Neotropics as a Cradle for Adaptive Radiations.

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.

Invasion by Cedrela odorata threatens long distance migration of Galapagos tortoises.

Invasive alien species are among the most pervasive threats to biodiversity. Invasive species can cause catastrophic reductions in populations of native and endemic species and the collapse of ecosystem function. A second major global conservation concern is the extirpation of large-bodied mobile animals, including long-distance migrants, which often have keystone ecological roles over extensive spatial extents. Here, we report on a potentially catastrophic synergy between these phenomena that threatens the endemic biota of the Galapagos Archipelago. We used GPS telemetry to track 140 migratory journeys by 25 Western Santa Cruz Island Galapagos tortoises. We plotted the spatial interaction between tortoise migrations and recently established non-native forest dominated by the invasive tree Cedrela odorata (Cedrela forest). We qualified (a) the proportion of migratory journeys that traversed Cedrela forest, and (b) the probability that this observed pattern occurred by chance. Tortoise migrations were overwhelmingly restricted to small corridors between Cedrela forest blocks, indicating clear avoidance of those blocks. Just eight of 140 migrations traversed extensive Cedrela stands. Tortoises avoid Cedrela forest during their migrations. Further expansion of Cedrela forest threatens long-distance migration and population viability of critically endangered Galapagos tortoises. Applied research to determine effective management solutions to mitigate Cedrela invasion is a high priority.

MADERA: A standardized Pan-Amazonian dataset for tropical timber species.

We compiled and presented a dataset for all timber species reported in the Amazon region from all nine South American Amazonian countries. This was based on official information from every country, as well as from two substantial scientific references. We verified the standard taxonomic names from each individual source, using the Taxonomic Name Resolution Service (TNRS) and considered all Amazonian tree species with diameter at breast height (DBH) ≥10 cm. We also obtained estimates of the current population size for most species from a published approach based on data from 1900 tree inventory plots (1-ha each) distributed across the Amazon region and part from the Amazon Tree Diversity Network (ATDN). We then identified the hyperdominant timber species. In addition, we overlapped our timber species list with data for species that are used for commercial purposes, according to the International Tropical Timber Organization (ITTO), the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) and the International Union for Conservation of Nature (IUCN) taxa assessment and Red List categories. Finally, we also included IUCN Red List categories based on combined deforestation, and climate change scenarios for these species. Our final Amazonian timber species dataset contains 1112 unique species records, which belong to 337 genera and 72 families from the lowland Amazonian rainforest, with associated information related to population, conservation, and trade status of each species. The authors of this research expect that the information provided will be useful to strengthen the public forestry policies of the Amazon countries, inform ecological studies, as well for forest management purposes. The data are released under the Creative Commons Attribution 4.0 International license.

Evolutionary genomics of oceanic island radiations.

A recurring feature of oceanic archipelagos is the presence of adaptive radiations that generate endemic, species-rich clades that can offer outstanding insight into the links between ecology and evolution. Recent developments in evolutionary genomics have contributed towards solving long-standing questions at this interface. Using a comprehensive literature search, we identify studies spanning 19 oceanic archipelagos and 110 putative adaptive radiations, but find that most of these radiations have not yet been investigated from an evolutionary genomics perspective. Our review reveals different gaps in knowledge related to the lack of implementation of genomic approaches, as well as undersampled taxonomic and geographic areas. Filling those gaps with the required data will help to deepen our understanding of adaptation, speciation, and other evolutionary processes.

A pilot study to estimate the population size of endangered Galápagos marine iguanas using drones.

