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Aim: Spatial analysis of the distribution and density of species is of continuing interest within theoretical and applied ecology. Species distribution models (SDMs) are being increasingly used to analyse count, presence-absence and presence-only data sets. There is a growing literature on dynamic SDMs (which incorporate temporal variation in species distribution), joint SDMs (which simultaneously analyse the correlated distribution of multiple species) and geostatistical models (which account for similarity between nearby sites caused by unobserved covariates). However, no previous study has combined all three attributes within a single framework. Innovation: We develop spatial dynamic factor analysis for use as a 'joint, dynamic SDM' (JDSDM), which uses geostatistical methods to account for spatial similarity when estimating one or more 'factors'. Each factor evolves over time following a density-dependent (Gompertz) process, and the logdensity of each species is approximated as a linear combination of different factors. We demonstrate a JDSDM using two multispecies case studies (an annual survey of bottom-associated species in the Bering Sea and a seasonal survey of butterfly density in the continental USA), and also provide our code publicly as an R package. Main conclusions: Case study applications show that that JDSDMs can be used for species ordination, i.e. showing that dynamics for butterfly species within the same genus are significantly more correlated than for species from different genera. We also demonstrate how JDSDMs can rapidly identify dominant patterns in community dynamics, including the decline and recovery of several Bering Sea fishes since 2008, and the 'flight curves' typical of early or late-emerging butterflies. We conclude by suggesting future research that could incorporate phylogenetic relatedness or functional similarity, and propose that our approach could be used to monitor community dynamics at large spatial and temporal scales.

The spatial patterns resulting from large fires include refugial habitats that support surviving legacies and promote ecosystem recovery. To better understand the diverse ecological functions of refugia on burn mosaics, we used remotely sensed data to quantify neighborhood patterns of areas relatively unchanged following the 2011 Las Conchas fire. Spatial patterns of refugia measured within 10-ha moving windows varied across a gradient from areas of high density, clustered in space, to sparsely populated neighborhoods that occurred in the background matrix. The scaling of these patterns was related to the underlying structure of topography measured by slope, aspect and potential soil wetness, and spatially varying climate. Using a nonmetric multidimensional scaling analysis of species cover data collected post-Las Conchas, we found that trees and forest associates were present across the refugial gradient, but communities also exhibited a range of species compositions and potential functions. Spatial patterns of refugia quantified for three previous burns (La Mesa 1977, Dome 1996, Cerro Grande 2000) were dynamic between fire events, but most refugia persisted through at least two fires. Efforts to maintain burn heterogeneity and its ecological functions can begin with identifying where refugia are likely to occur, using terrain-based microclimate models, burn severity models and available field data.

Protected areas are expected to harbour fewer invasive plants due to the absence of anthropogenic disturbance and greater resistance of natural vegetation to invasion. Our study aimed to quantify the impacts of selected invasive plants on native plant species richness, diversity, and composition in five protected areas of Nepal spread across ~ 3403 km 2 at the Himalayan foothill. Lantana camara , Mikania micrantha, and Parthenium hysterophorus were selected as target species based on their abundance in the study area. For each species, 30 pairs of invaded and uninvaded plots of 10 × 10 m were sampled to record the presence and covers of all vascular plants. The impacts of invaders on species diversity were analyzed using linear mixed-effect models, those on plant community composition by direct gradient ordination. The analysis of merged data, including all studied invaders, showed that the invasions reduced native species richness and diversity, which decreased to less than half of the values recorded in uninvaded plots. Similarly, each of the three species had a significant negative impact on native species richness and diversity when tested separately, with M. micrantha having the greatest impact, followed by P. hysterophorus and L. camara. In addition, the invasion by L. camara explained the greatest percentage of variation in the species composition of the invasive species studied. The results support the invasion meltdown theory, as the invasion promoted the presence of other alien species in the invaded plots.

The number of naturalizing non-native species continues to increase in the Anthropocene, with numerous species becoming invasive even after prolonged lag phases. A notably overlooked group among invasive trees and shrubs is the Rosaceae family, with Prunus cerasifera emerging as one of the species whose effects on forest ecosystems remain poorly understood despite its wide occurrence across the introduced range. We aimed to evaluate how the invasion of P. cerasifera affects the taxonomical, functional, and phylogenetic diversity of the understory of the early successional stages of oak-hornbeam forests. Using the P. cerasifera invasion gradient, defined as increasing cover of this invasive tree, and implementing the ordination and linear regression methods, we found the prominent effects of P. cerasifera on all three examined metrics of plant species diversity. We revealed that increasing the cover of P. cerasifera not only increased species richness but also altered the phylogenetic structure of the understory by introducing new clades. Additionally, it influenced community assembly processes by reducing the importance of habitat filtering and strengthening the role of interspecific competition in shaping the community structure. Our study presents the first assessment of P. cerasifera ’s impact on understory diversity along its invasion gradient, enabling a comprehensive evaluation of invasion-driven effects on the functioning of forest ecosystems during the early stages of succession. Our findings are not only essential for formulating effective management and conservation strategies but also critical for guiding how invasive tree species can influence the trajectories and mechanisms of the secondary forest succession.

