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Additional information for manuscript entiteld "Host-parasitoid associations in marine planktonic time series: can metabarcoding help reveal them?" (PONE-D-20-17825R1)
<p><strong>Description:</strong></p> <p>This repository contains material to reproduce metabarcoding analyses based on the q-zip pipeline (https://github.com/PyoneerO/qzip). Raw fastq files can be downloaded from https://www.ebi.ac.uk/ena/browser/view/PRJEB37135. The used reference file can be downloaded from https://github.com/pr2database/pr2database/releases/tag/4.11.1. Please select the files created for the classifier implemented in mothur.</p> <p>The dockerfile in this repository can be used to set up the environment which inludes the installation of the needed versions of the needed tools.</p> <p>Twelve different analyses had been conducted. For each analysis one zip file had been created which contains the following files:</p> <p>- q-zip_commands.sh: the shell script to launch the pipeline</p> <p>- q-zip_parameters.txt: pipeline parameter file as input of the shell script</p> <p>- q-zip_workflow.log: log file containing stdout and sdterr</p> <p>- q-zip_seq_of_coms.txt: file containing each command executed during the pipeline run (minimal set of command to reproduce the results)</p> <p>- seq_number_stats.txt: file containing the sequence numbers at each filtering step</p> <p>- OTU tables in tsv and biom format (sequences and taxonomic annotation included)</p> <p>- Meta data map (here only including the raw file names)</p> <p>- swarm sequences in fasta format</p> <p> </p> <p><strong>The following analyses had been conducted:</strong></p> <p>- otu formation at swarm distance 1; default settings for preceding sequence filtering and subsequent taxonomic annotation</p> <p>- otu formation at swarm distance 2; default settings for preceding sequence filtering and subsequent taxonomic annotation</p> <p>- otu formation at swarm distance 3; default settings for preceding sequence filtering and subsequent taxonomic annotation</p> <p>- otu formation at swarm distance 5; default settings for preceding sequence filtering and subsequent taxonomic annotation</p> <p>- otu formation at swarm distance 10; default settings for preceding sequence filtering and subsequent taxonomic annotation</p> <p>- otu formation at swarm distance 1; relaxt settings for preceding sequence filtering and subsequent taxonomic annotation</p> <p>- otu formation at swarm distance 2; relaxt settings for preceding sequence filtering and subsequent taxonomic annotation</p> <p>- otu formation at swarm distance 3; relaxt settings for preceding sequence filtering and subsequent taxonomic annotation</p> <p>- otu formation at swarm distance 1; strict settings for preceding sequence filtering and subsequent taxonomic annotation</p> <p>- otu formation at swarm distance 2; strict settings for preceding sequence filtering and subsequent taxonomic annotation</p> <p>- otu formation at swarm distance 3; strict settings for preceding sequence filtering and subsequent taxonomic annotation</p> <p>- otu formation at swarm distance 1; very strict settings settings for preceding sequence filtering and subsequent taxonomic annotation</p> <p><strong>Settings into more detail:</strong></p> <p>relaxt settings:</p> <ul> <li>trimmomatic filtering: sliding window length of 3 bp - threshold of average quality within of 5</li> <li>vsearch paired-end merging: length of minimum overlap of 25 bp - number of mismatches allowed of 5 bp</li> <li>cutadapt primer removal: percentage primer to sequence overlap of 75% - percentage mismatches allowed of 20%</li> <li>vsearch eeMax filtering: max number of errors expected per sequence of 1 bp</li> <li>minimum sequence length of 300 bp and maximum sequence length of 550 bp</li> <li>mothur classification cutoff (refers to confidence threshold of NBC) of 0.6</li> </ul> <p>default settings (used for the manuscript):</p> <ul> <li>trimmomatic filtering: sliding window length of 3 bp - threshold of average quality within of 8</li> <li>vsearch paired-end merging: length of minimum overlap of 50 bp - number of mismatches allowed of 5</li> <li>cutadapt primer removal: percentage primer to sequence overlap of 90% - percentage mismatches allowed of 10%</li> <li>vsearch eeMax filtering: max number of errors expected per sequence of 0.25 bp</li> <li>minimum sequence length of 300 bp and maximum sequence length of 550 bp</li> <li>mothur classification cutoff (refers to confidence threshold of NBC) of 0.8</li> </ul> <p>strict settings:</p> <ul> <li>trimmomatic filtering: sliding window length of 1 bp - threshold of average quality within of 15</li> <li>vsearch paired-end merging: length of minimum overlap of 50 bp - number of mismatches allowed of 0</li> <li>cutadapt primer removal: percentage primer to sequence overlap of 