Search for: All records

Human impacts are dramatically changing ecological communities, motivating research on resilience. Tropical reefs are increasingly undergoing transitions to short algal turf, a successional community that mediates either recovery to coral by allowing recruitment or transitions to longer turf/macroalgae. Intense herbivory limits turf height; subsequently, overfishing erodes resilience of the desirable coral-dominated reef state. Increased sedimentation also erodes resilience through smothering and herbivory suppression. In spite of this critical role, most herbivory studies on tropical reefs focus on fishes, and the contribution of urchins remains under-studied. To test how different herbivory and sedimentation scenarios impact turf resilience, we experimentally simulated, in situ, four future overfishing scenarios derived from patterns of fish and urchin loss in other reef systems and two future sedimentation regimes. We found urchins were critical to short turf resilience, maintaining this state even with reduced fish herbivory and increased sediment. Further, urchins cleared sediment, facilitating fish herbivory. This study articulates the likelihood of increased reliance on urchins on impacted reefs in the Anthropocene.

 

Obtaining body condition is an important life history challenge that directly impacts individual fitness and is particularly important for hibernating animals, whose maintenance of adequate body fat and mass is essential for survival. It is well-documented that host-associated microorganisms play a vital role in animal physiology and behavior. Recent work demonstrates that gut microbes are associated with fat accumulation and obesity, particularly the phyla Firmicutes and Bacteroidetes. The focus of most microbiome studies has been on human health or involved lab-reared animals used as a model system. However, these microbes likely are important for individual fitness in wild populations and provide potential mechanistic insights into the adaptability and survival of wildlife. Here we tested whether symbiotic microorganisms within the phyla of Firmicutes and Bacteroidetes were associated with summer mass gain in an exceptionally well-studied wild population of yellow-bellied marmots (Marmota flaviventer) by analyzing 207 fecal samples collected over 5 summer active seasons. Results showed that marmots with higher mass gain rates had a greater relative abundance of Firmicutes. In contrast, a higher relative abundance of Bacteroidetes was associated with lower mass gain rates, but only for marmots living in harsher environments. Similar patterns were found at the family level where Ruminococcaceae, a member of Firmicutes, was associated with higher mass gain rates, and Muribaculaceae, a member of Bacteroidetes, was associated with lower mass gain rates in harsher environments. Although correlative, these results highlight the potential importance of symbiotic gut microbiota to mass gain in the wild—a trait associated with survival and fitness in many taxonomic groups.

 

Coral reefs are shifting from coral to algal-dominated ecosystems worldwide. Recently, Turbinaria ornata, a marine alga native to coral reefs of the South Pacific, has spread in both range and habitat usage. Given dense stands of T. ornata can function as an alternative stable state on coral reefs, it is imperative to understand the factors that underlie its success. We tested the hypothesis that T. ornata demonstrates ontogenetic variation in allocation to anti-herbivore defense, specifically that blade toughness varied nonlinearly with thallus size. We quantified the relationship between T. ornata blade toughness and thallus size for individual thalli within algal stands (N=345) on 7 fringing reefs along the north shore of Moorea, French Polynesia. We found that blade toughness was greatest at intermediate sizes that typically form canopies, with overall reduced toughness in both smaller individuals that refuge within the understory and older reproductive individuals that ultimately detach and form floating rafts. We posit this variation in blade toughness reduces herbivory on the thalli that are most exposed to herbivores and may facilitate reproduction in dispersing stages, both of which may aid the proliferation of T. ornata. 

Understanding how evolutionary forces interact to drive patterns of selection and distribute genetic variation across a species' range is of great interest in ecology and evolution, especially in an era of global change. While theory predicts how and when populations at range margins are likely to undergo local adaptation, empirical evidence testing these models remains sparse. Here, we address this knowledge gap by investigating the relationship between selection, gene flow and genetic drift in the yellowtail clownfish, Amphiprion clarkii, from the core to the northern periphery of the species range. Analyses reveal low genetic diversity at the range edge, gene flow from the core to the edge and genomic signatures of local adaptation at 56 single nucleotide polymorphisms in 25 candidate genes, most of which are significantly correlated with minimum annual sea surface temperature. Several of these candidate genes play a role in functions that are upregulated during cold stress, including protein turnover, metabolism and translation. Our results illustrate how spatially divergent selection spanning the range core to the periphery can occur despite the potential for strong genetic drift at the range edge and moderate gene flow from the core populations. 

