Steven H. D. Haddock

Open-ocean biodiversity is structured by subtle environmental gradients rather than obvious geographic barriers, yet how genomes, morphology, and ecology interact during diversification in such systems remains unclear. Here we use Bargmannia siphonophores (Cnidaria: Hydrozoa) as a tractable model system for understanding the evolution of deep-sea pelagic biodiversity. Using museum specimens, genome-skimming data, and in situ observations and collections from remotely operated vehicles, we resolve species boundaries, clarify historical taxonomy, and describe two new species, B. marlena sp. nov. and B. pyrosa sp. nov. Our phylogenomic analyses recovered two major lineages within Bargmannia, one of which exhibits pronounced acceleration of mitochondrial genome evolution. This genomic divergence coincided with a transition to monoecy, suggesting a potential link between mitochondrial evolution and sexual system shift. Using geometric morphometrics we show that nectophore shape variation is strongly structured by phylogeny and follows lineage-specific allometric trajectories, while comparative cnidome analyses indicate functional divergence associated with differences in nematocyst size and tentillum architecture. Finally, although Bargmannia species overlap geographically, their distributions are structured along depth gradients, supporting vertical niche partitioning as an important driver of speciation in the open ocean. Together, these findings show how deep-sea biodiversity emerges from the interplay of genomic innovation, morphological divergence, and depth structuring.

Siphonophores (Cnidaria:Hydrozoa) are pelagic colonial marine invertebrates with many highly specialized bodies (zooids) within a single colony. Their unique biology and ecological importance have made them of particular interest. Recent work revealed siphonophore genomes to be larger than in most other cnidarians. To investigate siphonophores’ genome biology and develop resources for future studies, we sequenced the genome of a single Nanomia septata to chromosome scale. The haploid genome is 1.5GB across 8 chromosomes, a reduction relative to the 15 chromosomes seen in closely related hydrozoan genomes, and is highly rearranged, consistent with multiple mixing events. Genome expansion occurred through intergenic repeat expansion, with protein-coding genes shorter than in most cnidarians. We found no genomic features clearly associated with siphonophores’ exceptional colony-level complexity. Gene families that play critical roles in cnidarian development have not expanded, and gene proximity was not generally correlated to their expression across zooids, except in male gonophores. To contextualize these observations, we genome sequenced 20 additional Nanomia specimens across the globe and mapped them to our chromosome-scale reference. Population genomic analyses support three previously recognized species of Nanomia, and at least one additional undescribed species. Overlapping geographic distribution of some Nanomia species suggest reproductive isolation in sympatry. Phylogenetic analyses of genome size indicate Nanomia septata and Nanomia cara have similarly large genomes between 1.5-1.7GB, while Nanomia bijuga and an undescribed species show a secondary reduction to 0.7GB. These results highlight how genomic factors have shaped colony organization and genome diversity within Nanomia.

The open ocean is a vast, highly connected environment, and the organisms found there have been hypothesized to represent massive, well-mixed populations. Of these, the Portuguese man-o’-war ( Physalia ) is uniquely suited to dispersal, sailing the ocean surface with a muscular crest. We tested the hypothesis of a single, panmictic Physalia population by sequencing 133 genomes, and found five distinct lineages, with multiple lines of evidence showing strong reproductive isolation despite range overlap. We then scored thousands of citizen-science photos and identified four recognizable morphologies linked to these lineages. Within lineages, we detected regionally endemic subpopulations, connected by winds and currents, and identified individual long-distance dispersal events. We find that, even in these sailing species, genetic variation is highly partitioned geographically across the open ocean. Summary: The open ocean is a vast and highly connected environment. The organisms that live there have a significant capacity for dispersal and few geographic boundaries to separate populations. Of these, the Portuguese man-o’-war or bluebottle (genus Physalia ) is uniquely suited to long-distance travel, using its gas-filled float and muscular crest to catch the wind and sail the sea surface. Physalia are distributed across the globe, and like many pelagic organisms, have been hypothesized to represent a massive, well-mixed population that extends across ocean basins. We tested this hypothesis by sequencing whole genomes of 133 samples collected from waters of over a dozen countries around the globe. Our results revealed five distinct lineages, with multiple lines of evidence indicating strong reproductive isolation, despite regions of range overlap. We combined these data with an independent dataset of thousands of images of Physalia uploaded to the citizen-science website inaturalist.org, which we scored for morphological characters including sail size, tentacle arrangement, and color. From these images, we identified four recognizable morphologies, described their geographical distribution, and linked them to four of the lineages identified with genomic data. We conclude there are at least four species, three of which correspond to species proposed by scientists in the 18th and 19th centuries: P. physalis , P utriculus , and P. megalista , along with one as yet unnamed species Physalia sp. from the Tasman Sea. Within each species, we observe significant population structure, with evidence of persistent subpopulations at a regional scale, as well as evidence for individual long-distance dispersal events. Our findings indicate that, instead of one well-mixed, cosmopolitan species, there are in fact multiple Physalia species with distinct but overlapping ranges, each made up of regionally endemic subpopulations that are connected by major ocean currents and wind patterns.

