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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. [ABSTRACT FROM AUTHOR]

Odd ploidy-level cytotypes in sexually reproducing species are considered a dead end due to absent or reduced fertility. If sterility is only partial, however, their contribution to the population gene pool can be augmented by longevity and clonal growth. To test this, we investigated the cytotype origin and spatial pattern, and pollen viability in three relict shrub species of the genus Daphne (Thymelaeaceae Juss.) in central Europe. Daphne cneorum subsp. cneorum is a widespread European species that has a broad ecological amplitude, whereas D. cneorum subsp. arbusculoides and D. arbuscula are narrow endemics of the western Pannonian Plain and the Western Carpathians, respectively. Our study confirmed that all three taxa are diploid. However, of more than a thousand analysed individuals of D. cneorum subsp. cneorum , five in four different populations were triploid. Our data indicate that these triploids most likely originate from recurrent autopolyploidization events caused by the fusion of reduced and unreduced gametes. High pollen viability was observed in all three taxa and in both diploid and triploid cytotypes, ranging from 65 to 100 %. Our study highlights the significant role of odd ploidy-level cytotypes in interploidy gene flow, calling for more research into their reproduction, genetic variability, and overall fitness. Interestingly, while the endemic D. arbuscula differs from D. cneorum based on genetic and genome size data, D. cneorum subsp. arbusculoides was indistinguishable from D. cneorum subsp. cneorum. However, our study reveals that the subspecies differ in the number of flowers per inflorescence. This is the first comprehensive cytogeographic study of this intriguing genus at a regional scale, and in spite of its karyological stability, it contributes to our understanding of genomic evolution in plant species with a wide ecological amplitude. [ABSTRACT FROM AUTHOR]

We investigated if activity of the pre-infective juveniles (J2s) of root-knot nematodes is linked to the recruitment of a specific microbiome on the nematode surface and/or to the composition of the surrounding microbiota. For this, we determined the J2 activity (active vs. non-motile, which referred to dead and immobile J2s) upon a 3-day incubation in soil suspensions and studied the composition of bacteria, protists, and fungi present on the nematode surface and in the suspensions using amplicon sequencing of the 16S/18S rRNA genes, and ITS region. We also amended suspensions with Pseudomonas protegens strain CHA0 to study its effects on J2 activity and microbial composition. The J2 activity was suppressed in soil suspensions, but increased when suspensions were amended with P. protegens CHA0. The active and non-motile J2s differed in the composition of surface-attached bacteria, which was altered by the presence of P. protegens CHA0 in the soil suspensions. The bacterial genera Algoriphagus, Pedobacter , and Bdellovibrio were enriched on active J2s and may have protected the J2s against antagonists. The incubation time appeared short for attachment of fungi and protists. Altogether, our study is a step forward in disentangling the complex nematode-microbe interactions in soil for more successful nematode control. [ABSTRACT FROM AUTHOR]

Forest disturbance has well-characterized effects on soil microbial communities in tropical and northern hemisphere ecosystems, but little is known regarding effects of disturbance in temperate forests of the southern hemisphere. To address this question, we collected soils from intact and degraded Eucalyptus forests along an east–west transect across Tasmania, Australia, and characterized prokaryotic and fungal communities using amplicon sequencing. Forest degradation altered soil microbial community composition and function, with consistent patterns across soil horizons and regions of Tasmania. Responses of prokaryotic communities included decreased relative abundance of Acidobacteriota, nitrifying archaea, and methane-oxidizing prokaryotes in the degraded forest sites, while fungal responses included decreased relative abundance of some saprotrophic taxa (e.g. litter saprotrophs). Forest degradation also reduced network connectivity in prokaryotic communities and increased the importance of dispersal limitation in assembling both prokaryotic and fungal communities, suggesting recolonization dynamics drive microbial composition following disturbance. Further, changes in microbial functional groups reflected changes in soil chemical properties—reductions in nitrifying microorganisms corresponded with reduced NO3-N pools in the degraded soils. Overall, our results show that soil microbiota are highly responsive to forest degradation in eucalypt forests and demonstrate that microbial responses to degradation will drive changes in key forest ecosystem functions. [ABSTRACT FROM AUTHOR]

Soil microbial diversity and community composition are shaped by various factors linked to land management, topographic position, and vegetation. To study the effects of these drivers, we characterized fungal and bacterial communities from bulk soil at four soil depths ranging from the surface to below the rooting zone of two Swedish grasslands with differing land-use histories, each including both an upper and a lower catenary position. We hypothesized that differences in plant species richness and plant functional group composition between the four study sites would drive the variation in soil microbial community composition and correlate with microbial diversity, and that microbial biomass and diversity would decrease with soil depth following a decline in resource availability. While vegetation was identified as the main driver of microbial community composition, the explained variation was significantly higher for bacteria than for fungi, and the communities differed more between grasslands than between catenary positions. Microbial biomass derived from DNA abundance decreased with depth, but diversity remained relatively stable, indicating diverse microbial communities even below the rooting zone. Finally, plant-microbial diversity correlations were significant only for specific plant and fungal functional groups, emphasizing the importance of functional interactions over general species richness. [ABSTRACT FROM AUTHOR]

Species-level taxonomy is traditionally based on herbarium collections that typically include few, or even single, representatives per site. This can lead to underestimation of diversity when there are sympatric populations of superficially similar plants belonging to different lineages. Satyrium longicauda (Orchidaceae) represents a taxonomic challenge for the delimitation of species boundaries due to the high degree of morphological variation detected within and among populations. Currently, just two varieties are accepted based mainly on length differences of the lateral sepal and nectar spur. However, there is extensive morphological variation within South African populations and evidence for several pollination ecotypes, indicating that this taxon represents an actively diverging species complex. Here, we evaluate intraspecific morphological variation through uni- and multivariate morphometrics and analyse internal transcribed spacer sequences for individuals sampled from 36 sites, including 14 sites where divergent morphotypes occur sympatrically. Morphometric analyses of 1802 individuals revealed the presence of eight morphotypes based on vegetative and floral characters. Up to six morphologically and genetically distinct morphotypes can coexist in sympatry. Morphological and genetic distances among populations were significantly correlated. Phylogenetic analyses of 120 accessions indicated that neither of the two varieties nor S. longicauda as a species is monophyletic, and provided evidence for the monophyly of some of the morphotypes including the newly described S. cernuiflorum. The presence of distinct morphological and genetic sympatric variants, which in several cases scale up to distinct evolutionary lineages, is consistent with the existence of different taxa according to morphological and biological species concepts. Our results therefore confirm that taxonomy based mainly on herbarium collections can grossly under-estimate actual diversity of disparate lineages, although further work is required to finalize taxonomic decisions. These findings have implications for efforts to estimate species diversity in groups that are in the process of diversifying and for conservation practice. [ABSTRACT FROM AUTHOR]

In this study, we explore the relationships among taxa of Prunus subgenus Cerasus in Turkey using a combination of macromorphology, micromorphology and molecular techniques. We recorded qualitative and quantitative characteristics of flowers, leaves, seeds and endocarp for 96 populations representing 14 taxa of Prunus subgenus Cerasus. ITS, matK , ycf1 , trnL - trnF DNA sequence data were used to reconstruct phylogenetic trees for this group. Haplotype analyses results found 11 haplotypes among the samples used in this study. We also note that the infraspecific taxa of Cerasus angustifolia (= P. albicaulis), P. mahaleb , P. microcarpa and P. prostrata , as described by previous authors, do not exhibit significant differences even among the features of foliar morphology that are so often used to distinguish them from one another. As a general rule, our analyses indicate that the highly variable features of leaf micromorphology and endocarp and seed micromorphology are not taxonomically significant. In contrast, although floral morphology is often overlooked in systematic studies of Prunus subgenus Cerasus , we found several taxonomically useful flower characters, including sepal indumentum, hypanthium shape and indumentum and petal shape. This work clarifies the infraspecific relationships of members of Prunus subgenus Cerasus in Turkey and solves some taxonomic problems. [ABSTRACT FROM AUTHOR]

