Biology subjects

Torres, M. d. L.

Publications and source records attributed to Torres, M. d. L..

11 recordsLinked to original sources

bioRxiv2026

Vicariance and dispersal shape the colonization history of the Galapagos carpenter bee, Xylocopa darwini

Island colonization and subsequent diversification are often shaped by a complex interplay between organism-specific traits including dispersal capacity and ecological requirements, and the configuration of the landscape over geological time. Here, we investigate the evolutionary history and population genomics of the Galapagos carpenter bee, Xylocopa darwini, across six islands of the Galapagos archipelago. Despite the bees presumed strong flight ability, we find evidence of long-term isolation among all islands with the strongest divergence occurring between the eastern and western islands, and no evidence of contemporary gene flow between any island pairs. Our analyses indicate that the initial colonization of the archipelago by X. darwini occurred during the early Pleistocene, a period when most current islands except for the youngest islands of Isabela and Fernandina, were subaerial, and part of a large contiguous paleo-landmass. Diversification across the Galapagos islands closely tracks the timing of geological separation of the islands, with carpenter bees from the oldest eastern islands splitting first from the western clade over a million years ago. Subsequent diversification of the western clade tracks the sequential fragmentation of the western, central, and southern islands (Isabela, Santiago, Santa Cruz, and Floreana), rather than the geological age of the islands. Despite being on the oldest island, the bee population on Espanola appears to have been founded more recently (within the last 100,000 years) from San Cristobal, providing an exception to diversification tracking paleogeography and is the only example of founding via over-water dispersal among the sampled island populations. Measures of contemporary genetic diversity and runs of homozygosity (ROHs) suggest substantially smaller current population sizes on the southern island of Floreana and the eastern islands of Espanola and San Cristobal. These results are not consistent with a simple relationship between island area and genetic diversity and instead likely reflect a combination of evolution in isolation following vicariance, rare founder events following over-water dispersal, and possible episodes of secondary contact.

evolutionary biology↗

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

From nest to hatchling: nidobiome assembly and host selection in oviparous vertebrates without parental care

Early microbial assembly is fundamental for host development and fitness, yet in oviparous vertebrates lacking parental care, the mechanisms by which eggs and neonates acquire their microbiome remain poorly understood. The nidobiome concept predicts that maternal and environmental sources, and host selection, collectively shape early microbial communities. To test this, we conducted a longitudinal study on microbial assembly in the yellow-spotted Amazon river turtle (Podocnemis unifilis). We sampled maternal mucosa, freshly laid outer eggshells, and nest sand before incubation, along with hatchery sand, outer and inner eggshells, and hatchling cloaca after incubation. Using 16S and ITS amplicon sequencing to quantify microbial diversity, we observed that freshly laid outer eggshells shared bacterial diversity with maternal mucosa, whereas nest sand harboured a distinct community, providing evidence of early vertical transmission. After incubation, eggshell microbial communities became more even without a change in richness, while nest sand communities exhibited the opposite pattern, reflecting divergent host-environment assembly dynamics. SourceTracker analyses confirmed contributions from both maternal and environmental sources, yet inner eggshells and hatchling cloaca assembled distinct communities compared with outer eggshells, indicating that host selection is largely deterministic. Interkingdom interactions favoured beneficial microorganisms, suggesting active host filtering throughout development. Even in the presence of fusariosis, a widespread threat in turtle nests, host selection enriched protective taxa, linking microbiome composition to hatching success. These findings demonstrate that maternal seeding, priority effects, and deterministic host selection govern early-life microbiome assembly in oviparous reptiles without parental care, with direct implications for microbe-informed conservation strategies. ImportanceUnderstanding early-life microbial assembly is critical for uncovering the ecological and evolutionary drivers of host-microbiome interactions. This study reveals how microbial communities develop in oviparous vertebrates lacking parental care, highlighting key mechanisms such as vertical transmission, host selection, and environmental modulation that shape early-life microbiomes. Our results demonstrate that maternal microbiota seeding and priority effects play fundamental roles in structuring egg-associated microbial communities, directly influencing host fitness and survival. By identifying deterministic processes that enrich beneficial microorganisms during early development, this research underscores the pivotal role of microbiomes in host resilience and adaptation. These insights carry urgent conservation implications, offering microbe-informed strategies to mitigate emerging threats, such as diseases in vulnerable species like the yellow-spotted Amazon river turtle, and emphasising the broader importance of microbiome stewardship for ecosystem health.

