Seed macro- and micromorphology in Allium (Amaryllidaceae) and its phylogenetic significance.

BACKGROUND AND AIMS: Macro- and micromorphology of seeds are diagnostic characteristics of importance in delimiting taxa in Allium (Amaryllidaceae). However, there is no consensus on the phylogenetic significance of testa cell characteristics and whether they reflect the different evolutionary levels recognized in Allium. METHODS: Seeds of 95 species (98 samples) representing 14 subgenera and 58 sections of Allium were examined using scanning electron microscopy (SEM) for such traits as periclinal wall surface area of ten testa cells, distance between testa cells (macromorphology), testa cell shapes, and arrangement and structure of anticlinal and periclinal walls (micromorphology). The data matrix was subjected to cladistic analysis. The produced phylogenetic tree was examined against the molecular tree obtained from publically available ITS sequences. KEY RESULTS: The periclinal wall surface area of ten testa cells and the distance between them, examined for the first time, were found useful for delimitation of species in Allium. Based on seed macro- and micromorphology, we present a taxonomic key and a hypothetical reconstruction of the migration routes during the early stages of evolution of Allium. CONCLUSIONS: The ancestors of Allium originated in an area bounded by the Caucasus, Central Asia and Iran. The seed testa morphology-based evolutionary state of a species is determined by two parameters: the shape of the periclinal walls and curvature of the anticlinal walls.

Phylogenomics of Allium section Cepa (Amaryllidaceae) provides new insights on domestication of onion.

Allium sect. Cepa (Amaryllidaceae) comprises economically important plants, yet resolving the phylogenetic relationships within the section has been difficult as nuclear and chloroplast-based phylogenetic trees have been incongruent. Until now, phylogenetic studies of the section have been based on a few genes. In this study, we sequenced the complete chloroplast genome (plastomes) of four central Asian species of sect. Cepa: Allium oschaninii, A. praemixtum, A. pskemense and A. galanthum. Their chloroplast (cp) genomes included 114 unique genes of which 80 coded proteins. Seven protein-coding genes were highly variable and therefore promising for future phylogenetic and phylogeographic studies. Our plastome-based phylogenetic tree of Allium sect. Cepa revealed two separate clades: one comprising the central Asian species A. oschaninii, A. praemixtum, and A. pskemense, and another comprising A. galanthum, A. altaicum, and two cultivated species, A. cepa and A. fistulosum. These findings contradict previously reported phylogenies that relied on ITS and morphology. Possible explanations for this discrepancy are related to interspecific hybridization of species ancestral to A. galanthum and A. cepa followed by chloroplast capture; however, this is impossible to prove without additional data. Our results suggest that the central Asian Allium species did not play a role in the domestication of the common onion. Among the chloroplast genes, rpoC2 was identified as a gene of choice in further phylogeographical studies of the genus Allium.

Conservation-oriented restoration - a two for one method to restore both threatened species and their habitats.

There is an urgent need for a new conservation approach as mere designation of protected areas, the primary approach to conserving biodiversity, revealed its low conservation efficiency and inability to cope with numerous challenges faced by nature in the Anthropocene. The paper discusses the new concept, which proposes that ecological restoration becomes an integral part of conservation planning and implementation, and is done using threatened plant species that are introduced not only into locations where they currently grow or grew in the recent past, but also into suitable locations within their potential distribution range. This new concept is called conservation-oriented restoration to distinguish it from the traditional restoration. Although the number of restoration projects focusing on recreation of once existing natural habitats is instantly growing, the majority of ecological restoration projects, in contrast to conservation-oriented restoration, have predominantly utilitarian goals, e.g. improvement or air quality, erosion control or soil replenishment. Conservation-oriented restoration should not be seen as an alternative either to the latter, or to the conservation dealing with particular threatened species (species-targeted conservation). These three conservation approaches, traditional ecological restoration, species-targeted conservation, and conservation-oriented restoration differ not only in broadly defined goals and attributes of their targets, but also in the types of ecosystems they are applicable to, and complement each other in combating global deterioration of the environment and biodiversity loss.

Translocation of Otostegia bucharica, a highly threatened narrowly distributed relict shrub.

