Biology subjects

Chaves, J. A.

Publications and source records attributed to Chaves, J. A..

10 recordsLinked to original sources

bioRxiv2025

High-Quality De Novo Genome Assembly for the Galapagos Endemic Lava Gull Using Oxford Nanopore Technologies

High-quality reference genomes permit deeper investigation into species evolution and provide insight into species management and conservation. Next-generation sequencing technologies, such as Oxford Nanopore Technologies, allow researchers to generate high-accuracy long-read genetic data in real-time from anywhere in the world, increasing accessibility to sequence data. The lava gull (Leucophaeus fuliginosus), an endemic bird species of the Galapagos archipelago, is the worlds rarest gull with an estimated population of 300 to 600 individuals. Little genetic research has been done on this species due to its solitary nature and small population size. Here we present a chromosome-level reference genome assembly of an adult female lava gull, generated using ultra-long reads from the Oxford Nanopore Ultra-Long DNA Sequencing Kit and a PromethION 2 Solo device. Initial sequencing generated 1.78 million reads, consisting of 29.6 gigabases (Gbp), with a mean Q-score of 17.8 at an average 22.5x coverage. Our final assembly has a total length of 1.31 Gbp, with 450 scaffolds, and a scaffold N50 of 85.1 Mbp and contig N50 of 42.8 Mbp. The generation of a high-quality whole genome for the lava gull is an important step for investigation into the species phylogeography and population genetics.

genomics↗

bioRxiv2025

First Whole-Genome Assembly of the Galapagos Petrel (Pterodroma phaeopygia) Using Oxford Nanopore Sequencing to Advance Conservation Genomics in a Critically Endangered Seabird

The Galapagos petrel (Pterodroma phaeopygia) is a critically endangered procellariiform seabird endemic to the Galapagos Islands. Once abundant, its populations have sharply declined due to invasive predators, habitat degradation, and destruction of nest burrows. Although the species is distributed across several islands, the demographics of each population and their genetic relationships are poorly understood. To facilitate future studies of population structure and connectivity, we present the first high-quality reference genome for the Galapagos petrel. The genome was assembled from ultra-long Oxford Nanopore sequence data collected from an adult female sampled on San Cristobal Island. Sequencing was performed at the Galapagos Science Center, enabling local capacity-building and compliance with strict sample import-export regulations of endangered species. The final nuclear genome assembly spans 1.35 Gb in length, with average coverage of 36.07x, scaffold N50 of 74.2 Mb, and a BUSCO aves lineage completeness of 99.95%. The genome comprises 41 pseudo-chromosomes, with 23 spanning from telomere to telomere and 16, including W and Z chromosomes, containing a single telomere. Chromosomal-level scaffolding by reference was performed using the genome of Corys shearwater (Calonectris borealis) GCA_964196065.2 (Aranega et al., 2024), a related species. The Galapagos petrel reference genome represents a foundational tool for comparative genomics, conservation biology, and functional studies of island-endemic avifauna. It will also facilitate future efforts to characterize genetic diversity, structural variation, and adaptive responses in this critically endangered species.

genomics↗

bioRxiv2024

Genotypic Characterization and Antimicrobial Susceptibility of Human Campylobacter jejuni Isolates in Southern Spain

Campylobacter jejuni is the main cause of bacterial gastroenteritis and a public health problem worldwide. Little information is available on the genotypic characteristics of human Campylobacter jejuni in Spain. This study is based on an analysis of the resistome, virulome and phylogenetic relationship, antibiogram prediction and antimicrobial susceptibility of 114 human isolates of C. jejuni from a tertiary hospital in southern Spain from October 2020 to June 2023. The isolates were sequenced using Illumina technology, and bioinformatic analysis was subsequently performed. The susceptibility of C. jejuni isolates to ciprofloxacin, tetracycline, and erythromycin was tested. A high resistance rate was obtained for ciprofloxacin (90.6%) and tetracycline (66.7%), and a low resistance rate for erythromycin (0.85%) was detected among the C. jejuni isolates. CC-21 (n=23), ST-572 (n = 13) and ST-6532 (n=13) were the most prevalent clonal complexes (CCs) and sequence types (STs). Concerning the virulome, the cadF, ciaB, and cdtABC genes were detected in all the isolates. A prevalence of 20.1% was obtained for the genes wlaN and cstIII, which are related to the pathogenesis of Guillain-Barre syndrome (GBS). The prevalence of the main antimicrobial resistance markers detected were cmeABC (92.1%), RE-cmeABC (7.9%), the T86I substitution in gyrA (88.9%), blaOXA-61 (72.6%), tet(O) (65.8%) and ant(6)-Ia (17.1%). High antibiogram prediction rates (>97%) were obtained except for the erythromycin-resistant phenotype. This study contributes significantly to the knowledge of Campylobacter jejuni genomics for the prevention, treatment and control of infections caused by this pathogen, which is relevant to public health. ImportanceDespite being the pathogen with the greatest number of gastroenteritis cases worldwide, Campylobacter jejuni remains a poorly studied microorganism. The development of whole-genome sequencing (WGS) techniques has led to a better understanding of the genotypic characteristics of this pathogen. These techniques complement the data obtained from the phenotypic analysis of C. jejuni isolates. The zoonotic transmission of C. jejuni through the consumption of contaminated poultry implies approaching the study of this pathogen through the term "One Health." This is the first study, using WGS, conducted on human isolates of C. jejuni in Spain to date, which allows comparison of the results obtained with similar studies conducted in other countries and with animal and environmental isolates.