90% - percentage mismatches allowed of 10%</li> <li>vsearch eeMax filtering: max number of errors expected per sequence of 0.1 bp</li> <li>minimum sequence length of 300 bp and maximum sequence length of 550 bp</li> <li>mothur classification cutoff (refers to confidence threshold of NBC) of 0.9</li> </ul> <ul> </ul> <p>very strict settings:</p> <ul> <li>trimmomatic filtering: sliding window length of 1 bp - threshold of average quality within of 15</li> <li>vsearch paired-end merging: length of minimum overlap of 50 bp - number of mismatches allowed of 0</li> <li>cutadapt primer removal: percentage primer to sequence overlap of 100% - percentage mismatches allowed of 0%</li> <li>vsearch eeMax filtering: max number of errors expected per sequence of 0.1 bp</li> <li>minimum sequence length of 300 bp and maximum sequence length of 550 bp</li> <li>mothur classification cutoff (refers to confidence threshold of NBC) of 0.9</li> </ul>
Data from: Dense dwarfs versus gelatinous giants: the trade-offs and physiological limits determining the body plan of planktonic filter feeders
Most marine plankton have a high energy (carbon) density, but some are gelatinous with approximately hundred times more watery bodies. How do those distinctly different body plans emerge and what are the trade-offs? We address this question by modeling the energy budget of planktonic filter feeders across life forms from micron-sized unicellular microbes like choanoflagellates to centimeter-sized gelatinous tunicates such as salps. We find two equally successful strategies, one being small with high energy density (dense dwarf), and the other being large with low energy density (gelatinous giant). The constraint that forces large - but not small - filter feeders to be gelatinous is identified as a lower limit to the size-specific filter area, below which the energy costs lead to starvation. A further limit is found from the maximum size-specific motor force that restricts the access to optimum strategies. The quantified constraints are discussed in the context of other resource acquisition strategies. We argue that interception feeding strategies can only be accessed by large organisms if they are gelatinous. On the other hand, organisms that use remote prey sensing do not need to be gelatinous, even if they are large.
Data from: Nomenclature for the nameless: a proposal for an integrative molecular taxonomy of cryptic diversity exemplified by planktonic foraminifera
Investigations of biodiversity, biogeography and ecological processes rely on the identification of "species" as biologically significant, natural units of evolution. In this context, morpho-taxonomy only provides an adequate level of resolution if reproductive isolation matches morphological divergence. In many groups of organisms, morphologically defined species often disguise considerable genetic diversity, which may be indicative of the existence of cryptic species. The diversity hidden by morphological species can be disentangled through genetic surveys, which also provide access to data on the ecological distribution of genetically circumscribed units. These units can be identified by unique DNA sequence motifs and allow studies of evolutionary and ecological processes at different levels of divergence. However, the nomenclature of genetically circumscribed units within morphological species is not regulated and lacks stability. This represents a major obstacle to efforts to synthesize and communicate data on genetic diversity for multiple stakeholders. We have been confronted with such an obstacle in our work on planktonic foraminifera, where the stakeholder community is particularly diverse, involving geochemists, paleoceanographers, paleontologists and biologists, and the lack of stable nomenclature beyond the level of formal morphospecies prevents effective transfer of knowledge. To circumvent this problem, we have designed a stable, reproducible and flexible nomenclature system for genetically circumscribed units, analogous to the principles of a formal nomenclature system. Our system is based on the definition of unique DNA sequence motifs collocated within an individual, their typification (in analogy with holotypes), utilization of their hierarchical phylogenetic structure to define levels of divergence below that of the morphospecies, and a set of nomenclature rules assuring stability. The resulting molecular operational taxonomic units (MOTUs) remain outside the domain of current nomenclature codes, but are linked to formal morphospecies as regulated by the codes. Subsequently we show how this system can be applied to classify genetically defined units using the SSU rDNA marker in planktonic foraminifera and we highlight its potential use for other groups of organisms where similarly high levels of connectivity between molecular and formal taxonomies can be achieved.
