International Journal of Molecular Evolution and Biodiversity 2024, Vol.14, No.3, 120-132 http://ecoevopublisher.com/index.php/ijmeb 122 Simon et al. (2021) highlights the significant morphological diversity present within the Cerrado radiation clade, illustrating various growth forms, leaf structures, and flower arrangements. This diversity is notable given the low phylogenetic differentiation among these species, suggesting that significant phenotypic variation can occur even with limited genetic divergence. This phenomenon is particularly evident in the narrow endemic species restricted to specific localities within the Cerrado, emphasizing the adaptive versatility of these plants in different ecological niches. The detailed morphological descriptions alongside the phylogenetic tree provide valuable insights into the evolutionary processes driving diversification in this clade. 1.3 Early cultivators and cultivation practices The domestication of cassava was influenced by the cultural and agricultural practices of early cultivators. The transition from wild species to cultivated cassava involved changes in morphological traits and gene expression associated with the domestication syndrome (Carvalho et al., 2018). For instance, seedling morphology has evolved under domestication, with domesticated cassava exhibiting epigeal germination and photosynthetic cotyledons, traits that confer high initial growth rates in agricultural habitats (Pujol et al., 2005). Proteomic analysis between cultivated cassava and its wild relatives has revealed differences in photosynthesis and starch accumulation, which are critical for the selection in domestication syndrome phenomena (An et al., 2016). Additionally, the domestication process has been characterized by selection for traits such as high carbohydrate production, adaptability to diverse environments, and reduced cyanogenic glucoside accumulation. It can be seen that cassava’s domestication is rooted in the southern Amazon basin, with genetic evidence pointing to a single wild ancestor. The domestication process has been shaped by natural selection and human cultivation practices, leading to the crop’s adaptation to agricultural environments and its current genetic diversity (Olsen and Schaal, 2001; Pujol et al., 2005; An et al., 2016 Carvalho et al., 2018; Ogbonna et al, 2020). 2 Phylogenetic Analysis Techniques Used in Cassava Research 2.1 Genetic markers and DNA sequencing In cassava research, genetic markers such as single nucleotide polymorphisms (SNPs) are widely used due to their abundance and high-throughput detection capabilities. Additionally, because of the high heterozygosity of the cassava genome, it serves as an excellent system for studying diallelic differentiation. For instance, Hu et al. (2021) performed whole-genome sequencing on the cassava variety SC205, which is widely used as a breeding parent in China. They estimated the genome size of SC205 to be 770.3 Mb using flow cytometry (Figure 2). The study found that two haplotypes were assembled in the heterozygous regions of the genome and revealed allelic differentiation during the evolutionary process of cassava. Hu et al., (2021) provided a comprehensive analysis of the cassava SC205 genome, focusing on biallelic differentiation and expression profiles. The comparison with the AM560 genome (Panel A) and Hi-C data (Panel B) ensures the robustness of the assembly. Panels C through F highlight the expression dynamics of bialleles, revealing tissue-specific and developmental stage-specific expression patterns. Panel G’s analysis of sequence divergence and Panel H’s investigation into the relationship between Ka/Ks ratios and expression divergence offer deeper insights into the evolutionary pressures and functional differentiation of bialleles. This detailed genomic and expression analysis is crucial for understanding the genetic basis of important traits in cassava. 2.2 Phylogenetic tree construction To infer the evolutionary relationships among different cassava varieties and their wild relatives, researchers commonly use phylogenetic tree construction methods such as Maximum Likelihood (ML) (Simon et al., 2021) and Bayesian Inference (BI) (Yonis et al., 2020). These methods are employed to infer evolutionary relationships among different cassava genotypes by analyzing genetic marker data. ML is a statistical method that estimates the tree topology with the highest likelihood given the observed data, while BI uses probability distributions to estimate the uncertainty of phylogenetic trees.
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