Annals of botany最新文献

The importance of conserving plant genetic diversity has been recognised since the 1980's, but genetic research tools for improving conservation remain largely absent from standard planning. Using an Australian case study framework of the New South Wales Government's Saving our Species program, we outline the costs and benefits associated with conducting genomic analysis within a conservation strategy to inform for example, taxonomic resolution, targeted monitoring, translocations and ex situ collections. Despite a reported sentiment that costs are prohibitive, our study identified that where genetics reports have been provided (32 to date), the cost of genetic sampling, analysis and advice is less than 10% of the total Government investment (SoS program) and will continue decreasing proportionally throughout the years as other management occurs. We identified the largest Government investment was for maintenance and monitoring actions. On-ground practitioner feedback from the reports identified that the main reason for requesting genetics was to inform translocation or ex situ collection. However, from the total of two hundred and sixty-nine plant species with translocation or ex situ conservation actions planned, 75.4% still do not have provisions for genomics, suggesting that knowledge of the utility of this practice is low among practitioners. Responsive feedback also demonstrated that 90% of respondents seek additional learning, thus there is merit in providing future genomics focused workshops.

Background and aims: The cosmopolitan Botrychium lunaria group belong to the most species rich genus of the family Ophioglossaceae and was considered to consist of two species until molecular studies in North America and northern Europe led to the recognition of multiple new taxa. Recently, additional genetic lineages were found scattered in Europe, emphasizing our poor understanding of the global diversity of the B. lunaria group, while the processes involved in the diversification of the group remain unexplored.

Methods: We conducted the first global phylogenetic study of the group including 533 ingroup accessions sequenced for four plastid loci. We compared results of Bayesian and Maximum Likelihood based methods. We used the phylogenetic relationship we recovered to estimate the timing of divergence with BEAST. We explored ecological segregation between species with climatic variables (CHELSA database) and soil pH measurements. The ploidy level and genome size were estimated with flow cytometry.

Key results: We recovered nine well-supported clades, although relationships between clades were inconsistent between Bayesian and Maximum Likelihood analyses. We treated each clade at the species level, except for one clade including two ploidy levels and one including two recognized diploid species one of which appeared as subclade (B. nordicum) of the other (B. lunaria), resulting in the recognition of 11 species, 4 of which are unnamed. In contrast to previous studies, we found species diversity to be equally distributed across the northern hemisphere, with 6-8 species per continent. We estimated the stem age of the B. lunaria group at 2.5-5.3 million years, with most species 1.5-2.6 million years old, and subclades 0.2-1.0 million years old. Diversification thus coincided with Pleistocene climatic fluctuations that strongly affected the areas inhabited by the group, suggesting that diversification was driven by climatically induced cycles of extinction, dispersal, and migration. Furthermore, ecological differentiation between species suggests these complex population dynamics were associated with adaptations to specific environmental conditions. We found limited evidence that speciation is driven by polyploidization and hybridization.

Conclusions: The B. lunaria group radiation was most likely driven by the Pleistocene climatic shifts. For the first time, we show that ecological drivers may have played a role in the diversification of this group, rather than polyploidization. Furthermore, the B. lunaria group has greater species level diversity than previously assumed and we suspect that further cryptic species may await discovery, especially in the B. neolunaria clade.

Background and aims: Quantifying niche similarity among closely related species offers myriad insights into evolutionary history and ecology. In this study, our aim was to explore the interplay of geographic and niche space for rare, endemic plant species and determine if endemic habitats were environmentally similar or unique.

Methods: We characterized the niche of all Leavenworthia species, a genus of rare plants endemic to rocky glades in the eastern United States, using WorldClim data, surface geology, elevation, and slope. We calculated the area of range overlap and estimated niche similarity between species in their total occupied niche space and the subset of niche space shared by both species. We used Linear Discriminant Analyses to determine which niche dimensions differed the most between species. We used niche dimensions with consistently high discriminatory power to perform a Random Forest classification analysis and Principal Component Analysis. Using a linear model, we related geographic distance to distance in niche space.

Key results: Most species comparisons concluded that species' niches had diverged, with niche similarity increasing linearly with range overlap. Temperature variation, precipitation amount and seasonality, and surface geology were the most divergent niche dimensions among all species comparisons. Geographic distance explained 42% of the variation in niche space distance. Sites that were closer in niche space than expected were oriented east-west due to the strong correlation between latitude and PC1 scores.

Conclusions: Despite being endemic to seemingly very similar habitat, niche similarity is low among Leavenworthia species. Low niche similarity, combined with low geographic overlap suggests that this lineage of rare plants potentially diversified in isolation but across a very small geographic area. The correlation between geographic space and niche space has received considerable attention, but our results suggest that geographic distance is a weak predictor of distance in niche space.

Background and aims: Urbanization-induced environmental changes affect the geographical distribution of natural plant species. This study focused on how polyploidization, a dynamic genome change, influences the survival and distribution of Commelina communis (Cc) and its subspecies C. communis f. ciliata (Ccfc), which have variable chromosome numbers (e.g. Cc, 2n = 88 for Cc; Ccfc, 2n = 46 for Ccfc). The aim was to investigate polyploidization effects on natural plant distribution in urban environments.

