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AimWe used a phylogenetic approach to group assemblages of woody plant into major vegetation units in the Atlantic Forest, thus for the first time incorporating information on species evolutionary relationships into a bioregionalization of this critical hotspot. A phylogenetic regionalization will provide a spatially explicit framework for answering many basic and applied questions in biogeography, ecology and conservation.LocationAtlantic Forest.TaxonAngiospermsMethodsOur data set comprises 614 genera and 116 families, spread over 1,755 assemblages. To place assemblages in a multivariate evolutionary composition space, we used a phylogenetically informed ordination analysis, and to determine what the main phylogenetic groups of assemblages were, we used K‐means clustering based on phylogenetic dissimilarity of assemblages. To quantify how well environmental variables distinguish the phylogenetic groups found, we implemented classification tree approaches. Then, to explore the evolutionary turnover between the phylogenetic groups, we calculated phylogenetic beta diversity. Finally, we determined the lineages that are most strongly associated with individual phylogenetic groups using an indicator analysis for lineages.ResultsOur analyses suggest that there are seven principal groups, in terms of evolutionary lineage composition, in the Atlantic Forest. The greatest turnover of phylogenetic lineage composition separates tropical evergreen rain forest and semideciduous assemblages from subtropical and highland assemblages. The mixed subtropical forest showed the lowest phylogenetic compositional similarity values with other groups. Tropical rain forest had the highest number of significant indicator lineages, and the highest values of the indicator statistic for lineages.Main conclusionsWe found that the most pronounced evolutionary division separates southern and highland tree assemblages from those occurring under more tropical climates and at lower elevations. Our phylogenetic analyses point to an environmentally driven compositional division, likely based on the regular occurrence of freezing versus non‐freezing temperatures. Precipitation and edaphic regimes that assemblages experience had less definitive effects on their evolutionary lineage composition.

The Atlantic Forest in Brazil is a biodiversity hotspot, yet its diverse ecosystems and species are becoming increasingly threatened by habitat loss and extreme habitat fragmentation. Most habitat patches of Atlantic Forest are dispersed across agricultural landscapes (e.g., grazing and cropping) in relatively small and isolated fragments (80% < 50 ha). Forest fragments < 1 ha, scattered trees in pastures, tree lines on trenches and fences, and remnant riparian forest, collectively called here Small Landscape Elements (SLEs), are very common in this context. While these SLEs make up much of the Atlantic Forests footprint, very little is known about their role or impact on the persistence and conservation of species. In this study, we investigate the role of SLEs on landscape configuration, particularly their contribution toward landscape connectivity of individual species and the genetic flow of species between larger forest fragments. We randomly selected 20 buffers of 707 hectares within a 411,670 hectare area of the Atlantic Forest that was completely covered by forest in the past located in the south of Minas Gerais State, Brazil. The forest cover randomly varied between these buffers. We used graph theory to measure landscape connectivity as the probability of connectivity for different disperser movement types between landscape knots (habitat patches). We used three estimated dispersal distances in the models: pollen disperser insect (50 m), low-mobility seed disperser bird (100 m) and high-mobility seed disperser bird (760 m). The SLEs together increased the probability of connection by roughly 50%, for all model dispersers, if compared to a theoretical baseline landscape containing no SLEs. Of all SLEs, riparian forests contribute the most toward enhancing landscape connectivity. In these highly fragmented landscapes, such as the Atlantic Forest (>70%), the position of SLEs within the landscapes was more important than their respective areas for connectivity. Although the landscapes were deeply fragmented, we showed that the presence of SLEs can increase connectivity and reduce further biodiversity loss in the Atlantic Forest.

The campo rupestre sensu lato is among the most species-rich vegetation in the world, harbouring a high proportion of endemic species. We aimed to identify the processes that could generate a high level of phylogenetic diversity (PD) in campo rupestre for woody species and point out biodiversity hotspot areas which may provide additional information for conservation planning. We compiled a database of 2049 woody species from 185 community inventories. We calculated the evolutionary history using species richness (SR), PD, mean pairwise phylogenetic distance between species (MPD), the mean nearest taxon distance (MNTD) and their equivalents standardised (ses.PDss, ses.MPD, ses.MNTD), evolutionary distinctiveness (ED), and biogeographically weighted evolutionary distinctiveness (BED). Cloud dwarf-forests had the highest SR, PD, MPD and ses.MPD and lowest MNTD, while rupestrian cerrado presented the highest ses.PD and ses.MNTD. All areas are important for conservation, but the intersections between the hotspots should receive special attention in future conservation actions. The grids identified as hotspots by three or more metrics were localized mainly in Espinhaço Range in Minas Gerais State and a further expansion of protected areas is required. Moreover, the intersections between the hotspots obtained by mean ED and ses.PD are concentrated in the rocky dwarf forest and rupestrian cerrado, with considerable conservation gaps. The degree of protection of campo rupestre was low with unprotected areas comprising 56% of the species. Our results show an urgent need for increasing protected areas of campo rupestre in order to avoid the loss of valuable, endemic species with unique evolutionary history.

