Nuclear ITS Sequences Research Articles

Molecular, morphological, and morphometric evidence reveal a new, critically endangered rattlepod (Crotalaria, Fabaceae/Leguminosae, Papilionoideae) from tropical China.

Here, we describe a new species of Crotalaria L. discovered in Mengla County, Xishuangbanna Dai Autonomous Prefecture, Yunnan, China. The new species, Crotalariamenglaensis S.A.Rather, was confirmed by identifying diagnostic morphological characteristics, performing principal component analyses of phenotypic traits, and phylogenetic analyses based on nuclear ITS and plastid matK sequences. Phylogenetic analyses recovered the two accessions of the new species to be sister to C.bracteata Roxb. ex DC. In turn, these two species formed the sister clade to the two accessions of C.incana L. The morphometric analyses revealed that all three species were distinct, while the analyses of distinctive characters enabled unambiguous distinction of the new species by its growth habit, leaflets, flower structure and pod morphology. In contrast to the two related species, the new species is currently known only from ca. 100 mature individuals. Thus, this species is considered to be critically endangered.

Homoplasy rather than intergeneric hybridisation explains mammillose leaf cells in Schistidium mammillosum sp. nov. (Grimmiaceae)

We present a peculiar new species in the Grimmiaceae, Schistidium mammillosum, which is distinct in having mammillose leaf cells and pluristratose lamina. These features are rare in mosses but shared by a few Grimmia species including sympatric G. alpestris. Sporophyte characteristics of the new taxon, in contrast, indicated a species of Schistidium and suggested a possible intergeneric hybrid origin. Nuclear ITS and plastid rps4‒trnF sequence data consistently resolved the new taxon within species of Schistidium, thus contradicting the hybridogenic hypothesis. We suggest that the shared feature of mammillose cells evolved independently in the two genera in adaptation to similar environmental conditions, possibly prolonged snow cover. Supported by morphological similarity, our phylogenetic analyses indicate a sister relationship of S. mammillosum and S. marginale in the Confertum clade. Schistidium mammillosum colonises siliceous rocks in the alpine and nival zone and is to date known from the French Alps and a single locality in Switzerland.

Novelty in Arundinella (Arundinelleae, Panicoideae, Poaceae): Morphological and Molecular Evidences for a New Species from Sikkim Himalaya

Novelty in Arundinella (Arundinelleae, Panicoideae, Poaceae): Morphological and Molecular Evidences for a New Species from Sikkim Himalaya

Ixeridium malingheense (Asteraceae), a new species from southwestern Guizhou, China

A new Asteraceae species, Ixeridium malingheense Z.Li & Q.Xu sp. nov., from Xingyi City, south-western Guizhou, China, is described and illustrated based on morphological and molecular analyses. Compared with the other species of the genus, the species is most similar to I. yunnanense in a small stature, linear-lanceolate stem leaves, and short phyllaries. However, it is easily distinguished from the latter by its smaller basal leaves 18–34 × 5–13 mm (vs. 10–25 × 5 mm), spatulate or long-spatulate (vs. elliptic, lanceolate, or oblanceolate), petioles ca. 30–55 mm (vs. 10 mm to absent), outer phyllaries 1-seriate (vs. 2-seriate, unequal), achenes smaller 2.0–3.0 × 0.5–1.0 mm (vs. 3.2 × 0.6 mm), and a flowering period of March to May (vs. June). Molecular phylogenetic analyses based on nuclear ITS sequence data determined the systematic position of I. malingheense in Ixeridium.

Hedysarumqilianshanense sp. nov. (Fabaceae, Hedysareae), a new species from the Qilianshan Mountains in Gansu, China.

