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FIGURE 3 in A new species of the coral-symbiont crab genus Cymo de Haan, 1833 (Decapoda, Brachyura, Xanthidae) from Nansha Islands, the South China Sea

FIGURE 3. Cymo mazu sp. nov., holotype, male, CW 4.1 mm, CL 3.8 mm, MBM287035: A, carapace; B, front; C, maxilliped 1; D, maxilliped 3; E, pereopod 5; F, large cheliped; G, pleon; H, left G1, ventral view; I, left G1, distal part, ventral view; J, same, dorsal view; K, right G2, ventral view. Scale bar A, E, F = 1 mm, C, D, G = 0.5 mm, H = 0.2 mm, I–K = 0.1 mm.

FIGURE 4 in A new species of the coral-symbiont crab genus Cymo de Haan, 1833 (Decapoda, Brachyura, Xanthidae) from Nansha Islands, the South China Sea

FIGURE 4. Phylogenetic relationships among five species of Cymo based on COI sequences. The BI tree with posterior probabilities and ML bootstrap values labeled (PP/BS).

FIGURE 1 in A new species of the coral-symbiont crab genus Cymo de Haan, 1833 (Decapoda, Brachyura, Xanthidae) from Nansha Islands, the South China Sea

FIGURE 1. Colour in life, Cymo mazu sp. nov., holotype, male, CW 4.1 mm, CL 3.8 mm, MBM287035. Scale bar = 2 mm.

FIGURE 2 in A new species of the coral-symbiont crab genus Cymo de Haan, 1833 (Decapoda, Brachyura, Xanthidae) from Nansha Islands, the South China Sea

FIGURE 2. Cymo mazu sp. nov., holotype, male, CW 4.1 mm, CL 3.8 mm, MBM287035: A, dorsal habitus; B, carapace; C, frontal view; D, thoracic sternites and pleon; E, chelipeds. Scale bar A–C = 2 mm, D–E = 1 mm.

opencc-by-4.0Oct 2022View details →

Raw Data and Scripts used in Regulation of single-cell heterogeneity of capsular polysaccharide synthesis in a human gut symbiont

Raw data used in this publication.  Single-cell analysis of promoter inversions reveals differential inversion rates as a determinant of bacterial population heterogeneity.   Libx.zip contains raw sequencing reads scripts.zip contains code for analysis of reads and growth curve data SequencingRawDataFilesIndex.xls contains a description of all the raw data in each libx.zip.

opencc-by-4.0Nov 2024View details →

Recent genetic drift in the co-diversified gut bacterial symbionts of laboratory mice

Daniel D. Sprockett (1), Brian A. Dillard (1), Abigail A. Landers (2), Jon G. Sanders (1), Andrew H. Moeller (1,2)* 1 Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA 2 Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08540, USA *To whom correspondence should be addressed: andrew.moeller@princeton.edu   Abstract: Laboratory mice (Mus musculus domesticus) harbor gut bacterial strains that are distinct from those of wild mice but whose evolutionary histories are unclear. Understanding the divergence of laboratory-mouse gut microbiota (LGM) from wild-mouse gut microbiota (WGM) is critical, because LGM and WGM have been previously shown to differentially affect mouse immune-cell proliferation, infection resistance, cancer progression, and ability to model drug outcomes for humans. Here, we show that laboratory mice have retained gut bacterial symbiont lineages that diversified in parallel (co-diversified) with rodent species for > 25 million years, but that LGM strains of these ancestral symbionts have experienced accelerated accumulation of genetic load during the past ~ 120 years of captivity. Compared to closely related WGM strains, co-diversified LGM strains displayed significantly faster genome-wide rates of fixation of nonsynonymous mutations, indicating elevated genetic drift, a difference that was absent in non-co-diversified symbiont clades. Competition experiments in germ-free mice further indicated that LGM strains within co-diversified clades displayed significantly reduced fitness in vivo compared to WGM relatives to an extent not observed within non-co-diversified clades. Thus, stochastic processes (e.g., bottlenecks), not natural selection in the laboratory, have been the predominant evolutionary forces underlying divergence of co-diversified symbiont strains between laboratory and wild house mice. Our results show that gut bacterial lineages conserved in diverse rodent species have acquired novel mutational burdens in laboratory mice, providing an evolutionary rationale for restoring laboratory mice with wild gut bacterial strain diversity.