The fluid nature of the ocean, combined with planktonic dispersal of marine larvae, lowers physical barriers to gene flow. However, divergence can still occur despite gene flow if strong selection acts on populations occupying different ecological niches. Here, we examined the population genomics of an ectoparasitic snail,Coralliophila violacea(Kiener 1836), that specializes onPoritescorals in the Indo‐Pacific. Previous genetic analyses revealed two sympatric lineages associated with different coral hosts. In this study, we examined the mechanisms promoting and maintaining the snails’ adaptation to their coral hosts. Genome‐wide single nucleotide polymorphism (SNP) data from type II restriction site‐associated DNA (2b‐RAD) sequencing revealed two differentiated clusters ofC. violaceathat were largely concordant with coral host, consistent with previous genetic results. However, the presence of some admixed genotypes indicates gene flow from one lineage to the other. Combined, these results suggest that differentiation between host‐associated lineages ofC. violaceais occurring in the face of ongoing gene flow, requiring strong selection. Indeed, 2.7% of all SNP loci were outlier loci (73/2,718), indicative of divergence with gene flow, driven by adaptation of eachC. violacealineage to their specific coral hosts.

 

DNA metabarcoding is an increasingly popular technique to investigate biodiversity; however, many methodological unknowns remain, especially concerning the biases resulting from marker choice. Regions of the cytochromecoxidase subunit I (COI) and 18S rDNA (18S) genes are commonly employed “universal” markers for eukaryotes, but the extent of taxonomic biases introduced by these markers and how such biases may impact metabarcoding performance is not well quantified. Here, focusing on macroeukaryotes, we use standardized sampling from autonomous reef monitoring structures (ARMS) deployed in the world's most biodiverse marine ecosystem, the Coral Triangle, to compare the performance of COI and 18S markers. We then compared metabarcoding data to image‐based annotations of ARMS plates. Although both markers provided similar estimates of taxonomic richness and total sequence reads, marker choice skewed estimates of eukaryotic diversity. The COI marker recovered relative abundances of the dominant sessile phyla consistent with image annotations. Both COI and the image annotations provided higher relative abundance estimates of Bryozoa and Porifera and lower estimates of Chordata as compared to 18S, but 18S recovered 25% more phyla than COI. Thus, while COI more reliably reflects the occurrence of dominant sessile phyla, 18S provides a more holistic representation of overall taxonomic diversity. Ideal marker choice is, therefore, contingent on study system and research question, especially in relation to desired taxonomic resolution, and a multimarker approach provides the greatest application across a broad range of research objectives. As metabarcoding becomes an essential tool to monitor biodiversity in our changing world, it is critical to evaluate biases associated with marker choice.

 

Environmental DNA (eDNA) metabarcoding is a promising method to monitor species and community diversity that is rapid, affordable and non‐invasive. The longstanding needs of the eDNA community are modular informatics tools, comprehensive and customizable reference databases, flexibility across high‐throughput sequencing platforms, fast multilocus metabarcode processing and accurate taxonomic assignment. Improvements in bioinformatics tools make addressing each of these demands within a single toolkit a reality.

The new modular metabarcode sequence toolkitAnacapa(https://github.com/limey-bean/Anacapa/) addresses the above needs, allowing users to build comprehensive reference databases and assign taxonomy to raw multilocus metabarcode sequence data. A novel aspect ofAnacapais its database building module, “Creating Reference libraries Using eXisting tools” (CRUX), which generates comprehensive reference databases for specific user‐defined metabarcoding loci. TheQuality Control and ASV Parsingmodule sorts and processes multiple metabarcoding loci and processes merged, unmerged and unpaired reads maximizing recovered diversity.DADA2then detects amplicon sequence variants (ASVs) and theAnacapa Classifiermodule aligns these ASVs toCRUX‐generated reference databases usingBowtie2. Lastly, taxonomy is assigned to ASVs with confidence scores using a Bayesian Lowest Common Ancestor (BLCA) method. TheAnacapa Toolkitalso includes anrpackage,ranacapa, for automated results exploration through standard biodiversity statistical analysis.

Benchmarking tests verify that theAnacapa Toolkiteffectively and efficiently generates comprehensive reference databases that capture taxonomic diversity, and can assign taxonomy to both MiSeq and HiSeq‐length sequence data. We demonstrate the value of theAnacapa Toolkitin assigning taxonomy to seawater eDNA samples collected in southern California.

TheAnacapa Toolkitimproves the functionality of eDNA and streamlines biodiversity assessment and management by generating metabarcode specific databases, processing multilocus data, retaining a larger proportion of sequencing reads and expanding non‐traditional eDNA targets. All the components of theAnacapa Toolkitare open and available in a virtual container to ease installation.