Seed and capsule morphology of Iranian perennial species of Euphorbia (Euphorbiaceae) and its phylogenetic application

Of the 480 species of Euphorbia subgenus Esula, c. 290 occur in the Mediterranean and Irano‐Turanian regions. Turkey and Iran are the most species‐rich countries in Asia with 83 and 74 species, respectively. Following our previous paper on annual species of Iranian Euphorbia, we studied the quantitative and qualitative macro‐ and micromorphological traits of seeds and capsules of 47 perennial species, including E . ferdowsiana sp. nov. , E . sulphurea sp. nov. and E. glareosa, as a first report from Iran. A key for all Iranian perennial Euphorbia spp. based on seed and capsule morphology is provided. The phylogenetic relationships of Iranian species based on internal transcribed spacer (ITS) nuclear and ndhF plastid regions are updated and used for the characterization of the synapomorphies of each clade. Capsule shape, seed shape, seed surface and shape of the caruncle have been found to be homoplastic, whereas the presence or absence of granulate elements on seed surfaces represents a phylogenetically important trait for section delimitation. The capsule surface is synapomorphic for several sections, including Helioscopia (tuberculate‐verrucose), Myrsiniteae (vesiculate) and Esula (granulate), and seed shape is synapomorphic for sections Helioscopia (ellipsoidal), Myrsiniteae (ovoid‐quadrangular) and Herpetorrhizae (pseudo‐hexahedral). Reversals have also taken place in some features, including capsule surface (E. mazandaranica, E. altissima) and seed shape (E. densa, E. aleppica). It seems that ecarunculate seeds are plesiomorphic in sections Helioscopia (E. eriophora) and Herpetorrhizae (E. consanguinea and E. turczaninowii). © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 00 , 000–000.     

A systematic study of North American Angelica species (Apiaceae) based on nrDNA ITS and cpDNA sequences and fruit morphology

Angelica is a taxonomically complex genus widespread throughout the North Temperate Zone. Previous phylogenetic studies of the genus have focused primarily on its East Asian species. The relationships among its North American members, the monophyly of these species, and the value of fruit morphology in circumscribing its taxa have yet to be examined. This study represents the most comprehensive sampling of Angelica to date (100 species) and includes all 26 species in North America. Relationships are inferred using Bayesian inference, maximum likelihood, and maximum parsimony analyses of ITS sequences and, for multiple accessions of each North American species, cpDNA ndhF-rpl32, rpl32-trnL, and psbM-psbD sequences. The fruit morphological characters examined were those considered phylogenetically important in East Asian Angelica. The results revealed that the North American species fell into three major clades: North American Angelica clade, Archangelica clade, and the Eurasian Angelica clade. Angelica dawsonii has affinities with Lomatium brandegeei. Fourteen species within the North American Angelica clade were strongly supported as monophyletic. Two paraphyletic species resulted in new combinations in A. lineariloba and A. venenosa. Conflict between the ITS-derived and cpDNA-derived phylogenies and the lack of resolution in portions of the trees may be due to chloroplast capture and rapid species radiation. Fruit morphology supported some interspecific relationships based on molecular data, and relationships revealed by ITS and cpDNA data were roughly in accordance with fruit classification type and geographic distribution region, respectively. A diagnostic key based on fruit morphology is provided for the identification of the North American Angelica taxa.     

The infrageneric taxonomy of Chaerophyllum (Apiaceae) revisited: new evidence from nuclear ribosomal DNA ITS sequences and fruit anatomy

Evolutionary relationships among 65 Chaerophyllum spp. were inferred from nuclear ribosomal DNA internal transcribed spacer (ITS) sequence variation. Thirty‐one species, represented by 158 mericarp samples, were analysed for fruit anatomical character variation, employing phylogenetic and phenetic methods to explore their congruence with infrageneric divisions based on molecular data. Phylogenetic trees inferred from molecular data using maximum likelihood (ML) and Bayesian inference (BI) methods corroborated the division of the genus into four sections: Chaerophyllum, Dasypetalon, Physocaulis and Chrysocarpum. From among the newly sequenced species, the Greek endemic C. heldreichii was grouped with section Chaerophyllum, whereas the highly variable Asian C. reflexum–C. villosum complex formed an early‐branching paraphyletic assemblage in section Chrysocarpum. The recently described C. karsianum has an identical ITS sequence to C. bulbosum, whereas C. aksekiense was clearly separated from the morphologically similar C. macrospermum. Our study confirmed the postulated synonymy of several species on the basis of morphology, but also demonstrated distant relationships between some morphologically similar species. With the exception of the monotypic section Physocaulis, we were unable to find carpological traits matching sectional divisions. We hypothesize that fruit characters evolved rapidly as a result of diversification of members of the genus in different habitats. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 178 , 298–313.     