opencc-by-4.0Jul 2024View details →

Defensive symbiont genotype distributions are linked to parasitoid attack networks - Dataset and scripts

This R project includes data and scripts for paper - Defensive symbiont genotype distributions are linked to parasitoid attack networks Script for analysis:     Run all the scripts in order, to get all analyses and results in this paper.      Script_0_package_install_load.R:          Installs and loads the necessary R packages required for all subsequent scripts.         This R project     Script_1_Extract_from_Table_S2.R         Extracts information from:             Table_S2.csv (located in /Rawdata/)    Data_4_Aphid_sequences.fas         Generates 10 files for further analyses:             Aphid relatedness distance:               Aphid_phylogenetic_relatedness_16species.csv               Aphid_phylogenetic_relatedness_22species.csv               Aphid_phylogenetic_relatedness_31species.csv             Hamiltonella - Aphid Matrices:               Hamiltonella_Aphid_matrix_16species.csv               Hamiltonella_Aphid_matrix_22species.csv               Hamiltonella_Aphid_matrix_31species.csv             Parasitoid - Aphid Matrices:               Para_Aphid_matrix_16species.csv               Para_Aphid_matrix_22species.csv             Plant - Aphid Matrices:               Plant_Aphid_matrix_16species.csv               Plant_Aphid_matrix_31species.csv     Script_2_BarPlot_Fig1.R:          Generates Fig. 1 using:              Data_11_Parasitoid_genus_aphid_22_species_Fig.1.csv  Data_12_Plant_genus_aphid_31_species_Fig.1.csv         The bar order in Fig. 1 is arranged by proportion, which is not directly supported in the ggplot2 package in R. Therefore, we need manually reordered if using the first plot code; or, manually colour it using the second plot code.      Script_3_MMRR_analysis.R         Uses 10 distance/distribution matrices of Parasitoid, Plant, Hamiltonella, and Aphid relationships to compute matrix correlations with the MMRR (Multiple Matrix Regression with Randomization) model.     Script_4_Species_linkage_Fig2_FigS4.R         Uses 7 distribution matrices of Parasitoid, Plant, and Hamiltonella relationships with Aphids (excluding Aphid genetic distance matrices) to generate the species linkage diagrams for Fig. 2 and Fig. S4, For aesthetic purposes, unconnected sample points have been moved.     Script_5_MMRR_Fig3_FigS5.R         Plots the MMRR correlations using the 10 distance/distribution matrices for Parasitoid, Plant, Hamiltonella, and Aphid relationships (Fig. 3 & Fig. S5).      Script_6_parasitoid_specialization_Fig4.R         Computes specialization levels using the H2 Index for:             Parasitoid-Aphid             Aphid-Hamiltonella             Parasitoid-Hamiltonella relationships          Generates Figure 4.     Script_7_Ecologicial_indices&plots_Table1_FigS3.R         Uses 7 distribution matrices of Parasitoid, Plant, and Hamiltonella relationships with Aphids (excluding Aphid genetic distance matrices) to:             Calculate ecological indices (Richness, Shannon Index, Simpson Index).             Use linear models to analyze the relationships between Parasitoid/Plant-Aphid and Aphid-Hamiltonella communities.            Outputs results for Table 1 and Figure S3.     Script_8_Bubble_plot_FigS2.R         This script using              Hamiltonella_Aphid_matrix_31species.csv          and two phylogeny trees              Data_8_Aphid_species_phylogeny.txt &              Data_9_Hamiltonella_phylogeny.txt         To create a Cophylogeny tree of Hamiltonella strains and aphid species that we identified in this study and previously known strains. (Fig. S2)     Script_9_DADA2_pipeline.R         This script is the DADA2 pipeline used to processing the raw COI sequencing data into ASV (Amplicon Sequence Variant) count files. After processing, the ASV files required manual curation to link each ASV with a distinct parasitoid and aphid species name based on BLAST results. In our updated version, we have provided both the raw data (BioProject PRJNA1139364) as well as the manually curated files (Data_1 and Data_2) which includes the ASV species names. All subsequent analyses can be reproduced using the curated datasets (Data_1 and Data_2), ensuring clarity and replicability for users.         We have incorporated the SRA Toolkit to streamline the process. This allows users to download raw SRR sequencing files directly and convert them into FASTQ files, which can then be input into the DADA2 pipeline. The pipeline produces two ASV count files, one for each sequencing run.   Raw data and inofrmation:     Table_S2.csv         The Dataset from Supplementary Table S2: After manual pooling the Parasitoid/Aphid species based on the Data_1,2 and 6.             