Tropical forests are vast and scientifically underexplored places. Biotic losses, gains, and reorganization within these systems go undetected due to a lack of access to technologies needed to monitor forest cover, composition, and carbon content. Provision of forest cover-monitoring tools for non-scientists has, thus, become a focus of innovation in the remote-sensing community, while advances in high-resolution forest carbon and biodiversity mapping science has progressed more slowly. This paper focuses on high-resolution remote-sensing developments to measure and monitor tropical forest canopies at the “organismic scale,” which is the resolution that resolves individual canopies and species throughout the forest landscape. Emphasis is placed on how forest carbon stocks can be mapped with precision and accuracy comparable to that of field-based estimates. Biodiversity mapping poses the greatest challenge, but recent advances in three-dimensional functional and structural trait imaging can reveal variation in species richness, abundance, and functional diversity over large geographic regions. The pay-off in pursuing these studies will be a vastly improved understanding of tropical biodiversity patterns and their underlying ecological and evolutionary drivers, which will have positive cascading effects on conservation decision-making and resource policy development.

The interrelationships between smallholder agriculture, forest cover, and biodiversity loss have received insufficient research and analytic attention, though they stand at the center of the ongoing biodiversity crisis in tropical landscapes. Despite important advances in conservation science, knowledge generation remains fragmentary, and the formal institutions concerned with agriculture, forestry, social change, and climate change continue to work to a large extent in isolation, especially in developing countries. Drawing on our research program in the montane Eastern Himalaya of India, for example, two questions are explored: What types of landscapes can provide livelihood security for growing populations while maintaining healthy ecosystems? What kinds of knowledge, institutions, and policies will help us move toward land-use patterns that support livelihoods and protect biodiversity, given a regional economy based on small-scale agriculture? Here, we advocate for a greater integration of knowledge types (scientific, traditional, and participatory) and institutions (formal and informal, government and community) to foster better planning in order to reconcile several functions at the landscape level, including smallholder agriculture, the production of ecosystem goods and services, and the protection of biodiversity.

In the Cretaceous there were eight New World terrestrial ecosystems that were distinct or only shadowy versions of those present today. Now, 65 Ma later, 12 ecosystems constitute the recognizable subdivisions of the Earth's living and physical envelope. Knowledge of the intervening history is useful for conservation in several regards. It reveals how heterogeneous modern systems are in age and origin (e.g., lowland Neotropical rainforest formed between ca. 60 and 58 Ma; tundra and páramo between ca. 5 and 3 Ma), how individualized the response of component species to previous environmental change has been, and how levels of biodiversity have fluctuated through time. History provides approximate analogs for conditions anticipated in the near future and estimates of the biotic response. In addition, history documents that climatic events originally discovered and formerly associated with the high latitudes also affected tropical regions, and that discovery constitutes a valuable context for assessing previously held views about the stability of tropical communities and environments. There has been a rapid increase in the pace of both natural and human-induced environmental change and biotic response approaching modern times. Blurring the lines between neontology and paleontology, namely, conceptualizing ecosystems over Cretaceous and especially Late Cenozoic time, provides a dynamic view of these systems and furthers realistic strategies to conserve them.

I highlight new and emerging threats to tropical forests, the world's most biologically diverse ecosystems. The drivers of tropical forest destruction and key perils to biodiversity have changed over the past decade and will continue to evolve in the future. Industrial drivers of forest conversion, such as logging, large-scale soy and cattle farming, oil-palm plantations, and oil and gas development, have escalated in importance, buoyed by rapid globalization, economic growth, and rising standards of living in developing nations. Biofuels are likely to grow rapidly as a driver of future forest destruction. Climate change is similarly emerging as a potentially serious driver of change in the tropics, and many species, including certain amphibians, primates, and plants, are being harmed by emerging pathogens. In general, old-growth forests are vanishing rapidly and being replaced by fragmented, secondary, and selectively logged forests, particularly in impoverished tropical countries. Road expansion continues apace and is increasingly imperiling the world's last tropical frontiers. Human population growth, especially in developing nations, remains an important underlying threat to forests. These various environmental dangers often operate in concert, magnifying their impacts and posing an even greater threat to tropical forests and their biodiversity.