Hedysarumqilianshanensesp. nov. (Fabaceae, Hedysareae) is described and illustrated from the Qilianshan Mountains in Gansu, China. This new species is similar to H.przewalskii, but can be distinguished by its corolla being light purple to purple, standard 15-19 mm long, wings 14-16 mm long, keels 16-19 mm long, and the ovary and legume being glabrous. The new species can be easily distinguished from H.neglectum Ledeb. by its bract being shorter than the pedicel, and the ovary and legume being glabrous. Phylogenetic tree based on the nuclear ITS and ETS sequences shows that H.qilianshanense is sister to H.przewalskii, while the tree based on the plastid psbA-trnH, trnC-petN, trnL-F, trnS-G and petN-psbM sequences shows H.qilianshanense as sister to a clade consisting of H.hedysaroides, H.inundatum, H.americanum and H.neglectum. The new species is a diploid with the chromosome number 2n = 14. Based on morphological, phylogenetic and karyotypic evidence, the new species may originate from an ancient homoploid hybrid speciation event.

Genetic and morphological differentiation within Euphorbia japygica (Euphorbiaceae) suggests divergence of populations from the south-eastern Apennine Peninsula

Abstract The Mediterranean Basin is a hotspot of animal and plant diversity. Contrary to the Balkan and Iberian Peninsulas that were subject of many phylogeographic studies in past decades, the Apennine Peninsula and, in particular, the diversification of its flora has been neglected in contemporary phylogenetic studies. The few available studies showed a complex pattern of north–south differentiation of genetic diversity in Italy, both among the Alps, the Apuan Alps, and the Apennines, as well as within the Apennines. Here, we explore phylogeographic patterns within recently described Euphorbia adriatica, distributed in the central and northern Apennine Peninsula, the southern margin of the Eastern Alps and the north-western Balkan Peninsula, and its relationship to the southern Italian E. japygica. Our integrative approach using nuclear ITS sequences, amplified fragment length polymorphisms, relative genome size estimation combined with chromosome counting, as well as multivariate morphometrics inferred a weak genetic differentiation that only partly corresponds to the morphological differentiation. Whereas all southern populations have hairy capsules characteristic for E. japygica, only those in south-eastern Italy (Puglia and Basilicata) are genetically divergent. There are, however, additional morphological characters that differentiate them from other populations. Our data are thus in favour of recognizing a single species, E. japygica, which includes E. adriatica that should be treated as a subspecies, named E. japygica subsp. prostrata. We provide a revised taxonomic treatment for E. japygica, including the typification. Our study shows the necessity of further in-depth investigations of diversification of Italian biota.

A TIME-CALIBRATED PHYLOGENY OF VERBESINA (HELIANTHEAE – ASTERACEAE) BASED ON NUCLEAR RIBOSOMAL ITS AND ETS SEQUENCES

Verbesina L. is a genus of the tribe Heliantheae, subtribe Verbesininae (Asteraceae), with distribution in the Americas, where Mexico and the Andes harbour the richest concentration of species. The approximately 325 species in the genus are shrubs, subshrubs, trees and rarely herbs. Despite its high species diversity and biogeographical importance, the only available phylogenetic hypothesis for Verbesina was based on chloroplast DNA restriction site data. In the present study, nuclear ITS and ETS DNA sequence data were used with an expanded taxon sampling, particularly among the South American Verbesina species, to improve phylogenetic resolution and support, clarify infrageneric relationships, and resolve biogeographical questions in the genus. The results of our new analysis corroborate the monophyly of Verbesina, but its current classification into 12 taxonomic sections, based on morphological characters such as phyllotaxis, head size, corolla colour, and presence of ray flowers, is not congruent with the molecular phylogeny, in which most sections are polyphyletic. We also show that Verbesina diverged in the late Miocene of North America, about 8 Ma. At least two independent Pleistocene dispersals into South America across the Isthmus of Panama and along the Southern Andes are evident, beginning around 3.23 Ma (1.27–3.23 Ma) in the Middle Pliocene, and resulting in an extra-Amazonian distribution of the genus inSouth America. Diversification in South America began around 2.83 Ma with occupation of the Andes. Colonisation of Brazil is estimated to have occurred around 2.15 Ma, from Andean lineages.