Flowering rush (Butomus umbellatus L.), a perennial plant native to Eurasia, made a widespread appearance in the Upper Mississippi River in the United States in 2020, following extremely high river discharge during the previous year. Flowering rush expanded rapidly and was found at 1–10% of sites (n = 6,630 total sites) across a 400 km river reach within the first 4 years of invasion. Flowering rush invaded at least 12 of 31 wetland vegetation classes, including submersed aquatic, rooted-floating, deep marsh, and shallow marsh. Analysis of long-term macrophyte data and our targeted field study revealed that plant diversity declined with greater abundance of flowering rush over a 4-year early invasion period, suggesting that native species were displaced. Furthermore, species correlation plots showed a significant negative correlation (r < -0.1) between flowering rush and several native species, including wild celery, water stargrass, and wild rice. Non-metric multi-dimensional scaling (NMDS) ordination placed flowering rush near the center of the plot, which may indicate tolerance to a wide range of environmental conditions such as water depth, flow, and substrate. Centering on the NMDS plot also shows that flowering rush invades many types of vegetated aquatic land cover classes, which was also supported by our geographic information systems analysis of land cover invasion. These habitat associations and ecological impacts of the recent, widespread invasion of flowering rush in the Upper Mississippi River can help inform restoration and management actions during early invasion. Continuing long-term data collection can break limitations on modeling cause-effect relationships and provide insights to the future ecological trajectory of the macrophyte community to this non-native invasive species.

Natural coastal dune vegetation has changed drastically worldwide due to the stabilization of dune systems and the expansion of invasive plant species. On Ishikari Beach in Hokkaido, northern Japan, an invasive tall grass, Miscanthus sinensis , has rapidly expanded into the coastal dune grasslands. The purpose of this study was to clarify the temporal changes in the community structure and the responses of major coastal species to M . sinensis invasion. We investigated the species composition and abundance of individual plant species in a 100 m 2 survey plot over 17 years (2000–2017). Miscanthus sinensis increased the abundance by around 2006 and then maintained the highest cover of all species, during which a native dominant coastal dune grass, Leymus mollis , highly decreased. Additionally, other inland grasses expanded their distribution ranges into the communities dominated by M . sinensis . By 2017, the total cover of these invasive species exceeded 70%. Non-metric multidimensional scaling ordination analysis (NMDS) revealed that the coastal dune vegetation has shifted to a homogeneous grassland dominated by non-coastal graminoid species. Light conditions at the ground level were significantly darker in areas dominated by M. sinensis than in areas dominated by L. mollis . However, many coastal species survived, despite a decrease in their abundance. Coastal plants with horizontal rhizomes and creeping stems escaped from the shading stress by invasive grasses owing to their flexible mobility. Although the major species are replaced by non-coastal plants, the species diversity of coastal plants is maintained because of their high mobility in the dune grassland.

Aim In the current Anthropocene, many ecosystems are being simultaneously invaded by multiple alien species. Some of these invasive species become more dominant and have greater environmental impacts than others. If two potentially dominant species invade the same area, the combined impact has been reported to be either (a) domination by one species, that is, the competitive dominance of one invader, or (b) invasion meltdown, where the combined impact is much greater, that is, a synergistic effect. We studied the effects of the invasion of two alien plant species that are known to strongly decrease native plant species diversity: the Persian walnut Juglans regiaand goldenrod Solidago canadensis. Location We examined native vegetation diversity in abandoned fields (in Poland) where neither species had invaded, only one species had invaded, and both species had invaded. Methods Field survey data were analysed using generalized linear mixed models and ordination techniques. Results When goldenrod invaded alone, it caused a larger decrease in species richness and cover (74%) than when walnut invaded alone (58%). When walnut and goldenrod co‐occurred in abandoned fields, walnut was dominant and strongly decreased goldenrod density by 87%. However, the combined impact on native species diversity was much lower (15% decrease in native plant diversity) than when either goldenrod or walnut invaded alone. Main conclusions In contrast to many other studies, our study does not support the occurrence of an invasion meltdown. Instead, our results show that even when one invader dominates, its negative effect on plant diversity can be strongly modified by the presence of another invasive species.