BACKGROUND: Large-scale species monitoring remains a significant conservation challenge. Given the ongoing biodiversity crisis, the need for reliable and efficient methods has never been greater. Drone-based techniques have much to offer in this regard: they allow access to otherwise unreachable areas and enable the rapid collection of non-invasive field data. Herein, we describe the development of a drone-based method for the estimation of population size in Galápagos marine iguanas, Amblyrhynchus cristatus. As a large-bodied lizard that occurs in open coastal terrain, this endemic species is an ideal candidate for drone surveys. Almost all Amblyrhynchus subspecies are Endangered or Critically Endangered according to the IUCN yet since several colonies are inaccessible by foot, ground- based methods are unable to address the critical need for better census data. In order to establish a drone-based approach to estimate population size of marine iguanas, we surveyed in January 2021 four colonies on three focal islands (San Cristobal, Santa Fe and Espanola) using three techniques: simple counts (the standard method currently used by conservation managers), capture mark-resight (CMR), and drone-based counts. The surveys were performed within a 4-day window under similar ambient conditions. We then compared the approaches in terms of feasibility, outcome and effort. RESULTS: The highest population-size estimates were obtained using CMR, and drone-based counts were on average 14% closer to CMR estimates-and 17-35% higher-than those obtained by simple counts. In terms of field-time, drone-surveys can be faster than simple counts, but image analyses were highly time consuming. CONCLUSION: Though CMR likely produces superior estimates, it cannot be performed in most cases due to lack of access and knowledge regarding colonies. Drone-based surveys outperformed ground-based simple counts in terms of outcome and this approach is therefore suitable for use across the range of the species. Moreover, the aerial approach is currently the only credible solution for accessing and surveying marine iguanas at highly remote colonies. The application of citizen science and other aids such as machine learning will alleviate the issue regarding time needed to analyze the images.

Climate Constrains Photosynthetic Strategies in Darwin's Daisies: A Test of the Climatic Variability and Jack-of-All-Trades Hypotheses.

AbstractEmpirical evidence for the climate variability and performance trade-off hypotheses is limited to animals, and it is unclear whether climate constrains the photosynthetic strategies of plants. The plant genus Scalesia Arn. ex Lindl (family Asteraceae), endemic to the Galápagos archipelago, provides an ideal study system to test these hypotheses because of its species with markedly different leaf morphologies that occupy distinct climatic zones. In this study we tested the classic hypotheses that (1) climate constrains leaf size, (2) high climatic temperature variability selects for thermal generalists (i.e., the climate variability hypothesis), and (3) there is a trade-off between the breadth and rate of photosynthetic performance (i.e., jack-of-all-trades but master of none hypothesis). To do this we measured the leaf morphologies and photosynthetic temperature response curves of 11 Scalesia species. In support of a priori predictions, we found that small-leaved Scalesia species were more likely to occupy hotter and drier climates than large-leaved species, there was a positive relationship between climatic temperature variability and the breadth of photosynthetic performance, and photosynthetic performance was negatively correlated with photosynthetic breadth. Our study is among the first to provide evidence for the performance-breadth trade-off hypothesis in photosynthesis, suggesting that climate change may select for photosynthetic thermal generalists.

Global patterns of vascular plant alpha diversity.

Global patterns of regional (gamma) plant diversity are relatively well known, but whether these patterns hold for local communities, and the dependence on spatial grain, remain controversial. Using data on 170,272 georeferenced local plant assemblages, we created global maps of alpha diversity (local species richness) for vascular plants at three different spatial grains, for forests and non-forests. We show that alpha diversity is consistently high across grains in some regions (for example, Andean-Amazonian foothills), but regional 'scaling anomalies' (deviations from the positive correlation) exist elsewhere, particularly in Eurasian temperate forests with disproportionally higher fine-grained richness and many African tropical forests with disproportionally higher coarse-grained richness. The influence of different climatic, topographic and biogeographical variables on alpha diversity also varies across grains. Our multi-grain maps return a nuanced understanding of vascular plant biodiversity patterns that complements classic maps of biodiversity hotspots and will improve predictions of global change effects on biodiversity.

The genomic basis of the plant island syndrome in Darwin's giant daisies.

The repeated, rapid and often pronounced patterns of evolutionary divergence observed in insular plants, or the 'plant island syndrome', include changes in leaf phenotypes, growth, as well as the acquisition of a perennial lifestyle. Here, we sequence and describe the genome of the critically endangered, Galápagos-endemic species Scalesia atractyloides Arnot., obtaining a chromosome-resolved, 3.2-Gbp assembly containing 43,093 candidate gene models. Using a combination of fossil transposable elements, k-mer spectra analyses and orthologue assignment, we identify the two ancestral genomes, and date their divergence and the polyploidization event, concluding that the ancestor of all extant Scalesia species was an allotetraploid. There are a comparable number of genes and transposable elements across the two subgenomes, and while their synteny has been mostly conserved, we find multiple inversions that may have facilitated adaptation. We identify clear signatures of selection across genes associated with vascular development, growth, adaptation to salinity and flowering time, thus finding compelling evidence for a genomic basis of the island syndrome in one of Darwin's giant daisies.

