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Synopsis The city and its urban biome provides an extreme laboratory for studying fundamental biological questions and developing best practices for sustaining biodiverse and well-functioning ecological communities within anthropogenic built environments. We propose by studying urban organisms, urban biotic communities, the urban biome, and the interactions between the urban biome and peri-urban built and natural environments, we can (1) discover new “rules of life” for the structure, function, interaction, and evolution of organisms; (2) use these discoveries to understand how novel emerging biotic communities affect and are affected by anthropogenic environmental changes in climate and other environmental factors; and (3) apply what we have learned to engage residents of the urban biome, and design cities that are more biologically diverse, are provided with more and better ecosystem services, and are more equitable and healthier places to live. The built environment of the urban biome is a place that reflects history, economics, technology, governance, culture, and values of the human residents; research on and applications of the rules of life in the urban biome can be used by all residents in making choices about the design of the cities where they live. Because inhabitants are directly invested in the environmental quality of their neighborhoods, research conducted in and about the urban environment provides a great opportunity to engage wide and diverse communities of people. Given the opportunity to engage a broad constituency—from basic researchers to teachers, civil engineers, landscape planners, and concerned citizens—studying the translation of the rules of life onto the urban environment will result in an integrative and cross-cutting set of questions and hypotheses, and will foster a dialog among citizens about the focus of urban biome research and its application toward making more equitable, healthy, livable, sustainable, and biodiverse cities.

One of the remarkable aspects of the tremendous biodiversity found in tropical forests is the wide range of evolutionary strategies that have produced this diversity, indicating many paths to diversification. We compare two diverse groups of trees with profoundly different biologies to discover whether these differences are reflected in their genomes. Ficus (Moraceae), with its complex co-evolutionary relationship with obligate pollinating wasps, produces copious tiny seeds that are widely dispersed. Lithocarpus (Fagaceae), with generalized insect pollination, produces large seeds that are poorly dispersed. We hypothesize that these different reproductive biologies and life history strategies should have a profound impact on the basic properties of genomic divergence within each genus. Using shallow whole genome sequencing for six species of Ficus, seven species of Lithocarpus, and three outgroups, we examined overall genomic diversity, how it is shared among the species within each genus, and the fraction of this shared diversity that agrees with the major phylogenetic pattern. A substantially larger fraction of the genome is shared among species of Lithocarpus, a considerable amount of this shared diversity was incongruent with the general background history of the genomes, and each fig species possessed a substantially larger fraction of unique diversity than Lithocarpus.

Tropical Southeast (SE) Asia harbors extraordinary species richness and in its entirety comprises four of the Earth's 34 biodiversity hotspots. Here, we examine the assembly of the SE Asian biota through time and space. We conduct meta-analyses of geological, climatic, and biological (including 61 phylogenetic) data sets to test which areas have been the sources of long-term biological diversity in SE Asia, particularly in the pre-Miocene, Miocene, and Plio-Pleistocene, and whether the respective biota have been dominated by in situ diversification, immigration and/or emigration, or equilibrium dynamics. We identify Borneo and Indochina, in particular, as major "evolutionary hotspots" for a diverse range of fauna and flora. Although most of the region's biodiversity is a result of both the accumulation of immigrants and in situ diversification, within-area diversification and subsequent emigration have been the predominant signals characterizing Indochina and Borneo's biota since at least the early Miocene. In contrast, colonization events are comparatively rare from younger volcanically active emergent islands such as Java, which show increased levels of immigration events. Few dispersal events were observed across the major biogeographic barrier of Wallace's Line. Accelerated efforts to conserve Borneo's flora and fauna in particular, currently housing the highest levels of SE Asian plant and mammal species richness, are critically required.

