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A clear picture of animal relationships is a prerequisite to understand how the morphological and ecological diversity of animals evolved over time. Among others, the placement of the acoelomorph flatworms, Acoela and Nemertodermatida, has fundamental implications for the origin and evolution of various animal organ systems. Their position, however, has been inconsistent in phylogenetic studies using one or several genes. Furthermore, Acoela has been among the least stable taxa in recent animal phylogenomic analyses, which simultaneously examine many genes from many species, while Nemertodermatida has not been sampled in any phylogenomic study. New sequence data are presented here from organisms targeted for their instability or lack of representation in prior analyses, and are analysed in combination with other publicly available data. We also designed new automated explicit methods for identifying and selecting common genes across different species, and developed highly optimized supercomputing tools to reconstruct relationships from gene sequences. The results of the work corroborate several recently established findings about animal relationships and provide new support for the placement of other groups. These new data and methods strongly uphold previous suggestions that Acoelomorpha is sister clade to all other bilaterian animals, find diminishing evidence for the placement of the enigmatic Xenoturbella within Deuterostomia, and place Cycliophora with Entoprocta and Ectoprocta. The work highlights the implications that these arrangements have for metazoan evolution and permits a clearer picture of ancestral morphologies and life histories in the deep past.

Improved relations The accumulation of molecular data is reshaping our understanding of the evolutionary relationships between the major groups of animals. Early work in the field relied upon data from a small number of genes, but the availability of fully sequenced genomes and expressed sequence tags (ESTs, short sub-sequences obtained from large numbers of complementary DNA clones), means that huge swathes of the animal kingdom can now be subjected to such analysis. A new study describes and discusses almost 40 megabases-worth of ESTs from animals of 21 phyla, including 11 animals for which no genomic or EST data were previously available. The conclusions confirm ideas long established by anatomy, including the monophyletic nature of the molluscs, deriving from a common ancestor despite their remarkable variety. New and interesting evolutionary relationships are also uncovered, including a single origin for spiral cleavage of the early embryo. The cover illustrates animal diversity, including acorn, ribbon, arrow and velvet worms, jellyfish and sea spider. This paper describes and discusses almost 40 megabases of expressed sequence tags (EST) clones from the DNA of animals from 21 phyla, including 11 animals for which genomic or EST data were previously lacking. The conclusions confirm ideas long established by anatomy, but raise new and interesting evolutionary relationships. Long-held ideas regarding the evolutionary relationships among animals have recently been upended by sometimes controversial hypotheses based largely on insights from molecular data 1 , 2 . These new hypotheses include a clade of moulting animals (Ecdysozoa) 3 and the close relationship of the lophophorates to molluscs and annelids (Lophotrochozoa) 4 . Many relationships remain disputed, including those that are required to polarize key features of character evolution, and support for deep nodes is often low. Phylogenomic approaches, which use data from many genes, have shown promise for resolving deep animal relationships, but are hindered by a lack of data from many important groups. Here we report a total of 39.9 Mb of expressed sequence tags from 29 animals belonging to 21 phyla, including 11 phyla previously lacking genomic or expressed-sequence-tag data. Analysed in combination with existing sequences, our data reinforce several previously identified clades that split deeply in the animal tree (including Protostomia, Ecdysozoa and Lophotrochozoa), unambiguously resolve multiple long-standing issues for which there was strong conflicting support in earlier studies with less data (such as velvet worms rather than tardigrades as the sister group of arthropods 5 ), and provide molecular support for the monophyly of molluscs, a group long recognized by morphologists. In addition, we find strong support for several new hypotheses. These include a clade that unites annelids (including sipunculans and echiurans) with nemerteans, phoronids and brachiopods, molluscs as sister to that assemblage, and the placement of ctenophores as the earliest diverging extant multicellular animals. A single origin of spiral cleavage (with subsequent losses) is inferred from well-supported nodes. Many relationships between a stable subset of taxa find strong support, and a diminishing number of lineages remain recalcitrant to placement on the tree.

