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Fig. 10 in Defining the reproductive period of freshwater fish species using the Gonadosomatic Index: a proposed protocol applied to ten species of the Patos Lagoon basin
Fig. 10. Monthly variation of Trachelyopterus lucenai GSI values (adult females only) in Guaíba Lake (white) and Casamento Lake (dark gray), Rio Grande do Sul, Brazil (median, 25-75% quartiles and lower-upper GSI limits by month and site). Three GSI cut-off values were tested with respect to the maximum GSI recorded for each species, for delimitation of reproductive months: 20% (G20), 30% (G30) and 40% (G40).
Fig. 4 in Defining the reproductive period of freshwater fish species using the Gonadosomatic Index: a proposed protocol applied to ten species of the Patos Lagoon basin
Fig. 4. Monthly variation of Hoplias malabaricus GSI values (adult females only) in Guaíba Lake (white) and Casamento Lake (dark gray), Rio Grande do Sul, Brazil (median, 25-75% quartiles and lower-upper GSI limits by month and site). Three GSI cut-off values were tested with respect to the maximum GSI recorded for each species, for delimitation of reproductive months: 20% (G20), 30% (G30) and 40% (G40).
Multi-species models reveal that eDNA metabarcoding is more sensitive than backpack electrofishing for conducting fish surveys in freshwater streams
Environmental DNA (eDNA) sampling can provide accurate, cost-effective, landscape-level data on species distributions. Previous studies have compared the sensitivity of eDNA sampling to traditional sampling methods for single species, but similar comparative studies on multi-species eDNA metabarcoding are rare. Using hierarchical species occupancy-detection models, we examined whether key choices associated with eDNA metabarcoding (primer selection, low-abundance read filtering, and the number of positive water samples used to classify a species as present at a site) affect the sensitivity of metabarcoding, relative to backpack electrofishing for fish in freshwater streams. Under all scenarios (teleostei and vertebrate primers; 0%, 0.1% and 1% read filtering thresholds; 1 or 2 positive samples required to classify species as present), we found that eDNA metabarcoding is, on average, more sensitive than electrofishing. Combining vertebrate and teleostei markers resulted in higher detection probabilities relative to the use of either marker in isolation. Increasing the threshold used to filter low abundance reads decreased species detection probabilities but did not change our overall finding that eDNA metabarcoding was more sensitive than electrofishing. Using a threshold of two positive water samples (out of 5) to classify a species as present typically had negligible effects on detection probabilities compared to using one positive water sample. Our findings demonstrate that eDNA metabarcoding is generally more sensitive than electrofishing for conducting fish surveys in freshwater streams, and that this outcome is not sensitive to methodological decisions associated with metabarcoding.
Capacity for freshwater acclimation and differences in the transcription of ion transporter genes underlying different migratory life histories of Takifugu fish
<p>The genus<i> Takifugu </i>is a group of approximately 20 species of puffer fishes living in a wide range of salinity environments around East Asian countries. This group presents a broad spectrum of evolutionary stages adapted to anadromy as a result of speciation that occurred a short time (2–5 million years) ago on an evolutionary timescale. This group thus can be considered as a model for studying the evolutionary mechanisms of anadromy. We firstly conducted a transfer experiment from seawater to low-salinity waters on five <i>Takifugu</i> species: two anadromous species <i>T. obscurus</i> and <i>T. ocellatus</i>, two euryhaline wanderer marine species <i>T. rubripes</i> and <i>T. niphobles</i>, and a strictly marine species <i>T. snyderi</i>,<i> </i>and confirmed that the capacity for acclimation to hypotonic environments was associated with their life history strategies. Next, transcriptomes of the gill and intestine of these species in hypotonic condition were compared to those under hypertonic condition for each species using RNA-Sequencing so as to determine possible candidate transporters playing an important role on freshwater adaptation. As this analysis suggested that <i>cftr</i>, encoding an important ion transporter for seawater acclimation in the gill, and <i>ncc</i>, encoding a transporter that is suggested to play important osmoregulatory roles in the intestine, are important candidates, their expression was validated by quantitative real-time PCR analysis. Expression of<i> cftr</i> was downregulated in the gills of the four euryhaline species under the hypotonic condition, but no change was detected in the gill of stenohaline <i>T. snyderi</i>, which may be one reason for the poor hypotonic acclimation capacity of <i>T. snyderi</i>. Expression of <i>ncc</i> was clearly upregulated in the intestines of the two anadromous species under the hypotonic condition, but not in other three species.