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In the wake of widespread loss of old-growth forests throughout the tropics, secondary forests will likely play a growing role in the conservation of forest biodiversity. We considered a complex hierarchy of factors that interact in space and time to determine the conservation potential of tropical secondary forests. Beyond the characteristics of local forest patches, spatial and temporal landscape dynamics influence the establishment, species composition, and persistence of secondary forests. Prospects for conservation of old-growth species in secondary forests are maximized in regions where the ratio of secondary to old-growth forest area is relatively low, older secondary forests have persisted, anthropogenic disturbance after abandonment is relatively low, seed-dispersing fauna are present, and old-growth forests are close to abandoned sites. The conservation value of a secondary forest is expected to increase over time, as species arriving from remaining old-growth forest patches accumulate. Many studies are poorly replicated, which limits robust assessments of the number and abundance of old-growth species present in secondary forests. Older secondary forests are not often studied and few long-term studies are conducted in secondary forests. Available data indicate that both old-growth and second-growth forests are important to the persistence of forest species in tropical, human-modified landscapes.

Over the past 50 years, human agents of deforestation have changed in ways that have potentially important implications for conservation efforts. We characterized these changes through a meta-analysis of case studies of land-cover change in the tropics. From the 1960s to the 1980s, small-scale farmers, with state assistance, deforested large areas of tropical forest in Southeast Asia and Latin America. As globalization and urbanization increased during the 1980s, the agents of deforestation changed in two important parts of the tropical biome, the lowland rainforests in Brazil and Indonesia. Well-capitalized ranchers, farmers, and loggers producing for consumers in distant markets became more prominent in these places and this globalization weakened the historically strong relationship between local population growth and forest cover. At the same time, forests have begun to regrow in some tropical uplands. These changing circumstances, we believe, suggest two new and differing strategies for biodiversity conservation in the tropics, one focused on conserving uplands and the other on promoting environmental stewardship in lowlands and other areas conducive to industrial agriculture.

Aim: Cenozoic dynamics of large-scale species diversity patterns remain poorly understood, especially for the Western Pacific, in part, because of the paucity of well-dated fossil records from the tropics. This article aims to reveal the spatiotemporal dynamics of species diversity in the Western Pacific through the Cenozoic, focusing on the tropical Indo-Australian Archipelago (IAA) biodiversity hotspot. Location: Tropical and north-western Pacific Ocean. Methods: We analysed well-preserved fossil ostracodes from the tropical Western Pacific and combined their diversity data with other published data from the region to reconstruct Cenozoic dynamics of species diversity in the tropical and north-western Pacific Ocean. We fitted generalized additive models to test for differences in richness over time and across geographical regions while accounting for sample-size variation among samples. Results: Low-, mid- and high-latitude regions all show a similar diversity trajectory: diversity is low in the Eocene and Oligocène, increases from the Early Miocene to the Plio-Pleistocene but then declines to the present day. Present-day high biodiversity in these regions was established during the Pliocene with a remarkable diversity increase at that time. Latitudinal diversity patterns are relatively flat and never show a simple decline from the tropics to higher latitudes. Main conclusions: Western Pacific Cenozoic ostracodes exhibit a spatiotemporal pattern of species diversity that is inconsistent with the commonly reported and persistent pattern of declining diversity from the tropics to the extratropics. While this inconsistency could be interpreted as evidence that ostracodes are a contrarian clade, Atlantic ostracodes display a standard latitudinal species diversity gradient. Contrasting patterns between oceans suggest an important role for regional factors (e.g. plate tectonics and temporal geomorphological dynamics) in shaping the biodiversity of the Western Pacific.