A pattern of increasing species richness from the poles to the equator is frequently observed in many animal taxa. Ecological limits, determined by the abiotic conditions and biotic interactions within an environment, are one of the major factors influencing the geographical distribution of species diversity. Energy availability is often considered a crucial limiting factor, with temperature and productivity serving as empirical measures. However, these measures may not fully explain the observed species richness, particularly in marine ecosystems. Here, through a global comparative approach and standardised methodologies, such as Autonomous Reef Monitoring Structures (ARMS) and DNA metabarcoding, we show that the seasonality of primary production explains sessile animal richness comparatively or better than surface temperature or primary productivity alone. A Hierarchical Generalised Additive Model (HGAM) is validated, after a model selection procedure, and the prediction error is compared, following a cross-validation approach, with HGAMs including environmental variables commonly used to explain animal richness. Moreover, the linear effect of production magnitude on species richness becomes apparent only when considered jointly with seasonality, and, by identifying world coastal areas characterized by extreme values of both, we postulate that this effect may result in a positive relationship in environments with lower seasonality. The environmental drivers of species diversity at the global level are difficult to define. This paper, using standardised methodologies, shows that the seasonality of primary production explains marine pioneer metazoan richness comparatively or better than other measures like sea surface temperature.

ABSTRACT In this study, we trained an object‐detection model to classify 17 benthic invertebrate taxa in archived footage of a study site on the northern west coast of Sweden (a wall section of the Koster Fjord) within the Swedish marine protected area Kosterhavet National Park. The model displayed a mean average precision score of 0.738 and was applied to footage from 1997 to 2023, generating a dataset of 72,369 occurrence records. The dataset was used to quantify depth distributions and abundance trends of both individual taxa and functional groups over time. Depth distributions for 15 of 17 taxa occurred at depths ≥ 45 m. Distributions of 11 taxa aligned with empirical observations, and for the remaining six taxa, we propose expanded depth distributions in the area. Abundances over time significantly increased for eight taxa and decreased for five taxa, while the overall community structure throughout the study period shifted toward smaller, more heat‐tolerant suspension feeders. We found that temperature preference and size were significant drivers of the observed abundance trends in individual taxa. Community structure was altered by the loss of large, heat‐sensitive taxa to greater depths due to increased temperatures. We also observed a strong trend of increasing abundances in the remaining community, including six trawling‐sensitive taxa, highlighting the effectiveness of the park's protective measures. To protect key cold‐water species, we suggest that current fishery regulations of the national park should be expanded to deeper (colder) waters and that new marine protected areas should also be established in deep waters. Our study demonstrates the application potential of video surveillance combined with deep‐learning technology, and we recommend the implementation of standardized video monitoring in marine ecosystem management. We applied an object‐detection model to archived videos from 1997‐2023 of a submarine rock wall in a Swedish marine protected area. We modeled depth distributions and abundance trends of 17 invertebrate taxa. Most taxa resided at deeper wall sections and abundance trends were generally positive, but heat sensitivity was associated with population decline. This highlights a partially successful management strategy of the protected area that should be adapted to preserve key cold‐water species.

Conservation of horseshoe crabs has recently received increasing attention as several populations are in decline. However, scarce information on their distributions in Southeast Asia is impairing conservation efforts. In this study, we sought to improve our understanding of the geographical range and distinct populations of the three Asian horseshoe crabs species in order to identify optimal conservation areas. We mapped the geographic range of Carcinoscorpius rotundicauda, Tachypleus gigas, and T. tridentatus using recent data from field work, literature, Global Biodiversity Information Facility (GBIF), and unpublished data from our scientific network. The data were correlated with 23 different environmental variables of potential ecological importance for horseshoe crabs using the openModeller webservices, including new tidal variables. Ecological niche models were generated using two algorithms, Maximum Entropy and support vector machine, for the three species under present conditions, and projected into a climate change scenario of 2050. The niches of the Asian horseshoe crabs were mostly determined by tidal regime, chlorophyll A concentrations, depth, distance to land, and sea surface temperature. According to our predictions, horseshoe crabs in Southeast Asia are not expected to experience any severe change in extent and distribution of suitable habitat in the future. In order to conserve Asian horseshoe crabs, we suggest establishing Marine Protected Areas at locations where distinct populations and several species occur, such as northern Vietnam, China, Borneo, and southern Japan.