Background and Aims Grasses of the Festuca genus have complex phylogenetic relations due to morphological similarities among species and interspecific hybridization processes. Within Patagonian fescues, information concerning phylogenetic relationships is very scarce. In Festuca pallescens , a widely distributed species, the high phenotypic variability and the occurrence of interspecific hybridization preclude a clear identification of the populations. Given the relevance of natural rangelands for livestock production and their high degradation due to climate change, conservation actions are needed and knowledge about genetic variation is required. Methods To unravel the intraspecific phylogenetic relations and to detect genetic differences, we studied 21 populations of the species along its natural geographical distribution by coupling both molecular [internal transcribed spacer (ITS) and trn L-F markers] and morpho-anatomical analyses. Bayesian inference, maximum likelihood and maximum parsimony methods were applied to assemble a phylogenetic tree, including other native species. The morphological data set was analysed by discriminant and cluster analyses. Key Results The combined information of the Bayesian tree (ITS marker), the geographical distribution of haplotype variants (trn L-F marker) and the morpho-anatomical traits, distinguished populations located at the margins of the distribution. Some of the variants detected were shared with other sympatric species of fescues. Conclusions These results suggest the occurrence of hybridization processes between species of the genus at peripheral sites characterized by suboptimal conditions, which might be key to the survival of these populations. [ABSTRACT FROM AUTHOR]

Hybridization and polyploidy are key evolutionary forces in plant diversification, and their co-occurrence in the context of allopolyploid speciation is often associated with increased ability to colonize new environments and invasiveness. In the genus Ulex (Fabaceae), the European gorse (Ulex europaeus subsp. europaeus) is the only invasive and the only polyploid that has recently spread in different eco-geographical regions across the world. Understanding what confers such ecological advantages to this species, compared to its diploid and polyploid congeners, first requires clarification of the ecogeographical and evolutionary context of its formation. To achieve this, the geographical distributions of all Ulex spp. were estimated from species occurrence records, and phylogenetic analyses including all Ulex spp. were performed based on four nuclear (ITS and ETS nrDNA) and plastid (rps12 intron and trnK - matK) regions. The resulting trees were dated using a secondary calibration. Patterns of DNA sequence variation and dated phylogenetic trees were then interpreted in light of previous knowledge of chromosome numbers in Ulex to infer past events of polyploid speciation in the genus. We show that: (1) most current Ulex spp. radiated in the Iberian Peninsula during the past 1–2 Myr; (2) the history of Ulex was punctuated by multiple whole-genome duplication events; and (3) U. europaeus subsp. europaeus is the only gorse taxon that was formed by hybridization of two well-differentiated lineages (which separated c. 5 Mya) with wide climatic ranges (currently represented by Ulex minor and Ulex europaeus subsp. latebracteatus), possibly contributing to the invasive nature and wider climatic range of U. europaeus subsp. europaeus. These findings provide a much-needed evolutionary framework in which to explore the adaptive consequences of genome mergers and duplication in Ulex. [ABSTRACT FROM AUTHOR]

Ruagea (Meliaceae) comprises c. 15 species of small or medium-sized trees distributed in Central and South America, predominantly in montane rain forest and cloud forest of the Andes. The taxonomic position of Ruagea has changed several times in the past, and it was previously included in Guarea. Ruagea is currently accepted as a separate genus based on morphology and molecular phylogenetic analyses at the family level. However, its monophyly has not been accurately tested, and phylogenetic relationships among species are still largely unknown. In addition, delimitation of species boundaries is not straightforward due to morphological diversity within species. Here, we present the first phylogenetic reconstruction of Ruagea based on two nuclear ribosomal (ITS, ETS) and two plastid DNA regions (rps4-trnT , psbA-trnH). Our results show that Ruagea is monophyletic and composed of four main clades (A, B, C and D). Clade D, comprising the Ecuadorian endemic R. membranacea and a potentially new species from Colombia, is sister to the rest of the genus. Our results demonstrate that R. membranacea and R. insignis are monophyletic and provide support for the recognition of two new species with divergent morphologies. The delimitation of the remaining species remains unresolved as they are recovered as either poly- or paraphyletic. Our results highlight the complexity of the taxonomy of Ruagea , as found in other rainforest taxa, and the need for further detailed analyses to delimit these taxa. This study provides the first and most extensive phylogenetic analysis of the genus so far, representing a contribution towards understanding the evolutionary history of Ruagea. [ABSTRACT FROM AUTHOR]

Polyploidization is a key factor in the diversification of flowering plants, but appears to be of only minor importance in the evolution of Euphorbia subgenus Esula. An exception is Euphorbia section Esula , including c. 100 species, many of which are widespread, but several have restricted distribution areas. We used ITS sequencing and relative genome size estimation to explore the evolutionary origin of E. gayi , E. graminifolia , E. tommasiniana , E. valliniana and E. variabilis , which are endemic to disjunct areas along the southern and western margins of the Alps, Corsica and Sardinia. In addition, we explored the incidence of polyploidy across different lineages of E. section Esula. Our phylogenetic results revealed several lineages with unresolved relationships that probably diverged in the Late Miocene, but only one (the Eurasian Group) underwent considerable diversification, probably due to numerous polyploidization events. Several polyploid species or mixed ploidy species in this group are distributed across large areas of Eurasia. All other lineages remained mostly diploid and species-poor, but dispersed to various continents, where most of the species have restricted distribution areas. The five focal species are diploid, but they do not share a common ancestor. Euphorbia graminifolia and E. tommasiniana belong to the Eurasian Group, whereas E. gayi , E. valliniana and E. variabilis belong to the Cosmopolitan Group and are thus not closely related to other European members of the section. Phylogenetic analyses recovered E. valliniana and E. variabilis as genetically distinct, although closely related. This, in combination with a clear morphological differentiation as revealed by morphometric analyses, supports their recognition as independent species. Our study highlights the important role polyploidization had for plant diversification as well as the effects of other factors such as vicariance in disjunct refugia, which probably led to the origin of the five endemic species from Euphorbia section Esula. [ABSTRACT FROM AUTHOR]

Background and Aims Polyploidy is an important process that often generates genomic diversity within lineages, but it can also cause changes that result in loss of genomic material. Island lineages, while often polyploid, typically show chromosomal stasis but have not been investigated in detail regarding smaller-scale gene loss. Our aim was to investigate post-polyploidization genome dynamics in a chromosomally stable lineage of Malvaceae endemic to New Zealand. Methods We determined chromosome numbers and used fluorescence in situ hybridization to localize 18S and 5S rDNA. Gene sequencing of 18S rDNA, the internal transcribed spacers (ITS) with intervening 5.8S rDNA, and a low-copy nuclear gene, GBSSI-1 , was undertaken to determine if gene loss occurred in the New Zealand lineage following polyploidy. Key Results The chromosome number for all species investigated was 2 n  = 42, with the first published report for the monotypic Australian genus Asterotrichion. The five species investigated all had two 5S rDNA signals localized interstitially on the long arm of one of the largest chromosome pairs. All species, except Plagianthus regius , had two 18S rDNA signals localized proximally on the short arm of one of the smallest chromosome pairs. Plagianthus regius had two additional 18S rDNA signals on a separate chromosome, giving a total of four. Sequencing of nuclear ribosomal 18S rDNA and the ITS cistron indicated loss of historical ribosomal repeats. Phylogenetic analysis of a low-copy nuclear gene, GBSSI-1 , indicated that some lineages maintained three copies of the locus, while others have lost one or two copies. Conclusions Although island endemic lineages show chromosomal stasis, with no additional changes in chromosome number, they may undergo smaller-scale processes of gene loss and concerted evolution ultimately leading to further genome restructuring and downsizing. [ABSTRACT FROM AUTHOR]

