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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.

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. Maintaining long‐distance elevational migration in the face of environmental change is important to ensure both the reproductive success and keystone ecological role of giant tortoises on Santa Cruz Island, Galapagos. Here, we show that rapid range expansion by Cedrela odorata, an invasive tree, threatens the last migration corridors of western Santa Crus Galapagos tortoises. Finding effective management solutions to Cedrela expansion is critical for conservation for critically endangered Galapagos tortoises and their ecosystem.

Cedrela odorata is considered the second most invasive tree species of the Galapagos Islands. Although it is listed in CITES Appendix II and there are population losses in mainland Ecuador, in Galapagos it is paradoxically a species of concern due to its invasive potential. Genetic studies can shed light on the invasion history of introduced species causing effects on unique ecosystems like the Galapagos. We analyzed nine microsatellite markers in C. odorata individuals from Galapagos and mainland Ecuador to describe the genetic diversity and population structure of C. odorata in the Galapagos and to explore the origin and invasion history of this species. The genetic diversity found for C. odorata in Galapagos (He = 0.55) was lower than reported in the mainland (He = 0.81), but higher than other invasive insular plant species, which could indicate multiple introductions. Our results suggest that Ecuador's northern Coastal region is the most likely origin of the Galapagos C. odorata, although further genomic studies, like Whole Genome Sequencing, Rad‐Seq, and/or Whole Genome SNP analyses, are needed to confirm this finding. Moreover, according to our proposed pathway scenarios, C. odorata was first introduced to San Cristobal and/or Santa Cruz from mainland Ecuador. After these initial introductions, C. odorata appears to have arrived to Isabela and Floreana from either San Cristobal or Santa Cruz. Here, we report the first genetic study of C. odorata in the Galapagos and the first attempt to unravel the invasion history of this species. The information obtained in this research could support management and control strategies to lessen the impact that C. odorata has on the islands' local flora and fauna. Resumen Cedrela odorata es considerada la segunda especie más invasora de árboles en las Islas Galápagos. Esta especie está catalogada en el Apéndice II de CITES y sus poblaciones se encuentran amenazadas en Ecuador continental, pero paradójicamente en Galápagos es una especie de preocupación por su potencial invasor. Estudios genéticos pueden ayudar a entender la historia de invasión de especies introducidas que causan efectos en ecosistemas únicos como Galápagos. En este estudio, analizamos 9 marcadores microsatélites en individuos de Galápagos y Ecuador continental para describir la diversidad genética y estructura poblacional de C. odorata en Galápagos y explorar el origen e historia de invasión de esta especie. La diversidad genética encontrada para C. odorata en Galápagos (He = 0.55) fue menor que la reportada en continente (He = 0.81), pero mayor que la de otras especies de plantas insulares invasoras, lo que podría sugerir múltiples introducciones de esta especie a Galápagos. Nuestros resultados sugieren que la costa norte ecuatoriana es el origen más probable de C. odorata en Galápagos, aunque más estudios, como secuenciación del genoma completo, Rad‐Seq y/o análisis de SNPs, son necesarios para confirmar este hecho. Además, de acuerdo con los escenarios propuestos, es posible que C. odorata haya sido introducida primero a San Cristóbal y/o Santa Cruz desde Ecuador continental. Después de estas introducciones iniciales, parece haber llegado a Isabela y Floreana desde San Cristóbal o Santa Cruz. Este es el primer estudio genético de C. odorata en Galápagos y el primer intento de esclarecer la historia de invasión de esta especie. La información obtenida en esta investigación podría apoyar estrategias de manejo para disminuir el impacto que C. odorata tiene sobre la flora y fauna nativa de estas islas. Cedrela odorata is the second most invasive tree species in the Galapagos Islands. Using nine microsatellite markers, we found that the genetic diversity of C. odorata in Galapagos is lower (He = 0.55) than in mainland Ecuador (He = 0.81). Our preliminary findings suggest multiple introduction events and that the origin of C. odorata in Galapagos could have been the north coast of mainland Ecuador. Possibly, it first reached San Cristobal or Santa Cruz and then extended to Isabela and Floreana, information that provides insights for its management.

Research to date on Amazonian swamps has reinforced the impression that tree communities there are dominated by a small, morphologically specialized subset of the regional flora capable of surviving physiologically challenging conditions. In this paper, using data from a large‐scale tree inventory in upland, floodplain, and mixed palm swamp forests in Amazonian Ecuador, we report that tree communities growing on well‐drained and saturated soils are more similar than previously appreciated. While our data support the traditional view of Amazonian swamp forests as low‐diversity tree communities dominated by palms, they also reveal four patterns that have not been well documented in the literature to date: 1) tree communities in these swamp forests are dominated by a phylogenetically diverse oligarchy of 30 frequent and common species; 2) swamp specialists account for < 10% of species and a minority of stems; 3) most tree species recorded in swamps (> 80%) also occur in adjacent well‐drained forest types; and 4) many tree species present in swamps are common in well‐drained forests (e.g. upland oligarchs account for 34.1% of all swamp stems). These observations imply that, as in the temperate zone, the composition and structure of Amazonian swamp vegetation are determined by a combination of local‐scale environmental filters (e.g. plant survival in permanently saturated soils) and landscape‐scale patterns and processes (e.g. the composition and structure of tree communities in adjacent non‐swamp habitats, the dispersal of propagules from those habitats to swamps). We conclude with suggestions for further research to quantify the relative contributions of these factors in structuring tree communities in Amazonian swamps.

