Biology subjects

McCartin, L. J.

Publications and source records attributed to McCartin, L. J..

4 recordsLinked to original sources

bioRxiv2025

Environmental filtering shapes patch dynamics across isolated mesophotic reefs

Mesophotic coral ecosystems (MCEs; [~]30-150 m) are major but poorly understood benthic habitats. We used Autonomous Reef Monitoring Structures (ARMS) and integrated metabarcoding (mtCOI, 18S), image analysis, and hydrodynamic modeling across six mesophotic banks in the Gulf of Mexico to test whether community assembly is governed by environmental filtering or dispersal limitation. Local environmental conditions explained nearly twice as much compositional variance as geographic effects. Differences in depth and turbidity predicted community dissimilarity up to tenfold better than geographic distance. Turbidity, driven by the benthic nepheloid layer (BNL), was the dominant filter, while depth effects were weaker and taxon-specific. Hydrodynamic simulations revealed dispersal is variable but not limiting. These findings identify the BNL as a key physical driver linking shelf oceanography, biodiversity, and ecosystem function. Suspended particle dynamics associated with BNLs merit integration into conservation planning as critical mediators of ecological connectivity in mesophotic and other patchy reef systems globally. TeaserSuspended particle layers, not dispersal barriers, determines which species colonize mesophotic coral reefs on the TX-LA continental shelf.

ecology↗

bioRxiv2024

Environmental DNA Transport at an Offshore Mesophotic Bank in the Northwestern Gulf of Mexico

Environmental DNA (eDNA) offers a powerful, non-invasive means of assessing biodiversity in marine ecosystems, yet the spatial resolution of eDNA remains poorly understood. We investigated the vertical and horizontal dispersion of eDNA from an isolated mesophotic coral reef (Bright Bank) in the stratified offshore waters of the northern Gulf of Mexicos shelf edge. We conducted comprehensive vertical and horizontal water column eDNA sampling across multiple radial directions and depths. We characterized invertebrate communities using a paired metabarcoding approach targeting broad (18S) and taxon-specific (28S) markers. We found that vertical transport of benthic eDNA was limited by water column stratification, with distinct benthic community signals confined to the near-bottom layers. In contrast, horizontal dispersal of eDNA extended beyond at least 1.5 km, though the prevalence of eDNA from benthic invertebrates declined with increasing distance from the bank. Taxon-specific primers showed greater detection sensitivity and dispersal range, particularly for benthic corals, than primers that are used to broadly assess eukaryotic biodiversity. These findings demonstrate that water column structure and marker selection critically influence the spatial interpretation of marine eDNA data. The study represents a snapshot of late-summer conditions. Seasonal variability should be considered in future studies. Our results provide a realistic framework for integrating eDNA into offshore environmental surveillance, biodiversity monitoring, and spatial management.

ecology↗

bioRxiv2023

Nuclear eDNA Metabarcoding Primers for Anthozoan Coral Biodiversity Assessment

The distributions of anthozoan corals are under-characterized due to their wide bathymetric range, occurrences in remote locales, and difficulties of identification from morphology alone. Environmental DNA (eDNA) sequencing promises to be a non-invasive strategy to complement conventional approaches for mapping and monitoring coral communities. Primers for eDNA meta-barcoding have been designed to amplify nuclear and mitochondrial DNA barcodes in shallow scleractinians and mitochondrial MutS in deep-sea octocorals. However, a comprehensive method for eDNA meta-barcoding from all anthozoan corals, including black corals, has not been developed. We leveraged a sequence database of global coral collections, from shallow water to the deep sea, to design new PCR primers for coral eDNA sequencing that target the 28S rRNA gene. We tested the performance of these primers by amplifying and sequencing eDNA from water samples collected in the Gulf of Mexico near mesophotic and deep-sea corals that were also imaged, sampled, and sequenced. Sequencing libraries produced using the primers were highly enriched in coral eDNA, with up to 99.8% of the reads originating from corals. Further, the 28S barcode amplified using the primers distinguished coral genera. We recovered amplicon sequencing variants (ASVs) identical to DNA barcodes derived from Sanger sequencing and genome skimming of corals sampled at the same field sites. This new eDNA meta-barcoding strategy permits targeted eDNA sequencing of black corals, octocorals, and scleractinians at sites where they co-occur and expands our current toolkit for mapping and monitoring coral communities in shallow coral reefs and the deep sea.

ecology↗

bioRxiv2023

Skimming genomes for systematics and DNA barcodes of corals

1: Numerous genomic methods developed over the past two decades have enabled the discovery and extraction of orthologous loci to help resolve phylogenetic relationships across various taxa and scales. Genome skimming (or low-coverage whole genome sequencing) remains a low-cost, promising method to not only extract high-copy loci, but also 100s to 1000s of phylogenetically informative single-copy nuclear loci (e.g., ultraconserved elements [UCEs] and exons) from contemporary and historical museum samples. The subphylum Anthozoa, which includes important ecosystem engineers (e.g., stony corals, black corals, anemones and octocorals) in the marine environment, is in critical need of phylogenetic resolution and thus might benefit from a genome-skimming approach. 2: Genome skimming was conducted on 242 hexacorals and octocorals collected from 1890 to 2022. Using previously developed target-capture baitsets, we bioinformatically obtained UCEs and exons from the genome-skimming data and incorporated them with data from previously published target-capture studies. We also extracted partial to whole mitogenomes and nuclear rRNA genes from the skim data. 3: The mean number of UCE and exon loci extracted from the genome skimming data was 1,837 {+/-} 662 SD for octocorals and 1,422 {+/-} 720 loci for hexacorals; phylogenetic relationships were well resolved within each class. A mean of 1,422 {+/-} 720 loci were obtained from the historical museum specimens, with 1,253 loci recovered from the oldest specimen collected in 1886 and 1,336 loci recovered from a holotype. The nuclear rRNA genes and the majority of mitochondrial genes were successfully obtained from >95% of samples. Out of 99 circularized mitogenomes, 88% were recovered in samples from which we obtained >15M paired-end (PE) reads (>30M total reads); there was more variability in whether mitogenomes were circularized or not in samples with <15M PE reads. 4: Bioinformatically pulling UCEs, exons, mitochondrial genomes, and nuclear rRNA genes from genome skimming is a viable and low-cost option for phylogenetic studies. This approach can be used to review and support taxonomic revisions and reconstruct evolutionary histories, including historical museum and type specimens.

evolutionary biology↗