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Fig. 2 in Local ecological and taxonomic knowledge of snapper fish (Teleostei: Actinopterygii) held by fishermen in Ilhéus, Bahia, Brazil

Fig. 2. Similarity dendogram for the morphologic and color criteria used by the interviewed fishermen from Ilhéus, Bahia State, Brazil, to classify the species of the snapper group (number of interviews = 15; for the E. oculatus and P. furcifer n = 7).

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Fig. 3 in Local ecological and taxonomic knowledge of snapper fish (Teleostei: Actinopterygii) held by fishermen in Ilhéus, Bahia, Brazil

Fig. 3. Similarity dendrogram for the species of the snapper group according to the environments in which they are found, according to the perception of the fishermen from Ilhéus, Bahia State, Brazil (number of interviews = 15; for the E. oculatus and P. furcifer n = 7).

Fig. 8 in Ecology and life history of an Amazon floodplain cichlid: the discus fish Symphysodon (Perciformes: Cichlidae)

Fig. 8. Length vs. weight plots for male and female Symphysodon haraldi from a single colony in Uxi Bay, lago Amanã.

Fig. 12 in Ecology and life history of an Amazon floodplain cichlid: the discus fish Symphysodon (Perciformes: Cichlidae)

Fig. 12. Histogram showing size distribution of n = 1271 ovules from a pre-spawning (stage 4) female Symphysodon haraldi. Column bin-intervals are 0.05 mm.

Fig. 9 in Ecology and life history of an Amazon floodplain cichlid: the discus fish Symphysodon (Perciformes: Cichlidae)

Fig. 9. Frequency distribution of the size of Symphysodon haraldi from a single large colony in Uxi Bay, lago Amanã. Column bin-intervals are 3 mm. See Fig. 2 for the timing of sampling in (a) 1998 and (b) 1997. Specimens parasitized with Braga cichlae are excluded. Major modes in the multi-modal distribution of SL are marked with dotted lines and labeled as putative cohort groups (0, 1a, 1b, 2a, 2b, 3, 4) (refer to Fig. 2). Arrows on the x-axis mark the maximum known size of females. X refers to a male specimen marked and released on 20 December 1997 (X1), and recaptured (X2) on 16 November 1998. The overlapping shaded histogram for the 1998 data refers to seven discus captured in adjacent shore scrub. The histograms distributions marked by the beginnings and ends of the dotted triangles for 1a, 1b, and 2 in 1998, and 2a, 2b and 3 in 1997 fit normal distributions (p <0.01, one sample Kolmogorov-Smirnov tests).

Fig. 6 in Ecology and life history of an Amazon floodplain cichlid: the discus fish Symphysodon (Perciformes: Cichlidae)

Fig. 6. Shoreline distance dispersed by 104 tagged Symphysodon haraldi over a 7-9 day period in Uxi Bay, lago Amanã subsequent to release at their original capture site. Each bar represents a 5 m distance range.

Fig. 5 in Ecology and life history of an Amazon floodplain cichlid: the discus fish Symphysodon (Perciformes: Cichlidae)

Fig. 5. Seasonal changes in the proportional composition of food items within stomachs of Symphysodon haraldi from blackwater habitats of the Tefé region. Calculations of mean food item contribution excluded specimens with empty stom- achs. Error bars (displayed above bars) refer to one standard deviation from mean. Algae = periphyton identified as a mass of bright green filamentous structures. FOD = Fine organic detritus. GPM = green plant (macrophytes) matter – apparently mostly small triturated pieces of leaves. Periphyton, FOD and GPM were difficult to separate volumetrically, and are there- fore combined into a single category. GPM represented only a small portion of the volume of this category (perhaps less than 15%). COD = Coarse organic detritus – mainly pieces of wood and bark.

Fig. 11 in Ecology and life history of an Amazon floodplain cichlid: the discus fish Symphysodon (Perciformes: Cichlidae)

Fig. 11. Reproductive status and sex of putative (a) 1+ and (b) 2+ cohort members Symphysodon haraldi from a single large discus colony in Uxi Bay, lago Amanã, 1998. Only specimens that were dissected for sex determination are included. The single 1+ specimen with a stage 4 gonad is illustrated in Fig. 12c.

