Legume Genomics and Genetics 2024, Vol.15, No.1, 27-36 http://cropscipublisher.com/index.php/lgg 32 and 76 taxa, respectively, employing methods such as maximum likelihood, Bayesian inference, and multispecies coalescent summary methods. The results indicate that all six subfamilies originated nearly simultaneously, challenging the traditional view of some subfamilies as 'basal' or 'early-diverging' (Koenen et al., 2019). 4.2 Evolutionary insights The phylogenomic analyses have also provided profound evolutionary insights into the Fabaceae family. One significant insight is the recognition of incomplete lineage sorting as a prevalent evolutionary process within the family. The study found strongly supported conflicts in the nuclear genes, which suggest that incomplete lineage sorting has played a crucial role in the evolutionary history of Fabaceae. This finding underscores the complexity of evolutionary processes and highlights the limitations of phylogenetic resolution when dealing with rapid successive speciation events (Koenen et al., 2019). Additionally, the simultaneous origin of all six subfamilies has important implications for understanding the evolution of legume diversity and traits, suggesting a more complex evolutionary history than previously thought. 4.3 Case studies Case studies within the Fabaceae family have further illustrated the utility of phylogenomic approaches in resolving complex evolutionary relationships. For instance, the comparative and phylogenetic analyses of plastid genomes in the Fagaceae family, which is closely related to Fabaceae, have demonstrated the effectiveness of plastid phylogenomics in resolving phylogenetic relationships. This study highlighted the impact of codon composition bias on phylogenetic inference, revealing that the first two codon sites dataset recovered nearly all relationships with high support. Such findings emphasize the importance of considering codon composition bias in phylogenomic studies and provide a methodological framework that can be applied to Fabaceae phylogenomics (Yang et al., 2018). 5 Implications for Understanding Evolutionary Processes 5.1 Gene flow and hybridization Gene flow and hybridization are critical processes in the evolution of the Fabaceae family. The extensive phylogenomic analyses conducted on over 1 500 nuclear genes from 391 species have revealed numerous polyploidization events within the family, which are indicative of historical gene flow and hybridization events. These polyploidization events, including whole-genome duplications (WGD) and whole-genome triplications (WGT), have been identified at various ancestral nodes within the Fabaceae, suggesting that hybridization has played a significant role in the diversification and adaptation of this family (Zhao et al., 2021). The study also supports the hypothesis of multiple switches to rhizobial nodulation followed by several losses, which could be attributed to gene flow and hybridization events that facilitated the spread and subsequent loss of this trait (Zhao et al., 2021). 5.2 Molecular evolution Molecular evolution within the Fabaceae family has been profoundly influenced by polyploidization events. The phylogenomic analyses have provided a highly resolved phylogeny that supports the monophyly of the subfamilies and reveals the early radiation of these subfamilies near the K/Pg boundary, a period marked by mass extinction. This timing suggests that the molecular evolution of Fabaceae was significantly impacted by global environmental changes (Zhao et al., 2021). The study's molecular clock estimation indicates that most tribe-level clades diverged within approximately 15 million years, highlighting a rapid evolutionary radiation that could be driven by molecular adaptations to changing environments (Zhao et al., 2021). Additionally, the comparative analysis of plastid genomes in related families, such as Fagaceae, underscores the importance of codon composition bias in phylogenetic inference, which can affect our understanding of molecular evolution in these complex families (Yang et al., 2018).
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