microbiology↗

bioRxiv2024

SIEGA the integrated genomic surveillance system of Andalusia, a One Health regional resource connected with the clinic

The One Health approach, recognizing the interconnectedness of human, animal, and environmental health, has gained significance amid emerging zoonotic diseases and antibiotic resistance concerns. This paper aims to demonstrate the utility of a collaborative tool, the SIEGA, for monitoring infectious diseases across domains, fostering a comprehensive understanding of disease dynamics and risk factors, highlighting the pivotal role of One Health surveillance systems. Raw whole-genome sequencing is processed through different species-specific open software that additionally reports the presence of genes associated to anti-microbial resistances and virulence. The SIEGA application is a Laboratory Information Management System, that allows customizing reports, detect transmission chains, and promptly alert on alarming genetic similarities. The SIEGA initiative has successfully accumulated a comprehensive collection of more than 1900 bacterial genomes, including Salmonella enterica, Listeria monocytogenes, Campylobacter jejuni, Escherichia coli, Yersinia enterocolitica and Legionella pneumophila, showcasing its potential in monitoring pathogen transmission, resistance patterns, and virulence factors. SIEGA enables customizable reports and prompt detection of transmission chains, highlighting its contribution to enhancing vigilance and response capabilities. Here we show the potential of genomics in One Health surveillance when supported by an appropriate bioinformatic tool. By facilitating precise disease control strategies and antimicrobial resistance management, SIEGA enhances global health security and reduces the burden of infectious diseases. The integration of health data from humans, animals, and the environment, coupled with advanced genomics, underscores the importance of a holistic One Health approach in mitigating health threats.

microbiology↗

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↗

bioRxiv2023

Does urbanization lead to parallel demographic shifts across the world in a cosmopolitan plant?

Urbanization is occurring globally, leading to dramatic environmental changes that are altering the ecology and evolution of species. In particular, the expansion of human infrastructure and the loss and fragmentation of natural habitats in cities is predicted to increase genetic drift and reduce gene flow by reducing the size and connectivity of populations. Alternatively, the "urban facilitation model" suggests that some species will have greater gene flow into and within cities leading to higher diversity and lower differentiation in urban populations. These alternative hypotheses have not been contrasted across multiple cities. Here, we used the genomic data from the Global Urban Evolution project (GLUE), to study the effects of urbanization on non-adaptive evolutionary processes of white clover (Trifolium repens) at a global scale. We found that white clover populations presented high genetic diversity and no evidence of a reduction in Ne linked to urbanization. On the contrary, we found that urban populations were less likely to experience a recent decrease in effective population size than rural ones. In addition, we found little genetic structure among populations both globally and between urban and rural populations, which showed extensive gene flow between habitats. Interestingly, white clover displayed overall higher gene flow within urban areas than within rural habitats. Our study provides one of the largest comprehensive tests of demographic effects of urbanization and our results contrast the common perception that heavily altered and fragmented urban environments will reduce the effective population size and genetic diversity of populations and contribute to their isolation.

evolutionary biology↗

bioRxiv2023

Urban living can rescue Darwin's finches from the lethal effects of invasive vampire flies

Human activity changes multiple factors in the environment, which can have additive or neutralizing effects on organisms. However, few studies have explored the causal effects of multiple anthropogenic factors, such as urbanization and invasive species, on animals, and the mechanisms that mediate these interactions. This study examines the influence of urbanization on the detrimental effect of invasive avian vampire flies (Philornis downsi) on endemic Darwins finches in the Galapagos Islands. We experimentally manipulated nest fly abundance in an urban and non-urban area and then characterized nestling health, survival, diet, and gene expression patterns related to host defense. Survival of fumigated nestlings from urban and non-urban nests did not differ significantly. However, sham-fumigated, non-urban nestlings lost more blood and few nestlings survived compared to urban nestlings. Stable isotopic values ({delta}15N) from urban nestling feces were higher than non-urban nestlings, suggesting that urban nestlings are consuming more protein. {delta}15N values correlated negatively with parasite abundance, which suggests that diet might influence host defenses (e.g., tolerance and resistance). Parasitized urban nestlings differentially expressed genes within pathways associated with red blood cell production (tolerance) and pro-inflammatory response (innate immunological resistance), compared to sham-fumigated non-urban nestlings. In contrast, sham-fumigated non-urban nestlings differentially expressed genes within pathways associated with immunoglobulin production (adaptive immunological resistance). Our results suggest that urban nestlings are investing more in pro-inflammatory responses to resist parasites, but also recovering more blood cells to tolerate blood loss. Although non-urban nestlings are mounting an adaptive immune response, it is likely a last effort by the immune system rather than an effective defense against avian vampire flies since few nestlings survived.

