Biology subjects

McFadden, C. S.

Publications and source records attributed to McFadden, C. S..

11 recordsLinked to original sources

bioRxiv2026

The invasive soft coral Xenia umbellata has been confirmed in Cuban waters

Octocoral colonies with unusual morphology were detected in September 2022 and October 2023 in two coastal areas east of Havana, Cuba, and tentatively identified as Unomia stolonifera. U. stolonifera is an invasive octocoral from the Indo-Pacific that was first reported in the Caribbean off Venezuela in the 2000s, where it has spread rapidly, smothering coral reefs and substantially altering benthic communities. After obtaining tissue samples from a Cuban octocoral colony, we re-examined the specimen using molecular barcoding of three mitochondrial regions (16S/ND2, mtMutS, COI) and the nuclear large ribosomal subunit (28S rRNA), and we unequivocally identified it as Xenia umbellata. X. umbellata, a native of the Red Sea, was first identified in southern Puerto Rico in October 2023 and has since been found in various marine ecosystems along the southern coast of the island. The presence of either invasive octocoral species in Cuba or elsewhere in the Caribbean would be of a serious environmental concern due to their documented tolerance, totipotentiality, propagation capacity and significant negative interactions with local benthic fauna. Attempts to eradicate the invasive soft coral colonies from Cuban waters have been initiated with apparent success, helping to control further expansion. The most likely introduction pathway is the accidental or intentional releases from the aquarium trade but transport via ballast water cannot be ruled out. We cannot discount the possibility of independent invasion events from different routes to Puerto Rico and Cuba occurring within a year of each other. Propagation from Cuba to Puerto Rico, or vice versa, which we consider highly improbable, would likely imply that soft coral populations may also have been established on Hispaniola but have remained undetected in the Dominican Republic and Haiti to date.

ecology↗

bioRxiv2025

First record of a second invasive soft coral species, Latissimia ningalooensis, in southern Puerto Rico

Ever since the discovery of the invasive soft coral species Xenia umbellata (Anthozoa, Octocorallia, Malacalcyonacea, Xeniidae) on the reefs of southwestern Puerto Rico, ongoing surveys have documented its spread and potential impacts on native marine fauna. During benthic surveys conducted by scientific divers from Puerto Ricos DNER and the Department of Marine Sciences at UPRM, colonies of xeniid soft corals were observed with morphological and color characteristics distinct from those of X. umbellata. Morphological and genetic barcoding analyses of four gene regions confirmed the presence of a second invasive xeniid species, Latissimia ningalooensis, in the southern reefs of Puerto Rico. Originally described in Western Australia, L. ningalooensis has recently been reported in southeastern Brazilian waters, marking its expansion into the Atlantic. The discovery of a second xeniid species in Puerto Rico following the recent introduction of X. umbellata, is both surprising and concerning. Highly disturbed reefs, such as those along the southern coast of Puerto Rico and the wider Caribbean, seem highly susceptible to invasive species. Recent reports of invasive soft corals and other marine species in Puerto Rico highlight the potential for some species to become a regional issue, requiring coordinated management actions across the Caribbean.

ecology↗

bioRxiv2024

New mitochondrial gene order arrangements and evolutionary implications in the subclass Octocorallia

The complete mitochondrial genomes of octocorals typically range from 18.5 kb to 20.5 kb in length, and include 14 protein coding genes (PCGs), two ribosomal RNA genes and one tRNA. To date seven different gene orders (A-G) have been described, yet comprehensive investigations of the actual number of arrangements, as well as comparative analyses and evolutionary reconstructions of mitochondrial genome evolution within the whole subclass Octocorallia have been often overlooked. Here we considered the complete mitochondrial genomes available for octocorals and explored their structure and gene order variability. Our results updated the actual number of mitochondrial gene order arrangements so far known for octocorals from seven to twelve, and allowed us to explore and preliminarily discuss the role of some of the structural and functional factors in the mitogenomes. We performed comparative mitogenomic analyses on the existing and novel octocoral gene orders, considering different mitogenomic structural features such as genome size, GC percentage, AT- and GC-skewness. The mitochondrial gene order history mapped on a recently published nuclear loci phylogeny showed that the most common rearrangement events in octocorals are inversions, and that the mitochondrial genome evolution in the subclass is discontinuous, with rearranged gene orders restricted only to some regions of the tree. We believe that different rearrangement events arose independently and most likely that new gene orders, instead of being derived from other rearranged orders, came from the ancestral and most common gene order. Finally, our data demonstrate how the study of mitochondrial gene orders can be used to explore the evolution of octocorals and in some cases can be used to assess the phylogenetic placement of certain taxa.

genomics↗

bioRxiv2024

Shadows over Caribbean reefs: Identification of a new invasive soft coral species, Xenia umbellata, in southwest Puerto Rico

