Pulsatilla patens s.s. is a one of the most endangered plant species in Europe. The present range of this species in Europe is highly fragmented and the size of the populations has been dramatically reduced in the past 50 years. The rapid disappearance of P. patens localities in Europe has prompted the European Commission to initiate active protection of this critically endangered species. The aim of this study was to estimate the degree and distribution of genetic diversity within European populations of this endangered species. We screened 29 populations of P. patens using a set of six microsatellite primers. The results of our study indicate that the analyzed populations are characterized by low levels of genetic diversity (Ho = 0.005) and very high levels of inbreeding (FIS = 0.90). These results suggest that genetic erosion could be partially responsible for the lower fitness in smaller populations of this species. Private allelic richness was very low, being as low as 0.00 for most populations. Average genetic diversity over loci and mean number of alleles in P. patens populations were significantly correlated with population size, suggesting severe genetic drift. The results of AMOVA point to higher levels of variation within populations than between populations.The results of Structure and PCoA analyses suggest that the genetic structure of the studied P. patens populations fall into three clusters corresponding to geographical regions. The most isolated populations (mostly from Romania) formed a separate group with a homogeneous gene pool located at the southern, steppic part of the distribution range. Baltic, mostly Polish, populations fall into two genetic groups which were not fully compatible with their geographic distribution.Our results indicate the serious genetic depauperation of P. patens in the western part of its range, even hinting at an ongoing extinction vortex. Therefore, special conservation attention is required to maintain the populations of this highly endangered species of European Community interest.

Present study was designed to verify which or if any of plastome loci is a hotspot region for mutations and hence might be useful for molecular species identification in feather grasses. 21 newly sequenced complete plastid genomes representing 19 taxa from the genus of Stipa were analyzed in search of the most variable and the most discriminative loci within Stipa. The results showed that the problem with selecting a good barcode locus for feather grasses lies in the very low level of genetic diversity within its plastome. None of the single chloroplast loci is polymorphic enough to play a role of a barcode or a phylogenetic marker for Stipa. The biggest number of taxa was successfully identified by the analysis of 600 bp long DNA fragment comprising a part of rbcL gene, the complete rbcL-rpl23 spacer and a part of rpl23 gene. The effectiveness of multi-locus barcode composed of six best-performing loci for Stipa (ndhH, rpl23, ndhF-rpl32, rpl32-ccsA, psbK-psbI and petA-psbJ) didn’t reach 70% of analyzed taxa. The analysis of complete plastome sequences as a super-barcode for Stipa although much more effective, still didn’t allow for discrimination of all the analyzed taxa of feather grasses.

Aneura pinguis is known as a species complex with several morphologically indiscernible species, which are often reproductively isolated from each other and show distinguishable genetic differences. Genetic dissimilarity of cryptic species may be detected by genomes comparison. This study presents the first complete sequences of chloroplast and mitochondrial genomes of six cryptic species of A. pinguis complex: A. pinguis A, B, C, E, F, J. These genomes have been compared to each other in order to reconstruct phylogenetic relationships and to gain better understanding of the evolutionary process of cryptic speciation in this complex. The chloroplast genome with the nucleotide diversity 0.05111 and 1537 indels is by far more variable than mitogenome with π value 0.00233 and number of indels 1526. Tests of selection evidenced that on about 36% of chloroplast genes and on 10% of mitochondrial genes of A. pinguis acts positive selection. It suggests an advanced speciation of species. The phylogenetic analyses based on genomes show that A. pinguis is differentiated and forms three distinct clades. Moreover, on the cpDNA trees, Aneura mirabilis is nested among the cryptic species of A. pinguis. This indicates that the A. pinguis cryptic species do not derive directly from one common ancestor.

