Neotropical biodiversity: timing and potential drivers

The origin of extant neotropical biodiversity has been a controversial topic since the time of Darwin. In this review, I discuss the timing of, and potential driving factors associated with, diversification using recent evidence from molecular phylogenetics. Although these studies provide new insights into the subject, they are sensitive to dating approaches and targets, and can eventually lead to biased conclusions. A careful analysis suggests that the origin of extant neotropical biodiversity cannot be attributed to the action of one or few events during key time intervals. Rather, it is the result of complex ecological and evolutionary trends initiated by Neogene tectonic events and palaeogeographical reorganisations, and maintained by the action of Pleistocene climatic changes.     

Speciation timing and neotropical biodiversity: the Tertiary-Quaternary debate in the light of molecular phylogenetic evidence

The evolutionary origin of extant species in the Neotropics, one of the most biodiverse regions of the world, has been widely debated. One hypothesis is that neotropical species emerged primarily during the Quaternary (the last ~2 million years), favoured by alternating glacial/interglacial climates. An opposite view proposes an older Tertiary origin linked primarily to palaeogeographical changes. Here, a thorough review of the available literature on DNA molecular dating shows that the Tertiary–Quaternary debate no longer makes sense. Indeed, the > 1400 neotropical species whose origin has been dated have appeared in a continual fashion since the late Eocene/early Oligocene (~39 million years before present) to the Quaternary. Palaeogeographical mechanisms of speciation are relatively well accepted, but diversification processes linked to climate are still controversial. These results are important to unravel both the origin of present-day biodiversity patterns at both local and global scales and the genetic and environmental mechanisms involved, which are two crucial aspects for suitable biodiversity conservation strategies.     

Combining plant–frugivore networks for describing the structure of neotropical communities

Frugivory and seed dispersal are key processes for the maintenance of biodiversity. This is particularly true in the Neotropics, where most plant species depend on animals to disperse their seeds and most birds and mammals include fruits in their diets. We performed a continental‐scale literature review to build a database of interactions between neotropical fruits and fruit‐eating birds and mammals. Our objective was to evaluate the viability of combining literature data from different studies to describe the structure of highly diverse fruit–frugivore neotropical communities. We investigated sites that had been the focus of studies of at least four different avian and/or mammalian taxonomic orders and we included in our database only those conducted for at least a 6‐month period in order to account for the seasonality in fruit availability. In spite of a large number of study sites investigated for frugivory (n = 156), we found a huge gap in the knowledge of community‐wide fruit–frugivore interactions in the Neotropics, since most studies focused on single or a few species. Nevertheless, we were able to construct diverse plant–frugivore qualitative networks for 17 areas unevenly spread throughout the neotropical region. Using complex network analyses, we found that these networks were highly informative and non‐randomly organized. Most networks were both significantly nested and modular, characteristics related to stability and resilience in biological systems. We concluded that it is possible to use merged data to build networks for sites of conservation interest. The main advantage of using this approach is to optimize resources, avoiding exhaustive, costly and time‐consuming fieldwork when data is already available. Whilst bearing in mind the shortcomings of this methodology, these results can be used in studies aiming to understand the ecological processes structuring different communities in the neotropical region and to support conservation and restoration actions.     

Evolution on a shaky piece of Gondwana: is local endemism recent in New Caledonia?

New Caledonia is well known as a hot spot of biodiversity whose origin as a land mass can be traced back to the Gondwanan supercontinent. The local flora and fauna, in addition to being remarkably rich and endemic, comprise many supposedly relictual groups. Does the New Caledonian biota date back to Gondwanan times, building up its richness and endemism over 100 Myr or does it result from recent diversifications after Tertiary geological catastrophic events? Here we use a molecular phylogenetic approach to answer this question with the study of the Neocaledonian cockroach genus Angustonicus belonging to the subfamily Tryonicinae from Australia and New Caledonia. Both geological and molecular dating show that the diversification of this group is less than two million years old, whatever the date of its origin itself. This dating is not consistent with hypotheses of Gondwanan richness and endemism in New Caledonian biota. In other terms, local richness and endemism at the specific level are not necessarily related to an old Gondwanan origin of the Neocaledonian groups. © The Willi Hennig Society 2005.     

