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Diospyros L. is a large genus of flowering plants predominantly distributed in the tropics. It comprises over 700 species globally and around 300 are believed to occur in South-East Asia. Many species are economically important and exploited for the production of ebony wood and persimmons, yet taxonomic information on the genus is incomplete and inconsistent due to its morphological and nomenclatural complexity. Revisions of Diospyros in continental and insular South-East Asia were conducted independently by different authors, occasionally with different names used for the same species, or different species being given the same name in different countries. During our ongoing study of the genus Diospyros in Indochina (Cambodia, Laos, Thailand and Vietnam), we identified several such instances. Here, we clarify the most commonly misidentified species, including 1) D. apiculata Hiern, D. strigosa Hemsl. and D. tamiriensis Lecomte; 2) D. bejaudii Lecomte and D. retrofracta Bakh.; 3) D. dictyoneura Hiern and D. hasseltii Zoll.; 4) D. borneensis Hiern and D. fecunda H.R.Fletcher. Lectotypifications are also made for D. brachiata King & Gamble var. lanceolata H.R.Fletcher, D. fecunda, D. similis Craib and D. strigosa.
Abstract
Natural plant populations often harbour substantial heritable variation in DNA methylation. However, a thorough understanding of the genetic and environmental drivers of this epigenetic variation requires large-scale and high-resolution data, which currently exist only for a few model species. Here, we studied 207 lines of the annual weed Thlaspi arvense (field pennycress), collected across a large latitudinal gradient in Europe and propagated in a common environment. By screening for variation in DNA sequence and DNA methylation using whole-genome (bisulfite) sequencing, we found significant epigenetic population structure across Europe. Average levels of DNA methylation were strongly context-dependent, with highest DNA methylation in CG context, particularly in transposable elements and in intergenic regions. Residual DNA methylation variation within all contexts was associated with genetic variants, which often co-localized with annotated methylation machinery genes but also with new candidates. Variation in DNA methylation was also significantly associated with climate of origin, with methylation levels being lower in colder regions and in more variable climates. Finally, we used variance decomposition to assess genetic versus environmental associations with differentially methylated regions (DMRs). We found that while genetic variation was generally the strongest predictor of DMRs, the strength of environmental associations increased from CG to CHG and CHH, with climate-of-origin as the strongest predictor in about one third of the CHH DMRs. In summary, our data show that natural epigenetic variation in Thlaspi arvense is significantly associated with both DNA sequence and environment of origin, and that the relative importance of the two factors strongly depends on the sequence context of DNA methylation. T. arvense is an emerging biofuel and winter cover crop; our results may hence be relevant for breeding efforts and agricultural practices in the context of rapidly changing environmental conditions.
Author summary
Variation within species is an important level of biodiversity, and it is key for future adaptation. Besides variation in DNA sequence, plants also harbour heritable variation in DNA methylation, and we want to understand the evolutionary significance of this epigenetic variation, in particular how much of it is under genetic control, and how much is associated with the environment. We addressed these questions in a high-resolution molecular analysis of 207 lines of the common plant field pennycress (Thlaspi arvense), which we collected across Europe, propagated under standardized conditions, and sequenced for their genetic and epigenetic variation. We found large geographic variation in DNA methylation, associated with both DNA sequence and climate of origin. Genetic variation was generally the stronger predictor of DNA methylation variation, but the strength of environmental association varied between different sequence contexts. Climate-of-origin was the strongest predictor in about one third of the differentially methylated regions in the CHH context, which suggests that epigenetic variation may play a role in the short-term climate adaptation of pennycress. As pennycress is currently being domesticated as a new biofuel and winter cover crop, our results may be relevant also for agriculture, particularly in changing environments.
Tilletia caries and T. laevis, which are the causal agents of common bunt, as well as T. controversa, which causes dwarf bunt of wheat, threaten especially organic wheat farming. The three closely related fungal species differ in their teliospore morphology and partially in their physiology and infection biology. The gene content as well as intraspecies variation in these species and the genetic basis of their separation is unknown. We sequenced the genome of four T. caries, five T. controversa, and two T. laevis and extended this dataset with five publicly available ones. The genomes of the three species displayed microsynteny with up to 94.3% pairwise aligned regions excluding repetitive regions. The majority of functionally characterized genes involved in pathogenicity, life cycle, and infection of corn smut, Ustilago maydis, were found to be absent or poorly conserved in the draft genomes and the biosynthetic pathway for trimethylamine in Tilletia spp. could be different from bacteria. Overall, 75% of the identified protein-coding genes comprising 84% of the total predicted carbohydrate utilizing enzymes, 72.5% putatively secreted proteins, and 47.4% of effector-like proteins were conserved and shared across all 16 isolates. We predicted nine highly identical secondary metabolite biosynthesis gene clusters comprising in total 62 genes in all species and none were species-specific. Less than 0.1% of the protein-coding genes were species-specific and their function remained mostly unknown. Tilletia controversa had the highest intraspecies genetic variation, followed by T. caries and the lowest in T. laevis. Although the genomes of the three species are very similar, employing 241 single copy genes T. controversa was phylogenetically distinct from T. caries and T. laevis, however these two could not be resolved as individual monophyletic groups. This was in line with the genome-wide number of single nucleotide polymorphisms and small insertions and deletions. Despite the conspicuously different teliospore ornamentation of T. caries and T. laevis, a high degree of genomic identity and scarcity of species-specific genes indicate that the two species could be conspecific.
