We used a plastid ndhC-trnV intergenic spacer to reconstruct the genealogy of haplotypes and phylogenetic relationships of major taxonomic groups of the genus Rosa. We analyzed the data using the statistical parsimony, maximum likelihood, and NeighborNet approaches. According to our results, the majority of species may be subdivided into three groups roughly corresponding to the taxonomic sections Pimpinellifoliae, Rosa (former Cinnamomeae) and Synstylae + Chinenses + Gallicanae + Caninae. We assess their relationships as broadly paraphyletic, since the first group appears to be ancestral to the second and the third. The fourth group distanced from these three by many mutational steps consists of R. persica (subgenus Hulthemia) sequences. We argue that R. persica together with the North American R. minutifolia and R. stellata (section Minutifoliae) probably represent the only remnants of an ancient group of roses widely distributed in the Northern Hemisphere in the Oligocene. Two major lineages of the section Caninae arose independently from different ancestors belonging to Synstylae.

Trifolium polyphyllum is a Caucasian endemic of the Fabaceae family peculiar for its inability of nitrogen fixation. Despite this unique trait, the species is insufficiently studied; in particular, little is known about its propagation and dispersal modes. Analyses of ISSR markers in specimens from a population at the Malaya Khatipara Mountain revealed that the species is capable of both sexual and vegetative propagation; however, the former mode dominates. We found out that separate patches within a local population are considerably genetically differentiated within an area of about 2000 m 2 (PhiPT = 0.349; p = 0.001). We suppose this may happen owing to a lack of adaptations to seed dispersal. We also suppose that the observed concentration of genetically admixed individuals in the upper parts of slopes is due to peculiarities of the behavior of pollinators. The size of vegetative clones does not exceed 1 m 2 .

. We have studied the genetic structure of Eversmannia subspinosa (Fisch. ex DC.) B. Fedtsch. populations from the Russian Federation (the Bolshoe Bogdo Mt., the Astrakhan Region; Kegul'ta gully, Republic of Kalmykia) and a number of specimens from the Middle Asia (Kazakhztan and Kyrgyzstan) using inter-simple sequence repeats (ISSR) markers, sequenced nuclear (ITS 1, 2) and chloroplast markers (trnL-trnF, atpB-rbcL, rpl32-trnL(UAG), trnV-ndhC). The analysis of ISSR markers divided samples into three genetic clusters: the population from the Bolshoe Bogdo Mt., the population from the Kegul'ta gully, and samples from the Middle Asia. The population from the Kegul'ta gully ap-peared to be genetically variable, whereas the population from the Bolshoe Bogdo Mt. exhibited no variation. Popula-tions from the Bolshoe Bogdo and Kegul'ta are more closely related according to the results of the chloroplast DNA analysis. At the same time, these westernmost populations turned out to be related to the samples from the Western Tian Shan: Syr-Darya Karatau, Talas Alatau (Ichkele-Too Mts.) and Kyzylorda Region of Kazakhstan.

We have studied a population of Rosa kokanica from slopes of the Greater Chimgan Mt. in Tashkent Region of Uzbekistan. We reconstructed a statistical parsimony network of ndhC-trnV chloroplast intergenic spacer for 34 samples from three subpopulations found in valleys of the northern, southern and south-western macro slopes of the mountain. The study revealed 19 haplotypes, one of which, the basal internal haplotype 1, was shared between the northern and southern subpopulations, while 13 unique haplotypes were found in the south-western subpopulation. We suppose that such a kind of genetic structure could arise during long lasting isolation of the subpopulations in glacial times.

As part of our revision of the genus Ophiorrhiza for the Flora of Thailand, 24 species names are taxonomically reassessed and lectotypified, mostly those described by W.G. Craib from A.F.G. Kerr's collections. Thirteen species names are synonymized based on morphological comparisons of type specimens with modern collections from the same geographical areas and, partly, on molecular data.