Most studies on the impacts of plant invasions focus on species richness or diversity of invaded communities, but much less attention has been paid to structural changes such as the representation of species with different traits. To bridge this knowledge gap, we assess the impact of dominant species on the trait composition of recipient communities (i.e., how species with certain height, seed mass, specific leaf area, clonality, and life form are represented in the vegetation plots sampled). We sampled vegetation that comprised three species native to Eurasia and invasive in North America (i.e., Agrostis capillaris, Bromus tectorum, and Cirsium arvense) and three species native to North America and invasive in Europe (i.e., Aster novi‐belgii, Lupinus polyphyllus, and Solidago canadensis), in both their native and invaded ranges. This study system based on reciprocal inter‐continental invasions allowed us to assess whether the impact on trait composition differed (1) between the native and invaded ranges and (2) between the two continents. The relationships between species’ dominance and trait composition were tested using linear mixed‐effect models and ordination methods. A general trend was that dominant species with an impact on species richness also had an impact on trait composition, especially in North America, where even the native dominants affected the trait composition of the community. Further, the impact of Eurasian dominants in North America was stronger than that associated with the opposite direction of invasion, due to a strong negative effect of Eurasian invaders on local tall clonal perennials. Our results show that (1) the traits of species in the invaded community co‐determine the impact of invasion and are related to the impacts on species richness and composition; (2) the impacts on trait composition differ between the native and invaded ranges; and (3) the direction of invasion affects the impact on trait composition.

1. Fire-prone woodlands and savannas world-wide face management challenges resulting from fire exclusion and subsequent encroachment of fire-sensitive trees. In the Pacific Northwest (USA), Quercus garryana oak woodlands and savannas are threatened by encroachment from the native conifer Pseudotsuga menziesii in the absence of fire. 2. In the Bald Hills of Redwood National Park (California, USA), prescribed fire and conifer removal have been used to restore encroached woodlands. We examined the effects of encroachment and restoration on understorey vegetation, comparing four treatments: prescribed fire, prescribed fire and conifer removal, conifer removal, and encroached (control). 3. Treatments including prescribed fire had the greatest native species richness. These two treatments also had the greatest non-native species richness, at both the site level and the treatment level. Woodlands treated with conifer removal and no prescribed fire were intermediate in species richness and diversity compared to burned treatments and encroached woodlands. Encroached woodlands had diminished richness and diversity compared to all restoration treatments. Non-metric multidimensional scaling (NMS) ordination demonstrated that conifer basal area, conifer litter and fine wood were associated with low species richness and diversity and that elevation and thatch were associated with higher species richness and diversity. Indicator species analysis identified that most native species and non-native species were associated with burned woodlands that were never encroached. 4. Synthesis and applications. Our results suggest that both prescribed fire and conifer removal have benefits for understorey plant communities, increasing species richness, diversity and cover in oak woodlands and shifting understorey communities from forest-associated species to more woodland-associated species. Restoration of remnant Quercus garryana oak woodlands is complicated by the persistence and abundance of non-native herbaceous plants.

Aim To examine whether the tree flora of the Atlantic forest of northeastern Brazil has experienced detectable taxonomic homogenization via the proliferation of native pioneer species in response to habitat loss and fragmentation. Location Biotic homogenization (BH) was examined across the Atlantic forest of northeast Brazil, i.e. a 56,000 km² piece of tropical forest and a distinct centre of species endemism in South America. Methods We assessed a dataset consisting of 5122 tree records and compared the similarity of tree floras from 12 semi-natural sub-regions of the Atlantic forest between two time periods: pre-1980 (plant records between 1902 and 1980), and post-1980 (between 1981 and 2006). To understand the mechanisms leading to BH (1) tree floras were ordered (via non-metric multidimensional scaling - NMDS) by date (pre/post 1980) based on species occurrence and frequency, (2) NMDS axes were regressed against the proportion of those species that increased their occurrence post-1980 (i.e. the winner species), and (3) patterns of geographic distribution and frequency of particular life-history traits were examined across winner species and a control group. Results Tree floras across the Atlantic forest became c. 20-40% more similar to each other post-1980, but patterns of species similarity were also influenced by between-plot geographical distance. NMDS ordination clearly segregated pre- and post-1980 floras with a clear signal of floristic convergence. Furthermore, winner tree species were largely composed of short-lived and small-seeded pioneer species that exhibit wide geographic distributions. Main conclusions Our results suggest that tropical forest biotas are susceptible to taxonomic homogenization (i.e. increasing levels of similarity) in the context of severe human-disturbance via the proliferation of particular groups of native species comprised mainly by ecologically-plastic, generalist species. We are thus extending the concept of homogenization to address and highlight a pervasive biological shift in the structure of tropical forest communities currently taking place across hyper-fragmented landscapes.