Two cryptic species of California mustard within Caulanthus lasiophyllus.

PREMISE: Cryptic species are evolutionarily distinct lineages lacking distinguishing morphological traits. Hidden diversity may be lurking in widespread species whose distributions cross phylogeographic barriers. This study investigates molecular and morphological variation in the widely distributed Caulanthus lasiophyllus (Brassicaceae) in comparison to its closest relatives. METHODS: Fifty-two individuals of C. lasiophyllus from across the species' range were sequenced for the nuclear ribosomal internal transcribed spacer region (ITS) and the chloroplast trnL-F region. A subset of these samples were examined for the chloroplast ndhF gene. All 52 individuals were scored for 13 morphological traits, as well as monthly and annual climate conditions at the collection locality. Morphological and molecular results are compared with the closest relatives-C. anceps and C. flavescens-in the "Guillenia Clade." To test for polyploidy, genome size estimates were made for four populations. RESULTS: Caulanthus lasiophyllus consists of two distinct lineages separated by eight ITS differences-eight times more variation than what distinguishes C. anceps and C. flavescens. Fewer variable sites were detected in trnL-F and ndhF regions, yet these data are consistent with the ITS results. The two lineages of C. lasiophyllus are geographically and climatically distinct; yet morphologically overlapping. Their genome sizes are not consistently different. CONCLUSIONS: Two cryptic species within C. lasiophyllus are distinguished at the molecular, geographic, and climatic scales. They have similar genome sizes and are morphologically broadly overlapping, but an ephemeral basal leaf character may help distinguish the species.

Genome constitution and evolution of Elytrigia lolioides inferred from Acc1, EF-G, ITS, TrnL-F sequences and GISH.

BACKGROUND: Elytrigia lolioides (Kar. et Kir.) Nevski, which is a perennial, cross-pollinating wheatgrass that is distributed in Russia and Kazakhstan, is classified into Elytrigia, Elymus, and Lophopyrum genera by taxonomists on the basis of different taxonomic classification systems. However, the genomic constitution of E. lolioides is still unknown. To identify the genome constitution and evolution of E. lolioides, we used single-copy nuclear genes acetyl-CoA carboxylase (Acc1) and elongation factor G (EF-G), multi-copy nuclear gene internal transcribed space (ITS), chloroplast gene trnL-F together with fluorescence and genomic in situ hybridization. RESULTS: Despite the widespread homogenization of ITS sequences, two distinct lineages (genera Pseudoroegneria and Hordeum) were identified. Acc1 and EF-G sequences suggested that in addition to Pseudoroegneria and Hordeum, unknown genome was the third potential donor of E. lolioides. Data from chloroplast DNA showed that Pseudoroegneria is the maternal donor of E. lolioides. Data from specific FISH marker for St genome indicated that E. lolioides has two sets of St genomes. Both genomic in situ hybridization (GISH) and fluorescence in situ hybridization (FISH) results confirmed the presence of Hordeum genome in this species. When E genome was used as the probe, no signal was found in 42 chromosomes. The E-like copy of Acc1 sequences was detected in E. lolioides possibly due to the introgression from E genome species. One of the H chromosomes in the accession W6-26586 from Kazakhstan did not hybridize H genome signals but had St genome signals on the pericentromeric regions in the two-color GISH. CONCLUSIONS: Phylogenetic and in situ hybridization indicated the presence of two sets of Pseudoroegneria and one set of Hordeum genome in E. lolioides. The genome formula of E. lolioides was designed as StStStStHH. E. lolioides may have originated through the hybridization between tetraploid Elymus (StH) and diploid Pseudoroegneria species. E and unknown genomes may participate in the speciation of E. lolioides through introgression. According to the genome classification system, E. lolioides should be transferred into Elymus L. and renamed as Elymus lolioidus (Kar. er Kir.) Meld.

Extensive interlineage hybridization in the predominantly clonal Hydrilla verticillata.

