Biology subjects

Americo, J. A.

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

8 recordsLinked to original sources

bioRxiv2025

The globally dispersed sun-coral species is _Tubastraea coccinea_ (Cnidaria: Anthozoa)

Species of the genus Tubastraea (sun corals) have dispersed globally over recent decades, but morphological trait identification has led to taxonomic confusion, with multiple authors proposing conflicting species identifications due to high morphological plasticity and overlapping diagnostic traits. We combined global-scale molecular phylogenetics with chromosome-level genome assemblies to resolve this taxonomic issue. Using mitochondrial and nuclear markers from 287 specimens across five ocean regions, including type localities in Bora Bora (T. coccinea) and Galapagos (T. tagusensis), we reconstructed phylogenetic relationships and inferred demographic history through approximate Bayesian computation. We also generated high-quality, chromosome-level genome assemblies for three morphologically distinct morphotypes from the Brazilian coastline. Phylogenetic and species delimitation analyses revealed two well-supported clades: a small, geographically restricted T. tagusensis clade confined to the Galapagos Islands, and a large cosmopolitan clade containing all worldwide samples, including T. coccinea from its type locality. Chromosome-level genomic analyses confirmed that the three morpho-types represent a single species, sharing a triploid karyotype of 14 chromosomes with extensive synteny and gene-tree discordance consistent with incomplete lineage sorting. Dispersed-route analyses identified the Centralwestern Pacific as the ancestral source, with at least three independent, humanmediated colonization events establishing populations in the Southwestern Atlantic, Gulf of Mexico, and Western Pacific. However, preliminary analysis suggests a Galapagos (Southeastern Pacific) origin rather than Centralwestern Pacific for the T. tagusensis and T. coccinea cluster. Our results definitively establish Tubastraea coccinea as the cosmopolitan species responsible for global dissemination, while T. tagusensis is endemic to the Galapagos and not involved in the worldwide dis-persion.

genetics↗

bioRxiv2025

eDNA enables proof-of-origin of samples from reservoirs with rich and abundant biodiversity

Environmental DNA (eDNA) is increasingly used for biodiversity monitoring, but its application in verifying the geographic origin of samples remains limited. Here, we evaluated whether eDNA profiles from water samples can indicate sample provenance across three large Brazilian reservoirs. Using multi-marker metabarcoding (COI, 12S, 16S), we showed that biodiversity signatures enable spatial attribution. To ensure traceability, each report was encoded in a machine-readable format, hashed, and registered on the blockchain. This framework demonstrates a novel approach to independently verifying sample origin through molecular and cryptographic evidence.

ecology↗

bioRxiv2024

Insights into the representativeness of biodiversity assessment in large reservoir through eDNA metabarcoding

Monitoring biodiversity on a large scale, such as in hydropower reservoirs, poses scientific challenges. Conventional methods such as passive fishing gear are prone to various biases, while the utilization of environmental DNA (eDNA) metabarcoding has been restricted. Most eDNA studies have primarily focused on replicating results from traditional methods, which themselves have limitations regarding representativeness and bias. In our study, we employed eDNA metabarcoding with three markers (12SrRNA, COI, and 16SrRNA) to evaluate the biodiversity of an 800 km{superscript 2} reservoir. We utilized hydrodynamic modeling to determine water flow velocity and the water renewal ratio throughout the study area. Additionally, we conducted statistical comparisons - rarefaction curves and multivariate methods - among samples as an alternative approach to assess biodiversity representation. The eDNA identified taxa previously documented in the reservoir by traditional monitoring methods, as well as revealed 29 - nine fishes and 20 non-fish - previously unreported species. These results highlight the robustness of eDNA as a biodiversity monitoring technique. Our findings also indicated that by randomly sampling 30% of the original number of samples, we could effectively capture the same biodiversity. This approach enabled us to comprehend the reservoirs biodiversity profile and propose a straightforward, cost-effective monitoring protocol for the future based on eDNA.

molecular biology↗

bioRxiv2022

A high quality chromosome-level genome assembly for the golden mussel (Limnoperna fortunei)

The golden mussel (Limnoperna fortunei) is a highly adaptive species that causes environmental and socioeconomic losses in invaded areas. Reference genomes have proven to be a valuable resource for studying the biology of invasive species. While the current golden mussel genome has been useful for identifying new genes, its high fragmentation hinders some applications. In this Data Note, we provide the first chromosome-level reference genome for the golden mussel. The genome was built using Hi-C, PacBio HiFi and 10X sequencing data. The final assembly contains 99.4% of its total length assembled to the 15 chromosomes of the species and a scaffold N50 of 97.05 Mb. Approximately 47% of the genome was annotated as repetitive sequences. A total of 34 862 protein-coding genes were predicted, of which 84.7% were functionally annotated. This new high quality genome is expected to support both basic and applied research on this invasive species. Species taxonomyEukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Spiralia; Lophotrochozoa; Mollusca; Bivalvia; Autobranchia; Pteriomorphia; Mytilida; Mytiloidea; Mytilidae; Arcuatulinae; Limnoperna; Limnoperna fortunei (Dunker, 1857) (NCBI Taxonomy ID: 356393)

genomics↗

bioRxiv2021

Environmental DNA from a small sample of reservoir water can tell volumes about its biodiversity.

