The rough limpet, Lottia scabra, a generalist grazer in the upper intertidal zone of the northeastern Pacific, spans the California Transition Zone, where southern warm-water populations gradually replace northern cold-water ones, providing a valuable system for studying genomic adaptation. We present the first high-quality reference genome for L. scabra, making a significant advancement over previously available molecular resources for both L. scabra and the genus Lottia. We used PacBio HiFi long reads and Omni-C chromatin proximity sequences to assemble a genome comprising 70 scaffolds spanning 414.08 Mb, with an N50 of 5.33 Mb and a completeness of 96.4% single-copy ortholog genes. The assembly contains 10 chromosome-scale scaffolds, consistent with previously published karyotypes of sister taxa. This high-quality genome will enhance our understanding of the mechanisms underlying adaptation to environmental differences and species responses to environmental change, with implications for coastal biodiversity conservation.

The pink volcano barnacle, Tetraclita rubescens, has experienced a poleward range expansion along the eastern Pacific coastline amidst recent climate changes, likely facilitated by high gene flow and high genetic diversity in a large population. A high-quality reference genome provides the next step to investigate these patterns in more detail. We present a highly contiguous, chromosome-level genome assembly for T. rubescens using long-read sequencing and short-read proximity ligation data. The genome assembly is 2.44 Gb, contains 92.5% complete ortholog genes based on the known Arthropoda gene list, the largest N50 compared with other high-quality barnacle genomes (~107 Mb), and a low L50 score (10 scaffolds). With this chromosome-level assembly, we will be better able to contrast the roles of drift, migration, and selection in population and spatial expansion dynamics and the roles of dispersal and adaptation within the range and to investigate the genomic diversity of the species, including the roles of transposable elements in the genome. T. rubescens is an iconic barnacle on central and southern Californian rocky intertidal shores, and understanding its dynamics can help inform and support the conservation of intertidal communities along the northeastern Pacific coastline.

The Pismo clam, Tivela stultorum, is an ecologically and economically important species inhabiting sandy beaches and subtidal zones in central and southern California, USA, and northern Baja California, Mexico. This long-lived venerid clam species is of great management, cultural and conservation interest in California where it was harvested for centuries by indigenous people and then nearly extirpated by intense commercial and recreational overfishing in the mid-1900s. A recreational fishery continues today in California; however, T. stultorum faces pressure from poaching, overharvest, and the loss of sandy beaches from rising sea levels and beach erosion. Understanding the susceptibility and resilience of Pismo clams to these pressures is essential for their conservation. We used Pacific Biosciences HiFi long sequencing reads and Dovetail Omni-C proximity reads to assemble a highly contiguous genome of 763 Mb. The genome had a contig N50 of 13 Mb and a scaffold N50 of 38 Mb with a BUSCO completeness score of 95%. Most of the genome sequences (96%) were contained in 19 scaffolds at least 10MB long, consistent with prior evidence that venerid clam genomes are composed of 19 autosomes. This reference genome will enable a more complete understanding of the ecology and evolutionary dynamics of T. stultorum via population genomic analyses, which will help assess risks from climate, fishing, environmental change, and susceptibilities due to life history. Our goal is to better support the continued recovery, informed management and conservation, and future persistence of T. stultorum, a long-lived and highly valued clam species.

Local adaptation represents the balance of selection and gene flow. Increasingly, studies find that adaptation can occur on spatial scales much smaller than the scale of dispersal, resulting in balanced polymorphisms within populations. However, microgeographic adaptation might be facilitated or hindered by large-scale environmental heterogeneity, such as across latitude. Marine systems present a special case, as many marine species have high dispersal capacity so that dispersal 'neighbourhoods' may encompass environmental heterogeneity over both small and large spatial scales. Here, we leverage fine-scale sampling across the California range of the Pacific purple sea urchin (Strongylocentrotus purpuratus), a species with previous evidence of both local adaptation and extremely high gene flow. We find that despite the complete absence of neutral population structure, satellite-based sea surface temperature and tidal zone are associated with subtle genetic differences among populations, suggesting that balanced polymorphisms can lead to adaptation across both large (latitudinal) and small (subtidal vs. intertidal) scales. In fact, some of the same genetic variants differentiate populations at both spatial scales, potentially because both environmental parameters are related to temperature. Further, we find that genes that are expressed at a single tissue or life history stage are more divergent than expected across both latitudinal and tidal zone comparisons, suggesting that these genes have specific functions that might generate phenotypic variation important for local adaptation. Together, these results suggest that even in species with little population structure, genetic variation can be sorted across varying spatial scales, potentially resulting in local adaptation across complex environmental mosaics.