The aim of DNA barcoding is to enable fast and accurate species identification. However, universal plant DNA barcodes often do not provide species-level discrimination, especially in taxonomically complex groups. Here we use Lauraceae for the design and evaluation of DNA barcoding strategies, considering: (1) the efficacy of taxon-specific DNA barcode regions compared with universal barcodes for species discrimination; and (2) how the extent of intra- and interspecific sampling affects species discrimination rates. To address these areas, we targeted the highly polymorphic, taxon-specific barcode regions ycf1 + ndhH – rps15 + trnL – ycf2 for Lauraceae and compared them against the suite of standard plastid loci used for DNA barcoding (rbcL + matK + trnH – psbA) and the standard nuclear barcode ITS. The highest discrimination success came from nrDNA ITS, whereas the plastid regions (rbcL + matK + trnH – psbA) and the taxon-specific regions (ycf1 + ndhH – rps15 + trnL – ycf2) showed limited and inconsistent resolution. These results highlight that taxon-specific plastid barcodes may provide limited gains in discriminatory power in complex, closely related groups like Lauraceae. Moreover, our study showed that species discrimination greatly depends on the taxon sampling scheme, with relatively lower species discrimination observed where there is more comprehensive intra- and interspecific sampling. The outstanding challenge for plant DNA barcoding is the development of assays that allow routine low-cost access to large numbers of nuclear markers to facilitate the sequencing of large numbers of individuals. [ABSTRACT FROM AUTHOR]

Malaxidinae are a cosmopolitan higher Epidendroid subtribe of > 1250 species that exhibit wide morphological and ecological diversity. Despite almost two centuries of taxonomic deliberation, controversy persists regarding the delimitation of practically all Malaxidinae genera, the most important of which are Crepidium , Dienia , Liparis and Malaxis. Previous attempts to classify these genera using a molecular phylogenetic approach showed Liparis and Malaxis to be polyphyletic and the floral characters traditionally used to define them as homoplastic. Emphasis has instead shifted to vegetative and ecological traits. Here, we conduct an expanded analysis of nuclear (ITS) and plastid (matK) sequences focused on terrestrial taxa, with the resulting phylogram largely corroborating the emerging picture, and we test the efficacy of four previously highlighted traits to recover the same relationships. Although growth habit is underscored as important for resolving a natural distinction between epiphytic Liparis and terrestrial ' Crepidium clade' plus ' Malaxis clade' taxa, leaf shape and venation and habitat preference are shown to be poor predictors of phylogenetic affiliation. Instead, perennating organ structure (heteroblastic or homoblastic) and placement (predominantly above- or below-ground) – are incisive, with leaf number and texture apparently correlated. These findings are discussed in the context of an inferred evolutionary history of the subtribe. Although homoplastic at the subtribe level, some floral characters are shown to be useful for resolving identities at the species level. Accordingly, the status of four long-confused species (Crepidium acuminatum , C. allanii , C. purpureum and Microstylis biloba) is resolved. [ABSTRACT FROM AUTHOR]

Fungi are present in all environments. They fulfil important ecological functions and play a crucial role in the food industry. Their accurate characterization is thus indispensable, particularly through metabarcoding. The most frequently used markers to monitor fungi are ITSs. These markers are the best documented in public databases but have one main weakness: polymerase chain reaction amplification may produce non-overlapping reads in a significant fraction of the fungi. When these reads are filtered out, traditional metabarcoding pipelines lose part of the information and consequently produce biased pictures of the composition and structure of the environment under study. We developed a solution that enables processing of the entire set of reads including both overlapping and non-overlapping, thus providing a more accurate picture of fungal communities. Our comparative tests using simulated and real data demonstrated the effectiveness of our solution, which can be used by both experts and non-specialists on a command line or through the Galaxy-based web interface. [ABSTRACT FROM AUTHOR]

Aims: To characterize the geo‐distinct isolates of Ustilaginoidea virens for morpho‐molecular and mating‐type locus diversity. Methods and Results: Sixty‐one isolates of U. virens collected from Southern India exhibited significant diversity in mycelial width (3·45–5·50 µm), colony colour (yellow, pale yellow, and white), and growth pattern (thick leather mat, raised‐fluffy, flat‐fluffy, and raised). Field‐borne chlamydospores of each isolate were significantly smaller in size (3·34–5·26 µm2) compared to those formed on culture media (18·6–100·89 µm2). The phylogenetic study based on internal transcribed sequences revealed two clusters; however, most isolates (n = 54) were grouped in cluster‐I, indicating common ancestral origin. We also identified 42 haplotypes; among them, Hap_3 has the highest number of isolates (n = 19). Mating‐type locus (MAT1) analysis revealed all sixty‐one isolates as heterothallic, wherein 37 and 24 isolates belonging to MAT1‐1‐1 and MAT1‐2‐1 heterothallic mating types, respectively. The microsynteny analysis of MAT1 loci of one of the Indian strain (Uv‐Gvt) along with Uv‐8b (China) strain revealed synteny conservation at MAT1 locus, which is flanked by conserved genes SLA2 and a hypothetical protein in the upstream and APN2, COX12 and APC5 in the downstream of the locus. Conclusions: Morpho‐molecular study revealed the significant diversity among geo‐distinct isolates, and MAT1 loci analysis indicated the distribution of heterothallic mating types in south Indian paddy fields. And also, complete synteny conservation between Indian and Chinese strain was observed at the MAT1 locus. Significance and Impact of the Study: This is the first report describing the sexuality of Indian strains of the U. virens, which would help better understand the genetic diversity of the U. virens prevailing in Southern India and aid in developing resistant rice cultivars against this pathogen population. [ABSTRACT FROM AUTHOR]

Rhynchospora is one of the most species-rich genera of Cyperaceae, comprising c. 400 species in 28 sections. Rhyncospora section Tenues is one of the largest sections and one of the most problematic. Because it is morphologically similar to sections Laevinuces , Luzuliformes and Spermodontes , the characters traditionally used to distinguish section Tenues cannot be reliably used to place species into one of these four sections. These four sections are included in the Psilocarya group of Rhynchospora subgenus Rhynchospora with sections Psilocarya and Dichromena. Previous molecular studies of Rhynchospora indicate that species of the Psilocarya group form a clade and are sister to at least some species of the sections being studied here. Since only 11 of the estimated 41 species in these four sections were included in earlier phylogenetic studies, the relationships among these sections remain unclear. To elucidate these relationships, we conducted a molecular phylogenetic analysis for Rhynchospora , based on plastid trnL -F and nuclear ETS and ITS markers, emphasizing species in these four sections. Results show that sections Laevinuces , Spermodontes and Tenues are individually not monophyletic but, grouped together, form a well-supported clade, Rhynchospora section Tenues s.l. Rhynchospora section Luzuliformes is monophyletic but is not a sister clade of section Tenues. [ABSTRACT FROM AUTHOR]

Aims: This study investigated the diversity of Colletotrichum isolates recovered from Conyza bonariensis leaves through the use of morphological characteristics, growth rate, carbon sources utilization and phylogenetic analysis. Methods and Results: In all, 30 Colletotrichum isolates recovered from C. bonariensis leaves showing symptoms of disease were included in the present study. Based on the analysis of morphology and sequences, the isolates were distributed into six Colletotrichum species complexes. The concatenated alignment of GAPDH and ITS sequences showed that 20 out of 30 isolates were included in four species complexes which comprise the most important pathogens causing anthracnose in soybean or anthracnose and stalk rot in maize: C. truncatum, C. orchidearum, C. gloeosporioides and C. graminicola. The remaining 10 isolates were included in the C. boninense and C. destructivum species complexes or could not be assigned to any complex with the available information. Conclusion: Weeds belonging to genus Conyza are host to soybean and maize potential pathogenic species of Colletotrichum and could have a role as inoculum reservoir for cross contamination in the agroecosystem. Significance and Impact of the Study: The combined use of morphological, kinetics and physiological parameters of growth and phylogenetic analysis in Colletotrichum isolates from Conyza leaves allowed the detection of species complexes previously not identified in Argentina. [ABSTRACT FROM AUTHOR]

