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The complex phylogenetic relationship of polyploid species provides an opportunity for a comprehensive study of gene introgression. Oil camellias refer to a class of important woody oil plant in the camellia genus, including octoploid, hexaploid, tetraploid, and diploid plants, but the phylogeny relationship of these species remains poorly investigated. Here, based on multiple types of evidence, including phylogenetic conflict, gene flow analysis, and representative metabolite, we reconstructed the phylogenetic relationship of oil camellias. Camellia shensiensis and C. grijsii formed a distinct branch. Phylogenetic conflict suggested that hexaploid C. oleifera probably originated from hybridization and clustered with diploid C. kissi and tetraploid C. meiocarpa. Tetraploid C. confusa probably originated from crossing the ancestor of C. kissi and C. brevistyla, and C. brevistyla probably was the maternal progenitor of hexaploid C. sasanqua. Furthermore, the composition of anthocyanin in tender leaves showed a strong correlation with phylogenetic distinctions. This study proves the feasibility of using iconic metabolic components to solve phylogenetic relationships and lays a foundation for analyzing genetic breeding and utilizing oil camellia resources. [ABSTRACT FROM AUTHOR]

Since 2011, massive new strandings of holopelagic Sargassum have been reported on the coasts of the Caribbean, northern Brazil, Guiana, and West Africa, causing severe economic and ecological damage. Three common morphotypes (S. fluitans III, S. natans I, and S. natans VIII) were identified as responsible for these catastrophic events, with dominance shifts between them over time. However, the taxonomic status of these holopelagic Sargassum morphotypes remains unclear. Using an integrative taxonomy framework, combining a morphological study and molecular analyses, this study aimed to clarify their taxonomic status. Morphological analyses of 54 characters revealed no intermediate form between the three morphotypes, with the overall shape, nature of the axis, and size and shape of blades and vesicles being the most discriminating. An analysis of mitochondrial (IGS, cox2, cox3, mt16S rRNA, and nad6) and plastid (rbcL) markers confirmed the genetic divergence among the three morphotypes, with a lower level of divergence between the two S. natans morphotypes. Without additional molecular characterization, these morphotypes cannot be classified as three distinct species. However, due to their distinct morphological characteristics and sympatry within drifting aggregations, a revision of holopelagic species names is proposed, with Sargassum fluitans var. fluitans (for S. fluitans III), Sargassum natans var. natans (for S. natans I), and S. natans var. wingei (for S. natans VIII). This revision provides necessary clarity on the species involved in inundations of the tropical Atlantic. [ABSTRACT FROM AUTHOR]

Coccoid cyanobacteria represent an important part of cyanobacterial freshwater diversity, with many studied strains in public databases identified as Synechococcus. This is a diverse genus, both morphologically and ecologically, with a global distribution. However, many of the so-called Synechococcus-like cyanobacteria strains could represent several independent genera that require further studies. In this work, four strains of a Synechococcus-like cyanobacteria isolated from freshwater lakes and terrestrial atmophytic habitats on São Miguel and Flores Islands (Azores archipelago) were studied genetically using the 16S rRNA and 16S–23S rRNA ITS, morphologically with light and transmission electron microscopy, and ecologically. A draft genome was produced from the reference strain by Illumina sequencing, which allowed a more complete phylogenetic study and a deeper taxonomic analysis, revealing a divergent phylogenetic evolution and low ANI and AAI values (69.4% and 66.3%, respectively) to Thermosynechococcus, the closest phylogenetic genus. Although morphologically similar to Synechococcus, the 16S rRNA and genome phylogenetic analysis placed the studied strains in a clade sister to Thermosynechococcus, inside the Thermosynechococcaceae. Thus, Pseudocalidococcus azoricus gen. sp. nov. is described as a new coccoid freshwater genus and species from the Azores archipelago. A detailed comparison with similar morphological taxa is provided, supporting the separation of the new genus. The 16S rRNA with a high genetic similarity to other strains from several continents identified as Synechococcus sp. suggests that the new genus probably has a worldwide distribution. Future studies should be performed to clarify the taxonomic identity of those strains. [ABSTRACT FROM AUTHOR]