Translocation is a recognized means of rescuing imperiled species but the evidence for the long-term success of translocations is limited. We report the successful translocation of reproductive individuals of a critically endangered shrub Otostegia bucharica from a site facing imminent habitat destruction into a nearby natural population of the species. The relocated plants were visited the year after planting and 13 years later to assess short- and long-term plant survival. Significant percentage of plants that survived transplanting shock and very dry spring following transplanting (around 36%), and further decrease of this number in the next 12 years by only 14%, indicated that O. bucharica is amenable to translocation using reproductive plants. Based on results of species distribution modeling, and failed attempts of ex situ cultivation, we propose introduction of this species into areas with suitable climatic and soil conditions. However, because there is currently no nature reserve in Uzbekistan having suitable conditions for the species under the present climate and that expected in the near future, and because all known habitats of O. bucharica are exposed to the very strong anthropogenic pressure, establishment of a new protected area, awareness building and involvement of local community in conservation activities are required to prevent extinction of this extremely rare species.

Alkaloid chemodiversity in Mandragora spp. is associated with loss-of-functionality of MoH6H, a hyoscyamine 6ß-hydroxylase gene.

Mandrakes (Mandragora spp., Solanaceae) are known to contain tropane alkaloids and have been used since antiquity in traditional medicine. Tropane alkaloids such as scopolamine and hyoscyamine are used in modern medicine to treat pain, motion sickness, as eye pupil dilators and antidotes against organo-phosphate poisoning. Hyoscyamine is converted to 6ß-hydroxyhyoscyamine (anisodamine) and scopolamine by hyoscyamine 6ß-hydroxylase (H6H), a 2-oxoglutarate dependent dioxygenase. We describe here a marked chemo-diversity in the tropane alkaloid content in Mandragora spp. M. officinarum and M. turcomanica lack anisodamine and scopolamine but display up to 10 fold higher hyoscyamine levels as compared with M. autumnalis. Transcriptomic analyses revealed that H6H is highly conserved among scopolamine-producing Solanaceae. MoH6H present in M. officinarum differs in several amino acid residues including a homozygotic mutation in the substrate binding region of the protein and its prevalence among accessions was confirmed by Cleaved-Amplified-Polymorphic-Sequence analyses. Functional expression revealed that MaH6H, a gene isolated from M. autumnalis encodes an active H6H enzyme while the MoH6H sequence isolated from M. officinarum was functionally inactive. A single G to T mutation in nucleotide 663 of MoH6H is associated with the lack of anisodamine and scopolamine in M. officinalis.

Conservation implications of population genetic structure in a threatened orchid Cypripedium tibeticum.

Cypripedium tibeticum is a threatened orchid which efficient conservation requires knowledge of its extent and structure of genetic variation. Using two chloroplast DNA fragments (rps16 and trnL-F), we analyzed 157 individuals from 9 populations representing the species range in China. Seven haplotypes were identified. C. tibeticum had high total genetic diversity (H T = 0.80) with major contribution to this diversity made by among-population component (G ST  = 0.64, Φ ST  = 0.86). However, despite high population differentiation there was no clear phylogeographic structure. The populations CY and DC made the greatest contribution to the total gene diversity as well as allelic richness. The possible mechanisms and implications of these findings for conservation of the species are discussed.

Securing a future for China's plant biodiversity through an integrated conservation approach.

The severely threatened Chinese flora urgently needs a new, well adapted to China and properly formulated conservation strategy. The present review provides a detailed conservation methodology that complements previously described guidelines for preservation of plant species with extremely small populations (PSESP) in China. This review adds to the above concept in several aspects, making it relevant to all threatened Chinese plant species. The proposed integral conservation strategy has the following crucial components:-ecoregional basis for conservation planning and implementation;-a unified scoring system that is used in regional systematic planning for reserve design, monitoring and assessment of efficiency of a reserve network, and creation of seed banks and living collections;-a focus on population demography and the presence of naturally occurring regeneration as the key criteria for defining the conservation status of a species and the appropriate major focus of the species recovery plan;-creation of multi-species living collections that preserve species genetic variation and provide material for in situ actions;-experimental translocation of threatened species into multiple locations within and outside their known range. Adopting and implementing these strategies successfully and more fully in China requires that the country changes PA legislation and improves PA management, the National Science Foundation of China (NSFC) re-prioritizes the type of research that receives research funds, and local scientists improve their approach toward information sharing.

Evolutionary history and biogeography of Mandragora L. (Solanaceae).