Insights into Neogene Mediterranean biogeography based on phylogenetic relationships of mountain and lowland lineages of Narcissus (Amaryllidaceae)

Aim Our aims were: (1) to reconstruct the phylogenetic relationships of daffodils (Narcissus), focusing on the lowland subgenus Hermione and the mountain section Apodanthi; (2) to estimate the temporal setting of diversification; (3) to reconstruct the migration patterns of the lineages; and (4) to examine the microevolutionary differentiation of the wide‐ranging Narcissus tazetta group across the Mediterranean. Location The Mediterranean Basin. Methods Plastid (trnT–L, trnL–F and ndhF) sequences were obtained from 63 populations representing 23 species of Narcissus and combined with published data from 16 species. Phylogenetic relationships and dating were inferred by Bayesian analysis based on geological events and divergence estimates of closely related taxa. A dispersal–extinction–cladogenesis analysis was performed using maximum likelihood methods to infer ancestral geographical distributions, and phylogeographical reconstruction was performed using coalescence analysis. Results Subgenus Hermione is not recognized as a monophyletic group because two of the nine species were found to have a close relationship with the subgenus Narcissus. The results on section Apodanthi confirmed previous findings of its monophyly and phylogenetic relationships within this mountain group. Molecular dating and ancestral range reconstructions suggest that the ancestor of Narcissus originated in the Iberian Peninsula during the Late Oligocene–Early Miocene. Eastward expansion of the lineage range proceeded from the western Mediterranean and involved colonization of mountain ranges in northern Africa. The phylogeography of the N. tazetta group revealed a widespread distribution of certain haplotypes, suggesting wide dispersal and a high level of colonization in the Mediterranean Basin. Main conclusions Our study points to the role of three key historical events in Narcissus diversification: tectonic shifts of the Alboran domain in the western Mediterranean, the Messinian salinity crisis, and the onset of the Mediterranean climate followed by periods of repeated glaciation. Diversification of section Apodanthi probably resulted from allopatric speciation, while subgenus Hermione may have shown more sympatric speciation and high dispersal, despite the lack of apparent adaptations to long‐distance dispersal. This is best exemplified by the presence of both ancestral and recent haplotypes of N. tazetta across the Mediterranean.     

Did tree‐Betula,Pinus and Picea survive the last glaciation along the west coast of Norway? A review of the evidence,in light of Kullman (2002)

Aim We discuss the hypotheses proposed by Kullman [Geo‐Öko 21 (2000) 141; Nordic Journal of Botany 21 (2001) 39; Journal of Biogeography 29 (2002) 1117] on the basis of radiocarbon‐dated megafossils of late‐glacial age from the central Swedish mountains that boreal trees survived the glaciation along the south‐west coast of Norway and subsequently migrated eastward early in the late‐glacial to early deglaciated parts of the central Swedish Scandes mountains. Methods We assess these hypotheses on the basis of glacial geological evidence and four lines of palaeoecological evidence, namely macrofossil records of the tree species, vegetation and climate reconstructions from plant evidence, independent climate reconstructions from other proxies for the late‐glacial environment of south‐west Norway, and the patterns of post‐glacial spread of the tree species. Location South and west Norway, central Swedish Scandes mountains (Jämtland). Results and conclusions South‐west Norway and the adjacent continental shelf were under ice at the last‐glacial maximum (LGM). The late‐glacial vegetation of south‐west Norway was treeless and summer temperatures were below the thermal limits for Betula pubescens Ehrh., Pinus sylvestris L. and Picea abies (L.) Karst. Instead of spreading immediately after the onset of Holocene warming, as might have been expected if local populations were surviving, B. pubescens showed a lag of local arrival of 600 to > 1000 years, Pinus lagged by 1500 to > 2000 years, and Picea only reached southern Norway c. 1500 years ago and has not colonized most of south‐west Norway west of the watershed. Glacial geological evidence shows the presence of an ice sheet in the Scandes at the LGM and in the Younger Dryas, which was cold‐based near or at the area where the late‐glacial‐dated megafossils were recovered by Kullman. We conclude that the samples dated by Kullman (2002) should be evaluated carefully for possible sources of contamination. All the available evidence shows that the biogeographical hypotheses, based on these radiocarbon dates taken at face value, of late‐glacial tree survival at the Norwegian coast and subsequent eastwards spread to the mountains, are unsupportable.     

