Biology subjects

Ready, J. S.

Publications and source records attributed to Ready, J. S..

8 recordsLinked to original sources

bioRxiv2025

Geographical variation in mitogenomes of the largetooth sawfish Pristis pristis: challenges and perspectives for conservation efforts

Sawfishes (Pristidae) have been severely impacted by coastal development and unregulated fisheries and are considered Critically Endangered by the IUCN Red List. Environmental DNA (eDNA) analyses have shown potential for monitoring elasmobranch species, with various studies focusing on using species-specific approaches to detect Pristis species. However positive detection using existing probes has not been confirmed in some geographic regions where they would be expected. Here, we aimed to test whether mutations at key sites have been detrimental to species-specific detection of P. pristis (Linnaeus, 1758) using the existing probe set. To test this hypothesis mitogenomes were assembled that were found to follow the typical pattern of vertebrate mitogenomic organization. Phylogenetic trees showed similar topologies and confirmed geographic mitochondrial variation in P. pristis. Mismatches for the published 12S species-specific probe set for P. pristis were identified that prevent amplification of positive control samples from Brazil. However, ddPCR detection of the positive control was possible using a newly designed species-specific probe set. This study highlights how geographical variation can severely impact the success of generally applying species-specific detection systems developed based on data from only one geographical region. The new mitogenomes and species-specific probe set developed here may also contribute to improving the potential to map and monitor these Critically Endangered species across the globe. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/639618v1_ufig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@1fb30fborg.highwire.dtl.DTLVardef@4cd3a8org.highwire.dtl.DTLVardef@1dbd985org.highwire.dtl.DTLVardef@a5d7d3_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO C_FIG

ecology↗

bioRxiv2025

Investigating the dynamics of the aquatic community in Oslofjord through time series analysis of eDNA

Understanding temporal dynamics of marine communities is critical for assessing ecosystem health and guiding conservation efforts. Here, we conducted a survey using environmental DNA (eDNA) metabarcoding with two primer sets, MiFish and Elas02, to investigate seasonal and interannual changes in the fish community of Oslofjord (Norway) over two consecutive years. Using the MitoFish reference database through the GBIF querying tool, we identified 61 fish species and found significant changes in the dominant taxa between seasons and years. Clupea harengus (Atlantic herring) consistently peaked in early spring, while Scomber scombrus (Atlantic mackerel) dominated winter months in the second year. The MiFish primer set showed increased species richness in the second year, whereas the Elas02 primer set showed stable richness despite compositional turnover. Non-metric multidimensional scaling (NMDS) revealed distinct community separation between years in presence/absence data, driven by species turnover rather than abundance read changes. Our findings support the use of eDNA metabarcoding to capture fine-scale temporal dynamics and emphasise the importance of multi-year datasets for distinguishing ecological trends from stochastic changes. This strategy improves monitoring practices for marine ecosystems under anthropogenic stressors.

ecology↗

bioRxiv2025

From Nets to Molecules: A Comparative Study of Stream Fish Diversity Recovery Using Different Sampling Methods in Eastern Amazonia

The Neotropical freshwaters of South America host an exceptional level of ichthyofaunal diversity with over 5,160 species, making it the richest continental fauna worldwide. Despite their richness, these freshwater ecosystems face severe threats from human activities, leading to significant declines in fish populations. Traditional fish sampling techniques, such as netting, have been fundamental to ichthyology, offering insights into species richness and abundance. However, the complexity of stream environments limits the effectiveness of conventional sampling tools. As a result, more elusive or niche species are often missed. In recent years, water environmental DNA (eDNA) has emerged as a complementary method to traditional sampling. It allows for detection of aquatic organisms from water samples, expanding the scope of biodiversity assessments. Nevertheless, eDNA filtration faces challenges, especially in turbid waters, including the likelihood of co-extracting inhibitors that can affect amplification and detection processes, as well as the downstream flow of eDNA signals, which means that samples predominantly detect upstream fauna. To address these limitations, the use of bulk samples, such as stomach contents, provides a robust alternative by directly analyzing biological tissues and leveraging the bidirectional mobility of organisms within the stream, enabling the detection of taxa from both upstream and downstream regions. Given these issues, this study combines traditional netting, water eDNA analysis, and dietary metabarcoding to assess the fish biodiversity in three Neotropical streams in the Capim River basin, Para, Brazil. The integration of multiple sampling techniques offers a more accurate picture of biodiversity, helping to overcome the limitations of each individual method and providing essential insights for conservation efforts.

genetics↗

bioRxiv2024

eDNA replicates, polymerase and amplicon size impact inference of richness across habitats

Environmental DNA-based monitoring has been increasingly used in the last decade to monitor biodiversity in aquatic and terrestrial systems. Molecular-based surveys now allow quick and reliable production of baseline knowledge of species community composition on a large scale, allowing better understanding of ecosystem function and mitigation of stressors linked to anthropogenic activities. Despite this, technical hurdles often remain, and the impact of replicates, PCR polymerases and amplicon size on the recovered species richness is still poorly understood. Here, we conducted a large controlled experiment, with bulk samples collected from terrestrial, marine and freshwater environments to assess the impact of natural and technical replicates, PCR polymerases with different degrees of fidelity or proofreading activity, as well as amplicon size on species richness recovery across habitats. In this study, we consistently found variations in sample species richness depending on PCR polymerase choice. We further demonstrate the dissimilar impacts between natural and technical replicates on species richness recovery, and the necessity of increasing natural replications in eDNA based surveys. We highlight the benefits and limitations of replication strategies, polymerase choice and amplicon size across terrestrial, marine and freshwater habitats, and provide recommendations to increase the reliability of future eDNA-based metabarcoding studies.