Xishuangbanna has been largely transformed from biodiverse natural forests and mixed-use farms into monoculture rubber plantations in just twenty years. This conversion has expanded into forests previously protected by the community and onto marginal sites at high-elevation. Market-based ecosystem payments, especially carbon financing, are potential tools to prevent further forest loss in China. Here, we compare rubber net present value (NPV), carbon sequestration, and seed-plant species diversity for Xishuangbanna given three land-use scenarios: Business-As-Usual (BAU), Economic Oriented Scenario (EOS) and Conservation Oriented Scenario (COS) using a previously published spatial map of rubber profitability. The EOS achieved the greatest rubber profit but caused substantial reductions in natural forest area, biodiversity and carbon stocks. The EOS also requires substantial immigration of workers into a remote and ecologically important region with little social infrastructure for basic security, food security, health-care and education, causing frequently ignored costs. As expected, the COS will maintain the highest levels of natural forest area, sequester 57% more carbon, and 71% more biodiversity than EOS. Given the conservation value of the carbon stores and rich biodiversity residing in Xishuangbanna's natural forests, reducing rubber NPV only marginally would probably cost less than attempting to recover these resources. We recommend that rubber plantations be limited to established, productive lowland areas whilst protecting intact high-elevation forest and reforesting low-productivity plantations. These actions will enhance carbon sequestration and biodiversity conservation. Management policies focused solely on profits, like the EOS scenario, will fail to sustain the entire range of natural resources and ecosystem services. The prices in the carbon market would have to be considerably larger than they are currently to compete with the profitability of rubber.

To protect biodiversity and improve environmental conditions, China has invested billions of dollars in reforestation and payments for ecosystem service programs. Here, we examine the Sloping Land Conversion Program, the largest such program in the world and found that after 13 years of implementation at our study site, it has had negative impacts on natural tropical forests. GIS and remote sensing techniques revealed that both natural forests and natural shrub and grasslands were replaced by non-native monocultural plantations on Hainan Island, China, a key tropical biodiversity hotspot. Under current Chinese policy, these plantations are classified simply as "forests", with the assumption that they are equivalent to natural forests. This lack of a distinction in forest quality has led to substantial deforestation and plantation expansion, including encroachment into protected areas on Hainan. Additional social and economic drivers of these changes were identified by examining the participants in this program and their actions. Without a new ecologically based definition of forests and new goals for reforestation, such programs designed to improve ecosystem services, and forest quality may actually threaten remaining natural forests and other vegetation types in Hainan and in other areas of mainland China.

The recent mass fruiting of forest trees in Borneo is an urgent wakeup call: existing policy instruments, financial mechanisms, and forestry infrastructure are inadequate to take full advantage of these infrequent opportunities for forest restoration and conservation. Tropical forest restoration can provide substantial benefits for biodiversity conservation, climate change mitigation, and poverty alleviation. Yet the unpredictability of the synchronized flowering and consequent mass fruiting of many forest trees in Borneo presents a distinctive set of challenges for forest restoration. Significant financing and a considerable coordinated effort are required to prepare for future mass fruiting events if we are to capitalize on opportunities for ecological restoration. The continued high rate of forest clearance in this region and the rarity of mass fruiting events suggest that there may be few remaining opportunities to prevent widespread species extinctions. In this article we propose a facilitatory policy framework for forest restoration in Borneo to stimulate action in advance of the next mass fruiting of forest trees.

The extent of Dipterocarp rainforests on the emergent Sundaland landmass in Southeast Asia during Quaternary glaciations remains a key question. A better understanding of the biogeographic history of Sundaland could help explain current patterns of biodiversity and support the development of effective forest conservation strategies. Dipterocarpaceae trees dominate the rainforests of Sundaland, and their distributions serve as a proxy for rainforest extent. We used species distribution models (SDMs) of 317 Dipterocarp species to estimate the geographic extent of appropriate climatic conditions for rainforest on Sundaland at the last glacial maximum (LGM). The SDMs suggest that the climate of central Sundaland at the LGM was suitable to sustain Dipterocarp rainforest, and that the presence of a previously suggested transequatorial savannah corridor at that time is unlikely. Our findings are supported by palynologic evidence, dynamic vegetation models, extant mammal and termite communities, vascular plant fatty acid stable isotopic compositions, and stable carbon isotopic compositions of cave guano profiles. Although Dipterocarp species richness was generally lower at the LGM, areas of high species richness were mostly found off the current islands and on the emergent Sunda Shelf, indicating substantial species migration and mixing during the transitions between the Quaternary glacial maxima and warm periods such as the present.