Mandragora L. (Solanaceae) is the only genus of the tribe Mandragoreae, one of the two tribes of the cosmopolitan nightshade family, which occur exclusively in Eurasia and northern Africa. The genus occurs discontinuously in the Mediterranean region, Turanian region, and on the Tibetan Plateau, representing a classical disjunction pattern in the biogeography of the Old World flora. In this study, we reconstructed the genus phylogeny using AFLP, eight plastid DNA regions and one nuclear (ITS) gene, and evaluated the taxonomic value of quantitative traits time to flowering, fruit and seed size. We also analyzed the evolutionary history of the genus based on a phylogenetic framework and dating inferred from a combined data set of seven plastid regions with one fossil calibration point. Our data suggest that Mandragora originated in the Eocene, apparently along the Tethyan coast in broadleaf deciduous mesophytic forests that covered most of the Mediterranean region at that time. The Mediterranean-Turanian clade diverged from the Tibetan Plateau clade about 20.5 million years ago (Ma) as a result of the plateau uplift which probably was enhanced by aridification in the interior of Eurasia. A second split within the genus occurred about 11.1 Ma and resulted in Western Mediterranean and Near East-Turanian clades. Mandragora turcomanica was found to have very closely related evolutionary history with plants from the Near East indicating a possible ancient human assisted migration from Israel to Persia in historic times. In the Tibetan Plateau area, the morphologically distinctive M. chinghaiensis is nested within the M. caulescens clade indicating a very recent diversification within this lineage.

Role of the Qinghai-Tibetan Plateau uplift in the Northern Hemisphere disjunction: evidence from two herbaceous genera of Rubiaceae.

To assess the role of the Qinghai-Tibetan Plateau uplift in shaping the intercontinental disjunction in Northern Hemisphere, we analyzed the origin and diversification within a geological timeframe for two relict herbaceous genera, Theligonum and Kelloggia (Rubiaceae). Phylogenetic relationships within and between Theligonum and Kelloggia as well as their relatives were inferred using five chloroplast markers with parsimony, Bayesian and maximum-likelihood approaches. Migration routes and evolution of these taxa were reconstructed using Bayesian relaxed molecular clock and ancestral area reconstruction. Our results suggest the monophyly of each Theligonum and Kelloggia. Eastern Asian and North American species of Kelloggia diverged at ca.18.52 Mya and the Mediterranean species of Theligonum diverged from eastern Asian taxa at ca.13.73 Mya. Both Kelloggia and Theligonum are Tethyan flora relicts, and their ancestors might have been occurred in warm tropical to subtropical environments along the Tethys coast. The Qinghai-Tibetan Plateau separated the eastern and western Tethyan area may contribute significantly to the disjunct distributions of Theligonum, and the North Atlantic migration appears to be the most likely pathway of expansion of Kelloggia to North America. Our results highlight the importance role of the QTP uplift together with corresponding geological and climatic events in shaping biodiversity and biogeographic distribution in the Northern Hemisphere.

Conservation utility of botanic garden living collections: Setting a strategy and appropriate methodology.

In the realities of the modern world, when the natural habitat is rapidly disappearing and the number of imperiled plants is constantly growing, ex situ conservation is gaining importance. To meet this challenge, botanic gardens need to revise both their strategic goals and their methodologies to achieve the new goals. This paper proposes a strategy for the management of threatened plants in living collections, which includes setting regional conservation priorities for the species, creation of genetically representative collections for the high priority species, and usage of these collections in in situ actions. In this strategy, the value of existing and future species living collections for conservation is determined by the species' conservation status and how well the accessions represent their natural genetic variation.

Complementarities of two existing intermediate conservation approaches.

The need for integration of ex situ and in situ approaches in conservation of plants has long been recognized. However, ex situ collections have numerous limitations that reduce their utility for conservation, necessitating the introduction of new, more appropriate, flexible and less costly approaches. Two new approaches that can be called "intermediate" between in situ and ex situ, and bridging them in some way have been proposed over the last two decades. In these approaches material collected in natural populations is planted and maintained outside the original location, but with a different purpose. While the purpose of the inter situs approach is reintroduction, the concern of the quasi in situ approach is long-term storage of species genetic diversity. I view these two approaches as complementary and necessary components of conservation-oriented restoration. In restoration of a degraded habitat using threatened species (i.e. inter situs), quasi in situ collections can serve an important role in providing long-term preservation of these species' genetic diversity and production of seeds needed for restoration.