PREMISE: The submersed aquatic plant Hydrilla verticillata ("hydrilla") is important ecologically and economically due to its aggressive growth in both indigenous and nonindigenous regions. Substantial morphological variation has been documented in hydrilla, including the existence of monoecious and dioecious "biotypes." Whereas plastid sequence data have been used previously to explore intraspecific diversity, nuclear data have yet to be analyzed in a phylogenetic context. Molecular and morphological analyses were used to evaluate the genetic diversity and phylogenetic relationships of native and introduced populations. METHODS: Nuclear (internal transcribed spacer-ITS; phytoene desaturase-PDS) and plastid (trnL-F) sequence data were evaluated phylogenetically using likelihood and Bayesian methods. Leaf morphologies were compared among clades that were identified in phylogenetic analyses. RESULTS: Data from both ITS and PDS show multiple instances of polymorphic sequences that could be traced to two or more lineages, including both invasive biotypes in the Americas. Leaf morphological data support the distinctness of lineages and provide a metric for distinguishing monoecious and dioecious biotypes in the United States. CONCLUSIONS: Nuclear molecular data indicate far greater genetic diversity than could be estimated using plastid markers. Substantially divergent copies of nuclear genes, found in multiple populations worldwide, likely result from interlineage hybridization. Invasive monoecious and dioecious hydrilla biotypes in the Americas are genetically distinct, with both biotypes resulting from admixture among Eurasian progenitors. Genetic similarity to populations in India and South Korea, respectively, implicates these as likely origins for the dioecious and monoecious biotypes.

Testing the monophyly of Simaba (Simaroubaceae): Evidence from five molecular regions and morphology.

Generic circumscriptions in the mostly pantropical family Simaroubaceae are somewhat controversial. Simaba is the largest genus, currently defined as exclusively neotropical, with around 25 species of trees and shrubs, but both its limits and infrageneric classification have been a matter of discussion and divergence. Traditionally, species of the genus have been treated in three sections: Simaba sect. Tenuiflorae, S. sect. Floribundae and S. sect. Grandiflorae, but a phylogenetic analysis suggested that the latter two may not be monophyletic. To test the monophyly of Simaba and its infrageneric classification, we used a molecular approach based on DNA sequence data from two nuclear ribosomal spacer regions (ITS and ETS) and three plastid regions (rps16 intron, and intergenic spacers psbA-trnH and trnL-trnF), including a comprehensive sampling of species from Simaba and closely related genera. We also performed ancestral character reconstructions to identify morphological characters that could serve as synapomorphies for major clades and to explore patterns of homoplasy in the morphological dataset. Our results show Simaba as traditionally circumscribed is not monophyletic, with taxa segregated into two strongly supported but distinct clades, one of which is more closely related to Simarouba. The three main clades that emerged in the phylogeny include a mostly Amazonian Simaba clade (which includes the type species of Simaba and the remaining species of S. sect. Tenuiflorae, here proposed to be recognized as Simaba sensu stricto), a mostly extra-Amazonian Simaba clade (a distinct lineage that will be recognized as Homalolepis, a genus currently treated in synonymy and equivalent to Simaba sections Grandiflorae and Floribundae), and the Simarouba clade (including all of its current species). These three clades are characterized by a combination of morphological characters, described in detail herein, some of which are novel features for Simaba not previously reported in the literature. Mapping character-states on the phylogenetic tree provides tests for evolutionary hypotheses. For example, our reconstruction of habit and geographic distribution suggests that the diversification of several shrubby species within the extra-Amazonian lineage in the South American cerrados probably occurred from ancestors inhabiting tropical forests, involving transitions in morphological and ecological traits.

Phylogeny and maternal donors of Elytrigia Desv. sensu lato (Triticeae; Poaceae) inferred from nuclear internal-transcribed spacer and trnL-F sequences.