Understanding the phylogenetic structure provides evidence about the importance of the different processes that shape an ecological community. We addressed the following questions: i) What is the intensity of the role of the phylogenetic component on variations in the tree species composition in a large biogeographic transition zone in the Neotropics? ii) Have forest and savanna habitats similar answers to the above questions? We built an ultrametric phylogenetic tree for 2475 tree species and obtained eigenvectors for each site using the PCPS method (Principal Coordinates of Phylogenetic Structure). We used a variation partitioning framework coupled with Moran’s Spectral Randomization with three explanatory tables - a novel methodological approach - from canonical models expecting that the phylogenetic component would better explain the floristic variation than spatial and environmental components. The model containing the selected phylogenetic, spatial and environmental predictors explained 18.98 % of the floristic variation; the explanation provided by the phylogenetic component, after partitioning out the influence of spatial and environmental factors, accounted for 17.61 % of the total variation. The predominance of phylogenetic component was also found at other spatial levels (habitats and vegetation types). Variations in species composition in tree communities are thus strongly influenced by phylogenetic structure, and this pattern is consistent for both savanna and forest habitats. We confirmed that evolutive relationships are a synthetic indicator that can be correlated with patterns of floristic variation. This approach is unprecedented for tropical communities and brings promising contributions not only to understanding beta diversity in biogeographic transitions, but to the most varied ecological groups.

Studies that provide support for the conservation of transitions between biogeographic regions should be encouraged, given the ecological and evolutionary specificities of these environments. Investigations on evolutionary history may, for example, influence the prioritization of areas for biological conservation, as they enable a better understanding of the processes that shape communities in space and time. We used the occurrence data of tree species available for 87 sites of the Cerrado-Amazon Transition from the NeoTropTree database, together with 73 environmental variables, and investigated the phylogenetic structure (overdispersed, clustered, or randomly distributed communities) and diversity in this region. We evaluated the relationship between phylogenetic metrics and environmental variables using generalized least squares models. Our results demonstrated a predominant pattern of phylogenetic overdispersion, as well as high phylogenetic diversity. Phylogenetic metrics were strongly influenced by bioclimatic variables. Our study demonstrates that the Cerrado-Amazon Transition plays a fundamental role in the conservation of the regional flora both in terms of phylogenetic structure and diversity, but the protected areas in this region harbor only a restricted portion of this high diversity. These results not only confirm that transitional environments are areas of high biological diversity, but, unprecedentedly, this observation occurs from phylogenetic analyses of communities and to a biogeographic region so widely distributed and highly impacted by anthropogenic actions. Such findings point to the urgent need to take varied dimensions of biodiversity in establishing new areas of environmental protection in transition zones into account.

In South America the biogeographic history has produced different biomes with different vegetation types and distinct floras. As these vegetation types may diverge in evolutionary histories, we analysed how alpha and beta phylogenetic diversity vary across them and determine the main drivers of variation in phylogenetic diversity. To this end, we compiled a list of 205 sites and 1222 tree species spread over four biomes and eight vegetation types in central South America. For each site we evaluated six measures of evolutionary alpha diversity (species richness, phylogenetic diversity sensu stricto and the standardized effect size of phylogenetic diversity, mean phylogenetic distance and mean nearest taxon distance) and beta diversity (phylogenetic Sorensen's similarity). We checked the influence of spatial and environmental variables using generalized least squares models. The greatest phylogenetic differentiation was found between west and east of central South America, mainly between the Chaco communities and the other vegetation types, suggesting that species found in this biome come from different lineages, comparing with the others vegetation types. Our results also showed a clustered phylogenetic structure for the Dry Chaco woodlands, which may be associated with harsh environmental conditions. In addition to historical process, climatic conditions are the main drivers shaping phylogenetic patterns among the distinct vegetation types. Understanding patterns of phylogenetic diversity and distribution can greatly improve conservation planning and management since it allows the conservation of unique biome characteristics.

The southern portion of South America, which encompasses high and exceptional lineage diversity, is well-suited to studies addressing the interaction between biogeography and local environmental conditions and how this historical process and environmental variables affect distribution patterns. We here assessed the role of environmental variables and spatially autocorrelated processes in driving tree species distribution patterns in the whole southern South America forests. We compiled a dataset containing 110,087 occurrence records of 3183 species distributed into 742 sites across six countries and 13 biomes. We modeled the influence of both environmental and spatial variables related to geographic distribution limitations on the variations of species composition through partial canonical redundancy analysis. We built such models for each of our four datasets: the whole extratropical area of South America; Atlantic and Pampa Biomes; dry communities east of the Andes; and communities west of the Andes. Both spatial and environmental variables affect tree species composition in the southern region of South America, although a major role is played by the “pure” spatial fraction. This greatest significance of spatial structures reinforces the importance of historical process for this region and the floristic dissociation existing between the tropical and extratropical portion of South America. We argue that the southern South American forests (especially their temperate portion) should not be lumped into the Neotropical Floristic Province, an idea of utmost importance for the conservation of these high-diversity austral forests.

