Biology subjects

Rivas-Torres, G.

Publications and source records attributed to Rivas-Torres, G..

7 recordsLinked to original sources

bioRxiv2026

A Highly Contiguous Reference Genome for Scalesia gordilloi (Asteraceae), a Critically Endangered Plant Endemic to the Galapagos Islands

Scalesia gordilloi is a critically endangered species endemic to San Cristobal Island in the Galapagos archipelago and represents one of the most unique and vulnerable lineages within the adaptive radiation of the genus Scalesia. Despite its evolutionary distinctiveness and conservation importance, no genomic resources have been available for this species. Here, we present the first high-quality reference genome of S. gordilloi, generated using Oxford Nanopore long-read sequencing. Across three PromethION R10.4.1 flow cells, we obtained 80.5 Gb of long reads ([~]25x coverage), which enabled a highly contiguous 3.61 Gb assembly composed of only 549 contigs and an N50 of 106.6 Mb. BUSCO completeness reached 98.6%, with assembly metrics comparable to other high-quality Asteraceae genomes. Repeat annotation revealed that 76.2% of the genome is composed of interspersed elements, dominated by LTR retrotransposons. Structural annotation resulted in 47,913 high-confidence protein-coding genes, consistent with expectations for large, repetitive Asteraceae genomes. This genome provides a critical foundation for conservation genomics, enabling assessments of genetic diversity, inbreeding, and adaptive potential in the species. It further establishes a framework for comparative genomics across the Scalesia radiation and supports future efforts to protect and restore one of the most threatened plant lineages of the Galapagos Islands.

genomics↗

bioRxiv2026

Hiding in Plain Sight: Novel Observations of Plant Crypsis in a Well-Known Symbiotic System of a Hyperdiverse Tropical Forest

Devils gardens are among the most striking ant-plant mutualisms in Amazonian forests. In this system, the tree Duroia hirsuta is associated with the ant Myrmelachista schumanni, which actively removes neighboring vegetation and maintains nearly monodominant patches of the host plant. Despite the apparent efficiency of this system, repeated field observations at the Tiputini Biodiversity Station, Yasuni Biosphere Reserve, revealed that individuals of Palicourea alba recurrently occur within active devils gardens. Palicourea alba closely resembles dead plant material, exhibiting leaf morphology and coloration that strongly mimic the surrounding litter layer, and appears to be uncommon outside these gardens. To our knowledge, this "dead-leaf" masquerade has not been previously documented in this intensively studied system, making it a particularly striking and unexpected observation. To evaluate whether this masquerade facilitates persistence within devils gardens, we surveyed 35 gardens and recorded P. alba in 19 (52.8%). When present, P. alba covered on average 27% of plot area, while mean herbivory across sampled leaves remained low (8.6%). Generalized linear mixed models showed that P. alba cover decreased significantly with increasing herbivory (F = 8.09, p = 0.0159), whereas herbivory increased with leaf-litter cover (F = 8.73, p = 0.0120). Field observations further revealed that many individuals are nearly indistinguishable from dry leaf litter, suggesting a role for visual crypsis or masquerade. Together, these results indicate initially, that the persistence of P. alba within devils gardens is mediated by a multi-layered ecological filtering process. First, masquerade likely reduces detection by M. schumanni, allowing seedlings to escape ant-mediated removal. Second, low herbivory suggests either enemy avoidance or reduced apparency to herbivores within the simplified understory. Third, spatial heterogeneity in leaf-litter cover may create microhabitats where both ant activity and herbivore pressure are modulated, reinforcing establishment success. This system thus represents a previously undocumented mechanism in which plant-litter resemblance enables persistence within a highly structured, biotically filtered habitat, highlighting how subtle trait-mediated interactions may modulate outcomes in otherwise strongly deterministic mutualisms.

ecology↗

bioRxiv2025

Seeing the forest and the trees: a workflow for automatic acquisition of ultra-high resolution drone photos of tropical forest canopies to support botanical and ecological studies

Tropical forest canopies contain many tree and liana species, and foliar and reproductive characteristics useful for taxonomic identification are often difficult to see from the forest floor. As such, taxonomic identification often becomes a bottleneck in tropical forest inventories. Here we present a drone-based workflow to automatically acquire large volumes of close-up, ultra-high resolution photos of selected tree crowns (or specific locations over the canopy) to support tropical botanical and ecological studies (https://youtu.be/80goMEifpc4). Our workflow is built around the small, easy-to-use DJI Mavic 3 Enterprise (M3E) drone, which is equipped with a wide-angle and a telephoto camera. On day one, the pilot maps a forest area of up to [~]200 ha with the wide-angle camera to generate a high-resolution digital surface model (DSM) and orthomosaic using structure-from-motion (SfM) photogrammetry. On subsequent days, the pilot acquires close-up photos with the telephoto camera from up to 300 selected canopy trees per day. These close-up photos are acquired from 6 m above the canopy and contain a high level of visual detail that allows botanists to reliably identify many tree and liana species. The photos are geolocated with survey-grade accuracy using RTK GNSS, thus facilitating spatial co-registration with other data sources, including the photogrammetry products. The primary operational challenge of our workflow is the need to maintain RTK corrections with the drone to ensure that close-up photos are acquired exactly at the predefined locations. The maximum operational range we achieved was 3 km, which would allow the pilot to reach any tree within a [~]2800 ha area from the take-off point. Although our workflow was developed to support taxonomic identification of tropical trees and lianas, it could be extended to any other forest or vegetation type to support botanical, phenological, and ecological studies. We provide harpia, an open-source Python library to program these automatic close-up photo missions with the M3E drone (https://github.com/traitlab/harpia). Data/code for peer review statementWe provide harpia, an open-source Python library to program these automatic close-up photo missions (https://github.com/traitlab/harpia). Drone imagery and labelled close-up photo data are not yet publicly available because they were acquired with the goal of publishing benchmark machine learning datasets and models for tree and liana species classification and prior publication of the data would jeopardize this future publication.