Rediscovery of Gasteranthusextinctus L.E.Skog & L.P.Kvist (Gesneriaceae) at multiple sites in western Ecuador.

We report the rediscovery of the Critically Endangered cloud forest herb Gasteranthusextinctus, not seen since 1985. In 2019 and 2021, G.extinctus was recorded at five sites in the western foothills of the Ecuadorian Andes, 4-25 km from the type locality at the celebrated Centinela ridge. We describe the species' distribution, abundance, habitat and conservation status and offer recommendations for further research and conservation efforts focused on G.extinctus and the small, disjunct forest remnants it occupies.

Global tropical dry forest extent and cover: A comparative study of bioclimatic definitions using two climatic data sets.

There is a debate concerning the definition and extent of tropical dry forest biome and vegetation type at a global spatial scale. We identify the potential extent of the tropical dry forest biome based on bioclimatic definitions and climatic data sets to improve global estimates of distribution, cover, and change. We compared four bioclimatic definitions of the tropical dry forest biome-Murphy and Lugo, Food and Agriculture Organization (FAO), DryFlor, aridity index-using two climatic data sets: WorldClim and Climatologies at High-resolution for the Earth's Land Surface Areas (CHELSA). We then compared each of the eight unique combinations of bioclimatic definitions and climatic data sets using 540 field plots identified as tropical dry forest from a literature search and evaluated the accuracy of World Wildlife Fund tropical and subtropical dry broadleaf forest ecoregions. We used the definition and climate data that most closely matched field data to calculate forest cover in 2000 and change from 2001 to 2020. Globally, there was low agreement (< 58%) between bioclimatic definitions and WWF ecoregions and only 40% of field plots fell within these ecoregions. FAO using CHELSA had the highest agreement with field plots (81%) and was not correlated with the biome extent. Using the FAO definition with CHELSA climatic data set, we estimate 4,931,414 km2 of closed canopy (≥ 40% forest cover) tropical dry forest in 2000 and 4,369,695 km2 in 2020 with a gross loss of 561,719 km2 (11.4%) from 2001 to 2020. Tropical dry forest biome extent varies significantly based on bioclimatic definition used, with nearly half of all tropical dry forest vegetation missed when using ecoregion boundaries alone, especially in Africa. Using site-specific field validation, we find that the FAO definition using CHELSA provides an accurate, standard, and repeatable way to assess tropical dry forest cover and change at a global scale.

The Radiation of Darwin's Giant Daisies in the Galápagos Islands.

Evolutionary radiations on oceanic islands have fascinated biologists since Darwin's exploration of the Galápagos archipelago [1, 2]. Island radiations can provide key insights for understanding rapid speciation, including evolutionary patterns and the processes behind them. However, lack of resolution of species relationships has historically hindered their investigation, particularly in the plant kingdom [3-5]. Here, we report a time-calibrated phylogenomic analysis based on genotyping-by-sequencing data [6] of the 15 species of Scalesia (Darwin's giant daisies), an iconic and understudied plant radiation endemic to the Galápagos Islands and considered the plant counterpart to Darwin's finches [1, 7-9]. Results support a Pliocene to early Pleistocene divergence between Scalesia and the closest South American relatives, and rapid diversification of extant Scalesia species from a common ancestor dated to the Middle Pleistocene. Major evolutionary patterns in Scalesia include the following: (1) lack of compliance with the "progression rule" hypothesis, in which earlier diverging lineages are expected to occupy older islands; (2) a predominance of within-island speciation over between-island speciation; and (3) repeated convergent evolution of potentially adaptive traits and habitat preferences on different islands during the course of diversification. Massive sequencing provided the essential framework for investigating evolutionary and ecological processes in the complex natural laboratory of the Galápagos, thereby advancing our understanding of island plant radiations.