How many flowering plant species are there? Where are they? How many are going extinct, and how fast are they doing so? Interesting in themselves, these are questions at the heart of modern conservation biology. Determining the answers will dictate where and how successfully conservation efforts will be allocated. Plants form a large taxonomic sample of biodiversity. They are important in themselves and directly determine the diversity of many other taxonomic groups. Inspired by conversations with Peter Raven, we set out to provide quantitative answers to these questions. We argue that there are 450,000 species, two thirds of which live in the tropics, a third of all species are at risk of extinction, and they are going extinct 1000 to 10,000 times the background rate. In obtaining these results, we point to the critical role of dedicated taxonomic effort and biodiversity monitoring. We will only get a good answer to the age-old question of “how many species are there?” when we understand the population biology and social behavior of taxonomists. That most missing species will be found in biodiversity hotspots reaffirms their place as the foci of extinction for decades to come. Important, but not yet addressed, are future studies of how long plant species take to become extinct in habitat fragments. These will deliver not only better estimates of extinction rates, but also the critical timeframe of how quickly one needs to act to prevent extinctions.

This paper is the first in a series that documents the diversity, distribution, and evolution of palynological characters across angiosperms in a contemporary phylogenetic context, using modern optimization methods. The objectives of the series are: (1) to describe the diversity of pollen morphologies across the angiosperms; (2) to estimate ancestral palynological character states, diagnostic characters, and synapomorphies for monophyletic groups; (3) to highlight and interpret inferred patterns and processes of evolution in palynological characters; and (4) to provide a framework for the placement of enigmatic taxa (including fossil taxa) based on pollen morphology. This first paper examines the methods available for such a study and presents an overview of palynological characters across angiosperms as a whole. Using a well-supported, recent, molecular phylogeny, we consider the effects of coding strategy, method of optimization, and starting tree topology upon inference of trait evolution. Coding strategy and optimization method had significant effects upon inferred ancestral character states, the latter probably due to the different evolutionary models applied. Phylogenetic topology had little effect upon inferred ancestral character states, because the uncertainty in topology at this level involved only nodes where few character state changes occurred. Several palynological characters showed consistent, structured patterns in the context of phylogeny: angiosperms are distinguished from other seed plants by character states including supratectal elements echinate and less than 1 μm in size, and infratectum structure columellate; eudicots, as recognized in previous studies, may be defined by globose, isopolar, radially symmetrical grains with three equatorial apertures. We present a framework for the remainder of the series, in which the angiosperms are divided into nine monophyletic and paraphyletic groups each having a similar level of pollen variability, and a set of recommendations for the analysis of these groups. The series will provide a reference for future palynological and systematic studies and an approach that may be replicated for other character sets.

Recently, evolutionary relationships among the five major lineages of the basal angiosperms, i.e., Amborellanae, Nymphaeanae, Austrobaileyanae, Magnolianae, and Ceratophyllanae, still remain incompletely or controversially resolved. This study reviews and reevaluates the origin, evolution, and systematic significance of pollen morphology in basal angiosperms. Pollen grains from 34 species of 31 genera in 23 families of the basal angiosperms are investigated, using light microscopy (LM) and scanning electron microscopy (SEM), to illustrate the pollen diversity across the grade. Pollen data for 57 genera, representing all nine orders and 28 families of the basal angiosperms, were obtained from previous work and new investigations and were used to optimize character states onto recent molecular phylogenetic estimates. Two 18-character datasets were generated: a comprehensively coded dataset optimized with Fitch parsimony onto 12 recent phylogenies with differing topologies to evaluate the degree of pollen systematic significance of each topology, and a democratically coded dataset optimized by using Fitch parsimony, maximum likelihood, and hierarchical Bayesian inference onto a single recent phylogeny based on molecular data from Soltis et al. to evaluate the disparity of pollen evolutionary patterns among the three methods. Pollen morphology of the basal angiosperms is highly diverse, particularly in terms of pollen size, aperture number, aperture position, ectoaperture shape, tectum sculpture, and infratectal structure. Based on both datasets, the plesiomorphic pollen type for angiosperms was inferred to comprise monads of heteropolar, spheroidal, mono-apertural grains, with distal, colpate apertures, sculptured aperture membranes, and an infratectum and foot layer. Of the basal angiosperm phylogenies considered, when taxon sampling is taken into account, pollen characters provide greatest support for the topology represented in the three-mitochondrial-gene study from Qiu et al., in terms of number of synapomorphies plus what we term “likely synapomorphies” in which the subtending node is ambiguous and, therefore, the exact position of the synapomorphy is ambiguous. Thirty-six various lineages above family level are supported by pollen morphological synapomorphies or likely synapomorphies. We discuss the systematic significance of pollen morphology in basal angiosperm clades including the ANITA group (Amborellaceae, Nymphaeaceae, Schisandraceae, Trimeniaceae, and Austrobaileyaceae), Ceratophyllales, Chloranthales, and magnoliids, as well as in related lineages, i.e., monocots and basal eudicots. We also discuss present limitations in inferring the evolutionary history of pollen morphology in basal angiosperms.