dynamics that connect with micro-ecological patterns and ultimately leave macro-evolutionary signatures. We study spatially distributed populations that evolve under selection for mito-nuclear compatibility [38]. The genetic interaction between the mitochondrial and nuclear genomes is necessary for respiration, and is known to induce molecular co-evolution [39,40].…”