Data from: The cryptic and the apparent reversed: lack of genetic differentiation within the morphologically diverse plexus of the planktonic foraminifer Globigerinoides sacculifer
Previous genetic studies of extant planktonic foraminifera have provided evidence that the traditional, strictly morphological definition of species in these organisms underestimates their biodiversity. Here, we report the first case where this pattern is reversed. The modern (sub)tropical species plexus Globigerinoides sacculifer is characterized by large morphological variability, which has led to the proliferation of taxonomic names attributed to morphological end-members within the plexus. In order to clarify the taxonomic status of its morphotypes and to investigate the genetic connectivity among its currently partly disjunct (sub)tropical populations, we carried out a global survey of two ribosomal RNA regions (SSU and ITS-1) in all recent morphotypes of the plexus collected throughout (sub)tropical surface waters of the global ocean. Unexpectedly, we find an extremely reduced genetic variation within the plexus and no correlation between genetic and morphological divergence, suggesting taxonomical overinterpretation. The genetic homogeneity within the morphospecies is unexpected, considering its partly disjunct range in the (sub)tropical Atlantic and Indo-Pacific and its old age (early Miocene). A sequence variant in the rapidly evolving ITS-1 region indicates the existence of an exclusively Atlantic haplotype, which suggests an episode of relatively recent (last glacial) isolation, followed by subsequent resumption of unidirectional gene flow from the Indo-Pacific into the Atlantic. This is the first example in planktonic foraminifera where the morphological variability in a morphospecies exceeds its rDNA genetic variability. Such evidence for inconsistent scaling of morphological and genetic diversity in planktonic foraminifera could complicate the interpretation of evolutionary patterns in their fossil record.
Data from: Evolutionary ecology of Early Paleocene planktonic foraminifera: size, depth habitat and symbiosis
The carbon stable isotope (δ13C) composition of the calcitic tests of planktonic foraminifera has an important role as a geochemical tracer of ocean carbon system changes associated with the Cretaceous/Paleogene (K/Pg) mass extinction event and its aftermath. Questions remain, however, about the extent of δ13C isotopic disequilibrium effects and the impact of depth habitat evolution on test calcite δ13C among rapidly evolving Paleocene species, and the influence this has on reconstructed surface-to-deep ocean dissolved inorganic carbon (DIC) gradients. A synthesis of new and existing multispecies data, on the relationship between δ13C and δ18O and test size, sheds light on these issues. Results suggest that early Paleocene species quickly radiated into a range of depths habitats in a thermally stratified water column. Negative δ18O gradients with increasing test size in some species of Praemurica suggest either ontogenetic or ecotypic dependence on calcification temperature that may reflect depth/light controlled variability in symbiont photosynthetic activity. The pattern of positive δ13C test-size correlations allows us to (1) identify metabolic disequilibrium δ13C effects in small foraminifera tests, as occur in the immediate aftermath of the K/Pg event, (2) constrain the timing of evolution of foraminiferal photosymbiosis to 63.5 Ma, ∼0.9 Myr earlier than previously suggested, and (3) identify the apparent loss of symbiosis in a late-ranging morphotype of Praemurica. These findings have implications for interpreting δ13C DIC gradients at a resolution appropriate for incoming highly resolved K/Pg core records.