ecology↗

bioRxiv2020

Evolutionary history of the Galapagos Rail revealed by ancient mitogenomes and modern samples

The biotas of the Galapagos Islands are probably one of the best studied island systems and have provided a broad model of insular species origins and evolution. Nevertheless, some Galapagos species remain poorly characterized, such as the Galapagos Rail Laterallus spilonota. This bird species is one of the less explored groups of endemic vertebrates on these islands, due to its elusive behavior, cryptic plumage and restricted distribution. To date there is no genetic assessment of its origins and sister relationships to other taxa, and importantly, there is no data on its current genetic diversity. This lack of information is critical given the adverse fate of island rail species around the world in the recent past. Here we examine the genetics of Galapagos Rails using a combination of mitogenome de novo assembly with multi-locus sequencing (mtDNA+nuDNA) from both modern and historical samples. We show that the Galapagos Rail is part of the American black rail clade, sister to Black Rail L. jamaicensis, with a colonization of Galapagos dated to 1.2 Mya. The separate analysis of cytb, ND2, and RAG-1 markers demonstrates shallow population structure across sampled islands, possibly due to elevated island connectivity. Additionally, birds sampled from Pinta possessed the lowest levels of genetic diversity, most likely reflecting the impact of past bottlenecks due to habitat loss caused by invasive goats grazing on sensitive habitat. The data presented here highlights the low genetic diversity in this endemic rail species and suggests the use of genetic data (both modern and historical) to guide conservation efforts.

evolutionary biology↗

bioRxiv2020

Urbanization alters ecological and evolutionary interaction between Darwin's Finches and Tribulus cistoides on the Galapagos Islands

Emerging evidence suggests that urbanization shapes the ecology and evolution of species interactions. Islands are particularly susceptible to urbanization due to the fragility of their ecosystems; however, few studies have examined the effects of urbanization on species interactions on islands. To address this gap, we studied the effects of urbanization on interactions between Darwins finches and its key food resource, Tribulus cistoides, in three towns on the Galapagos Islands. We assessed the effects of urbanization on seed and mericarp removal, mericarp morphology, and finch community composition using natural population surveys, experimental manipulations, and finch observations. We found that both seed and fruit removal rates were higher in urban compared to non-urban populations in the natural and experimental populations, and that urbanization modified selection on mericarp size and defense. Urban environments supported smaller and less diverse finch communities than non-urban environments. Together, our results suggest that urbanization can dramatically alter ecological interactions between Darwins finches and T. cistoides, leading to modified selection on T. cistoides populations. Our study demonstrates that urban development on islands can have profound effects on the ecology and evolution of trophic interactions.

evolutionary biology↗

bioRxiv2020

Sex identification in embryos and adults of Darwins finches

Darwins finches, endemic to the Galapagos and Cocos islands, are an iconic example of adaptive radiation and evolution under natural selection. Comparative genetic studies using embryos of Darwins finches have shed light on the possible evolutionary processes underlying the speciation of this clade. Molecular identification of the sex of embryonic samples is important for such studies, where this information often cannot be inferred otherwise. We tested a fast and simple chicken embryo protocol for extraction of genomic DNA on Darwins finch embryos. In addition, we suggest modifications to two of the previously reported PCR primer sets for CHD1, a gene used for sexing in adult passerine birds. The sex of all 29 tested embryos of six species of Darwins finches was determined successfully by PCR, using both primer sets. Hatchlings/nestlings and fledglings are also impossible to distinguish visually. This includes juveniles of sexually dimorphic species which are yet to moult in adult-like plumage and beak colouration. Furthermore, four species of Darwins finches are monomorphic, males and females looking alike. Therefore, sex assessment in the field can be a source of error, especially with respect to juveniles and mature monomorphic birds outside of the mating season. We caught 567 juveniles and adults belonging to six species of Darwins finches and only 44% had unambiguous sex-specific morphology. We sexed 363 birds by PCR, including individuals sexed based on marginal sex specific morphological traits (N=278) and birds which were impossible to classify in the field (N=39). For birds with marginal sex specific traits, PCR results revealed a 13% sexing error rate. This demonstrates that PCR based sexing can improve field studies on Darwins finches, especially when individuals with unclear sex-related morphology are involved. The protocols used here provide an easy and reliable way to sex Darwins finches throughout ontogeny, from embryos to adults.

molecular biology↗