<b> </b>Different ion transporter expression patterns between the five species indicate that the transcriptional regulation of <i>cftr</i> in the gill and <i>ncc</i> in the intestine may be important for the improvement of hypotonic acclimation capacity and evolution of anadromy in the <i>Takifugu</i> species.</p>
Figure 2 from: Wang I-C, Lin H-D, Liang C-M, Huang C-C, Wang R-D, Yang J-Q, Wang W-K (2020) Complete mitochondrial genome of the freshwater fish Onychostoma lepturum (Teleostei, Cyprinidae): genome characterization and phylogenetic analysis. ZooKeys 1005: 57-72. https://doi.org/10.3897/zookeys.1005.57592
Figure 2 Comparison of codon usage in mitochondrial genomes of Onychostoma lepturuma Relative synonymous codon usage (RSCU) in the Onychostoma lepturum mitogenome. Codon families are provided on the X-axis, and the RSCU values, on the Y-axis b Codon distribution in the Onychostoma lepturum mitogenome. CDspT, codons per thousand codons. Codon families are provided on the X-axis.
Figure 1 from: Wang I-C, Lin H-D, Liang C-M, Huang C-C, Wang R-D, Yang J-Q, Wang W-K (2020) Complete mitochondrial genome of the freshwater fish Onychostoma lepturum (Teleostei, Cyprinidae): genome characterization and phylogenetic analysis. ZooKeys 1005: 57-72. https://doi.org/10.3897/zookeys.1005.57592
Figure 1 Gene map of the mitochondrial genome of Onychostoma lepturum. Two rRNA genes (in red); 13 coding genes (in green); 22 tRNA genes and control region (D-loop) (in yellow). (Color figure online).
Supplementary material 1 from: Wang I-C, Lin H-D, Liang C-M, Huang C-C, Wang R-D, Yang J-Q, Wang W-K (2020) Complete mitochondrial genome of the freshwater fish Onychostoma lepturum (Teleostei, Cyprinidae): genome characterization and phylogenetic analysis. ZooKeys 1005: 57-72. https://doi.org/10.3897/zookeys.1005.57592
Table S1
Figure 3 from: Wang I-C, Lin H-D, Liang C-M, Huang C-C, Wang R-D, Yang J-Q, Wang W-K (2020) Complete mitochondrial genome of the freshwater fish Onychostoma lepturum (Teleostei, Cyprinidae): genome characterization and phylogenetic analysis. ZooKeys 1005: 57-72. https://doi.org/10.3897/zookeys.1005.57592
Figure 3 Phylogenetic trees derived from Maximum-Likelihood (ML) and Neighbor Joining (NJ) approaches based on whole mitochondrial genomes. The numbers on the nodes are the bootstrap values of ML/NJ. The number after the species name is the GenBank Accession Number.
Adaptation to herbivory and detritivory drives the convergent evolution of large abdominal cavities in a diverse freshwater fish radiation (Otophysi: Characiformes)
<p>Convergent evolution is often interpreted as evidence of natural selection favoring an optimal phenotype during adaptation. Morphological convergence is frequently found among lineages that converge on diet, but most studies have focused on morphological traits that relate exclusively to food handling and processing. In vertebrates, there is a strong inverse relationship between intestine length and trophic level. However, little is known about whether adaptation to a low trophic level influences the evolution of abdominal cavities that can accommodate larger intestines. Here, I reconstruct the evolutionary history of trophic ecology and examine abdominal cavity shape across 157 species of the fish order Characiformes to determine whether adaptation to an herbivorous-detritivorous diet drives convergent evolution of large abdominal cavities. Herbivorous-detritivorous species evolved significantly larger abdominal cavities than other trophic groups and repeatedly converged on a similar abdominal cavity morphology. Other trophic groups evolved abdominal cavity morphologies either stochastically or by selective pressures from an untested ecological character. These findings demonstrate that the selective demands of a larger intestinal tract promote the repeated convergence of a large abdominal cavity within herbivorous-detritivorous characiform fishes, while allowing other lineages to evolve randomly or adapt in response to other selection pressures, contributing to the overall body shape diversity of the order.</p>
FIGURE 2 in Freshwater fishes from Paraná State, Brazil: an annotated list, with comments on biogeographic patterns, threats, and future perspectives
FIGURE 2. Specific richness in freshwater fish species by orders in the Paraná State, Brazil.
