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Neotropical ecosystems are renowned for numerous examples of adaptive radiation in both plants and animals resulting in high levels of biodiversity and endemism. However, we still lack a comprehensive review of the abiotic and biotic factors that contribute to these adaptive radiations. To fill this gap, we delve into the geological history of the region, including the role of tectonic events such as the Andean uplift, the formation of the Isthmus of Panama, and the emergence of the Guiana and Brazilian Shields. We also explore the role of ecological opportunities created by the emergence of new habitats, as well as the role of key innovations, such as novel feeding strategies or reproductive mechanisms. We discuss different examples of adaptive radiation, including classic ones like Darwin's finches and Anolis lizards, and more recent ones like bromeliads and lupines. Finally, we propose new examples of adaptive radiations mediated by ecological interactions in their geological context. By doing so, we provide insights into the complex interplay of factors that contributed to the remarkable diversity of life in the Neotropics and highlight the importance of this region in understanding the origins of biodiversity.

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Fire plays a dominant role in deforestation, particularly in the tropics, but the relative extent of transformations and influence of fire frequency on eventual forest loss remain unclear. Here, we analyze the frequency of fire and its influence on postfire forest trajectories between 2001 and 2018. We account for ~1.1% of Latin American forests burnt in 2002-2003 (8,465,850 ha). Although 40.1% of forests (3,393,250 ha) burned only once, by 2018, ~48% of the evergreen forests converted to other, primarily grass-dominated uses. While greater fire frequency yielded more transformation, our results reveal the staggering impact of even a single fire. Increasing fire frequency imposes greater risks of irreversible forest loss, transforming forests into ecosystems increasingly vulnerable to degradation. Reversing this trend is indispensable to both mitigate and adapt to climate change globally. As climate change transforms fire regimes across the region, key actions are needed to conserve Latin American forests.

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Preventing extinctions requires understanding macroecological patterns of vulnerability or persistence. However, correlates of risk can be nonlinear, within-species risk varies geographically, and current-day threats cannot reveal drivers of past losses. We investigated factors that regulated survival or extinction in Caribbean mammals, which have experienced the globally highest level of human-caused postglacial mammalian extinctions, and included all extinct and extant Holocene island populations of non-volant species (219 survivals or extinctions across 118 islands). Extinction selectivity shows a statistically detectable and complex body mass effect, with survival probability decreasing for both mass extremes, indicating that intermediate-sized species have been more resilient. A strong interaction between mass and age of first human arrival provides quantitative evidence of larger mammals going extinct on the earliest islands colonized, revealing an extinction filter caused by past human activities. Survival probability increases on islands with lower mean elevation (mostly small cays acting as offshore refugia) and decreases with more frequent hurricanes, highlighting the risk of extreme weather events and rising sea levels to surviving species on low-lying cays. These findings demonstrate the interplay between intrinsic biology, regional ecology and specific local threats, providing insights for understanding drivers of biodiversity loss across island systems and fragmented habitats worldwide.

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Populations along steep environmental gradients are subject to differentiating selection that can result in local adaptation, despite countervailing gene flow, and genetic drift. In montane systems, where species are often restricted to narrow ranges of elevation, it is unclear whether the selection is strong enough to influence functional differentiation of subpopulations differing by a few hundred meters in elevation. We used targeted capture of 12 501 exons from across the genome, including 271 genes previously implicated in altitude adaptation, to test for adaptation to local elevations for 2 highland hummingbird species, Coeligena violifer (n = 62) and Colibri coruscans (n = 101). For each species, we described population genetic structure across the complex geography of the Peruvian Andes and, while accounting for this structure, we tested whether elevational allele frequency clines in single nucleotide polymorphisms (SNPs) showed evidence for local adaptation to elevation. Although the 2 species exhibited contrasting population genetic structures, we found signatures of clinal genetic variation with shifts in elevation in both. The genes with SNP-elevation associations included candidate genes previously discovered for high-elevation adaptation as well as others not previously identified, with cellular functions related to hypoxia response, energy metabolism, and immune function, among others. Despite the homogenizing effects of gene flow and genetic drift, natural selection on parts of the genome evidently optimizes elevation-specific cellular function even within elevation range-restricted montane populations. Consequently, our results suggest local adaptation occurring in narrow elevation bands in tropical mountains, such as the Andes, may effectively make them "taller" biogeographic barriers.

