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ABSTRACT How reproductive barriers arise in early stages of divergence among broadcast spawning organisms that exist in sympatry remains poorly understood. Reproductively isolated lineages (Clade A and B) ofStichopuscf.horrenswere previously reported across the western Pacific, with an additional putative cryptic species detected within the Clade B lineage warranting further examination. The present study further examines the hypothesis that the two mitochondrial lineages (Clade A and Clade B) ofStichopuscf. horrensrepresent putative cryptic species and whether another cryptic species within the Clade B lineage exists using a reduced representation genomic approach. Using double‐digest RAD (ddRAD) sequencing, a total of 9788 single nucleotide polymorphism (SNP) markers were used to examine divergence amongStichopuscf. horrenslineages (n = 82). Individuals grouped into three SNP genotype clusters, broadly concordant with their mitochondrial lineages and microsatellite genotype clusters, with limited gene flow inferred among clusters. Outlier analysis recovered highly divergent SNP loci with significant homology to proteins related to rhodopsin and tachykinin receptor signaling, sperm motility, transmembrane transport, and hormone response. This study confirms the existence of three reproductively isolated genotype clusters withinStichopuscf.horrensand highlights gene regions related to reproduction that may contribute to establishing reproductive barriers between broadcast spawning species at an early stage of divergence. 

<bold>Abstract</bold> Mitochondrial tRNA gene loss and cytosolic tRNA import to mitochondria are two common phenomena in mitochondrial biology, but their importance is often under-appreciated in animals. This is because most bilaterally symmetrical animals (Bilateria) encode a complete set of tRNAs needed for mitochondrial translation. By contrast, studies of mitochondrial genomes in non-bilaterian animals have shown a reduced tRNA gene content in several lineages, necessitating tRNA import. Interestingly, in most of these lineages tRNA gene content appears to be set early in the evolution of the group and conserved thereafter. Here we demonstrate that Clade B of Haplosclerid Sponges (CBHS) represent an exception to this pattern. We determined mt-genome sequences for eight species from this group and analyzed them with six that had been previously available. In addition, we determined mt-genome sequences for two species of haploslerid sponges outside the CBHS and used them with eight previously available sequences as outgroups. We found that tRNA gene content varied widely among CBHS species: from three in an undescribedHaliclonaspecies (Haliclona sp. TLT785) to 25 inXestospongia mutaandX. testudinaria. Furthermore, we found that all CBHS species outside the genusXestospongialackedatp9, while some also lackedatp8. Analysis of nuclear sequences fromNiphates digitalisrevealed that bothatp8andatp9had transferred to the nuclear genome, while the absence of mt-tRNA genes represented their genuine loss. Overall, CBHS can be a useful animal system to study mt-tRNA genes loss, mitochondrial import of cytosolic tRNA, and the impact of both of these processes on mitochondrial evolution. Significance statementIt is generally believed that the gene content is stable in animal mitochondrial (mt) DNA. Indeed, mtDNA in most bilaterally symmetrical animals encompasses a conserved set of 37 genes coding for 13 proteins, two rRNAs and 22 tRNAs. By contrast, mtDNA in non-bilaterian animals shows more variation in mt gene content, in particular in the number of tRNA genes. However, most of this variation occurs between major non-bilaterian lineages. Here we demonstrate that a group of demosponges called Clade B of Haplosclerid Sponges (CBHS) represents a fascinating exception to this pattern, with species experiencing recurrent losses of up to 22 mt-tRNA genes. We argue that this group constitutes a promising system to investigate the effects of tRNA gene loss on evolution of mt-genomes as well as mitochondrial tRNA import machinery. 

Understanding connectivity between populations is key to identifying hotspots of diversity, dispersal sinks and sources, and effective management units for natural resources. Multi-species connectivity seeks to overcome species-specific idiosyncrasies to identify shared patterns that are most critical to spatial management. The linear Hawaiian archipelago provides an excellent platform to assess multi-species connectivity patterns, with shared boundaries to gene flow identified across a majority of the 41 coral reef species surveyed to date. Here, we evaluate genome-scale data by comparing consistency and resolution to previous connectivity studies using far fewer loci. We used pool-seq to genotype 22,503–232,730 single nucleotide polymorphisms per species (625,215 SNPs total) from the same individuals published in previous studies of two fishes, two corals, and two lobsters. Additionally, one coral species (Pocillopora meandrina) without previous archipelago-wide population genetic data was included. With greater statistical power, most genetic differences between pairwise comparisons of islands were significant (250 of 308), consistent with the most recent larval dispersal models for the Hawaiian Archipelago. These data reveal significant differentiation at a finer scale than previously reported using single-marker studies, yet did not overturn any of the conclusions or management implications drawn from previous studies. We confirm that population genomic datasets are consistent with previously reported patterns of multispecies connectivity but add a finer layer of population resolution that is pertinent to management. 