Supplementary material 3 from: Manjarrés-Hernández A, Guisande C, García-Roselló E, Heine J, Pelayo-Villamil P, Pérez-Costas E, González-Vilas L, González-Dacosta J, R. Duque S, Granado-Lorencio C, Lobo JM (2021) Predicting the effects of climate change on future freshwater fish diversity at global scale. Nature Conservation 43: 1-24. https://doi.org/10.3897/natureconservation.43.58997
Appendix 2
Supplementary material 4 from: Manjarrés-Hernández A, Guisande C, García-Roselló E, Heine J, Pelayo-Villamil P, Pérez-Costas E, González-Vilas L, González-Dacosta J, R. Duque S, Granado-Lorencio C, Lobo JM (2021) Predicting the effects of climate change on future freshwater fish diversity at global scale. Nature Conservation 43: 1-24. https://doi.org/10.3897/natureconservation.43.58997
Appendix 3
Supplementary material 1 from: Manjarrés-Hernández A, Guisande C, García-Roselló E, Heine J, Pelayo-Villamil P, Pérez-Costas E, González-Vilas L, González-Dacosta J, R. Duque S, Granado-Lorencio C, Lobo JM (2021) Predicting the effects of climate change on future freshwater fish diversity at global scale. Nature Conservation 43: 1-24. https://doi.org/10.3897/natureconservation.43.58997
Appendix 1
Supplementary material 2 from: Manjarrés-Hernández A, Guisande C, García-Roselló E, Heine J, Pelayo-Villamil P, Pérez-Costas E, González-Vilas L, González-Dacosta J, R. Duque S, Granado-Lorencio C, Lobo JM (2021) Predicting the effects of climate change on future freshwater fish diversity at global scale. Nature Conservation 43: 1-24. https://doi.org/10.3897/natureconservation.43.58997
Table S1
Data from: Shape up or ship out: migratory behaviour predicts morphology across spatial scale in a freshwater fish
1. Migration is a widespread phenomenon, with powerful ecological and evolutionary consequences. Morphological adaptations to reduce the energetic costs associated with migratory transport are commonly documented for migratory species. However, few studies have investigated whether variation in body morphology can be explained by variation in migratory strategy within a species. 2. We address this question in roach Rutilus rutilus, a partially migratory freshwater fish that migrates from lakes into streams during winter. We both compare body shape between populations that differ in migratory opportunity (open vs. closed lakes), and between individuals from a single population that vary in migratory propensity (migrants and residents from a partially migratory population). Following hydrodynamic theory, we posit that migrants should have a more shallow body depth, to reduce the costs associated with migrating into streams with higher flow conditions than the lakes the residents occupy all year round. 3. We find evidence both across and within populations to support our prediction, with individuals from open lakes and migrants from the partially migratory population having a more slender, shallow-bodied morphology than fish from closed lakes and all-year residents. 4. Our data suggest that a shallow body morphology is beneficial to migratory individuals and our study is one of the first to link migratory strategy and intraspecific variation in body shape.