The traditionally conceived genera Orthotrichum Hedw. and Ulota F.Weber are here reclassified into six genera, Orthotrichum, Dorcadion Lindb., Nyholmiella Holmen & E.Warncke, Pulvigera Plášek, Sawicki & Ochyra, Plenogemma Plášek, Sawicki & Ochyra, and Ulota, based on morphological differences and partially on molecular evidence. The genus Pulvigera includes P. lyellii (Hook. & Taylor) Plášek, Sawicki & Ochyra (Orthotrichum lyellii Hook. & Taylor) which was selected as its generitype. The genus Plenogemma includes P. phyllantha (Brid.) Plášek, Sawicki & Ochyra (Ulota phyllantha Brid.) which was selected as its generitype.

The genus Stipa L. comprises over 150 species, all native to the Old World, where they grow in warm temperate regions throughout Europe, Asia, and North Africa. It is one of the largest genera in the family Poaceae in Middle Asia, where one of its diversity hotspots is located. However, identification of Middle Asian Stipa species is difficult because of the lack of new, comprehensive taxonomic studies including all of the species recorded in the region. We present a critical review of the Mid-Asian representatives of Stipa, together with an identification key and taxonomic listing. We relied on both published and unpublished information for the taxa involved, many of which are poorly known. For each taxon, we present a taxonomic and nomenclatural overview, habitat preferences, distribution, altitudinal range, and additional notes as deemed appropriate. We describe four new nothospecies: S. ×balkanabatica M. Nobis & P. D. Gudkova, S. ×dzungarica M. Nobis, S. ×pseudomacroglossa M. Nobis, S. ×subdrobovii M. Nobis & A. Nowak, one subspecies S. caucasica Schmalh. subsp. nikolai M. Nobis, A. Nobis & A. Nowak, and eight varieties: S. araxensis Grossh. var. mikojanovica M. Nobis, S. caucasica var. fanica M. Nobis, P. D. Gudkova & A. Nowak, S. drobovii (Tzvelev) Czerep. var. jarmica M. Nobis, S. drobovii var. persicorum M. Nobis, S. glareosa P. A. Smirn. var. nemegetica M. Nobis, S. kirghisorum P. A. Smirn. var. balkhashensis M. Nobis & P. D. Gudkova, S. richteriana Kar. & Kir. var. hirtifolia M. Nobis & A. Nowak, and S. ×subdrobovii var. pubescens M. Nobis & A. Nowak. Additionally, 12 new combinations, Achnatherum haussknechtii (Boiss.) M. Nobis, A. mandavillei (Freitag) M. Nobis, A. parviflorum (Desf.) M. Nobis, Neotrinia chitralensis (Bor) M. Nobis, S. badachschanica Roshev. var. pamirica (Roshev.) M. Nobis, S. borysthenica Klokov ex Prokudin var. anomala (P. A. Smirn.) M. Nobis, S. holosericea Trin. var. transcaucasica (Grossh.) M. Nobis, S. kirghisorum P. A. Smirn. var. ikonnikovii (Tzvelev) M. Nobis, S. macroglossa P. A. Smirn. var. kazachstanica (Kotuchov) M. Nobis, S. macroglossa var. kungeica (Golosk.) M. Nobis, S. richteriana var. jagnobica (Ovcz. & Czukav.) M. Nobis & A. Nowak, and S. zalesskii Wilensky var. turcomanica (P. A. Smirn.) M. Nobis are proposed, and the lectotypes for 14 taxa (S. arabica Trin. & Rupr., S. bungeana Trin. ex Bunge, S. caspia K. Koch, S. ×consanguinea Trin. & Rupr., S. effusa Mez, S. ×heptapotamica Golosk., S. jacquemontii Jaub. & Spach., S. kungeica Golosk., S. margelanica P. A. Smirn., S. richteriana, S. rubentiformis P. A. Smirn., S. sareptana A. K. Becker, S. tibetica Mez, and Timouria saposhnikovii Roshev.) are designated. In Middle Asia the genus Stipa comprises 98 taxa, including 72 species, four subspecies, and 22 varieties. Of the 72 species of feather grasses, 23 are of hybrid origin (nothospecies). In Middle Asia, feather grasses can be found at elevations from (0 to)300 to 4500(to 5000) m, but most are montane species. The greatest species richness is observed at altitudes between 1000 and 2500 m. Nineteen species grow above 3000 m, but only nine above 4000 m. The number of taxa (species and subspecies) growing in each country also varies considerably, with the highest noted in Kazakhstan (42), Tajikistan (40), and Kyrgyzstan (35). Of the 76 taxa of Stipa (species and subspecies) recorded in Middle Asia, 41 are confined to the region, with some being known only from a single country or mountain range. Distribution maps of selected species are provided.