molecular biology↗

bioRxiv2024

Molecular identification of whole squids and calamari at fairs and markets in regions of Latin America

In recent decades, the commercial importance of cephalopods has increased considerably, being an important fishing resource around the world. However, during the preparation for commercialization of those species, especially those sold in markets, they suffer the process known as "calamari" which includes removing and separating the head, arm, skin or even having the body structure cut into rings, which ends up making it difficult or often prevents the identification of the species, which can lead to replacements. In this sense, the present study aimed to use the large ribosomal region, rrnL (also known as 16S rDNA) to genetically identify cephalopod species sold in markets and fairs in Latin America. Whole and processed samples were collected from supermarkets and directly from local fishers the approximate collection location. Each generated sequence was submitted to the website Genbank for molecular comparison and included in the database for subsequent genetic identification. Comparison of sequences using the Blastn revealed the presence of eight species that are widely traded in the Latin American region. Our results indicate labeling errors in samples from the State of Para that contained the species Dosidicus gigas (d Orbigny, 1823) found only in the Pacific Ocean and were generically labeled as "National Lula". No type of substitution was found among the samples that were being sold at fairs and markets, only labeling errors. Thus, our results demonstrate the effectiveness of the rrnL for identifying species and evaluating labeling errors.

genetics↗

bioRxiv2023

The role of Miocene-Pleistocene environmental change in diversification of the genus Hypoclinemus Chabanaud, 1928.

The Neotropical region stands out as one of the most taxonomically diverse areas on the planet, garnering significant attention in the context of marine incursions and their role in shaping this diversity. Among marine-derived taxa, pleuronectiform fishes exhibit distinctive morphological characteristics that have attracted significant scientific interest. However, the biogeography of Hypoclinemus mentalis, initially described as Solea mentalis and subsequently assigned to the genus Achirus, was eventually reclassified into its current monotypic genus due to its limited distribution in freshwater environments, in contrast to the species of Achirus. The broad distribution of a single species across multiple South American river basins positions H. mentalis as an ideal candidate for biogeographic studies within South America, with an emphasis on the detection of cryptic lineages associated with major drainage basins. In our study, we employed mitochondrial and nuclear markers to investigate the potential existence of such lineages within the broader context of a molecular phylogeny that encompasses all valid genera in the flatfish family Achiridae. Our findings reveal that Hypoclinemus comprises seven operational taxonomic units (OTUs), as deduced from specimens collected across the majority of its documented range. Furthermore, our phylogeographic analyses support the hypothesis that colonization of freshwater habitats occurred through connections between the Caribbean Sea and Lake Pebas approximately 21.28 million years ago. Moreover, we observed that differentiation of lineages within the Hypoclinemus genus was significantly influenced by pronounced sea level fluctuations during the Plio-Pleistocene epoch, underscoring the impact of glaciations and interglacial periods on the biogeographic patterns.

evolutionary biology↗

bioRxiv2021

eDNA in a bottleneck: obstacles to fish metabarcoding studies in megadiverse freshwater systems

The current capacity of environmental DNA (eDNA) to provide accurate insights into the biodiversity of megadiverse regions (e.g., the Neotropics) requires further evaluation to ensure its reliability for long-term monitoring. In this study, we first evaluated the taxonomic resolution capabilities of a short fragment from the 12S rRNA gene widely used in fish eDNA metabarcoding studies, and then compared eDNA metabarcoding data from water samples with traditional sampling using nets. For the taxonomic discriminatory power analysis, we used a specifically curated reference dataset consisting of 373 sequences from 264 neotropical fish species (including 47 newly generated sequences) to perform a genetic distance-based analysis of the amplicons targeted by the MiFish primer set. We obtained an optimum delimitation threshold value of 0.5% due to lowest cumulative errors. The barcoding gap analysis revealed only a 50.38% success rate in species recovery (133/264), highlighting a poor taxonomic resolution from the targeted amplicon. To evaluate the empirical performance of this amplicon for biomonitoring, we assessed fish biodiversity using eDNA metabarcoding from water samples collected from the Amazon (Adolpho Ducke Forest Reserve and two additional locations outside the Reserve). From a total of 84 identified Molecular Operational Taxonomic Units (MOTUs), only four could be assigned to species level using a fixed threshold. Measures of -diversity analyses within the Reserve showed similar patterns in each site between the number of MOTUs (eDNA dataset) and species (netting data) found. However, {beta}-diversity revealed contrasting patterns between the methods. We therefore suggest that a new approach is needed, underpinned by sound taxonomic knowledge, and a more thorough evaluation of better molecular identification procedures such as multi-marker metabarcoding approaches and tailor-made (i.e., order-specific) taxonomic delimitation thresholds.

ecology↗

bioRxiv2019

Species specificity and intraspecific variation in the chemical profiles of Heliconius butterflies across a large geographic range

In many animals, mate choice is important for the maintenance of reproductive isolation between species. Traits important for mate choice and behavioural isolation are predicted to be under strong stabilising selection within species, however such traits can also exhibit variation at the population level driven by neutral and adaptive evolutionary processes. Here, we describe patterns of divergence among androconial and genital chemical profiles at inter- and intra-specific levels in mimetic Heliconius butterflies. Most variation in chemical bouquets was found between species, but there were also quantitative differences at the population level. We found a strong correlation between interspecific chemical and genetic divergence, however, this correlation varied in intraspecific comparisons. We identified indicator compounds characteristic of particular species that included known biologically active compounds, suggesting an approach for identification of candidate compounds for future behavioural studies in novel systems. Overall, the strong signal of species identity suggests a role for these compounds in species recognition, but with additional potentially neutral variation at the population level.

evolutionary biology↗