Bloodstream infections (BSI) caused by Candida species are the fourth cause of healthcare associated infections worldwide. Non- albicans Candida species emerged in the last decades as agents of serious diseases. In this study, clinical and microbiological aspects of six patients with BSI due to the Meyerozyma (Candida) guilliermondii species complex from an oncology reference center in Brazil, were evaluated. To describe demographic and clinical characteristics, medical records of the patients were reviewed. Molecular identification of the isolates was performed by ITS1-5.8S-ITS2 region sequencing. Antifungal susceptibility was evaluated by the EUCAST method and the minimal inhibitory concentrations (MIC) assessed according to the epidemiological cutoff values. Virulence associated phenotypes of the isolates were also studied. Ten isolates from the six patients were evaluated. Five of them were identified as Meyerozyma guilliermondii and the others as Meyerozyma caribbica. One patient was infected with two M. caribbica isolates with different genetic backgrounds. High MICs were observed for fluconazole and echinocandins. Non-wild type isolates to voriconazole appeared in one patient previously treated with this azole. Additionally, two patients survived, despite infected with non-wild type strains for fluconazole and treated with this drug. All isolates produced hemolysin, which was not associated with a poor prognosis, and none produced phospholipases. Aspartic proteases, phytase, and esterase were detected in a few isolates. This study shows the reduced antifungal susceptibility and a variable production of virulence-related enzymes by Meyerozyma spp. In addition, it highlights the poor prognosis of neutropenic patients with BSI caused by this emerging species complex. Lay Abstract Our manuscript describes demographic, clinical and microbiological characteristics of patients with bloodstream infection by the Meyerozyma guilliermondii species complex at a reference center in oncology in Brazil. [ABSTRACT FROM AUTHOR]

Paepalanthus is a diverse monocot genus with remarkable diversity distributed in the Neotropical highlands of South America. The genus comprises 410 species arranged in subgenera, sections, subsections and series. Added to this complex classification, Paepalanthus shows considerable morphological heterogeneity and includes three other genera in it, Actinocephalus (Körn.) Sano, Lachnocaulon Kunth and Tonina Aubl. A broadly sampled phylogenetic inference for the genus is still missing, precluding a better understanding of its delimitation and further studies in the group. Here we present the most comprehensive phylogenetic study for Paepalanthus to date, as well as morphological survey of characters that delimit the main lineages found. We assembled a morphologically and geographically representative sampling of Paepalanthus and associated genera comprising 356 accessions in a combined dataset of plastid (trnL-F , psbA-trnH) and nuclear (ITS, ETS) regions. Bayesian inference and maximum likelihood methods were used for phylogenetic reconstruction. We found that Paepalanthus and 16 of its 28 infrageneric categories are not monophyletic, as well as the closely related genus Actinocephalus. Thirty-six well-supported clades are recognized. Morphological characters show high levels of homoplasy, and concepts traditionally used in the classification of Paepalanthus were found to be inconsistent. We confirmed that Paepalanthus as currently circumscribed is not monophyletic and revealed several new relationships in Eriocaulaceae. To make Paepalanthus monophyletic, the genus must be re-circumscribed. These results also provide a foundation for future investigations of the diversification and evolution of flora of the Neotropical highlands of South America. [ABSTRACT FROM AUTHOR]

The Mediterranean region is one of the 25 biodiversity hotspots, with several species distributed on both sides of the Adriatic Sea, i.e. on the Apennine and the Balkan Peninsulas. One of these is Euphorbia spinosa , distributed in the coastal regions of the Ligurian, Tyrrhenian, Ionian and Adriatic Seas, whereas its closest relative, E. glabriflora , occurs in continental regions of the western and southern Balkan Peninsula, mostly on serpentine substrates. They differ morphologically, but transitional forms resembling E. glabriflora can be found within the range of E. spinosa and in the overlapping areas of both species, and phylogenetic relationships between them remain unclear. Using nuclear ribosomal ITS sequences, we here show that these two species form a monophyletic group closely related to the E. acanthothamnos alliance, but the relationships between them remain unresolved. Also, amplified fragment length polymorphism (AFLP) fingerprints are weakly structured, but indicate a north-west to south-east trend in genetic differentiation and two main genetic groups; however, these are not entirely congruent with morphological species boundaries. In addition, morphometric analyses indicate only weak differentiation between the taxa, mostly due to occurrence of morphologically transitional forms in contact areas between the two genetic groups. Based on our results we propose to treat both taxa as subspecies of E. spinosa and provide a taxonomic treatment with descriptions. Finally, based on the high genetic variability on the Balkan Peninsula, we hypothesize a trans-Adriatic dispersal from the Balkans to the Apennine Peninsula, probably during the Pleistocene. This is in line with previous studies of different plants with amphi-Adriatic distributions, with the exception that in E. spinosa the distributions on both peninsulas are of similar size, whereas in most other cases the distribution area on the Balkan Peninsula is larger than on the Apennine Peninsula. [ABSTRACT FROM AUTHOR]

Background and Aims While nuclear DNA content variation and its phenotypic consequences have been well described for animals, vascular plants and macroalgae, much less about this topic is known regarding unicellular algae and protists in general. The dearth of data is especially pronounced when it comes to intraspecific genome size variation. This study attempts to investigate the extent of intraspecific variability in genome size and its adaptive consequences in a microalgal species. Methods Propidium iodide flow cytometry was used to estimate the absolute genome size of 131 strains (isolates) of the golden-brown alga Synura petersenii (Chrysophyceae, Stramenopiles), identified by identical internal transcribed spacer (ITS) rDNA barcodes. Cell size, growth rate and genomic GC content were further assessed on a sub-set of strains. Geographic location of 67 sampling sites across the Northern hemisphere was used to extract climatic database data and to evaluate the ecogeographical distribution of genome size diversity. Key Results Genome size ranged continuously from 0.97 to 2.02 pg of DNA across the investigated strains. The genome size was positively associated with cell size and negatively associated with growth rate. Bioclim variables were not correlated with genome size variation. No clear trends in the geographical distribution of strains of a particular genome size were detected, and strains of different genome size occasionally coexisted at the same locality. Genomic GC content was significantly associated only with genome size via a quadratic relationship. Conclusions Genome size variability in S. petersenii was probably triggered by an evolutionary mechanism operating via gradual changes in genome size accompanied by changes in genomic GC content, such as, for example, proliferation of transposable elements. The variation was reflected in cell size and relative growth rate, possibly with adaptive consequences. [ABSTRACT FROM AUTHOR]

Stenoglottis is a small genus of forest orchids endemic to continental Africa. Nine taxa have so far been described, but species boundaries in the genus are problematic and several of these taxa are not widely accepted. In this study, taxon boundaries were investigated by means of a combination of morphometric and phylogenetic analyses, with the aim of resolving species-level relationships and identifying practical diagnostic characters. Sequence variation was low, particularly in plastid DNA (atpI-atpH), and Bayesian inference and maximum likelihood analyses of nuclear markers (ITS and ETS) did not resolve all of the putative taxa. Multivariate morphometrics (PCA, PCoA, cluster analysis) likewise did not support the recognition of all described Stenoglottis taxa, but they reliably distinguished some taxa that DNA data did not. Combined morphological and phylogenetic evidence supports the delimitation of five species and two varieties, for which characteristics of floral spurs, labella, leaves, bracts and auricles provide reliable diagnostic traits. These findings will form the basis of a taxonomic revision in which the proposed changes will be formalized. [ABSTRACT FROM AUTHOR]

There is little understanding about how soil water stress history and host genotype influence the response of wheat-associated microbiome under short-term decreases in soil moisture. To address this, we investigated how plant breeding history (four wheat genotypes; two with recognized drought resistance and two without) and soil water stress history (same wheat field soil from Saskatchewan with contrasting long-term irrigation) independently or interactively influenced the response of the rhizosphere, root and leaf bacterial and fungal microbiota to short-term decreases in soil water content (SWC). We used amplicon sequencing (16S rRNA gene for bacteria and ITS region for fungi) to characterize the wheat microbiome. Fungal and bacterial communities responses to short-term decreases in SWC were mainly constrained by soil water stress history, with some smaller, but significant influence of plant genotype. One exception was the leaf-associated fungal communities, for which the largest constraint was genotype, resulting in a clear differentiation of the communities based on the genotype's sensitivity to water stress. Our results clearly indicate that soil legacy does not only affect the response to water stress of the microbes inhabiting the soil, but also of the microorganisms more closely associated with the plant tissues, and even of the plant itself. [ABSTRACT FROM AUTHOR]