ABSTRACT In marine environments, nonindigenous species (NIS) are especially difficult to manage since they are often first detected when fully established and near impossible to eradicate. The development and implementation of effective monitoring methods for marine NIS are therefore crucial for early detection valuable to management. In this study, we develop and evaluate environmental DNA monitoring using quantitative digital PCR (dPCR) to assess the presence of the euryhaline round goby (Neogobius melanostomus) in a seascape environment close to Scandinavia's largest shipping port. We developed a dPCR assay for the species, targeting a region of the 12S gene, and verified its specificity compared to other locally common species from the gobiid family. Using captive live fish, we also experimentally determined the decaying rate of N. melanostomus DNA in water to a half‐life of 9.8 h in 15 ppt salinity and 15°C. Finally, we sampled 10 sites within a 400 km2 area using eDNA, fyke nets, and baited remote video to validate the accuracy of the water samples to predict the presence and abundance of the species. We found that the number of DNA copies extracted from the water samples varied strongly at sites where N. melanostomus were caught in nets or on video, but the average value from four water samples significantly correlated with an average value from four video samples and also with the total catch at each site. The eDNA assay also detected signals from the species at sites where no fish were caught by fishing or on video. These results show that this method is sensitive for the species at low abundance, and with enough replicates, it can be possible to determine the relative abundance between sites. Effective monitoring of marine invasive species is crucial for early detection valuable to management. In this study, we develop and evaluate environmental DNA monitoring to assess the presence of the round goby fish (Neogobius melanostomus) in a seascape environment. We found that with a half‐life of 9.8 h in 15 PSU salinity and 15°C temperature and eDNA presence of the species confirmed with fishing and video, it is possible to monitor the current presence and abundance to support conservation management.

We investigated the use of eDNA metabarcoding for supplementing traditional diver-based monitoring of biodiversity of marine boulder reefs within the photic zone. The applied sampling design made it possible to evaluate the usefulness of eDNA monitoring as a supplement for traditional monitoring. Specifically, this study aimed to (1) assess the local influence of boulder reefs on biodiversity across the North Sea to Baltic Sea transition zone and (2) investigate the importance of environmental gradients for patterns in community structure. On samples collected during August 2020, we compared the composition and abundance of species associated with nine reefs, representing an environmental gradient of salinity (16–33 psu), water temperature (16–21°C) and water depth (6–29 m). At each reef site, water was sampled near the bottom just above the reef and on average 2.6 km upstream and downstream (location) and sequenced with metabarcoding using COI, 18S and 12S rDNA primers. eDNA identified 400 species, diver-based observations identified 184 with an overlap of 70 species (12%) and 81 genera (18%). While eDNA identified many infaunal species, it did not detect several macroalgal species which dominated in the diver-based observations. Multivariate analysis of eDNA and diver-based community structure both distinguished between reef communities, with a significant match between patterns observed by the two methods ( r = 0.37, p = 0.02). Furthermore, the eDNA approach made it possible to identify significant differences in species composition between upstream, above-reef and downstream locations, suggesting that eDNA leaves a local footprint in benthic habitats. Patterns in both eDNA and diver-based species composition and richness were significantly related to geographical distance, salinity, water temperature and water depth. Despite of low detection of macroalgae, the eDNA sampling provided a substantial supplement to traditional diver-based monitoring of biodiversity around benthic hotspots in the Danish marine waters and therefore we recommend to add eDNA methods to conventional monitoring programs in the future.

The increasing access to autonomously-operated technologies offer vast opportunities to sample large volumes of biological data. However, these technologies also impose novel demands on ecologists who need to apply tools for data management and processing that are efficient, publicly available and easy to use. Such tools are starting to be developed for a wider community and here we present an approach to combine essential analytical functions for analysing large volumes of image data in marine ecological research. This paper describes the Koster Seafloor Observatory, an open-source approach to analysing large amounts of subsea movie data for marine ecological research. The approach incorporates three distinct modules to: manage and archive the subsea movies, involve citizen scientists to accurately classify the footage and, finally, train and test machine learning algorithms for detection of biological objects. This modular approach is based on open-source code and allows researchers to customise and further develop the presented functionalities to various types of data and questions related to analysis of marine imagery. We tested our approach for monitoring cold water corals in a Marine Protected Area in Sweden using videos from remotely-operated vehicles (ROVs). Our study resulted in a machine learning model with an adequate performance, which was entirely trained with classifications provided by citizen scientists. We illustrate the application of machine learning models for automated inventories and monitoring of cold water corals. Our approach shows how citizen science can be used to effectively extract occurrence and abundance data for key ecological species and habitats from underwater footage. We conclude that the combination of open-source tools, citizen science systems, machine learning and high performance computational resources are key to successfully analyse large amounts of underwater imagery in the future.

