Plastome-based backbone phylogeny of East Asian Phedimus (Subgenus Aizoon: Crassulaceae), with special emphasis on Korean endemics

Abstract

Although the monophyly of Phedimus has been strongly demonstrated, the species relationships among approximately 20 species of Phedimus have been difficult to determine because of the uniformity of their floral characteristics and extreme variation of their vegetative characters, often accompanied by high polyploid and aneuploid series and diverse habitats. In this study, we assembled 15 complete chloroplast genomes of Phedimus species from East Asia and generated a plastome-based backbone phylogeny of the subgenus Aizoon. As a proxy for nuclear phylogeny, we reconstructed the nuclear ribosomal DNA internal transcribed spacer (nrDNA ITS) phylogeny independently. The 15 plastomes of subg. Aizoon were highly conserved in structure and organization; hence, the complete plastome phylogeny fully resolved the species relationships with strong support. We found that P. aizoon and P. kamtschaticus were polyphyletic and morphologically distinct or ambiguous species, and they most likely evolved from the two species complex. The crown age of subg. Aizoon was estimated to be 27 Ma, suggesting its origin to be in the late Oligocene; however, the major lineages were diversified during the Miocene. The two Korean endemics, P. takesimensis and P. zokuriensis, were inferred to have originated recently during the Pleistocene, whereas the other endemic, P. latiovalifolium, originated in the late Miocene. Several mutation hotspots and seven positively selected chloroplast genes were identified in the subg. Aizoon.

Phylogenetic relationships and genetic diversity of the Korean endemic Phedimus latiovalifolius (Crassulaceae) and its close relatives

“…Recently, Moon and Jang 25 reported that P. latiovalifolius, P. takesimensis , and P. middendorffianus should be recognized as distinct taxa based on their morphological characteristics. Molecular phylogenetic studies on interspecific relationships within the subgenus Aizoon species in Korea have encountered challenges in establishing robust phylogenetic relationships 26 , 27 . For instance, Seo et al (2020) 26 conducted a phylogenetic analysis of five Korean taxa ( P. takesimensis , P. aizoon , P. kamtschaticus , P. ellacombeanus , and P. latiovalifolius ) to assess the anagenetic speciation of P. takesimensis on Ulleung Island.…”

“…However, the overall lack of resolution and support, along with insufficient sampling, prevented the determination of the closest sister species to P. latiovalifolius . Recently, Kim et al (2023) 27 explored overall species relationships within the subgenus Aizoon using complete plastomes and nrDNA ITS sequences. Despite these efforts, neither the monophyly of P. latiovalifolius nor the phylogenetic relationships within Aizoon were adequately addressed, attributed to insufficient sampling and/or limited tree resolution and node support.…”

Multispectral Phenotyping and Genetic Analyses of Spring Appearance in Greening Plant, Phedimus spp.

“…The genus Phedimus is mainly distributed in Asia and Europe, with about 20 species [ 8 , 9 ]. P. takesimensis is narrowly restricted to Ulleung Island [ 8 ].…”

“…The genus Phedimus is mainly distributed in Asia and Europe, with about 20 species [ 8 , 9 ]. P. takesimensis is narrowly restricted to Ulleung Island [ 8 ]. It has been suggested that the species is monophyletic with an ancestral species of continental origin [ 10 ].…”

“…[ 10 ] suggest that P. kamchaticus and P. aizoon may be the ancestral species of P. takesimensis , and Kim et al. [ 8 ] suggest that the species P. middendorffianus , P. aizoon , P. litoralis , and P. selskianus , are likely to be the ancestral species of P. takesimensis . However, there are no reports on the relationship based on cross-compatibility among these species.…”