The Clade Replacement Theory: a framework to study age-dependent extinction.

There is no scientific consensus about whether and how species' evolutionary age, or the elapsed time since their origination, might affect their probability of going extinct. Different age-dependent extinction (ADE) patterns have been proposed in theoretical and empirical studies, while the existence of a consistent and universal pattern across the tree of life remains debated. If evolutionary age predicts species extinction probability, then the study of ADE should comprise the elapsed time and the ecological process acting on species from their origin to their extinction or to the present for extant species. Additionally, given that closely related species share traits associated with fitness, evolutionary proximity could generate similar ADE patterns. Considering the historical context and extinction selectivity based on evolutionary relatedness, we build on previous theoretical work to formalize the Clade Replacement Theory (CRT) as a framework that considers the ecological and evolutionary aspects of species age and extinction probability to produce testable predictions on ADE patterns. CRT's domain is the diversification dynamics of two or more clades competing for environmental space throughout time, and its propositions or derived hypotheses are as follows: (i) incumbency effects by an early arriving clade that limit the colonization and the diversification of a younger clade leading to a negative ADE scenario (younger species more prone to extinction than older ones) and (ii) an ecological shift triggered by an environmental change that imposes a new selective regime over the environmental space and leads to a positive ADE scenario (extinction probability increasing with age). From these propositions, we developed the prediction that the ADE scenario would be defined by whether an ecological shift happens or not. We discuss how the CRT could be tested with empirical data and provide examples where it could be applied. We hope this article will provide a common ground to unify results from different fields and foster new empirical tests of the mechanisms derived here while providing insights into CRT theoretical structuration.

Global importance of Indigenous Peoples, their lands, and knowledge systems for saving the world's primates from extinction.

Primates, represented by 521 species, are distributed across 91 countries primarily in the Neotropic, Afrotropic, and Indo-Malayan realms. Primates inhabit a wide range of habitats and play critical roles in sustaining healthy ecosystems that benefit human and nonhuman communities. Approximately 68% of primate species are threatened with extinction because of global pressures to convert their habitats for agricultural production and the extraction of natural resources. Here, we review the scientific literature and conduct a spatial analysis to assess the significance of Indigenous Peoples' lands in safeguarding primate biodiversity. We found that Indigenous Peoples' lands account for 30% of the primate range, and 71% of primate species inhabit these lands. As their range on these lands increases, primate species are less likely to be classified as threatened or have declining populations. Safeguarding Indigenous Peoples' lands, languages, and cultures represents our greatest chance to prevent the extinction of the world's primates.

The role of protected areas in maintaining natural vegetation in Brazil.

The destruction of natural vegetation in recent decades has been concentrated in the tropics, where ecosystem processes underpin global homeostasis and harbor most of the world's biodiversity. Protected areas (PAs) are the primary societal tool to avoid this destruction, yet their effectiveness is often questioned. Here, we quantified the impact of PAs and indigenous lands in avoiding 34 years of vegetation destruction in forested and nonforested biomes in Brazil. We showed that the odds of destruction in the PA network are four times lower than in unprotected areas, and generally, this positive effect extends to a buffer zone around PAs. Among the most effective groups of PAs are those that are older, larger, located in the Amazonian region, and indigenous lands. Despite recent setbacks for the Brazilian PA system, we highlight the benefits of PAs for biodiversity and climate if they were instead strengthened.

Historical range contractions can predict extinction risk in extant mammals.

Climate change is amongst the main threats to biodiversity. Considering extant mammals endured Quaternary climate change, we analyzed the extent to which this past change predicts current mammals' extinction risk at global and biogeographical scales. We accessed range dynamics by modeling the potential distribution of all extant terrestrial mammals in the Last Glacial Maximum (LGM, 21,000 years ago) and in current climate conditions and used extinction risk from IUCN red list. We built General Linear Mixed-Effects Models to test the magnitude with which the variation in geographic range (ΔRange) and a proxy for abundance (ΔSuitability) between the LGM and present-day predicts current mammal's extinction risk. We found past climate change most strongly reduced the geographical range and climatic suitability of threatened rather than non-threatened mammals. Quaternary range contractions and reduced suitability explain around 40% of species extinction risk, particularly for small-bodied mammals. At global and biogeographical scales, all groups that suffered significant Quaternary range contractions now contain a greater proportion of threatened species when compared to groups whose ranges did not significantly contract. This reinforces the importance of using historical range contractions as a key predictor of extinction risk for species in the present and future climate change scenarios and supports current efforts to fight climate change for biodiversity conservation.

