International Journal of Molecular Evolution and Biodiversity 2024, Vol.14, No.4, 162-173 http://ecoevopublisher.com/index.php/ijmeb 168 functional and clinical relevance (Schulze and Lammers, 2020). The integration of these sequencing technologies with bioinformatics tools, such as the Molecular Evolutionary Genetics Analysis (MEGA) software, has further enhanced our ability to reconstruct evolutionary histories, estimate rates of molecular evolution, and infer selective forces shaping the evolution of genes and genomes. 8.2 Comparative genomics and phylogenetics Comparative genomics and phylogenetics play a crucial role in understanding the evolutionary relationships between species. By comparing DNA and protein sequences, researchers can infer phylogenetic trees, estimate evolutionary distances, and test evolutionary hypotheses. The development of user-friendly computational tools, such as MEGA, has made it easier to perform these analyses, thereby expanding the scope of molecular evolutionary studies. These methods have been instrumental in identifying conserved genetic elements and understanding the genetic basis of adaptation and speciation (Ansai and Kitano, 2022). 8.3 Functional genomics and gene editing Functional genomics aims to understand the roles of genes and their interactions by perturbing the flow of genetic information from DNA to RNA to protein. The CRISPR/Cas9 system has emerged as a powerful tool in this field, allowing precise and efficient genome editing across a wide range of organisms. This technology has revolutionized functional genomics by enabling researchers to create genetic knockouts, transgenics, and other forms of gene manipulation with unprecedented ease and accuracy (Bono et al., 2015; Hartenian and Doench, 2015). The CRISPR/Cas9 system has been applied to study gene function in non-model organisms, investigate the genetic basis of adaptive traits, and explore the roles of specific genes in development and disease (Chen et al., 2014; Gilles and Averof, 2014; Ahmad et al., 2018). The versatility of CRISPR/Cas9 extends to various applications, including targeted gene knock-out, gene knock-in, precise gene replacement, and chromosomal rearrangement. These techniques have been used to conduct functional analyses of naturally occurring genetic variations, providing insights into the genetic basis of reproductive isolation and adaptive traits in natural populations. 9 Integrating Genomic and Environmental Data 9.1 Environmental influences on gene expression Environmental factors play a significant role in shaping gene expression, which in turn affects various organism-level traits. Functional genomics has provided new insights into how these environmental inputs influence gene regulation. For instance, research has shown that the social and physical environment can impact health, reproduction, and survival across mammalian species by altering gene expression patterns (Snyder‐Mackler and Lea, 2018). Additionally, studies on genotype-by-environment interactions (GxE) in Simmental cattle have revealed that environmental variables significantly contribute to phenotypic variance in growth traits, highlighting the importance of understanding these interactions for predicting population vulnerability to climate change (Braz et al., 2020). 9.2 Adaptation to climate and habitat changes Adaptation to changing climates and habitats is a critical aspect of mammalian evolution. Research has shown that species inhabiting variable environments tend to maintain a higher proportion of small-scale duplication (SSD) genes, which are essential for adapting to novel environments and surviving environmental changes (Tamate et al., 2014). In the context of climate change, phenotypic plasticity and microevolution are the primary mechanisms through which mammals adapt. However, most observed phenotypic changes in wild mammal populations have been attributed to plasticity rather than evolutionary changes (Boutin and Lane, 2013). Studies on US beef cattle have also provided evidence of local adaptation to different environmental conditions, with numerous genomic loci associated with environmental variables, indicating ongoing selection for traits that enhance survival and productivity in diverse climates (Rowan et al., 2021). 9.3 Role of ecological interactions in trait evolution Ecological interactions are fundamental in shaping trait evolution in mammals. For example, the adaptation of marine mammals to aquatic environments has involved convergent evolution in genes associated with
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