HeartCV: a tool for transferrable, automated measurement of heart rate and heart rate variability in transparent animals.

Heart function is a key component of whole-organismal physiology. Bioimaging is commonly, but not exclusively, used for quantifying heart function in transparent individuals, including early developmental stages of aquatic animals, many of which are transparent. However, a central limitation of many imaging-related methods is the lack of transferability between species, life-history stages and experimental approaches. Furthermore, locating the heart in mobile individuals remains challenging. Here, we present HeartCV: an open-source Python package for automated measurement of heart rate and heart rate variability that integrates automated localization and is transferrable across a wide range of species. We demonstrate the efficacy of HeartCV by comparing its outputs with measurements made manually for a number of very different species with contrasting heart morphologies. Lastly, we demonstrate the applicability of the software to different experimental approaches and to different dataset types, such as those corresponding to longitudinal studies.

Global Distribution and Variation of the Invasive Cheilostome Bryozoan Cribrilina mutabilis.

Viable populations of the cheilostome bryozoan Cribrilina mutabilis Ito, Onishi & Dick exist in the NW Pacific (Russian Far East and northern Japan), NE Atlantic (Scandinavia and Scotland), and NW Atlantic (Maine, USA). The first NE and NW Atlantic records are from Norway (2008) and Casco Bay, Maine, USA (2018), respectively, indicating a relatively recent introduction to the region. Mitochondrial COI gene sequences from North Atlantic populations (Sweden, Norway, and Maine) showed two haplotypes differing by one substitution, but differed from two haplotypes from Akkeshi, northern Japan, by 6-8 substitutions. North Atlantic populations differed morphologically from the Akkeshi population in that some zooids formed a suboral projection, and frontal zooids were more common. While C. mutabilis in northern Japan has been found only on natural or artificial eelgrass (Zostera marina), across its range it has been found on several species of algae, plastic panels and strips, several species of Zostera, and mollusc shells. Similar frequencies of heteromorphic zooids with differing degree of frontal wall calcification, i.e., R (rib)-, I (intermediate)-, and S (shield)-type zooids, in colonies on eelgrass at comparable times of the season and across populations suggest an innate response to seasonal environmental fluctuations, although zooid frequencies were different on non-eelgrass substrates. The increase in trans-Arctic shipping along the Northern Sea Route in recent decades, and previous documentation of C. mutabilis on ship hulls in the Sea of Japan, indicate a clear mechanism for anthropogenic introduction from the Far East to Europe in recent decades.

Developing a list of invasive alien species likely to threaten biodiversity and ecosystems in the European Union.

The European Union (EU) has recently published its first list of invasive alien species (IAS) of EU concern to which current legislation must apply. The list comprises species known to pose great threats to biodiversity and needs to be maintained and updated. Horizon scanning is seen as critical to identify the most threatening potential IAS that do not yet occur in Europe to be subsequently risk assessed for future listing. Accordingly, we present a systematic consensus horizon scanning procedure to derive a ranked list of potential IAS likely to arrive, establish, spread and have an impact on biodiversity in the region over the next decade. The approach is unique in the continental scale examined, the breadth of taxonomic groups and environments considered, and the methods and data sources used. International experts were brought together to address five broad thematic groups of potential IAS. For each thematic group the experts first independently assembled lists of potential IAS not yet established in the EU but potentially threatening biodiversity if introduced. Experts were asked to score the species within their thematic group for their separate likelihoods of i) arrival, ii) establishment, iii) spread, and iv) magnitude of the potential negative impact on biodiversity within the EU. Experts then convened for a 2-day workshop applying consensus methods to compile a ranked list of potential IAS. From an initial working list of 329 species, a list of 66 species not yet established in the EU that were considered to be very high (8 species), high (40 species) or medium (18 species) risk species was derived. Here, we present these species highlighting the potential negative impacts and the most likely biogeographic regions to be affected by these potential IAS.

CASA in invertebrates.