We performed morphology, molecular study and antifungal susceptibility test on 10 Talaromyces sp. isolates: eight clinical isolates (human immunodeficiency virus (HIV) and non-HIV-patient) and two isolates from rats. All strains produced red soluble pigment and microscopically showed Penicillium -like structure in room temperature and yeast-like structure in 37°C. Based on molecular analysis, nine isolates were identified as Talaromyces atroroseus (including the isolates from rats) and one as T. marneffei. Our susceptibility result of T. marneffei supports the use of amphotericin B, itraconazole for talaromycosis marneffei management. Talaromyces atroroseus showed variable MIC to echinocandin, azole derivatives, 5-flucytosine and amphotericin B. [ABSTRACT FROM AUTHOR]

Background and Aims Whole-genome duplication (WGD) events are considered important driving forces of diversification. At least 11 out of 52 Brassicaceae tribes had independent mesopolyploid WGDs followed by diploidization processes. However, the association between mesopolyploidy and subsequent diversification is equivocal. Herein we show the results from a family-wide diversification analysis on Brassicaceae, and elaborate on the hypothesis that polyploidization per se is a fundamental driver in Brassicaceae evolution. Methods We established a time-calibrated chronogram based on whole plastid genomes comprising representative Brassicaceae taxa and published data spanning the entire Rosidae clade. This allowed us to set multiple calibration points and anchored various Brassicaceae taxa for subsequent downstream analyses. All major splits among Brassicaceae lineages were used in BEAST analyses of 48 individually analysed tribes comprising 2101 taxa in total using the internal transcribed spacers of nuclear ribosomal DNA. Diversification patterns were investigated on these tribe-wide chronograms using BAMM and were compared with family-wide data on genome size variation and species richness. Key Results Brassicaceae diverged 29.9 million years ago (Mya) during the Oligocene, and the majority of tribes started diversification in the Miocene with an average crown group age of about 12.5 Mya. This matches the cooling phase right after the Mid Miocene climatic optimum. Significant rate shifts were detected in 12 out of 52 tribes during the Mio- and Pliocene, decoupled from preceding mesopolyploid WGDs. Among the various factors analysed, the combined effect of tribal crown group age and net diversification rate (speciation minus extinction) is likely to explain sufficiently species richness across Brassicaceae tribes. Conclusions The onset of the evolutionary splits among tribes took place under cooler and drier conditions. Pleistocene glacial cycles may have contributed to the maintenance of high diversification rates. Rate shifts are not consistently associated with mesopolyploid WGD. We propose, therefore, that WGDs in general serve as a constant 'pump' for continuous and high species diversification. [ABSTRACT FROM AUTHOR]

Lake Baikal is populated by an endemic genus of oligochaetes (Baikalodrilus), which currently comprises 24 morphospecies. The genus can be considered as a 'species flock'. However, the validity of many species is questionable: the great similarity in their description and the lack of unequivocal diagnostic characters often lead species identification to an impasse. In order to clarify the systematics of this genus, we analysed two nuclear and two mitochondrial DNA markers of 40 Baikalodrilus specimens. DNA and morphological approaches are mostly congruent in suggesting ten candidate species, although two additional species are suspected. A reassessment of the taxonomic value of the morphological characteristics of Baikalodrilus suggests that there are few that can be used as distinctive, specific criteria in the genus. The association between candidate and nominal species remains problematic, except for three species identified prior to molecular analyses. Baikalodrilus trituberculum sp. nov. is described. Phylogenetic inferences suggests that the earliest split in Baikalodrilus and the time of divergence of most lineages corresponding to species are consistent with the hypothesis of a general rearrangement of the Baikal fauna, following major environmental changes due to a general cooling in the Early Pleistocene. [ABSTRACT FROM AUTHOR]

Leaf blight and fruit rot disease caused by Phomopsis vexans is a devastating disease of brinjal. The detection of P. vexans in plant parts and seeds of brinjal can be complicated, mainly when the inoculum is present at low levels and/or overgrown by fast‐growing saprophytic fungi or other seed‐borne fungi. A PCR‐based diagnostic method was developed with specific primers designed based on sequence data of a region consisting of the 5·8S RNA gene and internal transcribed spacers, ITS 1 and ITS 2 of nuclear ribosomal RNA gene (rDNA) repeats of P. vexans. The efficiency and specificity of primer pairs PvexF/PvexR designed were established by PCR analysis of DNA from P. vexans strains isolated from India and fungal isolates of other genera. A single amplification product of 323‐bp was detected from DNA of P. vexans isolates. No cross‐reaction was observed with any of the other isolates tested. The specific primers designed and employed in PCR detected P. vexans up to 10 pg from DNA isolated from pure culture. This is the first report on the development of species‐specific PCR assay for identification and detection of P. vexans. Thus, PCR‐based assay developed is very specific, rapid, confirmatory and sensitive tool for the detection of pathogen P. vexans at early stages. Significance and Impact of the Study: Phomopsis vexans is an important seed‐borne pathogenic fungus responsible for leaf blight and fruit rot in brinjal. Current detection methods, based on culture and morphological identification is time consuming, laborious and are not always reliable. A PCR‐based diagnostic method was developed with species‐specific primers designed based on sequence data of a region consisting of the 5·8S RNA gene and internal transcribed spacers, ITS 1 and ITS 2 of nuclear ribosomal RNA gene (rDNA) repeats of P. vexans. [ABSTRACT FROM AUTHOR]

Distribution, taxonomy, nomenclature and molecular genetic data are presented for two closely related pairs of birch taxa: (1) dark-barked Betula pubescens var. sibakademica (Baran.) Kuzeneva (basionym B. sibakademica Baranov) and white-barked B. pubescens var. pubescens , and (2) dark-barked B. kotulae Zaverucha = B. pendula var. obscura (Kotula ex Fiek) Olšavská (basionym B. obscura Kotula ex Fiek, heterotypic synonym B. kotulae) and white-barked B. pendula , respectively. Using published data and sequences obtained in this study, it was found that, although these pairs can be distinguished not only by morphological characters but also by two diagnostic single nucleotide polymorphisms (SNPs) in the internal transcribed spacers ITS1 and ITS2, no sequence differences within each pair were detected. These results suggest that the colour of the bark cannot be used as a taxonomic trait at the species level, and the dark-barked birches within each pair should not be treated as separate species or varieties, but as forms, respectively. Therefore, we reassessed the taxonomic status of B. sibakademica and B. kotulae using morphological traits and molecular genetic markers and suggest that B. pubescens f. sibakademica (Baranov) Tarieiev comb. nov. and B. pendula f. obscura (Kotula ex Fiek) Tarieiev comb. nov. should be used for them, respectively. Betula pubescens f. sibakademica was described in Ukraine for the first time. [ABSTRACT FROM AUTHOR]

The article discusses the evolution of deception based on floral chemistry in Dactylorhiza orchids. Topics discussed include demonstration of the role of different floral traits in deception strategies of orchids, difference between sexually deceptive orchids and food-deceptive plants; and comparison of the floral chemical signals of food-deceptive orchids with co-flowering rewarding species.

Gastrochilus and related taxa is a diverse group of horticultural and threatened orchids occurring mainly in South-East Asia. Although Gastrochilus is a small genus, the generic and interspecific relationships of it are still not well understood. Here, we present a molecular study using sequence data from nuclear internal transcribed spacer (ITS) and four plastid DNA regions (matK, psbA-trnH, psbM-trnD, trnL-F) to clarify these relationships. Our results indicated that Gastrochilus is monophyletic and subdivided into five clades. Haraella is nested in Pomatocalpa, and together they are sister to Gastrochilus. Five morphological characters (epichile hairs, stem type, leaf size, dorsal sepal size and presence of leaf spots) agree well with the molecular phylogenetic trees and can be used to subdivide Gastrochilus. Two new species are separated from G. calceolaris, and the status of the confused species G. somai and G. fuscopunctatus is clarified as a distinct species. The molecular phylogenetic trees and evaluation of characters indicate that shifts in pollination system in Gastrochilus have occurred independently at least three times. [ABSTRACT FROM AUTHOR]