Due to massive energetic investments in woody support structures, trees are subject to unique physiological, mechanical, and ecological pressures not experienced by herbaceous plants. Despite a wealth of studies exploring trait relationships across the entire plant kingdom, the dominant traits underpinning these unique aspects of tree form and function remain unclear. Here, by considering 18 functional traits, encompassing leaf, seed, bark, wood, crown, and root characteristics, we quantify the multidimensional relationships in tree trait expression. We find that nearly half of trait variation is captured by two axes: one reflecting leaf economics, the other reflecting tree size and competition for light. Yet these orthogonal axes reveal strong environmental convergence, exhibiting correlated responses to temperature, moisture, and elevation. By subsequently exploring multidimensional trait relationships, we show that the full dimensionality of trait space is captured by eight distinct clusters, each reflecting a unique aspect of tree form and function. Collectively, this work identifies a core set of traits needed to quantify global patterns in functional biodiversity, and it contributes to our fundamental understanding of the functioning of forests worldwide.
The lianescent genus Tinospora Miers in Singapore is revised. Four species are recognised, two of which are newly described. Tinospora krispura I.M.Turner sp. nov. is known from Christmas Island and Singapore. Tinospora singapura I.M.Turner sp. nov. is known only from Singapore. Two new lectotypifications are included, one at the second step.
Around 400 BC, pottery- and iron-producing populations immigrated into the Inner Congo Basin (ICB) and subsequently spread upstream some major tributaries of the Congo River. Until recently, their subsistence was almost completely unknown. We present an archaeobotanical study of three sites in the ICB covering parts of the Early Iron Age (ca. 400 BC-AD 650) and of the Late Iron Age (LIA) as well as subrecent times (ca. AD 1300–2000). We studied 82 flotated samples of botanical macroremains, and 68 soil phytolith samples, recovered from the terra firme sites Iyonda and Mbandaka, and the floodplain fishing camp site of Bolondo. The EIA assemblage from Iyonda yielded domesticated Cenchrus americanus (pearl millet), Vigna unguiculata (cowpea), Canarium schweinfurthii, Elaeis guineensis (oil palm), several wild plants, and parenchyma fragments tentatively attributed to Dioscorea sp. (yams). The exploitation of these plants originated in the savannas and forest-savanna ecotones of West Africa. The presence of C. americanus in LIA contexts at Bolondo and Mbandaka, dated to ca. AD 1350–1550, indicates that its cultivation is not dependent on a seasonal climate with a distinct dry season, contrary to previous views. The role of C. americanus as a staple is difficult to assess; it might have been used for special purposes, e.g. beer brewing. In spite of extensive screening, we did not detect any banana phytoliths in the EIA samples. Musa phytoliths were only present in LIA contexts after ca. AD 1400, leaving room for the possibility that the introduction and spread of Musa spp. AAB ‘Plantain’ in the ICB was a late phenomenon.
A comprehensive checklist of Habenaria from Chapada dos Veadeiros, State of Goiás, was performed alongside morphologic and molecular phylogenetic studies, revealing three new taxa endemic to this region. A total of 61 taxa (59 species and two varieties) of Habenaria are recorded for Chapada dos Veadeiros, representing a two-fold increase compared to previous lists and comprising one of the greatest diversities of the genus in Brazil. Of this total, four taxa are locally endemic. Habenaria cultellifolia, until recently known only from the type collection, was rediscovered in the region after 127 years without records and represents this species’ only known extant population. Three proposed new taxa of Habenaria (H. minuticalcar J.A.N. Bat. & Bianch. sp. nov., H. proiteana J.A.N. Bat., A.A. Vale & Bianch. sp. nov., and H. lavrensis var. xanthodactyla J.A.N. Bat. & Bianch. var. nov.) are corroborated by molecular phylogenetic analyses based on nuclear and plastid markers. They are described, illustrated, tentatively assessed as threatened, and compared to phylogenetically and morphologically related species. Since some areas of this mountain range have not yet been floristically sampled, additional taxonomic novelties and new records are still expected in the future.