The potato is one of the most important food crops in the world. Improving the efficiency of potato breeding is of great importance for solving the global food problem. Today, researchers distinguish between six potato cytoplasm types: A, M, P, T, W, D. In the current study, the complete chloroplast genomes of Solanum tuberosum accessions with five out of the six major cytoplasmic genome types were sequenced (T-, W-, D-, A-, and P-genomes). A comparative analysis of the plastomes in potato accessions with different cytoplasm types was carried out for the first time. The time of origin of the different cytoplasm types was estimated. The presence of two main groups of chloroplast genomes among cultivated potato was confirmed. Based on the phylogenetic analysis of the complete plastome sequences, five main evolutionary branches of chloroplast genomes can be distinguished within the Petota section. Samples with A- and P- cytoplasm formed isolated and distant groups within a large and polymorphic group of samples with M-type cytoplasm, suggesting that A and P genomes arose independently. The findings suggest that the diversity of the T-genome in S. tuberosum Group Tuberosum could be initially low due to a bottle neck already existing at the origin of the Chilean clade. Differences in the rbcL gene sequence may be one of the factors causing differences in economically important traits in species with A and T-type cytoplasm. The data obtained will contribute to the development of methods for molecular marking of cytoplasm types and increase knowledge about the evolution and diversity of potato. [ABSTRACT FROM AUTHOR]

Tomato cv. super strain B was widely cultivated in Saudi Arabia under drought stress. Illumina Hiseq-2000 was used to create the transcriptional profile of tomato cultivar super strain B. A total of 98,069 contigs were gathered, with an average length of 766 bp. Most of the genes in the gene ontology (GO) analysis were categorized into molecular function (MF) of ATP binding (1301 genes), metal ion binding (456 genes), protein kinase activity (392 genes), transferase activity (299 genes), Biological process (BP) of DNA-templated genes (366 genes), and regulation of transcription genes (209 genes), while cellular components (CC) of integral component of membrane (436 genes). The most dominant enzymes expressed were transferases (645 sequences). According to the KEGG pathway database, 15,638 transcripts were interpreted in 125 exclusive pathways. The major pathway groups were metabolic pathways (map01100, 315 genes) and biosynthesis of secondary metabolites (map01110, 188 genes). The total number of variants in the twelve chromosomes of super strain B compared with the tomato genome was 5284. The total number of potential SSRs was 5047 in 4806 unigenes. Trinucleotide repeats (3006, 59.5%) were the most found type in the transcriptome. A total of 4541 SNPs and 744 INDELs in tomato super strain B were identified when compared with the tomato genome. [ABSTRACT FROM AUTHOR]

Central American and Mexican Pinguicula species are characterized by enormous divergence in size and color of flowers and are pollinated by butterflies, flies, bees, and hummingbirds. It is known that floral trichomes are key characters in plant–pollinator interaction. The main aim of our study was to verify our hypothesis that the distribution and diversity of non-glandular and glandular trichomes are related to the pollinator syndromes rather than the phylogenetic relationships. The studied sample consisted of Central American and Mexican species. In our study, we relied on light microscopy and scanning electron microscopy with a phylogenetic perspective based on ITS DNA sequences. The flower morphology of species pollinated by butterflies and hummingbirds was similar in contrast to species pollinated by flies and bees. Species pollinated by butterflies and hummingbirds contained low diversity of non-glandular trichomes, which occurred mostly in the tube and basal part of the spur. Surprisingly, in P. esseriana and P. mesophytica, non-glandular trichomes also occurred at the base of lower lip petals. In the case of species pollinated by flies/bees, we observed a high variety of non-glandular trichomes, which occurred on the surface of corolla petals, in the tube, and at the entrance to the spur. Furthermore, we did not identify any non-glandular trichomes in the spur. The capitate glandular trichomes were of similar morphology in all examined species. There were minor differences in the shape of the trichome head, as well as the length and the number of stalk cells. The distribution and the diversity of non-glandular and glandular trichomes and pollinator syndromes were mapped onto a phylogenetic reconstruction of the genus. Most micromorphological characters appear to be associated more with floral adaptation to pollinators and less with phylogeny. [ABSTRACT FROM AUTHOR]

Plant debris are habitats favoring survival and multiplication of various microbial species. During continuing mycological surveys of saprobic microfungi from plant debris in Yunnan Province, China, several Corynespora-like and Dendryphiopsis-like isolates were collected from dead branches of unidentified perennial dicotyledonous plants. Four barcodes, i.e., ITS, LSU, SSU and tef1-α, were amplified and sequenced. Morphological studies and multigene phylogenetic analyses by maximum likelihood and Bayesian inference revealed three new Corynespora species (C. mengsongensis sp. nov., C. nabanheensis sp. nov. and C. yunnanensis sp. nov.) and a new Kirschsteiniothelia species (K. nabanheensis sp. nov.) within Dothideomycetes, Ascomycota. A list of identified and accepted species of Corynespora with major morphological features, host information and locality was compiled. This work improves the knowledge of species diversity of Corynespora and Kirschsteiniothelia in Yunnan Province, China. [ABSTRACT FROM AUTHOR]