BACKGROUND: Elytrigia Desv. is a genus with a varied array of morphology, cytology, ecology, and distribution in Triticeae. Classification and systematic position of Elytrigia remain controversial. We used nuclear internal-transcribed spacer (nrITS) sequences and chloroplast trnL-F region to study the relationships of phylogenetic and maternal genome donor of Elytrigia Desv. sensu lato. RESULTS: (1) E, F, P, St, and W genomes bear close relationship with one another and are distant from H and Ns genomes. Ee and Eb are homoeologous. (2) In ESt genome species, E genome is the origin of diploid Elytrigia species with E genome, St genome is the origin of Pseudoroegneria. (3) Diploid species Et. elongata were differentiated. (4) Et. stipifolia and Et. varnensis sequences are diverse based on nrITS data. (5) Et. lolioides contains St and H genomes and belongs to Elymus s. l. (6) E genome diploid species in Elytrigia serve as maternal donors of E genome for Et. nodosa (PI547344), Et. farcta, Et. pontica, Et. pycnantha, Et. scirpea, and Et. scythica. At least two species act as maternal donor of allopolyploids (ESt and EStP genomes). CONCLUSIONS: Our results suggested that Elytrigia s. l. species contain different genomes, which should be divided into different genera. However, the genomes of Elytrigia species had close relationships with one another. Diploid species were differentiated, because of introgression and different geographical sources. The results also suggested that the same species and the same genomes of different species have different maternal donor. Further study of molecular biology and cytology could facilitate the evaluation of our results of phylogenetic in a more specific and accurate way.

Asymmetrical natural hybridization varies among hybrid swarms between two diploid Rhododendron species.

Background and Aims: The extent to which hybridization leads to gene flow between plant species depends on the structure of hybrid populations. However, if this varies between locations, species barriers might prove permeable in some locations but not in others. To assess possible variation in hybrid population structure, the magnitude and direction of natural hybridization between two Chinese endemic species, Rhododendron spiciferum and Rhododendron spinuliferum , were evaluated. Methods: Thirteen nuclear microsatellite markers were employed to characterize 566 individuals collected from 15 non-allopatric populations and nine allopatric parental populations. Chloroplast DNA (cpDNA) sequences were obtained from a subset of samples. Genetic structure and direction of gene flow was determined using a combination of STRUCTURE and NEWHYBRIDS analysis. Key Results: Nuclear analysis revealed that parental taxa formed two genetically distinct clusters and hybrids shared the genetic background of both parents and did not form a separate genetic lineage. Overall, hybrid swarms were dominated by early- and later-generation hybrids, with a significantly higher proportion of hybrids (59·6 %) possessing >50 % R. spiciferum-like nuclear germplasm. The cpDNA analysis further indicated that a significantly greater proportion of hybrids (61·1 %) possessed the R. spiciferum cpDNA haplotype. Conclusions: Gene flow between R. spiciferum and R. spinuliferum was found to be bidirectional in 14 of the 15 hybrid swarms and asymmetrical in six hybrid swarms. Asymmetrical gene flow was evident for only nuclear DNA (nDNA) in two populations, for only cpDNA in three populations, and for both nDNA and cpDNA in one population. Collectively, the variation in genetic structure found among the 15 hybrid swarms suggests that introgression rather than hybrid speciation is a more likely outcome of hybridization between these hybridizing taxa.

The Intra-familial Relationships of Pentaphylacaceae s.l. as Revealed by DNA Sequence Analysis.

During the past three decades, molecular taxonomy has made considerable changes in the systematic delimitations of several families in the order Ericales which were formed earlier based on morphology. For instance, the Pentaphylacaceae s.l. has been treated differently by both modern and traditional taxonomists. Modern molecular taxonomists constituted this family by combining the traditionally defined Pentaphylacaceae s.s. (Pentaphylax), Sladeniaceae s.s. (Sladenia), the subfamily Ternstroemioideae with 11 genera of Theaceae s.l. and the genus Ficalhoa. There are also treatments placing the genus Pentaphylax with Ternstroemioideae in Pentaphylacaceae and Ficalhoa with Sladenia in Sladeniaceae. Because most of these genera are poorly studied, investigations on all aspects are important to understand the phylogeny to settle the issues surrounding the treatment of the 14 genera in this family. In the present study, DNA sequences of nrITS and trnL-F genes from species of 11 genera from these 14 genera were generated and analyzed together with sequences from other closely related members of Ericales. The results suggested existence of four distinct lineages viz., Sladenia, Pentaphylax, and tribes Frezierieae (9 genera) and Ternstroemieae (2 genera). Further, it demonstrated that within the biggest lineage, Frezierieae, the Visnea remained sister to the clades Adinandra+Cleyera, Euryodendron+Symplococarpon, Freziera, and finally, Eurya. Based on the evidence, it can be concluded that Sladeniaceae and Pentaphylacaceae are very close to each other and the proposal of merging them into a mega family Pentaphylacaceae s.l. with four tribes, i.e., Sladenieae, Pentaphylaceae, Ternstroemieae, and Freziereae should be considered seriously.