Data from: Using geography to infer the importance of dispersal for the synchrony of freshwater plankton
Spatial synchrony in population dynamics is a ubiquitous ecological phenomenon that can result from predator-prey interactions, synchronized environmental variation (Moran effects), or dispersal. Of these, dispersal historically has been the least well studied in natural systems, partly because of the difficulty in quantifying dispersal in situ. We hypothesized that dispersal routes of plankton were based on the major and consistent water current movements in Kentucky Lake, a large reservoir in western Kentucky, USA. Then, using 26-year time series collected at 16 locations, we used matrix regression techniques to test whether spatial heterogeneity in strengths of hypothesized dispersal predicted spatial patterns of synchrony of phytoplankton and zooplankton, thereby testing for evidence of dispersal as a possible mechanism of synchrony in this system. Nearly all taxa showed significant spatial synchrony that did not decline with increasing linear distance between locations. All taxa also showed substantial geographic structure in synchrony that was not explained by linear distance. Matrix regression revealed that our hypothesized matrix of dispersal pathways, which differed substantially from linear distance, was a significant predictor of spatial variability in synchrony in phytoplankton biomass, and Bosmina longirostris and Daphnia lumholtzi densities. Thus dispersal was a likely mechanism of synchrony for these taxa. Our hypothesized dispersal matrix was a significant predictor of spatial patterns of synchrony for these taxa even after accounting for numerous alternative possible mechanisms, including possible Moran effects through any of ten physical/abiotic constraints. Our findings indicate that statistically comparing hypothesized or measured dispersal pathway information to synchrony data via matrix regressions can provide valuable evidence for the importance of dispersal as a mechanism of spatial synchrony.
FIGURE 6 in Planktonic ostracods (Myodocopa: Halocyprididae) from abyssopelagic depths in the Atlantic, North Pacific and Gulf of Oman: Chavturia abyssopelagica (n. gen., n. sp.), Halocypretta profunda (n. sp.), Halocypretta parvirostrata Chavtur and Stovbun, 2008 and Halocypretta striata (Müller, 1906)
FIGURE 6. Known geographical distribution of Chavturia abyssopelagica, n. sp.
Figure 3. Chlorophyll-a in First observation and seasonal dynamics of the new invasive planktonic copepod Oithona davisae Ferrari and Orsi, 1984 along the southern Black Sea (Anatolian Coast)
Figure 3. Chlorophyll-a distributions during the sampling period.
Figure 2 in First observation and seasonal dynamics of the new invasive planktonic copepod Oithona davisae Ferrari and Orsi, 1984 along the southern Black Sea (Anatolian Coast)
Figure 2. The average monthly sea surface temperature in 2007 and 2015 (°C).
Figure 3. Chlorophyll-a in First observation and seasonal dynamics of the new invasive planktonic copepod Oithona davisae Ferrari and Orsi, 1984 along the southern Black Sea (Anatolian Coast)
Figure 3. Chlorophyll-a distributions during the sampling period.
Figure 2 in First observation and seasonal dynamics of the new invasive planktonic copepod Oithona davisae Ferrari and Orsi, 1984 along the southern Black Sea (Anatolian Coast)
Figure 2. The average monthly sea surface temperature in 2007 and 2015 (°C).
Figure 8 from: Komeda S, Ohtsuka S, Huys R (2024) A new genus and species of oceanic planktonic Tisbidae (Crustacea, Copepoda, Harpacticoida) with enlarged modified eyes. ZooKeys 1191: 307-338. https://doi.org/10.3897/zookeys.1191.114974
Figure 8 Schematic diagram of left caudal ramus of Gyorome gen. nov. A dorsal view B ventral view. I–VII, caudal ramus setae I–VII; IT, inner branching tube-pore; OT, outer branching tube-pore.
Figure 3 from: Komeda S, Ohtsuka S, Huys R (2024) A new genus and species of oceanic planktonic Tisbidae (Crustacea, Copepoda, Harpacticoida) with enlarged modified eyes. ZooKeys 1191: 307-338. https://doi.org/10.3897/zookeys.1191.114974
Figure 3 Gyorome guttatum gen. et sp. nov., adult female, paratype A, B urosome, dorsal and ventral views, respectively (surface denticles partly omitted to reveal other structures) C, D left caudal ramus, dorsal and ventral views, respectively (surface denticles omitted). Abbreviations: P6, sixth pair of legs; I–VII, caudal ramus setae I–VII; IT, inner branching tube-pore; OT, outer branching tube-pore. Scale bars: 0.1 mm.
