International Journal of Molecular Evolution and Biodiversity 2024, Vol.14, No.4, 162-173 http://ecoevopublisher.com/index.php/ijmeb 163 2 Evolutionary Framework 2.1 Overview of mammalian evolutionary history Mammalian evolution is marked by significant diversification and adaptation events that have shaped the vast array of species we see today. The emergence of the six-layered neocortex in reptilian ancestors of mammals represents a fundamental evolutionary landmark, enabling the remarkable sensory, motor, and cognitive abilities of mammals (Franchini, 2021). The evolutionary history of mammals also includes the divergence of major lineages such as placentals, marsupials, and monotremes, each adapting uniquely to their environments (Figure 1) (Brawand et al., 2011; Franchini, 2021). Additionally, the study of marine mammals from different orders has provided insights into convergent evolution, where similar phenotypic traits have evolved independently in response to aquatic environments (Foote et al., 2015). Figure 1 Phylogenetic tree of mammalian evolution (Adopted from Franchini, 2021) Image caption: The schematic phylogenetic tree has been based on phylogenetic trees built by Goffinet (2017) and Rowe (2017). Red lines mark the mass extinction events. In every lineage two examples of lissencephalic and gyrencephalic brains are shown. Extinct lineages show examples of species that have been described from fossils specimens (Adopted from Franchini, 2021) 2.2 Key evolutionary milestones and speciation events Several key milestones have punctuated mammalian evolution. The diversification of the neocortex in different mammalian lineages, particularly its expansion in primates, has been crucial for the development of complex behaviors and cognitive functions. The sequencing of the platyfish genome has revealed evolutionary stability in chromosomes and identified genes associated with viviparity and cognition, highlighting instances of parallel evolution and positive selection (Schartl et al., 2013). Furthermore, the study of gene expression evolution across mammalian organs has shown that selective pressures have shaped the transcriptome differently across tissues and lineages, contributing to the unique biology of various mammals. 2.3 Importance of genetic diversity in trait evolution Genetic diversity plays a critical role in the evolution of mammalian traits. Differences in gene regulation, rather than protein-coding sequences, are often responsible for species-specific traits (Hernando-Herraez et al., 2015)1. The evolution of gene expression levels, influenced by selective pressures, has been a major driver of phenotypic diversity among mammals (Chen et al., 2018; Sun et al., 2020). Additionally, the identification of loci of adaptive
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