The taxonomic status of endemic Callitriche taxa from western Beringia (C. subanceps) and the Lower Volga (C. fimbriata, C. transvolgensis) has been poorly studied. To investigate this question we compared endemic taxa with close Callitriche species. To achieve this goal we studied nuclear (ITS) and plastid (trnS-trnG, petL-psbE, trnH-psbA) genetic variation of almost 200 Callitriche samples and incorporated data on fruit shape variation and chromosome numbers. We found two genetically well-differentiated evolutionary lineages within C. heterophylla s.l. with rounded, wingless fruits, which diversification was likely associated with Beringia. One lineage occurs in western Beringia (known as C. subanceps), Greenland and northern North America, while another is confined to North America. Callitriche palustris, bearing winged, ovate fruits, is well-differentiated genetically from both C. heterophylla s.l. lineages. We refrain from any taxonomic decisions in C. heterophylla s.l. unless revision of full spectrum of diagnostic characters coupled with genetic studies with inclusion of abundant material from the both sides of the Bering Strait will be done. We demonstrated that Lower Volga endemics (C. fimbriata and C. transvolgensis) are separate species and their divergence might have been associated with dynamics of the Mediterranean, Black and Caspian seas. We point out importance of northern cryptic refugia (e.g. Lena River Delta) for cold-tolerant aquatic plants diversification.

The grass Deschampsia cespitosa is a variable taxon out of which many varieties, subspecies and endemic species have been separated. In this paper, the variation in genome size (GS) and ploidy of this grass including several of its subspecies and two related species in Eurasia was investigated by flow cytometric (FCM) measurements. GS and ploidy data were also related to specific environments and reproduction mode. Ploidy levels found by FCM were confirmed by chromosome counts of diploid (2n = 28) and tetraploid (2n = 52) samples. Seminiferous (seed bearing) D. cespitosa was mainly diploid (GS between 3.754 and 5.438 pg/1C). GS variation in diploids showed a geographic pattern with a significant difference (H = 41,441, P < 0.001) between European (median = 4.377 pg) and Asian (median = 4.881 pg) accessions. Genome size (1C) in tetraploids ranged from 7.9426 to 9.0399 pg. Tetraploid seminiferous D. cespitosa was found mostly in disturbed habitats in western and southern Europe, while tetraploids in Asia were registered in wet Arctic habitats. Genome size (1C between 8.3278 and 8.8603 pg) of the pseudoviviparous plants (spikelets produce plantlets asexually) of wet habitats in central and northern Europe indicated tetraploidy. A putative triploid (GS 6.6817 pg) was detected in Iceland. Summing up, we found a high variation in GS on the geographic scale with significant regional differences in diploid D. cespitosa. Among the tetraploids, the asexually reproducing plants were bound to specific habitats, while the seminiferous plants showed a habitat preference similar to the diploids.

Comparison of genetic variation among closely related species with well-known ecological preferences may provide insights into the role of specific traits in biogeographic processes. Three widely distributed birddispersed species of the genus Vaccinium L. provide a good model system for such an inference. We report the first comprehensive range-wide dataset on genetic variation in V. myrtillus that can be directly used for interspecific comparisons. In contrast to its congeners V. uliginosum and V. vitis-idaea, V. myrtillus is characterized by extremely low plastid DNA variation, with a single haplotype occupying vast territories in Eurasia and two more haplotypes occurring in the Caucasus. We suggest that the main reason for the genetic impoverishment of V. myrtillus, which is relatively cold-intolerant, is bottlenecking during the Pleistocene glaciations. We reinforce this view using niche modeling, predicting that no suitable habitats for V. myrtillus existed during the Last Glacial Maximum in Beringia and Siberia. We aggregate our new data and published information on genetic diversity in the three species and explain the differences between them based on their ecology, reproductive biology and demographic history.

Salix fursaevii, a species endemic to the Volga River flood plain, was described by E. Mavrodiev and co-authors in Byull. Moskovsk. Obshch. Isp. Prir. in 2012. It differs from the closely related and widespread S. triandra by a few quantitative morphological characters and, most of all by its much later flowering time. This late-flowering willow was known and studied before as an ecotype of S. triandra. Our study of a large sample of S. triandra s. l. revealed that 1) S. triandra s. str. and S. fursaevii could not be clearly distinguished using several morphological characters and the time of flowering; 2) specimens morphologically corresponding to S. fursaevii are with a single exception strictly confined to the Volga River flood plain; 3) the populations of S. triandra and S. fursaevii do not differ by nrITS sequences; 4) the populations of S. triandra and S. fursaevii are poorly differentiated by chloroplast atpB-rbcL sequences; 5) representatives of both taxa are tetraploids 2n = 4x = 76. Poor differentiation of populations by chloroplast sequences is indicative of the intraspecific variability, the geographic pattern of which suggests that the Volga River valley was a probable glacial refugium and a source of post glacial spread of S. triandra.