ecology↗

bioRxiv2024

First whole genome assembly of Vaccinium floribundum Kunth, an emblematic Andean species

BackgroundVaccinium floribundum Kunth, known as "mortino," is an endemic shrub species of the Andean region adapted to harsh conditions in high-altitude ecosystems. It plays an important ecological role as a pioneer species in the aftermath of deforestation and human-induced fires within paramo ecosystems, emphasizing its conservation value. While previous studies have offered insights into the genetic diversity of mortino, comprehensive genomic studies are still missing to fully understand the unique adaptations of this species and its population status, highlighting the importance of generating a reference genome for this plant. ResultsONT and Illumina sequencing were used to establish a reference genome for this species. Three different de novo genome assemblies were generated and compared for quality, continuity and completeness. The Flye assembly was selected as the best and refined by filtering out short ONT reads, screening for contaminants and genome scaffolding. The final assembly has a genome size of 529 MB, containing 1,317 contigs and 97% complete BUSCOs, indicating a high level of integrity of the genome. Additionally, the LAI Index of 12.93, further categorizes this assembly as a reference genome. ConclusionsThe genome of V. floribundum reported in this study is the first reference genome generated for this species, providing a valuable tool for further studies. This high-quality genome, based on the quality and completeness parameters obtained, will not only help uncover the genetic mechanisms responsible for its unique traits and adaptations to high-altitude ecosystems, but will also contribute to conservation strategies for a species endemic to the Andes.

genomics↗

bioRxiv2023

First whole genome sequence and assembly of the Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps), a critically endangered species, using Oxford Nanopore Technologies

The Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps) is currently considered one of the most endangered primates in the world and is classified as critically endangered (IUCN). It faces multiple threats, the most significant one being habitat loss due to deforestation in western Ecuador. Genomic tools are key for the management of endangered species, but this requires a reference genome which until now was unavailable for A. f. fusciceps. The present study reports the first whole genome sequence and assembly of A. f. fusciceps generated using Oxford Nanopore long reads. DNA was extracted from a subadult male and libraries were prepared for sequencing following the Ligation Sequencing Kit SQK-LSK112 workflow. Sequencing was performed using a MinION Mk1C sequencer. The sequencing reads were processed to generate a genome assembly. Two different assemblers were used to obtain draft genomes using raw reads, of which the Flye assembly was found to be superior. The final assembly has a total length of 2.63 Gb and contains 3,861 contigs, with an N50 of 7,560,531 bp. The assembly was analyzed for annotation completeness based on primate ortholog prediction using a high-resolution database, and was found to be 84.3% complete, with a low number of duplicated genes indicating a precise assembly. The annotation of the assembly predicted 31,417 protein-coding genes, comparable to other mammal assemblies. A reference genome for this critically endangered species will allow researchers to gain insight into the genetics of its populations and thus aid conservation and management efforts of this vulnerable species.

genomics↗

bioRxiv2022

Local exclusion and regional decline of an endemic Galapagos tree species (Psidium galapageium) by an invasive relative (P. guajava)