Mazus sunhangii (Mazaceae), a New Species Discovered in Central China Appears to Be Highly Endangered.

Mazus sunhangii, a new species of Mazaceae from central China is described and illustrated based on evidence from morphology and molecular phylogeny. This new species is morphologically similar to M. puchellus and M. omeiensis but differs in erect habit, inflorescence position, leaf pattern and corolla color. Phylogenetic analysis based on four chloroplast DNA regions (rbcL, rps16, trnL-F, and psbA-trnH) identified the new species as the independent lineage sister to the other East Asian Mazus species. The new species is known only from a single location in Mt. Shennongjia area in northwest Hubei province, at the elevation of 760 m. The species grows on the limestone cliff, and, because a tourist arterial highway is located along this cliff, its habitat can be easily disturbed or destroyed. We propose that the only known species location is recognized as critical habitat (i.e., as the habitat required to ensure the persistence of a species) and the species listed as Critically Endangered based on the International Union for Conservation of Nature Red List Categories and Criteria B2a.

Seed heteromorphism in Triticum dicoccoides: association between seed positions within a dispersal unit and dormancy.

Variation in seed size and dormancy can take the form of seed heteromorphism, i.e., production of different kinds of seeds by a single individual. In this paper, I tested for the effect of seed position within a spikelet on its germination over time, and the contribution of this effect to population differentiation along an aridity gradient in an annual grass, Triticum dicoccoides. The results show that the upper grain in a spikelet is larger than the bottom grain, and either germinates in the season following dispersal, or dies. In contrast, a substantial fraction of the bottom grains do not germinate in the first season, but remain dormant in the soil seed bank for 1 and, very rarely, 2 years. This pattern was observed in seeds of all origins, but the bottom grains from the most arid location had the lowest, and from the least arid location, the highest germination fraction in the 1st year and vice versa in the 2nd year. This difference in germination fraction was observed under controlled irrigation conditions but not in the field experiment. These mixed results suggest that seed dimorphism is a life history trait with a complicated evolutionary history and wide adaptive implications. Seed dimorphism in T. dicoccoides could initially be an adaptation for reducing competition in productive (i.e., high precipitation) environments. In addition to this, seed dimorphism under increasing aridity could become a bet-hedging trait allowing a population to survive periods of insufficient rainfall through dormancy.

How to conserve threatened Chinese plant species with extremely small populations?

The Chinese flora occupies a unique position in global plant diversity, but is severely threatened. Although biodiversity conservation in China has made significant progress over the past decades, many wild plant species have extremely small population sizes and therefore are in extreme danger of extinction. The concept of plant species with extremely small populations (PSESPs), recently adopted and widely accepted in China, lacks a detailed description of the methodology appropriate for conserving PSESPs. Strategies for seed sampling, reintroduction, protecting PSESP locations, managing interactions with the local human population, and other conservation aspects can substantially differ from those commonly applied to non-PSESPs. The present review is an attempt to provide a detailed conservation methodology with realistic and easy-to-follow guidelines for PSESPs in China.

Fine-scale spatial genetic structure in predominantly selfing plants with limited seed dispersal: A rule or exception?

Gene flow at a fine scale is still poorly understood despite its recognized importance for plant population demographic and genetic processes. We tested the hypothesis that intensity of gene flow will be lower and strength of spatial genetic structure (SGS) will be higher in more peripheral populations because of lower population density. The study was performed on the predominantly selfing Avena sterilis and included: (1) direct measurement of dispersal in a controlled environment; and (2) analyses of SGS in three natural populations, sampled in linear transects at fixed increasing inter-plant distances. We found that in A. sterilis major seed dispersal is by gravity in close (less than 2 m) vicinity of the mother plant, with a minor additional effect of wind. Analysis of SGS with six nuclear SSRs revealed a significant autocorrelation for the distance class of 1 m only in the most peripheral desert population, while in the two core populations with Mediterranean conditions, no genetic structure was found. Our results support the hypothesis that intensity of SGS increases from the species core to periphery as a result of decreased within-population gene flow related to low plant density. Our findings also show that predominant self-pollination and highly localized seed dispersal lead to SGS at a very fine scale, but only if plant density is not too high.

