Abstract1. There is growing interest among conservationists in biodiversity mapping based on stacked species distribution models (SSDMs), a method that combines multiple individual species distribution models to produce a community-level model. However, no user-friendly interface specifically designed to provide the basic tools needed to fit such models was available until now.2. The "ssdm" package is a computer platform implemented in r providing a range of methodological approaches and parameterisation at each step in building the SSDM: e.g. pseudo-absence selection, variable contribution and model accuracy assessment, inter-model consensus forecasting, species assembly design, and calculation of weighted endemism.3. The object-oriented design of the package is such that: users can modify existing methods, extend the framework by implementing new methods, and share them to be reproduced by others.4. The package includes a graphical user interface to extend the use of SSDMs to a wide range of conservation scientists and practitioners.

Increases in drought-induced tree mortality are being observed in tropical rain forests worldwide and are also likely to affect the geographical distribution of tropical vegetation. However, the mechanisms underlying the drought vulnerability and environmental distribution of tropical species have been little studied. We measured vulnerability to xylem embolism (P ) of 13 woody species endemic to New Caledonia and with different xylem conduit morphologies. We examined the relation between P , along with other leaf and xylem functional traits, and a range of habitat variables. Selected species had P values ranging between -4.03 and -2.00 MPa with most species falling in a narrow range of resistance to embolism above -2.7 MPa. Embolism vulnerability was significantly correlated with elevation, mean annual temperature and percentage of species occurrences located in rain forest habitats. Xylem conduit type did not explain variation in P . Commonly used functional traits such as wood density and leaf traits were not related to embolism vulnerability. Xylem embolism vulnerability stands out among other commonly used functional traits as a major driver of species environmental distribution. Drought-induced xylem embolism vulnerability behaves as a physiological trait closely associated with the habitat occupation of rain forest woody species.

Tree crowns play a central role in stand dynamics. Remotely sensed canopy images have been shown to allow inferring stand structure and biomass which suggests that allometric scaling between stems and crowns may be tight, although insufficiently investigated to date. Here, we report the first broad-scale assessment of stem vs. crown scaling exponents using measurements of bole diameter (DBH), total height (H), and crown area (CA) made on 4148 trees belonging to 538 species in five biogeographic areas across the wet tropics. Allometries were fitted with power functions using ordinary least-squares regressions on log-transformed data. The inter-site variability and intra-site (sub-canopy vs. canopy trees) variability of the allometries were evaluated by comparing the scaling exponents. Our results indicated that, in contrast to both DBH-H and H-CA allometries, DBH-CA allometry shows no significant inter-site variation. This fairly invariant scaling calls for increased effort in documenting crown sizes as part of tree morphology. Stability in DBH-CA allometry, indeed, suggests that some universal constraints are sufficiently pervasive to restrict the exponent variation to a narrow range. In addition, our results point to inverse changes in the scaling exponent of the DBH-CA vs. DBH-H allometries when shifting from sub-canopy to canopy trees, suggesting a change in carbon allocation when a tree reaches direct light. These results pave the way for further advances in our understanding of niche partitioning in tree species, tropical forest dynamics, and to estimate AGB in tropical forests from remotely sensed images. (Résumé d'auteur

Frost risk assessment is of critical importance in tropical highlands like the Andes where human activities thrives at altitudes up to 4200 m, and night frost may occur all the year round. In these semiarid and cold regions with sparse meteorological networks, remote sensing and topographic modeling are of potential interest for understanding how physiography influences the local climate regime. After integrating night land surface temperature from the MODIS satellite, and physiographic descriptors derived from a digital elevation model, we explored how regional and landscape-scale features influence frost occurrence in the southern altiplano of Bolivia. Based on the high correlation between night land surface temperature and minimum air temperature, frost occurrence in early-, middle-and late-summer periods were calculated from satellite observations and mapped at a 1-km resolution over a 45000 km² area. Physiographic modeling of frost occurrence was then conducted comparing multiple regression (MR) and boosted regression trees (BRT). Physiographic predictors were latitude, elevation, distance from salt lakes, slope steepness, potential insolation, and topographic convergence. Insolation influence on night frost was tested assuming that ground surface warming in the daytime reduces frost occurrence in the next night. Depending on the time period and the calibration domain, BRT models explained 74% to 90% of frost occurrence variation, outperforming the MR method. Inverted BRT models allowed the downscaling of frost occurrence maps at 100-m resolution, illustrating local processes like cold air drainage. Minimum temperature lapse rates showed seasonal variation and mean values higher than those reported for temperate mountains. When applied at regional and subregional scales successively, BRT models revealed prominent effects of elevation, latitude and distance to salt lakes at large scales, whereas slope, topographic convergence and insolation gained influence at local scales. Our results highlight the role of daytime insolation on night frost occurrence at local scale, particularly in the early-and midsummer periods when solar astronomic forcing is maximum. Seasonal variations and interactions in physiographic effects are also shown. Nested effects of physiographic factors across scales are discussed, as well as potential applications of physiographic modeling to downscale ecological processes in complex terrains.