Trees of Amazonian Ecuador: a taxonomically verified species list with data on abundance and distribution.

We compiled a data set for all tree species collected to date in lowland Amazonian Ecuador in order to determine the number of tree species in the region. This data set has been extensively verified by taxonomists and is the most comprehensive attempt to evaluate the tree diversity in one of the richest species regions of the Amazon. We used four main sources of data: mounted specimens deposited in Ecuadorian herbaria only, specimen records of a large-scale 1-hectare-plot network (60 plots in total), data from the Missouri Botanical Garden Tropicos® database (MO), and literature sources. The list of 2,296 tree species names we provide in this data set is based on 47,486 herbarium records deposited in the following herbaria: Alfredo Paredes Herbarium (QAP), Catholic University Herbarium (QCA), Herbario Nacional del Ecuador (QCNE), Missouri Botanical Garden (MO), and records from an extensive sampling of 29,768 individuals with diameter at breast height (dbh) ≥10 cm recorded in our plot network. We also provide data for the relative abundance of species, geographic coordinates of specimens deposited in major herbaria around the world, whether the species is native or endemic, current hypothesis of geographic distribution, representative collections, and IUCN threat category for every species recorded to date in Amazonian Ecuador. These data are described in Metadata S1 and can be used for macroecological, evolutionary, or taxonomic studies. There are no copyright restrictions; data are freely available for noncommercial scientific use (CC BY 3.0). Please see Metadata S1 (Class III, Section B.1: Proprietary restrictions) for additional information on usage.

Scaling issues of neutral theory reveal violations of ecological equivalence for dominant Amazonian tree species.

Neutral models are often used as null models, testing the relative importance of niche versus neutral processes in shaping diversity. Most versions, however, focus only on regional scale predictions and neglect local level contributions. Recently, a new formulation of spatial neutral theory was published showing an incompatibility between regional and local scale fits where especially the number of rare species was dramatically under-predicted. Using a forward in time semi-spatially explicit neutral model and a unique large-scale Amazonian tree inventory data set, we show that neutral theory not only underestimates the number of rare species but also fails in predicting the excessive dominance of species on both regional and local levels. We show that although there are clear relationships between species composition, spatial and environmental distances, there is also a clear differentiation between species able to attain dominance with and without restriction to specific habitats. We conclude therefore that the apparent dominance of these species is real, and that their excessive abundance can be attributed to fitness differences in different ways, a clear violation of the ecological equivalence assumption of neutral theory.

Estimating and interpreting migration of Amazonian forests using spatially implicit and semi-explicit neutral models.

With many sophisticated methods available for estimating migration, ecologists face the difficult decision of choosing for their specific line of work. Here we test and compare several methods, performing sanity and robustness tests, applying to large-scale data and discussing the results and interpretation. Five methods were selected to compare for their ability to estimate migration from spatially implicit and semi-explicit simulations based on three large-scale field datasets from South America (Guyana, Suriname, French Guiana and Ecuador). Space was incorporated semi-explicitly by a discrete probability mass function for local recruitment, migration from adjacent plots or from a metacommunity. Most methods were able to accurately estimate migration from spatially implicit simulations. For spatially semi-explicit simulations, estimation was shown to be the additive effect of migration from adjacent plots and the metacommunity. It was only accurate when migration from the metacommunity outweighed that of adjacent plots, discrimination, however, proved to be impossible. We show that migration should be considered more an approximation of the resemblance between communities and the summed regional species pool. Application of migration estimates to simulate field datasets did show reasonably good fits and indicated consistent differences between sets in comparison with earlier studies. We conclude that estimates of migration using these methods are more an approximation of the homogenization among local communities over time rather than a direct measurement of migration and hence have a direct relationship with beta diversity. As betadiversity is the result of many (non)-neutral processes, we have to admit that migration as estimated in a spatial explicit world encompasses not only direct migration but is an ecological aggregate of these processes. The parameter m of neutral models then appears more as an emerging property revealed by neutral theory instead of being an effective mechanistic parameter and spatially implicit models should be rejected as an approximation of forest dynamics.