Questions: Both species turnover and intraspecific trait variation can affect plant assemblage dynamics along environmental gradients. Here, we asked how community assemblage patterns in relation to species turnover and intraspecific variation differ between endemic and non-endemic species. We hypothesized that endemic species show lower intraspecific variation than non-endemic species because they tend to have high rates of in situ speciation, whereas non-endemic species are expected to have a larger gene pool and higher phenotypic plasticity.
Location: La Palma, Canary Islands.
Methods: We established 44 sampling sites along a directional gradient of precipitation, heat load, soil nitrogen, phosphorus and pH. Along this gradient, we estimated species abundances and measured three traits (plant height, leaf area and leaf thickness) on perennial endemic and non-endemic plant species. In total, we recorded traits for 1,223 plant individuals of 43 species. Subsequently, we calculated community-weighted mean traits to measure the relative contribution of species turnover, intraspecific variation and their covariation along the analysed gradient.
Results: The contribution of intraspecific variation to total variation was similar in endemic and non-endemic assemblages. For plant height, intraspecific variation explained roughly as much variation as species turnover. For leaf area and leaf thickness, intraspecific variation explained almost no variation. Species turnover effects mainly drove trait responses along the environmental gradient, but intraspecific variation was important for responses in leaf area to precipitation.
Conclusions: Despite their distinct evolutionary history, endemic and non-endemic plant assemblages show similar patterns in species turnover and intraspecific variation. Our results indicate that species turnover is the main component of trait variation in the underlying study system. However, intraspecific variation can increase individual species’ fitness in response to precipitation. Overall, our study challenges the theory that intraspecific trait variation is more important for the establishment of non-endemic species compared with endemic species.
Differential derepression of the genome of potato tuber cells can be initiated by slicing the tissue into disks. The consequence of this procedure on the cells of the wound surface is dedifferentiation and cell division followed by redifferentiation to a suberized phellem cell. The drift of glucose-, glucose-1-phosphate-, glucose-6-phosphate-, fructose-6-phosphate- and 6-phospho-gluconatelevels has been determined in the derepressed tissue. With the exception of 6-phospho-gluconate all intermediates so far investigated showed a rise in concentration after derepression.
This is interpreted as a consequence of altered enzymic activities which were estimated for phosphoglucomutase, hexokinase, phosphoglucoisomerase, gluco-6-phosphate- and 6-phosphogluconatedehydrogenase. The two dehydrogenases were activated after derepression, the activation represented a de-novo-synthesis, as was demonstrated with the inhibitors Actidione (translation) and p-Fluorophenyl-alanine (protein synthesis in general). Hexokinase and phosphoglucoisomerase were not severely affected by cutting the tissue. Phosphoglucomutase was degrated rapidly, the degradation being dependent on protein synthesis. The importance of an enhanced activity of the pentose phosphate shunt for the stressed cell is emphasized and the possibility of an alteration in the osmotic pressure within the cell and especially in the nucleus — a primary consequence of wounding — as a cause of derepression in potato tuber cells is discussed.
Positive plant–plant interactions are thought to drive vegetation patterns in harsh environments, such as semi-arid areas. According to the stress-gradient hypothesis (SGH), the role of positive interactions between species (facilitation) is expected to increase with harshness, predicting associated variation in species composition along environmental gradients. However, the relation between stress and facilitation along environmental gradients is debated. Furthermore, differentiating facilitative interactions from other underlying mechanisms, such as microtopographic heterogeneity, is not trivial. We analysed the spatial co-occurrence relationships of vascular plant species that form patchy vegetation in arid lapilli fields (tephra) from recent volcanic eruptions on La Palma, Canary Islands. Assuming a harshness gradient negatively correlated with elevation because the lower elevations are more arid and water availability is considered the most limiting resource, and that an outcome of facilitation is plants co-occurring in the same patch, from the SGH we expected a greater degree of co-occurrence at lower elevation. We tested this at both the species and the individual plant level. We analysed the species composition of 1277 shrubby vegetation patches at 64 different sampling points, ranging from the coast to around 700 m a.s.l. Patch morphology and microtopographic heterogeneity variables were also measured, to account for their potential effects on the species composition of patches. We used generalized linear models and generalized mixed-effects models to analyse species richness, number of individuals in patches and percentage of patches with positive co-occurrences, and a pairwise co-occurrence analysis combined with a graphical network analysis to reveal positive links between 13 of the species. We found that the percentage of patches with positive co-occurrences increased at higher elevations, in contrast to the predictions of the SGH, but in accordance with a refined stress-gradient hypothesis for arid sites, in which characteristics of the interacting species are incorporated.