Ethanol from sugarcane in Brazil: a ‘midway’ strategy for increasing ethanol production while maximizing environmental benefits

This article reviews the history and current state of ethanol production from sugarcane in Brazil and presents a strategy for improving ecosystem services and production. We propose that it is possible to produce ethanol from sugarcane while maintaining or even recovering some of Brazil's unique neotropical biodiversity and ecosystem climate services. This approach to the future of sustainable and responsible ethanol production is termed the ‘midway’ strategy. The ‘midway’ strategy involves producing the necessary biotechnology to increase productivity while synergistically protecting and regenerating rainforest. Three main areas of scientific and technological advance that are key to realizing the ‘midway’ strategy are: (i) improving the quality of scientific data on sugarcane biology as pertains to its use as a bioenergy crop; (ii) developing technologies for the use of bagasse for cellulosic ethanol; and (iii) developing policies to improve the ecosystem services associated with sugarcane landscapes. This article discusses these three issues in the general context of biofuels production and highlights examples of scientific achievements that are already leading towards the ‘midway’ strategy.     

The role of the uplift of the Qinghai‐Tibetan Plateau for the evolution of Tibetan biotas

Biodiversity is unevenly distributed on Earth and hotspots of biodiversity are often associated with areas that have undergone orogenic activity during recent geological history (i.e. tens of millions of years). Understanding the underlying processes that have driven the accumulation of species in some areas and not in others may help guide prioritization in conservation and may facilitate forecasts on ecosystem services under future climate conditions. Consequently, the study of the origin and evolution of biodiversity in mountain systems has motivated growing scientific interest. Despite an increasing number of studies, the origin and evolution of diversity hotspots associated with the Qinghai‐Tibetan Plateau (QTP) remains poorly understood. We review literature related to the diversification of organisms linked to the uplift of the QTP. To promote hypothesis‐based research, we provide a geological and palaeoclimatic scenario for the region of the QTP and argue that further studies would benefit from providing a complete set of complementary analyses (molecular dating, biogeographic, and diversification rates analyses) to test for a link between organismic diversification and past geological and climatic changes in this region. In general, we found that the contribution of biological interchange between the QTP and other hotspots of biodiversity has not been sufficiently studied to date. Finally, we suggest that the biological consequences of the uplift of the QTP would be best understood using a meta‐analysis approach, encompassing studies on a variety of organisms (plants and animals) from diverse habitats (forests, meadows, rivers), and thermal belts (montane, subalpine, alpine, nival). Since the species diversity in the QTP region is better documented for some organismic groups than for others, we suggest that baseline taxonomic work should be promoted.     

Biogeography of cedrela (meliaceae, sapindales) in central and South america

Dated phylogenies have helped clarify the complex history of many plant families that today are restricted to the world's tropical forests, but that have Eocene, Oligocene, and Miocene fossils from the northern hemisphere. One such family is the Meliaceae. Here we infer the history of the neotropical Meliaceae genus Cedrela (17 species), the sister clade of which today is restricted to tropical Asia. Sequences from the nuclear ribosomal spacer region and five plastid loci obtained for all ingroup species and relevant outgroups were used to infer species relationships and for molecular-clock dating under two Bayesian relaxed clock models. The clock models differed in their handling of rate autocorrelation and sets of fossil constraints. Results suggest that (1) crown group diversification in Cedrela started in the Oligocene/Early Miocene and intensified in the Late Miocene and Early Pliocene, and (2) Central American Cedrela species do not form a clade, implying reentry into Central America after the closure of the Panamanian Isthmus. At present, Cedrela is distributed in both dry and humid habitats, but morphological features suggest an origin in dry forest under seasonal climates, fitting with Miocene and Pliocene Cedrela fossils from deciduous forests.     

Role of Caribbean Islands in the diversification and biogeography of Neotropical Heraclides swallowtails

Numerous hypotheses on the evolution of Neotropical biodiversity have stimulated research to provide a better understanding of diversity dynamics and distribution patterns of the region. However, few studies integrate molecular and morphological data with complete sampling of a Neotropical group, and so there has been little synthesis of the multiple processes governing biodiversity through space and time. Here, a total‐evidence phylogenetic approach is used to reconstruct the evolutionary history of the butterfly subgenus Heraclides. We used DNA sequences for two mitochondrial genes and one nuclear gene and coded 133 morphological characters of larvae and adults. A robust and well‐resolved phylogeny was obtained using several analytical approaches, while molecular dating and biogeographical analyses indicated an early Miocene origin (22 Mya) in the Caribbean Islands. We inferred six independent dispersal events from the Caribbean to the mainland, and three from the mainland to the Caribbean, and we suggest that cooling climates with decreasing sea levels may have contributed to these events. The time‐calibrated tree is best explained by a museum model of diversity in which both speciation and extinction rates remained constant through time. By assessing both continental and fine‐scale biodiversity patterns, this study provides new findings, for instance that islands may act as source of diversity rather than as a sink, to explain spatio‐temporal macroevolutionary processes within the Neotropical region.     