Invasive species can interact with native relatives in a variety of ways which may jeopardize their long-term coexistence. Here we show that interactions with an invasive species of guava (Psidium guajava) appear to be driving the local exclusion and regional decline of guayabillo (Psidium galapageium), a tree species endemic to the Galapagos archipelago. We find evidence consistent with recent historic exclusion of guayabillo from the highlands of San Cristobal Island, signatures of ongoing demographic decline in sympatric populations at lower elevations, and evidence suggesting that the four coinhabited islands represent points along a time series of regional decline, with the extent of guayabillo decline depending on the date that guava was introduced to each island. Based on these results, we then use the percentage of guava cover surrounding guayabillo populations to target populations that are at imminent risk of exclusion to aid in prioritizing management targets.

ecology↗

bioRxiv2020

Characterizing the genetic diversity of the Andean blueberry (Vaccinium floribundum Kunth.) across the Ecuadorian Highlands

The Ecuadorian paramo, a high altitude tundra-like ecosystem, is a unique source of various ecosystem services and distinct biodiversity. Anthropogenic activities are associated with its fragmentation, which alters ecological factors and directly threatens resident species. Vaccinium floribundum Kunth., commonly known as Andean blueberry or mortino, is a wild shrub endemic to the Andean region and highly valued in Ecuador for its berries, which are widely used in food preparations and hold an important cultural value. Since it is a wild species, mortino could be vulnerable to environmental changes, resulting in a reduction of the size and distribution of its populations. To evaluate the extent of these effects on the mortino populations, we assessed the genetic diversity and population structure of the species along the Ecuadorian highlands. We designed and developed a set of 30 homologous SSR markers and used 16 of these to characterize 100 mortino individuals from 27 collection sites. Our results revealed a high degree of genetic diversity (HE=0.73) for the Ecuadorian mortino, and a population structure analyses suggested the existence of distinct genetic clusters present in the northern, central and southern highlands. A fourth, clearly differentiated cluster was also found and included individuals from locations at higher elevations. We suggest that the population structure of the species could be explained by an isolation-by-distance model and can be associated to the geological history of the Andean region. Our results suggest that elevation could also be a key factor in the differentiation of mortino populations. This study provides an extensive overview of the species across its distribution range in Ecuador, contributing to a better understanding of its conservation status. These results can assist the development of conservation programs for this valuable biological and cultural resource and for the paramo ecosystems as a whole.

genetics↗

bioRxiv2020

Understanding the genetic diversity of the guayabillo (Psidium galapageium), an endemic plant of the Galapagos Islands

Oceanic archipelagos are known to host a variety of endemic plant species. The genetic diversity and structure of these species is an important indicator of their evolutionary history and can inform appropriate conservation strategies that mitigate the risks to which theyre exposed, including invasive species and environmental disturbances. A comprehensive consideration of the role of their natural history, as well as the landscape features and the geological history of the islands themselves is required to adequately understand any emerging patterns. Such is the case for the guayabillo (Psidium galapageium), an understudied endemic plant from the Galapagos Islands with important ecological and economic roles. In this study we designed and evaluated 13 informative SSR markers and used them to investigate the genetic diversity, population structure and connectivity of the guayabillo populations from San Cristobal, Isabela and Santa Cruz islands. A total of 208 guayabillo individuals were analyzed, revealing a strong population structure between islands and two distinct genetic lineages for the Santa Cruz population. Overall, the guayabillo genetic diversity is relatively high, an unusual pattern for an insular endemic species which is possibly explained by its polyploidy and the geographical features of the islands. These include their broad altitudinal ranges and habitat heterogeneity. For populations displaying a lower genetic diversity such as San Cristobal, the history of human disturbance could be an important factor explaining these observations. Some similarities between individuals in Santa Cruz and the San Cristobal population could be explained by population differentiation or distinct natural histories of separate lineages. Our findings highlight the complex population dynamics that shape the genetic diversity of species like the guayabillo and emphasize the need to explore the currently unresolved questions about this Galapagos endemic plant.

plant biology↗

bioRxiv2020

Reconstructing the history and biological consequences of a plant invasion on the Galapagos islands