We explored the effects of Quaternary climate changes on the campos rupestre sky island ecosystem in central and eastern Brazil studying the phylogeography of Richterago discoidea (Asteraceae) to better understand the effect of historical biogeographic processes on species diversification in this region. DNA sequences of nuclear (ITS) and plastid (psbA - trnH, rpl32 - trnL UAG , trnK UUU - rps16 and ycf3 - trnS) markers and 83 AFLP loci were used to genotype up to 90 individuals from 19 populations of R. discoidea. We investigated intraspecific genetic structure, demographic history and spatiotemporal diversification. Also, ecological niche modelling was used to infer palaeodistribution. Three lineages (without strong geographical structure) were identified in the Bayesian genetic structure analysis of 25 haplotypes, whereas AFLPs revealed two lineages with considerable levels of admixture. The origin of diversification of R. discoidea is on the Diamantina Plateau (Espinhaço Meridional, Minas Gerais), from where lineages expanded to the central highlands of Brazil during glacial periods in the Mid-Pleistocene. The current disjunct distribution is a relict of an ancient wide distribution, resulting from retraction during interglacial periods, confining populations to mountain-top sky islands that acted as refugia (Espinhaço Range and Goiás highlands). Expansion within refugium sites during the LGM blurred deeper genetic structure, and pressure of selection in ecological outliers favoured high genetic diversity outside refugia. © 2018 The Linnean Society of London, Biological Journal of the Linnean Society, 2018, YY, 000–000 [ABSTRACT FROM AUTHOR]

Ceratophyllum (Ceratophyllaceae) is among the most enigmatic of angiosperm taxa, with its phylogenetic placement changing almost continuously over the last few decades. Ceratophyllum spp. are difficult to identify using vegetative morphology alone, which is commonly all that is available for these highly clonal plants. A molecular phylogenetic approach was used to examine relationships in the genus and provide molecular markers to facilitate the identification of Ceratophyllum spp. This study included all known Ceratophyllum spp. that have been distinguished in the last two taxonomic treatments of the genus. Sequence data for ITS and matK were used to examine phylogenetic relationships among species. The molecular analyses readily distinguish five clades which correspond taxonomically to C. echinatum, C. demersum, C. australe (including C. tanaiticum), C. submersum and C. muricatum (including C. muricatum subsp. muricatum and C. m. subsp. kossinskyi). In these analyses, accessions of the morphologically distinct C. platyacanthum were not clearly differentiated from some accessions of C. demersum, perhaps as a consequence of the probable polyploid origin of this taxon. Overall, the molecular data disagree with some previous studies based on morphology by indicating (1) the presence of more than two species in the genus, (2) that C. echinatum is not the closest relative of C. submersum, (3) that C. muricatum is related more closely to C. submersum than to C. australe and (4) that C. tanaiticum is resolved in a well-supported clade with C. australe, which is distinct from accessions of C. muricatum. Although C. tanaiticum and C. australe fall in the same clade in the current analysis, their high level of genetic divergence, extreme geographical isolation and significantly different morphologies support their recognition as distinct species. We also discuss the chorological and palaeobotanical aspects of the new results. [ABSTRACT FROM AUTHOR]

The ‘out of Australia’ hypothesis describes taxa with ancestors present on the Australian continent before the contact of the Australian plate with Southeast Asia and the subsequent biological interchange between these regions across Wallacea. Our study supports the ‘out of Australia’ hypothesis for the tropical tree genus Alphitonia and its closest relatives. A common ancestor of the entire clade inhabited Australia in the Miocene, and westward dispersal into Wallacea, the Philippines and the Asian continent was reconstructed to be of Quaternary origin. Furthermore, our study supports the currently applied taxonomy in Alphitonia and related genera, although it highlights potentially underestimated diversity. Finally, our study highlights the need for further investigations in Alphitonia and related genera and for including fossil-rich related taxa. The need for these investigations also arises from a potential human-mediated dispersal of Alphitonia spp. in Polynesia, which cannot be clearly proven by our approach. [ABSTRACT FROM AUTHOR]

Paspalum stellatum is widely distributed in the American continent and it is known to include diploid cytotypes (2 n = 2 x = 20) and polyploid cytotypes (2 n = 32 and 52). It is closely related to P. eucomum, P. malmeanum and P. schesslii. After chromosome counting and geographical mapping of the different cytotypes, phylogenetic relationships between them were explored in order to infer the origin and evolution of the polyploid complex P. stellatum and related species. Additionally, several unusual chromosome numbers are here reported for P. stellatum (2 n = 30, 46, 48, 56 and 60) from the Brazilian cerrado. Phylogenetic analysis using plastid DNA showed that the cytotypes of P. stellatum split into two clades, one of which included all accessions with 2 n = 32 and P. schesslii. Using ITS for phylogenetic analysis showed that P. schesslii, P. malmeanum and P. eucomum were grouped together as expected. The origin of the cytotype 2 n = 32 of P. stellatum may have involved P. schesslii as one of the putative progenitors with a diploid cytotype of P. stellatum as the other. [ABSTRACT FROM AUTHOR]

We developed two ligase-dependent probe amplification assays based on rolling circle amplification (RCA) and the ligase-dependent reaction (LDR) to differentiate species of Exophiala targeting the rDNA internal transcribed spacer region. We focused on Exophiala dermatitidis and E. phaeomuriformis , two opportunistic inhabitants of indoor wet cells, and further detected E. heteromorpha , E. xenobiotica , and E. crusticola ; 57 reference isolates representing the five species were tested. Depending on the RCA probes used, the sensitivity was 100%, and the specificity ranged from 3.7% to 88.6% (median: 46.1%). In contrast, the sensitivity and specificity of the LDR probes targeting the same isolates were 88.6–100% (median: 95.8%) and 95.4–100% (median: 97.7%), respectively. We analyzed 198 additional environmental isolates representing the same Exophiala species. Overall, the sensitivity and specificity of LDR ranged from 89.7% to 100% (median: 94.1%) and from 93.9% to 100% (median: 96.9%), respectively. The assessment of performance and validation of LDR probes using SYBR Green quantitative polymerase chain reaction revealed high reproducibility and an acceptable range limit, in line with the guidelines of the European Network of GMO Laboratories. In conclusion, the LDR assay was more reliable and less expensive than RCA for species-level identification of Exophiala isolates. [ABSTRACT FROM AUTHOR]

Aloe (Asphodelaceae) is a typical element of the succulent flora of the eastern Indian Ocean islands of Madagascar, the Mascarene Islands of Mauritius, and Réunion and the Seychelles. In this region, there are 129 native Aloe spp., all of which are endemic. The most recent classification of Aloe in Madagascar, completed by Reynolds in the 1960s, defined nine morpho-groups. The present study is the first phylogenetic analysis of Aloe in Madagascar and the Mascarenes, encompassing approximately one-third of the regional species diversity. Bayesian inference and maximum likelihood analyses of ITS, matK and trnQ-rps16 DNA sequences suggest that numerous dispersal events occurred from the African continent to Madagascar. As a result, close evolutionary relationships exist among geographically distant aloes, such as A. suzannae, the nocturnal-flowered species and Kumara in southern Africa. Aloe section Lomatophyllum is the only morpho-group to correspond to a phylogenetic clustering. Our findings confirm that Aloe spp. native to the eastern Indian Ocean islands do not comprise a monophyletic unit and emphasize the need for a revised infrageneric classification of Aloe. [ABSTRACT FROM AUTHOR]

With limited resources for curtailing the escalating biodiversity crisis, a rational means of setting priorities among threatened species is of pre-eminent concern. Combining phylogenetic history and conservation status to estimate the evolutionary distinctiveness that would be lost in the event of a given species becoming extinct has gained momentum in analyses of animal taxa, but has not previously been attempted for plants. Focusing on the heavily impacted Indo-Burma Biodiversity Hotspot, we examine the utility of various phylogenetic metrics in prioritizing members of Orchidaceae, the largest family in the eco-region. Reconstructing a time-calibrated phylogenetic tree for 592 of the known 2170 species in the region reveals Thailand, South China and Vietnam as the areas harbouring the highest phylogenetic diversity and Tropidia curculigoides, Thaia saprophytica and Risleya atropurpurea as accounting for disproportionately great evolutionary distinctiveness. Although patchy, integrating global and national Red List data justifies several priorities, particularly in the intensively poached genera Paphiopedilum and Dendrobium. Addressing biases in the phylogenetic and conservation status data sets requires that botanical gardens in the region accession under-represented taxa and that citizen scientists and professional researchers contribute more fully to Red Lists. Governments are urged to step-up protection of habitats highlighted as cradles of exceptional orchid diversity. [ABSTRACT FROM AUTHOR]