Identification of neotropical felid faeces using RCP-PCR

Faeces similarity among sympatric felid species has generally hampered their use in distributional, demographic and dietary studies. Here, we present a new and simple approach based on a set of species-specific primers, for the unambiguous identification of faeces from sympatric neotropical felids (i.e. puma, jaguar, jaguarundi and ocelot/ margay). This method, referred to as rapid classificatory protocol-PCR (RCP-PCR), consists of a single-tube multiplex PCR yielding species-specific banding patterns on agarose gel. The method was optimized with samples of known origin (14 blood and 15 fresh faeces) and validated in faecal samples of unknown origin (n = 138), for some of which (n = 40) we also obtained species identification based on mtDNA sequencing. This approach proved reliable and provides high identification success rates from faeces. Its simplicity and cost effectiveness should facilitate its application for routine surveys of presence and abundance of these species.     

A review of the chronology of the European Middle Pleistocene hominid record

Over the last seventy years, European hominid fossils and associated archaeological remains have been dated by reference to the classical, fourfold glacial/interglacial subdivision of the Pleistocene. This method seemed relatively straightforward and precise especially as new discoveries were fitted into the schemes, apparently strengthening the correlations and increasing their validity. However, recent studies of deep-sea cores and terrestrial deposits, combined with new developments in relative and absolute dating, have shown that the fourfold schemes are oversimplified. This paper critically reviews some of the dating evidence from sites with hominid remains generally considered as Middle Pleistocene (ca. 700,000–128,000 BP). The hominid and archaeological remains are shown to require independent dating and a cautious approach is adopted towards the use of mammalian faunal remains as chronological indicators. The techniques and results of absolute dating are discussed with reference to present problems and future prospects. At a time of transition from an old framework to new correlations, it is inevitable that some conclusions seem tentative and others rather negative. Nevertheless, the Middle Pleistocene in Europe is more fully understood and better dated than the equivalent period in other parts of the world.     

Connectance of species interaction networks and conservation value: Is it any good to be well connected?

Recently, the focus of conservation efforts gradually changed from a species-centred approach to a broader ambition of conserving functional ecosystems. This new approach relies on the understanding that much ecosystem function is a result of the interaction of species to form complex interaction networks. Therefore measures summarising holistic attributes of such ecological networks have the potential to provide useful indicators to guide and assess conservation objectives. The most generally accepted insight is that complexity in species interactions, measured by network connectance, is an important attribute of healthy communities which usually protects them from secondary extinctions. An implicit and overlooked corollary to this generalization is that conservation efforts should be directed to conserve highly connected communities. We conducted a literature review to search for empirical evidence of a relationship between connectance (complexity) and conservation value (communities on different stages of degradation). Our results show that the often assumed positive relationship between highly connected and desirable (i.e. with high conservation value) communities does not derive from empirical data and that the topic deserves further discussion. Given the conflicting empirical evidence revealed in this study, it is clear that connectance on its own cannot provide clear information about conservation value. In the face of the ongoing biodiversity crisis, studies of species interaction networks should incorporate the different ‘conservation value’ of nodes (i.e. species) in a network if it is to be of practical use in guiding and evaluating conservation practice.     

Ecological palaeoecology in the neotropical Gran Sabana region: Long-term records of vegetation dynamics as a basis for ecological hypothesis testing

