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Conservation Status, Plastome Diversity, and Evolutionary Diversification of Three Arabian Desmidorchis Endemics (Apocynaceae)
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Department of Biology, Faculty of Science, Umm Al-Qura University, Makkah 24381, Saudi Arabia
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Biology Department, Faculty of Science, University of Aden, Khormaksar, Aden P.O. Box 6235, Yemen
*
Author to whom correspondence should be addressed.
Biology 2026, 15(10), 798; https://doi.org/10.3390/biology15100798 (registering DOI)
Submission received: 25 March 2026
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Revised: 10 May 2026
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Accepted: 13 May 2026
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Published: 17 May 2026
Simple Summary
Many unique plant species native to the Arabian Peninsula are increasingly threatened by habitat loss and climatic change. Among these are members of the genus Desmidorchis, succulent plants traditionally valued for their medicinal importance. This study evaluated the extinction risk of three endemic species and characterized their complete chloroplast genomes to better understand their evolutionary history and genomic diversity. The results classified all three species as Near Threatened (NT), indicating that they may become more vulnerable without effective conservation measures. Comparative plastome analyses revealed a highly conserved genome structure, although several regions, particularly ycf1 and clpP1, showed comparatively elevated sequence divergence and a useful phylogenetic signal. Codon usage and selection-pressure analyses further demonstrated that most plastid genes remain under strong purifying selection, reflecting overall genomic conservation within Stapeliinae. Molecular dating suggested that Arabian Desmidorchis diversified relatively recently during the Pleistocene, likely in association with climatic fluctuations and habitat fragmentation in Arabian mountain systems. These findings provide important baseline data for future taxonomic, evolutionary, and conservation studies of rare Arabian succulent plants.
Abstract
The genus Desmidorchis Ehrenb. (Apocynaceae) is a characteristic component of the succulent flora of the Arabian Peninsula, where high levels of endemism and increasing environmental pressures highlight the need for integrated genomic and conservation research. This study assessed the conservation status of three ethnomedicinally important endemics—D. adenensis, D. arabica, and D. awdeliana—and characterizes their complete plastomes to resolve their evolutionary and temporal history. Conservation assessments were conducted following IUCN Red List criteria, and complete plastomes were sequenced and compared within a dataset of 15 subtribe Stapeliinae taxa. Comparative analyses examined the genome structure, divergence hotspots, repetitive sequences, codon usage bias, and selection pressure, while divergence times were estimated using fossil-calibrated molecular clock analyses. All three species were classified as Near Threatened (NT), primarily due to anthropogenic and environmental pressures. Plastome analyses revealed a highly conserved genome structure; however, hypervariable regions, particularly ycf1 and clpP1, exhibited elevated sequence divergence and phylogenetic informativeness. Simple sequence repeats (SSRs) were also identified as potentially informative features at the genus level. Codon usage and Ka/Ks analyses further indicated that most plastid protein-coding genes are under strong purifying selection, whereas only a few loci, particularly clpP1, showed comparatively elevated evolutionary rates. Phylogenomic analyses supported the monophyly of Desmidorchis, with molecular dating indicating recent Pleistocene diversification (~0.34–1.51 Ma), potentially associated with Quaternary climatic oscillations. Overall, this study provides an important genomic foundation for future taxonomic, evolutionary, and conservation studies of rare Arabian taxa.
