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Supplementary material 2 from: Alter SE, Arroyave J (2022) Environmental DNA metabarcoding is a promising method for assaying fish diversity in cenotes of the Yucatán Peninsula, Mexico. Metabarcoding and Metagenomics 6: e89857. https://doi.org/10.3897/mbmg.6.89857
OTU (Operational Taxonomic Unit) table
Supplementary material 1 from: Alter SE, Arroyave J (2022) Environmental DNA metabarcoding is a promising method for assaying fish diversity in cenotes of the Yucatán Peninsula, Mexico. Metabarcoding and Metagenomics 6: e89857. https://doi.org/10.3897/mbmg.6.89857
Summary results from initial eDNA raw data processing
Freshwater fishes dataset–Fish diversity of post-conflict Colombian Andes-Amazon streams
Open the record for dataset details and reuse information.
Figure 38 in Diversity, distribution and community composition of fish in perialpine lakes – "Projet Lac" synthesis report
Figure 38: Examples of Scardinius spp caught in Projet Lac. Upper panel are northern S. erythrophthalmus caught in their native lakes. Upper middle panel are southern S. hesperidicus from their native southern perialpine lakes. Lower middle panel are S. hesperidicus from northern perialpine lakes. Bottom panel are a phenotypic hybrid from Chalain and a backcross hybrid from Zurich, i.e. a phenotypic S. erythrophthalmus that carried S. hesperidicus mitochondrial DNA. * indicates that the identity was confirmed by DNA barcoding.
Figure 61 in Diversity, distribution and community composition of fish in perialpine lakes – "Projet Lac" synthesis report
Figure 61: Two gillnet protocols used to sample all major lake habitats. The European standard, also called the CEN protocol, uses separate, horizontally-oriented nets to sample the benthic and pelagic zones. The vertical protocol uses columns of nets that simultaneously sample the fish community from the surface to the lake floor.
Figure 52 in Diversity, distribution and community composition of fish in perialpine lakes – "Projet Lac" synthesis report
Figure 52: Stickleback were dramatically larger in Upper Lake Constance compared to other lakes. Length frequency distribution of all Gasterosteus spp caught in Projet Lac. Scaled photos on the right show one of the larger individuals from each lake.
Figure 40 in Diversity, distribution and community composition of fish in perialpine lakes – "Projet Lac" synthesis report
Figure 40: The three different Phoxinus species recorded in Projet Lac. P. septimaniae from lakes Chalain and Poschiavo. P. csikii from lakes Thun, Lucerne, Walen. P. lumaireul from Lake Garda.
Figure 31 in Diversity, distribution and community composition of fish in perialpine lakes – "Projet Lac" synthesis report
Figure 31: Four adult Gobio caught in Upper Lake Constance in the same electrofishing action near the mouth of the Rhein-
Figure 30 in Diversity, distribution and community composition of fish in perialpine lakes – "Projet Lac" synthesis report
Figure 30: Underwater image of a fish very likely to be Rutilus pigus in Lake Maggiore. The photo was taken during Projet Lac sampling. The fish was mixed into a shoal of Rutilus rutilus, several individuals of which can be seen in the background.
Figure 31 in Diversity, distribution and community composition of fish in perialpine lakes – "Projet Lac" synthesis report
Figure 31: Four adult Gobio caught in Upper Lake Constance in the same electrofishing action near the mouth of the Rhein- taler Binnenkanal. Genetic barcoding revealed that two individuals had the mitochondrial DNA of Gobio gobio (upper) and two of Gobio obtusirostris (lower).
Figure 25 in Diversity, distribution and community composition of fish in perialpine lakes – "Projet Lac" synthesis report
Figure 25: Left panel compares the "uniqueness" of the fish community to the number of native species to reveal outlier lakes with particularly "unique" fish assemblages for their size (lakes above the dashed line). Sils and Poschiavo were severe outliers and were excluded from estimation of the fitline and calculation of residuals. Sils was the only lake surveyed in the Danube catchment and Poschiavo was the only high-altitude lake surveyed in the Po catchment. Hence they shared few of their species with other lakes. Right panel shows that the uniqueness of the lake fish community relative to the number of recorded native fish species (i.e. residuals from the relationship in the left panel) decreased with the maximum total phosphorus that had been measured in the lake in the past (R2 = 0.248, p = 0.013). Relationships of the residuals with other lake characteristics (lake surface area, lake maximum depth, present-day phosphorus) were not significant (Figure 83).
Figure 4 in Diversity, distribution and community composition of fish in perialpine lakes – "Projet Lac" synthesis report
Figure 4: Estimate of phylogenetic relationships based on COI sequence variation between fish species caught in Projet Lac: endemic species, species native in at least some surveyed lakes, species non-native in some lakes, exotic species.
Figure 13 in Diversity, distribution and community composition of fish in perialpine lakes – "Projet Lac" synthesis report
Figure 13: Species-area relationships for lakes in the Rhine catchment when, additionally to the species recorded in Projet Lac, all known recently extant, and all known extinct and locally extirpated species are included. Left panel: dark green = native species, but each species radiatation only counted as one taxon, medium green = all native species, i.e. counting each radiation species separately, light green = endemic species only. Right panel: black = total number of present-day fish species (species recorded in Projet Lac, plus other species recorded in the lake in other recent surveys), orange = non-native and exotic species (species recorded in Projet Lac, plus other species recorded in the lake in other recent surveys but excluding species that have failed to establish self-sustaining populations), red = extinct and extirpated native species. Regression statistics are provided in Table 9.