Simple Summary: Species of Sarcoscyphaceae are saprobic on branches, stumps, trunks, or twigs. The majority of members in this family are widespread in tropical areas, with only a fraction of the known species found in temperate areas. All species have typical disc- or cup-shaped fruiting bodies in a variety of colours ranging from white, grey, orange, red to brown. A high diversity of Sarcoscyphaceae has been reported in southwestern China and Thailand. In this study, we provide redescriptions of five known species and establish three new species in Sarcoscyphaceae from these regions based on morphology and phylogeny. We also propose an amendment for Phillipsia gelatinosa. Cookeina sinensis, a common species in China, is reported from Thailand for the first time. Sarcoscyphaceae (Pezizales) is distinguished by small to large, vividly-coloured sessile to stipitate apothecia, plurinucleate and pigmented paraphyses, operculate asci with thick walls, and plurinucleate, uniguttulate to multiguttulate ascospores with smooth walls or ornamentations. We collected more than 40 Sarcoscyphaceae specimens from dead twigs or wood. Based on morphology and phylogeny, these species belong to Cookeina, Nanoscypha, Phillipsia, Pithya, and Sarcoscypha. Among these, we introduce three new species–Nanoscypha aequispora, Pithya villosa, and Sarcoscypha longitudinalis. Phylogenetic analyses based on ITS, LSU, SSU, rpb2, and tef-1α gene regions indicate the relationships of these species within Sarcoscyphaceae. Meanwhile, we propose Ph. gelatinosa as a synonym of Ph. domingensis. One new record of C. sinensis is reported from Thailand. [ABSTRACT FROM AUTHOR]

The delimitation of Limonium taxa is highly complicated due to hybridization, polyploidy, and apomixis. Many "microspecies" were described and aggregated into groups, most of which are still poorly known from both molecular and morphological points of view. The aim of this study is to investigate four endemic species from the Tyrrhenian coast of central Italy and the Ponziane Archipelago belonging to the L. multiforme group (L. amynclaeum, L. circaei, L. pandatariae, and L. pontium) by means of molecular and morphometric analyses. Molecular data by sequencing ITS and three plastid markers and morphometric data highlight new information about the taxonomy of these taxa so as to reduce them into a single specific entity. In fact, the better taxonomic choice is to consider the populations studied as part of a single species, i.e., Limonium pontium. Three subspecies are recognized, i.e., subsp. pontium [= L. circaei = L. amynclaeum; from Circeo to Gianola localities (excluding Terracina) and from islands Ponza, Palmarola, Zannone, and Santo Stefano], subsp. pandatariae comb. et stat. nov. (from island of Ventotene), and subsp. terracinense subsp. nov. (from Terracina). [ABSTRACT FROM AUTHOR]

Taxonomic studies of bambusicolous fungi in China and Thailand have resulted in the collection of three fascinating saprobic coelomycetes strains. Morphology coupled with combined gene analysis of ITS, LSU, TUB2, and TEF1-α DNA sequence data showed that they belong to the genus Apiospora, family Apiosporaceae. A new species from Thailand, Apiospora mukdahanensis, and new records of A. locuta-pollinis from China are herein described. In addition, based on both morphological data coupled with phylogenetics and nomenclatural analyses, A. mori is proposed as a new combination. Maximum likelihood, maximum parsimony and Bayesian analyses were performed to clarify the phylogenetic affinities of the species obtained in this study. Newly obtained strains are compared with morphologically- and phylogenetically-related taxa. The comprehensive descriptions, illustrations, and updated phylogeny are provided and discussed for intra-and intergeneric relationships within Apiospora species. [ABSTRACT FROM AUTHOR]

A new Choiromyces species was discovered at local wild mushroom markets in Songpan County, Sichuan, southwest China where it has been considered as a Chinese white truffle. Based on both morphological and phylogenetic analyses, the collection was described as Choiromyces sichuanensis sp. nov. This study confirms the occurrence of members of Choiromyces in China. In addition, the mycorrhizal synthesis via spore inoculation between C. sichuanensis and Pinus armandii or two Picea species of Pi. likiangensis and Pi. crassifolia was attempted in a greenhouse. Both morphoanatomical and molecular analyses evidenced well-developed mycorrhization between C. sichuanensis and P. armandii, but not in Picea seedlings. Our current study provides data about the species diversity and mycorrhizal research of this genus for further studies. In addition, a successful mycorrhization between C. sichuanensis and selected tree species, irrespective of Pinus genus or other plant species, would broaden the set of species for a successful mycorrhization in greenhouse conditions and potential outplanting for cultivation purposes. [ABSTRACT FROM AUTHOR]