Primates in peril: the significance of Brazil, Madagascar, Indonesia and the Democratic Republic of the Congo for global primate conservation.

Primates occur in 90 countries, but four-Brazil, Madagascar, Indonesia, and the Democratic Republic of the Congo (DRC)-harbor 65% of the world's primate species (439) and 60% of these primates are Threatened, Endangered, or Critically Endangered (IUCN Red List of Threatened Species 2017-3). Considering their importance for global primate conservation, we examine the anthropogenic pressures each country is facing that place their primate populations at risk. Habitat loss and fragmentation are main threats to primates in Brazil, Madagascar, and Indonesia. However, in DRC hunting for the commercial bushmeat trade is the primary threat. Encroachment on primate habitats driven by local and global market demands for food and non-food commodities hunting, illegal trade, the proliferation of invasive species, and human and domestic-animal borne infectious diseases cause habitat loss, population declines, and extirpation. Modeling agricultural expansion in the 21st century for the four countries under a worst-case-scenario, showed a primate range contraction of 78% for Brazil, 72% for Indonesia, 62% for Madagascar, and 32% for DRC. These pressures unfold in the context of expanding human populations with low levels of development. Weak governance across these four countries may limit effective primate conservation planning. We examine landscape and local approaches to effective primate conservation policies and assess the distribution of protected areas and primates in each country. Primates in Brazil and Madagascar have 38% of their range inside protected areas, 17% in Indonesia and 14% in DRC, suggesting that the great majority of primate populations remain vulnerable. We list the key challenges faced by the four countries to avert primate extinctions now and in the future. In the short term, effective law enforcement to stop illegal hunting and illegal forest destruction is absolutely key. Long-term success can only be achieved by focusing local and global public awareness, and actively engaging with international organizations, multinational businesses and consumer nations to reduce unsustainable demands on the environment. Finally, the four primate range countries need to ensure that integrated, sustainable land-use planning for economic development includes the maintenance of biodiversity and intact, functional natural ecosystems.

Impending extinction crisis of the world's primates: Why primates matter.

Nonhuman primates, our closest biological relatives, play important roles in the livelihoods, cultures, and religions of many societies and offer unique insights into human evolution, biology, behavior, and the threat of emerging diseases. They are an essential component of tropical biodiversity, contributing to forest regeneration and ecosystem health. Current information shows the existence of 504 species in 79 genera distributed in the Neotropics, mainland Africa, Madagascar, and Asia. Alarmingly, ~60% of primate species are now threatened with extinction and ~75% have declining populations. This situation is the result of escalating anthropogenic pressures on primates and their habitats-mainly global and local market demands, leading to extensive habitat loss through the expansion of industrial agriculture, large-scale cattle ranching, logging, oil and gas drilling, mining, dam building, and the construction of new road networks in primate range regions. Other important drivers are increased bushmeat hunting and the illegal trade of primates as pets and primate body parts, along with emerging threats, such as climate change and anthroponotic diseases. Often, these pressures act in synergy, exacerbating primate population declines. Given that primate range regions overlap extensively with a large, and rapidly growing, human population characterized by high levels of poverty, global attention is needed immediately to reverse the looming risk of primate extinctions and to attend to local human needs in sustainable ways. Raising global scientific and public awareness of the plight of the world's primates and the costs of their loss to ecosystem health and human society is imperative.

Climate and land use changes will degrade the configuration of the landscape for titi monkeys in eastern Brazil.

Land use changes have profound effects on populations of Neotropical primates, and ongoing climate change is expected to aggravate this scenario. The titi monkeys from eastern Brazil (Callicebus personatus group) have been particularly affected by this process, with four of the five species now allocated to threatened conservation status categories. Here, we estimate the changes in the distribution of these titi monkeys caused by changes in both climate and land use. We also use demographic-based, functional landscape metrics to assess the magnitude of the change in landscape conditions for the distribution predicted for each species. We built species distribution models (SDMs) based on maximum entropy for current and future conditions (2070), allowing for different global circulation models and contrasting scenarios of glasshouse gas concentrations. We refined the SDMs using a high-resolution map of habitat remnants. We then calculated habitat availability and connectivity based on home-range size and the dispersal limitations of the individual, in the context of a predicted loss of 10% of forest cover in the future. The landscape configuration is predicted to be degraded for all species, regardless of the climatic settings. This include reductions in the total cover of forest remnants, patch size and functional connectivity. As the landscape configuration should deteriorate severely in the future for all species, the prevention of further loss of populations will only be achieved through habitat restoration and reconnection to counteract the negative effects for these and several other co-occurring species.