Hydrostatic pressure increases with depth in the ocean, but little is known about the molecular bases of biological pressure tolerance. We describe a mode of pressure adaptation in comb jellies (ctenophores) that also constrains these animals’ depth range. Structural analysis of deep-sea ctenophore lipids shows that they form a nonbilayer phase at pressures under which the phase is not typically stable. Lipidomics and all-atom simulations identified phospholipids with strong negative spontaneous curvature, including plasmalogens, as a hallmark of deep-adapted membranes that causes this phase behavior. Synthesis of plasmalogens enhanced pressure tolerance in Escherichia coli , whereas low-curvature lipids had the opposite effect. Imaging of ctenophore tissues indicated that the disintegration of deep-sea animals when decompressed could be driven by a phase transition in their phospholipid membranes.

Many metazoans contain molecules capable of fluorescence, the absorption and re-emission of light. Since the anatomical distribution, or patterning, of these molecules is variable across taxa, patterns of fluorescence may serve as a powerful diagnostic tool in taxonomy and ecology. However, species-specific fluorescence patterns among marine invertebrates are poorly understood. Here, we show that hydrozoans have diverse fluorescence patterns, which may result from molecules that are produced intrinsically or obtained from dietary sources. We surveyed hydrozoans including siphonophores, hydromedusae, and hydroids across 5 orders from pelagic and benthic marine environments in Bocas del Toro, Panama. Our findings show that fluorescence patterns are highly prevalent and may vary across hydrozoan species and throughout development. Most of the examined hydrozoan taxa exhibited some form of fluorescence, with variation observed between life stages and body parts. Fluorescence was documented in 88% of hydromedusae (Leptothecata, Anthoathecata, Limnomedusae and Narcomedusae), 50% of hydroid, and 75% of siphonophore taxa that were observed in this study. Our results illustrate how fluorescence patterns may serve as a useful diagnostic tool to explore marine biodiversity, highlighting the need for further documentation of fluorescence patterns across marine diversity and research into the molecules that underlie this phenomenon. Muchos metazoos contienen moléculas capaces de fluorescencia, absorción y reemisión de luz. Dado que la distribución anatómica, o el patrón, de estas moléculas es variable entre taxones, los patrones de fluorescencia pueden servir como una poderosa herramienta diagnóstica en taxonomía y ecología. Sin embargo, los patrones de fluorescencia específicos de especie entre invertebrados marinos están poco comprendidos. Aquí, mostramos que los hidrozoos tienen diversos patrones de fluorescencia, que pueden ser el resultado de moléculas producidas intrínsecamente u obtenidas de fuentes dietéticas. Estudiamos hidrozoos, incluidos sifonóforos, hidromedusas e hidroides, en 5 órdenes de ambientes marinos pelágicos y bentónicos en Bocas del Toro, Panamá. Nuestros hallazgos muestran que los patrones de fluorescencia son muy prevalentes y pueden variar entre especies de hidrozoos y a lo largo del desarrollo. La mayoría de los taxa de hidrozoos examinados exhibieron alguna forma de fluorescencia, con variación observada entre las etapas de vida y las partes del cuerpo. Se documentó fluorescencia en el 88% de las hidromedusas (Leptothecata, Anthoathecata, Limnomedusae y Narcomedusae), el 50% de los hidroides y el 75% de los sifonóforos que se observaron en este estudio. Nuestros resultados ilustran cómo los patrones de fluorescencia pueden servir como una herramienta diagnóstica útil para explorar la biodiversidad marina, resaltando la necesidad de una mayor documentación de los patrones de fluorescencia en la diversidad marina y de investigar las moléculas que subyacen a este fenómeno.

