Biodiversity monitoring based on DNA metabarcoding depends on primer performance. Here, we develop a new metabarcoding primer pair that targets a ~ 318 bp fragment of the 28S rRNA gene. We validate the primer pair in assessing sponges, a notoriously challenging group for coral reef metabarcoding studies, by using mock and natural complex reef communities to examine its performance in species detection, amplification efficiency, and quantitative potential. Mock community experiments revealed a high number of sponge species (n = 94) spanning a broad taxonomic scope (15 orders), limited taxon-specific primer biases (only a single species exceeded a two-fold deviation from the expected number of reads), and its suitability for quantitative metabarcoding – there was a significant relationship between read abundance and visual percent coverage of sponge taxa (R = 0.76). In the natural complex coral reef community experiments, commonly used COI metabarcoding primers detected only 30.9% of sponge species, while the new 28S primer increased detection to 79.4%. These new 28S primers detect a broader taxonomic array of species across phyla and classes within the complex cryptobiome of coral reef communities than the Leray-Geller COI primers. As biodiversity assessments using metabarcoding tools are increasingly being leveraged for environmental monitoring and guide policymaking, these new 28S rRNA primers can improve biodiversity assessments for complex ecological coral reef communities.

Signals of natural selection can be quickly eroded in high gene-flow systems, curtailing efforts to understand how and when genetic adaptation occurs in the ocean. This long-standing, unresolved topic in ecology and evolution has renewed importance because changing environmental conditions are driving range expansions that may necessitate rapid evolutionary responses. One example occurs in Kellet’s whelk (Kelletia kelletii), a common subtidal gastropod with a ~ 40-60 day pelagic larval duration that expanded their biogeographic range northward in the 1970s by over 300 kilometers. To test for genetic adaptation, we performed a series of experimental crosses with Kellet’s whelk adults collected from their historical (HxH) and recently expanded range (ExE), and conducted RNA-Seq on offspring that we reared in a common garden environment. We identified 2,770 differentially expressed genes (DEGs) between 54 offspring samples with either only historical-range (HxH offspring) or expanded-range (ExE offspring) ancestry. Using SNPs called directly from the DEGs, we assigned samples of known origin back to their range of origin with unprecedented accuracy for a marine species (92.6 and 94.5% for HxH and ExE offspring, respectively). The SNP with the highest predictive importance occurred on triosephosphate isomerase (TPI), an essential metabolic enzyme involved in cold stress response. TPI was significantly upregulated and contained a non-synonymous mutation in the expanded range. Our findings pave the way for accurately identifying patterns of dispersal, gene flow, and population connectivity in the ocean by demonstrating that experimental transcriptomics can reveal mechanisms for how marine organisms respond to changing environmental conditions.

Signals of natural selection can be quickly eroded in high gene-flow systems, severely challenging efforts to understand how and when genetic adaptation occurs in the ocean. This long-standing, unresolved topic in ecology has renewed importance because rapidly changing environmental conditions are driving range expansions that, in many cases, necessitate rapid evolutionary responses. To test for genetic adaptation in a coastal marine species with high dispersal potential, we performed a series of crosses on Kellet’s whelk (Kelletia kelletii) collected from its historical and recently colonized range, and conducted RNA-Seq on offspring that we reared in a common garden environment. We identified 2,770 differentially expressed genes between 54 samples with historical-range and expanded-range ancestry. Using SNPs called directly from the differentially expressed genes, we revealed parental population structure that enabled us to assign “unknown” samples back to their range of origin with unprecedented accuracy for a marine species (92.6 to 94.5%). The SNP with the highest predictive importance occurred on triosephosphate isomerase (TPI), an essential enzyme for glycolysis and glucogenesis, which also plays a role in cold stress response. TPI is both highly upregulated and contains a non-synonymous mutation in the expanded range, where ocean temperatures are colder than in the historical range. Our findings pave the way for accurately identifying patterns of dispersal, gene flow, and population connectivity in the ocean by demonstrating that rapid genetic adaptation can occur even in high gene flow species and that experimental transcriptomics can reveal mechanisms for how marine organisms respond to changing environmental conditions.