In October 2023, several colonies of an alien soft coral species were reported on shallow reefs in southwest Puerto Rico. The soft coral was identified as a xeniid octocoral (species undetermined), resembling the octocoral Unomia stolonifera, which has invaded and overgrown reefs in Venezuela in recent years. To conclusively characterize the species of the invading xeniid, we employed multilocus barcoding targeting four genes (ND2, mtMutS, COI, and 28S) of three separate colonies across three locations in southwest Puerto Rico. Sequence comparisons with xeniid sequences from GenBank, including those from the genera Xenia and Unomia, indicated a 100% sequence identity (>3,000 bp combined) with the species Xenia umbellata (Octocorallia : Malacalcyonacea : Xeniidae). Xenia umbellata is native to the Red Sea and to our knowledge, this represents the first confirmed case of this species as an invader on Caribbean reefs. Similar to U. stolonifera, X. umbellata is well known for its ability to rapidly overgrow substrate as well as tolerate environmental extremes. In addition, X. umbellata has recently been proposed as a model system for tissue regeneration having the ability to regenerate completely from a single tentacle. These characteristics greatly amplify X. umbellatas potential to adversely affect any reef it invades. Our findings necessitate continued collaborative action between local management agencies and stakeholders in Puerto Rico, as well as neighboring islands, to monitor and control this invasion prior to significant ecological perturbation.

genetics↗

bioRxiv2024

Phylogenomics reveals coincident divergence between giant host sea anemones and the clownfish adaptive radiation.

The mutualism between clownfishes (or anemonefishes) and their giant host sea anemones are among the most immediately recognizable animal interactions on the planet and have attracted a great deal of popular and scientific attention [1-5]. However, our evolutionary understanding of this iconic symbiosis comes almost entirely from studies on clownfishes-- a charismatic group of 28 described species in the genus Amphiprion [2]. Adaptation to venomous sea anemones (Anthozoa: Actiniaria) provided clownfishes with novel habitat space, ultimately triggering the adaptive radiation of the group [2]. Clownfishes diverged from their free-living ancestors 25-30 MYA with their adaptive radiation to sea anemones dating to 13.2 MYA [2, 3]. Far from being mere habitat space, the host sea anemones also receive substantial benefits from hosting clownfishes, making the mutualistic and co-dependent nature of the symbiosis well established [4, 5]. Yet the evolutionary consequences of mutualism with clownfishes have remained a mystery from the host perspective. Here we use bait-capture sequencing to fully resolve the evolutionary relationships among the 10 nominal species of clownfish-hosting sea anemones for the first time (Figure 1). Using time-calibrated divergence dating analyses we calculate divergence times of less than 25 MYA for each host species, with 9 of 10 host species having divergence times within the last 13 MYA (Figure 1). The clownfish-hosting sea anemones thus diversified coincidently with clownfishes, potentially facilitating the clownfish adaptive radiation, and providing the first strong evidence for co-evolutionary patterns in this iconic partnership. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=187 SRC="FIGDIR/small/576469v1_fig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@7053b4org.highwire.dtl.DTLVardef@876c65org.highwire.dtl.DTLVardef@dd6d9forg.highwire.dtl.DTLVardef@147fddd_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO Diversification of the clownfish-hosting sea anemones was coincident with the clownfish adaptive radiation. A) Time-calibrated maximum likelihood cladogram of Order Actiniaria based on 328 ultra-conserved element and exon loci (75% data occupancy matrix). The three clades containing the clownfish hosting sea anemones are highlighted reflecting the multiple evolutionary origins of symbiosis with clownfishes within superfamily Actinioidea. B-D) Detailed time-calibrated maximum likelihood cladograms of Entacmaea quadricolor, Clade Stichodactylina, and Clade Heteractina, respectively. In all panels, the orange line denotes the beginning of the clownfish adaptive radiation 13 MYA. Sea anemone superfamilies Actinostoloidea, Metridioidea, Actiniernoidea, and Edwardsioidea are collapsed for clarity. C_FIG

evolutionary biology↗

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↗

bioRxiv2022

Extreme mito-nuclear discordance within Anthozoa, with notes on unique properties of their mitochondrial genomes

Whole mitochondrial genomes are often used in phylogenetic reconstruction. However, discordant patterns in species relationships between mitochondrial and nuclear phylogenies are commonly observed. Within Anthozoa (Phylum Cnidaria), mitochondrial-nuclear discordance has not yet been examined using a large and comparable dataset. Here, we used data obtained from target-capture enrichment sequencing to assemble and annotate mitochondrial genomes and reconstruct phylogenies for comparisons to phylogenies inferred from 100s of nuclear loci obtained from the same samples. The datasets comprised 108 hexacorals and 94 octocorals representing all orders and >50% of extant families. Results indicated rampant discordance between datasets at every taxonomic level. This discordance is not attributable to substitution saturation, but rather likely caused by recent and ancient introgressive hybridization and selection. We also found strong purifying selection across the mitochondrial genomes, cautioning their use in analyses that rely on assumptions of neutrality. Furthermore, unique properties of the mitochondrial genomes were noted, including genome rearrangements and the presence of nad5 introns. Specifically, we note the presence of the homing endonuclease in ceriantharians. This large dataset of mitochondrial genomes further demonstrates the utility of off-target reads generated from target-capture data for mitochondrial genome assembly and adds to the growing knowledge of anthozoan evolution.

