Biology subjects

Paight, C.

Publications and source records attributed to Paight, C..

3 recordsLinked to original sources

bioRxiv2021

Utility of Occupancy Models with Environmental DNA (eDNA) fromOlympic Coast National Marine Sanctuary

Adjacent to the spectacular, rugged coastline bordering the Olympic Peninsula of Washington State, Olympic Coast National Marine Sanctuary (OCNMS) encompasses 8257 km2 of coastal waters that support one of North Americas most productive marine ecosystems. These rich waters support important recreational, commercial and subsistence fisheries for Washington state and four sovereign tribal governments: the Quinault Indian Nation and the Makah, Quileute and Hoh Tribes. Given its ecological, cultural and economic significance, managers from OCNMS are tasked with monitoring and management towards conserving the areas ecological integrity. The development of metabarcoding with environmental DNA (eDNA) as an effective freshwater monitoring tool has potential applications in marine systems, but the statistical analysis and the interpretation of those eDNA results are still under development. One promising strategy to analyze eDNA is through the use of occupancy models. Occupancy models enable us to calculate probabilities of detection from each taxon sequenced and are designed to work with presence-absence data. To inform our long term monitoring design of this coastal ecosystem, we collected 44 eDNA samples at nine of OCNMS long term mooring sites in 2019 and tested four different molecular markers for species reported and taxonomic richness. Additionally, we assessed occupancy models for use with eDNA to estimate the number of samples required to accurately predict the presence of a species. Occupancy models show great promise for use in eDNA studies provided there is sufficient replication; additionally, the choice of molecular marker strongly influences a taxas probability of detection. Author SummaryWe show the utility of using occupancy models with eDNA in Olympic Coast National Marine Sanctuary for monitoring near-shore marine biological communities. Based on probabilities of detection, long term coastal monitoring projects using eDNA would benefit from designs prioritizing sample number (10-20 samples per site) over sites sampled. With proper study design, occupancy models provide a statistical framework for comparisons between sites and over time. By accounting for simple non-detection vs true absence, occupancy models help to eliminate noise from eDNA studies, increasing detection of true shifts in community composition. We also demonstrate that marker choice is an important study design consideration not only for the types of taxa recovered, but also for consistency between samples and timepoints.

bioinformatics↗

bioRxiv2020

Metabolic contributions of an alphaproteobacterial endosymbiont in the apicomplexanCardiosporidium cionae

Apicomplexa is a diverse protistan phylum composed almost exclusively of metazoan-infecting parasites, including the causative agents of malaria, cryptosporidiosis, and toxoplasmosis. A single apicomplexan genus, Nephromyces, was described in 2010 as a mutualist partner to its tunicate host. Here we present genomic and transcriptomic data from the parasitic sister species to this mutualist, Cardiosporidium cionae, and its associated bacterial endosymbiont. Cardiosporidium cionae and Nephromyces both infect tunicate hosts, localize to similar organs within these hosts, and maintain bacterial endosymbionts. Though many other protists are known to harbor bacterial endosymbionts, these associations are completely unknown in Apicomplexa outside of the Nephromycidae clade. Our data indicate that a vertically transmitted -proteobacteria has been retained in each lineage since Nephromyces and Cardiosporidium diverged. This -proteobacterial endosymbiont has highly reduced metabolic capabilities, but contributes the essential amino acid lysine, and essential cofactor lipoic acid to C. cionae. This partnership likely reduces resource competition with the tunicate host. However, our data indicate that the contribution of the single -proteobacterial endosymbiont in C. cionae is minimal compared to the three taxa of endosymbionts present in the Nephromyces system, and is a potential explanation for the virulence disparity between these lineages.

evolutionary biology↗

bioRxiv2020

Codependence in the Nephromyces species swarm depends on heterospecific bacterial endosymbionts

The phylum Apicomplexa encompasses 6000 ubiquitous animal parasites, including Plasmodium, the most deadly human parasite on Earth. Anciently parasitic lineages, like apicomplexans, lose core metabolic pathways over time, as they evolve less costly scavenging mechanisms. The recent description of a mutualistic apicomplexan, Nephromyces, from deep within this parasitic group, opened the possibility of an evolutionary innovation that allowed an escape from a parasitic lifestyle. Nuclear genome data from Nephromyces, as well as the three bacterial symbionts that live within this species complex, demonstrate that the bacteria within Nephromyces contribute essential cofactors and amino acids that have enabled Nephromyces to abandon a parasitic lifestyle. Among these, bacterial lipoic acid appears to be a key cofactor for the reduction of virulence in Nephromyces. However, whereas we use FISH microscopy to reveal that each individual Nephromyces harbors no more than one endosymbiont type, no single bacterial endosymbiont can account for all missing metabolites. Based on the unique habitat of Nephromyces, as well as genomic, culturing, and wild population data, we conclude that Nephromyces has evolved as an extraordinary clade of codependent species, unlike any previously described.

evolutionary biology↗