Background: The European continent is presently colonized by nine species of the genus Pulsatilla, five of which are encountered only in mountainous regions of southwest and south-central Europe. The remaining four species inhabit lowlands in the north-central and eastern parts of the continent. Most plants of the genus Pulsatilla are rare and endangered, which is why most research efforts focused on their biology, ecology and hybridization. The objective of this study was to develop genomic resources, including complete plastid genomes and nuclear rRNA clusters, for three sympatric Pulsatilla species that are most commonly found in Central Europe. The results will supply valuable information about genetic variation, which can be used in the process of designing primers for population studies and conservation genetics research. The complete plastid genomes together with the nuclear rRNA cluster can serve as a useful tool in hybridization studies. Methodology/principal findings: Six complete plastid genomes and nuclear rRNA clusters were sequenced from three species of Pulsatilla using the Illumina sequencing technology. Four junctions between single copy regions and inverted repeats and junctions between the identified locally-collinear blocks (LCB) were confirmed by Sanger sequencing. Pulsatilla genomes of 120 unique genes had a total length of approximately 161–162 kb, and 21 were duplicated in the inverted repeats (IR) region. Comparative plastid genomes of newly-sequenced Pulsatilla and the previously-identified plastomes of Aconitum and Ranunculus species belonging to the family Ranunculaceae revealed several variations in the structure of the genome, but the gene content remained constant. The nuclear rRNA cluster (18S-ITS1-5.8S-ITS2-26S) of studied Pulsatilla species is 5795 bp long. Among five analyzed regions of the rRNA cluster, only Internal Transcribed Spacer 2 (ITS2) enabled the molecular delimitation of closely-related Pulsatilla patens and Pulsatilla vernalis. Conclusions/significance: The determination of complete plastid genome and nuclear rRNA cluster sequences in three species of the genus Pulsatilla is an important contribution to our knowledge of the evolution and phylogeography of those endangered taxa. The resulting data can be used to identify regions that are particularly useful for barcoding, phylogenetic and phylogeographic studies. The investigated taxa can be identified at each stage of development based on their species-specific SNPs. The nuclear and plastid genomic resources enable advanced studies on hybridization, including identification of parent species, including their roles in that process. The identified nonsynonymous mutations could play an important role in adaptations to changing environments. The results of the study will also provide valuable information about the evolution of the plastome structure in the family Ranunculaceae.

No abstract

Background: Molecular research revealed that some of the European Calypogeia species described on the basis of morphological criteria are genetically heterogeneous and, in fact, are species complexes. DNA barcoding is already commonly used for correct identification of difficult to determine species, to disclose cryptic species, or detecting new taxa. Among liverworts, some DNA fragments, recommend as universal plant DNA barcodes, cause problems in amplification. Super-barcoding based on genomic data, makes new opportunities in a species identification. Results: On the basis of 22 individuals, representing 10 Calypogeia species, plastid genome was tested as a superbarcode. It is not effective in 100%, nonetheless its success of species discrimination (95.45%) is still conspicuous. It is not excluded that the above outcome may have been upset by cryptic speciation in C. suecica, as our results indicate. Having the sequences of entire plastomes of European Calypogeia species, we also discovered that the ndhB and ndhH genes and the trnT-trnL spacer identify species in 100%. Conclusions: This study shows that even if a super-barcoding is not effective in 100%, this method does not close the door to a traditional single-or multi-locus barcoding. Moreover, it avoids many complication resulting from the need to amplify selected DNA fragments. It seems that a good solution for species discrimination is a development of so-called "specific barcodes" for a given taxonomic group, based on plastome data.