Evolution of leaf blade anatomy in Allium (Amaryllidaceae) subgenus Amerallium with a focus on the North American species.

PREMISE OF THE STUDY: Reconstructing ancestral states is a useful method to understand the pathway and patterns of character evolution and to test specific hypotheses within a phylogenetic context. Using a phylogenetic hypothesis of the subgenus Amerallium and related subgenera based on molecular data, we reconstructed the evolutionary history of leaf blade anatomical characters and identified those characters that are most congruent with phylogenetic relationships. Furthermore, we used these character histories to investigate the evolution of terete leaves and explore a possible correlation between environment and leaf anatomy in the North American species. METHODS: Sixty-seven North American and Old World species were sampled from all major infrageneric taxa and lineages for transectional leaf anatomy. To provide a phylogenetic framework for interpretation, representatives of Old World Amerallium and related subgenera were added to a published data matrix of North American taxa and ITS, ETS, trnL-F, and rpL32-trnL sequences. KEY RESULTS: Four anatomical characters, namely leaf-blade shape in transection, presence versus absence of palisade mesophyll, distribution and orientation of vascular bundles, and position of laticifer cells, were found to be congruent with phylogenetic relationships and useful diagnostic traits within North American species. Character reconstructions show that terete leaves in North American species evolved from flattened leaves via a possible transition from subterete to terete leaves. Furthermore, terete leaves possess traits that are indicative of possible adaptation to xeric environments. CONCLUSIONS: The findings from this study provide valuable information for understanding the evolution of leaf-blade anatomy in North American Allium species.

New insight into the taxonomy of Cephaloziellaceae (Marchantiophyta): the family of the smallest higher plants on Earth.

An analysis of the phylogeny of Cephaloziellaceae was carried out based on trees constructed for previously and newly obtained sequences of five genes: nuclear ITS1-2 and chloroplast trnL-F, trnG, rbcL, and psbA. Phylogenetic trees inferred from different genes are congruent for the main details; however, the position of several taxa is variable. As a result, a new phylogenetic system of the family was proposed. The narrow genus concept seems to be more appropriate for the family. Cephaloziella spinicaulis is segregated into the new genus Douiniella, the generic status for Prionolobus and Metacephalozia is confirmed, and the dubious generic status of Kymatocalyx is substantiated. The generic independence of Cylindrocolea from Cephaloziella s. str. is confirmed. The small amount of data hinders the description of two more genera from Cephaloziella s.l.

Integrative Taxonomy Reveals Hidden Diversity in the Aloina catillum Complex (Pottiaceae, Bryophyta).

Aloina catillum is a variable moss typical of xerophytic environments in the Neotropics, characterized against other closely allied Aloina species with well-differentiated leaf border by its setae twisted to the left throughout. In order to clarify its variability and its relationships with the allied species with differentiated leaf border A. brevirostris, A. obliquifolia, and A. rigida, we performed an integrative study including sequence data from four markers (nuclear ITS, plastid atpB-rbcL, trnG, trnL-F), morphometry, and species assembling by automatic partitioning (ASAP) algorithm. Our data suggest that A. catillum consists of at least three species: A. calceolifolia (an earlier name for A. catillum), and two species described here as a new, A. bracteata sp. nov. and A. limbata sp. nov. This latter species includes the specimens previously identified as A. obliquifolia from South America. Additionally, some morphological and molecular variability was also detected in A. limbata, but was not consistent enough to be recognized taxonomically. The study supports the presence of A. brevirostris in the Neotropics and A. rigida is tentatively excluded from South America. Full descriptions of the A. catillum s.l. species and a diagnostic key to this complex in South America are provided.