Long-term palaeoecological records are needed to test ecological hypotheses involving time, as short-term observations are of insufficient duration to capture natural variability. In this paper, we review the published palaeoecological evidence for the neotropical Gran Sabana (GS) region, to record the vegetation dynamics and evaluate the potential effects of natural climatic and anthropogenic (notably fire) drivers of change. The time period considered (last 13,000 years) covers major global climate changes and the arrival of humans in the region. The specific points addressed are climate–vegetation equilibrium, reversibility of vegetation changes, the origin of extant biodiversity and endemism patterns and biodiversity conservation in the face of global warming. Vegetation dynamics is reconstructed by pollen analysis and fire incidence is deduced from microscopic charcoal records. Palaeoclimatic inferences are derived from global and regional records using independent physico-chemical evidence to avoid circular reasoning. After analyzing all the long-term records available from both GS uplands and highlands, we conclude that: (1) Upland vegetation (mostly treeless savannas and savanna–forest mosaics, with occasional Mauritia palm swamps) is not in equilibrium with the dominant climates, but largely conditioned by burning practices; (2) a hypothetical natural or “original” vegetation type for these uplands has not been possible to identify due to continuous changes in both climate and human activities during the last 13,000 years; (3) at the time scale studied (millennial), the shift from forest to savanna is abrupt and irreversible due to the existence of tipping points, no matter the cause (natural or anthropogenic); (4) on the contrary, the shift from savanna to palm swamps is reversible at centennial time scales; (5) some of the reconstructed past vegetation types have no modern analogues owing to the individual species response to environmental shifts, leading to variations in community composition; (6) extant biodiversity and endemism patterns are not the result of a long history of topographical isolation, as previously proposed but, rather, the consequence of the action of climatic and palaeogeographic variations; (7) the projected global warming will likely exacerbate the expansion of upland savannas by favouring positive fire-climate feedbacks; (8) in the highlands, extinction by habitat loss will likely affect biodiversity but to a less extent that prognosticated by models based only on present-day climatic features; (9) future highland communities will likely be different to present ones due to the prevalence of individual species responses to global warming; and (10) conservation strategies at individual species level, rather than at community level, are enriched by long-term palaeoecological studies analyzed here. None of these conclusions would have been possible to derive from short-term neoecological observations.     

Historical biogeography of the Southeast Asian and Malesian tribe Dissochaeteae (Melastomataceae)

The region of Tropical Southeast Asia and the Malay Archipelago is a very appealing area for research due to its outstanding biodiversity, being one of the most species-rich areas in the world with high levels of endemism, and due to its complex geological history. The high number of species in tribe Dissochaeteae (Melastomataceae) and their tendency to narrow endemism makethe tribe an ideal group for examining biogeographic patterns. We sampled 58 accessions spread over 42 accepted and two undescribed species of the Dissochaeteae. Two nuclear (ETS, ITS) and four chloroplast regions (ndhF, psbK-psbL, rbcL, rpl16) were used for divergence time estimation and ancestral area reconstruction. Results from the molecular dating analysis suggest that the diversity of Dissochaeteae in the Southeast Asian region resulted from a South American ancestor in the late Eocene. The ancestor of the Dissochaeteae might have migrated from South America to Southeast Asia via North America and then entered Eurasia over the North Atlantic land bridge during the Eocene. The origin and early diversification of the Dissochaeteae in Southeast Asia dates back to the middle Oligocene, and most of the genera originated during the Miocene. Indochina and Borneo are most likely the area of origin for the most recent common ancestor of the Dissochaeteae and for many of the early diverging clades of some genera within Southeast Asia.     

Assessing the conservation value of waterbodies: the example of the Loire floodplain (France)

In recent decades, two of the main management tools used to stem biodiversity erosion have been biodiversity monitoring and the conservation of natural areas. However, socio-economic pressure means that it is not usually possible to preserve the entire landscape, and so the rational prioritisation of sites has become a crucial issue. In this context, and because floodplains are one of the most threatened ecosystems, we propose a statistical strategy for evaluating conservation value, and used it to prioritise 46 waterbodies in the Loire floodplain (France). We began by determining a synthetic conservation index of fish communities (Q) for each waterbody. This synthetic index includes a conservation status index, an origin index, a rarity index and a richness index. We divided the waterbodies into 6 clusters with distinct structures of the basic indices. One of these clusters, with high Q median value, indicated that 4 waterbodies are important for fish biodiversity conservation. Conversely, two clusters with low Q median values included 11 waterbodies where restoration is called for. The results picked out high connectivity levels and low abundance of aquatic vegetation as the two main environmental characteristics of waterbodies with high conservation value. In addition, assessing the biodiversity and conservation value of territories using our multi-index approach plus an a posteriori hierarchical classification methodology reveals two major interests: (i) a possible geographical extension and (ii) a multi-taxa adaptation.     