Wildlife diseases, such as the sea star wasting (SSW) epizootic that outbroke in the mid-2010s, appear to be associated with acute and/or chronic abiotic environmental change; dissociating the effects of different drivers can be difficult. The sunflower sea star, Pycnopodia helianthoides, was the species most severely impacted during the SSW outbreak, which overlapped with periods of anomalous atmospheric and oceanographic conditions, and there is not yet a consensus on the cause(s). Genomic data may reveal underlying molecular signatures that implicate a subset of factors and, thus, clarify past events while also setting the scene for effective restoration efforts. To advance this goal, we used Pacific Biosciences HiFi long sequencing reads and Dovetail Omni-C proximity reads to generate a highly contiguous genome assembly that was then annotated using RNA-seq-informed gene prediction. The genome assembly is 484 Mb long, with contig N50 of 1.9 Mb, scaffold N50 of 21.8 Mb, BUSCO completeness score of 96.1%, and 22 major scaffolds consistent with prior evidence that sea star genomes comprise 22 autosomes. These statistics generally fall between those of other recently assembled chromosome-scale assemblies for two species in the distantly related asteroid genus Pisaster. These novel genomic resources for P. helianthoides will underwrite population genomic, comparative genomic, and phylogenomic analyses-as well as their integration across scales-of SSW and environmental stressors.

As the sister group to all other animals, ctenophores (comb jellies) are important for understanding the emergence and diversification of numerous animal traits. Efforts to explore the evolutionary processes that promoted diversification within Ctenophora are hindered by undersampling genomic diversity within this clade. To address this gap, we present the sequence, assembly and initial annotation of the genome of Beroe ovata. Beroe possess unique morphology, behavior, ecology and development. Unlike their generalist carnivorous kin, beroid ctenophores feed exclusively on other ctenophores. Accordingly, our analyses revealed a loss of chitinase, an enzyme critical for the digestion of most non-ctenophore prey, but superfluous for ctenophorivores. Broadly, our genomic analysis revealed that extensive gene loss and changes in gene regulation have shaped the unique biology of B. ovata. Despite the gene losses in B. ovata, our phylogenetic analyses on photosensitive opsins and several early developmental regulatory genes show that these genes are conserved in B. ovata. This additional sampling contributes to a more complete reconstruction of the ctenophore ancestor and points to the need for extensive comparisons within this ancient and diverse clade of animals. To promote further exploration of these data, we present BovaDB (http://ryanlab.whitney.ufl.edu/bovadb/), a portal for the B. ovata genome.

The interaction between selection and gene flow can determine to what degree populations are able to adapt to local environmental conditions. This presents a particular conundrum in marine systems, as many marine species have high dispersal capacity resulting in nearly panmictic populations. Increasingly, genomic studies find that even in systems with little or no population structure divergence at particular loci may indicate local adaptation in the presence of high gene flow. However we are just beginning to understand which environmental variables might be the strongest drivers of selection in marine systems and the functional outcomes of genetic variants that are candidates for selection. Here, we leverage fine-scale sampling across the California range of the Pacific Purple Urchin (Strongylocentrutus purpuratus), a species with previous evidence of both local adaptation and extremely high gene flow. We find that despite complete absence of neutral population structure, sea surface temperature and tidal height drive genetic differences among populations, suggesting that balanced polymorphisms can lead to adaptation across both large scale (latitudinal) and small scale (subtidal v. intertidal) scales. Further, we find that genes that are expressed at a single tissue or life history stage are more divergent than expected across both latitudinal and tidal height comparisons, suggesting that these genes have specific functions that might generate phenotypic variation important for local adaptation. Together these results suggest that even in panmictic populations genetic variation can be sorted across even small spatial scales, potentially resulting in local adaptation across a complex environmental mosaic.

Innexins facilitate cell-cell communication by forming gap junctions or nonjunctional hemichannels, which play important roles in metabolic, chemical, ionic, and electrical coupling. The lack of knowledge regarding the evolution and role of these channels in ctenophores (comb jellies), the likely sister group to the rest of animals, represents a substantial gap in our understanding of the evolution of intercellular communication in animals. Here, we identify and phylogenetically characterize the complete set of innexins of four ctenophores: Mnemiopsis leidyi, Hormiphora californensis, Pleurobrachia bachei, and Beroe ovata. Our phylogenetic analyses suggest that ctenophore innexins diversified independently from those of other animals and were established early in the emergence of ctenophores. We identified a four-innexin genomic cluster, which was present in the last common ancestor of these four species and has been largely maintained in these lineages. Evidence from correlated spatial and temporal gene expression of the M. leidyi innexin cluster suggests that this cluster has been maintained due to constraints related to gene regulation. We describe the basic electrophysiological properties of putative ctenophore hemichannels from muscle cells using intracellular recording techniques, showing substantial overlap with the properties of bilaterian innexin channels. Together, our results suggest that the last common ancestor of animals had gap junctional channels also capable of forming functional innexin hemichannels, and that innexin genes have independently evolved in major lineages throughout Metazoa.