The Position of Lophozia dubia (Lophoziaceae, Marchantiophyta) in the Phylogenetic System of Lophozia and the Distribution of Lophozia in Southeast Eurasia, Extending to Indonesia.

Lophozia pallida, the commonly used name for a rare and little-known Sino-Himalayan species, was found to be a synonym of Lophozia dubia, a forgotten and previously misinterpreted species known in Indonesia. A comparative study of herbarium materials and our collections made it possible to 'extend' the distribution of Lophozia s. str. southward to Indonesia. The description of oil bodies from the species is provided for the first time. The position of the species in the Lophozia phylogenetic system demonstrates its clear differences from the morphologically similar Lophozia guttulata and its phylogenetic relationship with the Japanese-Korean Lophozia koreana.

Phylogenetic relationships in Brassicaceae tribe Alysseae inferred from nuclear ribosomal and chloroplast DNA sequence data.

Numerous molecular systematic studies within Brassicaceae have resulted in a strongly improved classification of the family, as morphologically defined units at and above the generic level were often found to poorly reflect phylogenetic relationships. Here, we focus on tribe Alysseae, which despite its size (accounting for about 7% of all species) has only received limited coverage in previous phylogenetic studies. Specifically, we want to test phylogenetic hypotheses implied by current tribal and generic circumscriptions and to put diversification within tribe Alysseae into a temporal context. To this end, sequence data from the nrDNA ITS and two plastid regions (ndhF gene, trnL-F intergenic spacer) were obtained for 176 accessions, representing 16 out of 17 currently recognized genera of the tribe, and were phylogenetically analysed, among others, using a relaxed molecular clock. Due to large discrepancies with respect to published ages of Brassicaceae, age estimates concerning Alysseae are, however, burdened with considerable uncertainty. The tribe is monophyletic and contains four strongly supported major clades and Alyssum homalocarpum, whose relationships among each other remain uncertain due to incongruences between nuclear and plastid DNA markers. The largest genus of the tribe, Alyssum, is not monophyletic and contains, apart from A. homalocarpum, two distinct lineages, corresponding to sections Alyssum, Psilonema, Gamosepalum and to sections Odontarrhena and Meniocus, respectively. Clypeola, whose monophyly is supported only by the plastid data, is very closely related to and possibly nested within the second Alyssum lineage. Species of the genus Fibigia intermingle with those of Alyssoides, Clastopus, Degenia, and Physoptychis, rendering Fibigia polyphyletic. The monotypic genera Leptoplax and Physocardamum are embedded in Bornmuellera.

Genetic evaluation and germplasm identification analysis on ITS2, trnL-F, and psbA-trnH of alfalfa varieties germplasm resources.

In this study, genetic diversity and germplasm identification of 28 alfalfa germplasm cultivars materials were evaluated by analyzing their internal transcribed spacer 2 (ITS2), trnL-F, and psbA-trnH sequences to provide the innovative reference of alfalfa varieties genetic diversity and identify research. The results showed that the fragment average length of ITS2, trnL-F, and psbA-trnH sorting sequences were 455.7 bp, 230.3 bp, and 345.6 bp, respectively. The ITS2 sequence was too conservative to reflect the individual differences between intercultivars and intracultivars in the preliminary experiment. Furthermore, trnL-F and psbA-trnH sequence differences were relatively small between intercultivars but significant between intracultivars. Alfalfa cultivars were divided into four groups by sequence similarity clustering. Alfalfa cultivars trnL-F and psbA-trnH sequences have apparent differences, showing that chloroplast conservative sequences were independent evolution. Compared with trnL-F and psbA-trnH sequences of alfalfa cultivars, psbA-trnH sequence has abundant variation sites and can better reflect the differences between cultivars than the trnL-F sequence. Therefore, the psbA-trnH sequence can identify different alfalfa cultivars and establish the DNA sequence fingerprint.