Phylogenetic relationships of the callitrichinae (Platyrrhini,Primates) based on β2‐microglobulin DNA sequences

The phylogenetic relationships of callitrichine primates have been determined by DNA sequence analyses of exons 1, 2, and 3 of the β₂‐microglobulin gene. Parsimony, distance, and maximum likelihood analyses of ca. 900 base pairs of 21 taxa, representing all callitrichine genera, indicated that Saguinus was the most basal offshoot. Within Saguinus, S. fuscicollis appeared as the first divergent lineage followed by an unresolved trichotomy formed by S. mystax/S. imperator, S. midas/S. bicolor, and S. oedipus. A second callitrichine lineage was formed by Leontopithecus; each of the three species studied showed identical nucleotide sequences. Callimico appeared as the sister taxon of Callithrix/Cebuella. Genetic distances within this latter group were very small, although a stronger association between Cebuella and species of the Callithrix argentata group was observed. The inclusion of Cebuella in the genus Callithrix is suggested. These studies indicated that tamarins are more plesiomorphic than marmosets in agreement with the phyletic dwarfism hypothesis. Am. J. Primatol. 48:225–236, 1999. © 1999 Wiley‐Liss, Inc.     

Molecular phylogeny and divergence times of Onosma (Boraginaceae s.s.) based on nrDNA ITS and plastid rpl32‐trnL(UAG) and trnH–psbA sequences

We analysed 87 species of Onosma (Boraginaceae) from throughout its distribution range to investigate its evolutionary history. Using nrDNA ITS and two plastid (rpl32‐trnL_(UAG) and trnH–psbA) markers, we reconstructed phylogenetic relationships within Onosma by conducting maximum parsimony, maximum likelihood, Bayesian, and BEAST analyses. The analyses revealed that Onosma as currently circumscribed is not monophyletic. However, the vast majority of Onosma species appear to belong to a single clade, the so‐called Onosma s.s. Outside of this core clade is a clade containing O. rostellata, a subclade of Sino‐Indian species and Maharanga emodii. Podonosma orientalis (as O. orientalis) appear only distantly related to Onosma but is more closely related to Alkanna, as also suggested in previous molecular studies. The Onosma s.s. clade includes all representatives of O. sect. Onosma, and encompasses three subsections, i.e. Onosma, Haplotricha and Heterotricha, corresponding to asterotrichous, haplotrichous and heterotrichous groups, respectively, but none of these subsections was retrieved as monophyletic. We observed significant incongruence between nuclear and chloroplast phylogenies regarding the phylogenetic status of the heterotrichous group. A dozen of the Iranian haplotrichous species formed a lineage which may not hybridize with asterotrichous species. Divergence time estimates suggested that the early radiation of Onosma s.l. took place at the Oligocene‐Miocene boundary and the diversification within Onosma s.s. occurred during middle to late Miocene and Pliocene.     

Species‐delimitation and phylogenetic analyses of some cosmopolitan species of Hypnea (Rhodophyta) reveal synonyms and misapplied names to H. cervicornis,including a new species from Brazil

Hypnea has an intricate nomenclatural history due to a wide pantropical distribution and considerable morphological variation. Recent molecular studies have provided further clarification on the systematics of the genus; however, species of uncertain affinities remain due to flawed taxonomic identification. Detailed analyses coupled with literature review indicated a strong relationship among H. aspera, H. cervicornis, H. flexicaulis, and H. tenuis, suggesting a need for further taxonomic studies. Here, we analyzed sequences from two molecular markers (COI‐5P and rbcL) and performed several DNA‐based delimitation methods (mBGD, ABGD, SPN, PTP and GMYC). These molecular approaches were contrasted with morphological and phylogenetic evidence from type specimens and/or topotype collections of related species under a conservative approach. Our results demonstrate that H. aspera and H. flexicaulis represent heterotypic synonyms of H. cervicornis and indicate the existence of a misidentified Hypnea species, widely distributed on the Brazilian coast, described here as a new species: H. brasiliensis. Finally, inconsistencies observed among our results based on six different species delimitation methods evidence the need for adequate sampling and marker choice for different methods.     

