New Phytologist最新文献

Phylogenies of long-lived plants often exhibit short molecular branch lengths and high levels of gene-tree conflict. However, the biological mechanisms underlying these patterns remain unclear. We examine this with simulations and through empirical examination of several large seed plant clades. We used an agent-based simulation model varying lifespan, degree of overlapping generations, and somatic mutation. We also compared simulated outcomes to phylogenomic patterns in several datasets of seed plants that include life-history shifts. Lifespan and overlapping generations together can generate both short branches and elevated gene-tree conflict. Somatic mutation can amplify these effects, although available evidence suggests mutation rates are often too low to drive major phylogenetic consequences. Variation across simulation parameterizations can mirror the diversity of phylogenomic patterns observed among lineages with differing life histories. Lifespan and generation overlap are potentially major contributors to characteristic phylogenetic signatures in long-lived plants. Consequently, life history should be considered when interpreting evolutionary patterns, substitution rates, and among-lineage heterogeneity in long-lived plant lineages.

Plasmids contribute to the efficient adaptation of bacteria to specific niches in nature. The gram-positive bacterium Clavibacter michiganensis carries two plasmid-borne important virulence genes, celA and pat-1, necessary for wilting in tomato. The 88 C. michiganensis field isolates collected between 2011 and 2020 were examined for phenotypic variation, including virulence in host plants. Four isolates lacking plasmids with celA, pat-1, or both failed to cause wilting, and nine isolates, including these four, failed to cause wilting in Nicotiana benthamiana. Whole genome analyses revealed 11 distinct plasmid types, including 9 newly identified, and 10 bacterial groups with different plasmid compositions, despite having almost identical chromosomes. Comparative genomic analyses revealed significant genetic diversity among the plasmids, while three plasmids containing the genomic island (GI) α with celA or GIβ with pat-1 and three newly identified plasmids carrying both islands shared large blocks of synteny. In addition, GIα is closely associated with mobile genetic elements, suggesting the genetic rearrangement or transfer at this locus. These results suggest that C. michiganensis harbors a wide variety of virulence and nonvirulence plasmids, and that there is genetic rearrangement among plasmids in GI regions, determining bacterial virulence in plants.

High-throughput molecular studies of museum specimens (museomics) have great potential in biodiversity research, but fungal historical collections have scarcely been examined, leading to no comprehensive methodological assessments. Here we present a whole genome sequencing (WGS) project conducted at the Fungarium of the Royal Botanic Gardens, Kew. DNA was extracted from 2104 specimens collected between 1770 and 2023, and we found that the specimen age had the smallest effect, while DNA purification and taxonomic identity had the greatest effect on DNA yield. We barcoded 771 specimens, and WGS was conducted on a subset of 394 specimens that were empirically selected for in-depth analysis. We developed an automated assembly pipeline, integrating 16 different approaches. Starting from 220 libraries (excluding lichenised specimens), we produced 3143 assemblies using these approaches and found that there is no universal assembly method that can provide good-quality genomes for all; rather, different approaches should be used depending on the library size and the specimen's age. Producing high-quality genomes from specimens over 100 yr old is possible by using customised DNA extraction protocols and applying a multimethod bioinformatic approach. Whole genomes from historical collections will enrich genomics resources, accelerating biodiversity and evolutionary research, amongst others.

Phenological response to global climate change can impact ecosystem functions. There are various data sources from which spatiotemporal and taxonomic phenological data may be obtained: mobilized herbaria, community science initiatives, observatory networks, and remote sensing. However, analyses conducted to date have generally relied on single sources of these data. Siloed treatment of data in analyses may be due to the lack of harmonization across different data sources that offer partially nonoverlapping information and are often complementary. Such treatment precludes a deeper understanding of phenological responses at varying macroecological scales. Here, we describe a detailed vision for the harmonization of phenological data, including the direct integration of disparate sources of phenological data using a common schema. Specifically, we highlight existing methods for data harmonization that can be applied to phenological data: data design patterns, metadata standards, and ontologies. We describe how harmonized data from multiple sources can be integrated into analyses using existing methods and discuss the use of automated extraction techniques. Data harmonization is not a new concept in ecology, but the harmonization of phenological data is overdue. We aim to highlight the need for better data harmonization, providing a roadmap for how harmonized phenological data may fill gaps while simultaneously being integrated into analyses.

Epiphytes and their associated biota are increasingly recognized as contributing to biodiversity and to filling critical ecosystem functions in world forests. However, the attributes that have made them successful in canopy environments also make them vulnerable to natural and human-induced disturbances. Drawing upon ecological frameworks to understand disturbance, I categorized and synthesized the drivers and the consequences of disturbances on epiphytic materials. Across all impacts, disturbance agents were significantly more likely to lead to negative, rather than positive, effects in both tropical and temperate locales. Significantly more studies reported negative effects on abundance, diversity, community composition and connectivity, but some studies showed that disturbances enhanced these attributes. Although particular disturbance agents did not differently influence individual consequences, they explained a significant portion of variation in aggregated totals. Surprisingly, relative to human disturbances, natural disturbances were more likely to lead to negative effects. Many studies provided recommendations for effective societal responses to mitigate negative impacts, such as retaining large, old trees in forestry operations, patch-clearing for epiphyte harvest, maximizing forest fragment size, using epiphytes as bioindicators of disturbance, and applying principles of community forestry to land management. Future actions should also include communication of these results to policymakers and land managers.

The formation of inflorescences and flowers is essential for the successful reproduction of angiosperms. In the past few decades, genetic studies have identified the LEAFY transcription factor and the UNUSUAL FLORAL ORGANS (UFO) F-box protein as two major regulators of flower development in a broad range of angiosperm species. Recent research has revealed that UFO acts as a transcriptional cofactor, redirecting the LEAFY floral regulator to novel cis-elements. In this review, we summarize the various roles of UFO across species, analyze past results in light of new discoveries and highlight the key questions that remain to be solved.