Temperate-zone species have responded to warming temperatures by shifting their distributions poleward and upslope. Thermal tolerance data suggests that tropical species may respond to warming temperatures even more strongly than temperate-zone species, but this prediction has yet to be tested. We addressed this data gap by conducting resurveys to measure distributional responses to temperature increases in the elevational limits of the avifaunas of two geographically and faunally independent New Guinean mountains, Mt. Karimui and Karkar Island, 47 and 44 y after they were originally surveyed. Although species richness is roughly five times greater on mainland Mt. Karimui than oceanic Karkar Island, distributional shifts at both sites were similar: upslope shifts averaged 113 m (Mt. Karimui) and 152 m (Karkar Island) for upper limits and 95 m (Mt. Karimui) and 123 m (Karkar Island) for lower limits. We incorporated these results into a metaanalysis to compare distributional responses of tropical species with those of temperate-zone species, finding that average upslope shifts in tropical montane species match local temperature increases significantly more closely than in temperate-zone montane species. That tropical species appear to be strong responders has global conservation implications and provides empirical support to hitherto untested models that predict widespread extinctions in upper-elevation tropical endemics with small ranges.

Global climate change is driving species poleward and upward in high-latitude regions, but the extent to which the biodiverse tropics are similarly affected is poorly known due to a scarcity of historical records. In 1802, Alexander von Humboldt ascended the Chimborazo volcano in Ecuador. He recorded the distribution of plant species and vegetation zones along its slopes and in surrounding parts of the Andes. We revisited Chimborazo in 2012, precisely 210 y after Humboldt’s expedition. We documented upward shifts in the distribution of vegetation zones as well as increases in maximum elevation limits of individual plant taxa of >500 m on average. These range shifts are consistent with increased temperatures and glacier retreat on Chimborazo since Humboldt’s study. Our findings provide evidence that global warming is strongly reshaping tropical plant distributions, consistent with Humboldt’s proposal that climate is the primary control on the altitudinal distribution of vegetation.

Landscape dynamics are widely thought to govern the tempo and mode of continental radiations, yet the effects of river network rearrangements on dispersal and lineage diversification remain poorly understood. We integrated an unprecedented occurrence dataset of 4,967 species with a newly compiled, time-calibrated phylogeny of South American freshwater fishes—the most species-rich continental vertebrate fauna on Earth—to track the evolutionary processes associated with hydrogeographic events over 100 Ma. Net lineage diversification was heterogeneous through time, across space, and among clades. Five abrupt shifts in net diversification rates occurred during the Paleogene and Miocene (between 30 and 7 Ma) in association with major landscape evolution events. Net diversification accelerated from the Miocene to the Recent (c. 20 to 0 Ma), with Western Amazonia having the highest rates of in situ diversification, which led to it being an important source of species dispersing to other regions. All regional biotic interchanges were associated with documented hydrogeographic events and the formation of biogeographic corridors, including the Early Miocene (c. 23 to 16 Ma) uplift of the Serra do Mar and Serra da Mantiqueira and the Late Miocene (c. 10 Ma) uplift of the Northern Andes and associated formation of the modern transcontinental Amazon River. The combination of high diversification rates and extensive biotic interchange associated with Western Amazonia yielded its extraordinary contemporary richness and phylogenetic endemism. Our results support the hypothesis that landscape dynamics, which shaped the history of drainage basin connections, strongly affected the assembly and diversification of basin-wide fish faunas.

There is broad consensus that the diversity of functional traits within species assemblages drives several ecological processes. It is also widely recognized that rare species are the first to become extinct following human-induced disturbances. Surprisingly, however, the functional importance of rare species is still poorly understood, particularly in tropical species-rich assemblages where the majority of species are rare, and the rate of species extinction can be high. Here, we investigated the consequences of local and regional extinctions on the functional structure of species assemblages. We used three extensive datasets (stream fish from the Brazilian Amazon, rainforest trees from French Guiana, and birds from the Australian Wet Tropics) and built an integrative measure of species rarity versus commonness, combining local abundance, geographical range, and habitat breadth. Using different scenarios of species loss, we found a disproportionate impact of rare species extinction for the three groups, with significant reductions in levels of functional richness, specialization, and originality of assemblages, which may severely undermine the integrity of ecological processes. The whole breadth of functional abilities within species assemblages, which is disproportionately supported by rare species, is certainly critical in maintaining ecosystems particularly under the ongoing rapid environmental transitions.