A species well travelled – the Dodonaea viscosa (Sapindaceae) complex based on phylogenetic analyses of nuclear ribosomal ITS and ETSf sequences

Aim To determine the evolutionary history of the widely studied, cosmopolitan polymorphic species Dodonaea viscosa (hop bush, varnish tree). Location All continents except Antarctica, extending from 44° S (in the South Island of New Zealand) to 33° N (in California and Arizona). Methods For 50 samples across the worldwide distribution, Bayesian analyses of nuclear ribosomal transcribed spacers (ITS 1, ITS 2 and partial ETS) were performed. The alignment was partitioned by secondary structure and analysed using separate models of sequence evolution for each spacer’s stem and loop partition. Bayesian relaxed‐clock estimations of divergence times were used to investigate the tempo of the transoceanic dispersal history of Dodonaea viscosa. Results The widely distributed Dodonaea viscosa evolved in Australia from its most recent common ancestor in the Late Pliocene to Early Pleistocene and subsequently split into two distinct, geographically based, intraspecific lineages. There are a number of regional subclades that are also supported by specific molecular elements. Main conclusions Dodonaea viscosa is not an old lineage, as has often been speculated based primarily on its vast distribution. It diverged from its most recent common ancestor and subsequently dispersed and established around the world within the last 2 Myr. Two distinct lineages within Dodonaea viscosa, which have been shaped by Quaternary climatic change, have separate dispersal histories. The molecular investigations have identified that, although there are least two evolutionary lineages within the complex, they do not correlate with any distinct morphological subunits. It is proposed that Dodonaea viscosa (including D. biloba and D. procumbens) be recognized as an ochlospecies.     

Limber pine (Pinus flexilis James) genetic map constructed by exome‐seq provides insight into the evolution of disease resistance and a genomic resource for genomics‐based breeding

Limber pine ( Pinus flexilis ) is a keystone species of high‐elevation forest ecosystems of western North America, but some parts of the geographic range have high infection and mortality from the non‐native white pine blister rust caused by Cronartium ribicola . Genetic maps can provide essential knowledge for understanding genetic disease resistance as well as local adaptation to changing climates. Exome‐seq was performed to construct high‐density genetic maps in two seed families. Composite maps positioned 9612 unigenes across 12 linkage groups ( LG s). Syntenic analysis of genome structure revealed that the majority of orthologs were positional orthologous genes ( POG s) with localization on homologous LG s among conifer species. Gene ontology ( GO) enrichment analysis showed relatively fewer constraints for POG s with putative roles in adaptation to environments and relatively more conservation for POG s with roles in basic cell function and maintenance. The mapped genes included 639 nucleotide‐binding site leucine‐rich repeat genes ( NBS ‐ LRR s) , 290 receptor‐like protein kinase genes ( RLK s), and 1014 genes with potential roles in the defense response and induced systemic resistance to attack by pathogens. Orthologous loci for resistance to rust pathogens were identified and were co‐positioned with multiple members of the R gene family, revealing the evolutionary pressure acting upon them. This high‐density genetic map provides a genomic resource and practical tool for breeding and genetic conservation programs, with applications in genome‐wide association studies ( GWASs ), the characterization of functional genes underlying complex traits, and the sequencing and assembly of the full‐length genomes of limber pine and related Pinus species.     

Molecular phylogeny of Solms‐laubachia (Brassicaceae) s.l., based on multiple nuclear and plastid DNA sequences,and its biogeographic implications