A phylogenetic hypothesis for tribe Podochileae with emphasis on subtribe Eriinae s.s. is based on nucleotide sequences of the nuclear ITS and four plastid regions (matK, trnL-F spacer, trnL intron and ycf1). The strict consensus tree based on parsimony is largely congruent with the maximum likelihood tree with a few major differences; most importantly, monophyly of Podochileae as recently circumscribed is strongly supported by the maximum likelihood tree but not recovered in the parsimony analysis. Monophyly of Thelasiinae s.s. (without Ridleyella) and Eriinae s.l. (including Podochilinae) is supported, whereas Eria s.l. appears polyphyletic. The generic circumscription of Eriinae s.s. (excluding Podochilinae) is revised, and 21 genera are accepted, including two not previously recognized. Nomenclatural changes and a key to genera in Eriinae are provided. [ABSTRACT FROM AUTHOR]

Deschampsia antarctica is the only grass naturally occurring in Antarctica, and it is also indigenous to southern South America. We aimed to evaluate patterns of within-population genetic diversity and between the focal areas Patagonia and Antarctica by using 144 sequences of nuclear internal transcribed spacer and non-coding plastid regions. We analysed phylogenetic relationships between these two main areas and performed demographic and landscape analysis. To test the divergence time between Antarctic and Patagonian populations we used approximate Bayesian computation. We found 17 nuclear and eight plastid haplotypes. For both molecular markers, Patagonia was the most genetically variable area in the range of D. antarctica. The divergence time between populations from Antarctica and Patagonia was dated to the mid to late Pleistocene. The large number of private haplotypes found in Patagonia and the great genetic variability support the hypothesis of a South American origin of the Antarctic populations of D. antarctica. Finally, we suggest that D. antarctica probably survived the Last Glacial Maximum and possibly earlier glaciations in ice-free refugia in Patagonia and Antarctica. Dispersal to Antarctica possibly occurred in the mid to late Pleistocene through bird-aided long-distance transport from South America. [ABSTRACT FROM AUTHOR]

Despite the biological, ecological and conservational interest of halo-gypsophytes, which are frequently found in endangered ecosystems, such plant species have received little attention from a phylogeographical point of view. Jacobaea auricula is an endangered perennial member of Asteraceae, which has a fragmented distribution restricted to gypsum and/or saline outcrops in the Iberian Peninsula. It includes populations with few individuals. Amplified fragment length polymorphism markers and nuclear and plastid sequences were used to explore the phylogeographical and evolutionary history of the species and to determine whether the classical taxonomic differentiation in subspecies is genetically supported. Estimation of divergence times indicated that intraspecific divergence took place during the Pleistocene glaciations. Unlike other species from the area that grow under unusual soil conditions, northern and central Spain appeared to be ancestral with respect to the southern areas. Overall population differentiation was low, which does not completely match with the expected pattern in plant species from discontinuous habitats. Considering the bi-edaphic character of J. auricula, low levels of among-population differentiation may be explained by the fact that more continuous habitat availability could have favoured connectivity among fragments in the past. Haplotype differentiation reflects survival of ancestral polymorphism, instead of phylogeographical structure. Finally, a poor correlation among genetic groups and subspecies was found. This study illustrates the importance of exploring the evolutionary history of each particular species more deeply when determining conservation strategies for edaphoendemics. [ABSTRACT FROM AUTHOR]

The amphipod genus Niphargus comprises hundreds of eyeless and depigmented species with narrow ranges in Western Palaearctic subterranean freshwaters. Niphargus hrabei and N. valachicus, two morphologically and ecologically similar species, are atypical due to their epigean lifestyle and large ranges. Given their wide and largely sympatric distributions, we explored their potential ecological niche overlap by comparing morphological functional traits, patterns of co-occurrence and habitat selection, and tested for cryptic diversity by examining variation of mitochondrial and nuclear markers in selected populations. Mitochondrial sequences and the presence of shared nuclear alleles among individuals collected along the study area did not support the existence of cryptic lineages; two other Niphargus species described in the past from Hungary seem to be their younger synonyms. Except for body size, both species were morphologically similar and seem only weakly differentiated ecologically. Though smaller in size, N. hrabei is ecologically more tolerant, while N. valachicus might be a superior competitor due to its larger size. Despite large-scale sympatry, co-occurrence of both species was rare. Their present distributions may result from a dynamic relationship between dispersal ability and competitive strength. These widespread and euryoecious Niphargus species demonstrate that the genus may be successful not only in the subterranean realm but also in various surface waters. [ABSTRACT FROM AUTHOR]

Several plant and animal species exhibit amphi-Adriatic distributions spanning the Italian and Balkan peninsulas. Such distribution patterns have traditionally been explained mostly by land connections between the two peninsulas during the Messinian salinity crisis (Miocene/Pliocene), but recent studies employing molecular dating pointed to more recent, i.e. Pleistocene, dispersals from the Balkans to Italy. One of the plant groups exhibiting such a distribution pattern is the Euphorbia barrelieri group (Euphorbiaceae), in which six taxa (variously treated as species or subspecies) have been traditionally included. We employed AFLPs and nuclear (ITS) and plastid (trnT-trnL) DNA sequences to disentangle relationships among them and infer their spatio-temporal diversification. Our results clearly show that E. hercegovina and E. saxatilis do not belong to the group, which thus consists of four species. The common ancestor of the E. barrelieri group originated and diversified in the Pleistocene, giving rise to E. barrelieri distributed in Italy and France on one side of the Adriatic and E. kerneri in the south-eastern Alps and E. triflora and E. thessala on the Balkan Peninsula on the other side. Phylogeographical analysis inferred a trans-Adriatic dispersal of the lineage leading to E. barrelieri from the Balkan Peninsula, thus underlining the importance of this area for the origin of Italian biota. Last but not least, E. hercegovina subsp. javoriensis is clearly nested in E. triflora. Based on our results we provide a taxonomic treatment of all four species and designate five lectotypes. [ABSTRACT FROM AUTHOR]

Acantholimon is an important component of the subalpine steppe flora in the Irano-Turanian region and the second largest genus of Plumbaginaceae with c. 200 cushion-forming subshrubby species. Because the genus has been poorly represented in previous phylogenetic studies, questions regarding its monophyly, phylogenetic relationships and infrageneric classification have not been addressed in a solid evolutionary framework. We used sequences from the nuclear ribosomal internal transcribed spacers and the plastid trnY(GUA)-trnT(GGU) intergenic spacer for 197 accessions of Acantholimon and nine putatively closely related Asian genera in Limonioideae. Contrary to previous results, Bayesian, maximum likelihood and maximum parsimony analyses show that Acantholimon is not monophyletic unless its limits are extended to include species currently placed in eight of these Asian genera. As circumscribed, the new Acantholimon s.l. is sister to Goniolimon and includes the following genera: Bamiania, Bukiniczia, Chaetolimon, Cephalorhizum, Dictyolimon, Gladiolimon, Popoviolimon and Vassilczenkoa. Our phylogenetic analyses also challenge the existing classification at the generic and infrageneric levels. A maximum likelihood reconstruction of ancestral states for morphological characters illustrates the possible scenarios by which the cushion architecture combined with linear acuminate leaves, also present in other steppic Irano-Turanian elements, were acquired in this group of Plumbaginaceae. Our study shows the importance of extensive taxon sampling for phylogenetic reconstruction of species-rich lineages. [ABSTRACT FROM AUTHOR]

