International Journal of Molecular Evolution and Biodiversity 2024, Vol.14, No.3, 120-132 http://ecoevopublisher.com/index.php/ijmeb 128 5.2 Impact of human intervention Human cultivation practices have had a profound impact on the evolutionary pathways of cassava. The practice of incorporating seedlings from sexual reproduction into planting stocks has exposed cassava to selection pressures favoring rapid growth in agricultural environments (Pujol et al., 2005). This has led to morphological changes, such as the reversion to epigeal germination and the development of photosynthetic cotyledons, which confer high initial growth rates in cultivated habitats (Pujol et al., 2005). Meanwhile, selecting traits that can improve agricultural productivity and resilience also significantly affects the genetic structure of cassava, which has been shaped to enhance yield, improve drought resistance, and increase pest resistance(Okogbenin et al., 2012; Oliveira et al., 2017; Ntui et al., 2023). For instance, the selection for larger root size and higher starch content has led to varieties that are vastly more productive than their wild counterparts. Similarly, in response to the challenge of variable water availability, especially in regions like Northeast Brazil and sub-Saharan Africa, cultivars with enhanced drought tolerance have been developed. These traits are not only the result of direct selection but also of sophisticated breeding techniques, including hybridization and, more recently, genetic engineering. The modifications in genetic traits have also had ecological impacts, such as changes in plant architecture and root system depth, which in turn affect soil health and agricultural sustainability. 5.3 Comparative analysis Comparing cassava’s domestication trajectory with that of other staple crops reveals both unique and common patterns of domestication. Like many other crops, cassava has undergone selection for traits favored by humans, such as increased palatability and yield, while experiencing a reduction in genetic diversity due to selective sweeps and genetic bottlenecks (Smýkal et al., 2018). Unlike some other crops, cassava’s clonal propagation has allowed for the effective exploitation of nonadditive genetic effects, such as dominance and epistasis, particularly for traits like root yield and disease resistance (Elias et al., 2000). This contrasts with crops that are primarily sexually reproduced, where additive genetic effects are more commonly selected. 6 Challenges and Limitations in Current Research 6.1 Gaps in phylogenetic data Despite advancements in genetic sequencing and phylogenetic analysis, significant gaps remain in the phylogenetic data available for cassava. One major limitation is the incomplete representation of wild and ancestral varieties in genetic studies, which are crucial for understanding the full phylogenetic landscape of cassava. This lack of comprehensive sampling can lead to biased interpretations of cassava’s evolutionary history and its domestication process. Additionally, many existing phylogenetic studies rely on limited genetic markers, which may not provide a complete picture of the genetic diversity and evolutionary relationships within the Manihot genus (Simon et al., 2021). Expanding the types of genetic markers used, such as incorporating more single nucleotide polymorphisms (SNPs) and whole-genome sequencing data, could greatly enhance the resolution and accuracy of phylogenetic trees. 6.2 Complexities in interpreting data The interpretation of genetic and phylogenetic data in cassava is compounded by the complexity of its genome. Cassava possesses a highly heterozygous genome, which presents challenges for genetic assembly and accurate variant calling. This heterozygosity can obscure phylogenetic signals and complicate efforts to identify clear genetic relationships among different cassava varieties and their wild counterparts. Furthermore, cassava’s genome shows evidence of past polyploidy events, adding another layer of complexity to genetic analyses (Bredeson et al., 2016; Chen et al., 2021). These polyploidy events can result in multiple copies of genes, which may undergo independent evolutionary paths, thus complicating phylogenetic interpretations and functional genomic studies. Additionally, environmental adaptations and artificial selection pressures have led to convergent evolutionary traits in cassava, which can be mistaken for close genetic relationships in phylogenetic analyses. Distinguishing between convergence due to adaptive traits and genuine phylogenetic closeness requires careful genomic and phenotypic characterization, which is often limited by the current methodologies and data availability.
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