Systematic implications from a robust phylogenetic reconstruction of the genus Helianthemum (Cistaceae) based on genotyping-by-sequencing (GBS) data

Molecular systematics requires the establishment of a robust phylogenetic framework including extensive geographical and taxonomic sampling. In this work, we proposed systematic changes in the genus Helianthemum based on phylogenetic trees obtained by both maximum likelihood and Bayesian analyses of GBS data. The implications of these phylogenetic results for the systematics of Helianthemum entail the establishment of a new subgenus and novel re-ascriptions of sections and species along with some nomenclatural novelties. The following new combinations are proposed: Helianthemum subg. Eriocarpum (Dunal) Martín-Hernanz, Velayos, Albaladejo & Aparicio; H. oelandicum subsp. conquense (Borja & Rivas Goday ex G.López) Martín-Hernanz, Velayos, Albaladejo & Aparicio; H. nummularium subsp. cantabricum (M.Laínz) Martín-Hernanz, Velayos, Albaladejo & Aparicio; H. nummularium subsp. tinetense (M.Mayor & Fern.Benito) Martín-Hernanz, Velayos, Albaladejo & Aparicio.

Finding missing diversity from synonyms of Haplopteris (Pteridaceae)

Although taxonomists target the remote wild regions to discover new species, taxa lacking a comprehensive and modern systematic treatment may be the new hotspot for biodiversity discovery. The development of molecular systematics integrated with microscopic observation techniques has greatly improved the ability of taxonomists to identify species correctly. Vittaria centrochinensis Ching ex J.F. Cheng, regarded as a synonym of Haplopteris fudzinoi (Makino) E.H.Crane, remained hidden from the eyes of fern taxonomists for more than 20 years. Herein, we collected several population samples of V. centrochinensis by performing molecular phylogenetic analysis of five cpDNA regions (rbcL, atpA, matK, ndhF, and trnL-trnF) and through micromophological observation of specimens which differs from H. fudzinoi by lamina width and exospores. Considering the differences in morphology, geographical range, and genetic distance between these two species, we formally recognized V. centrochinensis as an authentic species and proposed a new combination Haplopteris centrochinensis (Ching ex J.F.Cheng) Y.H.Yan, Z.Y.Wei & X.C.Zhang, comb. nov. Our findings demonstrate that several taxa in synonyms are missing, and nowadays taxonomy should also include re-evaluation of the past taxonomy.

Assessing the suitability of mitochondrial and nuclear DNA genetic markers for molecular systematics and species identification of helminths

Background Genetic markers are employed widely in molecular studies, and their utility depends on the degree of sequence variation, which dictates the type of application for which they are suited. Consequently, the suitability of a genetic marker for any specific application is complicated by its properties and usage across studies. To provide a yardstick for future users, in this study we assess the suitability of genetic markers for molecular systematics and species identification in helminths and provide an estimate of the cut-off genetic distances per taxonomic level. Methods We assessed four classes of genetic markers, namely nuclear ribosomal internal transcribed spacers, nuclear rRNA, mitochondrial rRNA and mitochondrial protein-coding genes, based on certain properties that are important for species identification and molecular systematics. For molecular identification, these properties are inter-species sequence variation; length of reference sequences; easy alignment of sequences; and easy to design universal primers. For molecular systematics, the properties are: average genetic distance from order/suborder to species level; the number of monophyletic clades at the order/suborder level; length of reference sequences; easy alignment of sequences; easy to design universal primers; and absence of nucleotide substitution saturation. Estimation of the cut-off genetic distances was performed using the ‘K-means’ clustering algorithm. Results The nuclear rRNA genes exhibited the lowest sequence variation, whereas the mitochondrial genes exhibited relatively higher variation across the three groups of helminths. Also, the nuclear and mitochondrial rRNA genes were the best possible genetic markers for helminth molecular systematics, whereas the mitochondrial protein-coding and rRNA genes were suitable for molecular identification. We also revealed that a general gauge of genetic distances might not be adequate, using evidence from the wide range of genetic distances among nematodes. Conclusion This study assessed the suitability of DNA genetic markers for application in molecular systematics and molecular identification of helminths. We provide a novel way of analyzing genetic distances to generate suitable cut-off values for each taxonomic level using the ‘K-means’ clustering algorithm. The estimated cut-off genetic distance values, together with the summary of the utility and limitations of each class of genetic markers, are useful information that can benefit researchers conducting molecular studies on helminths.