No: the number of this sample             City: The city that collected this sample             Location: the location of sample collection             Sample category: Aphid mummies or alive aphids             Sample code: the name of sample (self defined)             Collection year: when this sample was collected             Aphid taxa / Wasp taxa / Plant species /Hamiltonella strain: The Aphid/Parasitoid/Plant/Hamiltonella species              Sequencing method: Illumina or Sanger sequencing                Sequencing date: the date of sending this sample to sequencing             Data source: From this study or from Wu et al. 2022: Local adaptation to hosts and parasitoids shape Hamiltonella defensa genotypes across aphid species     Data_1_Deep_sequencing_data_block_1.xlsx & Data_2_Deep_sequencing_data_block_2.xlsx          Sample: The sample name from Illumina sequencing, which can later be found on GenBank (BioProject PRJNA1139364).         Aphid: The detected aphid species for each sample.         Parasitoid: The detected parasitoid species.         The remaining columns contain ASV (Amplicon Sequence Variant) data derived from high-throughput barcoding sequencing.         Data1 and Data_2 are the manually curated versions of the BioProject PRJNA1139364 with added species names for each ASV.      Data_3_Parasitoid sequences.fas &      Data_4_Aphid sequences.fas &      Data_5_Hamiltonella sequences.fas,         FASTA files for:             Parasitoid species             Aphid species             Hamiltonella strains         These sequences were used for phylogenetic reconstruction and subsequent analyses.     Data_6_Parasitoid_Aphid_pooled_table.xlsx          Contains the OTU (Operational Taxonomic Unit) manual pooling results for Parasitoid and Aphid species based on 99% (4 base pair) sequence similarity:             Parasitoid pooling together group & Aphid pooling together group: Original names from Illumina sequencing.             Original name: Representative sequences for each group.             Pooled species name: Final species names used in all analyses.             Pooled sequences: Final representative sequences used in all analyses.             The result of manual pooling see the Table_S2.csv     Data_7_Parasitoid_species_phylogeny.txt & Data_8_Aphid_species_phylogeny.txt & Data_9_Hamiltonella_phylogeny.txt          Phylogenetic trees for:             Parasitoid species             Aphid species             Hamiltonella strains         These trees were generated using the PhyML tool on the ATGC Montpellier platform, original fasta file was Data_3, 4 & 5.     Data_10_aphid_host_info.csv          Provides aphid host information for generating Figure 2 and Figure S4:         Aphid: Names of aphid species included in this study.         Host: Host categories:             1: Herb aphids             2: Grass aphids             3: Tree aphids         Host_category: Detailed descriptions of host categories.     Data_11_Parasitoid_genus_aphid_22_species_Fig.1.csv & Data_12_Plant_genus_aphid_31_species_Fig.1.csv          Reduced matrices used for Figure 1, created by merging data from:             OTUs associated with the same parasitoid species.             Plant species belonging to the same genus.     7 Distribution Matrices (from Script_1_Extract_from_Table_S2.R)         Hamiltonella-Aphid Matrices:            Hamiltonella_Aphid_matrix_16species.csv             Hamiltonella_Aphid_matrix_22species.csv             Hamiltonella_Aphid_matrix_31species.csv         Parasitoid-Aphid Matrices:             Para_Aphid_matrix_16species.csv             Para_Aphid_matrix_22species.csv         Plant-Aphid Matrices:             Plant_Aphid_matrix_16species.csv             Plant_Aphid_matrix_31species.csv         Structure:             Rows represent aphid species.             Columns represent Hamiltonella strains, parasitoid species, or host plant species linked to each aphid species.         Usage: These matrices were used to generate Figures 2, 3, 4, Figures S2, S3, S4, S5, and for MMRR tests, ecological indices, and H2 index calculations.     3 Aphid phylogenetic relatedness matrices derived from Script_1_Extract_from_Table_S2.R         Aphid_phylogenetic_relatedness_16species.csv         Aphid_phylogenetic_relatedness_22species.csv         Aphid_phylogenetic_relatedness_31species.csv         These matrices provide phylogenetic distance information, showing pairwise genetic distances between the 31 aphid species included in this study.     SraRunTable.csv         The BioProject (PRJNA1139364) information downloaded directly from Genbank.