Palm wine produced traditionally and consumed by many people in the South-West of Burkina Faso is subject to alteration. In this study, we carried out a follow-up of two palm wines' fermentation during the 10 days in which palm wines are classically produced and consumed. We monitored biochemical characteristics of fermenting wines as well as followed the microflora kinetics using culture-dependent and culture-independent methods. The analysis of the acid content and the bacterial population revealed the correlation between the development of Lactic acid bacteria, acetic acid, and total acidity. Ribosomal intergenic spacer analysis and sequencing results revealed different yeast and bacterial populations for the two palm wines. Although Saccharomyces cerevisiae remained the sole yeast species in one fermentation, it was quickly replaced by Clavispora lusitaniae in the second fermentation, which had never been described until now in palm wine. When considering bacteria, the species Corynebacterium sp. , Lactobacillus casei, Lactobacillus paracasei and Leuconostoc sp. were detected in both palm wines . But we also detected Acetobacter pasteurianus, Bacillus cereus and Bacillus thuringiensis in the second fermentation. Significance and Impact of the Study Our results highlight the evolution of palm wine during the 10 days separating palm tapping and consumption of the fermented wine. The fermentation step is performed within few hours and completed after 24 h. The next days, its acidity increases progressively with the production of lactic and acetic acids by bacteria. The high production of acetic acid is very likely one of the main cause of palm wine degradation during this period. This indicates that the solution to palm wine preservation might be protection against oxygen, as well as the limit of bacterial growth through the use of preservatives. [ABSTRACT FROM AUTHOR]

Three termite species currently placed into Nasutitermes Dudley, 1890 (Isoptera: Termitidae), occurring in Taiwan, N. kinoshitai (Hozawa, 1915), N. parvonasutus (Nawa, 1911), and N. takasagoensis (Nawa, 1911), are redescribed and keyed. The soldier and worker castes of N. kinoshitai are described for the first time. Neotypes are designated for N. parvonasutus and N. takasagoensis. Significant difference in their morphology and gene sequences of mitochondrial 16S rRNA and internal transcribed spacer (ITS) indicate that N. kinoshitai and N. parvonasutus do not belong to Nasutitermes; however, as the genus and several morphologically similar and systematically related genera are in need of revision, currently it is not possible to propose a revised generic placement. Based on 438 colony samples, the distribution pattern, dispersal flight season, polymorphism of soldier and worker castes, and termitophiles of the three species are discussed. [ABSTRACT FROM AUTHOR]

• Background and Aims Betula L. (birch) is a genus of approx. 60 species, subspecies or varieties with a wide distribution in the northern hemisphere, of ecological and economic importance. A new classification of Betula has recently been proposed based on morphological characters. This classification differs somewhat from previously published molecular phylogenies, which may be due to factors such as convergent evolution, hybridization, incomplete taxon sampling or misidentification of samples. While chromosome counts have been made for many species, few have had their genome size measured. The aim of this study is to produce a new phylogenetic and genome size analysis of the genus. • Methods Internal transcribed spacer (ITS) regions of nuclear ribosomal DNA were sequenced for 76 Betula samples verified by taxonomic experts, representing approx. 60 taxa, of which approx. 24 taxa have not been included in previous phylogenetic analyses. A further 49 samples from other collections were also sequenced, and 108 ITS sequences were downloaded from GenBank. Phylogenetic trees were built for these sequences. The genome sizes of 103 accessions representing nearly all described species were estimated using flow cytometry. • Key Results As expected for a gene tree of a genus where hybridization and allopolyploidy occur, the ITS tree shows clustering, but not resolved monophyly, for the morphological subgenera recently proposed. Most sections show some clustering, but species of the dwarf section Apterocaryon are unusually scattered. Betula corylifolia (subgenus Nipponobetula) unexpectedly clusters with species of subgenus Aspera. Unexpected placements are also found for B. maximowicziana, B. bomiensis, B. nigra and B. grossa. Biogeographical disjunctions were found within Betula between Europe and North America, and also disjunctions between North-east and South-west Asia. The 2C-values for Betula ranged from 0·88 to 5·33 pg, and polyploids are scattered widely throughout the ITS phylogeny. Species with large genomes tend to have narrow ranges. • Conclusions Betula grossa may have formed via allopolyploidization between parents in subgenus Betula and subgenus Aspera. Betula bomiensis may also be a wide allopolyploid. Betula corylifolia may be a parental species of allopolyploids in the subsection Chinenses. Placements of B. maximowicziana, B. michauxii and B. nigra need further investigation. This analysis, in line with previous studies, suggests that section Apterocaryon is not monophyletic and thus dwarfism has evolved repeatedly in different lineages of Betula. Polyploidization has occurred many times independently in the evolution of Betula. [ABSTRACT FROM AUTHOR]

Homoploid hybrid speciation, the origin of a hybrid species without change in chromosome number, is currently considered to be a rare form of speciation. In the present study, we examined the phylogenetic origin of Hippophaë gyantsensis, a diploid species occurring in the western Qinghai-Tibet Plateau. Some of its morphological and molecular traits suggest a close relationship to H. rhamnoides ssp. yunnanensis while others indicate H. neurocarpa. We conducted phylogenetic analyses of sequence data of two maternally inherited chloroplast (cp) DNA fragments and the bi-parentally inherited nuclear ribosomal internal transcribed spacer ( ITS) from 17 populations of H. gyantsensis, 15 populations of H. rhamnoides ssp. yunnanensis and 27 populations of H. neurocarpa across their distributional ranges, and modelled the niche differentiation of the three taxa. Multiple lines of evidence suggested that H. gyantsensis is a morphologically stable, genetically independent and ecologically distinct species. The inconsistent phylogenetic placements of the H. gyantsensis clade that comprised the dominant cp DNA haplotypes and ITS ribotypes suggested a probable diploid hybrid origin from multiple crosses between H. rhamnoides ssp. yunnanensis and H. neurocarpa. This tentative hypothesis is more parsimonious than alternative explanations according to the data available, although more evidence based on further testing is needed. [ABSTRACT FROM AUTHOR]

Accurate specimen identification is challenging in groups with subtle or scarce taxonomically diagnostic characters, and the use of DNA barcodes can provide an effective means for consistent identification. Here, we investigate the utility of DNA barcode identification of species in a cosmopolitan genus of lichen-forming fungi, Parmelia (Parmeliaceae). Two hundred and two internal transcribed spacer (ITS) sequences generated from specimens collected from all continents, including Antarctica, were analysed, and DNA barcodes of 14 species of Parmelia s.s. are reported. Almost all species show a barcode gap. Overall, intraspecific divergence values were lower than the threshold previously established for Parmeliaceae. However, the mean and range were elevated by deep barcode divergences in three species, indicating the likely occurrence of overlooked specieslevel lineages. Here, we provide a DNA barcode reference library with well-identified specimens sampled worldwide and sequences from most of the type material to enable easy and fast accurate sample identification and to assist in uncovering overlooked species in Parmelia s.s. Further, our results confirm the efficiency of the ITS region in the identification of species of Parmelia s.s. [ABSTRACT FROM AUTHOR]

V eronica subsection P entasepalae is a diploid-polyploid complex of c. 20 species distributed in Eurasia and North Africa, in which species boundaries are difficult to determine. Here, we present the first comprehensive phylogenetic analysis of V. subsection P entasepalae based on nucleotide sequences [internal transcribed spacer ( ITS) and the plastid trnH-psbA and ycf6-psbM spacers] combined with ploidy estimations. Our results support the monophyly of the subsection. Five well-supported clades are recovered in the ITS sequence analyses, corresponding to broad geographical areas. The causes of the extensive incongruence found between the ITS and plastid DNA datasets, namely incomplete lineage sorting and/or hybridization and polyploidization, are discussed. Most of the diploids traditionally recognized based on morphological characters and one tetraploid are each recovered as monophyletic by the ITS sequence analyses. The Balkan species V . kindlii is resurrected. DNA ploidy level for V . teucrioides is reported here for the first time (2 x). Diploid populations have been found for V . orbiculata, which was previously thought to be only tetraploid. Past contact in the amphi- Adriatic area between V . orsiniana and V . orbiculata is suggested. Finally, molecular analyses show that diploid V . jacquinii and diploid V . orbiculata are unrelated. This study contributes to our understanding of the evolutionary history of polyploid complexes, especially those in southern Europe, and highlights the importance of using multiple lines of evidence to investigate species boundaries in such actively diversifying groups. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179, 670-692. [ABSTRACT FROM AUTHOR]