Although the Pleosporaceae is one of the species-richest families in the Pleosporales, research into less-explored substrates can contribute to widening the knowledge of its diversity. In our ongoing survey on culturable Ascomycota from freshwater sediments in Spain, several pleosporacean specimens of taxonomic interest were isolated. Phylogenetic analyses based on five gene markers (ITS, LSU, gapdh, rbp2, and tef1) revealed that these fungi represent so far undescribed lineages, which are proposed as two novel genera in the family, i.e., Neostemphylium typified by Neostemphylium polymorphum sp. nov., and Scleromyces to accommodate Scleromyces submersus sp. nov. Neostemphylium is characterized by the production of phaeodictyospores from apically swollen and darkened conidiogenous cells, the presence of a synanamorph that consists of cylindrical and brown phragmoconidia growing terminally or laterally on hyphae, and by the ability to produce secondary conidia by a microconidiation cycle. Scleromyces is placed phylogenetically distant to any genera in the family and only produces sclerotium-like structures in vitro. The geographic distribution and ecology of N. polymorphum and Sc. submersus were inferred from metabarcoding data using the GlobalFungi database. The results suggest that N. polymorphum is a globally distributed fungus represented by environmental sequences originating primarily from soil samples collected in Australia, Europe, and the USA, whereas Sc. submersus is a less common species that has only been found associated with one environmental sequence from an Australian soil sample. The phylogenetic analyses of the environmental ITS1 and ITS2 sequences revealed at least four dark taxa that might be related to Neostemphylium and Scleromyces. The phylogeny presented here allows us to resolve the taxonomy of the genus Asteromyces as a member of the Pleosporaceae. [ABSTRACT FROM AUTHOR]

We studied the taxonomy of Pluteus romellii, and morphologically similar Holarctic species in the/romellii clade of section Celluloderma, using morphological and molecular data (nrITS, TEF1-α). Pluteus romellii is lectotypified and epitypified and accepted as an exclusively Eurasian species. Pluteus lutescens and P. pallescens are considered synonyms of P. romellii. Pluteus fulvibadius is accepted as a related, but separate, North American species. Five species in the/romellii clade are described as new to science: two from North America (P. austrofulvus and P. parvisporus), one from Asia (P. parvicarpus), one from Europe (P. siccus), and one widely distributed across the Holarctic region (P. vellingae). Basidioma size, pileus color, lamellae color, basidiospore size, hymenial cystidia shape and size, habitat and geographical distribution help separate the species described here, but in some instances only molecular data allows for confident identification. The current status of P. californicus, P. melleipes, P. romellii var. luteoalbus, P. splendidus, P. sternbergii and P. sulphureus is discussed. [ABSTRACT FROM AUTHOR]

In the large and morphologically diverse phylum of Chlorophyta, new taxa are discovered every year and their phylogenetic relationships are reconstructed by the incorporation of molecular phylogenetic methods into traditional taxonomy. Herein, we aim to contribute to the photosynthetic microorganisms' diversity knowledge in the Mediterranean area, a relatively unexplored ecoregion with high diversity. Based on a polyphasic approach, 18 Chlorophyta isolates were investigated and characterized. Morphological characteristics and ultrastructure, the phylogeny based on 18S rRNA gene (small subunit ribosomal RNA), 18S–28S internal transcribed spacer (ITS region), and the ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit region (rbcL gene), support establishing four new genera (Nomia, Ava, Akraea, Lilaea) and five new species (Spongiosarcinopsis limneus, N. picochloropsia, Av. limnothalassea, Ak. chliaropsychia, and L. pamvotia) belonging to orders Sphaeropleales, Chlorellales, and Chlamydomonadales. For some of them, this is the first report of their occurrence in specific aquatic environments. [ABSTRACT FROM AUTHOR]

The genus Dalbergia has a pantropical distribution and comprises approximately 250 species. Previous phylogenetic studies on the genus revealed that Dalbergia is monophyletic and is sister to Machaerium and Aeschynomene sect. Ochopodium. However, due to limited samples or DNA regions in these studies, relationships among the major clades are still unresolved, and divergence dates and biogeographical history of the genus have not been addressed. In this study, phylogenetic analyses of Dalbergia were conducted using broad taxon sampling and a combined dataset of two plastid DNA markers (matK and rbcL) and one nuclear marker (ITS). We evaluated the infrageneric classification of the genus based on the reconstructed tree, and investigated biogeographical history of this genus through molecular dating and ancestral area reconstruction analyses. The monophyly of Dalbergia was strongly supported and the genus was resolved into five major clades with high support, several of which correspond to the previous recognized sections. We inferred that Dalbergia originated in South America during the Early Miocene (c. 22.9 Ma) and achieved its current pantropical distribution through multiple recent transoceanic long-distance dispersals (LDD). We highlighted the important historical events which may explain the pantropical distribution pattern of Dalbergia. [ABSTRACT FROM AUTHOR]