Haplosclerid sponges (Porifera: Demospongiae: Heteroscleromorpha), and particularly the family Chalinidae, are notoriously difficult to identify through taxonomic methods alone. Here we use an integrative approach to confirm the identification and report both polymorphic characters and different morphotypes exhibited from a recruitment stage that complicate identification of introduced haplosclerid species Haliclona (Soestella) caerulea and Gelliodes conulosa sp. nov. in Hawaiʻi. Using these same methods, we also describe three new species Haliclona (Gellius) pahua sp. nov., Haliclona (Reniera) kahoe sp. nov., Haliclona (Rhizoniera) loe sp. nov. from our collections in Kāne‘ohe Bay. Using a combination of mitochondrial and ribosomal RNA sequences, we compile a phylogeny that is consistent with previous molecular work but is at odds with the morphological characters used to classify species belonging to Chalinidae and Niphatidae families within Haplosclerida. Although shared morphological traits were distributed across taxa throughout the tree, both mitochondrial and ribosomal RNA sequences were diagnostic, with an average of at least 3 % sequence divergence among species and their closest relative. This study highlights both the use of standardized Autonomous Reef Monitoring Structures (ARMS) to access the hidden diversity of haplosclerid sponges, and the potential for competition between these introduced and newly described and potentially endemic species.   

Coral reefs are among the most sensitive ecosystems affected by ocean warming and acidification, and are predicted to collapse over the next few decades. Reefs are predicted to shift from net accreting calcifier-dominated systems with exceptionally high biodiversity to net eroding algal-dominated systems with dramatically reduced biodiversity. Here, we present a two-year experimental study examining the responses of entire mesocosm coral reef communities to warming (+2 °C), acidification (−0.2 pH units), and combined future ocean (+2 °C, −0.2 pH) treatments. Contrary to modeled projections, we show that under future ocean conditions, these communities shift structure and composition yet persist as novel calcifying ecosystems with high biodiversity. Our results suggest that if climate change is limited to Paris Climate Agreement targets, coral reefs could persist in an altered state rather than collapse. 

Recent collection efforts along the Brazilian coast revealed a Haliclona species preliminarily identified as a likely new species. However, sequencing of the 28S rRNA C-Region, a barcode marker in sponges, showed its high genetic similarity with a Haliclona sp. from Hawaiʻi (GenBank MW016137–MW016139). We applied an integrated morphological and molecular assessment, which allowed us to identify both Brazilian and Hawaiian specimens as H. (Reniera) laubenfelsi, a species with an Indo-Pacific distribution. We postulate this species to be exotic both in the Brazilian coast and in Hawaiʻi. Our evidence is based on the arrival of the species in Brazil after 2001, being first registered next to an international port. In turn, the species is distributed discontinuously in Hawaiʻi, being mainly restricted to sheltered bays and vicinities of ports, showing a predilection for anthropogenic substrates, which strengthen the hypothesis of its exotic origin. Recent collections in Hawaiʻi (2016–2018) failed to find this species in natural habitats, though it was an abundant pioneer species in Autonomous Reef Monitoring Structures. Its capacity to colonize artificial substrata may indicate either a cryptobenthic nature or an invasive potential. We highlight the need of monitoring its abundance, spatial distribution, and biotic interactions along the Brazilian coast to assess its potential environmental impacts. The full morphological description, and the molecular sequences we provided certainly will speed up the identification of this species, allowing to track its range extension. 

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. 

Reef-building coral populations are at serious risk of collapse due to the combined effects of ocean warming and acidification. Nonetheless, many corals show potential to adapt to the changing ocean conditions. Here we examine the broad sense heritability (H²) of coral calcification rates across an ecologically and phylogenetically diverse sampling of eight of the primary reef-building corals across the Indo-Pacific. We show that all eight species exhibit relatively high heritability of calcification rates under combined warming and acidification (0.23–0.56). Furthermore, tolerance to each factor is positively correlated and the two factors do not interact in most of the species, contrary to the idea of trade-offs between temperature and pH sensitivity, and all eight species can co-evolve tolerance to elevated temperature and reduced pH. Using these values together with historical data, we estimate potential increases in thermal tolerance of 1.0–1.7°C over the next 50 years, depending on species. None of these species are probably capable of keeping up with a high global change scenario and climate change mitigation is essential if reefs are to persist. Such estimates are critical for our understanding of how corals may respond to global change, accurately parametrizing modelled responses, and predicting rapid evolution.