Hainan, the largest tropical island in China, belongs to the Indo-Burma biodiversity hotspot. The Changhua watershed is a center of endemism for plants and birds and the cradle of Hainan’s main rivers. However, this area has experienced recent and ongoing deforestation and habitat fragmentation. To quantify habitat loss and fragmentation of natural forests, as well as the land-cover changes in the Changhua watershed, we analyzed Landsat images obtained in 1988, 1995, and 2005. Land-cover dynamics analysis showed that natural forests increased in area (97,909 to 104,023 ha) from 1988 to 1995 but decreased rapidly to 76,306 ha over the next decade. Rubber plantations increased steadily throughout the study period while pulp plantations rapidly expanded after 1995. Similar patterns of land cover change were observed in protected areas, indicating a lack of enforcement. Natural forests conversion to rubber and pulp plantations has a general negative effect on biodiversity, primarily through habitat fragmentation. The fragmentation analysis showed that natural forests area was reduced and patch number increased, while patch size and connectivity decreased. These land-cover changes threatened local biodiversity, especially island endemic species. Both natural forests losses and fragmentation should be stopped by strict enforcement to prevent further damage. Preserving the remaining natural forests and enforcing the status of protected areas should be a management priority to maximize the watershed’s biodiversity conservation value.

Uganda's forests are globally important for their conservation values but are under pressure from increasing human population and consumption. In this study, we examine how conversion of natural forest affects soil bacterial and fungal communities. Comparisons in paired natural forest and human-converted sites among four locations indicated that natural forest soils consistently had higher pH, organic carbon, nitrogen, and calcium, although variation among sites was large. Despite these differences, no effect on the diversity of dominant taxa for either bacterial or fungal communities was detected, using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). Composition of fungal communities did generally appear different in converted sites, but surprisingly, we did not observe a consistent pattern among sites. The spatial distribution of some taxa and community composition was associated with soil pH, organic carbon, phosphorus and sodium, suggesting that changes in soil communities were nuanced and require more robust metagenomic methods to understand the various components of the community. Given the close geographic proximity of the paired sampling sites, the similarity between natural and converted sites might be due to continued dispersal between treatments. Fungal communities showed greater environmental differentiation than bacterial communities, particularly according to soil pH. We detected biotic homogenization in converted ecosystems and substantial contribution of β-diversity to total diversity, indicating considerable geographic structure in soil biota in these forest communities. Overall, our results suggest that soil microbial communities are relatively resilient to forest conversion and despite a substantial and consistent change in the soil environment, the effects of conversion differed widely among sites. The substantial difference in soil chemistry, with generally lower nutrient quantity in converted sites, does bring into question, how long this resilience will last.

The rapid disruption of tropical forests probably imperils global biodiversity more than any other contemporary phenomenon(1-3). With deforestation advancing quickly, protected areas are increasingly becoming final refuges for threatened species and natural ecosystem processes. However, many protected areas in the tropics are themselves vulnerable to human encroachment and other environmental stresses(4-9). As pressures mount, it is vital to know whether existing reserves can sustain their biodiversity. A critical constraint in addressing this question has been that data describing a broad array of biodiversity groups have been unavailable for a sufficiently large and representative sample of reserves. Here we present a uniquely comprehensive data set on changes over the past 20 to 30 years in 31 functional groups of species and 21 potential drivers of environmental change, for 60 protected areas stratified across the world's major tropical regions. Our analysis reveals great variation in reserve `health': about half of all reserves have been effective or performed passably, but the rest are experiencing an erosion of biodiversity that is often alarmingly widespread taxonomically and functionally. Habitat disruption, hunting and forest-product exploitation were the strongest predictors of declining reserve health. Crucially, environmental changes immediately outside reserves seemed nearly as important as those inside in determining their ecological fate, with changes inside reserves strongly mirroring those occurring around them. These findings suggest that tropical protected areas are often intimately linked ecologically to their surrounding habitats, and that a failure to stem broad-scale loss and degradation of such habitats could sharply increase the likelihood of serious biodiversity declines.

The marked biogeographic difference between western (Malay Peninsula and Sumatra) and eastern (Borneo) Sundaland is surprising given the long time that these areas have formed a single landmass. A dispersal barrier in the form of a dry savanna corridor during glacial maxima has been proposed to explain this disparity. However, the short duration of these dry savanna conditions make it an unlikely sole cause for the biogeographic pattern. An additional explanation might be related to the coarse sandy soils of central Sundaland. To test these two nonexclusive hypotheses, we performed a floristic cluster analysis based on 111 tree inventories from Peninsular Malaysia, Sumatra, and Borneo. We then identified the indicator genera for clusters that crossed the central Sundaland biogeographic boundary and those that did not cross and tested whether drought and coarse-soil tolerance of the indicator genera differed between them. We found 11 terminal floristic clusters, 10 occurring in Borneo, 5 in Sumatra, and 3 in Peninsular Malaysia. Indicator taxa of clusters that occurred across Sundaland had significantly higher coarse-soil tolerance than did those from clusters that occurred east or west of central Sundaland. For drought tolerance, no such pattern was detected. These results strongly suggest that exposed sandy sea-bed soils acted as a dispersal barrier in central Sundaland. However, we could not confirm the presence of a savanna corridor. This finding makes it clear that proposed biogeographic explanations for plant and animal distributions within Sundaland, including possible migration routes for early humans, need to be reevaluated.