Bougainvillea Comm. ex Juss. is one of the renowned genera in the Nyctaginaceae, but despite its recognized horticultural value, the taxonomy and phylogeny of the genus is not well-studied. Phylogenetic reconstructions based on plastid genomes showed that B. pachyphylla and B. peruviana are basal taxa, while B. spinosa is sister to two distinct clades: the predominantly cultivated Bougainvillea clade (B. spectabilis, B. glabra, B. arborea, B. cultivar, B. praecox) and the clade containing wild species of Bougainvillea (B. berberidifolia, B. campanulata, B. infesta, B. modesta, B. luteoalba, B. stipitata, and B. stipitata var. grisebachiana). Early divergence of B. peruviana, B. pachyphylla and B. spinosa is highly supported, thus the previously proposed division of Bougainvillea into two subgenera (Bougainvillea and Tricycla) was not reflected in this study. Morphological analysis also revealed that leaf arrangement, size, and indumentum together with the perianth tube and anthocarp shape and indumentum are important characteristics in differentiating the species of Bougainvillea. In the present study, 11 species and one variety are recognized in Bougainvillea. Six names are newly reduced to synonymy, and lectotypes are designated for 27 names. In addition, a revised identification key and illustrations of the distinguishing parts are also provided in the paper. [ABSTRACT FROM AUTHOR]

Phylogenetic conflicts limit our understanding of the evolution of terrestrial life under multiple whole genome duplication events, and the phylogeny of early terrestrial plants remains full of controversy. Although much incongruence has been solved with so-called robust topology based on single or lower copy genes, the evolutionary mechanisms behind phylogenetic conflicts such as polyploidization remain poorly understood. Here, through decreasing the effects of polyploidization and increasing the samples of species, which represent all four orders and eight families that comprise early leptosporangiate ferns, we have reconstructed a robust phylogenetic tree and network with 1125 1-to-1 orthologs based on both coalescent and concatenation methods. Our data consistently suggest that Matoniales, as a monophyletic lineage including Matoniaceae and Dipteridaceae, should be redefined as an ordinal rank. Furthermore, we have identified and located at least 11 whole-genome duplication events within the evolutionary history of four leptosporangiates lineages, and associated polyploidization with higher speciation rates and mass extinction events. We hypothesize that paleopolyploidization may have enabled leptosporangiate ferns to survive during mass extinction events at the end Permian period and then flourish throughout the Mesozoic era, which is supported by extensive fossil records. Our results highlight how ancient polyploidy can result in rapid species radiation, thus causing phylogenetic conflicts yet allowing plants to survive and thrive during mass extinction events. [ABSTRACT FROM AUTHOR]

A collection of 30 Phytophthora cactorum and 12 P. pseudotsugae (subclade 1a) strains isolated from several recent surveys across California was phylogenetically compared to a worldwide collection of 112 conspecific strains using sequences from three barcoding loci. The surveys baited P. cactorum from soil and water across a wide variety of forested ecosystems with a geographic range of more than 1000 km. Two cosmopolitan lineages were identified within the widespread P. cactorum, one being mainly associated with strawberry production and the other more closely associated with apple orchards, oaks and ornamental trees. Two other well-sampled P. cactorum lineages, including one that dominated Californian restoration outplantings, were only found in the western United States, while a third was only found in Japan. Coastal California forest isolates of both Phytophthora species exhibited considerable diversity, suggesting both may be indigenous to the state. Many isolates with sequence accessions deposited as P. cactorum were determined to be P. hedraiandra and P. ×serendipita, with one hybrid lineage appearing relatively common across Europe and Asia. This study contains the first report of P. pseudotsugae from the state of California and one of the only reports of that species since its original description. [ABSTRACT FROM AUTHOR]

