مطالعه روابط فرگشتی در جنس Heterorhabditis، تجزیه و تحلیل نسب‌شناختی مبتنی بر نواحی ژنومی مختلف و طراحی آغازگرهای اختصاصی برای هر ناحیه

This research introduces a suite of novel primers targeting phylogenetically informative genetic loci including Internal Transcribed Spacer 1 (ITS1), ITS2, ITS, Cytochrome Oxidase I (COX1) and large subunit ribosomal DNA (28s-rDNA) within Heterorhabditis species and provide phylogenetically insights on the efficiency of these regions in unravelling phylogeny relationships. Two regions, namely ITS and 28S rDNA, proved instrumental in attaining highly resolved trees accompanied by solid branch supports. The ITS1-constructed phylogenetic tree exhibited decreased confidence ratings at deeper nodes by having low bootstrap values. Contrastingly, the ITS2-based tree registered augmented bootstrap scores for interior nodes. Root node polytomy characterized the tree arising from ITS1 and ITS2 analysis. Nonetheless, the composite ITS1 & ITS2 tree failed to align logically with singular ITS1 or ITS2 trees. Noteworthy disparities emerged among the reconstructed trees concerning the placement of a monophyletic assemblage consisting of H. bacteriophora, H. beicherriana, and H. georgiana. Specifically, disagreements materialized when assigning this cohesive unit as either a sibling entity or being nested within another cluster. Such incongruities led to varying interpretations of evolutionary histories depending on the chosen ITS fragment used for reconstruction. However, despite these inconsistencies, there remained remarkable uniformity observed in terms of consistency indices (CI) and retention indices (RI) across all ITS-derived trees. These congruent measures reflected the overall stability and reliability of the resulting phylogenetic structures regardless of minor fluctuations in branch arrangements. Nevertheless, the COXI-based phylogenetic tree exhibited inferior CI and RI indices, suggesting lower fit of the tree to the data and a higher degree of homoplasy, respectively. Ultimately, the ITS region offered unrivaled discriminating prowess and dependable branch supports, cementing itself as the optimal choice for unequivocal demarcation of Heterorhabditis species delineations. Employment of the proposed primer set shall facilitate informed decision-making processes reliant upon robust phylogenetic frameworks.