Peering through the hedge: Multiple datasets yield insights into the phylogenetic relationships and incongruences in the tribe Lilieae (Liliaceae).

The increasing use of genome-scale data has significantly facilitated phylogenetic analyses, contributing to the dissection of the underlying evolutionary mechanisms that shape phylogenetic incongruences, such as incomplete lineage sorting (ILS) and hybridization. Lilieae, a prominent member of the Liliaceae family, comprises four genera and approximately 260 species, representing 43% of all species within Liliaceae. They possess high ornamental, medicinal and edible values.

Phylogeny, adaptive evolution, and taxonomy of (Apiaceae): evidence from plastid phylogenomics and morphological data.

Introduction: The genus , belonging to Apiaceae, includes approximately 25 species distributed in the high-altitude Sino-Himalayan region from E Nepal to SW China. This genus is a taxonomically complex genus with often indistinct species boundaries and problematic generic delimitation with and other close genera, largely due to the varied morphological characteristics.

Methods: To explore the phylogenetic relationships and clarify the limits of the genus and its related genera, we reconstructed a reliable phylogenetic framework with high support and resolution based on two molecular datasets (plastome data and ITS sequences) and performed morphological analyses.

Morphology and ITS sequences provide insights into the phylogeny of Tongoloa (Apiaceae) from China.

Background: Tongoloa is a genus comprising approximately 20 species, primarily distributed in the mountainous regions of southwest China. The insufficiency of specimen materials and morphological similarities among species render it a taxonomically challenging genus within the Apiaceae family. To elucidate the phylogenetic relationships and taxonomy of Chinese Tongoloa, this study utilized a total of 115 nrITS sequences, including 47 recently obtained sequences, for phylogenetic reconstruction.

The Micromorphology and Its Taxonomic Value of the Genus L. in China (Apiaceae).

The genus L. possesses many medically important plants, belonging to the family Apiaceae. It is one of the most taxonomically difficult taxa, largely due to the great variability in habit, foliage, flowers and fruits.

Plastid phylogenomics contributes to the taxonomic revision of taxa within the genus L. and acceptance of two new members of the genus.

Introduction: The genus L. is a taxonomically complicated taxa within Apiaceae, as its high variability in morphology. Although taxonomists have performed several taxonomic revisions for this genus, the interspecific relationships and species boundaries have not been satisfactorily resolved, especially for those endemic to China.

Phylogeny and Taxonomic Revision of the Genus (Apiaceae), Based on Plastid Genomes and Morphological Evidence.

is considered a monotypic genus and is also endemic to the southwest of China. No detailed phylogenetic studies or plastid genomes have been identified in . In this study, the plastid genome sequence and nrDNA sequence were used for the phylogenetic analysis of and its related groups.

The complete plastomes of thirteen Libanotis (Apiaceae, Apioideae) plants: comparative and phylogenetic analyses provide insights into the plastome evolution and taxonomy of Libanotis.

Background: The genus Libanotis Haller ex Zinn, nom. cons., a contentious member of Apiaceae, encompasses numerous economically and medicinally significant plants, comprising approximately 30 species distributed across Eurasia.

Phylogeny and diversification of genus Sanicula L. (Apiaceae): novel insights from plastid phylogenomic analyses.

Background: The genus Sanicula L. is a unique perennial herb that holds important medicinal values. Although the previous studies on Sanicula provided us with a good research basis, its taxonomic system and interspecific relationships have not been satisfactorily resolved, especially for those endemic to China.

Plastid Phylogenomic Analyses Reveal a Cryptic Species of (Apiaceae, Angiosperms).

is identified and described as a cryptic species from Sichuan Province, China. Although the distribution of this cryptic species overlaps with that of and , the morphological boundaries between them are explicit and have obviously distinguishable characters. The main distinguishing features of the cryptic species are as follows: long conical multi-branched roots, very short pedicels in compound umbels, unequal rays, oblong-globose fruits, 1-2 vittae per furrow and 3-4 vittae on the commissure.

Backbone phylogeny and adaptive evolution of s. l.: New insights from phylogenomic analyses of complete plastome data.

is a taxonomically challenging taxon of Apiaceae, as its circumscription and composition remain controversial for morphological similarities with several related genera, leading to a dispute between in the broad sense and strict sense. While evidence from previous molecular studies recognized plural branching lineages within the s. l.

Morphological and molecular evidence gives insight into the taxonomic position of (Apiaceae, Selineae).

In this study, morphological and molecular evidences were combined to determine the taxonomic position of Hand.-Mazz. Morphologically, is similar to the species of the genus in having fibrous remnant sheaths at the stem base, pinnate and linear coexisted bracts, strongly compressed dorsally mericarps, filiform median and lateral ribs, winged marginal ribs, numerous vittae in each furrow and commissure, but can also be easily distinguished from members of by its hispid fruit and linear-lanceolate bracteoles.

Phylogeny and adaptive evolution of subgenus Rhizirideum (Amaryllidaceae, Allium) based on plastid genomes.

The subgenus Rhizirideum in the genus Allium consists of 38 species worldwide and forms five sections (A. sect. Rhizomatosa, A.

Plastid Phylogenomic Analyses Reveal the Taxonomic Position of .

is a famous folk medicinal plant in China. However, the taxonomy of the has not been sufficiently resolved. Due to similar morphological features between and members, the World Flora Online (WFO) Plant List suggested that this species transformed into the genus and merged with .

Plastid Phylogenomics Provide Evidence to Accept Two New Members of (Apiaceae, Angiosperms).

and are recognized as members of the genus because of their dorsally compressed mericarps with slightly prominent dorsal ribs and narrowly winged lateral ribs. However, these species are not similar to other taxa but resemble in overall morphology. To check the taxonomic positions of and , we sequenced their complete plastid genome (plastome) sequences and, together with eleven previously published plastomes, performed comprehensively comparative analyses.