We evaluated the potential of metabarcoding in assessing the environmental DNA (eDNA) biodiversity profile in the water column of an hydroelectric power plant reservoir in southeast Brazil. Samples were obtained in three technical replicates at 1 km from the dam at 1, 13 and 25 m depths. For each minibarcodes -- COI, 12S and 16S -- 1.5 million paired-reads (150 base pairs) were sequenced. A total of 44 unique taxa were found. COI identified most of the taxa (34 taxa; 77.2 %) followed by 16S (14; 31.8 %) and 12S (10; 22.7 %). All minibarcodes identified fishes (13 taxa), however, COI detected other aquatic macro-invertebrates (18), algae (3) and amoebas (2). Richness was the same across the three depths (35 taxa), although, beta diversity suggested slightly divergent profiles. In just one location we identified 15 taxa never reported previously, 50% of the fish species identified in the last year of fishery monitoring and 13% of the species in biodiversity surveys performed from 2012 to 2021. Clustering into Amplicon Sequence Variants (ASV) showed that 12S and 16S are able to detect predominant haplotypes of fishes, suggesting they are suitable to study population genetics of this group. In this study we reviewed the species occurring within the Tres Irmaos reservoir according to previous conventional surveys and demonstrated that eDNA metabarcoding can be applied to monitor its biodiversity.

molecular biology↗

bioRxiv2020

Population structure of the invasive golden mussel (Limnoperna fortunei) on reservoirs from five Brazilian drainage basins

The golden mussel (Limnoperna fortunei) is a freshwater bivalve that was introduced in South America almost 30 years ago, likely through ballast water of Asian ships. Since then, it has spread across the continent, causing both economic and environmental impacts. The study of the population structure of an invasive species may bring valuable insights towards understanding its pattern of dispersion, which in turn will help to create more effective management plans. Here, we have compared mussel populations from 5 different Brazilian reservoirs and tested for the presence of geographic genetic structure. In order to obtain a high number of single nucleotide variants (SNVs) at good cost-benefit, we have for the first time applied the double digest restriction-site associated DNA sequencing (ddRAD-seq) protocol for the golden mussel. The ddRAD-seq protocol allowed us to obtain 2046 SNVs, which were then used to assess population structure by applying three independent methodologies: Principal Component Analysis (PCA), Bayesian Clustering and Phylogenetic Tree. All methodologies have indicated absent geographic structure.

genetics↗

bioRxiv2019

Identification of suitable reference genes for qPCR expression analysis on the gonads of the invasive mussel Limnoperna fortunei

Limnoperna fortunei -- popularly known as the Golden mussel -- is an aggressive invasive species that has been causing environmental damage and adversely affecting economic sectors dependent on freshwater ecosystems in South America. As a non-model species, knowledge about its biology is very limited, especially molecular mechanisms that contribute to its invasiveness, such as its high reproduction rate. Quantitative PCR (qPCR) is considered the gold standard technique to determine gene expression levels and its accuracy relies on the use of stably expressed reference genes for data normalization and to minimize technical variability. Our goal was to identify reliable reference genes to perform gene expression analysis on the gonads of L. fortunei. The stability of five candidate genes (RPS3, EF1a, HS6ST3B, NAPA and UBE2F) in the gonads of male and female mussels was evaluated by using two algorithms, Bestkeeper and Genorm. Results show that NAPA, UBE2F and RPS3 genes are stable enough to compose a reliable normalization factor for gene expression analyses comparing both sexes. HS6ST3B and NAPA were found to be more stable in female gonads; thus, their application as a normalization factor is preferable for studies limited to female processes only.

molecular biology↗

bioRxiv2019

Gonad transcriptome of golden mussel Limnoperna fortunei reveals potential sex differentiation genes

The golden mussel Limnoperna fortunei is an Asian invasive bivalve that threats aquatic biodiversity and causes economic damage, especially to the hydroelectric sector in South America. Traditional control methods have been inefficient to stop the advance of the invasive mollusk, which currently is found in 40% of Brazilian hydroelectric power plants. In order to develop an effective strategy to stop golden mussel infestations, we need to better understand its reproductive and sexual mechanisms. In this study, we sequenced total RNA samples from male and female golden mussel gonads in the spawning stage. A transcriptome was assembled resulting in 200,185 contigs with 2,250 bp N50 and 99.3% completeness. Differential expression analysis identified 3,906 differentially expressed transcripts between the sexes. We searched for genes related to the sex determination/differentiation pathways in bivalves and model species and investigated their expression profiles in the transcriptome of the golden mussel gonads. From a total of 187 genes identified in the literature, 131 potential homologs were found in the L. fortunei transcriptome, of which 15 were overexpressed in males and four in females. To this group belong gene families relevant to sexual development in various organisms, from mammals to invertebrates, such as Dmrt (doublesex and mab3-related-transcription factor), Sox (SRY-related HMG-box) and Fox (forkhead box).

bioinformatics↗