Bioeroding sponges interact and compete with corals on tropical reefs. Experimental studies have shown global change alters this biotic interaction, often in favour of the sponge. Ocean acidification in particular increases sponge bioerosion and reduces coral calcification, yet little is known about the molecular basis of these changes. We used RNA-Seq data to understand how acidification impacts the interaction between the bioeroding sponge, Cliona varians, and the coral, Porites furcata, at the transcriptomic level. Replicate sponge and coral genets were exposed to ambient (8.1 pH) and acidified (7.6 pH) conditions in isolation and in treatments where they were joined for 48 h. The coral had a small gene expression response (tens of transcripts) to the sponge, suggesting it does little at the transcriptomic level to deter sponge overgrowth. By contrast, the sponge differentially expressed 7320 transcripts in response to the coral under ambient conditions and 3707 transcripts in response to acidification. Overlap in the responses to acidification and the coral, 2500 transcripts expressed under both treatments, suggests a similar physiological response to both cues. The sponge expressed 50× fewer transcripts in response to the coral under acidification, suggesting energetic costs of bioerosion, and other cellular processes, are lower for sponges under acidification. Our results suggest how acidification drives ecosystem-level changes in the accretion/bioerosion balance on coral reefs. This shift is not only the result of changes to the thermodynamic balance of these chemical reactions but also the result of active physiological responses of organisms to each other and their abiotic environment.

Cnidarians are critical members of aquatic communities and have been an experimental system for a diversity of research areas ranging from development to biomechanics to global change biology. Yet, we still lack a well-resolved, taxonomically balanced cnidarian tree of life to place this research in appropriate phylogenetic context. To move towards this goal, we combined data from 26 new anthozoan transcriptomes with 86 previously published cnidarian and outgroup datasets to generate two 748-locus alignments containing 123,051 (trimmed) and 449,935 (untrimmed) amino acids. We estimated maximum likelihood phylogenies for both matrices under partitioned and unpartitioned site-homogeneous and site-heterogenous models of substitution. We used the resulting topology to constrain a phylogenetic analysis of 1,814 small subunit ribosomal (18S) gene sequences from GenBank. Our results confirm the position of Ceriantharia (tube-dwelling anemones), a historically recalcitrant group, as sister to the rest of Hexacorallia across all phylogenies regardless of data matrix or model choice. We find unanimous support for the sister relationships of Scleractinia and Corallimorpharia and of Endocnidozoa and Medusozoa. We propose the name Coralliformes for the clade uniting scleractinians and corallimorpharians and the name Operculozoa for the clade uniting endocnidozoans and medusozoans. Of the 229 genera with more than a single representative in our 18S hybrid phylogeny, 47 (21%) were identified as monophyletic, providing a starting point for a number of taxonomic revisions. Together, these data are an invaluable resource for comparative cnidarian research and provide perspective to guide future refinement of cnidarian systematics.

The California ribbed mussel, Mytilus californianus, is an ecosystem engineer crucial for the survival of many marine species inhabiting the intertidal zone of California. Here, we describe the first reference genome for M. californianus and compare it to previously published genomes from three other Mytilus species: M. edulis, M. coruscus, and M. galloprovincialis. The M. californianus reference genome is 1.65 Gb in length, with N50 sequence length of 118 Mb, and an estimated 86.0% complete single copy genes. Compared with the other three Mytilus species, the M. californianus genome assembly is the longest, has the highest N50 value, and the highest percentage complete single copy genes. This high-quality genome assembly provides a foundation for population genetic analyses that will give insight into future conservation work along the coast of California.

Keystone species are known to play a critical role in kelp forest health, including the well-known killer whales, sea otter, sea urchin, kelp trophic cascade in the Aleutian Islands, Alaska, USA. In California, a major player in the regulation of sea urchin abundance, and in turn, the health of kelp forests ecosystems, is a large wrasse, the California Sheephead, Semicossyphus pulcher. We present a reference genome for this ecologically important species that will serve as a key resource for future conservation research of California's inshore marine environment utilizing genomic tools to address changes in life-history traits, dispersal, range shifts, and ecological interactions among members of the kelp forest ecological assemblages. Our genome assembly of S. pulcher has a total length of 0.794 Gb, which is similar to many other marine fishes. The assembly is largely contiguous (N50 = 31.9 Mb) and nearly complete (BUSCO single-copy core gene content = 98.1%). Within the context of the California Conservation Genomics Project (CCGP), the genome of S. pulcher will be used as an important reference resource for ongoing whole genome resequencing efforts of the species.