Resolution of relationships at lower taxonomic levels is crucial for answering many evolutionary questions, and as such, sufficiently varied species representation is vital. This latter goal is not always achievable with relatively fresh samples. To alleviate the difficulties in procuring rarer taxa, we have seen increasing utilization of historical specimens in building molecular phylogenies using high throughput sequencing. This effort, however, has mainly focused on large‐bodied or well‐studied groups, with small‐bodied and under‐studied taxa under‐prioritized. Here, we utilize both historical and contemporary specimens, to increase the resolution of phylogenetic relationships among a group of under‐studied and small‐bodied metazoans, namely, cheilostome bryozoans. In this study, we pioneer the sequencing of air‐dried cheilostomes, utilizing a recently developed library preparation method for low DNA input. We evaluate a de novo mitogenome assembly and two iterative methods, using the sequenced target specimen as a reference for mapping, for our sequences. In doing so, we present mitochondrial and ribosomal RNA sequences of 43 cheilostomes representing 37 species, including 14 from historical samples ranging from 50 to 149 years old. The inferred phylogenetic relationships of these samples, analyzed together with publicly available sequence data, are shown in a statistically well‐supported 65 taxa and 17 genes cheilostome tree, which is also the most broadly sampled and largest to date. The robust phylogenetic placement of historical samples whose contemporary conspecifics and/or congenerics have been sequenced verifies the appropriateness of our workflow and gives confidence in the phylogenetic placement of those historical samples for which there are no close relatives sequenced. The success of our workflow is highlighted by the circularization of a total of 27 mitogenomes, seven from historical cheilostome samples. Our study highlights the potential of utilizing DNA from micro‐invertebrate specimens stored in natural history collections for resolving phylogenetic relationships among species. Here, we present a workflow that utilizes historical and contemporary specimens, to increase the resolution of phylogenetic relationships among understudied and small‐bodied metazoans, namely, cheilostome bryozoans. In doing so, we present mitochondrial and ribosomal RNA sequences of 43 cheilostomes representing 37 species, including 14 from historical samples ranging from 50 to 149 years old, circularizing a total of 27 mitogenomes, seven from historical cheilostome samples. Our study highlights the potential of utilizing DNA from micro‐invertebrate specimens stored in natural history collections for resolving phylogenetic relationships between species.

Hares from Iran can be divided into three morphological groups, with Lepus europaeus inhabiting the western parts of Iran. Hares from lowland areas along the southeastern corner of the Caspian Sea are morphologically similar to both L. tolai and L. tibetanus , but diagnosis is complicated by a lack of taxonomic agreement. Mitochondrial DNA suggests L. tibetanus rather than L. tolai , although comparative material is not incontestable. The third group, in more xeric habitats of eastern Iran, shows a mixture of traits characteristic of both the west Iranian L. europaeus and the Golestan population, the southeast Caspian Sea. Mitochondrial and nuclear loci reveal conflicting patterns, where hares from eastern Iran cluster with L. europaeus based on mtDNA, but with the Golestan population based on nuclear transferrin, suggesting a mixed ancestry. Ecological niche modeling indicates that the preferred habitat of the Golestan population is more restricted than that of the other two groups. Pure L. europaeus occur in areas of high seasonality, low temperature, and high precipitation, whereas the population in eastern Iran inhabits areas characterized by high contrast in daily temperatures and the highest isothermality in eastern Iran. Parts of the range of this population are also indicated to correspond to the fundamental niche of L. europaeus , yet both parental forms appear to be absent from this area occupied by individuals of apparent mixed ancestry. This suggests that the population of mixed ancestry may have selective advantages over the parental forms, and that the absence of the latter from this area may be due to competitive exclusion. As the population of mixed ancestry thus appears to be self-sustaining, incipient speciation of a stabilized hybrid may be implied.