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The IUCN provides a spatial database for many species, including terrestrial mammals. This database includes shapefiles with taxonomic information and the extent of occurrence for each species, and has been used in hundreds of studies in ecology, biogeography and conservation. Here we provide updated distribution maps that comprise the extent of occurrence of the neotropical bat species in the superfamily Noctilionoidea (Mammalia: Chiroptera) after a thorough research of new records published between January 2008 and March 2018. The main motivation for this update was the inclusion of spatial and climatic variables in explaining the ecological and taxonomic diversity of noctilionoid bats. The core of the superfamily (246 species distributed in five families out of 250 species) occurs in the Neotropics and shows ecological diversity unparalleled among mammals. This clade also shows the only evolutionary shift towards higher speciation rates within the order Chiroptera. Updating the range maps for these bats resulted in the modification of maps of 94 species, and the creation of new maps for 37 species missing from the IUCN database. From the 94 modified maps, 55 species increased their latitudinal range and 38 increased their longitudinal range. These modifications did not change the overall extent of occurrence of the clade. Altogether, modified and new maps represent 53% of Noctilionoidea. No copyright or proprietary restrictions are associated with the use of this data set other than citation of this Data Paper.

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The role of trophic specialisation in taxonomic diversification remains unclear. Plant specialists diversify faster than omnivores and animalivores, but at shorter macroevolutionary scales this pattern sometimes reverses. Here, we estimate the effect of diet diversification on speciation rates in noctilionoid bats, controlling for tree shape, rate heterogeneity and macroevolutionary regimes. We hypothesise that niche subdivision among herbivores positively relates to speciation rates, differing between macroevolutionary regimes. We found the rate at which new herbivorous lineages originate decreases as rates of diet evolution increase. Herbivores experience higher speciation rates, but generalist herbivores and predominantly herbivorous omnivores speciate faster than specialised herbivores, omnivores and animalivores. Generalised herbivory is not a dead end. We show that analysing ecological traits and diversification requires accounting for macroevolutionary regimes and within- and between-clade variation in evolutionary rates. Our approach overcomes the high false-positive rates of other methods and illuminates the roles of herbivory and specialisation in speciation.

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Fire is an important tool in tropical forest management, as it alters forest composition, structure, and the carbon budget. The United Nations program on Reducing Emissions from Deforestation and Forest Degradation (REDD+) aims to sustainably manage forests, as well as to conserve and enhance their carbon stocks. Despite the crucial role of fire management, decision-making on REDD+ interventions fails to systematically include fires. Here, we address this critical knowledge gap in two ways. First, we review REDD+ projects and programs to assess the inclusion of fires in monitoring, reporting, and verification (MRV) systems. Second, we model the relationship between fire and forest for a pilot site in Colombia using near-real-time (NRT) fire monitoring data derived from the Moderate Resolution Imaging Spectroradiometer (MODIS). The literature review revealed fire remains to be incorporated as a key component of MRV systems. Spatially explicit modeling of land use change showed the probability of deforestation declined sharply with increasing distance to the nearest fire the preceding year (multi-year model area under the curve [AUC] 0.82). Deforestation predictions based on the model performed better than the official REDD early-warning system. The model AUC for 2013 and 2014 was 0.81, compared to 0.52 for the early-warning system in 2013 and 0.68 in 2014. This demonstrates NRT fire monitoring is a powerful tool to predict sites of forest deforestation. Applying new, publicly available, and open-access NRT fire data should be an essential element of early-warning systems to detect and prevent deforestation. Our results provide tools for improving both the current MRV systems, and the deforestation early-warning system in Colombia.