Data from: Molecular diversity of Germany's freshwater fishes and lampreys assessed by DNA barcoding
This study represents the first comprehensive molecular assessment of freshwater fishes and lampreys from Germany. We analysed COI sequences for almost 80% of the species mentioned in the current German Red List. In total, 1056 DNA barcodes belonging to 92 species from all major drainages were used to (i) build a reliable DNA barcode reference library, (ii) test for phylogeographic patterns, (iii) check for the presence of barcode gaps between species and (iv) evaluate the performance of the barcode index number (BIN) system, available on the Barcode of Life Data Systems. For over 78% of all analysed species, DNA barcodes are a reliable means for identification, indicated by the presence of barcode gaps. An overlap between intra- and interspecific genetic distances was present in 19 species, six of which belong to the genus Coregonus. The Neighbour-Joining phenogram showed 60 nonoverlapping species clusters and three singleton species, which were related to 63 separate BIN numbers. Furthermore, Barbatula barbatula, Leucaspius delineatus, Phoxinus phoxinus and Squalius cephalus exhibited remarkable levels of cryptic diversity. In contrast, 11 clusters showed haplotype sharing, or low levels of divergence between species, hindering reliable identification. The analysis of our barcode library together with public data resulted in 89 BINs, of which 56% showed taxonomic conflicts. Most of these conflicts were caused by the use of synonymies, inadequate taxonomy or misidentifications. Moreover, our study increased the number of potential alien species in Germany from 14 to 21 and is therefore a valuable groundwork for further faunistic investigations.
Data from: Conflict between background matching and social signalling in a colour-changing freshwater fish
The ability to change coloration allows animals to modify their patterning to suit a specific function. Many freshwater fishes, for example, can appear cryptic by altering the dispersion of melanin pigment in the skin to match the visual background. However, melanin-based pigments are also used to signal dominance among competing males; thus colour change for background matching may conflict with colour change for social status signalling. We used a colour-changing freshwater fish to investigate whether colour change for background matching influenced aggressive interactions between rival males. Subordinate males that had recently darkened their skin for background matching received heightened aggression from dominant males, relative to males whose coloration had not changed. We then determined whether the social status of a rival male, the focal male's previous social status, and his previous skin coloration, affected a male's ability to change colour for background matching. Social status influenced skin darkening in the first social encounter, with dominant males darkening more than subordinate males, but there was no effect of social status on colour change in the second social encounter. We also found that the extent of skin colour change (by both dominant and subordinate males) was dependent on previous skin coloration, with dark males displaying a smaller change in coloration than pale males. Our findings suggest that skin darkening for background matching imposes a significant social cost on subordinate males in terms of increased aggression. We also suggest that the use of melanin-based signals during social encounters can impede subsequent changes in skin coloration for other functions, such as skin darkening for background matching.
Data from: Native freshwater species get out of the way: Prussian carp (Carassius gibelio) impacts both fish and benthic invertebrate communities in North America
Prussian Carp (Carassius gibelio) are one of the most noxious non-native species in Eurasia. Recently, Prussian Carp, a non-native freshwater fish species, were genetically confirmed in Alberta, Canada and have been rapidly expanding their range in North America since establishment. Given their rapid range expansion, there is an increasing need to determine how Prussian Carp may impact native species. We assessed the severity of the Prussian Carp invasion by 1) determining their impact on fish communities, 2) assessing their impact on benthic invertebrate communities, 3) evaluating if Prussian Carp alter abiotic conditions, and 4) identifying where we find higher abundances of Prussian Carp. When Prussian Carp were established, we found significant changes to the fish community. Correspondingly, the degree of impact to benthic invertebrate communities was related to the stage of invasion (none, early, or recent), where changes in fish communities were significantly concordant with changes in benthic invertebrate communities. Finally, we found that higher abundances of Prussian Carp were significantly associated with lower abundances of a majority of native fish species. Altogether, using three lines of evidence, we determine that Prussian Carp can have wide ranging impacts on freshwater ecosystems in North America, pressing the need for management intervention.
FIGURE 4 in Orientocreadium elegans n. sp. and Orientocreadium pseudobagri Ya m a g u t i (Digenea: Orientocreadiidae), from freshwater fish of the Primorsky region (southern far east, Russia) with a description of their life cycles
FIGURE 4. Arrangement of the sensillae of the cercaria of Orientocreadium elegans n. sp..
FIGURE 3 in Orientocreadium elegans n. sp. and Orientocreadium pseudobagri Ya m a g u t i (Digenea: Orientocreadiidae), from freshwater fish of the Primorsky region (southern far east, Russia) with a description of their life cycles
FIGURE 3. Arrangement of the sensillae of the cercaria of Orientocreadium pseudobagri.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.