The Lotus angustissumus Group (Fabaceae): Can Phylogenetic Patterns Be Accommodated by a Taxonomic Concept?

The Lotus angustissimus group represents an example of obvious contradictions between the molecular and morphological data. This group includes from six to eight mostly annual species of Lotus section Lotus, with the center of species diversity in the Mediterranean. We performed a phylogenetic analysis of the genus Lotus with an expanded representation of all known species of the L. angustissimus group using both nuclear (nrITS) and a set of plastid DNA markers and compared the results with traditional taxonomy of this group. Our results demonstrated a non-monophyletic nature of the study group. In addition, the nrITS and plastid dataset tree topologies were incongruent with each other in both Bayesian and ML analyses. We revealed very complex phylogenetic relationships among the species of the group. Important results obtained in this study are: (1) genetic and geographical differentiation in the latitudinal direction (between L. angustissimus and L. praetermissus) and in the longitudinal direction among closely related accessions identified as L. castellanus, L. lourdes-santiagoi and L. palustris; (2) close genetic links between the Anatolian endemic L. macrotrichus and L. praetermissus from Eastern Europe and Central Asia; and (3) the hybrid nature of L. subbiflorus with L. parviflorus as its presumed male parent species. These results are discussed in the context of morphology, biogeography and taxonomy.

Screening of universal DNA barcodes for identifying grass species of Gramineae.

There is currently international interest in applying DNA barcoding as a tool for plant species discrimination and identification. In this study, we evaluated the utility of four candidate plant DNA barcoding regions [rbcL, matK, trnL-F, and internal transcribed spacer (ITS)] in seven genera of Gramineae including Agropyron, Bromus, Elymus, Elytrigia, Festuca, Leymus, and Lolium. Fourteen accessions were analyzed, and matK and ITS showed the highest species, subspecies, and variety discriminatory power, each resolving 11 accessions. Species discrimination using rbcL and trnL-F was lower, resolving 7 and 8 accessions, respectively. Subspecies and variety discrimination using rbcL and trnL-F could not identify 4 accessions of Agropyron. A technical system can be established using the proposed DNA barcode to rapidly and reliably identify the seven genera of Gramineae. This study serves as a "useful reference" for identifying the genetic diversity of grass germplasm resources. DNA barcoding can be utilized to uncover the relatives of different species within the same family or between different families. It can also be used to determine the related groups of important herbage, turfgrass, and crops and provide crucial background information for discovering excellent genes and improving existing crop varieties.

Hemiboeakaiyangensis, a new species of Gesneriaceae endemic to Guizhou, China.

A new species of Gesneriaceae from Guizhou, China, Hemiboeakaiyangensis sp. nov., is described and illustrated. We investigated its phylogenetic position and relationships with 13 other species of Hemiboea C.B.Clarke, which present large morphological diversity in the genus, based on molecular analyses of the nuclear ribosomal internal transcribed spacer (ITS) and the chloroplast trnL-F intron-spacer sequences. The molecular phylogenetic analyses revealed that the new species is most closely related to H.ovalifolia. A diagnostic table and discussion of morphological characters are provided to differentiate the new species from H.longisepala, H.flaccida and H.ovalifolia.

Circumscription and Phylogenetic Position of Two Propagulose Species of Syntrichia (Pottiaceae, Bryophyta) Reveals Minor Realignments within the Tribe Syntricheae.

