Maize Genomics and Genetics 2024, Vol.15, No.5, 218-227 http://cropscipublisher.com/index.php/mgg 220 The major evolutionary relationships revealed among Zea species indicate that despite the close genetic relationships, there are significant variations in mutation rates. For instance, the study of five Zea species, including Zea diploperennis, Zea perennis, Zea luxurians, Zea nicaraguensis, and Zea mays subsp. huehuetenangensis, showed that tandem repeat indels were the most common type of microstructural change observed. These findings are consistent with previous studies that have examined mitochondrial and nuclear data, confirming the robustness of the phylogenetic trees constructed using plastome alignments (Orton et al., 2017). 3.2 Divergence time estimation Estimating divergence times within the Zea genus involves sophisticated methods that model rate variation among lineages. One effective approach is the noncorrelated relaxed clock method, which allows for the estimation of divergence dates without assuming a constant rate of evolution across all branches of the phylogenetic tree. This method has been applied to calculate divergence times for specific nodes within Zea, revealing that the stem lineage of all Zea species diverged approximately 176 000 years before present (YBP) (Orton et al., 2017). Key divergence events within the Zea genus include the separation of subspecies around 38 000 YBP and the divergence of section Luxuriantes around 23 000 YBP. These temporal contexts provide a framework for understanding the evolutionary history and speciation events within the genus. The calculated mutation rates for Zea, ranging from 1.7E-8 to 3.5E-8 microstructural changes per site per year, highlight the non-uniformity of evolutionary rates despite the close relationships among taxa (Orton et al., 2017). 3.3 Evolutionary history of major Zea species The evolutionary pathways of major Zea species, such as maize (Zea mays), are shaped by a combination of genetic, environmental, and ecological factors. Maize, in particular, has undergone significant evolutionary changes that have been well-documented through phylogenomic studies. The use of complete plastid genomes has provided a detailed understanding of the microstructural changes and divergence times within the genus (Figure 1) (Orton et al., 2017). Figure 1 Plastid genome of Zeamays subsp. mays cv. ‘INIA 601’(Adopted from Orton et al., 2017) Image caption: The thick lines indicate the IR1 and IR2 regions, which separate the SSC and LSC regions. Genes inside the circle are transcribed in the clockwise direction and genes outside the circle in the counterclockwise direction. Colors of genes indicate their function as shown in the legend. Genes containing introns are marked with an asterisk (*) (Adopted from Orton et al., 2017) Factors influencing speciation within Zea include genetic mutations, environmental pressures, and hybridization events. The study of plastid genomes has revealed that tandem repeat indels are a common type of mutation,
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