We have studied several samples from Lotus corniculatus s. l. and L. zhegulensis populations with the use of SSR and sequenced nuclear (ITS) and plastid (atpB-rbcL, ndhC-trnV, rpl32-trnL(UAG), trnH-psbA, trnL-trnF) markers. We analysed 9 local populations from the Volga River valley ranging from Ulyanovsk in the north to Volgograd in the south, as well as two local populations from Moscow and Lipetsk Provinces. Analyses of SSR markers using the STRUCRURE program divided the sample into three genetic clusters. Populations from Moscow and Lipetsk Provinces, and three local populations from the ‘locus classicus’ location of L. zhegulensis in Samara Province appeared to be the most genetically differentiated while all the other populations were variously genetically admixed. Low pairwise Fst values indicate low genetic differentiation of Lotus populations and the intraspecific nature of the revealed diversity. The nuclear and plastid DNA sequences analyzed yielded little information. Substitutions and indels revealed were mostly autapomorphies characteristic of separate specimens or small groups of specimens but not of populations. Our study enables to firmly conclude that Lotus populations from the right bank of the Volga River in vicinity of Zhiguli upland described as L. zhegulensis are weakly genetically differentiated from other populations of Lotus corniculatus s. l. and, hence, cannot be regarded as a separate species.

The Mediterranean region is a center of species and genetic diversity of many plant groups, which served as a source of recolonization of temperate regions of Eurasia in Holocene. We investigate the evolutionary history of species currently classified in Lotus sect. Bonjeanea in the context of the evolution of the genus Lotus as a whole, using phylogenetic, phylogeographic and dating analyses. Of three species of the section, L. rectus and L. hirsutus have wide Mediterranean distribution while L. strictus has a disjunctive range in Bulgaria, Turkey, Armenia, Eastern Kazakhstan, and adjacent parts of Russia and China. We used entire nuclear ribosomal ITS1-5.8S-ITS2 region (nrITS) and a plastid dataset (rps16 and trnL-F) to reconstruct phylogenetic relationships within Lotus with an extended representation of Bonjeanea group. We analyzed the phylogeographic patterns within each species based on the plastid dataset. For divergence time estimation, the nrITS dataset was analyzed. Our results confirmed the non-monophyletic nature of the section Bonjeanea. They indicate that Lotus is likely to have diverged about 15.87 (9.99–19.81) million years ago (Ma), which is much older than an earlier estimate of ca. 5.54 Ma. Estimated divergence ages within L. strictus, L. rectus, and L. hisrutus (6.1, 4.94, and 4.16 Ma, respectively) well predate the onset of the current type of Mediterranean climate. Our data suggest that relatively ancient geological events and/or climatic changes apparently played roles in early diversification of Lotus and its major clades, as well as in formation of phylogeographic patterns, in at least some species.

Rosa × archipelagica is a spontaneous hybrid between Rosa rugosa and R. maximowicziana distributed, together with its parental taxa, on the coast of a small Stenina Island in the Peter the Great Gulf, the Sea of Japan (Russian Far East). Its hybrid origin is confirmed by direct electropherogram comparisons of PCR products and maximum likelihood analyses of nuclear ITS 1–2 and plastid intergenic spacers trnH–psbA and ndhC–trnV. The plastome markers indicate R. maximowicziana as the maternal genome donor of Rosa × archipelagica, however, one specimen shows also signs of heteroplasmy. This is the first evidence of possible biparental inheritance of plastids in rose hybrids. The results do not show whether the hybrid plants all belong to F1 or further generations of hybrids.

