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Stylophora pistillata is a widely used coral “lab-rat” species with highly variable morphology and a broad biogeographic range (Red Sea to western central Pacific). Here we show, by analysing Cytochorme Oxidase I sequences, from 241 samples across this range, that this taxon in fact comprises four deeply divergent clades corresponding to the Pacific-Western Australia, Chagos-Madagascar-South Africa, Gulf of Aden-Zanzibar- Madagascar, and Red Sea-Persian/Arabian Gulf-Kenya. On the basis of the fossil record of Stylophora, these four clades diverged from one another 51.5-29.6 Mya, i.e., long before the closure of the Tethyan connection between the tropical Indo-West Pacific and Atlantic in the early Miocene (16–24 Mya) and should be recognised as four distinct species. These findings have implications for comparative ecological and/or physiological studies carried out using Stylophora pistillata as a model species, and highlight the fact that phenotypic plasticity, thought to be common in scleractinian corals, can mask significant genetic variation. Stylophora sequence files for DryadAligned sequence files used for phylogeny analysis. ReadMe files also included.

The Tara Pacifc expedition (2016–2018) provided an opportunity to investigate calcifcation patterns in extant corals throughout thePacifc Ocean. Cores from colonies of the massive Porites and Diploastrea genera were collected fromdiferent environments to assess calcifcation parameters of long-lived reef-building corals. In this study, we compared the calcifcation and carbonate chemistryup-regulation of Diploastrea heliopora and Porites corals from across a range of environments. To this, we analyzed the skeletal geochemistry and growth parameters of 39 colonies of Porites (n=33) and Diploastrea (n=6) collected across the tropical Pacifc Ocean during the Tara Pacifc expedition (2016–2018). Te collected corals represent a suite of cores exposed to various hydrological conditions of seawater temperature (SST: 22.4–29.8 °C), salinity (SSS: 31.5–36.1), and carbonate chemistry (total scale pHsw: 8.01–8.09). Te average chemical composition of the calcifying fuid (pHcf, [CO32−]cf, DICcf, Ωcf) was derived from paired boron isotope (δ11B) and B/Ca analyses of core-top samples corresponding to the last 6 years of growth (2010–2016). Based on these data, we assessed the impact of the ambient seawater properties (SST, salinity, carbonate chemistry) on the cf composition of these slow-growing reef-building genera at the Pacifc basin scale. In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2024) was used to compute a complete and consistent set of carbonate system variables, as described by Nisumaa et al. (2010). In this dataset the original values were archived in addition with the recalculated parameters (see related PI). The date of carbonate chemistry calculation by seacarb is 2024-04-08.

Abstract Background The Nile tilapia (Oreochromis niloticus) is the third most important freshwater fish for aquaculture. Its success is directly linked to continuous breeding efforts focusing on production traits such as growth rate and weight. Among those elite strains, the Genetically Improved Farmed Tilapia (GIFT) programme initiated by WorldFish is now distributed worldwide. To accelerate the development of the GIFT strain through genomic selection, a high-quality reference genome is necessary. Results Using a combination of short (10X Genomics) and long read (PacBio HiFi, PacBio CLR) sequencing and a genetic map for the GIFT strain, we generated a chromosome level genome assembly for the GIFT. Using genomes of two closely related species (O. mossambicus, O. aureus), we characterised the extent of introgression between these species and O. niloticus that has occurred during the breeding process. Over 11 Mb of O. mossambicus genomic material could be identified within the GIFT genome, including genes associated with immunity but also with traits of interest such as growth rate. Conclusion Because of the breeding history of elite strains, current reference genomes might not be the most suitable to support further studies into the GIFT strain. We generated a chromosome level assembly of the GIFT strain, characterising its mixed origins, and the potential contributions of introgressed regions to selected traits.