Intersectional polyphyly of the puzzling Scapania obcordata (Marchantiidae) suggests convergent evolution: resurrection and European occurrence of S. jensenii

We present an example of morphological convergence among two species of Scapania that were considered to be conspecific. We resurrect S. jensenii from synonymy with the morphologically and molecularly variable S. obcordata because our molecular data show that they are distantly related. Chloroplast trnL-trnF and nuclear ITS sequences resolved S. obcordata in sect. Curtae and S. jensenii in sect. Apiculatae sister to S. obscura and we detected morphological differences in secondary pigmentation and leaf anatomy. The similarity comprises the absence of a pronounced keel in vegetative leaves and a weakly defined stem cortex. These features are virtually unknown in other species of Scapania and probably result from convergence in adaptation to the same environmental conditions, as both taxa inhabit alluvial plains characterised by regular disturbance by flooding and covering with sand and silt. While S. obcordata is widespread in the northern Holarctic and known from the Antarctic, S. jensenii is known from a few localities in Greenland, mainland Norway, the Chukchi Peninsula and the Swiss Alps. Its rarity, the absence of female plants, and the lack of genetic variability suggest that S. jensenii underwent a bottleneck event.

Kiluluma ceratotherii (Nematoda: Strongylida) in a White Rhinoceros (Ceratotherium simum) from the United States: Case Report

Nematodes of the genus Kiluluma (Strongylidae, Cyathostominae) parasitize African rhinoceros. We describe the case of a one-year-old male white rhinoceros calf that presented with colonic inflammation and hemorrhage at necropsy. The animal had died following a neurological episode. We recovered and identified adult nematodes from the colon using morphology and ITS2 gene sequences as Kiluluma ceratotherii. We also generated nuclear ITS1, 5.8S, ITS2, and mitochondrial cox1 sequences for future studies and deposited them in GenBank (OR142644–OR142653). Since the animal was born in the same zoo and never transported, infection likely originated within the herd. This is the first report of this nematode from a white rhinoceros in the United States.

A new species of the genus Aleurodiscus sensu lato (Russulales, Basidiomycota) from Hachijo Island, Japan.

Aleurodiscus sagittisporus sp. nov. is described and illustrated. This species is characterized by producing basidiomata with a monomitic hyphal system, clampless-septate hyphae, arrowhead-shaped, amyloid, finely verrucose basidiospores, gloeocystidia, dendrohyphidium-like branched paraphysoid hyphae, and variously shaped swelling cells in the hymenium. Phylogenetic analyses based on nuclear rDNA LSU and ITS sequences revealed that the species is distinct from the lineage of Aleurodiscus s. str. and related genera in the Aleurodiscus s. lat. clade. Basidiomata of A. sagittisporus have been collected only from dead petioles attached to living trees of Livistona chinensis var. subglobosa on Hachijo Island, Japan.

Resolving relationships despite past hybridization in Aliciella subsection Subnuda (Polemoniaceae)

AbstractPhylogenetics is crucial in the study of evolutionary processes and events transpiring in the course of species diversification. Phylogenetic studies within kingdom Plantae often reveal hybridization and introgression. Here, we study a subsection rife with historic hybridization and discuss the impacts of such processes on evolutionary trajectories. Aliciella subsection Subnuda comprises seven species of herbaceous plants occurring in Utah, the Navajo Nation, and the Four Corners region of North America. Previous molecular and morphological work left relationships in the subsection unresolved. Here, we use comparative DNA sequencing of nuclear ITS and chloroplast DNA regions and genome‐wide RAD‐seq data to clarify phylogenetic relationships and examine the role of hybridization in the subsection. We construct haplotype and nucleotype networks from chloroplast and nuclear ITS sequence matrices and compare nuclear and chloroplast phylogenies to identify multiple putative chloroplast capture events. The RAD‐seq maximum likelihood phylogeny and multispecies coalescent species tree robustly resolve relationships between six species‐level clades. We use STRUCTURE and HyDe on the RAD‐seq data to evaluate the influence of hybridization within the subsection. The HyDe results suggest that hybridization has occurred among all species in the subsection at some point in their history. Cytonuclear discordance reveals historic chloroplast capture, and we discuss potential causes of the observed discordance. Our study robustly resolves relationships in Aliciella subsection Subnuda and provides a framework for discussing its speciation despite a history of hybridization and introgression.