embargoedcc-by-4.0May 2024View details →

Marine heatwaves and bleaching impact on a photosynthetic symbiont-bearing nudibranch (Dataset)

Open the record for dataset details and reuse information.

opencc-zeroNov 2021View details →

Strong genotype-by-genotype interactions between aphid-defensive symbionts and parasitoids persist across different biotic environments

The dynamics of coevolution between hosts and parasites are influenced by their genetic interactions. Highly specific interactions, where the outcome of an infection depends on the precise combination of host and parasite genotypes (G × G interactions), have the potential to maintain genetic variation by inducing negative frequency-dependent selection. The importance of this effect also rests on whether such interactions are consistent across different environments or modified by environmental variation (G × G × E interaction). In the black bean aphid, Aphis fabae, resistance to its parasitoid Lysiphlebus fabarum is largely determined by the possession of a heritable bacterial endosymbiont, Hamiltonella defensa, with strong G × G interactions between H. defensa and L. fabarum. A key environmental factor in this system is the host plant on which the aphid feeds. Here, we exposed genetically identical aphids harbouring three different strains of H. defensa to three asexual genotypes of L. fabarum and measured parasitism success on three common host plants of A. fabae, namely Vicia faba, Chenopodium album and Beta vulgaris. As expected, we observed the pervasive G × G interaction between H. defensa and L. fabarum, but despite strong main effects of the host plants on average rates of parasitism, this interaction was not altered significantly by the host plant environment (no G × G × E interaction). The symbiont-conferred specificity of resistance is thus likely to mediate the coevolution of A. fabae and L. fabarum, even when played out across diverse host plants of the aphid.

opencc-zeroNov 2021View details →

More or less? The effect of symbiont density in protective mutualisms

Symbionts can provide hosts with effective protection from natural enemies, but it can sometimes come at a cost. It is unclear to what extent the density of symbionts modulates the cost and benefits of conferred protection. Here we use a meta-analysis of 103 effect sizes from a broad taxonomic range of protective symbioses, to show that the degree of both protection and cost afforded to hosts is a positive function of symbiont density. We found that the effects of symbiont density on protection and cost are robust across ecological contexts. Density-function relationships did not vary with host type, symbiont localization or transmission mode, nor the method of density manipulation. Together, our results suggest symbiont density can be a key variable determining the costs and benefits of a protective interaction.

opencc-zeroDec 2021View details →

Data from: Loss of fungal symbionts at the arid limit of the distribution range in a native Patagonian grass – resource ecophysiological relations

1. Crucial to our understanding of plant ecology is the consideration of the eco-physiological responses and constraints of plant-fungal symbioses throughout the native distribution range of their host. 2. We examined key eco-physiological roles of two co-occurring fungal symbionts [Epichloë endophytes and arbuscular mycorrhizal fungi (AMF)] in the endemic grass Hordeum comosum across a wide bioclimatic gradient and contrasting grazing severity. We sampled H. comosum plants along four humid-to-arid transects in Patagonia, Argentina, covering its entire distribution range and determined Epichloë presence, AMF root colonization, nitrogen and phosphorus concentration, intrinsic water use-efficiency (iWUE, the ratio of photosynthesis to stomatal conductance) and 18O-enrichment of cellulose in shoots. 3. Root colonization by AMF increased with Epichloë-presence. All plants hosted Epichloë in the humid range of the gradient, but symbioses occurrence decreased towards arid sites which also displayed severe grazing symptoms at site level. 4. Symbiosis with Epichloë correlated positively with shoot nitrogen concentration in the centre of the distribution range, and with shoot phosphorus concentration across the entire distribution range. 5. The site-level relationship of AMF colonization with 18O-enrichment and iWUE suggested that mycorrhiza boosted stomatal conductance in humid environments but curbed it in arid environments. 6. While the interpretation of interactions and potential causalities from observational studies should be done with caution, this study demonstrates distinct correlations between plant-fungal symbiont associations and key resource parameters (phosphorus, nitrogen, and iWUE vs 18O-enrichment). Such correlations may suggest particular functional roles for these symbionts in the ecology of their host plant.