The extent of glacial survival of woody plants in temperate Asia is still poorly known. A reliable way to clarify this issue in the absence of sufficient paleontological data is a phylogeographic analysis of contemporary populations. A recent study of Juniperus communis genetic diversity in Eurasia suggested that this species with wide ecological tolerance survived the glaciation in many periglacial microrefugia at high latitudes and subsequently spread to new areas during interglacials (Hantemirova et al. in J Biogeogr 44:271–282, 2017. https://doi.org/10.1111/jbi.12867). This pattern was termed a “new Eurasian phylogeographical paradigm” as opposed to survival in few major refugia. We have tested the proposed “paradigm” with another hardy species with wide Eurasian area, Prunus padus, to find out if any general phylogeographic patterns may exist for cold-tolerant Eurasian arboreal plant species. We interpret the observed genetic structure [nuclear (ITS) and plastid DNA] of the Eurasian populations of P. padus as plausibly resulted from at least two cycles of glacial survivals in refugia followed by post-glacial colonization events. The species likely originated in East Asia and subsequently spread across all Eurasia. Its continuous range had been fragmented by early-Pleistocene glaciations, when the species survived in the Caucasian and Far Eastern refugia as well as in northern periglacial microrefugia with an active gene flow between them. The known major glacial refugia, such as Iberian Peninsula, the Colchis, the Southern Urals, and the Beringia, played little role as a source of the species post-glacial expansion.

In the cold periods of Quaternary climatic fluctuations, many temperate species underwent severe range contractions, and their survival during these periods was associated with climatically more favorable regions, so-called glacial refugia, from which subsequent range expansions took place. In this regard, the relative roles of the Southern (“main”), Northern (i.e., cryptic northern), and Eastern European (e.g., Colchis) refugia in shaping the evolutionary history of European temperate plants should be evaluated. In this study, we investigated the phylogeographic structure of Primula vulgaris, a European mesophilous species, by comparing DNA sequences derived from the nuclear (nrITS) and the plastid (trnL-trnF and rpl32-trnL) genomes of specimens covering the entire distribution range of the species. The variability in flower morphology was also studied on an area-wide scale with geometric morphometry. Our results clearly show the importance of the northern and eastern refugia (the Carpathian Basin and Colchis) as sources of genetic variation among European mesophilous plant species. Primula vulgaris spread initially from the Colchis refugium westwards, and a proportion of the colonists survived during the last glacial period in the Carpathian Basin, which may have served as a secondary center of diversity from which all Europe was subsequently populated.

The results of a molecular genetic study of Potentilla multifida agg. using two plastid markers (ndhC-trnV and psbA-trnH) and a nuclear ITS marker suggested that this group comprises a number of relatively young and incompletely differentiated species widely distributed in Northern Eurasia. The sequences were analyzed using tree-based (maximum likelihood) and network-based (statistical parsimony network) approaches. The plastid data suggested incomplete lineage sorting, characteristic of the group as a whole. The nuclear ITS results demonstrated quite a different pattern, with mostly conspecific accessions shaping monophyletic clades. The majority of the Potentilla sect. Multifidae species studied possess few, usually closely related plastid haplotypes, or are even monomorphic. In contrast, P. volgarica, a narrow endemic from the Volga River valley, presents plastid haplotypes belonging to two distantly related groups. Such a pattern of genetic diversity in P. volgarica may be explained by a long persistence of the species within an extremely small distribution range, on the right bank of the Volga River, most likely representing a contemporary refugium. The genealogy of plastid markers in P. volgarica suggests that this species is ancestral to P.eversmanniana, another narrow endemic from the S Urals.

We studied genetic diversity in 54 populations of nine sexual and apomictic species of the genus Chondrilla (C. acantholepis, C. ambigua, C. brevirostris, C. canescens, C. graminea, C. juncea, C. laticoronata, C. latifolia and C. pauciflora) in SE European Russia and neighboring territories of NW Kazakhstan. We analysed the trnT–trnF region of plastid DNA and the internal transcribed spacer of ribosomal DNA (ITS1–5.8S–ITS2) using statistical parsimony, maximum likelihood and neighbor net methods. Two major evolutionary lineages, roughly corresponding to the two subgenera traditionally recognized in the region, were revealed. Within the first evolutionary lineage (subgenus Brachyrhynchus), the sexual diploid C. ambigua and its putatively hybrid apomictic derivatives C. brevirostris, C. laticoronata and C. pauciflora could be recognized. Their identity was also confirmed by analyses of ISSR markers. The second evolutionary lineage (subgenus Chondrilla) comprises C. juncea, C. acantholepis, C. canescens, C. graminea and C. latifolia in European Russia, but analyses of morphological variability and the genealogy of plastid and nuclear markers favor their treatment as the single facultatively apomictic species C. juncea. The results demonstrate that an apomictic mode of reproduction does not necessarily result in the formation of genetically separated microspecies.