An integrative approach supports the taxonomic distinction of the Sardo-Corsican endemic Euphorbia semiperfoliata from the widespread E. amygdaloides (Euphorbiaceae)

In the western Mediterranean, Corsica and Sardinia are characterised by high plant diversity and endemism, and exhibit a tight biogeographic connection. One of the endemic taxa thriving in forests, macchia, along riversides and in mountain grasslands of both islands is Euphorbia semiperfoliata. It was often considered a subspecies of the widespread European forest plant Euphorbia amygdaloides, or deemed closely related with the western Asian E. macroceras and E. oblongifolia. Here, we explored the evolutionary origin of E. semiperfoliata using nuclear ITS sequences that showed that E. semiperfoliata is divergent from E. amygdaloides and the other species of E. sect. Patellares, which indicates its old, likely Tertiary origin. In addition, its relative genome size is different from E. amygdaloides and other species and several morphological characters revealed by morphometric analyses differentiate E. semiperfoliata from E. amygdaloides. Finally, we provide a taxonomic treatment for E. semiperfoliata, including the typification and a morphological description.

Underestimated diversity in high elevations of a global biodiversity hotspot: two new endemic species of Aethionema (Brassicaceae) from the alpine zone of Iran.

Although the mountains in South-West Asia are a global biodiversity hotspot, our understanding of their biodiversity, especially in the commonly remote alpine and subnival zones, is still limited. This is well exemplified here by Aethionema umbellatum (Brassicaceae), a species considered to have a wide yet disjoint distribution in the Zagros and Yazd-Kerman mountains of western and central Iran. Morphological and molecular phylogenetic data (based on plastid trnL-trnF and nuclear ITS sequences) show that A. umbellatum is restricted to a single mountain range in southwestern Iran (Dena Mts., southern Zagros), whereas populations from central Iran (Yazd-Kerman and central Zagros) and from western Iran (central Zagros) belong to species new to science, A. alpinum and A. zagricum, respectively. Both new species are phylogenetically and morphologically close to A. umbellatum, with which they share unilocular fruits and one-seeded locules. However, they are easily distinguishable by leaf shape, petal size, and fruit characters. This study confirms that the alpine flora of the Irano-Anatolian region is still poorly known. As the proportion of rare and local endemic species in alpine habitats is high, these habitats are of prime interest for conservation efforts.

Inflorescences of Cuscuta (Convolvulaceae): Diversity, evolution and relationships with breeding systems and fruit dehiscence modes.

Cuscuta (dodder) includes ca. 200 species of plant obligate stem parasites with enormous ecological and economical significance. Inflorescences have been historically used in Cuscuta for species descriptions and identification keys, but no comprehensive study exists to date. The main objectives of this study were to survey the diversity and evolution of inflorescences and to uncover their possible form-function relationships. The inflorescence architecture of 132 Cuscuta taxa was analysed using herbarium specimens and eight species were grown to study their inflorescence development. Inflorescence traits were mapped into a genus phylogeny obtained from a combined analysis of nuclear ITS and plastid trnL-F sequences. To test the hypothesis that inflorescence architecture is connected to sexual reproduction, correlations between inflorescence traits (using Principal Components), sexual reproductive traits (pollen/ovule ratios, corolla length and diameter), fruit charaters (fruit length and width), and the modes of dehiscence were analyzed. Based on their development, three major types of inflorescences were observed: "Cuscuta type", a simple, monochasial scorpioid cyme; "Monogynella type", a compound monochasial scorpioid cymes with the longest primary axes having prolonged vegetative growth and giving the appearance of thyrses; and "Grammica type", a compound monochasial scorpiod cymes with up to five orders of axes. Maximum likelihood analyses suggested Monogynella as the ancestral type, while Cuscuta and Grammica were derived. Overall, the total length of axes exhibited a reduction trend throughout the genus evolution, but it was not correlated with the pedicels length. Inflorescences with similar architectures may exhibit contrasting pollen-ovule ratios. Positive significant correlations were noted between the size of the flower traits and pollen-ovule ratios. Several modes of dehiscence had statistically significant different total axes lengths, suggesting that the infructescence architecture is connected to the modes of dehiscence in Cuscuta and therefore seed dispersal.

Langbiangia, a new genus of Gesneriaceae endemic to Langbiang Plateau, southern Vietnam and a taxonomic endeavor to achieve key targets of the post-2020 global biodiversity framework.