The relationships between parasites and their hosts are intimate, dynamic and complex; the evolution of one is inevitably linked to the other. Despite multiple origins of parasitism in the Cnidaria, only parasites belonging to the Myxozoa are characterized by a complex life cycle, alternating between fish and invertebrate hosts, as well as by exceptionally high species diversity. This inspired us to examine the history of reciprocal interactions and adaptive radiations in myxozoans and their hosts by determining the degree of congruence between their phylogenies and by timing the emergence of myxozoan lineages in relation to their hosts. Recent genomic analyses suggested a common origin of Polypodium hydriforme, a cnidarian parasite of acipenseriform fishes, and the Myxozoa, and proposed fish as original hosts for both sister lineages. We clearly demonstrate that the Myxozoa emerged long before fish populated Earth and that phylogenetic congruence with their invertebrate hosts is evident down to the most basal branches of the tree, indicating bryozoans and annelids as original hosts and challenging previous hypothesis. We provide evidence that, following invertebrate invasion, fish hosts were acquired multiple times, leading to parallel cospeciation patterns in all major phylogenetic lineages. We identify the acquisition of vertebrate hosts that facilitate alternative transmission and dispersion strategies as reason for the distinct success of the Myxozoa, and identify massive host specification-linked parasite diversification events. The results of this study transform our understanding of the origins and evolution of parasitism in the most basal metazoan parasites known. Trees for cophylogeny reconciliationHost and parasite trees (24) used for cophylogeny reconciliation and based on the alignments of 18S rDNA and 16S rRNA gene sequences deposited in the same dryad folder.trees for cophylogeny reconciliation.nexMolClock_alignmentAlignment of 6 concatenated protein-coding genes, i.e. aldolase (200 aa), triosephosphate isomerase (217 aa), phosphofructokinase (175 aa), methionine adenosyltransferase (348 aa), elongation factor 1 alpha (418 aa) and ATP synthase beta chain (430 aa), for molecular clock analysis of myxozoan and other metazoan taxa.18S rDNA aligment_myxozoans_in_vertebrate_hostsCut alignment of 18S rDNA sequences of 682 taxa of myxozoans from vertebrate hosts in fasta format18S_myxozoans_in_vertebrate_hosts.fasta18S rDNA_myxozoans_from_invertebrate_hostsCut alignment of 18S rDNA sequences of 124 taxa of myxozoans from invertebrate hosts in fasta format18S_myxozoans_from_invertebrates_53M.fasta18S rDNA alignment_invertebrate hostsCut alignment of 18S rDNA sequences of 25 taxa of invertebrate hosts of myxozoans in fasta format18S_invertebrate hosts.fasta16S rRNA_vertebrate_hostsCut alignment of 16S rRNA gene sequences of 246 taxa of vertebrate hosts of myxozoans in fasta format16S_vertebrate_hosts.fastafull__mitogenome_vertebrate_hostsCut alignment of full mitogenome sequences of 105 taxa of invertebrate host families of myxozoans in fasta format

Additional file 6: Supplementary Table 3. Genes identified within O. mossambicus introgressed regions including corresponding orthologs in medaka.

All experimental trials were performed in 12-well polystyrene plates. Three food choice treatment groups were defined: (1) Artemia sp. nauplii only (n = 10 nauplii in each replicate); (2) microplastic particles only (n = 10 microplastic particles in each replicate); (3) evenly split food choice of Artemia sp. nauplii and microplastic (n = 5 each). A total of 12 replicates of each treatment group were set up, and a randomized design was created to assign treatments to wells. A total of five specimens of A. gibbosa were placed into each well. Approximately 24 hours after the initiation of the experiment, feeding activity of A. gibbosa on nauplii and microplastic was assessed visually under a Leica binocular microscope, by counting the number of remaining nauplii and feeding attempts on microplastic particles and nauplii. For the purpose of this experiment, feeding on microplastic is defined as any physical interaction with the LBFs’ pseudopodia. Two trials were conducted, with a total of 24 replicates (12 per trial) in each treatment. None of the specimens were used in both trials. To ensure counting accuracy, an additional four counting controls per treatment were established, in which no LBF were placed in the well. Increasing marine microplastic pollution has detrimentally impacted organismal physiology and ecosystem functioning. While previous studies document negative effects of microplastics on coral reef animals, the potential responses of organisms such as Large Benthic Foraminifera (LBF) are largely unknown. Here, we document the impact of microplastics on heterotrophic feeding behavior of LBF. Specimens of Amphistegina gibbosa were incubated in three experimental treatments: (1) Artemia sp. nauplii only; (2) pristine microplastic particles only; (3) choice of nauplii and pristine microplastic. Feeding rates were observed 24 h after initiation of treatments. A separate experiment was conducted to compare the effect of conditioned vs. pristine microplastic. Our results indicate that A. gibbosa is able to selectively feed on Artemia, avoiding interactions with pristine microplastic. However, the presence of conditioned microplastic causes similar feeding interaction rates as with Artemia. This suggests microplastics with longer residence times may have a larger impact on facultative detritivores. There are no missing values in the dataset. Pristine Microplastic, Exp. 1 trial refers to the time points at which the Experiment was conducted (trial 1 vs. trial 2) Food choice refers to the food source that was presented to the foraminifera (Artemia sp. Nauplii vs. Pristine Microplastic) Treatment represents the food choices that were offered to the foraminifera (single choice vs. Mixed choice) Feeding rate represents the number of particles ingested and/or pseudopodal interactions (Particles fed upon day-1) Soaked Microplastic, Exp. 2 trial refers to the time points at which the Experiment was conducted (trial 1 vs. trial 2) Food choice refers to the food source that was presented to the foraminifera (Artemia sp. Nauplii vs. soaked Microplastic) Treatment represents the food choices that were offered to the foraminifera (single choice vs. Mixed choice) Feeding rate represents the number of particles ingested and/or pseudopodal interactions (Particles fed upon day-1)

Additional file 1. Figure S1: Alpha rarefaction curves of epiphytic microbial communities in samples of each mesocosm treatment

Additional file 8: Supplementary Table 4. Ontology terms significantly enriched among genes identified within O. mossambicus introgressed regions.