The article examines the genetic diversity in 54 populations of 9 Chondrilla species (C. acantholepis, C. ambigua, C. brevirostris, C. canescens, C. graminea, C. juncea, C. laticoronata, C. latifolia, and C. pauciflora) in European Russia. Plastid DNA segments trnT–trnF are selected as markers. Reconstruction of evolutionary networks based on the principle of maximum parsimony reveals that the sample is divided into four groups, where group 1 is C. ambigua, 2 – C. brevirostris, 3 – C. laticoronata, 4 – C. acantholepis, C. canescens, C. graminea, C. juncea, and C. latifolia. The findings show that C. acantholepis, C. canescens, C. graminea, C. juncea and C. latifolia are to be treated as synonyms under the name of C. juncea.

The Lotus corniculatus complex (Fabaceae, Loteae) includes diploids (2n = 2x = 12) and tetraploids (2n = 4x = 24). Monophyly of the complex was supported by recent phylogenetic analyses, but evolutionary relationships within it remain debatable. The present study aims to outline species relationships in the L. corniculatus complex and evolutionary history of the group in eastern Europe and northern Asia. Genetic variability (based on plastid trnL-trnF sequences and eight nuclear microsatellite loci) is described for 51 local populations of six species in the complex (the diploids L. krylovii, L. frondosus, L. tenuis and L. stepposus and the tetraploids L. corniculatus and L. xucrainicus) in northern Eurasia and compared to the patterns of morphological differentiation. A representative set of species of Lotus section Lotus was also included in phylogenetic and phylogeographic analyses. The morphological and genetic variation patterns indicate sporadic interspecific hybridization in sympatric zones. The genetic structure of the species is different in the European and Asian parts of the distribution area. Taxonomic significance of indels in the trnL-F region is confirmed by phylogenetic studies of section Lotus. A reconstructed plastid haplotype network of the L. corniculatus group indicated that haplotype A is closest to the hypothetical ancestral type in one of the Mediterranean glacial refugia. The proposed phylogeographic scenario suggests a European origin of the L. corniculatus complex and its geographical expansion parallel to the changes in plastid haplotypes from group A in Western Europe to group D in Central Asia, as well as the existence of a possible 'southern' lineage represented by the haplotype E group. The decrease of population genetic variability in Asia is probably due to the change of prevailing mating system from cross-pollination to autogamy.

A survey of populations of invasive Amelanchier spicata and A. alnifolia species has been carried out in the European part of Russia. Along with typical morphotypes, some hardly identified variants with intermediate traits have been revealed. Molecular genetic analysis of ITS1-2 nuclear regions has revealed an intragenomic polymorphism probably indicating a hybridogenic origin of A. spicata. Genealogic relations between ITS1-2 haplotypes of the invasive A. spicata species have been traced, resulting in the conclusion that its formation was connected with hybridization between A. humilis and A. alnifolia; a hypothetical area of origin of its initial forms in North America has been established.

Variability of M. arvensis from five geographically distanced populations was examined using morphological traits and phytochemical composition of essential oil and with the help of DNA fingerprinting using ISSR markers. The population differentiation based on morphological traits was weak. Analysis of the essential oil composition provided the subdivision of the sample into three groups and, on the basis of the composition of ISSR amplicons, into four groups of specimens. A high degree of genetic polymorphism of M. arvensis and substantial, though incomplete, population differentiation were identified. It was demonstrated that the population of M. arvensis from the Komi Republic was the most genetically isolated, while the populations from Moscow and Penza provinces were weakly differentiated from each other. The population from the Republic of Belarus (near Grodno) was genetically and phytochemically considerably different from the other studied populations, although morphologically indistinguishable from them. We argue that the differentiation was caused not only by the isolation by distance but also owing to the formation of three different ecotypes adapted to different climatic conditions.