The humid highlands of the Galapagos are the islands’ most biologically productive regions and a key habitat for endemic animal and plant species. These areas are crucial for the region’s food security and for the control of invasive plants, but little is known about the spatial distribution of its land cover. We generated a baseline high-resolution land cover map of the agricultural zones and their surrounding protected areas. We combined the high spatial resolution of PlanetScope images with the high spectral resolution of Sentinel-2 images in an object-based classification using a RandomForest algorithm. We used images collected with an unmanned aerial vehicle (UAV) to verify and validate our classified map. Despite the astounding diversity and heterogeneity of the highland landscape, our classification yielded useful results (overall Kappa: 0.7, R2: 0.69) and revealed that across all four inhabited islands, invasive plants cover the largest fraction (28.5%) of the agricultural area, followed by pastures (22.3%), native vegetation (18.6%), food crops (18.3%), and mixed forest and pioneer plants (11.6%). Our results are consistent with historical trajectories of colonization and abandonment of the highlands. The produced dataset is designed to suit the needs of practitioners of both conservation and agriculture and aims to foster collaboration between the two areas.

Population surveys are essential for conservation, but are often resource-intensive. Modern technologies, like drones, facilitate data collection but increase the analysis burden. Citizen Science (CS) offers a solution by engaging non-specialists in data analysis. We evaluated CS for monitoring marine iguanas, focusing on volunteers’ accuracy in detecting and counting individuals in aerial images. During three phases of our Zooniverse project, over 13,000 volunteers contributed 1,375,201 classifications from 57,838 images; each classified up to 30 times. Using a Gold Standard dataset of expert counts from 4,345 images, we evaluated optimal aggregation methods for CS-inputs. Volunteers achieved 68–94% accuracy in detection, with more false negatives than false positives. The standard ‘majority vote’ aggregation approach (where the answer given by the majority of individual inputs is selected) produced less accuracy than when a minimum threshold of five volunteers (from the total independent classifications) was used. Image quality significantly influenced accuracy; by excluding suboptimal pilot-phase data, volunteer counts were 91–92% accurate. HDBSCAN clustering yielded the best results. We conclude that volunteers can accurately identify and count marine iguanas from drone images, though there is a tendency for undercounting. However, even CS-based data analysis remains relatively resource-intensive, underscoring the need to develop an automated approach.

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.

Transposable elements (TEs) have been hypothesized to play a pivotal role in driving diversification by facilitating the emergence of novel phenotypes and the accumulation of divergence between species. Hybridization and adaptation to novel niches have been proposed to destabilize mechanisms constraining TE proliferation, potentially inducing a ‘TE burst’ that promotes TE accumulation on the genome. The rapid speciation and ecological diversification characteristic of adaptive radiations offer a unique opportunity to examine the link between TE accumulation and speciation, diversification, hybridization and adaptation. Here, focusing on all 15 species of the genus Scalesia (Asteraceae), a radiation endemic to the Galápagos Islands, we test whether diversification, hybridization, or shifts in ecological niche are associated with changes in TE accumulation in genomes. Our analyses reveal little to no variation in TE accumulation among Scalesia species nor its hybrid populations. Shifts in ecological niches, linked to climatic variation, did not result in discernible changes in TE accumulation, a surprising finding given the anticipated selective pressure imposed by aridity, a factor often linked to genome size reduction. We found no distinct patterns in the temporal accumulation of TEs, and no effects at the class or superfamily level. Our findings suggest that while TEs may play a key role in evolution at the locus level, their macroevolutionary association with diversification or speciation appears weak. Rather than actively driving evolutionary diversification, TEs may simply be'along for the ride.

The Ecuadorian Amazon holds more biodiversity than most other places on Earth. Palms are a particularly dominant component of the vegetation; however, it remains unknown to what degree the pattern has persisted through time. Here, we investigate the persistence of palm dominance through time and the degree to which past human activities (e.g., fire, cultivation, and forest opening) have affected changes in palm abundances across five regions of the Ecuadorian Amazon. We analyzed soil cores (40–80 cm depth) from each region for charcoal (evidence of past fire) and phytoliths (evidence of past vegetation change). The timings of fires (based on 14C radiocarbon dates), the occurrence, recurrence, and number of fires (based on charcoal presence and abundance in samples), and the amount of change in palm abundances (based on phytoliths) varied within and between the studied regions. The charcoal and phytolith results indicate the presence of low levels of past human activity at all sites. Our results show that patterns of modern palm hyperdominance found in Amazonian forests have not been persistent through time, and that even low levels of past human activities can affect palm abundance.

Within the tropics, a marked gradient in rainfall between dry and wet forests correlates with a well documented turnover of plant species. While water availability along these gradients is an important determinant of species distributions, other abiotic and biotic factors correlate with rainfall and may also contribute to limit species distribution. One of these is soil fertility, which is often lower in the wetter forests. To test its possible role in species distribution along a rainfall gradient, we performed a screen-house experiment where we measured the growth performance of seedlings of 23 species with contrasting distributions across the Isthmus of Panama. We grew seedlings in soils collected from the drier Pacific side and the wetter Atlantic side. Differences in soil fertility across the Isthmus were large enough to significantly influence the growth performance of the seedlings. However, we found no evidence of home-soil advantage among species with contrasting distributions. Dry-distribution species grew on average slower than wet-distribution species suggesting a cost to drought adaptations. The response to soil differences correlated with the growth rate of the species, such that fast-growing species responded more to changes in soil quality. We hypothesize that inherently slow growth rates of some dry-distribution tropical species may be a more important factor limiting their colonization of wetter sites along the rainfall gradient.