International Journal of Molecular Evolution and Biodiversity 2024, Vol.14, No.2, 52-61 http://ecoevopublisher.com/index.php/ijmeb 53 1 Systematic Classification of Cucurbitaceae 1.1 Historical perspective on the classification of Cucurbitaceae The Cucurbitaceae family, with approximately 800 species across 130 genera, has been traditionally divided into subfamilies such as Cucurbitoideae and Nhandiroboideae, with further classification into tribes and subtribes. Historically, the classification within Cucurbitaceae has been based on morphological and floral characteristics, which have been used to delineate genera and species. However, this approach has often led to polyphyletic or paraphyletic groupings due to convergent evolution and the plasticity of certain morphological traits (Kocyan et al., 2007; Rahman, 2013). 1.2 Current systematic framework and taxonomic updates Recent systematic studies have proposed a new classification for the Cucurbitaceae family, based on comprehensive molecular data from multiple DNA regions across the three plant genomes. This has resulted in a more natural classification system that comprises 95 genera in 15 tribes, with the introduction of five new tribes: Actinostemmateae, Indofevilleeae, Thladiantheae, Momordiceae, and Siraitieae. This reclassification necessitated 44 new combinations and two new names within the family, reflecting a significant update to the systematic framework of Cucurbitaceae (Schaefer and Renner, 2011). 1.3 Role of molecular markers and phylogenetic studies in reshaping classification Molecular markers, such as chloroplast DNA sequences, nuclear ribosomal RNA genes, and low-copy nuclear genes, have played a pivotal role in reshaping the classification of Cucurbitaceae. Phylogenetic analyses using these markers have provided insights into the relationships among species and genera, often challenging traditional classifications based on morphology alone. For instance, the internal transcribed spacer (ITS) regions have revealed genus-specific variations in length and have suggested a polyphyletic origin for New World species within the family (Jobst et al., 1998). Additionally, molecular systematics has clarified species boundaries within genera, such as Psiguria, and has provided DNA barcodes for species identification (Steele et al., 2010). Phylogenetic informativeness analyses have also been employed to interpret phylogenomic datasets, leading to a better understanding of diversification processes within the family (Bellot et al., 2020). Moreover, molecular phylogenetics has unraveled relationships within the Cucumis genus, indicating multiple introductions from Africa to Asia and highlighting the complex biogeographical history of these species (Ghebretinsae et al., 2007). Seed coat diversity studies have further supported the findings of molecular phylogenetic research, providing additional evidence for the systematic classification of tribes and genera within Cucurbitaceae (Heneidak and Khalik, 2015). The comprehensive phylogeny of the Cucurbitales order, based on DNA sequences from nine loci across three genomes, has implications for the evolution of morphological traits and sexual systems, offering a broader context for the classification of Cucurbitaceae (Zhang et al., 2006; Jaklitsch et al., 2017). In conclusion, the integration of molecular markers and phylogenetic studies has been instrumental in developing a more robust and natural classification system for the Cucurbitaceae family, highlighting the dynamic nature of plant taxonomy in the era of molecular systematics. 2 Phylogenesis of Cucurbitaceae 2.1 Overview of phylogenetic methods used in Cucurbitaceae studies Phylogenetic studies within the Cucurbitaceae family have employed a variety of methods to elucidate the evolutionary relationships among its species. Genome skimming and target sequence capture have been commonly used, despite their limitations such as representation bias and sometimes insufficient resolution of relationships even with hundreds of loci (Bellot et al., 2020). Phylogenetic informativeness and tree confidence analyses have also been applied to interpret phylogenomic datasets, which can help clarify tribe-level relationships within the family (Bellot et al., 2020). Chloroplast DNA sequences from multiple genes and spacers have been used to infer phylogenies, providing insights into the systematic classification of the family (Kocyan et al., 2007). Additionally, the rbcL gene and protein sequences have been utilized to address systematic questions,
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