opencc-zeroMar 2022View details →

Fluctuating starvation conditions modify host-symbiont relationship between a leaf beetle and its newly identified gregarine species

Gregarines are ubiquitous endosymbionts in invertebrates, including terrestrial insects. However, the biodiversity of gregarines is probably vastly underestimated and the knowledge about their role in shaping fitness-related traits of their host in dependence of fluctuating environmental conditions is limited. Using morphological and molecular analyses, we identified a new gregarine species, Gregarina cochlearium sp. n., in the mustard leaf beetle, Phaedon cochleariae. Applying a full-factorial design, we investigated the effects of a gregarine infection in combination with fluctuating starvation conditions during the larval stage on the development time and fitness-related traits of adult beetles. Under benign environmental conditions, the relationship between gregarines and the host seemed neutral, as host development, body mass, reproduction and survival were not altered by a gregarine infection. However, when additionally exposed to starvation, the combination of gregarine infection and this stress resulted in the lowest reproduction and survival of the host, which points to a parasitic relationship. Furthermore, when the host experienced starvation, the development time was prolonged and the adult females were lighter compared to non-starved individuals, independent of the presence of gregarines. Counting of gregarines in the guts of larvae revealed a lower gregarine load with increasing host body mass under stable food conditions, which indicates a regulation of the gregarine burden in dependence of the host condition. Contrary, in starved individuals the number of gregarines was the highest, hence the already weakened host suffered additionally from a higher gregarine burden. This interactive effect between gregarine infection and fluctuating starvation conditions led to an overall reduced fitness of P. cochleariae. Our study emphasises the need to study endosymbionts as important components of the natural environment and to investigate the role of host-symbiont relationships under fluctuating environmental conditions in an evolutionary and ecological context.

opencc-zeroApr 2022View details →

Intermediate results for: Large differences in carbohydrate degradation and transport potential among lichen fungal symbionts

Lichen symbioses are thought to be stabilized by the transfer of fixed carbon from a photosynthesizing symbiont to a fungus. In other fungal symbioses, carbohydrate subsidies correlate with reductions in plant cell wall-degrading enzymes, but whether this is true of lichen fungal symbionts (LFSs) is unknown. We predicted genes encoding carbohydrate-active enzymes (CAZymes) and sugar transporters in 46 genomes from the Lecanoromycetes, the largest extant clade of LFSs. All LFSs possess a robust CAZyme arsenal including enzymes acting on cellulose and hemicellulose, confirmed by experimental assays. However, the number of genes and predicted functions of CAZymes vary widely, with some fungal symbionts possessing arsenals on par with well-known saprotrophic fungi. These results suggest that stable fungal association with a phototroph does not in itself result in fungal CAZyme loss, and lends support to long-standing hypotheses that some lichens may augment fixed CO2 with carbon from external sources.

opencc-zeroJun 2022View details →

The impacts of host association and perturbation on symbiont fitness

Symbiosis benefits hosts in numerous ways, but much less is known about how host-association affects symbionts. While symbiont fitness can be mediated by host, symbiont, and/or environmental factors, recent works indicate that symbiont performance can depend on whether the symbiont is needed by the host, suggesting that symbiosis is not always beneficial for symbionts. To determine the impact of symbiosis on symbionts across the Tree of Life, we conducted a meta-analysis across 83 unique host-symbiont pairings under a range of spatial and temporal contexts. Specifically, we asked how symbiont fitness is altered outside of symbiosis, when host-symbiont interaction is under suboptimal conditions, or as hosts age. We found that intracellular symbionts associated with protists tend to have greater fitness outside of symbiosis, with the opposite trend for animal hosts. This result suggests that animals may be better at maintaining symbionts. Symbiont fitness also generally increased as hosts grow older. Moreover, symbionts that can proliferate in- and outside host cells performed better than those found exclusively inside or outside cells, suggesting that flexibility in growing location may help symbionts thrive. We discuss these fitness patterns in light of host-driven factors, where hosts exert influence over symbionts to suit their needs.