South American palaeobotany and the origins of neotropical rainforests

Extant neotropical rainforest biomes are characterized by a high diversity and abundance of angiosperm trees and vines, high proportions of entire-margined leaves, high proportions of large leaves (larger than 4500 mm2), high abundance of drip tips and a suite of characteristic dominant families: Sapotaceae, Lauraceae, Leguminosae (Fabaceae), Melastomataceae and Palmae (Arecaceae). Our aim is to define parameters of extant rainforests that will allow their recognition in the fossil record of South America and to evaluate all known South American plant fossil assemblages for first evidence and continued presence of those parameters. We ask when did these critical rainforest characters arise? When did vegetative parameters reach the level of abundance that we see in neotropical forests? Also, when do specific lineages become common in neotropical forests? Our review indicates that evidence of neotropical rainforest is exceedingly rare and equivocal before the Palaeocene. Even in the Palaeocene, the only evidence for tropical rainforest in South America is the appearance of moderately high pollen diversity. By contrast, North American sites provide evidence that rainforest leaf physiognomy was established early in the Palaeocene. By the Eocene in South America, several lines of evidence suggest that neotropical rainforests were diverse, physiognomically recognizable as rainforest and taxonomically allied to modern neotropical rainforests. A mismatch of evidence regarding the age of origin between sites of palaeobotanical high diversity and sites of predicted tropical climates should be reconciled with intensified collecting efforts in South America. We identify several lines of promising research that will help to coalesce previously disparate approaches to the origin, longevity and maintenance of high diversity floras of South America.     

Dating placentalia: Morphological clocks fail to close the molecular fossil gap

Dating the origin of Placentalia has been a contentious issue for biologists and paleontologists. Although it is likely that crown‐group placentals originated in the Late Cretaceous, nearly all molecular clock estimates point to a deeper Cretaceous origin. An approach with the potential to reconcile this discrepancy could be the application of a morphological clock. This would permit the direct incorporation of fossil data in node dating, and would break long internal branches of the tree, so leading to improved estimates of node ages. Here, we use a large morphological dataset and the tip‐calibration approach of MrBayes. We find that the estimated date for the origin of crown mammals is much older, ～130–145 million years ago (Ma), than fossil and molecular clock data (～80–90 Ma). Our results suggest that tip calibration may result in estimated dates that are more ancient than those obtained from other sources of data. This can be partially overcome by constraining the ages of internal nodes on the tree; however, when this was applied to our dataset, the estimated dates were still substantially more ancient than expected. We recommend that results obtained using tip calibration, and possibly morphological dating more generally, should be treated with caution.     

A Toolkit for Ecosystem Ecologists in the Time of Big Science

Ecosystem ecologists are being challenged to address the increasingly complex problems that comprise Big Science. These problems include multiple levels of biological organization that cross multiple interacting temporal and spatial scales, from individual plants, animals, and microbes to landscapes, continents, and the globe. As technology improves, the availability of data, derived data products, and information to address these complex problems are increasing at finer and coarser scales of resolution, and legacy, dark data are brought to light. Data analytics are improving as big data increase in importance in other fields that are improving access to these data. New data sources (crowdsourcing, social media) and ease of communication and collaboration among ecosystem ecologists and other disciplines are increasingly possible via the internet. It is increasingly important that ecosystem ecologists be able to communicate their findings, and to translate their concepts and findings into concrete bits of information that a general public can understand. Traditional approaches that portray ecosystem sciences as a dichotomy between empirical research and theoretical research will keep the field from fully contributing to the complexity of global change questions, and will keep ecosystem ecologists from taking full advantage of the data and technology available. Building on previous research, we describe a more forward-looking, integrated empirical–theoretical modeling approach that is iterative with learning to take advantage of the elements of Big Science. We suggest that training ecosystem ecologists in this integrated approach will be critical to addressing complex Earth system science questions, now and in the future.     

Mobilizing and integrating big data in studies of spatial and phylogenetic patterns of biodiversity

The current global challenges that threaten biodiversity are immense and rapidly growing. These biodiversity challenges demand approaches that meld bioinformatics, large-scale phylogeny reconstruction, use of digitized specimen data, and complex post-tree analyses (e.g. niche modeling, niche diversification, and other ecological analyses). Recent developments in phylogenetics coupled with emerging cyberinfrastructure and new data sources provide unparalleled opportunities for mobilizing and integrating massive amounts of biological data, driving the discovery of complex patterns and new hypotheses for further study. These developments are not trivial in that biodiversity data on the global scale now being collected and analyzed are inherently complex. The ongoing integration and maturation of biodiversity tools discussed here is transforming biodiversity science, enabling what we broadly term “next-generation” investigations in systematics, ecology, and evolution (i.e., “biodiversity science”). New training that integrates domain knowledge in biodiversity and data science skills is also needed to accelerate research in these areas. Integrative biodiversity science is crucial to the future of global biodiversity. We cannot simply react to continued threats to biodiversity, but via the use of an integrative, multifaceted, big data approach, researchers can now make biodiversity projections to provide crucial data not only for scientists, but also for the public, land managers, policy makers, urban planners, and agriculture.