evolutionary biology↗

bioRxiv2020

New approaches to species delimitation and population structure of corals: two case studies using ultraconserved elements and exons

As coral populations decline worldwide in the face of ongoing environmental change, documenting their distribution, diversity and conservation status is now more imperative than ever. Accurate delimitation and identification of species is a critical first step. This task, however, is not trivial as morphological variation and slowly evolving molecular markers confound species identification. New approaches to species delimitation in corals are needed to overcome these challenges. Here, we test whether target enrichment of ultraconserved elements (UCEs) and exons can be used for delimiting species boundaries and population structure within species of corals by focusing on two octocoral genera, Alcyonium and Sinularia, as exemplary case studies. We designed an updated bait set (29,363 baits) to target-capture 3,040 UCE and exon loci, recovering a mean of 1,910 {+/-} 168 SD per sample with a mean length of 1,055 {+/-} 208 bp. Similar numbers of loci were recovered from Sinularia (1,946 {+/-} 227 SD) and Alcyonium (1,863 {+/-} 177 SD). Species-level phylogenies were highly supported for both genera. Clustering methods based on filtered SNPs delimited species and populations that are congruent with previous allozyme, DNA barcoding, reproductive and ecological data for Alcyonium, and offered further evidence of hybridization among species. For Sinularia, results were congruent with those obtained from a previous study using Restriction Site Associated DNA Sequencing. Both case studies demonstrate the utility of target-enrichment of UCEs and exons to address a wide range of evolutionary and taxonomic questions across deep to shallow time scales in corals.

evolutionary biology↗

bioRxiv2019

A next generation approach to species delimitation reveals the role of hybridization in a cryptic species complex of corals

BackgroundOur ability to investigate processes shaping the evolutionary diversification of corals (Cnidaria: Anthozoa) is limited by a lack of understanding of species boundaries. Discerning species has been challenging due to a multitude of factors, including homoplasious and plastic morphological characters and the use of molecular markers that are either not informative or have not completely sorted. Hybridization can also blur species boundaries by leading to incongruence between morphology and genetics. We used traditional DNA barcoding and restriction-site associated DNA sequencing combined with coalescence-based and allele-frequency methods to elucidate species boundaries and simultaneously examine the potential role of hybridization in a speciose genus of octocoral, Sinularia.\n\nResultsSpecies delimitations using two widely used DNA barcode markers, mtMutS and 28S rDNA, were incongruent with one another and with the morphospecies identifications, likely due to incomplete lineage sorting. In contrast, 12 of the 15 morphospecies examined formed well-supported monophyletic clades in both concatenated RAxML phylogenies and SNAPP species trees of >6,000 RADSeq loci. DAPC and Structure analyses also supported morphospecies assignments, but indicated the potential for two additional cryptic species. Three morphologically distinct species pairs could not, however, be distinguished genetically. ABBA-BABA tests demonstrated significant admixture between some of those species, suggesting that hybridization may confound species delimitation in Sinularia.\n\nConclusionsA genomic approach can help to guide species delimitation while simultaneously elucidating the processes generating diversity in corals. Results support the hypothesis that hybridization is an important mechanism in the evolution of Anthozoa, including octocorals, and future research should examine the contribution of this mechanism in generating diversity across the coral tree of life.

evolutionary biology↗

bioRxiv2018

A Hybrid de novo Assembly of the Sea Pansy (Renilla muelleri) Genome

BackgroundOver 3,000 species of octocorals (Cnidaria, Anthozoa) inhabit an expansive range of environments, from shallow tropical seas to the deep-ocean floor. They are important foundation species that create coral \"forests\" which provide unique niches and three-dimensional living space for other organisms. The octocoral genus Renilla inhabits sandy, continental shelves in the subtropical and tropical Atlantic and eastern Pacific Oceans. Renilla is especially interesting because it produces secondary metabolites for defense, exhibits bioluminescence, and produces a luciferase that is widely used in dual-reporter assays in molecular biology. Although several cnidarian genomes are currently available, the majority are from hexacorals. Here, we present a de novo assembly of the R. muelleri genome, making this the first complete draft genome from an octocoral.\n\nFindingsWe generated a hybrid de novo assembly using the Maryland Super-Read Celera Assembler v.3.2.6 (MaSuRCA). The final assembly included 4,825 scaffolds and a haploid genome size of 172 Mb. A BUSCO assessment found 88% of metazoan orthologs present in the genome. An Augustus ab initio gene prediction found 23,660 genes, of which 66% (15,635) had detectable similarity to annotated genes from the starlet sea anemone, Nematostella vectensis, or to the Uniprot database. Although the R. muelleri genome is smaller (172 Mb) than other publicly available, hexacoral genomes (256-448 Mb), the R. muelleri genome is similar to the hexacoral genomes in terms of the number of complete metazoan BUSCOs and predicted gene models.\n\nConclusionsThe R. muelleri hybrid genome provides a novel resource for researchers to investigate the evolution of genes and gene families within Octocorallia and more widely across Anthozoa. It will be a key resource for future comparative genomics with other corals and for understanding the genomic basis of coral diversity.

genomics↗