Hyphodontia sensu lato, belonging to Hymenochaetales, accommodates corticioid woodinhabiting basidiomycetous fungi with resupinate basidiocarps and diverse hymenophoral characters. Species diversity of Hyphodontia sensu lato has been extensively explored worldwide, but in previous studies the six accepted genera in Hyphodontia sensu lato, viz. Fasciodontia, Hastodontia, Hyphodontia, Kneiffiella, Lyomyces and Xylodon were not all strongly supported from a phylogenetic perspective. Moreover, the relationships among these six genera in Hyphodontia sensu lato and other lineages within Hymenochaetales are not clear. In this study, we performed comprehensive phylogenetic analyses on the basis of multiple loci. For the first time, the independence of each of the six genera receives strong phylogenetic support. The six genera are separated in four clades within Hymenochaetales: Fasciodontia, Lyomyces and Xylodon are accepted as members of a previously known family Schizoporaceae, Kneiffiella and Hyphodontia are, respectively, placed in two monotypic families, viz. a previous name Chaetoporellaceae and a newly introduced name Hyphodontiaceae, and Hastodontia is considered to be a genus with an uncertain taxonomic position at the family rank within Hymenochaetales. The three families emerged between 61.51 and 195.87 million years ago. Compared to other families in the Hymenochaetales, these ages are more or less similar to those of Coltriciaceae, Hymenochaetaceae and Oxyporaceae, but much older than those of the two families Neoantrodiellaceae and Nigrofomitaceae. In regard to species, two, one, three and 10 species are newly described from Hyphodontia, Kneiffiella, Lyomyces and Xylodon, respectively. The taxonomic status of additional 30 species names from these four genera is briefly discussed; an epitype is designated for X. australis. The resupinate habit and poroid hymenophoral configuration were evaluated as the ancestral state of basidiocarps within Hymenochaetales. The resupinate habit mainly remains, while the hymenophoral configuration mainly evolves to the grandinioid-odontioid state and also back to the poroid state at the family level. Generally, a taxonomic framework for Hymenochaetales with an emphasis on members belonging to Hyphodontia sensu lato is constructed, and trait evolution of basidiocarps within Hymenochaetales is revealed accordingly. [ABSTRACT FROM AUTHOR]

Disturbance plays a key role in shaping forest composition and diversity. We used a community phylogeny and long-term forest dynamics data to investigate biotic and abiotic factors shaping tropical forest regeneration following both human and natural disturbance. Specifically, we examined shifts in seedling phylogenetic and functional (i.e., seed mass) community structure over a decade following a major hurricane in a human-impacted forest in Puerto Rico. Phylogenetic relatedness of the seedling community decreased in the first five years post-hurricane and then increased, largely driven by changes in the abundance of a common palm species. Functional structure (based on seed mass) became increasingly clustered through time, due to canopy closure causing small-seeded, light-demanding species to decline in abundance. Seedling neighbor density and phylogenetic relatedness negatively affected seedling survival, which likely acted to reduce phylogenetic relatedness within seedling plots. Across the study site, areas impacted in the past by high-intensity land use had lower or similar phylogenetic relatedness of seedling communities than low-intensity past land use areas, reflecting interactive effects of human and natural disturbance. Our study demonstrates how phylogenetic and functional information offer insights into the role of biotic and abiotic factors structuring forest recovery following disturbance. [ABSTRACT FROM AUTHOR]

Developmental genetic studies of Antirrhinum majus demonstrated that two transcription factors from the MYB gene family, RADIALIS (RAD) and DIVIRICATA (DIV), interact through antagonism to regulate floral dorsoventral asymmetry. Interestingly, similar antagonistic interaction found among proteins of FSM1 (RAD-like) and MYBI (DIV-like) in Solanum lycopersicum is involved in fruit development. Here, we report the reconstruction of the phylogeny of I-box-like and R-R-type clades, where RAD- and DIV-like genes belong, respectively. We also examined the homology of these antagonistic MYB proteins using these phylogenies. The results show that there are likely three paralogs of RAD-/I-box-like genes, RAD1, RAD2, and RAD3, which originated in the common ancestor of the core eudicots. In contrast, R-R-type sequences fall into two major clades, RR1 and RR2, the result of gene duplication in the common ancestor of both monocots and dicots. RR1 was divided into clades RR1A, RR1B, and RR1C, while RR2 was divided into clades RR2A/DIV1, RR2B/DIV2, and RR2C/DIV3. We demonstrate that among similar antagonistic interactions in An. Majus and So. lycopersicum, RAD-like genes originate from the RAD2 clade, while DIV-like genes originate from distantly related paralogs of the R-R-type lineage. The phylogenetic analyses of these two MYB clades lay the foundation for future comparative studies including testing the evolution of the antagonistic relationship of proteins. [ABSTRACT FROM AUTHOR]