Methods: The geographical distribution across urban-rural gradients was investigated at a total of 218 sites in Japan. Stomata size and density were measured and compared between Cc and Ccfc. Flow cytometry determined genome size and polyploidy. Chromosome karyotyping was performed using the genomic in situ hybridization (GISH) method.

Key results: Urban areas were exclusively dominated by Cc, while Cc and Ccfc coexisted in rural areas. Cc had larger and fewer stomata and a genome size more than twice that of Ccfc. GISH results indicated that Cc possesses Ccfc and another unknown genome, suggesting allopolyploidy.

Conclusions: Our results show that the ploidy difference affects the geographical distribution, stomata traits and genome size between two distinct taxa in the genus Commelina, C. communis as a neo-tetraploid and C. communis f. ciliata, the diploid. Cc is an allopolyploid and is therefore not only polyploidy but also has an additional genome that provides new sets of genes and alleles, contributing to Cc having enhanced survival potentials in urban environments compared with Ccfc. This is the first investigation to clarify the distribution difference related to urban environments, the difference in stomata traits and genome size, and to study chromosome composition in Commelina species.

Background and aims: Previous phylogenetic studies on the pharmaceutically significant genus Paris (Melanthiaceae) have consistently revealed substantial cytonuclear discordance, yet the underlying mechanism responsible for this phenomenon remains elusive. This study aims to reconstruct a robust nuclear backbone phylogeny and elucidate the potential evolutionarily complex events contributing to previously observed cytonuclear discordance within Paris.

Methods: Based on a comprehensive set of nuclear low-copy orthologous genes obtained from transcriptomic data, the intrageneric phylogeny of Paris, along with its phylogenetic relationships to allied genera, were inferred using coalescent and concatenated approaches. The analysis of gene tree discordance and reticulate evolution, in conjunction with an incomplete lineage sorting (ILS) simulation, was conducted to explore potential hybridization and ILS events in the evolutionary history of Paris and assess their contribution to the discordance of gene trees.

Key results: The nuclear phylogeny unequivocally confirmed the monophyly of Paris and its sister relationship with Trillium, while widespread incongruences in gene trees were observed at the majority of internal nodes within Paris. The reticulate evolution analysis identified five instances of hybridization events in Paris, indicating that hybridization events might have occurred recurrently throughout the evolutionary history of Paris. In contrast, the ILS simulations revealed that only two internal nodes within section Euthyra experienced ILS events.

Conclusions: Our data suggest that the previously observed cytonuclear discordance in the phylogeny of Paris can primarily be attributed to recurrent hybridization events, with secondary contributions from infrequent ILS events. The recurrent hybridization events in the evolutionary history of Paris not only drove lineage diversification and speciation but also facilitated morphological innovation, and enhanced ecological adaptability. Therefore, artificial hybridization has great potential for breeding medicinal Paris species. These findings significantly contribute to our comprehensive understanding of the evolutionary complexity of this pharmaceutically significant plant lineage, thereby facilitating effective exploitation and conservation efforts.

Background and aims: Plant-fungus symbioses may experience temporal turnover during the ontogenetic or phenological development of the host, which can influence the ecological requirements of the host plant. In this study, we investigate temporal turnover of Ceratobasidiaceae orchid mycorrhizal fungal (OMF) communities in Prasophyllum (Orchidaceae), asking whether OMF communities are subject to temporal change attributable to orchid phenology or ontogeny.

Methods: Roots of adult Prasophyllum frenchii, Prasophyllum lindleyanum and Prasophyllum sp. aff. validum from Australia were sampled between autumn and spring. Seed was sown in situ as 'baits' to explore the mycorrhizal associations of germinating protocorms, which were compared with OMF in roots of co-occurring adult plants. Culture-dependent and -independent sequencing methods were used to amplify the internal transcribed spacer and mitochondrial large subunit loci, with sequences assigned to operational taxonomic units (OTUs) in phylogenetic analyses. Germination trials were used to determine whether fungal OTUs were mycorrhizal.

Key results: A persistent core of OMF was associated with Prasophyllum, with Ceratobasidiaceae OMF dominant in all three species. Phenological turnover occurred in P. lindleyanum and P. sp. aff. validum, but not in P. frenchii, which displayed specificity to a single OTU. Ontogenetic turnover occurred in all species. However, phenological and ontogenetic turnover was typically driven by the presence or absence of infrequently detected OTUs in populations that otherwise displayed specificity to one or two dominant OTUs. Ex situ germination trials showed that 13 of 14 tested OTUs supported seed germination in their host orchid, including eight OTUs that were not found in protocorms in situ.

Conclusions: An understanding of OMF turnover can have practical importance for the conservation of threatened orchids and their mycorrhizal partners. However, frameworks for classifying OMF turnover should focus on OTUs important to the life cycle of the host plant, which we suggest are likely to be those that are frequently detected or functionally significant.