Effect of salinity on seed germination, growth and ion content in dimorphic seeds of Salicornia europaea L. (Chenopodiaceae).

The halophyte Salicornia europaea L. is a widely distributed salt-tolerant plant species that produces numerous dimorphic seeds. We studied germination and recovery in dimorphic seeds of Central Asian S. europaea under various salinity conditions. We also tested the effects of various salts on Na+ and K+ accumulation during plant development from germination to anthesis under greenhouse conditions. We found good germination (close to control) of large seeds under NaCl between 0.5 and 2%, Na2SO4 and 2NaCl + KCl + CaCl between 0.5 and 3%, and 2Na2SO4 + K2SO4 + MgSO4 between 0.5 and 5%. For the small seeds, we found stimulating effects of chloride salts (both pure and mixed) under 0.5-1% concentrations, and sulfate salts under 0.5-3%. Both types of seeds showed high germination recovery potential. Salt tolerance limits of the two seed types during germination and at the later stages of development were very similar (4-5%). During plant growth the optimal concentrations of mixed chloride and sulfate salts ranged from 0.5 to 2%. The mechanisms of salt tolerance in the two seed types of S. europaea appear to differ, but complement each other, improving overall adaptation of this species to high salinity.

Role of phenotypic plasticity and population differentiation in adaptation to novel environmental conditions.

Species can adapt to new environmental conditions either through individual phenotypic plasticity, intraspecific genetic differentiation in adaptive traits, or both. Wild emmer wheat, Triticum dicoccoides, an annual grass with major distribution in Eastern Mediterranean region, is predicted to experience in the near future, as a result of global climate change, conditions more arid than in any part of the current species distribution. To understand the role of the above two means of adaptation, and the effect of population range position, we analyzed reaction norms, extent of plasticity, and phenotypic selection across two experimental environments of high and low water availability in two core and two peripheral populations of this species. We studied 12 quantitative traits, but focused primarily on the onset of reproduction and maternal investment, which are traits that are closely related to fitness and presumably involved in local adaptation in the studied species. We hypothesized that the population showing superior performance under novel environmental conditions will either be genetically differentiated in quantitative traits or exhibit higher phenotypic plasticity than the less successful populations. We found the core population K to be the most plastic in all three trait categories (phenology, reproductive traits, and fitness) and most successful among populations studied, in both experimental environments; at the same time, the core K population was clearly genetically differentiated from the two edge populations. Our results suggest that (1) two means of successful adaptation to new environmental conditions, phenotypic plasticity and adaptive genetic differentiation, are not mutually exclusive ways of achieving high adaptive ability; and (2) colonists from some core populations can be more successful in establishing beyond the current species range than colonists from the range extreme periphery with conditions seemingly closest to those in the new environment.

Multi-approaches analysis reveals local adaptation in the emmer wheat (Triticum dicoccoides) at macro- but not micro-geographical scale.

Detecting local adaptation and its spatial scale is one of the most important questions of evolutionary biology. However, recognition of the effect of local selection can be challenging when there is considerable environmental variation across the distance at the whole species range. We analyzed patterns of local adaptation in emmer wheat, Triticum dicoccoides, at two spatial scales, small (inter-population distance less than one km) and large (inter-population distance more than 50 km) using several approaches. Plants originating from four distinct habitats at two geographic scales (cold edge, arid edge and two topographically dissimilar core locations) were reciprocally transplanted and their success over time was measured as 1) lifetime fitness in a year of planting, and 2) population growth four years after planting. In addition, we analyzed molecular (SSR) and quantitative trait variation and calculated the QST/FST ratio. No home advantage was detected at the small spatial scale. At the large spatial scale, home advantage was detected for the core population and the cold edge population in the year of introduction via measuring life-time plant performance. However, superior performance of the arid edge population in its own environment was evident only after several generations via measuring experimental population growth rate through genotyping with SSRs allowing counting the number of plants and seeds per introduced genotype per site. These results highlight the importance of multi-generation surveys of population growth rate in local adaptation testing. Despite predominant self-fertilization of T. dicoccoides and the associated high degree of structuring of genetic variation, the results of the QST - FST comparison were in general agreement with the pattern of local adaptation at the two spatial scales detected by reciprocal transplanting.