Abstract The Hengduan Mountains region of south‐west China is a noted biodiversity hotspot, but the geographic origins and historical assembly of its rich endemic flora, including the sky‐island species of Solms‐laubachia Muschl. (Brassicaceae), have been little studied. Previous molecular studies on the phylogeny of Solms‐laubachia showed it to be paraphyletic, leading to considerable expansion not only of its taxonomic limits, but also its geographic range, with the inclusion of taxa from outside the Hengduan region. However, these studies provided little resolution of interspecific relationships, preventing inferences about historical biogeography within the clade. In the present study, new sequence data from two nuclear genes (LEAFY and G3pdh) and two chloroplast intergenic spacers (petN–psbM and psbM–trnD) were combined with existing markers to increase phylogenetic signals. Phaeonychium villosum (Maxim.) Al‐Shehbaz was found to be nested within Solms‐laubachia s.l. In general, phylogenetic relationships appear to be a good predictor of geography, with the Hengduan Mountain endemics embedded in a paraphyletic grade of species from the western Himalayas and central Asia, but they also imply morphological homoplasy. Incongruence was detected between the nuclear and chloroplast gene trees, perhaps resulting from incomplete lineage sorting of ancestral polymorphisms. The crown age of Solms‐laubachia s.l. was estimated to be approximately 1.42–3.68 mya, using Bayesian relaxed molecular clock analysis. Historical biogeographic analysis using a parametric dispersal–extinction–cladogenesis model inferred central Asia and the western Himalayas as most probable ancestral range of Solms‐laubachia s.l., and estimated higher rates of eastward expansion than westward during the diversification of descendant lineages. In summary, our results suggest that Solms‐laubachia s.l. originated during the Pliocene in central Asia, and subsequently migrated eastward into the Hengduan Mountains, colonizing sky‐island, alpine scree‐slope habitats that may have provided novel ecological opportunity and accelerated speciation, ultimately establishing this region as the present center of diversity of the genus.     

Biooptical characteristics of PSII and PSI in 33 species (13 pigment groups) of marine phytoplankton,and the relevance for pulse‐amplitude‐modulated and fast‐repetition‐rate fluorometry1

We studied the variability of in vivo absorption coefficients and PSII‐scaled fluorescence excitation (fl‐ex) spectra of high light (HL) and low light (LL) acclimated cultures of 33 phytoplankton species that belonged to 13 different pigment groups (PGs) and 10 different phytoplankton classes. By scaling fl‐ex spectra to the corresponding absorption spectra by matching them in the 540–650 nm range, we obtained estimates for the fraction of total chl a that resided in PSII, the absorption of light by PSII, PSI, and photoprotective carotenoids. The in vivo red peak absorption maxima ranged from 673 to 679 nm, reflecting bonding of chl a to different pigment proteins. A simple approach is presented for quantifying intracellular self‐shading and evaluating the impact of photoacclimation on biooptical characteristics of the different PGs examined. In view of these results, parameters used in the calculation of oxygenic photosynthesis based on pulse‐amplitude‐modulated (PAM) and fast‐repetition‐rate (FRR) fluorometers are discussed, showing that the ratio between light available to PSII and total absorption, essential for the calculation of the oxygen release rate (using the PSII‐scaled fluorescence spectrum as a proxy) was dependent on species and photoacclimation state. Three subgroups of chromophytes exhibited 70%–80%, 60%–80%, and 50%–60% chl a in PSII‐LHCII; the two subgroups of chlorophytes, 70% or 80%; and cyanobacteria, only 12%. In contrast, the mean fraction for chromo‐ and chlorophytes of quanta absorbed by PSII was 73% in LL‐ and 55% in HL‐acclimated cells; thus, the corresponding ratios 0.55 and 0.73 might be used as correction factors adjusting for quanta absorbed by PSII for PAM and FRR measurements.     

Enantioresolution of Chiral Derivatives of Xanthones on (S,S)‐Whelk‐O1 and l‐Phenylglycine Stationary Phases and Chiral Recognition Mechanism by Docking Approach for (S,S)‐Whelk‐O1

The resolution of seven enantiomeric pairs of chiral derivatives of xanthones (CDXs) on (S,S)‐Whelk‐O1 and l ‐phenylglycine chiral stationary phases (CSPs) was systematically investigated using multimodal elution conditions (normal‐phase, polar‐organic, and reversed‐phase). The (S,S)‐Whelk‐O1 CSP, under polar‐organic conditions, demonstrated a very good power of resolution for the CDXs possessing an aromatic moiety linked to the stereogenic center with separation factor and resolution factor ranging from 1.91 to 7.55 and from 6.71 to 24.16, respectively. The chiral recognition mechanisms were also investigated for (S,S)‐Whelk‐O1 CSP by molecular docking technique. Data regarding the CSP–CDX molecular conformations and interactions were retrieved. These results were in accordance with the experimental chromatographic parameters regarding enantioselectivity and enantiomer elution order. The results of the present study fulfilled the initial objectives of enantioselective studies of CDXs and elucidation of intermolecular CSP–CDX interactions. Chirality 25:89–100, 2013. © 2012 Wiley Periodicals, Inc.