The introduction of non-native species into new habitats is one of the foremost risks to global biodiversity. Here, we evaluate a recent invasion of wild tomato (Solanum pimpinellifolium) onto the Galapagos islands from a population genomic perspective, using a large panel of novel collections from the archipelago as well as historical accessions from mainland Ecuador and Peru. We infer a recent invasion of S. pimpinellifolium on the islands, largely the result of a single event from central Ecuador which, despite its recency, has rapidly spread onto several islands in the Galapagos. By reconstructing patterns of local ancestry throughout the genomes of invasive plants, we uncover evidence for recent hybridization and introgression between S. pimpinellifolium and the closely related endemic species Solanum cheesmaniae. Two large introgressed regions overlap with known fruit color loci involved in carotenoid biosynthesis. Instead of red fruits, admixed individuals with endemic haplotypes at these loci have orange fruit colors that are typically characteristic of the endemic species. We therefore infer that introgression explains the observed trait convergence. Moreover, we infer roles for two independent loci in driving this pattern, and a likely history of selection favoring the repeated phenotypic transition from red to orange fruits. Together, our data reconstruct a complex history of invasion, expansion, and gene flow among wild tomatoes on the Galapagos islands. These findings provide critical data on the evolutionary importance of hybridization during colonization and its role in influencing conservation outcomes. Significance StatementThe isolation and unique diversity of the Galapagos Islands provide numerous natural experiments that have enriched our understanding of evolutionary biology. Here we use population genomic sequencing to reconstruct the timing, path, and consequences of a biological invasion by wild tomato onto the Galapagos. We infer that invasive populations originated from a recent human-mediated migration event from central Ecuador. Our data also indicate that invasive populations are hybridizing with endemic populations, and that this has led to some invasive individuals adopting both fruit color genes and the fruit color characteristic of the endemic island species. Our results demonstrate how hybridization can shape patterns of trait evolution over very short time scales, and characterize genetic factors underlying invasive success.

evolutionary biology↗

bioRxiv2019

Local extirpation is pervasive among populations of Galapagos endemic tomatoes

The Galapagos Islands are home to incredible endemic biodiversity that is of high conservation interest. Two such endemic species are the Galapagos tomatoes: Solanum cheesmaniae and Solanum galapagense. Both are known from historical location records, but like many endemic plant species on the Galapagos, their current conservation status is unclear. We revisited previously documented sites of endemic species on San Cristobal, Santa Cruz, and Isabela, and document the disappearance of >80% of these populations. In contrast, we find that two invasive relatives (Solanum pimpinellifolium and Solanum lycopersicum) are now highly abundant, and in some cases--based on morphological observations--might be hybridizing with endemics. Our findings suggest that expanding human developments and putative interspecific hybridization are among the major factors affecting the prevalence of invasives and the threatened persistence of the endemic populations.

evolutionary biology↗

bioRxiv2018

Psidium guajava in the Galapagos Islands: population genetics and history of an invasive species

The threat of invasive plant species in island populations prompts the need to better understand their population genetics and dynamics. In the Galapagos islands, this is exemplified by the introduced guava (Psidium guajava), considered one of the greatest threats to the local biodiversity due to its effective spread in the archipelago and its ability to outcompete endemic species. To better understand its history and genetics, we analyzed individuals from three inhabited islands in the Galapagos archipelago with 11 SSR markers. Our results reveal similar genetic diversity between islands, suggestive of gene flow between them. Populations appear to be distinct between the islands of San Cristobal and Isabela, with the population of Santa Cruz being composed as a mixture from both. Additional evidence for genetic bottlenecks and the inference of introduction events suggests an original introduction of the species in San Cristobal, from where it was later introduced to Isabela, and finally into Santa Cruz. Alternatively, an independent introduction event for Isabela is also possible. These results are contrasted with the historical record, providing a first overview of the history of P. guajava in the Galapagos islands and its current population dynamics.

evolutionary biology↗