Fig. 1. NASDA JERS-1 in Ecology and life history of an Amazon floodplain cichlid: the discus fish Symphysodon (Perciformes: Cichlidae)

Fig. 1. NASDA JERS-1 radar image of the Tefé region, Brazil: (a) high water (May 1995); (b) low water (September 1995). Flooded forests appear white, illustrating the maximum extent of the seasonal flooding. The area between the dotted lines is whitewater floodplain. R. Solimões is the local name for the Amazon River. Discus occur in the following habitats: 1, blackwater flooded forest (igapó), 2, blackwater lakes, 3, whitewater flooded forest, 4, whitewater floodplain lakes. Study are marked A (Uxi Bay) and B (lago Urini). Inset (c) shows Uxi Bay from Landsat TM-5 image, 1998. Here, the white dot represents the locality of a large discus colony and the line X-Y refer to the cross-sectional schematic (d). In (d) the dotted horizontal line represents the water level at the beginning of 1998 samples. The 4 m water-level (see also Fig. 2) marks the lower levels of shore scrub growing on beaches and sand bars. Shore scrub is dominated by Coccoloba ovata Benth. and Symmeria paniculata Benth. (Polygonaceae).

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Species ecology explains the various spatial components of genetic diversity in tropical reef fishes

<p>Generating genomic data for 19 tropical reef fish species of the Western Indian Ocean, we investigate how species ecology influences genetic diver- sity patterns from local to regional scales. We distinguish between the α, β and γ components of genetic diversity, which we subsequently link to six ecological traits. We find that the α and γ components of genetic diversity are strongly correlated so that species with a high total regional genetic diversity display systematically high local diversity. The α and γ diversity components are negatively associated with species abundance recorded using underwater visual surveys and positively with body size. Pelagic larval duration is found to be negatively related to genetic β diversity supporting its role as a dispersal trait in marine fishes. Deviation from the neutral theory of molecular evolution motivates further effort to understand the processes shaping genetic diversity and ultimately the diversification of the exceptional diversity of tropical reef fishes.</p>

Fig. 8 in Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species

Fig. 8 | Total microbial diversity across vertebrate hindguts and within multi- plebodysites of fish. a Hindgutmicrobiotasamplesfrom 569 speciesof vertebrates were rarified to 5000 reads and unique or shared ASVs determined for each class. b The percentage of unique ASVs only found in a given class (not shared in other classes) as compared to the total ASVs within that class. c Rarefaction of cumulative gamma diversity as a function of unique vertebrate species. Included is a single fish species, S. japonicus, sampled over 3 years "black dots" and the unrarefied FMP samples which had detectable bacteria in all four body sites (gill, skin, midgut, and hindgut).d Gammadiversity of 68 fishspeciesacrossfour bodysites.e Percentageof unique ASVs associatedwitha given bodysiteacrossthe 68 fish species.f Rarefaction curve of increasing gamma diversity (inclusive of four body sites) as a function of increasing fish species. ASV amplified sequence variant, 5k 5000.