Situated in the southern end of the Annamite Mountain Range, Langbiang Plateau is a major biodiversity hotspot of southern Vietnam known for high species diversity and endemicity. To achieve effective conservation, parts of the plateau were designated as the Langbiang Biosphere Reserve, an UNESCO World Network aiming to improve relationships between inhabitants and their environments. Amongst the rich endemic flora of the plateau are three gesneriads ascribed to Primulina, a calciphilous genus with high species diversity in the vast limestone karsts stretching from southern China to northern Vietnam. However, a recent phylogenetic study questioned the generic placement of the Langbiang Primulina, corroborating with observations on the geographical distribution, habitat preference, and phyllotaxy of the three species. Based on phylogenetic analyses of nuclear ITS and plastid trnL-F DNA sequences of a comprehensive sampling covering nearly all genera of the Old World Gesneriaceae, we demonstrate that the three Langbiang Primulina species form a fully supported clade distantly related to other Primulina. As this clade is biogeographically, ecologically, morphologically, and phylogenetically distinct worthy of generic recognition, we propose to name it Langbiangia gen. nov. to highlight the rich and unique biodiversity of the Langbiang Plateau. By means of this taxonomic endeavor, we are hoping to raise the conservation awareness of this biodiversity heritage of southern Vietnam and promote the importance of Langbiang Biosphere Reserve that is crucial for achieving action-oriented global targets of the post-2020 global biodiversity framework (GBF) of the UN Convention on Biological Diversity (CBD)-effective conservation and management of at least 30% of biodiverse terrestrial, inland water, and costal and marine areas by 2030-that has been agreed at the COP15 in Montréal in December 2022.

Multigene phylogeny reveals a cryptic diversity in the genus Dinobryon (Chrysophyceae) with integrative description of five new species.

The genus Dinobryon is one of the most recognizable chrysophyte genera, characterized by dendroid colonies with a biflagellate inside each cellulosic lorica. The representative forms of lorica are cylindrical, conical, vase, or funnel shaped, with undulation on the lorica wall. Traditionally, the morphological characteristics of the lorica and the colony organization have been used for the delimitation of Dinobryon species. To understand the taxonomy and phylogeny of colonial Dinobryon species, we performed molecular and morphological studies using 39 unialgal cultures and 46 single colony isolations from environmental specimens collected in Korea. We used a nuclear internal transcript spacer (ITS1-5.8S-ITS2) to find the genetic diversity of Dinobryon from environmental samples and a combined dataset from six gene sequences (nuclear SSU and LSU rRNA, plastid LSU rRNA, rbcL and psaA, and mitochondrial CO1 genes) for phylogenetic analysis. We found 15 different lineages based on the genetic diversity of the nuclear ITS sequences. The phylogenetic tree of the colonial species based on the combined multigene dataset were divided into 18 subclades, including five new species, each with unique molecular signatures for the E23-5 helix of the V4 region in the nuclear SSU rRNA and the E11-1 helix of D7b, and the E20-1 helix of D8 regions in the nuclear LSU rRNA. Morphological studies were focused on lorica dimension and shape, and stomatocyst morphology. The Dinobryon species showed similarities or differences in lorica morphologies between and within species, and also differences in lorica size between culture and environmental samples. Five Dinobryon species formed distinctive stomatocysts, their stomatocyst morphologies, including collar structure, surface ornamentation, and cyst shape, showed unique characteristics in each species and were useful for identification. Here, we propose five new species based on morphological and molecular evidences: D. cylindricollarium, D. exstoundulatum, D. inclinatum, D. similis, and D. spinum.

A deep dive into cryptic taxonomic diversity in the rare endemic mustard Draba maguirei.