Figure 18 in Diversity, distribution and community composition of fish in perialpine lakes – "Projet Lac" synthesis report
Figure 18: Zone of low oxygen in Lower Lake Zurich has been increasing in severity and vertical extent since around 1990, offsetting gains of oxygenated deepwater habitat that would otherwise be associated with the reduction of eutrophication. Severe hypoxia also occurred between 1940 and 1960 and is believed to be caused by a combination of elevated nutrients and inverse stratification in winter during this period [50]. Isobars for dissolved oxygen concentrations of 1 and 4 mg/L are indicated. Data source: Canton Zurich, Amt für Abfall, Wasser, Energie und Luft (AWEL) and Wasserversorgung Zurich. Black bars on the right side: depth distribution of Projet Lac fish catches by abundance (net per unit effort catch).
Species traits and CWM data: Recent warming causes functional borealization and diversity loss in deep fish communities east of Greenland
<p>Aim: We asessed whether functional turnover in east Greenland fish driven by increased occurrence of boreal species compensates for the climate-driven loss of species thereby maintaining functional diversity and ecological function.</p> <p>Location: The study region encompasses a shelf and slope area located offshore between 63° N and 66° N, east of Greenland.</p> <p>Methods: We investigated spatio-temporal changes in fish communities based on a unique dataset covering a depth range of 1500m over 18 years combined with a demersal fish trait dataset. We analyzed the species by trait matrix using principal component analysis (PCA). To investigate trait patterns across the communities (sites), community weighted mean (CWM) traits were calculated and analysed using PCA. The CWM traits matrix was further analysed by redundancy analysis (RDA) with depth-strata and year as explanatory variables.</p> <p>Results: We found signs of a taxonomic and functional borealization, associated with a loss in functional diversity, down to 1000m, characterized by an increase in mobile generalists, and a decrease in bottom dwelling benthivores. The functional turnover brought about by boreal species was not sufficient to compensate for the loss of Arctic species traits, hence the loss in functional diversity.</p> <p>Main conclusions: The functional turnover brought about by boreal species was not sufficient to compensate for the loss of Arctic species traits that may negatively affect ecosystem robustness to environmental change. These observations are most likely not unique to this study area, and calls for the inclusion of the deep sea in climate adaptation of management strategies.</p>
Supplementary material 1 from: Chen X, Wang M, Zhang E (2022) Updated species checklist of fishes from Lake Dongting in Hunan Province, South China: Species diversity and conservation. ZooKeys 1108: 51-88. https://doi.org/10.3897/zookeys.1108.79960
Table S1
Fig 3 in Helminth Diversity In Teleost Fishes From The South Orkney Islands Region, West Antarctica
Fig 3. Cluster analysis of the similarity between the helminth communities of the shallow-water (SW) and deepwater (DW) populations of fish species determined by the Bray-Curtis index.
Break-through fish diversity and locations
<p>Aim: While marine debris is entering the ocean at unprecedented rates, little is known about how biological communities engage with this introduced substrate. This study analyzes the community composition of debris-associated fishes and explores the role of plastics in transferring fish across biogeographic barriers.</p> <p>Location: Pacific Ocean, including North Pacific Garbage Patch.</p> <p>Results: Fish communities around marine debris have low diversity, individual debris items have highly dissimilar species compositions, and species composition is affected by horizontal debris item size. Debris items in Group I have significantly higher fish species diversity and differ in community composition from Group II. We observed four species (<em>Abudefduf vaigiensis, Histrio histrio, Oplegnathus punctatus, and Petroscirtes spp.</em>) surviving east of the Hawaiian Islands, where they have not been previously reported. While we have not yet detected juveniles of these "break through" species east of the Islands, the earlier transport by debris of <em>A. vaigiensis</em> and <em>H. histrio</em> to Hawaii in the 1990s and their subsequent successful establishment there suggest that these Indo-Pacific fish have found hospitable thermal regimes east of the Hawaiian Islands matching their original reproductive ranges.</p> <p>Main conclusion: We suggest that marine debris acts as a mechanism for fish to cross biogeographic barriers, such as the Eastern Pacific Barrier. While natural flotsam has long been a potential vector, long-lived and increasingly abundant plastic debris may set the stage for altering fish biogeography.</p>
Supplementary material 2 from: Li Y, Evans NT, Renshaw MA, Jerde CL, Olds BP, Shogren AJ, Deiner K, Lodge DM, Lamberti GA, Pfrender ME (2018) Estimating fish alpha- and beta-diversity along a small stream with environmental DNA metabarcoding. Metabarcoding and Metagenomics 2: e24262. https://doi.org/10.3897/mbmg.2.24262
GPS and environmental variables of each site. :
Supplementary material 1 from: Li Y, Evans NT, Renshaw MA, Jerde CL, Olds BP, Shogren AJ, Deiner K, Lodge DM, Lamberti GA, Pfrender ME (2018) Estimating fish alpha- and beta-diversity along a small stream with environmental DNA metabarcoding. Metabarcoding and Metagenomics 2: e24262. https://doi.org/10.3897/mbmg.2.24262
Control samples that were used to test for contamination during each step of the experiment. :
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