Conservation biogeography of the Cerrado's wild edible plants under climate change: Linking biotic stability with agricultural expansion.

UNLABELLED: REMISE OF THE STUDY: Wild edible plants (WEPs) have an important cultural and economic role in human population worldwide. Human impacts are quickly converting natural habitats in agricultural, cattle ranch, and urbanized lands, putting native species on peril of risk of extinction, including some WEPs. Moreover, global climate changes also can pose another threat to species persistency. Here, we established conservation priorities for the Cerrado, a neotropical region in South America with high levels of plant endemism and vulnerability, aiming to assure long-term persistency of 16 most important WEPs. We evaluated these conservation priorities using a conservation biogeography framework using ecological patterns and process at a biogeographical scale to deal with species conservation features. METHODS: We built ecological niche models for 16 WEPs from Cerrado in the neotropics using climate models for preindustrial, past (Last Glacial Maximum) and future (year 2080) time periods to establish climatically stable areas through time, finding refugias for these WEPs. We used a spatial prioritization algorithm based on the spatial pattern of irreplaceability across the neotropics, aiming to ensure the persistence of at least 25% of range size in climatically stable areas for each WEP, using agricultural models as constraints. KEY RESULTS: The Southeast Cerrado was the most biotically stable and irreplaceable region for the WEPs compared with other areas across the neotropics. CONCLUSIONS: Our findings strongly suggest that the Southeast Cerrado should be considered a conservation priority, with new protected areas to be sustainably managed and restored, to guarantee the supply of cultural and ecosystem services provided from the Cerrado's WEPs.

Forest structure drives global diversity of primates.

Geographic gradients in the species richness of non-human primates have traditionally been attributed to the variation in forest productivity (related to precipitation levels), although an all-inclusive, global-scale analysis has never been conducted. We perform a more comprehensive test on the role of precipitation and biomass production and propose an alternative hypothesis - the variation in vertical structure of forest habitats as measured by forest canopy height - in determining primate species richness on a global scale. Considering the potential causal relationships among precipitation, productivity and forest structure, we arranged these variables within a path framework to assess their direct and indirect associations with the pattern of primate species richness using structural equation modelling. The analysis also accounted for the influence of spatial autocorrelation in the relationships and assessed possible historical differences among biogeographical regions. The path coefficients indicate that forest canopy height (used as a proxy for vertical forest structure) is a better predictor of primate species richness than either precipitation or productivity on both global and continental scales. The only exception was Asia, where precipitation prevailed, albeit independently from productivity or forest structure. The influence of spatially structured processes varied markedly among biogeographical regions. Our results challenge the traditional rainfall-based viewpoint in favour of forest distribution and structure as primary drivers of primate species richness, which aggregate potential effects from both climatic factors and habitat complexity. These findings may support predictions of the impact of forest removal on primate species richness.

Is rich and rare the common share? Describing biodiversity patterns to inform conservation practices for South American anurans.

Species richness and range size are key features of biogeographic and macroecological analyses, which can yield a first assessment tool to define conservation priorities. Here we combined both features in a simultaneous analysis, based on range-diversity plots, to identify sets of rich-rare (high species richness with restricted ranges) and poor-rare cells (low species richness with restricted ranges). We applied this analysis to the anurans of South America and evaluated the representation of those sets of cells within the protected area system. South American anurans showed high species richness in the Brazilian Atlantic Forest and East Tropical Andes, while regions harboring most of the rare species were concentrated in the Andes and Atlantic Coast from North-Eastern Brazil to River Plate. Based on such patterns, we identified as rich-rare cells the Brazilian Atlantic Forest and Tropical Andes and as poor-rare cells the southern part of Andes and Uruguay. A low fraction of both sets of cells was represented within the protected area system. We show that a simultaneous consideration of species richness and rarity provides a rapid assessment of large-scale biodiversity patterns and may contribute to the definition of conservation priorities.

Mantel test in population genetics.