Background and aims: Understanding the biogeographical patterns and processes underlying the distribution of diversity within the Northern Hemisphere has fascinated botanists and biogeographers for over a century. However, as a well-known centre of species diversity in the Northern Hemisphere, whether East Asia acted as a source and/or a sink of plant diversity of the Northern Hemisphere remains unclear. Here, we used Thalictroideae, a subfamily widely distributed in the Northern Hemisphere with the majority of species in East Asia, to investigate the role of East Asia in shaping the biogeographical patterns of the Northern Hemisphere and to test whether East Asia acted as a museum or a cradle for herbaceous taxa.

Methods: Based on six plastid and one nuclear DNA regions, we generated the most comprehensive phylogeny for Thalictroideae, including 217 taxa (~66 % species) from all ten of the currently recognized genera. Within this phylogenetic framework, we then estimated divergence times, ancestral ranges and diversification rates.

Key results: The monophyletic Thalictroideae contains three major clades. All genera with more than one species are strongly supported as monophyletic except for Isopyrum, which is nested in Enemion. The most recent common ancestor of Thalictroideae occurred in East Asia in the late Eocene (~36 Mya). From the Miocene onwards, ≥46 dispersal events were inferred to be responsible for the current distribution of this subfamily. East Asian Thalictroideae lineages experienced a rapid accumulation at ~10 Mya.

Conclusions: The biogeographical patterns of Thalictroideae support the 'out of and in East Asia' hypothesis, i.e. East Asia is both a source and a sink of biodiversity of the Northern Hemisphere. The global cooling after the middle Miocene Climatic Optimum, combined with the exposed land bridges owing to sea-level decline, might jointly have caused the bidirectional plant exchanges between East Asia and other Northern Hemisphere regions. East Asia serves as evolutionary museums and cradles for the diversity of Thalictroideae and probably for other herbaceous lineages.

Background and aims: Durum wheat, Triticum turgidum, and bread wheat, Triticum aestivum, are two allopolyploid species of very recent origin that have been subjected to intense selection programmes during the thousands of years they have been cultivated. In this paper, we study the durum wheat satellitome and establish a comparative analysis with the previously published bread wheat satellitome.

Methods: We revealed the durum wheat satellitome using the satMiner protocol, which is based on consecutive rounds of clustering of Illumina reads by RepeatExplorer2, and we estimated abundance and variation for each identified satellite DNA (satDNA) with RepeatMasker v4.0.5. We also performed a deep satDNA family characterization including chromosomal location by fluorescence in situ hybridization (FISH) in durum wheat and its comparison with FISH patterns in bread wheat. BLAST was used for trailing each satDNA in the assembly of durum wheat genome through NCBI's Genome Data Viewer and the genome assemblies of both species were compared. Sequence divergence and consensus turnover rate between homologous satDNA families of durum and bread wheat were estimated using MEGA11.

Key results: This study reveals that in an exceedingly short period, significant qualitative and quantitative changes have occurred in the set of satDNAs of both species, with expansions/contractions of the number of repeats and the loci per satellite, different in each species, and a high rate of sequence change for most of these satellites, in addition to the emergence/loss of satDNAs not shared between the two species analysed. These evolutionary changes in satDNA are common between species but what is truly remarkable and novel is that these processes have taken place in less than the last ~8000 years separating the two species, indicating an accelerated evolution of their satDNAs.

Conclusions: These results, together with the relationship of many of these satellites with transposable elements and the polymorphisms they generate at the level of centromeres and subtelomeric regions of their chromosomes, are analysed and discussed in the context of the evolutionary origin of these species and the selection pressure exerted by humans throughout the history of their cultivation.

Background and aims: Mixed forest plantations are increasingly recognized for their role in mitigating the impacts of climate change and enhancing ecosystem resilience. Yet, there remains a significant gap in understanding the early-stage dynamics of species trait diversity and interspecies interactions, particularly in pure deciduous mixtures. This study aims to explore the timing and mechanisms by which trait diversity of deciduous species and competitive interactions influence yield, carbon allocation and space occupation in mixed forests, both above and below ground.

Methods: A forest inventory was conducted in planted monocultures, two-species and four-species mixtures of European Acer, Tilia, Carpinus and Quercus, representing a spectrum from acquisitive to conservative tree species. Effects of competition were assessed with linear mixed-effects models at the level of biomass and space acquisition, including leaf, canopy, stem and fine root traits.

Key results: Early above-ground growth effects were observed 6 years post-planting, with significant biomass accumulation after 8 years, strongly influenced by species composition. Mixtures, especially with acquisitive species, exhibited above-ground overyielding, 1.5-1.9 times higher than monocultures. Fine roots showed substantial overyielding in high-diversity stands. Biomass allocation was species specific and varied markedly by tree size and the level of diversity and between acquisitive Acer and the more conservative species. No root segregation was found.

Conclusions: Our findings underscore the crucial role of species trait diversity in enhancing productivity in mixed deciduous forest plantations. Allometric changes highlight the need to differentiate between (active) acclimatizations and (passive) tree size-related changes, but illustrate major consequences of competitive interactions for the functional relationship between leaves, stem and roots. This study points towards the significant contributions of both above- and below-ground components to overall productivity of planted mixed-species forests.