opencc-by-4.0Jun 2022View details →

Supplementary Tables: Host cellular immunity and nutrition respond to intracellular symbiont abundance in an obligate deep-sea symbiosis

Contains supplementary tables for the pre-print manuscript: Host cellular immunity and nutrition respond to intracellular symbiont abundance in an obligate deep-sea symbiosis

FIGURE 6. Quadrella boopsis Alcock, 1898 in Two new records of the coral symbiont crab genus Quadrella Dana, 1851, from Taiwan, with notes on the taxonomy of Q. boopsis Alcock, 1898 (Crustacea: Brachyura: Trapeziidae)

FIGURE 6. Quadrella boopsis Alcock, 1898, male (5.87 × 5.24 mm) (ZRC 2015.286), Taiwan. A, B, left G1; C, D, distal part of left G1; E, left G2; F, distal part of left G2. Specimens from Taiwan. Scales: A, B, E = 0.5 mm; C, D = 0.1 mm; F = 0.05 mm.

FIGURE 4. Quadrella boopsis Alcock, 1898, Taiwan. A in Two new records of the coral symbiont crab genus Quadrella Dana, 1851, from Taiwan, with notes on the taxonomy of Q. boopsis Alcock, 1898 (Crustacea: Brachyura: Trapeziidae)

FIGURE 4. Quadrella boopsis Alcock, 1898, Taiwan. A, ovigerous female (10.76 × 9.23 mm) (ZRC 2015.287); B–D ovigerous female (13.05 × 11.64 mm) (ZRC 2015.285). A, B, dorsal view of carapace front; C, dorsal view of left cheliped merus; D, dorsal view of right cheliped merus. Specimens from Taiwan.

FIGURE 3. Quadrella boopsis Alcock, 1898 in Two new records of the coral symbiont crab genus Quadrella Dana, 1851, from Taiwan, with notes on the taxonomy of Q. boopsis Alcock, 1898 (Crustacea: Brachyura: Trapeziidae)

FIGURE 3. Quadrella boopsis Alcock, 1898, overall habitus, Taiwan. A, male (5.87 × 5.24 mm) (ZRC 2015.286); B, ovigerous female (10.76 × 9.23 mm) (ZRC 2015.287); C, ovigerous female (13.05 × 11.64 mm) (ZRC 2015.285).

FIGURE 2. Quadrella boopsis Alcock, 1898 in Two new records of the coral symbiont crab genus Quadrella Dana, 1851, from Taiwan, with notes on the taxonomy of Q. boopsis Alcock, 1898 (Crustacea: Brachyura: Trapeziidae)

FIGURE 2. Quadrella boopsis Alcock, 1898, colours in life. A, female (8.32 × 7.44 mm) (NMMBCD); B, ovigerous female (10.76 × 9.23 mm) (NMMBCD); C, female (14.90 × 12.20 mm, with bopyrid) (ZRC 2015.287); D, female (6.05 × 7.05) (ZRC 2015.287); E, ovigerous female (13.05 × 11.64 mm) (ZRC 2015.285); F, male (5.87 × 5.24 mm) (ZRC 2015.286). All specimens from Taiwan.

FIGURE 5. Quadrella boopsis Alcock, 1898. A in Two new records of the coral symbiont crab genus Quadrella Dana, 1851, from Taiwan, with notes on the taxonomy of Q. boopsis Alcock, 1898 (Crustacea: Brachyura: Trapeziidae)

FIGURE 5. Quadrella boopsis Alcock, 1898. A, female (7.15 × 6.40 mm) (NMMBCD 4080); B – F, ovigerous female (10.76 × 9.23 mm) (ZRC 2015.287). A, dorsal view of carapace; B, left third maxilliped; C – F, P 2 – P 5 propodus and dactylus (denuded), respectively. Specimens from Taiwan. Scales = 1.0 mm.