Bioluminescence is the production of visible light by an organism. This phenomenon is particularly widespread in marine animals, especially in the deep sea. While the luminescent status of numerous marine animals has been recently clarified thanks to advancements in deep-sea exploration technologies and phylogenetics, that of others has become more obscure due to dramatic changes in systematics (themselves triggered by molecular phylogenies). Here, we combined a comprehensive literature review with unpublished data to establish a catalogue of marine luminescent animals. Inventoried animals were identified to species level in over 97% of the cases and were associated with a score reflecting the robustness of their luminescence record. While luminescence capability has been established in 695 genera of marine animals, luminescence reports from 99 additional genera need further confirmation. Altogether, these luminescent and potentially luminescent genera encompass 9405 species, of which 2781 are luminescent, 136 are potentially luminescent (e.g., suggested luminescence in those species needs further confirmation), 99 are non-luminescent, and 6389 have an unknown luminescent status. Comparative analyses reveal new insights into the occurrence of luminescence among marine animal groups and highlight promising research areas. This work will provide a solid foundation for future studies related to the field of marine bioluminescence.

A central question in evolutionary biology is whether sponges or ctenophores (comb jellies) are the sister group to all other animals. These alternative phylogenetic hypotheses imply different scenarios for the evolution of complex neural systems and other animal-specific traits^1–6. Conventional phylogenetic approaches based on morphological characters and increasingly extensive gene sequence collections have not been able to definitively answer this question^7–11. Here we develop chromosome-scale gene linkage, also known as synteny, as a phylogenetic character for resolving this question¹². We report new chromosome-scale genomes for a ctenophore and two marine sponges, and for three unicellular relatives of animals (a choanoflagellate, a filasterean amoeba and an ichthyosporean) that serve as outgroups for phylogenetic analysis. We find ancient syntenies that are conserved between animals and their close unicellular relatives. Ctenophores and unicellular eukaryotes share ancestral metazoan patterns, whereas sponges, bilaterians, and cnidarians share derived chromosomal rearrangements. Conserved syntenic characters unite sponges with bilaterians, cnidarians, and placozoans in a monophyletic clade to the exclusion of ctenophores, placing ctenophores as the sister group to all other animals. The patterns of synteny shared by sponges, bilaterians, and cnidarians are the result of rare and irreversible chromosome fusion-and-mixing events that provide robust and unambiguous phylogenetic support for the ctenophore-sister hypothesis. These findings provide a new framework for resolving deep, recalcitrant phylogenetic problems and have implications for our understanding of animal evolution.