The plastid genome of twenty-two species from Ferula, Talassia, and Soranthus: comparative analysis, phylogenetic implications, and adaptive evolution.

Background: The Ferula genus encompasses 180-185 species and is one of the largest genera in Apiaceae, with many of Ferula species possessing important medical value. The previous studies provided more information for Ferula, but its infrageneric relationships are still confusing. In addition, its genetic basis of its adaptive evolution remains poorly understood.

Evidence from Phylogenomics and Morphology Provide Insights into the Phylogeny, Plastome Evolution, and Taxonomy of .

Pimenov is one of the segregate genera of sensu lato within the Apiaceae. The phylogenetic position and morphological delimitation of have been controversial. In this study, we used plastid genome (plastome) and nuclear ribosomal DNA (nrDNA) sequences to reconstruct the phylogeny of , along with comparative plastome and morphological analyses between and related taxa.

The phylogeny of Seseli (Apiaceae, Apioideae): insights from molecular and morphological data.

Background: The genus Seseli L., which consists of 125-140 species distributed in the Old World from western Europe and northwestern Africa to China and Japan, is one of the largest and most taxonomically difficult genera of Apiaceae Lindl. Although several previous studies have been conducted on Seseli based on limited morphological characteristics and molecular fragments, a robust and comprehensive phylogeny of Seseli remains elusive.

Plastid phylogenomic insights into relationships, divergence, and evolution of Apiales.

Members of Apiales are monophyletic and radiated in the Late Cretaceous. Fruit morphologies are critical for Apiales evolution and negative selection and mutation pressure play important roles in environmental adaptation. Apiales include many foods, spices, medicinal, and ornamental plants, but the phylogenetic relationships, origin and divergence, and adaptive evolution remain poorly understood.

Molecular evolution and phylogenetic relationships of Ligusticum (Apiaceae) inferred from the whole plastome sequences.

Background: The genus Ligusticum belongs to Apiaceae, and its taxonomy has long been a major difficulty. A robust phylogenetic tree is the basis of accurate taxonomic classification of Ligusticum. We herein used 26 (including 14 newly sequenced) plastome-scale data to generate reliable phylogenetic trees to explore the phylogenetic relationships of Chinese Ligusticum.

Phylogenetic position of (Apiaceae, Apioideae): evidence from molecular data and carpological characters.

(Apiaceae, Apioideae) is now considered to have an East-Asia and Sino-Himalaya distribution. The genus was not recognized as a natural and separate genus and was treated as a synonym of both in and since first established, though Pimenov have made many taxonomic revisions to , phylogenetic relationships between and have been in dispute. Thirty-four plastomes and 35 nrITS from Apioideae were analysed by RAxML and MrBayes to reconstruct the phylogenetic relationships, along with carpology of 10 species and comparative analyses of 17 plastomes to investigate the evidence supporting the independence of .

Comparative Plastome Analysis of Three Amaryllidaceae Subfamilies: Insights into Variation of Genome Characteristics, Phylogeny, and Adaptive Evolution.

In the latest APG IV classification system, Amaryllidaceae is placed under the order of Asparagus and includes three subfamilies: Agapanthoideae, Allioideae, and Amaryllidoideae, which include many economically important crops. With the development of molecular phylogeny, research on the phylogenetic relationship of Amaryllidaceae has become more convenient. However, the current comparative analysis of Amaryllidaceae at the whole chloroplast genome level is still lacking.

The complete plastomes of seven Peucedanum plants: comparative and phylogenetic analyses for the Peucedanum genus.

Background: The Peucedanum genus is the backbone member of Apiaceae, with many economically and medically important plants. Although the previous studies on Peucedanum provide us with a good research basis, there are still unclear phylogenetic relationships and many taxonomic problems in Peucedanum, and a robust phylogenetic framework of this genus still has not been obtained, which severely hampers the improvement and revision of taxonomic system for this genus. The plastid genomes possessing more variable characters have potential for reconstructing a robust phylogeny in plants.

Phylogeny, Age, and Evolution of Tribe Lilieae (Liliaceae) Based on Whole Plastid Genomes.

Tribe Lilieae, encompassing , , , and , includes economically important crops with a horticultural and medicinal value. It is considered to be a core lineage of Liliaceae, but phylogenetic relationships within it, and the timing of the origin of individual clades, remain incompletely resolved. To address these issues, we reconstructed the evolutionary history of the tribe.

Phylogeny and Comparative Analysis for the Plastid Genomes of Five (Liliaceae).

Species of (Liliaceae) are of great horticultural importance and are distributed across Europe, North Africa, and Asia. The Tien Shan Mountain is one of the primary diversity centres of , but the molecular studies of species from this location are lacking. In our study, we assembled four plastid genomes from the Tien Shan Mountains, , , , and , combined with the plastid genome of to compare against other Liliaceae plastid genomes.

Effects of Mountain Uplift and Climatic Oscillations on Phylogeography and Species Divergence of (Apiaceae).

Exploring the effects of orographic events and climatic shifts on the geographic distribution of organisms in the Himalayas-Hengduan Mountains (HHM) region and Qinghai-Tibetan Plateau (QTP) is crucial to understand the impact of environmental changes on organism evolution. To gain further insight into these processes, we reconstructed the evolutionary history of nine species distributed across the HHM and QTP regions. In total, 525 individuals from 56 populations of the nine species were analyzed based on three maternally inherited chloroplast fragments (, , and ) and one nuclear DNA region (internal transcribed spacer, ITS).