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Identifying drivers of deforestation in tropical biodiversity hotspots is critical to assess threats to particular ecosystems and species and proactively plan for conservation. We analyzed land cover change between 2002 and 2007 in the northern Andes, Chocó, and Amazon forests of Colombia, the largest producer of coca leaf for the global cocaine market, to quantify the impact of this illicit crop on forest dynamics, evaluate the effectiveness of protected areas in this context, and determine the effects of eradication on deforestation. Landscape-level analyses of forest conversion revealed that proximity to new coca plots and a greater proportion of an area planted with coca increased the probability of forest loss in southern Colombia, even after accounting for other covariates and spatial autocorrelation. We also showed that protected areas successfully reduced forest conversion in coca-growing regions. Neither eradication nor coca cultivation predicted deforestation rates across municipalities. Instead, the presence of new coca cultivation was an indicator of municipalities, where increasing population led to higher deforestation rates. We hypothesize that poor rural development underlies the relationship between population density and deforestation in coca-growing areas. Conservation in Colombia's vast forest frontier, which overlaps with its coca frontier, requires a mix of protected areas and strategic rural development to succeed.

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Different frameworks have been proposed for using molecular data in systematic revisions, but there is ongoing debate on their applicability, merits and shortcomings. In this paper we examine the fit between morphological and molecular data in the systematic revision of Paroaria, a group of conspicuous songbirds endemic to South America. We delimited species based on examination of >600 specimens, and developed distance-gap, and distance- and character-based coalescent simulations to test species limits with molecular data. The morphological and molecular data collected were then analyzed using parsimony, maximum likelihood, and Bayesian phylogenetics. The simulations were better at evaluating the new species limits than using genetic distances. Species diversity within Paroaria had been underestimated by 60%, and the revised genus comprises eight species. Phylogenetic analyses consistently recovered a congruent topology for the most recently derived species in the genus, but the most basal divergences were not resolved with these data. The systematic and phylogenetic hypotheses developed here are relevant to both setting conservation priorities and understanding the biogeography of South America.

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For more than 30 years Colombia has waged an internal War on Drugs with the support of the international community. During this time, the illegal economy has evolved toward integrating cultivation with processing and trafficking, making Colombia the largest grower of coca in the world. The environmental impact of coca production and processing is vast, accounting for large quantities of toxic chemicals directly dumped onto the soil and watersheds, as well as most deforestation since the 1990s. The policies pursued to stem the coca economy, however, are based on unfounded assumptions about the behaviour of coca growers in the context of international markets. Despite their unfounded premises, these assumptions have acquired a mythical stature. In this article we review the most persistent myths about coca production with a view to understanding its links to environmental degradation. To this end, we present data on the economic and demographic background of coca growers, their impact on the environment, and their behaviour in the larger context of international markets and current eradication policies.

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Two assumptions have framed previous systematic and biogeographic studies of the family Natalidae: that it comprises a few widespread species, and that extant lineages originated in Mexico and/or Central America. This study analyzes new sequence data from the mitochondrial cytochrome b and the nuclear Rag2, to clarify species boundaries and infer relationships among extant taxa. Fixed differences in cytochrome b coincide with published morphological characters, and show that the family includes at least eight species. One newly recognized species is known to live from a single locality in Jamaica, suggesting immediate conservation measures and underscoring the urgency of taxonomic revision. Among the three genera, Chilonatalus and Natalus form a clade, to the exclusion of Nyctiellus. This phylogeny and the geographic distribution of natalids, both extant and extinct, are hardly compatible with a Middle American origin for the group. Instead, extant natalids appear to have originated in the West Indies. The threat of Caribbean hurricanes early in their evolutionary history might account for the specialized cave roosting that characterizes all natalids, even continental species.

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