The Leafless Vanilla Species-Complex from the South-West Indian Ocean Region: A Taxonomic Puzzle and a Model for Orchid Evolution and Conservation Research

Phylogenetic relationships and the identification of allopolyploidy in circumpolar Silene sect. Physolychnis

PREMISE

Species complexes are groups of closely related species with ambiguous delimitation, often composed of recently diverged lineages. Polyploidization and uniparental reproduction (i.e., selfing and apomixis) can play important roles in the origin of species complexes. These complexes pose challenges for species-based scientific questions, such as the estimation of species richness or conservation prioritization.

METHODS

We determined the potential of resolving taxonomically complex groups using target enrichment in the circumpolar Silene uralensis complex (Caryophyllaceae). We proposed a metric using genetic distances between phased alleles to distinguish diploids from allopolyploids.

RESULTS

Our results identified geographic structure of populations, with the northern American and Greenlandic samples having a common ancestor. We found little phylogenetic support for the most recent taxonomic treatment of the Silene uralensis complex.

CONCLUSIONS

The study highlights the use of target enrichment in testing taxonomic hypotheses in diploids and the challenges of studying recently diverged lineages.

Unveiling a Meaningful Form of Cypripedium × ventricosum Sw. (Cypripedioideae, Orchidaceae) from Changbai Mountain, China: Insights from Morphological, Molecular, and Plastome Analyses

A Cypripedium plant was discovered in Wangqing County, Changbai Mountain, Jilin Province. This newly discovered plant of Cypripedium not only inhabits the same natural habitat as Cypripedium calceolus L. and Cypripedium × ventricosum Sw. but also has a morphology intermediate between that of C. calceolus and C. × ventricosum. Its dorsal sepals, petals, and synsepal are similar to those of C. calceolus, while the color of its lip is intermediate between that of C. calceolus and C. × ventricosum. For the purpose of distinguishing the newly discovered plant of Cypripedium from other Cypripedium plants, we provisionally named it W1. To further verify the taxonomic status of W1, we introduced three identified forms of C. × ventricosum and conducted molecular biology analyses with W1, C. calceolus, and C. × ventricosum. The analyses further confirmed the relationship between W1 and C. × ventricosum, and the phylogenetic analysis of the nuclear region demonstrated a close relationship between W1 and C. calceolus. Collectively, the morphological and molecular evidence indicates that W1 is a product of the backcross between C. × ventricosum and C. calceolus. Although it shows morphological differences from typical C. × ventricosum, it can still be considered a form of C. × ventricosum. We further investigated the chloroplast genome of this form of C. × ventricosum and determined that its total genome length was 196,850 bp. The genome contains 132 genes, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. By analyzing the phylogenetic position and chloroplast genome of the form of C. × ventricosum, this study clarified the relationships among Cypripedium taxa with similar morphological characteristics, laying a foundation for research on orchid evolution and species conservation.

Assessing the phylogenetic relationship among varieties of Toona ciliata (Meliaceae) in sympatry with chloroplast genomes

Toona ciliata is an endangered species due to over-cutting and low natural regeneration in China. Its genetic conservation is of an increasing concern. However, several varieties are recognized according to the leaf and flower traits, which complicates genetic conservation of T. ciliata. Here, we sequenced the whole chloroplast genome sequences of three samples for each of four varieties (T. ciliata var. ciliata, T. ciliata var. yunnanensis, T. ciliata var. pubescens, and T. ciliata var. henryi) in sympatry and assessed their phylogenetic relationship at a fine spatial scale. The four varieties had genome sizes ranged from 159,546 to 159,617 bp and had small variations in genome structure. Phylogenomic analysis indicated that the four varieties were genetically well-mixed in branch groups. Genetic diversity from the whole chloroplast genome sequences of 12 samples was low among varieties (average π = 0.0003). Besides, we investigated genetic variation of 58 samples of the four varieties in sympatry using two markers (psaA and trnL-trnF) and showed that genetic differentiation was generally insignificant among varieties (Ф st = 0%-5%). Purifying selection occurred in all protein-coding genes except for the ycf2 gene that was under weak positive selection. Most amino acid sites in all protein-coding genes were under purifying selection except for a few sites that were under positive selection. The chloroplast genome-based phylogeny did not support the morphology-based classification. The overall results implicated that a conservation strategy based on the T. ciliata complex rather than on intraspecific taxon was more appropriate.

A new remarkable Vanilla Mill. (Orchidaceae) species endemic to the Espinhaço Range, Brazil: its phylogenetic position and evolutionary relationships among Neotropical congeners

During surveys conducted on Neotropical Vanilla, a new endemic species was found in the Brazilian campos rupestres of the Espinhaço Range. Here, this new remarkable Vanilla species, namely V.rupicola Pansarin & E.L.F. Menezes, is described and illustrated. A phylogeny for Vanilla is presented and the relationships between Neotropical species are discussed. The position of V.rupicola among Neotropical Vanilla is discussed within an evolutionary context. Vanillarupicola is recognized by its rupicolous habit, its reptant stems, and its sessile and rounded leaves. This remarkable new taxon emerges in a clade that includes V.appendiculata Rolfe and V.hartii Rolfe. Vegetative and floral features support a close relationship between V.rupicola and sister taxa, mainly regarding the apical inflorescence (V.appendiculata), the type of appendages of the central crest of the labellum, and the labellar color pattern. Phylogenetic inference suggests that the circumscription of Neotropical Vanilla groups needs revision.