Siphonophores (Cnidaria:Hydrozoa) are abundant predators found throughout the ocean and are important components in worldwide zooplankton. They range in length from a few centimeters to tens of meters. They are gelatinous, fragile, and difficult to collect, so many aspects of the biology of these 190 species remain poorly understood. To survey siphonophore genome diversity, we performed Illumina sequencing of 32 species sampled broadly across the phylogeny. Sequencing depth was sufficient to estimate nuclear genome size from k-mer spectra in 8 specimens, ranging from 0.7-4.8Gb. In 6 specimens we got heterozygosity estimates between 0.7-5.3%. Rarefaction analyses indicate k-mer peaks can be absent with as much as 30x read coverage, suggesting minimum genome sizes range from 1.0-3.8Gb in the remaining 27 samples without k-mer peaks. This work confirms most siphonophore nuclear genomes are large, but also identifies several with reduced size that are tractable targets for future siphonophore nuclear genome assembly projects. We also assembled mitochondrial genomes for 32 specimens from these new data, indicating a conserved gene order among Hydrozoa, Cystonectae and some Physonectae, also revealing the ancestral gene organization of siphonophores. There then was extensive rearrangement of mitochondrial genomes within other physonects and in Calycophorae, including the repeated loss of atp8. Though siphonophores comprise a small fraction of cnidarian species, this survey greatly expands our understanding of cnidarian genome diversity. This study further illustrates both the importance of deep phylogenetic sampling and the utility of Illumina genome skimming in understanding genomic diversity of a clade. Significance Descriptions of basic genome features, such as nuclear genome size and mitochondrial genome sequences, remain sparse across many clades in the tree of life, leading to over generalizations from very small sample sizes and often limiting selection of optimal species for genome assembly efforts. Here we use Illumina genome skimming to assess a variety of genome features across 35 siphonophores (Cnidaria). This deep dive within a single clade identifies six species that are optimal candidates of future genomic work, and reveals greater range in nuclear genome size and diversity of mitochondrial genome orders within siphonophores than had been described across all Cnidaria.

The study of evolution and speciation in non-model systems provides us with an opportunity to expand our understanding of biodiversity in nature. Connectivity studies generally focus on species with obvious boundaries to gene flow, but in open-ocean environments, such boundaries are difficult to identify. Due to the lack of obvious boundaries, speciation and population subdivision in the pelagic environment remain largely unexplained. Comb jellies (Phylum Ctenophora) are mostly planktonic gelatinous invertebrates, many of which are considered to have freely interbreeding distributions worldwide. It is thought that the lobate ctenophoreBolinopsis infundibulumis distributed throughout cooler northern latitudes andB. vitreawarmer. Here, we examined the global population structure for species ofBolinopsiswith genetic and morphological data. We found distinct evolutionary patterns within the genus, whereB. infundibulumhad a broad distribution from northern Pacific to Atlantic waters despite many physical barriers, while other species were geographically segregated despite few barriers. Divergent patterns of speciation within the genus suggest that oceanic currents, sea-level, and geological changes over time can act as either barriers or aids to dispersal in the pelagic environment. Further, we used population genomic data to examine evolution in the open ocean of a distinct lineage ofBolinopsisctenophores from the North Eastern Pacific. Genetic information and morphological observations validated this as a separate species,Bolinopsis microptera, which was previously described but has recently been calledB. infundibulum. We found that populations ofB. micropterafrom California were in cytonuclear discordance, which indicates a secondary contact zone for previously isolated populations. Discordance at this scale is rare, especially in a continuous setting.

Our perception of deep-sea communities has evolved as various sampling approaches have captured different components of deep-sea habitats. We sampled midwater zooplankton assemblages in Monterey Bay, California to quantify community composition (abundance and biomass) and biodiversity (at the Order level) across three depth ranges, and the effects of sampling methodology on community parameters. We collected zooplankton using two types of opening-closing trawls [Tucker Trawl and Multiple Opening/Closing Net and Environmental Sensing System (MOCNESS)] and video recordings from a remotely operated vehicle (ROV). We quantified the relative contributions of microbes to community biomass using synoptic water-bottle casts and flow cytometry. Overall, the pelagic community was most similar between the Tucker trawl and ROV (dissimilarity = 52.4%) and least similar between the MOCNESS and ROV (dissimilarity = 65.8%). Dissimilarity between sampling methods was driven by the relative abundances of crustaceans and gelatinous taxa, where gelatinous animals (cnidarians, ctenophores, tunicates) were more abundant in ROV surveys (64.2%) and Tucker trawls (46.8%) compared to MOCNESS samples (14.5%). ROV surveys were the only method that sufficiently documented the most physically delicate taxa (e.g., physonect siphonophores, lobate ctenophores, and larvaceans). Biomass was also one order of magnitude lower in MOCNESS trawls compared to Tucker trawls. Due to these large differences, the relative contributions of microbes to total biomass were substantially lower in Tucker trawl samples (mean = 7.5%) compared to MOCNESS samples (mean = 51%). These results illustrate that our view of planktonic composition and community biomass is strongly dependent on sampling methodology.