Biology subjects

Muffett, K. M.

Publications and source records attributed to Muffett, K. M..

6 recordsLinked to original sources

bioRxiv2026

Can an original be found? Mitochondrial species identity does not predict nuclear genome similarity in the photosymbiotic jellyfish Cassiopea andromeda and C. xamachana

The Upside-Down Jellyfish, Cassiopea, has become a mainstay of cnidarian photosymbiosis research. Two nominal sister species, C. xamachana and the globally introduced C. andromeda, supply most of the medusae used in American and European laboratory research within this genus. As founder identity can shape experimental outcomes, here we utilize whole genome resequencing of 21 Cassiopea medusae spanning the Florida Keys, Bocas del Toro (Panama), and a European laboratory line, to ask whether mitochondrial species assignment predicts nuclear genome identity. Across multiple population structure analyses using the nuclear genome, Floridian Cassiopea carrying C. xamachana or C. andromeda mitotypes are indistinguishable, and geography is the dominant axis of nuclear genetic structure. A population tree that groups the two Floridian mitotypes as a single interbreeding unit is strongly supported (Patterson's D {approx} 0.0, Z = 0.02), whereas a tree that respects mitochondrial species boundaries is rejected (D = 0.42, Z = 20.8). Strikingly, the European "true" C. andromeda line clusters with Panamanian C. xamachana rather than with Floridian C. andromeda-mitotype animals. From the same sequencing effort, we recover evidence of symbiont community variability (Cladocopium) in Panama and assemble two near-complete Tenacibaculum and Endozoicomonas metagenomically-assembled genomes from Floridian host tissue. Together these results indicate that the C. andromeda/C. xamachana hybridization zone may extend across ocean basins, and that a "pure" original of either species may be difficult to find. We urge Cassiopea researchers to establish new European laboratory lines with described genomes.

ecology↗

bioRxiv2026

Jelly belly: Recovery of fish eDNA from Cassiopea medusae gastrovascular cavities across the Florida Keys

Ranges of small benthic fauna are notoriously difficult to assess. In some of these cases, modern eDNA methods can shed light on species occurrence. Here we conduct an exploratory study on the fish eDNA recoverable from the gastrovascular cavities of the easy-to-sample pore water siphoning benthic invertebrate, Cassiopea, across six sites within the Florida Keys. Twenty-seven fish 12S identities were recovered from water samples, two from sediment samples, and seventeen from Cassiopea gut swabs. In total, thirty-two different species were identified from nineteen families, including one shark species (Ginglymostoma cirratum), and five species of cryptobenthic reef fishes (f: Gobiidae, Labrisomidae). Additionally, five species were identified from medusae samples that were not recovered in water or sediment samples. The species identities recovered may provide insight into the fish in direct proximity to Cassiopea assemblages, as well as indicate that Cassiopea may accrue disproportionate eDNA from cryptobenthic reef fish compared to surrounding environmental samples. The unorthodox sampling technique of using eDNA recovered from jellyfish stomachs yields another avenue for epibenthic community data acquisition.

ecology↗

bioRxiv2026

Combination of indomethacin and temperature produces reliable strobilation in Cassiopea xamachana but batch effects create high variability in ephyra outcomes

Indomethacin and temperature shocks are both widely used to induce ephyra production in Cassiopea polyps, yet the combined effect of these stimuli on strobilation rate, ephyra viability, and polyp survivorship has not been systematically examined. We designed a full factorial experiment crossing five indomethacin concentrations (0, 10, 25, 50, and 75 {micro}M) with four temperature treatments (22, 25, 28, and 31{degrees}C) across three independent experimental trials, exposing a total of 288 individual Cassiopea xamachana polyps for 29 days. Overall, 207 of 288 polyps (71.9%) released at least one ephyra. Temperature was the stronger predictor of strobilation: higher temperatures substantially increased the probability of producing a healthy ephyra (log-odds: +0.327 per {degrees}C; {chi}{superscript 2} p = 6.5 x 10-5), while indomethacin had a smaller but significant positive effect (log-odds: +0.024 per {micro}M; {chi}{superscript 2} p = 0.035). The two stimuli acted independently without significant interaction on healthy ephyra production ({chi}{superscript 2} p = 0.87), although their interaction on total ephyra production (including unhealthy releases) was significant ({chi}{superscript 2} p = 1.0 x 10-9). Notably, low indomethacin concentrations (10 and 25 {micro}M) significantly increased the proportion of unhealthy ephyrae relative to seawater controls (paired t-tests: p = 0.035 and p = 0.006, respectively), while higher concentrations (50-75 {micro}M) did not. Polyp survivorship declined significantly at 28{degrees}C and 31{degrees}C but was unaffected by indomethacin. Trial replicate was the most statistically significant predictor of every outcome measured with the third trial producing near-universal strobilation but zero viable ephyrae, a result of an unidentified perturbation. These results indicate that temperature elevation to 28-31{degrees}C is the most reliable induction strategy for C. xamachana and that low indomethacin concentrations should be avoided when ephyra quality is paramount. We also note that cryptic batch-level variables can overwhelm controlled factors and should be addressed in future experimental designs.