Hybridization in the Fringed Orchids: An Analysis of Species Boundaries in the Face of Gene Flow

Natural hybridization between closely related species in sympatry is an evolutionary process that is common in orchids. Once seen as a threat to parent species, interspecific genetic change is increasingly viewed as a source of novel variation in some ecological contexts. Terrestrial fringed orchids in the genus Platanthera contain several clades with high genetic compatibility among species and many putative hybrids. We used biallelic SNPs generated with 3RAD sequencing to study the hybrid complex formed from the parent species P. blephariglottis, P. ciliaris, and P. cristata with high resolution. The genetic structure and phylogenetic relationship of the hybrid complex revealed site-dependent gene flow between species. We documented extensive hybridization and cryptic hybrids in sympatric sites. Interspecific genetic exchange is particularly common between P. blephariglottis and P. ciliaris, with cryptic hybrids among putative P. ciliaris samples being more common than parental assignments in sympatric sites. Hybridization across the triad species complex can reticulate lineages and introduce adaptive alleles. Conversely, it can reduce diversification rates and introduce maladaptive alleles. Investigation into whether anthropogenic forces are eroding species boundaries, particularly the permeable P. blephariglottis and P. ciliaris boundary, is appropriate for conservation efforts.

Vanilla beyond Vanilla planifolia and Vanilla × tahitensis: Taxonomy and Historical Notes, Reproductive Biology, and Metabolites

Vanilla is a worldwide cherished condiment, and its volatile market is associated with the so-called "vanilla crisis". Even though only two species (Vanilla planifolia and V. × tahitensis) are cultivated on a large scale for commercial purposes, the Vanilla genus is comprised of 140 species. The present review article discusses the facets of this crisis, and vanilla crop wild relatives (WRs) are showcased as alternatives to overcome them. Historical, taxonomic, and reproductive biology aspects of the group were covered. Emphasis was given to the metabolic characterization of the vanilla crop WRs, highlighting their main chemical classes and the potential flavor descriptors. Many of these species can produce important flavor compounds such as vanillin, vanillic acid, and acetovanillone, among others. Overall, this review compiles valuable information that can help unravel new chapters of the history of this treasured product by evidencing the biotechnological potential of vanilla crop WRs.

Effect-directed profiling of 32 vanilla products, characterization of multi-potent compounds and quantification of vanillin and ethylvanillin

Food testing is of great importance to the food industry and organizations to verify the authenticity claims, to prove the quality of raw materials and products, and to ensure food safety. The market prices of vanilla differed by a factor of about 20 in the last three decades. Therefore the risk of adulteration and counterfeiting of vanilla products is high. Instead of commonly used target analyses and sum parameter assays, a complementary non-target multi-imaging effect-directed screening was developed, which provided a new perspective on the wide range of vanilla product qualities on the market. Planar chromatography was combined with effect-directed assays, and the obtained biological and biochemical profiles of 32 vanilla products from nine different categories revealed a variety of active ingredients. Depending on the region, typical vanilla product profiles and activity patterns were obtained for pods, tinctures, paste (inner part), oleoresin and powders. However, some vanilla products showed additional active compounds and a different intensity pattern. The vanilla product profiles substantially differed from those of vanilla aroma or products containing synthetic vanillin or vanilla-flavored food products. Bioactive compounds of interest were online eluted and further characterized via HPTLC-HRMS, which allowed their tentative assignment. After purchase of the standards, these were successfully confirmed by co-chromatography. Quantification of vanillin across nine different product categories revealed levels ranging from 1 µg/g to 36 mg/g with a mean repeatability of 1.9%. The synthetic ethylvanillin was not detected in the investigated samples in significant concentrations. The assessment of differences in the activity patterns pointed to highly active compounds, which were not detected at UV/Vis/FLD but first via the biological and enzymatic assays. This effect-directed profiling bridges the gap from analytical food chemistry to food toxicology, and thus, makes an important contribution to consumer safety. In the same way, it would accelerate investigations for Registration, Evaluation, Authorisation and Restriction of Chemicals (REACH) according to Regulation (EC) No. 1907/2006.

Drivers of population divergence and species differentiation in a recent group of indigenous orchids (Vanilla spp.) in Madagascar

With over 25,000 species, orchids are among families with remarkable high rate of diversification. Since Darwin's time, major advances attributed the exceptional diversity of orchids to plant-pollinator interactions. However, unraveling the processes and factors that determine the phenotypic and genotypic variation of natural orchid populations remains a challenge. Here, we assessed genetic population structure and floral differentiation in recently diverged leafless Vanilla species in a world biodiversity hotspot, Madagascar, using seven microsatellite loci and 26 morphometric variables. Additionally, analyses were performed to test for the occurrence of any patterns of isolation by distance, isolation by environment, and isolation by adaptation and to detect possible physical barriers that might have caused genetic discontinuities between populations. Positive inbreeding coefficients detected in 22 populations were probably due to the presence of null alleles, geitonogamy and/or some admixture (sympatric species). In contrast, the only high-altitude population showed an important rate of clonality leading to heterozygote excess. Genetic diversity was maximum in western populations, suggesting a postglacial colonization to the north and south. Clustering analyses identified seven genetic groups characterized by specific floral traits that matched five botanical descriptions in the literature. A contribution of montane refugia and river barriers on population differentiation was detected. We also detected combined effects of IBD/IBE and IBE/IBA on genetic differentiation and suggested this pattern is more likely determined by ecological isolation, although pollinator-mediated divergent selection could not be ruled out for some of the species. Overall, this study provides further insights on speciation in orchids, a group for which Madagascar shows one of the world's highest level of endemism and confirms the importance of the peculiar biogeography of the island in shaping species differentiation.