Efforts to protect the ecologically and economically significant California Current Ecosystem from global change will greatly benefit from data about patterns of local adaptation and population connectivity. To facilitate that work, we present a reference-quality genome for the giant pink sea star, Pisaster brevispinus, a species of ecological importance along the Pacific west coast of North America that has been heavily impacted by environmental change and disease. We used Pacific Biosciences HiFi long sequencing reads and Dovetail Omni-C proximity reads to generate a highly contiguous genome assembly of 550 Mb in length. The assembly contains 127 scaffolds with a contig N50 of 4.6 Mb and a scaffold N50 of 21.4 Mb; the BUSCO completeness score is 98.70%. The P. brevispinus genome assembly is comparable to the genome of the congener species P. ochraceus in size and completeness. Both Pisaster assemblies are consistent with previously published karyotyping results showing sea star genomes are organized into 22 autosomes. The reference genome for P. brevispinus is an important first step toward the goal of producing a comprehensive, population genomics view of ecological and evolutionary processes along the California coast. This resource will help scientists, managers, and policy makers in their task of understanding and protecting critical coastal regions from the impacts of global change.

Abstract Tunicates, the closest living relatives of vertebrates, have served as a foundational model of early embryonic development for decades. Comparative studies of tunicate phylogeny and genome evolution provide a critical framework for analyzing chordate diversification and the emergence of vertebrates. Toward this goal, we sequenced the genome of Corella inflata (Ascidiacea, Phlebobranchia), so named for the capacity to brood self-fertilized embryos in a modified, “inflated” atrial chamber. Combining the new genome sequence for Co. inflata with publicly available tunicate data, we estimated a tunicate species phylogeny, reconstructed the ancestral Hox gene cluster at important nodes in the tunicate tree, and compared patterns of gene loss between Co. inflata and Ciona robusta, the prevailing tunicate model species. Our maximum-likelihood and Bayesian trees estimated from a concatenated 210-gene matrix were largely concordant and showed that Aplousobranchia was nested within a paraphyletic Phlebobranchia. We demonstrated that this relationship is not an artifact due to compositional heterogeneity, as had been suggested by previous studies. In addition, within Thaliacea, we recovered Doliolida as sister to the clade containing Salpida and Pyrosomatida. The Co. inflata genome provides increased resolution of the ancestral Hox clusters of key tunicate nodes, therefore expanding our understanding of the evolution of this cluster and its potential impact on tunicate morphological diversity. Our analyses of other gene families revealed that several cardiovascular associated genes (e.g., BMP10, SCL2A12, and PDE2a) absent from Ci. robusta, are present in Co. inflata. Taken together, our results help clarify tunicate relationships and the genomic content of key ancestral nodes within this phylogeny, providing critical insights into tunicate evolution.

Extreme environmental gradients represent excellent study systems to better understand the variables that mediate patterns of genomic variation between populations. They also allow for more accurate predictions of how future environmental change might affect marine species. The Persian/Arabian Gulf is extreme in both temperature and salinity, whereas the adjacent Gulf of Oman has conditions more typical of tropical oceans. The sea urchin Echinometra sp. EZ inhabits both of these seas and plays a critical role in coral reef health as a grazer and bioeroder, but, to date, there have been no population genomic studies on this or any urchin species in this unique region. E sp. EZ’s life history traits (e.g., large population sizes, large reproductive clutches, and long life spans), in theory, should homogenize populations unless nonneutral processes are occurring. Here, we generated a draft genome and a restriction site-associated DNA sequencing data set from seven populations along an environmental gradient across the Persian/ Arabian Gulf and the Gulf of Oman. The estimated genome size of E. sp. EZ was 609 Mb and the heterozygosity was among the highest recorded for an echinoderm at 4.5%. We recovered 918 high-quality SNPs from 85 individuals which we then used in downstream analyses. Population structure analyses revealed a high degree of admixture between all sites, although there was population differentiation and significant pairwise FST values between the two seas. Preliminary results suggest migration is bidirectional between the seas and nine candidate loci were identified as being under putative natural selection, including one collagen gene. This study is the first to investigate the population genomicsof a sea urchin from this extreme environmental gradient and is an important contribution to our understanding of the complex spatial patterns that drive genomic divergence.