Sperm movement has been described in several phyla of invertebrates. Yet, sperm motility has only been quantified using computer-aided sperm analysis (CASA-Mot) in externally fertilising species (broadcast spawners) of two phyla, molluscs and echinoderms. In the present study we quantified in detail the nature of the sperm tracks, percentage motility groupings and detailed kinematics of rapid-, medium- and slow-swimming spermatozoa in the oyster Crassostrea gigas and four species never previously studied by CASA-Mot, namely the molluscs Choromytilus meridionalis, Donax serra and Haliotis midae and the echinoderm Parechinus angulosus. A feature common to all these species are the helical tracks, the diameter of which seems to be species specific. Using CASA-Mot, the behaviour of spermatozoa was also studied over time and in the presence of egg water and Ca2+ modulators such as caffeine and procaine hydrochloride. For the first time, we show that hyperactivation can be induced in all species in the presence of egg water (sea water that was mixed with mature eggs and then centrifuged) and/or caffeine, and these hyperactivated sperm tracks were characterised using CASA-Mot. We relate the different patterns of sperm motility and behaviour to reproductive strategies such as broadcast spawning and spermcasting, and briefly review studies using CASA-Mot on other invertebrates.

What causes female bias in the secondary sex ratios of the dioecious woody shrub Salix sitchensis colonizing a primary successional landscape?

UNLABELLED: • PREMISE OF THE STUDY: Females often outnumber males in Salix populations, although the mechanisms behind female bias are not well understood and could be caused by both genetic and ecological factors. We investigated several ecological factors that could bias secondary sex ratios of Salix sitchensis colonizing Mount St. Helens after the 1980 eruption.• METHODS: We determined whether S. sitchensis secondary sex ratios varied across disturbance zones created by the eruption and across mesic and hydric habitats within each zone. For one population, we tracked adult mortality, whole-plant reproductive allocation, the number of stems, and plant size for 2 years. In a field experiment, we created artificial streams to test whether vegetative reproduction via stem fragments was sex-biased.• KEY RESULTS: We found a consistent 2:1 female bias in S. sitchensis secondary sex ratios across all disturbance zones and habitats. Despite female plants sometimes allocating more resources (in terms of carbon, nitrogen, and phosphorus) to reproduction than males, we found no evidence of sex-biased mortality. The establishment rate of S. sitchensis experimental stems did not differ between the sexes, indicating that vegetative reproduction was not distorting secondary sex ratios.• CONCLUSIONS: We hypothesize that S. sitchensis secondary sex ratios depend on either early-acting genetic factors affecting the seed sex ratio or sex-specific germination or survival rates before maturity, as opposed to factors associated with reproduction in adult plants.

Gopher mounds decrease nutrient cycling rates and increase adjacent vegetation in volcanic primary succession.

Fossorial mammals may affect nutrient dynamics and vegetation in recently initiated primary successional ecosystems differently than in more developed systems because of strong C and N limitation to primary productivity and microbial communities. We investigated northern pocket gopher (Thomomys talpoides) effects on soil nutrient dynamics, soil physical properties, and plant communities on surfaces created by Mount St. Helens' 1980 eruption. For comparison to later successional systems, we summarized published studies on gopher effects on soil C and N and plant communities. In 2010, 18 years after gopher colonization, we found that gophers were active in ~2.5% of the study area and formed ~328 mounds ha(-1). Mounds exhibited decreased species density compared to undisturbed areas, while plant abundance on mound margins increased 77%. Plant burial increased total soil carbon (TC) by 13% and nitrogen (TN) by 11%, compared to undisturbed soils. Mound crusts decreased water infiltration, likely explaining the lack of detectable increases in rates of NO3-N, NH4-N or PO4-P leaching out of the rooting zone or in CO2 flux rates. We concluded that plant burial and reduced infiltration on gopher mounds may accelerate soil carbon accumulation, facilitate vegetation development at mound edges through resource concentration and competitive release, and increase small-scale heterogeneity of soils and communities across substantial sections of the primary successional landscape. Our review indicated that increases in TC, TN and plant density at mound margins contrasted with later successional systems, likely due to differences in physical effects and microbial resources between primary successional and older systems.