Stress in forest ecosystems (FES) occurs as a result of land-use intensification, disturbances, resource limitations or unsustainable management, causing changes in forest health (FH) at various scales from the local to the global scale. Reactions to such stress depend on the phylogeny of forest species or communities and the characteristics of their impacting drivers and processes. There are many approaches to monitor indicators of FH using in-situ forest inventory and experimental studies, but they are generally limited to sample points or small areas, as well as being time- and labour-intensive. Long-term monitoring based on forest inventories provides valuable information about changes and trends of FH. However, abrupt short-term changes cannot sufficiently be assessed through in-situ forest inventories as they usually have repetition periods of multiple years. Furthermore, numerous FH indicators monitored in in-situ surveys are based on expert judgement. Remote sensing (RS) technologies offer means to monitor FH indicators in an effective, repetitive and comparative way. This paper reviews techniques that are currently used for monitoring, including close-range RS, airborne and satellite approaches. The implementation of optical, RADAR and LiDAR RS-techniques to assess spectral traits/spectral trait variations (ST/STV) is described in detail. We found that ST/STV can be used to record indicators of FH based on RS. Therefore, the ST/STV approach provides a framework to develop a standardized monitoring concept for FH indicators using RS techniques that is applicable to future monitoring programs. It is only through linking in-situ and RS approaches that we will be able to improve our understanding of the relationship between stressors, and the associated spectral responses in order to develop robust FH indicators. [ABSTRACT FROM AUTHOR]

Ergot fungi (Claviceps spp.) are infamous for producing sclerotia containing a wide spectrum of ergot alkaloids (EA) toxic to humans and animals, making them nefarious villains in the agricultural and food industries, but also treasures for pharmaceuticals. In addition to three classes of EAs, several species also produce paspaline-derived indole diterpenes (IDT) that cause ataxia and staggers in livestock. Furthermore, two other types of alkaloids, i.e., loline (LOL) and peramine (PER), found in Epichloë spp., close relatives of Claviceps, have shown beneficial effects on host plants without evidence of toxicity to mammals. The gene clusters associated with the production of these alkaloids are known. We examined genomes of 53 strains of 19 Claviceps spp. to screen for these genes, aiming to understand the evolutionary patterns of these genes across the genus through phylogenetic and DNA polymorphism analyses. Our results showed (1) varied numbers of eas genes in C. sect. Claviceps and sect. Pusillae, none in sect. Citrinae, six idt/ltm genes in sect. Claviceps (except four in C. cyperi), zero to one partial (idtG) in sect. Pusillae, and four in sect. Citrinae, (2) two to three copies of dmaW, easE, easF, idt/ltmB, itd/ltmQ in sect. Claviceps, (3) frequent gene gains and losses, and (4) an evolutionary hourglass pattern in the intra-specific eas gene diversity and divergence in C. purpurea. [ABSTRACT FROM AUTHOR]

Australia has a very diverse pea-flowered legume flora with 1715 native and naturalised species currently recognised. Tribe Mirbelieae s.l. includes 44% of Australia's peas in 24 genera with 756 recognised species. However, several genera within the Pultenaea alliance in tribe Mirbelieae are considered to be non-monophyletic and two main options have been proposed: option one is to merge ca. 18 genera containing ca. 540 species (the largest genus, Pultenaea has nomenclatural priority); and option two is to re-circumscribe some genera and describe new genera as required to form monophyletic groups. At the species level, option one would require 76% of names to be changed; whereas based on available data, option two is likely to require, at most, 8.3% of names to change. Option two therefore provides the least nomenclatural disruption but cannot be implemented without a robust phylogenetic framework to define new generic limits. Here we present novel analyses of available plastid DNA data (trnL-F) which suggest that option two would be feasible once sufficient data are generated to resolve relationships. However, the reticulate evolutionary histories or past rapid speciation suggested for this group may prevent the resolution of all nodes. We propose targeted use of Next-Generation Sequencing technology as the best way to resolve relationships between the key clades in the tribe and present a framework for such a study. An overview of current taxonomy in the tribe is presented, along with the state of taxonomic knowledge and availability of published descriptions for electronic flora treatments. Several new combinations and typifications are published in an appendix. [ABSTRACT FROM AUTHOR]