The comparison of genetic divergence or genetic distances, estimated by pairwise FST and related statistics, with geographical distances by Mantel test is one of the most popular approaches to evaluate spatial processes driving population structure. There have been, however, recent criticisms and discussions on the statistical performance of the Mantel test. Simultaneously, alternative frameworks for data analyses are being proposed. Here, we review the Mantel test and its variations, including Mantel correlograms and partial correlations and regressions. For illustrative purposes, we studied spatial genetic divergence among 25 populations of Dipteryx alata ("Baru"), a tree species endemic to the Cerrado, the Brazilian savannas, based on 8 microsatellite loci. We also applied alternative methods to analyze spatial patterns in this dataset, especially a multivariate generalization of Spatial Eigenfunction Analysis based on redundancy analysis. The different approaches resulted in similar estimates of the magnitude of spatial structure in the genetic data. Furthermore, the results were expected based on previous knowledge of the ecological and evolutionary processes underlying genetic variation in this species. Our review shows that a careful application and interpretation of Mantel tests, especially Mantel correlograms, can overcome some potential statistical problems and provide a simple and useful tool for multivariate analysis of spatial patterns of genetic divergence.

The three phases of the ensemble forecasting of niche models: geographic range and shifts in climatically suitable areas of Utetheisa ornatrix (Lepidoptera, Arctiidae) / As três fases da projeção combinada de modelos de nicho: distribuição geográfica e deslocamento de áreas climaticamente adequadas para Utetheisa ornatrix (Lepidoptera, Arctiidae)

Species' geographic ranges are usually considered as basic units in macroecology and biogeography, yet it is still difficult to measure them accurately for many reasons. About 20 years ago, researchers started using local data on species' occurrences to estimate broad scale ranges, thereby establishing the niche modeling approach. However, there are still many problems in model evaluation and application, and one of the solutions is to find a consensus solution among models derived from different mathematical and statistical models for niche modeling, climatic projections and variable combination, all of which are sources of uncertainty during niche modeling. In this paper, we discuss this approach of ensemble forecasting and propose that it can be divided into three phases with increasing levels of complexity. Phase I is the simple combination of maps to achieve a consensual and hopefully conservative solution. In Phase II, differences among the maps used are described by multivariate analyses, and Phase III consists of the quantitative evaluation of the relative magnitude of uncertainties from different sources and their mapping. To illustrate these developments, we analyzed the occurrence data of the tiger moth, Utetheisa ornatrix (Lepidoptera, Arctiidae), a Neotropical moth species, and modeled its geographic range in current and future climates.

A distribuição geográfica das espécies tem sido considerada como a unidade básica em macroecologia e biogeografia, mas ainda há dificuldades em mensurá-la de forma adequada, por diferentes razões. Há cerca de 20 anos atrás, os pesquisadores começaram a utilizar dados locais da ocorrência das espécies para estimar essas distribuições utilizando modelos de nicho ecológico. Entretanto, ainda há uma série de problemas na avaliação dos modelos e em suas aplicações, e uma das soluções é utilizar um consenso de diferentes modelos, projeções climáticas, cenários de emissão e combinação de variáveis, que são fontes de incerteza durante o processo de modelagem de nicho. Neste artigo nós discutimos essa abordagem de consenso e a dividimos em três fases, com níveis crescentes de complexidade. A Fase I é simplesmente a combinação de mapas e a obtenção e interpretação de um único mapa de consenso. A Fase II envolve a descrição das diferenças entre os mapas utilizando técnicas de análise multidimensional, enquanto que a Fase III consiste em analisar quantitativamente e mapear a magnitude relativa das diferentes fontes de incerteza. A fim de ilustrar essa abordagem, nós analisamos dados de ocorrência de Utetheisa ornatrix (Lepidoptera, Arctiidae), uma mariposa distribuída na região Neotropical, modelando sua distribuição geográfica com base em dados climáticos atuais e projeções de mudança climática.

Lonofibrase, a novel alpha-fibrinogenase from Lonomia obliqua caterpillars.

Envenomation caused by Lonomia obliqua caterpillars is an increasing problem in Southern Brazil. The clinical profile is characterized by a profound hemorrhagic disorder. In the present study, we describe the characterization of a fibrin(ogen)olytic factor (lonofibrase) isolated from a venomous secretion of the caterpillars. The crude extract showed a dose-dependent inhibitory effect in the rate of thrombin-induced fibrinogen clotting and produced fragmentation of fibrinogen. Isolation of the fibrin(ogen)olytic enzyme was achieved by combining ion exchange chromatography followed by gel filtration in a fast protein liquid chromatography (FPLC) system. A single 35-kDa band was identified and the isolated enzyme named lonofibrase. Lonofibrase rapidly degrades Aalpha and Bbeta chains of fibrinogen, also being able to cleave fibrin in a distinct way from that observed with plasmin. The presence of lonofibrase with both fibrinogenolytic and fibrinolytic activities in L. obliqua secretion is coherent with the severe hemorrhagic clinical profile resulting from envenomation caused by these insects.