Genetic adaptation despite high gene flow in a range-expanding population.

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 an ~40- to 60-day pelagic larval duration that expanded their biogeographic range northwards in the 1970s by over 300 km. 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 2770 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.

Effects of macroalgae and sea urchin grazing pressure on zoantharians growth under laboratory conditions.

In the context of ocean warming, thermophilic organisms such as zoantharians are expanding and altering shallow benthic habitats. Here, a four-month laboratory experiment was performed to examine the influence of three types of macroalgae morphotypes common in the Canary Islands (turf algae, Lobophora spp., and crustose coralline algae) on the growth of two zoantharian species, Palythoa caribaeorum and Zoanthus pulchellus. Additionally, the grazing effects of echinoids Diadema africanum and Paracentrotus lividus were assessed as facilitators of substrate colonization by means of controlling macroalgae cover. Colony and algal coverages were measured at the beginning, middle and end of the experiment, and increments were calculated. Results indicated a general decrease in zoantharian colony sizes in contact with different algal types in the absence of sea urchins. However, P. caribaeorum colonies showed significant growth in the presence of D. africanum, highlighting the ecological importance of sea urchins in zoantharian population proliferation and subsequent community modification. This study represents the first investigation into zoantharian-macroalgae interactions under controlled conditions.

Genomic DNA extraction optimization and validation for genome sequencing using the marine gastropod Kellet's whelk.

Next-generation sequencing technologies, such as Nanopore MinION, Illumina Hiseq and Novaseq, and PacBio Sequel II, hold immense potential for advancing genomic research on non-model organisms, including the vast majority of marine species. However, application of these technologies to marine invertebrate species is often impeded by challenges in extracting and purifying their genomic DNA due to high polysaccharide content and other secondary metabolites. In this study, we help resolve this issue by developing and testing DNA extraction protocols for Kellet's whelk (Kelletia kelletii), a subtidal gastropod with ecological and commercial importance, by comparing four DNA extraction methods commonly used in marine invertebrate studies. In our comparison of extraction methods, the Salting Out protocol was the least expensive, produced the highest DNA yields, produced consistent high DNA quality, and had low toxicity. We validated the protocol using an independent set of tissue samples, then applied it to extract high-molecular-weight (HMW) DNA from over three thousand Kellet's whelk tissue samples. The protocol demonstrated scalability and, with added clean-up, suitability for RAD-seq, GT-seq, as well as whole genome sequencing using both long read (ONT MinION) and short read (Illumina NovaSeq) sequencing platforms. Our findings offer a robust and versatile DNA extraction and clean-up protocol for supporting genomic research on non-model marine organisms, to help mediate the under-representation of invertebrates in genomic studies.

Reef fish assemblages associated to new mat-forming zoantharian communities in the Canary Islands.

Proliferations of zoantharians along tropical and subtropical regions are increasingly common and usually associated with anthropogenic impacts and ecosystem degradation. In the Canary Islands, we studied how the dominance in the substrate of Palythoa caribaeorum and Zoanthus pulchellus affected fish communities. For that purpose, we recorded the composition and biodiversity of fish assemblages associated to both zoantharian and macroalgae dominated habitats. In general terms, we found significant reductions of total fish abundance and richness at P. caribaeorum dominated habitats compared with macroalgae stands. However, in terms of trophic structure, there were significant changes within both zoantharian habitats depending on their coverages of the substrate. Herbivores and small invertebrate feeders, which are more adapted to forage in the macroalgae canopy, were less abundant in zoantharian habitats. This study demonstrates that the increasing dominance of zoantharians throughout the archipelago restructure the ecosystems and impact the native fish communities, that may offer a positive feedback for invasive tropical species to thrive.

Atlantia, a new genus of Dendrophylliidae (Cnidaria, Anthozoa, Scleractinia) from the eastern Atlantic.

Atlantia is described as a new genus pertaining to the family Dendrophylliidae (Anthozoa, Scleractinia) based on specimens from Cape Verde, eastern Atlantic. This taxon was first recognized as Enallopsammia micranthus and later described as a new species, Tubastraea caboverdiana, which then changed the status of the genus Tubastraea as native to the Atlantic Ocean. Here, based on morphological and molecular analyses, we compare fresh material of T. caboverdiana to other dendrophylliid genera and describe it as a new genus named Atlantia in order to better accommodate this species. Evolutionary reconstruction based on two mitochondrial and one nuclear marker for 67 dendrophylliids and one poritid species recovered A. caboverdiana as an isolated clade not related to Tubastraea and more closely related to Dendrophyllia cornigera and Leptopsammia pruvoti. Atlantia differs from Tubastraea by having a phaceloid to dendroid growth form with new corallites budding at an acute angle from the theca of a parent corallite. The genus also has normally arranged septa (not Portualès Plan), poorly developed columella, and a shallow-water distribution all supporting the classification as a new genus. Our results corroborate the monophyly of the genus Tubastraea and reiterate the Atlantic non-indigenous status for the genus. In the light of the results presented herein, we recommend an extensive review of shallow-water dendrophylliids from the Eastern Atlantic.

Molecular Phylogeny Demonstrates the Need for Taxonomic Reconsideration of Species Diversity of the Hydrocoral Genus Millepora (Cnidaria: Hydrozoa) in the Pacific.

Millepora (Cnidaria: Hydrozoa: Milleporidae) spp. are distributed throughout shallow subtropical and tropical marine environments in the Indo-Pacific and Caribbean-Atlantic, and have traditionally been identified using pore characteristics and colony form. Until now, representatives of Millepora spp. on the island of Okinawa-jima, Japan, have been divided into five species; three branching species (Millepora intricata, M. tenera, M. dichotoma), one species with plate-like morphology (M. platyphylla), and one encrusting species (M. exaesa). There have been only a few reports from the Indo-Pacific that have studied the genetic diversity within Millepora spp., although phylogenetic analyses in the Caribbean-Atlantic have proven useful in delimiting closely-related species, while demonstrating that morphologically-based identification systems may have problems. In the present study, we sought to clarify taxonomic confusion of Millepora spp. in the Pacific by using sequence data of the ribosomal internal transcribed spacer (ITS-rDNA) of specimens from Okinawa, Japan and other localities (Johnston Atoll, Great Barrier Reef). Four separate clades were recovered from the ITS-rDNA analyses. Although we examined specimens of all three branching Millepora spp. previously reported from Okinawa-jima Island, in our phylogenetic analyses they were concentrated within a single clade, with only three specimens in other clades. Encrusting Millepora specimens were found within all clades, although it should be noted all species initially start as encrusting forms, and plate-like specimens were found within three clades. Our data also point to the existence of a previously unknown lineage within Millepora characterized by its ability to overgrow live scleractinian corals.