ecology↗

bioRxiv2024

Genomic stability in the Galapagos Scalesia adaptive radiation: Consistent transposable element accumulation despite hybridization and ecological niche shifts

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 are hypothesized to influence TE accumulation in genomes by disrupting genomic regulation, including the suppression of TE replication. 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 Galapagos Islands, we test whether 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 challenge the assertion that TEs have directly driven diversification, speciation and local adaptation. Instead, we suggest that TEs may simply be along for the ride, rather than actively contributing to plant diversification.

evolutionary biology↗

bioRxiv2024

Iguanas from above: Citizen scientists provide reliable counts of endangered Galapagos marine iguanas from drone imagery

Population surveys are vital for wildlife management, yet traditional methods often demand excessive time and resources, leading to data gaps for many species. Modern technologies such as drones can facilitate field surveys but may also increase data analysis challenges. Citizen Science (CS) can address this issue by engaging non-specialists for data collection and analysis. We evaluated CS for population monitoring using the endangered Galapagos marine iguana as a case study, assessing online volunteers ability to detect and count animals in aerial images. Comparing against a Gold Standard dataset of expert counts in 4345 images, we explored optimal aggregation methods from CS inputs, considering image quality and filtering data from infrequent and anonymous participants. During three phases of our project -- hosted on the Zooniverse platform -- over 13,000 volunteers made 1,375,201 classifications from 57,838 aerial images; each being independently classified 20 (phases 1 & 2) or 30 (phase 3) times. Volunteers achieved 68% to 94% accuracy in detecting iguanas, with more false negatives than false positives. Image quality strongly influenced accuracy; by excluding data from suboptimal pilot-phase images, volunteers counted with 90% to 92% of accuracy. For detecting presence or absence of iguanas, the commonly used majority vote aggregation approach (where the answer selected is that given by the majority of individual inputs) produced less accurate results than when a minimum threshold of five (from the 20/30 independent classifications) was used. For counting iguanas, HDBSCAN clustering yielded the best results. Excluding inputs from anonymous and inexperienced volunteers decreased accuracy. We conclude that online volunteers can accurately identify and count marine iguanas from drone images, though a tendency to underestimate warrants further consideration. CS-based data analysis is faster than manual counting but still resource-intensive, underscoring the need to develop a Machine Learning approach.

zoology↗

bioRxiv2023

Darwin's Overlooked Radiation: genomic evidence points to the early stages of a radiation in the Galapagos prickly pear cactus (Opuntia, Cactaceae)

The Galapagos Islands are a prime example of a natural laboratory for the study of evolutionary radiations. While much attention has been devoted to iconic species like Darwins finches 1-4, the islands offer an equally unique but often overlooked opportunity for plant radiations 5. Yet, compared to their animal counterparts, our understanding of the patterns and processes underpinning Galapagos plant radiations remains relatively limited 6,7. We present evidence of the early stages of a radiation in prickly-pear cactus (Opuntia, Cactaceae), a plant lineage widespread across the archipelago. Phylogenomic and population genomic analyses show that notwithstanding overall low genetic differentiation across populations, there is marked geographic structure that is broadly consistent with current taxonomy and the dynamic paleogeography of the Galapagos. Because such low genetic differentiation stands in stark contrast to the exceptional eco-phenotypic diversity displayed by cacti across islands, it is plausible that phenotypic plasticity precedes genetic divergence and is the source of adaptive evolution, or that introgression between populations facilitates local adaptation. Models of population relationships including admixture indicate that gene flow is common between certain islands, likely facilitated by dispersal via animals known to feed on Opuntia flowers, fruits, and seeds across the archipelago. Scans of genetic differentiation between populations reveal candidate loci associated with seed traits and environmental stressors, suggesting that a combination of biotic interactions and abiotic pressures due to the harsh conditions characterizing island life in a volcanic, equatorial archipelago may underlie the diversification of prickly-pear cacti. Considered in concert, these results are relevant to both the mechanisms of plant eco-phenotypic differentiation and the evolutionary history and conservation of the Galapagos biota.

evolutionary biology↗

bioRxiv2022

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

Oceanic archipelagos comprise multiple disparate environments over small geographic areas and are isolated from other biotas. These conditions have led to some of the most spectacular adaptive radiations, which have been key to our understanding of evolution, and offer a unique chance to characterise the genomic basis underlying rapid and pronounced phenotypic changes. Repeated patterns of evolutionary change in plants on oceanic archipelagos, i.e. the plant island syndrome, include changes in leaf morphology, acquisition of perennial life-style, and change of ploidy. Here, we describe the genome of the critically endangered and Galapagos endemic Scalesia atractyloides Arnot., obtaining a chromosome-resolved 3.2-Gbp assembly with 43,093 candidate gene models. Using a combination of fossil transposable elements, k-mer spectra analyses and orthologue assignment, we identify the two ancestral subgenomes and date their divergence and the polyploidization event, concluding that the ancestor of all Scalesia species on the Galapagos 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, life-growth, adaptation to salinity and changes in flowering time, thus finding compelling evidence for a genomic basis of island syndrome in Darwins giant daisy radiation. This work advances understanding of factors influencing subgenome divergence in polyploid genomes, and characterizes the quick and pronounced genomic changes in a specular and diverse radiation of an iconic island plant radiation.

evolutionary biology↗