Figure 7 from: Komeda S, Ohtsuka S, Huys R (2024) A new genus and species of oceanic planktonic Tisbidae (Crustacea, Copepoda, Harpacticoida) with enlarged modified eyes. ZooKeys 1191: 307-338. https://doi.org/10.3897/zookeys.1191.114974
Figure 7 Gyorome guttatum gen. et sp. nov., adult male, paratype A left antennule, ventral view A' segment 1 of left antennule showing detached seta B right maxilliped, anterior view C left basis of leg 1, posterior view D endopod of left leg 2, posterior view E right leg 5, anterior view. Abbreviation: RS, root of detached seta. Scale bars: 0.1 mm.
Figure 2 from: Komeda S, Ohtsuka S, Huys R (2024) A new genus and species of oceanic planktonic Tisbidae (Crustacea, Copepoda, Harpacticoida) with enlarged modified eyes. ZooKeys 1191: 307-338. https://doi.org/10.3897/zookeys.1191.114974
Figure 2 Gyorome guttatum gen. et sp. nov., adult female, holotype A habitus, internal structures omitted B habitus, dorsal view, surface ornamentation omitted C rostrum, ventral view D mouthparts, ventral view, right antenna, right mandibular palp, and both maxillules omitted. Abbreviations: A2, antenna; BO, baculiform ocellus; LB, labrum; LD, lipid droplets; MD, mandible; MX2, maxilla; MXP, maxilliped; OV, ovary; PG, paragnath; GO, globular organ; SP, semi-parabolic plate. Scale bars: 0.1 mm.
Figure 6 from: Komeda S, Ohtsuka S, Huys R (2024) A new genus and species of oceanic planktonic Tisbidae (Crustacea, Copepoda, Harpacticoida) with enlarged modified eyes. ZooKeys 1191: 307-338. https://doi.org/10.3897/zookeys.1191.114974
Figure 6 Gyorome guttatum gen. et sp. nov., adult male, paratype A, B habitus, internal structures omitted, dorsal and lateral views, respectively C, D urosome, dorsal and ventral views, respectively (surface denticles partly omitted to reveal other structures). Abbreviation: P6, leg 6. Scale bars: 0.1 mm.
Figure 1 from: Komeda S, Ohtsuka S, Huys R (2024) A new genus and species of oceanic planktonic Tisbidae (Crustacea, Copepoda, Harpacticoida) with enlarged modified eyes. ZooKeys 1191: 307-338. https://doi.org/10.3897/zookeys.1191.114974
Figure 1 Focus stacked micrographs of Gyorome guttatum gen. et sp. nov., adult female, holotype, using A reflected (incident) light microscopy and B transmitted light microscopy. Abbreviations: BO, baculiform ocelli; GO, globular organs. Scale bars: 0.5 mm.
Figure 5 from: Komeda S, Ohtsuka S, Huys R (2024) A new genus and species of oceanic planktonic Tisbidae (Crustacea, Copepoda, Harpacticoida) with enlarged modified eyes. ZooKeys 1191: 307-338. https://doi.org/10.3897/zookeys.1191.114974
Figure 5 Gyorome guttatum gen. et sp. nov., adult female, paratype A, B right leg 1, anterior and posterior views, respectively A', A'' distal exopodal (A') and endopodal (A'') segment of left leg 1, posterior view showing setae at full length C, D left leg 2 anterior and posterior views, respectively E, F left leg 3, anterior and posterior views, respectively G left leg 4, posterior view H endopod of left leg 4, anterior view I right leg 5, anterior view. Scale bar: 0.1 mm.
Figure 4 from: Komeda S, Ohtsuka S, Huys R (2024) A new genus and species of oceanic planktonic Tisbidae (Crustacea, Copepoda, Harpacticoida) with enlarged modified eyes. ZooKeys 1191: 307-338. https://doi.org/10.3897/zookeys.1191.114974
Figure 4 Gyorome guttatum gen. et sp. nov., adult female, paratype A right antennule, ventral view B right antenna C left mandible D right maxillule E right maxilla F left maxilliped, posterior view. Scale bars: 0.1 mm.
Data for: Ecological associations distribution modelling of marine plankton at global scale (2024)
<p>Datasets used to generate and project ADMs.</p> <p><a href="https://gitlab.univ-nantes.fr/combi-ls2n/adm">Click here to access to the git repository</a></p>
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