Fig. 7 in Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species

Fig. 7 | Microbial source tracking analysis. a Microbial sources of 60 sea water (blue circle) samples taken from 30 unique sampling stations from two timepoints are distributed on a 10 km transect from Torrey Pines beach to Mission Bay. Microbial sources of 108 marine sediment samples (red stars) from San Diego coastalenvironmentincludes 60 paired samples (samelocationsas seawater) from the same 10 km transect along with 58 samples from the various reef habitats near La Jolla. Geographic data presented using ArcGIS. b Sourcetracker2 analysis of likely sources for the four body sites of the fish comparing contributions of beach sand, marine sediment, sea water, and "unknown". Unknown refers to microbes from an unknown source which could include diet and other animals or locations not sampled. c Specific microbial contributions of sea water to the four mucosal body sites and d specific microbial contributions of marine sediment to the four mucosalbodysites b–d: distributionisin medianand interquartilerange.Statistical differences determined using non-parametrictesting Kruskal–Wallistest with 0.05 FDR Benjamini–Hochberg. e Proportion of microbes (distribution is in median and interquartile range) likely originating from the sea water vs. sediment for each unique body site (sea water vs. sediment pairwise comparison for each body site using Mann–Whitney test p <0.05).f Spearmanrho valuesfromcomparisons ofthe ratio of sea water "SW" and marine sediment "SED" against various continuous fish life history metadata variables for each unique body site (Spearman correlation p <0.05). g Comparison of the SW:SED ratios across the habitats from which the fish live. Comparisons performed on each unique body site (Kruskal–Wallis test, p <0.05). *p <0.05, **p <0.01, ***p <0.001, ****p <0.0001, ASV amplified sequence variant ~unique sub-Operational Taxonomic Unit, SD standard deviation, MG midgut, HG hindgut, KW Kruskal–Wallis test statistic "H", IQR inter quartile range, SW sea water.

Fig. 5 in Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species

Fig. 5 | Biological and life history drivers of mucosal microbiota in diverse sampling of marine fish from Southern California. a Multivariate analysis of biological and life history parameters evaluated using unweighted and weighted normalized UniFrac distances. Statistical significance (PERMANOVA p = 0.001) indicated by yellow blocks (left) and effect size (right). All samples compared together (all) along with individual sample types (gill, skin, midgut, hindgut). b Impact of trophic level on similarity between midgut and hindgut (within a species) (linear model:p p value, mslope,dottedlinesare 95% confidence interval). F-Stat test statistic used in PERMANOVA analysis, all row names in a are metadata column names used in the analysis, MG midgut, HG hindgut, Gen. Weighted UniFrac generalized weighted UniFrac.

Fig. 6 in Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species

Fig. 6 | Evidence forphylosymbiosis across fishbody sites. Effectof evolutionary distance (low divergence time indicates a short branch length or similar fish species) of all fish compared to a skin unweighted UniFrac distance, b gill generalized weighted UniFrac distance, c hindgut generalized weighted UniFrac distance. Comparisons performed using Mantel test with multiple testing by FDR. Divergence time between fish species calculated using timetree.org. Gen. Weighted UniFrac generalized weighted UniFrac.

Fig. 3 in Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species

Fig. 3 | Alpha diversity and biomass comparisons across ecological and biolo- gical gradients in marine fish. Comparison of microbial diversity a "Chao1", b "Faith's Phylogenetic Diversity", c "Shannon", or d microbial biomassacrossbody site (gill, skin, midgut, and hindgut). Distributions in "red" are median with inter- quartile range. Statistical differences determined using non-parametric testing Kruskal–Wallistest with 0.05 FDR Benjamini–Hochberg. Further testing computed for each unique body site for a variety of biological and ecological metadata categories. Metadata whichis e categorical istestedusing Kruskal–Wallis f whereas numeric metadata tested using Spearmancorrelation. Onlysignificant associations are represented in e (Kruskal–Wallis p <0.05) and f (Spearman p <0.05). KW or KW stat "H" test statistic from Kruskal–Wallis test, MG midgut, HG hindgut, Faith PD Faith's Phylogenetic Diversity metric, GI:TL gastrointestinal length to fish total length "ratio", TL total length of fish.

Fig. 4 in Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species

Fig. 4 | Associations between fishmass and collection location as measuredby and d distance from shore with gill microbial biomass. e Comparison of fish mass distancefrom shorewith fishgill microbialbiomassand alphadiversity. Subset and f distancefromshorewithalpha diversitymetrics (Chao1).g Comparison of fish of fish from EPO and Atlantic (n = 54) collected from ocean (excludes bay and mass and h distance from shore with alpha diversity metric: Faith's PD. estuary samples) and from the neritic zone (<200 m depth). a Correlation matrix c–h (Confidenceintervalsof 95% aredisplayedasdotted lines). habita- between sample metadata where values are rho and significance indicated by t_act_collection refers to the metadata column name from where this habitat clas- *p <0.05, **p <0.01, ***p <0.001, ****p <0.0001 (Spearmancorrelation). sification can be found…, SZsurf zone, RIT rocky intertidal, RST rocky subtidal, IS b Comparison of gill microbial biomass (log cells per gram) across habitat types inner shelf, KBRF kelp bed rocky reef, MDRF mid depth rocky reef, CP coastal from which the fish were collected. Distribution is in median and interquartile pelagic, P pelagic. Mass_g_log = log 10 (mass of the fish in grams), dis- range. Statistical differences determined using non-parametric testing tance_from_shore_m_log = log 10 (distance from nearest point on shore in meters Kruskal–Wallistest with 0.05 FDRBenjamini–Hochberg. c Comparison of fish mass from where the fish was caught).