In the course of a worldwide revision of the genus Syntrichia, we identified problems in the circumscription of some species of the genus as well as among some allied genera grouped in the tribe Syntricheae. This is the case for the two propagulose Syntrichia amphidiacea and S. gemmascens, closely related to Streptopogon. We analyzed phylogenetic relationships between these species, based on nuclear (ITS) and two plastid (trnL-F and trnG) markers and morphological features. Species delimitation using molecular data was consistent with our preliminary morphological inference. Phylogenetic analyses were performed using maximum likelihood and Bayesian inference methods. Our results placed Syntrichia amphidiacea in the Streptopogon clade. Syntrichia gemmascens is also included in Streptopogon in spite of the discrepancy of the ITS and plastid relationships, which could be evidence of an exchange of genetic material between species in various lineages in the Pottioideae. Streptopogon is maintained as a separate genus on the basis of morphology characters, and we consider the differentiation of laminal papillae and the presence of a stem central strand as new characters in the genus. We accept Sagenotortula as distinct genus sister to Syntrichia. We consider the lack of costal dorsal epidermis and the differentiation of a crescent-shaped costal dorsal stereid band as distinctive generic characters in Syntrichia. Additionally, we include Syntrichia percarnosa as a new synonym for S. breviseta. Three names are lectotypified.

When Morphology and Biogeography Approximate Nuclear ITS but Conflict with Plastid Phylogeny: Phylogeography of the Lotus dorycnium Species Complex (Leguminosae).

Lotus dorycnium s.l. is a complex of taxa traditionally regarded as members of Dorycnium. It has a wide Mediterranean range, extending in the north to Central and Eastern Europe, and in the east to the Crimea, the Caucasus, and the Western Caspian region. Molecular phylogenetic data support placement of the L. dorycnium complex in the genus Lotus. The present study investigated the phylogeny, phylogeography and morphological variability of the L. dorycnium complex across its distribution range to reveal the main trends in genetic and morphological differentiation in this group. The results of the morphological analyses demonstrated some degree of differentiation, with L. d. ssp. herbaceus, ssp. gracilis, and ssp. anatolicus more or less well defined, whereas ssp. dorycnium, ssp. germanicus, and ssp. haussknechtii can be hardly distinguished from each other using morphology. Analyses of the L. dorycnium complex based on nrITS revealed a tendency towards a geographic differentiation into Western, Eastern, and Turkish groups. Phylogenetic and phylogeographic analyses of the same set of specimens using concatenated plastid markers trnL-F, rps16, and psbA-trnH demonstrated a low resolution between the L. dorycnium complex and L. hirsutus, as well as among the taxa within the L. dorycnium complex, which can be interpreted as evidence of an incomplete lineage sorting or hybridization. The evolutionary processes responsible for incongruence in phylogenetic signals between plastid and nuclear sequences of the morphologically well-defined species L. dorycnium and L. hirsutus were most likely localized in the Eastern Mediterranean. A possibility of rare gene exchange between the L. dorycnium complex and the group of L. graecus is revealed for the first time.

Codonoblepharonteae, a New Major Lineage among Orthotrichoideae (Orthotrichaceae, Bryophyta).

Orthotrichoideae aggregates epiphytic mosses widespread throughout temperate regions and high tropical mountains of the world. Recently, important advances have been made in elucidating its phylogenetic relationships and evolutionary patterns. Fourteen genera are currently recognized within the subfamily, which are spread over two main tribes: Orthotricheae, comprising Orthotrichinae and Lewinskyinae, and Zygodonteae. Despite the progress, some groups have received little attention, as is the case of genus Codonoblepharon. Recent studies have suggested that this genus may represent a separate lineage from Zygodonteae, in which it traditionally has been considered. Although, none of the studies were conclusive as they did not include a representative sampling of the Codonoblepharon species. This work aims to evaluate the taxonomic position of Codonoblepharon and its phylogenetic relationships within Orthotrichoideae. For this purpose, we present an updated phylogenetic tree based on four different loci, one belonging to the nuclear genome (ITS2) and the rest to the plastid genome (rps4, trnG and trnL-F). The phylogenetic reconstruction recovers all samples of Codonoblepharon in a monophyletic group, sister to the rest of the subfamily, constituting a lineage independent of the two currently recognized tribes. For this reason, we propose the new tribe Codonoblepharonteae to accommodate Codonoblepharon.

Phylogenetic Placement and Phylogeography of Large-Flowered Lotus Species (Leguminosae) Formerly Classified in Dorycnium: Evidence of Pre-Pleistocene Differentiation of Western and Eastern Intraspecific Groups.

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.