Melting polar and alpine ice surfaces frequently exhibit blooms of dark pigmented algae. These microbial extremophiles significantly reduce the surface albedo of glaciers, thus accelerating melt rates. However, the ecology, physiology and taxonomy of cryoflora are not yet fully understood. Here, a Swiss and an Austrian glacier dominated either by filamentous Ancylonema nordenskioeldii or unicellular Mesotaenium berggrenii var. alaskanum, were sampled. Molecular analysis showed that both species are closely related, sharing identical chloroplast morphologies (parietal-lobed for Ancylonema vs. axial plate-like for Mesotaenium sensu stricto), thus the unicellular species was renamed Ancylonema alaskana. Moreover, an ecophysiological comparison of the two species was performed: pulse–amplitude modulated (PAM) fluorometry confirmed that they have a high tolerance to elevated solar irradiation, the physiological light preferences reflected the conditions in the original habitat; nonetheless, A. nordenskioeldii was adapted to higher irradiances while the photosystems of A. alaskana were able to use efficiently low irradiances. Additionally, the main vacuolar polyphenol, which effectively shields the photosystems, was identical in both species. Also, about half of the cellular fatty acids were polyunsaturated, and the lipidome profiles dominated by triacylglycerols were very similar. The results indicate that A. alaskana is physiologically very similar and closely related but genetically distinct to A. nordenskioeldii. [ABSTRACT FROM AUTHOR]

Sparsely vegetated habitats of cliffs and screes act as refugia for many regional and local endemic specialized plant taxa most of which have evolved precisely for that type of habitat. The interplay between taxonomic, phylogenetic, and functional plant diversity on rock and scree habitats of extreme environmental conditions, enlightens the relations of plant communities and ecosystems and facilitates management planning for the conservation of biodiversity and ecosystem services. The identification of biodiversity patterns and hotspots (taxonomic, phylogenetic, and functional) contributes to the integration of the ecosystem services (ES) approach for the mapping and assessment of ecosystems and their services (MAES) implementation in Greece and the creation of thematic maps based on the MAES reporting format. The overlap among the protected areas' network revealed that almost all areas of cliffs and screes of medium, high, and very high taxonomic and phylogenetic plant endemism are included in the Natura 2000 area network. The results of this study provide the baseline information for ES assessments at sparsely vegetated land of cliffs and screes. Our results contribute to the implementation of certain indicators of the national set of MAES indicators in Greece such as (a) floristic diversity and (b) microrefugia of endemic diversity and support of decision-making. [ABSTRACT FROM AUTHOR]

Floral nectar is a rich secretion produced by the nectary gland and is offered as reward to attract pollinators leading to improved seed set. Nectars are composed of a complex mixture of sugars, amino acids, proteins, vitamins, lipids, organic and inorganic acids. This composition is influenced by several factors, including floral morphology, mechanism of nectar secretion, time of flowering, and visitation by pollinators. The objective of this study was to determine the contributions of flowering time, plant phylogeny, and pollinator selection on nectar composition in Nicotiana. The main classes of nectar metabolites (sugars and amino acids) were quantified using gas chromatography/mass spectrometric analytical platforms to identify differences among fifteen Nicotiana species representing day- and night-flowering plants from ten sections of the genus that are visited by five different primary pollinators. The nectar metabolomes of different Nicotiana species can predict the feeding preferences of the target pollinator(s) of each species, and the nectar sugars (i.e., glucose, fructose, and sucrose) are a distinguishing feature of Nicotiana species phylogeny. Moreover, comparative statistical analysis indicate that pollinators are a stronger determinant of nectar composition than plant phylogeny. [ABSTRACT FROM AUTHOR]

Near full genome sequencing (NFGS) of HIV-1 is required to assess the genetic composition of HIV-1 strains comprehensively. Population-wide, it enables a determination of the heterogeneity of HIV-1 and the emergence of novel/recombinant strains, while for each individual it constitutes a diagnostic instrument to assist targeted therapeutic measures against viral components. There is still a lack of robust and adaptable techniques for efficient NFGS from miscellaneous HIV-1 subtypes. Using rational primer design, a broad primer set was developed for the amplification and sequencing of diverse HIV-1 group M variants from plasma. Using pure subtypes as well as diverse, unique recombinant forms (URF), variable amplicon approaches were developed for NFGS comprising all functional genes. Twenty-three different genomes composed of subtypes A (A1), B, F (F2), G, CRF01_AE, CRF02_AG, and CRF22_01A1 were successfully determined. The NFGS approach was robust irrespective of viral loads (≥306 copies/mL) and amplification method. Third-generation sequencing (TGS), single genome amplification (SGA), cloning, and bulk sequencing yielded similar outcomes concerning subtype composition and recombinant breakpoint patterns. The introduction of a simple and versatile near full genome amplification, sequencing, and cloning method enables broad application in phylogenetic studies of diverse HIV-1 subtypes and can contribute to personalized HIV therapy and diagnosis. [ABSTRACT FROM AUTHOR]