Extreme mito-nuclear discordance in a peninsular lizard: the role of drift, selection, and climate

Abstract

Nuclear and mitochondrial genomes coexist within cells but are subject to different tempos and modes of evolution. Evolutionary forces such as drift, mutation, selection, and migration are expected to play fundamental roles in the origin and maintenance of diverged populations; however, divergence may lag between genomes subject to different modes of inheritance and functional specialization. Herein, we explore whole mitochondrial genome data and thousands of nuclear single nucleotide polymorphisms to evidence extreme mito-nuclear discordance in the small black-tailed brush lizard, Urosaurus nigricaudus, of the Peninsula of Baja California, Mexico and southern California, USA, and discuss potential drivers. Results show three deeply divergent mitochondrial lineages dating back to the later Miocene (ca. 5.5 Ma) and Pliocene (ca. 2.8 Ma) that likely followed geographic isolation due to trans-peninsular seaways. This contrasts with very low levels of genetic differentiation in nuclear loci (FST < 0.028) between mtDNA lineages. Analyses of protein-coding genes reveal substantial fixed variation between mitochondrial lineages, of which a significant portion comes from non-synonymous mutations. A mixture of drift and selection is likely responsible for the rise of these mtDNA groups, albeit with little evidence of marked differences in climatic niche space between them. Finally, future investigations can look further into the role that mito-nuclear incompatibilities and mating systems play in explaining contrasting nuclear gene flow.

Are glacial refugia hotspots of speciation and cytonuclear discordances? Answers from the genomic phylogeography of Spanish common frogs

“…In this case, the rise and maintenance of T6 would simply stem from the lower effective size of mtDNA, eventually promoted by male-biased dispersal (but see Palo et al, 2004). Our SDMs indicate a minor role for climatic niche differences in maintaining the T6 and T4 mtDNA lineages apart (File S8b), but analyses of complete mitogenomes could inform on whether selection played a role in accelerating the divergence (e.g., Bernardo et al, 2019).…”

Evolution of Poecilimon jonicus group (Orthoptera: Tettigoniidae): a history linked to the Aegean Neogene paleogeography

“…The phylogenetic position of P. inflatus is especially intriguing, as it appears as an internal branch of the Balkan lineages with very high support in the ND2 + COI phylogeny, at the same time occurring at the opposite side of the Aegean Sea. Yet, based on the long history of the discussed lineages and contradictions in the trees, independent evolution of each genome is possible (Bernardo et al 2019). The instability at the base of the P. jonicus group tree may express a real situation.…”

A mirage of cryptic species: Genomics uncover striking mitonuclear discordance in the butterfly Thymelicus sylvestris

“…Although mitochondrial DNA (mtDNA) is widely used to assess genetic patterns, results obtained from mtDNA may differ from the ones based on nuclear DNA (Bernardo et al, ; Galtier, Nabholz, Glemin, & Hurst, ; Toews & Brelsford, ). Several mechanisms have been shown to generate mitonuclear discordance, namely incomplete lineage sorting, sex‐biased asymmetries, introgression, natural selection or genetic sweeps mediated by Wolbachia infection (Toews & Brelsford, ).…”