Regional species assemblages have been shaped by colonization, speciation and extinction over millions of years. Humans have altered biogeography by introducing species to new ranges. However, an analysis of how strongly naturalized plant species (i.e. alien plants that have established self-sustaining populations) affect the taxonomic and phylogenetic uniqueness of regional floras globally is still missing. Here, we present such an analysis with data from native and naturalized alien floras in 658 regions around the world. We find strong taxonomic and phylogenetic floristic homogenization overall, and that the natural decline in floristic similarity with increasing geographic distance is weakened by naturalized species. Floristic homogenization increases with climatic similarity, which emphasizes the importance of climate matching in plant naturalization. Moreover, floristic homogenization is greater between regions with current or past administrative relationships, indicating that being part of the same country as well as historical colonial ties facilitate floristic exchange, most likely due to more intensive trade and transport between such regions. Our findings show that naturalization of alien plants threatens taxonomic and phylogenetic uniqueness of regional floras globally. Unless more effective biosecurity measures are implemented, it is likely that with ongoing globalization, even the most distant regions will lose their floristic uniqueness.

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Aim In New Caledonia, relictual angiosperm lineages are over-represented. However, the mechanisms responsible for such a distribution remain unclear. Two key hypotheses are that: (1) the diversity reflects adaptation to ultramafic substrates that ecologically filtered plant colonists; and (2) the diversity stems from wet climatic conditions that have persisted in New Caledonia during the late Quaternary while Australia and some nearby islands experienced widespread extinction events. Here, we investigate which hypothesis better explains the disharmony of relict angiosperms in New Caledonia. Location New Caledonia (South West Pacific Ocean).Methods We built species distribution models from herbarium data to determine the environmental correlates for 60 relict angiosperm taxa. Environmental variables used to characterize habitats included vegetation, substrate, and climate variables. We then tested whether the variety of xylem conduit structures borne by New Caledonian relict angiosperms, which is expected to affect plant hydraulic capacity, was correlated with habitat preference. Finally, we analysed species prevalence on different substrates and projected habitat size and distribution to the Last Glacial Maximum (LGM).Results We found a clear habitat preference among relict angiosperms for rain forests located on non-ultramafic substrates, with the exception of taxa bearing true vessels with simple perforation plates, which harboured a wider habitat breadth. We also showed that these rain forest habitats experienced a range reduction and an eastward shift during the LGM, forming two refugial areas located on the warm and rainy east coast of Grande Terre.Main conclusions Prevalence of relict angiosperms in habitats characterized by low evaporative demand appears to be related to xylem hydraulic limitations. The disharmony of relict angiosperms in New Caledonia therefore arose from the persistence of rain forests in the island despite global fluctuations in climate during the Quaternary that affected floras in the region. Our study offers a new model to explain why certain angiosperm families are disharmonically represented in New Caledonia.

It is generally accepted that plants locally influence the composition and activity of their rhizosphere microbiome, and that rhizosphere community assembly further involves a hierarchy of constraints with varying strengths across spatial and temporal scales. However, our knowledge of rhizosphere microbiomes is largely based on single-location and time-point studies. Consequently, it remains difficult to predict patterns at large landscape scales, and we lack a clear understanding of how the rhizosphere microbiome forms and is maintained by drivers beyond the influence of the plant. By synthesizing recent literature and collating data on rhizosphere microbiomes, we point out the opportunities and challenges offered by advances in molecular biology, bioinformatics, and data availability. Specifically, we highlight the use of exact sequence variants, coupled with existing and newly generated data to decipher the rules of rhizosphere community assembly across large spatial and taxonomic scales. Unearthing the Macroecology of Rhizosphere Soil Microbes Recent advances in sequencing technologies have expanded our ability to study plantassociated microbial communities. This has transformed our perception of the interactions between the plant and its microbiome (see Glossary) [1], which are now increasingly regarded jointly as holobionts [2-5]. The rhizosphere (i.e., the interface of plant roots and soils [6]) hosts diverse communities of microorganisms that are crucial to the plants they associate with. The rhizosphere microbiome can supply plants with nutrients [7], and protect plants against pathogens [8]. Furthermore, microbiomes can stimulate plant growth by producing phytohormones [9,10], and improve plant resistance and tolerance to abiotic stressors. Recent research suggests that rhizosphere microbiomes can alter plant phenology (e.g., flowering time) [11], modify morphological and size-related traits (e.g., shoot and root length and biomass, and number of secondary roots and leaves) [12], have a major role in plant community dynamics [13-15], and mediate plant responses to global change [16,17]. While much progress has been made, we are still far from understanding the mechanisms that control rhizosphere microbiome assembly and maintain community structure and composition. It has long been hypothesized that the macroecological patterns (i.e., ecological patterns across large spatial scales) of the rhizosphere microbiome will relate to the macroecological patterns of plants [18]. However, few studies have found clear relationships between plant and rhizosphere diversity [19,20]. This is likely because there is a disconnect between the plant and the microbial scales (Box 1). For other (non-rhizosphere) microbiomes, large-scale sampling campaigns are leading the way by generating standardized raw data and metadata (e.g., the Earth Microbiome Project [21] or the Human Microbiome Project [22]). For macro-organisms, macroecological patterns are frequently identified by collating existing and newly generated data from ...