Symmetrical reproductive compatibility of two species in the Ciona intestinalis (Ascidiacea) species complex, a model for marine genomics and developmental biology.

The sea squirt Ciona intestinalis species complex is a widely used model system for genomics and developmental biology, as well as ecology. Contrary to previous reports, here we show no difference in the success of development and hatching between hybrid and conspecific crosses between the two species within this complex known as types A and B, from a region in the English Channel where they are sympatric. We grew laboratory hybrids in the field for three months, and successfully obtained reproductive adults. In back-crosses of F1 laboratory hybrids to parental types, normal larvae were obtained. We conclude that hybrid crosses generate viable offspring and the resulting hybrids are interfertile with types A and B. However we also show that introgression in the natural sympatric population remains low. We discuss possible pre-zygotic and post-zygotic mechanisms which reproductively isolate these species.

Molecular and morphological discrimination between an invasive ascidian, Ascidiella aspersa, and its congener A. scabra (Urochordata: Ascidiacea).

The solitary ascidian Ascidiella aspersa (Müller, 1776) has sometimes been regarded as conspecific with A. scabra (Müller, 1776), although previous detailed morphological comparisons have indicated that the two are distinguishable by internal structures. Resolution of this taxonomic issue is important because A. aspersa has been known as a notoriously invasive ascidian, doing much damage to aquaculture e.g. in Hokkaido, Japan. We collected many specimens from European waters (including the Swedish coast, near the type localities of these two species) and Hokkaido, Japan (as an alien population) and made molecular phylogenetic analyses using the mitochondrial cytochrome c oxidase subunit I (COI) gene, and found that in terms of COI sequences all the analyzed specimens were clustered into two distinct groups, one of which is morphologically referable to A. aspersa and the other to A. scabra. Thus, these two species should be regarded as distinct from each other.

The genome sequence of the sand star, Astropecten irregularis (Pennant, 1777).

We present a genome assembly from an individual Astropecten irregularis (the sand star; Echinodermata; Asteroidea; Paxillosida; Astropectinidae). The genome sequence spans 475.80 megabases. Most of the assembly is scaffolded into 22 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.34 kilobases in length.

The genome sequence of the Orange-tipped sea squirt, Corella eumyota Traustedt, 1882.

We present a genome assembly from an individual specimen of Corella eumyota (the Orange-tipped sea squirt; Chordata; Ascidiacea; Phlebobranchia; Corellidae). The genome sequence is 129.3 megabases in span. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 14.53 kilobases in length.

The genome sequence of a segmented worm, Terebella lapidaria Linnaeus, 1767.

We present a genome assembly from an individual Terebella lapidaria (segmented worm; Annelida; Polychaeta; Terebellida; Terebellidae). The genome sequence spans 765.20 megabases. Most of the assembly is scaffolded into 16 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.97 kilobases in length.

The genome sequence of the ruby bryozoan, Bugula neritina (Linnaeus, 1758).

We present a genome assembly from a specimen of Bugula neritina (the ruby bryozoan; Bryozoa; Gymnolaemata; Cheilostomatida; Bugulidae). The genome sequence has total length of 216.00 megabases. Most of the assembly is scaffolded into 9 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.25 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,264 protein-coding genes.

Heterogeneity in maternal mRNAs within clutches of eggs in response to thermal stress during the embryonic stage.

