Evolutionary ecology is at the precipice of a paradigm shift. For many years and through the early years of the 21st century, mitochondrial genomes were dismissed as unimportant to the evolution of complex life. Variation within mitochondrial genomes was proposed to be functionally neutral. These conceptions about mitochondrial genomes and mitonuclear genomic interactions have begun to change within the past decade, but currently accepted theories of sexual selection and speciation were proposed before the discovery of the mitochondrial genome. Evolutionary ecology has yet to fully appreciate the fundamental implications of two genomes coding for the core respiratory enzymes of eukaryotes. This chapter promotes a fundamental rethinking of key theories in evolutionary ecology with full consideration of the necessity of coadaptation of mitochondrial and nuclear genes.
Keywords: New theory, paradigm shift, mitonuclear ecology, mitonuclear mate choice, the mitonuclear compatibility species concept, mitochondrial adaptation, mitochondrial theory of aging, the evolution of sex, compensatory coevolution
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