Species Delimitation and Conservation in Taxonomically Challenging Lineages: The Case of Two Clades of Capurodendron (Sapotaceae) in Madagascar

Target capture and genome skimming for plant diversity studies

Recent technological advances in long-read high-throughput sequencing and assembly methods have facilitated the generation of annotated chromosome-scale whole-genome sequence data for evolutionary studies; however, generating such data can still be difficult for many plant species. For example, obtaining high-molecular-weight DNA is typically impossible for samples in historical herbarium collections, which often have degraded DNA. The need to fast-freeze newly collected living samples to conserve high-quality DNA can be complicated when plants are only found in remote areas. Therefore, short-read reduced-genome representations, such as target capture and genome skimming, remain important for evolutionary studies. Here, we review the pros and cons of each technique for non-model plant taxa. We provide guidance related to logistics, budget, the genomic resources previously available for the target clade, and the nature of the study. Furthermore, we assess the available bioinformatic analyses, detailing best practices and pitfalls, and suggest pathways to combine newly generated data with legacy data. Finally, we explore the possible downstream analyses allowed by the type of data generated using each technique. We provide a practical guide to help researchers make the best-informed choice regarding reduced genome representation for evolutionary studies of non-model plants in cases where whole-genome sequencing remains impractical.

Understanding the Taxonomic Complexes and Species Delimitation within Sambucus L. (Viburnaceae)

The genus Sambucus belongs to the family Viburnaceae, and has long been a debatable taxon regarding its systematics and taxonomic assignment. It is known for its morphological and genetic variations and thus the taxonomic delimitation remains uncertain. Phenotypic and genotypic variations within plant species causes difficulties in the detection of species boundaries. In the present review, we compiled a set of studies that assessed species discrimination within Sambucus genus by morphological and molecular markers as well as the taxonomic uncertainties in the re-circumscription of the segregated genera i.e., Viburnum L., Sambucus L., and Adoxa L., (syn. Sinadoxa C.Y. Wu, Z.L. Wu & R.F. Huang/Tetradoxa C.Y. Wu) from Caprifoliaceae and their family assignment. The data was obtained from published journal articles and various online databases. Morphological and molecular diagnostic characters were employed to distinguish Sambucus species. Our findings indicated that high intraspecific variations within narrow-ranged populations and their widespread counterparts contribute to its taxonomic complications. Additionally, intraspecific variations within Sambucus species leads to misidentifications and the misapplication of names, occasioning the publication of many putative synonyms and ambiguous names. Possible interspecific hybridizations experienced between Sambucus species increases complexity in character evolution. A morphological analysis showed that the endocarp seed morphological characters can reliably support the segregation of Sambucus taxa into discrete taxonomic entities. In molecular analysis, the NeighborNet (NN) phylogenetic split network revealed three distinct genera including Viburnum, Sambucus, and Adoxa, which clustered separately. The Maximum Likelihood (ML) analysis indicated that the Sambucus species formed a monophyletic group and clustered into two major clades, a small clade containing S. maderensis, S. peruviana, S. nigra, and S. canadensis, and a large clade encompassing the rest of the species with significantly supported clades (<52%). The preferred family assignment for Sambucus is Viburnaceae.