Extreme environmental gradients represent excellent study systems to better understand the variables that mediate patterns of genomic variation between populations. They also allow for more accurate predictions of how future environmental change might affect marine species. The Persian/Arabian Gulf is extreme in both temperature and salinity, whereas the adjacent Gulf of Oman has conditions more typical of tropical oceans. The sea urchin Echinometra sp. EZ inhabits both of these seas and plays a critical role in coral reef health as a grazer and bioeroder, but, to date, there have been no population genomic studies on this or any urchin species in this unique region. E sp. EZ's life history traits (e.g., large population sizes, large reproductive clutches, and long life spans), in theory, should homogenize populations unless nonneutral processes are occurring. Here, we generated a draft genome and a restriction site-associated DNA sequencing data set from seven populations along an environmental gradient across the Persian/Arabian Gulf and the Gulf of Oman. The estimated genome size of E. sp. EZ was 609 Mb and the heterozygosity was among the highest recorded for an echinoderm at 4.5%. We recovered 918 high-quality SNPs from 85 individuals which we then used in downstream analyses. Population structure analyses revealed a high degree of admixture between all sites, although there was population differentiation and significant pairwise F-ST values between the two seas. Preliminary results suggest migration is bidirectional between the seas and nine candidate loci were identified as being under putative natural selection, including one collagen gene. This study is the first to investigate the population genomics of a sea urchin from this extreme environmental gradient and is an important contribution to our understanding of the complex spatial patterns that drive genomic divergence.

Research products that lack transparency and are influenced by confirmation bias lead to barriers that, when left unchecked, propagate throughout the scientific record and lead to wasted research effort. Phylogenetics is particularly vulnerable given its ever-evolving methodology and wide choice of options for conducting analyses. Great strides in transparency have been achieved in clinical research by the implementation of a priori protocols. Here we propose a similar approach—phylotocol—a straightforward, protocol-driven strategy tailored to the needs of phylogenetic studies. We provide a simple template and offer a flexible range of implementation frameworks, including preregistration options. Besides increasing transparency and accountability, phylotocol has the added benefits of improving study design and reproducibility, enhancing collaboration and education, and increasing the likelihood of project completion. The increased transparency afforded by wide adoption of an a priori system like phylotocol would have extensive benefits to science.

ANISEED (https://www.aniseed.cnrs.fr) is the main model organism database for the worldwide community of scientists working on tunicates, the vertebrate sister-group. Information provided for each species includes functionally-annotated gene and transcriptmodels with orthology relationships within tunicates, and with echinoderms, cephalochordates and vertebrates. Beyond genes the system describes other genetic elements, including repeated elements and cis-regulatory modules. Gene expression profiles for several thousand genes are formalized in both wild-type and experimentally-manipulated conditions, using formal anatomical ontologies. These data can be explored through three complementary types of browsers, each offering a different viewpoint. A developmental browser summarizes the information in a gene- or territory-centric manner. Advanced genomic browsers integrate the genetic features surrounding genes or gene sets within a species. A Genomicus synteny browser explores the conservation of local gene order across deuterostome. This new release covers an extended taxonomic range of 14 species, including for the first time a non-ascidian species, the appendicularian Oiko-pleura dioica. Functional annotations, provided for each species, were enhanced through a combination of manual curation of gene models and the development of an improved orthology detection pipeline. Finally, gene expression profiles and anatomical territories can be explored in 4D online through the newly developed Morphonet morphogenetic browser.

Addressing theorigin of axial-patterning machinery is essential for understanding the evolution of animal form. Historically, sponges, a lineage that branched off early in animal evolution, were thought to lack Hox and ParaHox genes, suggesting that these critical axial-patterning genes arose after sponges diverged. However, a recent study has challenged this long-held doctrine by claiming to identify ParaHox genes (Cdx family) in two calcareous sponge species, Sycon ciliatum and Leucosolenia complicata. We reanalyzed the main data sets in this paper and analyzed an additional data set that expanded the number of bilaterians represented and removed outgroup homeodomains. As in the previous study, our Neighbor-Joining analyses of the original data sets recovered a clade that included sponge and Cdx genes, whereas Bayesian analyses placed these sponge genes within the NKL subclass of homeodomains. Unlike the original study, only one of our two maximum-likelihood analyses was congruent with Cdx genes in sponges. Our analyses of our additional data set led to the sponge genes consistently being placed within the NKL subclass of homeodomains regardless of method or model. Our results show more support for these sponge genes belonging to the NKL subclass, and therefore imply that Hox and ParaHox genes arose after Porifera diverged from the rest of animals.