Biology subjects

Hernandez-Agreda, A.

Publications and source records attributed to Hernandez-Agreda, A..

3 recordsLinked to original sources

bioRxiv2021

Hidden in the deep: distinct benthic trajectories call for monitoring of mesophotic reefs

Long-term monitoring studies are central to coral reef ecology and conservation management. However, ongoing monitoring programs are almost exclusively focused on shallow depths, and it remains unclear to what extent those are representative of the whole ecosystem. Here, we present a temporal comparison (2012-2017) of directly adjacent shallow and mesophotic benthic communities across seven sites from the Great Barrier Reef and Western Coral Sea. We found a positive correlation initially between shallow and mesophotic coral cover, with higher cover at shallow depths. However, this correlation broke down after multiple disturbances, with coral cover declining only at shallow depths. Point-based tracking revealed the dynamic nature of mesophotic communities, with their consistent coral cover reflecting a net balance between substantial growth and mortality. Overall, the divergent trajectories highlight the urgency to expand monitoring efforts into mesophotic depths, to decipher the processes governing these habitats and enable better-informed management of the overall ecosystem.

ecology↗

bioRxiv2021

Inconsistent patterns of microbial diversity and composition between highly similar sequencing protocols: a case study with reef-building corals

16S rRNA gene profiling (amplicon sequencing) is a popular technique for understanding host-associated and environmental microbial communities. Most protocols for sequencing amplicon libraries follow a standardized pipeline that can differ slightly depending on laboratory facility and user. Given that the same variable region of the 16S gene is targeted, it is generally accepted that sequencing output from differing protocols are comparable and this assumption underlies our ability to identify universal patterns in microbial dynamics through meta-analyses. However, discrepant results from a combined 16S rRNA dataset prepared by two labs whose protocols differed only in DNA polymerase and sequencing platform led us to scrutinize the outputs and challenge the idea of confidently combining them for standard microbiome analysis. Using technical replicates of reef-building coral samples from two species, Montipora aequituberculata and Porites lobata, we evaluated the consistency of alpha and beta diversity metrics between data resulting from these highly similar protocols. While we found minimal variation in alpha diversity between platform, significant differences were revealed with most beta diversity metrics, dependent on host species. These inconsistencies persisted following removal of low abundance taxa and when comparing across higher taxonomic levels, suggesting that bacterial community differences associated with sequencing protocol are likely to be context dependent and difficult to correct without extensive validation work. The results of this study encourage caution in the statistical comparison and interpretation of studies that combine rRNA sequence data from distinct protocols and point to a need for further work identifying mechanistic causes of these observed differences. ImportanceAmplicon sequencing remains a popular technique for characterizing organism and environmental microbiomes. The publication of sequence data from microbiome studies on open-access repositories provides an opportunity to identify universal patterns in microbial dynamics. To this end, it has been widely accepted that sequencing output from differing protocols are comparable and can be combined for analysis, so long as the same gene region is targeted. While most protocols for amplicon sequencing follow standardized pipelines, they can differ slightly between laboratory facility and user. In this study, we compared technical replicates of coral samples to evaluate the efficacy of combining organism-associated microbial datasets derived from two differing protocols. We found inconsistencies in the differences between bacterial communities, which persisted following data manipulations intended to increase comparability. These results suggest caution must be taken in the statistical comparison and interpretation of studies that combine data derived from distinct protocols.

microbiology↗

bioRxiv2020

Cryptic diversity masks ecologically distinct coral species on tropical reefs

Coral reefs are the epitome of species diversity, yet the number of described scleractinian coral species, the framework-builders of coral reefs, remains moderate by comparison. DNA sequencing studies are rapidly challenging this notion by exposing a wealth of undescribed diversity, but the evolutionary and ecological significance of this diversity remains largely unclear. Here, we present an annotated genome for one of the most ubiquitous corals in the Indo-Pacific (Pachyseris speciosa), and uncover through a comprehensive genomic and phenotypic assessment that it comprises morphologically indistinguishable, but ecologically divergent cryptic lineages. Demographic modelling based on whole-genome resequencing disproved that morphological crypsis was due to recent divergence, and instead indicated ancient morphological stasis. Although the lineages occur sympatrically across shallow and mesophotic habitats, extensive genotyping using a rapid diagnostic assay revealed differentiation of their ecological distributions. Leveraging "common garden" conditions facilitated by the overlapping distributions, we assessed physiological and quantitative skeletal traits and demonstrated concurrent phenotypic differentiation. Lastly, spawning observations of genotyped colonies highlighted the potential role of temporal reproductive isolation in the limited admixture, with consistent genomic signatures in genes related to morphogenesis and reproduction. Overall, our findings demonstrate how ecologically and phenotypically divergent coral species can evolve despite morphological stasis, and provide new leads into the potential mechanisms facilitating such divergence in sympatry. More broadly, they indicate that our current taxonomic framework for reef-building corals may be scratching the surface of the ecologically relevant diversity on coral reefs, consequently limiting our ability to protect or restore this diversity effectively.

evolutionary biology↗