Predicting community and species responses to disturbance is complicated by incomplete knowledge about species traits. A phylogenetic framework should partially solve this problem, as trait similarity is generally correlated with species relatedness, closely related species should have similar sensitivities to disturbance. Disturbance should thus result in community assemblages of closely related species. We tested this hypothesis with 18 disturbed and 16 reference whole-lake, long-term zooplankton data sets. Regardless of disturbance type, communities generally contained more closely related species when disturbed. This effect was independent of species richness, evenness, and abundance. Communities already under stress (i.e., those in acidic lakes) changed most when disturbed. Species sensitivities to specific disturbances were phylogenetically conserved, were independent of body size, and could be predicted by the sensitivities of close relatives within the same community. Phylogenetic relatedness can effectively act as a proxy for missing trait information when predicting community and species responses to disturbance.

Tropical botanical gardens (TBGs) should have a leading role in in situ conservation by directly promoting several initiatives, including the reintroduction of important or valuable native species, focused habitat restoration, 'assisted migration' of species that are vulnerable to climate change, and creative local collaboration with governments, NGOs and indigenous peoples. Compared with temperate gardens, TBGs face heightened challenges for ex situ conservation, including greater absolute amounts of biodiversity, need for resource mobilization, risk of introducing invasive species and potential genetic introgression within living collections. Meanwhile, the ecosystems surrounding TBGs have undergone widespread and rapid conversion. Here, we provide several illustrations of the effectiveness of TBGs in achieving their mission of preserving tropical biodiversity at the frontier of in situ ecosystem management.

Aim Identify environmental correlates for tropical tree diversity and composition. Location Borneo, Southeast Asia. Methods A GIS-environmental database with 5 arc minute ( c . 10 × 10 km) resolution was combined with tree inventory data. Tree diversity, phylogenetic diversity (PD) and the two main compositional gradients were determined for 46 tree inventories. Akaike’s information criterion and a data jackknifing procedure were used to select 50 explanatory models for diversity and composition gradients. The average of these models was used as our final diversity and compositional model. We applied Moran’s I to detect spatial autocorrelation of residuals. Results Tree diversity, PD and the two main compositional gradients in Borneo were all significantly correlated with the environment. Tree diversity correlated negatively with elevation, soil depth, soil coarseness (texture) and organic carbon content, whereas it correlated positively with soil C:N ratio, soil pH, moisture storage capacity and annual rainfall. Tree PD was correlated positively with elevation and temperature seasonality and was largely determined by gymnosperms. However, angiosperm PD also correlated positive with elevation. Compositional patterns were strongly correlated with elevation but soil texture, cation-exchange-capacity, C:N ratio, C and N content and drainage were also important next to rainfall seasonality and El Nino Southern Oscillation drought impact. Main conclusions Although elevation is the most important correlate for diversity and compositional gradients in Borneo, significant additional variability is explained by soil characteristics (texture, carbon content, pH, depth, drainage and nutrient status) and climate (annual rainfall, rainfall seasonality and droughts). The identified environmental correlates for diversity and composition gradients correspond to those found in other tropical regions of the world. Differences between the regions are mainly formed by differences in the relative importance of the environmental variables in explaining diversity and compositional gradients.

For 68 months, we observed the reproductive behaviour of 7288 woody plants (172 figs, 1457 climbers and 5659 trees) spanning major soil and elevational gradients. Two 2‐3 month community-wide supra-annual fruiting events were synchronized across five forest types, coinciding with ENSO events. At least 27 genera in 24 families restricted their reproduction to these events, which involved a substantial proportion of tree diversity (> 80% of phylogenetic diversity). During these events, mean reproductive levels (8.5%) represented an almost four-fold increase compared with other months. These patterns indicate a strong behavioural advantage to this unusual reproductive behaviour. Montane forest experienced a single, separate fruiting peak while the peat swamp forest did not participate. Excluding these events, no temporal reproductive pattern was detectible, at either the landscape or forest type. These phenological patterns have major implications for the conservation of frugivore communities, with montane and swamp forests acting as keystone forests.