Altitude is one of the major environmental variables influencing the distribution of tree taxa around the world, and can be a useful parameter for the development of conservation strategies. Our objectives were to obtain an overview of the conservation status of taxa from the Atlantic semideciduous seasonal forests of southeastern Brazil and check, among the floristically consistent altitudinal zones, which had the largest number of endemic, threatened and indicator species. To accomplish this, we used species occurrence and geo-climatic data from the ‘NeoTropTree’ database. First, we checked which zones were floristically consistent using an ordination method (non-metric multidimensional scaling, NMS) followed by an analysis of variance. Then, we conducted an indicator species analysis, estimated species richness, calculated the taxonomic distinctness index for all zones and evaluated important aspects for conservation, such as endemism and threat of extinction. Taxa richness, and number of endemic and threatened species decreased with increasing altitude, while the amount of indicator species for each zone increased with altitudinal elevation. These variations related to the altitudinal gradient should be considered when developing conservation strategies. We also should prioritise the conservation of the entire gradient and, whenever possible, include endemic and endangered species in forest recovery programs.

The present-day southern South American flora comprises a group of lineages with southern temperate affinities, which have been suggested to have evolved during and after the breakup of Gondwana, as well as a group of Neotropical elements which are largely found in northern South America. Here, I aim to assess the floristic coherence of the main vegetation types that inhabit this region and determine the principal drivers of variation in the evolutionary diversity of these forest communities. I compiled a database of 3662 species of shrubs and trees at 781 sampling sites spread over six countries in South America. To understand the vegetation types that occur in the region I conducted clustering and ordination analyses. I then compared the defined vegetation types using taxonomic distinction, indicator species and phylogenetic diversity analyses. My results indicated a high diversity of vegetation types in terms of woody floristic composition, with a large number of indicator species, many of which are endemic. Contradicting the idea that temperate floras are recently derived and evolutionarily poor subsets of tropical floras, I demonstrated that the forests of the far south of South America are characterized by exceptional evolutionary diversity.

AimWe aimed to assess the contribution of marginal habitats to the tree species richness of the Mata Atlântica (Atlantic Forest) biodiversity hotspot. In addition, we aimed to determine which environmental factors drive the occurrence and distribution of these marginal habitats.LocationThe whole extension of the South American Atlantic Forest Domain plus forest intrusions into the neighbouring Cerrado and Pampa Domains, which comprises rain forests (“core” habitat) and five marginal habitats, namely high elevation forests, rock outcrop dwarf-forests, riverine forests, semi deciduous forests and restinga (coastal white-sand woodlands).MethodsWe compiled a dataset containing 366,875 occurrence records of 4,431 tree species from 1,753 site-checklists, which were a priori classified into 10 main vegetation types. We then performed ordination analyses of the species-by-site matrix to assess the floristic consistency of this classification. In order to assess the relative contribution of environmental predictors to the community turnover, we produced models using 26 climate and substrate-related variables as environmental predictors.ResultsOrdination diagrams supported the floristic segregation of vegetation types, with those considered as marginal habitats placed at the extremes of ordination axes. These marginal habitats are associated with the harshest extremes of five limiting factors: temperature seasonality (high elevation and subtropical riverine forests), flammability (rock outcrop dwarf-forests), high salinity (restinga), water deficit severity (semi deciduous forests) and waterlogged soils (tropical riverine forests). Importantly, 45% of all species endemic to the Atlantic Domain only occur in marginal habitats.Main conclusionsOur results showed the key role of the poorly protected marginal habitats in contributing to the high species richness of the Atlantic Domain. Various types of environmental harshness operate as environmental filters determining the distribution of the Atlantic Domain habitats. Our findings also stressed the importance of fire, a previously neglected environmental factor.

The Atlantic Forest encompasses a high level of biodiversity, endemism and degradation; hence, it is a biome of particular interest for biological conservation. We aimed to investigate the actual geographic distribution of tree species and, among the indicator species of each vegetation type, the conservation status and potential distribution of each species along a vegetation gradient of the Subtropical Atlantic Forest. We analysed the species’ relative constancy to determine their actual distribution, obtained 21 indicator species of the different vegetation types and modelled their potential distribution using the maximum entropy algorithm. The potential distribution models were pooled to yield a single map, which was used to predict the distribution of climatic suitability for these species in South America. Our results showed that the actual geographic distribution is restricted for most species (~72 %). Araucaria angustifolia and Euterpe edulis were categorized as threatened species. The sum of the indicator-species maps showed reduced climatic suitability across most of South America. The southern region of Brazil and the southeastern Brazilian highlands, as well as a few areas of seasonal forests on higher elevations of the Bolivian Chiquitania and Andean Piedmont, exhibited the best climatic suitability. Elevation was the most important variable in our models. Given the concerning level of forest degradation and the presence of endangered and geographic restricted species, our results are a relevant contribution to biodiversity conservation in the Subtropical Atlantic Forest areas, highlighting their floristic and environmental uniqueness and, therefore, the urgent necessity of preserving their biological heritage.