In recent decades the rate and geographic extent of land-use and land-cover change has increased throughout the world's humid tropical forests. The pan-tropical geography of forest change is a challenge to assess, and improved estimates of the human footprint in the tropics are critical to understanding potential changes in biodiversity. We combined recently published and new satellite observations, along with images from Google Earth and a literature review, to estimate the contemporary global extent of deforestation, selective logging, and secondary regrowth in humid tropical forests. Roughly 1.4% of the biome was deforested between 2000 and 2005. As of 2005, about half of the humid tropical forest biome contained 50% or less tree cover. Although not directly comparable to deforestation, geographic estimates of selective logging indicate that at least 20% of the humid tropical forest biome was undergoing some level of timber harvesting between 2000 and 2005. Forest recovery estimates are even less certain, but a compilation of available reports suggests that at least 1.2% of the humid tropical forest biome was in some stage of long-term secondary regrowth in 2000. Nearly 70% of the regrowth reports indicate forest regeneration in hilly, upland, and mountainous environments considered marginal for large-scale agriculture and ranching. Our estimates of the human footprint are conservative because they do not resolve very small-scale deforestation, low-intensity logging, and unreported secondary regrowth, nor do they incorporate other impacts on tropical forest ecosystems, such as fire and hunting. Our results highlight the enormous geographic extent of forest change throughout the humid tropics and the considerable limitations of the science and technology available for such a synthesis.

The Eastern Arc Mountains of Tanzania and the Atlantic Forest of Brazil are two of the most fragmented biodiversity hotspots. Species–area relationships predict that their habitat fragments will experience a substantial loss of species. Most of these extinctions will occur over an extended time, and therefore, reconnecting fragments could prevent species losses and allow locally extinct species to recolonize former habitats. An empirical relaxation half-life vs. area relationship for tropical bird communities estimates the time that it takes to lose one-half of all species that will be eventually lost. We use it to estimate the increase in species persistence by regenerating a forest connection 1 km in width among the largest and closest fragments at 11 locations. In the Eastern Arc Mountains, regenerating 8,134 ha of forest would create >316,000 ha in total of restored contiguous forest. More importantly, it would increase the persistence time for species by a factor of 6.8 per location or ∼2,272 years, on average, relative to individual fragments. In the Atlantic Forest, regenerating 6,452 ha of forest would create >251,000 ha in total of restored contiguous forest and enhance species persistence by a factor of 13.0 per location or ∼5,102 years, on average, relative to individual fragments. Rapidly regenerating forest among fragments is important, because mean time to the first determined extinction across all fragments is 7 years. We estimate the cost of forest regeneration at $21–$49 million dollars. It could provide one of the highest returns on investment for biodiversity conservation worldwide.

In recent years, rising gold prices have exacerbated the global proliferation of artisanal-scale gold mining (ASGM), with catastrophic consequences for human and ecological health. Much of this burgeoning industry has occurred in biodiversity hot spots, notably in the tropical forests of South America. While the loss of tropical forests and floodplains as a result of ASGM has been well characterized, ASGM impacts on riverine hydrological properties are less understood. Previous fieldwork on ASGM-affected and gully-eroded tropical streams and rivers has demonstrated that increases in suspended-sediment concentration (SSC) can substantially impact fish diversity and aquatic community structure, yet our understanding of the timing and scope of impacts of such increases is limited by the lack of long-term records of SSC. To address this challenge, we present a 34-y analysis of the direct effect of ASGM on 32 river reaches in the Madre de Dios region of Peru, which has been heavily impacted by ASGM since the 1980s. We evaluate spatial and temporal patterns of impacts using estimated SSC derived from Landsat satellite imagery. We find that 16 of 18 stretches of river impacted by ASGM show significant increasing trends in SSC (P < 0.05), while only 5 of 14 unaffected sites do so. Additionally, ASGM appears to reverse natural seasonal cycles of SSC, which may imperil aquatic species. Overall, our findings indicate that ASGM is fundamentally altering optical water quality dynamics of a critical tropical biodiversity hot spot and provide guidance for future regulation of these activities.