Previously published evidence suggests that Draba maguirei, a mustard endemic to a few localities in the Bear River, Wellsville, and Wasatch Mountains of northern Utah, may represent a cryptic species complex rather than a single species. Conservation concerns prompted an in-depth systematic study of this taxon and its putative relatives. Sampling most known populations of D. maguirei s.l. (D. maguirei var. maguirei and D. maguirei var. burkei), we integrate data from geography, ecology, morphology, cytogenetics and pollen, enzyme electrophoresis, and the phylogenetic analysis of nuclear ITS sequences to explore potential taxonomic diversity in the species complex. Draba maguirei var. burkei is shown here to be a distinct species (D. burkei) most closely related to D. globosa, rather than to D. maguirei. Within D. maguirei s.s., the northern (high elevation) and southern (low elevation) population clusters are genetically isolated and morphologically distinguishable, leading to the recognition here of the southern taxon as D. maguirei subsp. stonei. Our study reveals that plants traditionally assigned to D. maguirei comprise three genetically divergent lineages (D. burkei and two newly recognized subspecies of D. maguirei), each exhibiting a different chromosome number and occupying a discrete portion of the geographic range. Although previously overlooked and underappreciated taxonomically, the three taxa are morphologically recognizable based on the distribution and types of trichomes present on the leaves, stems, and fruit. Our clarification of the diversity and distribution of these taxa provides an improved framework for conservation efforts. This article is protected by copyright. All rights reserved.

Alleniella aegaea Blockeel & Hugonnot (Neckeraceae), a new moss species from the Aegean islands of Greece

A new moss species, Alleniella aegaea (Neckeraceae) is described and illustrated from the Greek islands of Crete, Samos and Evvia based on morphological and molecular evidence. According to phylogenetic analysis of nuclear ITS and plastid trnS-F sequences it is sister to A. com planata, which it also morphologically resembles, but it differs from that species e.g. in its distinctly flattened habit, lack of caducous branchlets, more rounded leaf apices, and shorter median laminal cells. Alleniella aegaea is dioicous and the sporophytes remain unknown

A huge undescribed diversity of the subgenus Hystricochaetonotus (Gastrotricha, Chaetonotidae, Chaetonotus) in Central Europe

The subgenus Hystricochaetonotus Schwank, 1990 is one of the most species-rich subgenera of Chaetonotus Ehrenberg, 1830. It has a worldwide distribution and encompasses 37 species predominantly living in the benthos and periphyton of limnetic habitats. We have discovered further nine new species in running and stagnant waters in Slovakia (Central Europe): Ch. (H.) arcanus sp. nov., Ch. (H.) avarus sp. nov., Ch. (H.) gulosus sp. nov., Ch. (H.) iratus sp. nov., Ch. (H.) luxus sp. nov., Ch. (H.) mirabilis sp. nov., Ch. (H.) optabilis sp. nov., Ch. (H.) slavicus sp. nov., and Ch. (H.) superbus sp. nov. Their morphology was studied using differential interference contrast microscopy and subsequent morphometric analyses were carried out. In addition, the primary and secondary structures of their 18S, ITS2, and 28S rRNA molecules as well as their barcoding mitochondrial gene encoding for cytochrome c oxidase (COI) were analyzed. Species boundaries were tested also using the compensatory base change analysis. The new species could be well separated both morphologically and molecularly. The present barcoding analyses revealed that the nuclear ITS2 sequences represent a powerful DNA barcode in addition to the mitochondrial COI gene. According to the multi-gene phylogenetic analyses, the lineage leading to the last common ancestor of the ‘Hystricochaetonotus’ clade is the longest internal branch within the family Chaetonotidae Gosse, 1864. Since members of the subgenus Hystricochaetonotus are morphologically highly heterogeneous, parallel evolution of Chaetonotus-like and/or Hystricochaetonotus-like characters of scales and spines occurred during its radiation.

Two new species of Impatiens (Balsaminaceae) from Gaoligong Mountains, Yunnan, China

Impatiens longyangensis and I. yaojiapingensis, two new species from Gaoligong Mountains, Yunnan, China, are described here. The former species is morphologically similar to I. shangjiangensis, but differs by its shorter petioles and peduncle, ovate bract, shortly saccate lower sepal with a longer spur and suborbicular dorsal petal. The latter is similar to I. sterilis, and differs by its pubescent leaf, petiole with one to three pairs of clavate glands, persistent bract, lower sepal with a straight spur and suborbicular dorsal petal. Molecular phylogenetic analysis based on nuclear ITS and plastid atpB-rbcL sequences shows that the two new species belong to I. sect. Racemosae.