zoology↗

bioRxiv2025

Low-abundance taxa drive host microbiome response to temperature stress

Global climate change (GCC) will lead to the deterioration of host and microbiome health, posing a significant threat to complex symbioses. To gauge the reproducibility of thermal warming associated with GCC and the time scales on which it occurs, we monitored shifts in the Exaiptasia microbiome in 24 populations of the model cnidarian Exaiptasia diaphana over the course of six months. We identified a small cohort of temperature-sensitive amplicon sequence variants (ASVs) that reproducibly declined with increases in temperature before changes in host fitness occurred. After comparing these ASVs to global datasets, we found that the heat-impacted ASVs from our experiment were also present in many other cnidarian species, highlighting their potential as widespread indicators of thermal stress. Overall, we find that fewer than 1% of the microbiome within E. diaphana are heat indicator taxa, suggesting that a small but consistent group of ASVs signals the early stages of thermal stress.

ecology↗

bioRxiv2025

Notes on the diet and size of Cassiopea

Medusae of the genus Cassiopea are common components of tropical and subtropical coastlines globally. Despite the broad distribution of this benthic scyphozoan, much about their ecology remains poorly described. Here, we collected over 100 adult Cassiopea individuals from Panama, the eastern United States, Cuba, the Philippines, Italy and Australia to examine continuity and differences in their diet across space, and to investigate whether their unique lifestyle is reflected in their diet. We found the majority of prey items to be associated with the epibenthos. The recovered prey were supermajority crustaceans, mainly harpacticoid copepods, with pteropods, nematodes, and miscellaneous eggs common as secondary components. Within the gastrovascular cavity of a single medusa, we found up to 379 items. There was a limited relationship between medusa size and prey items. Location had an impact on gut content diversity and medusa size had a small impact on the number of taxa found within the gut. In some sites, prey were scarce or absent from all medusae sampled. Overall, we reaffirm the diet previously recorded for small medusae in Puerto Rico and show that similar components are common in large and small medusae from throughout the East and West Atlantic and the Philippines.

ecology↗

bioRxiv2024

Bacterial communities of Cassiopea in the Florida Keys share major bacterial taxa with coral microbiomes

Interactions with microbial communities fundamentally shape metazoans physiology, development, and health across marine ecosystems. This is especially true in zooxanthellate (symbiotic algae-containing) cnidarians. In photosymbiotic anthozoans (eg. shallow water anemones and corals), the key members of the associated microbiota are increasingly well studied, however there is limited data on photosymbiotic scyphozoans (true jellyfish). Using 16S rRNA barcoding, we sampled the internal and external mucus of the zooxanthellate Upside- Down Jellyfish, Cassiopea xamachana throughout eight sites covering the full length of the Florida Keys. We find that across sites, these medusae to have low-diversity internal microbial communities distinct from the communities of their external surfaces and their environment. These internal communities are dominated by only three taxa: Endozoicomonas cf. atrinae, an uncultured novel Mycoplasma, and Vibrio cf. coralliilyticus. Cassiopea bell mucosal samples conform largely to the communities of surrounding sediment with the addition of Endozoicomonas cf. atrinae. The microbial taxa we identify associated with wild Florida Keys Cassiopea bear a strong resemblance to those found within photosymbiotic anthozoans, increasing the known links in ecological position between these groups.

ecology↗