Fig. 2 in Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species

Fig. 2 | Limit of detection, sample exclusion, and microbial biomassestimation for FMP101 dataset. a Application of KatharoSeq formula to calculate limit of detection of microbiota platesusing the Bacillus/Paracoccus mock community (1150 reads at 90%). b Limit of detection based on cell counts of Bacillus/ Paracoccus mock community (~16 cells into extraction at 90%). c Model fit of the log(sequencing read counts) of positive extraction controls vs. the log cell counts of those positive extraction controls (empirically determined using plate counts. The linear regression of the line is indicative of the quality of method to estimate microbial biomass from sequencing read counts. Con- fidenceintervalsof 95% aredisplayedas dottedlines. Thismethodissimilar to a qPCR curvewherethe log (Ct) would beequivalent to the log(read counts).This equation is then used to estimate the number of "microbial density" of the existing samples which is then further normalized by the volume of the DNA extraction,biomass of materialgoinginto theextraction and finallynormalized to at estimated microbial cells per gram of tissue. d Community analysis comparison and validation of compositionality of controls of twosets of mock community controls (section 1 = Bacillus/Paracoccus mock community; section 2 = zymo mock community). Putative contaminant g__Geobacillus identified (presentin 93% of negatives and higherrelative abundance ascompared to positives and samples). e Number of samples successful across the four body sites collected from the broad fish microbiota dataset. QC quality control, g__ refers to a genus of bacteria, HM mock homemade mock or human made mixture of bacteria to use as a control whereas zymo mock = mock microbial community created by a company "Zymo".

Fig. 1 in Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species

Fig. 1 | Samplingdesignof 116 speciesof marine fish. a Using ArcGIS todepictthe general area from which fish were sampled: black dots indicate the locations of the 101 unique species of marine fish sampled from the California Current Ecosystem in the Eastern Pacific Ocean primarily in the waters of San Diego CA. Red circles depict the locations of an additional 17 species of fish (15 unique species with 2 species duplicates) collected from the Western Atlantic primarily in the waters of New York. When multiple species of fish were caught in the same location, a single circle is used to indicate the location. b Fish were sampled across a gradient of depth and distances from shore. c Biometric measurements taken for nearly all fish include total length, fork length, mass, gape, and GI length. Various ratios from these lengths were also calculated. Microbiota samples from the gill were primarily whole tissue specimens from the entire left second gill arch or a section of the top middle and bottom of the entire filament. Skin mucus samples were taken by scraping using a razor blade. Midgut digesta material was collected from directly posterior of the stomach or if stomach was absent, the beginning of the GI tract. Hindgut digesta samples were taken from near the anus. Image from phylopic. MG midgut, HG hindgut, GI gastrointestinal tract, m meters.

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Figure 5 in A review of amphidromous freshwater fishes of the Chocó biogeographical region (Colombia and Ecuador): diversity, ecology, fisheries and conservation

Figure 5. – Representative habitat of freshwater amphidromous fishes in western of Colombia. A: photo of Valle River, 20 m collection site; B: Photo of Aguaclara River (Anchicayá Basin), 70 m collection site; C: Representative habitat in which post-larval Awaous transandeanus, Hemieleotris latifasciata, Hemieleotris levis and Sicydium spp. were collected in western Colombia. Photo of San Juan River, 18 m collection site; D: Type locality of Sicydium hildebrandi, photo of Dagua River in Cisneros, 350 m collection site.