BACKGROUND: The origin of variation is of central interest in evolutionary biology. Maternal mRNAs govern early embryogenesis in many animal species, and we investigated the possibility that heterogeneity in maternal mRNA provisioning of eggs can be modulated by environmental stimuli. RESULTS: We employed two sibling species of the ascidian Ciona, called here types A and B, that are adapted to different temperature regimes and can be hybridized. Previous study showed that hybrids using type B eggs had higher susceptibility to thermal stress than hybrids using type A eggs. We conducted transcriptome analyses of multiple single eggs from crosses using eggs of the different species to compare the effects of maternal thermal stress on heterogeneity in egg provisioning, and followed the effects across generations. We found overall decreases of heterogeneity of egg maternal mRNAs associated with maternal thermal stress. When the eggs produced by the F1 AB generation were crossed with type B sperm and the progeny ('ABB' generation) reared unstressed until maturation, the overall heterogeneity of the eggs produced was greater in a clutch from an individual with a heat-stressed mother compared to one from a non-heat-stressed mother. By examining individual genes, we found no consistent overall effect of thermal stress on heterogeneity of expression in genes involved in developmental buffering. In contrast, heterogeneity of expression in signaling molecules was directly affected by thermal stress. CONCLUSIONS: Due to the absence of batch replicates and variation in the number of reads obtained, our conclusions are very limited. However, contrary to the predictions of bet-hedging, the results suggest that maternal thermal stress at the embryo stage is associated with reduced heterogeneity of maternal mRNA provision in the eggs subsequently produced by the stressed individual, but there is then a large increase in heterogeneity in eggs of the next generation, although itself unstressed. Despite its limitations, our study presents a proof of concept, identifying a model system, experimental approach and analytical techniques capable of providing a significant advance in understanding the impact of maternal environment on developmental heterogeneity.

Neuropathological Applications of Microscopy with Ultraviolet Surface Excitation (MUSE): A Concordance Study of Human Primary and Metastatic Brain Tumors.

Whereas traditional histology and light microscopy require multiple steps of formalin fixation, paraffin embedding, and sectioning to generate images for pathologic diagnosis, Microscopy using Ultraviolet Surface Excitation (MUSE) operates through UV excitation on the cut surface of tissue, generating images of high resolution without the need to fix or section tissue and allowing for potential use for downstream molecular tests. Here, we present the first study of the use and suitability of MUSE microscopy for neuropathological samples. MUSE images were generated from surgical biopsy samples of primary and metastatic brain tumor biopsy samples (n = 27), and blinded assessments of diagnoses, tumor grades, and cellular features were compared to corresponding hematoxylin and eosin (H&E) images. A set of MUSE-treated samples subsequently underwent exome and targeted sequencing, and quality metrics were compared to those from fresh frozen specimens. Diagnostic accuracy was relatively high, and DNA and RNA integrity appeared to be preserved for this cohort. This suggests that MUSE may be a reliable method of generating high-quality diagnostic-grade histologic images for neuropathology on a rapid and sample-sparing basis and for subsequent molecular analysis of DNA and RNA.

The genome sequence of a solitary sea squirt, Ascidia mentula (Müller, 1776).

We present a genome assembly from an individual Ascidia mentula (the (a solitary sea squirt); Chordata; Ascidiacea; Phlebobranchia; Ascidiidae). The genome sequence is 197.0 megabases in span. Most of the assembly is scaffolded into 9 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.46 kilobases in length.

The genome sequence of the sea mat, Membranipora membranacea (Linnaeus, 1767).

We present a genome assembly from an adult colony of Membranipora membranacea (the sea mat; Bryozoa; Gymnolaemata; Cheilostomatida; Membraniporidae). The genome sequence is 339 megabases in span. Most of the assembly (99.95%) is scaffolded into 11 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 14.7 kilobases in length.

The genome sequence of an erect bryozoan, Bugulina stolonifera (Ryland, 1960).

We present a genome assembly from a Bugulina stolonifera colony (an erect bryozoan; Bryozoa; Gymnolaemata; Cheilostomatida; Bugulidae). The genome sequence is 235 megabases in span. Most of the assembly (99.85%) is scaffolded into 11 chromosomal pseudomolecules. The mitochondrial genome was also assembled and is 14.4 kilobases long.

The genome sequence of the light-bulb sea squirt, Clavelina lepadiformis (Müller, 1776).

We present a genome assembly from an individual Clavelina lepadiformis (the light-bulb sea squirt; Chordata; Ascidiacea; Aplousobranchia; Clavelinidae). The genome sequence is 210.1 megabases in span. Most of the assembly is scaffolded into 9 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 14.48 kilobases in length.