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opencc-by-4.0Sep 2024View details →

Sequential migrations of diverse fish community provide seasonally prolonged and stable nutrient inputs to a river

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Figure 6 in Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes)

Figure 6. Phylogeny of Acestrorhamphidae and subfamilies Stethaprioninae, Pristellinae, Jupiabinae, Tyttobryconinae, and Hyphessobryconinae based on 1348 nuclear loci of ultraconserved elements (538 472 bp). Numbers near nodes represent bootstrap support.

Figure 4 in Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes)

Figure 4. Phylogeny of Characidae and subfamilies Aphyocharacinae, Cheirodontinae, Exodontinae, Tetragonopterinae, and Characinae based on 1348 nuclear loci of ultraconserved elements (538 472 bp). Numbers near nodes represent bootstrap support.

Figure 3 in Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes)

Figure 3. Phylogeny of Spintherobolidae and Stevardiidae and subfamilies Landoninae, Xenurobryconinae, Glandulocaudinae, Argopleurinae, Hemibryconinae, Stevardiinae, Planaltininae, Creagrutinae, and Diapominae based on 1348 nuclear loci of ultraconserved elements

Figure 2 in Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes)

Figure 2. Phylogenetic relationships of the major clades of Spintherobolidae, Stevardiidae, Characidae, and Acestrorhamphidae based on the 75% complete matrix of 1348 ultraconserved elements (575 taxa; 538 472 bp).

Figure 7 in Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes)

Figure 7. Phylogeny of Acestrorhamphidae and subfamilies Thayeriinae, Rhoadsiinae, Grundulinae, and Acestrorhamphinae based on 1348 nuclear loci of ultraconserved elements (538 472 bp). Numbers near nodes represent bootstrap support.

Figure 1 in Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes)

Figure 1. Accumulation curve of the original descriptions of current valid genera of Characidae s.l. highlighting the three periods of active descriptions of genera: (i) 1777–1900, (ii) 1900–1955, and (iii) 1955–present.

Figure 5 in Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes)

Figure 5. Phylogeny of Acestrorhamphidae and subfamilies Oxybryconinae, Trochilocharacinae, Stygichthyinae, Megalamphodinae, and Stichonodontinae based on 1348 nuclear loci of ultraconserved elements (538 472 bp). Numbers near nodes represent bootstrap support.

opencc-by-4.0Sep 2024View details →

Fish Diversity and Assemblages along the Altitudinal Gradients of Ghamot National Park Forest Streams the State Biosphere-Reserve Neelum Valley, Pakistan

Fish Diversity and Assemblages along the Altitudinal Gradients of  Ghamot National Park Forest Streams the State Biosphere-Reserve  Neelum Valley, Pakistan

opencc-zeroDec 2019View details →

Data from: Comparison of fish detections, community diversity, and relative abundance using environmental DNA metabarcoding and traditional gears

Background Detecting species at low abundance, including aquatic invasive species (AIS), is critical for making informed management decisions. Environmental DNA (eDNA) methods have become a powerful tool for rare or cryptic species detection; however, many eDNA assays offer limited utility for community‐level analyses due to their use of species‐specific (presence/absence) 'barcodes'. Metabarcoding methods provide information on entire communities based on sequencing of all taxon‐specific barcodes within an eDNA sample. Aims Evaluate measures of fish species detections, community diversity, and estimates of relative abundance based on eDNA metabarcoding and traditional fisheries sampling approaches in the context of fish community characterization and AIS survellience. Materials and Methods In 2016, eight limnologically diverse lakes (surface area range: 13 – 1,728 ha) in Michigan, USA were sampled using a variety of traditional fisheries gears to characterize fish community composition. Environmental DNAs from surface (33 ± 6, mean ± 1 SD) and benthic (14 ± 2) water samples from each lake were isolated and amplified for two metabarcoding markers (mitochondrial 12S and 16S rDNA loci) using fish‐specific primers. Fish species detected within each lake were determined by comparing the sequencing data to a database of sequences from native Michigan fish species and 19 AIS on the Michigan's Watch List. Results Analysis of species accumulation curves indicated multi‐locus eDNA metabarcoding assays can enhance species detection capacities and characterize 95% of a fish community in fewer sampling efforts than traditional gear (range: 2 – 62, median: 14). In addition, all AIS detected in traditional gear samples were also detected by eDNA, while some AIS detected by eDNA assays were absent from traditional gear samples. Discussion Results reported here are, in part, driven by the lack of species‐selectivity during eDNA sampling events. Given the efficacy of eDNA assays, we suggest multi‐locus eDNA metabarcoding assays be implemented in early detection efforts.

opencc-zeroDec 2011View details →

Data from: Genetic diversity and differentiation in a wide ranging anadromous fish, American shad (Alosa sapidissima), is correlated with latitude

Studies that span entire species ranges can provide insight into the relative roles of historical contingency and contemporary factors that influence population structure and can reveal patterns of genetic variation that might otherwise go undetected. American shad is a wide ranging anadromous clupeid fish that exhibits variation in demographic histories and reproductive strategies (both semelparity and iteroparity) and provides a unique perspective on the evolutionary processes that govern the genetic architecture of anadromous fishes. Using 13 microsatellite loci, we examined the magnitude and spatial distribution of genetic variation among 33 populations across the species' range to (i) determine whether signals of historical demography persist among contemporary populations and (ii) assess the effect of different reproductive strategies on population structure. Patterns of genetic diversity and differentiation among populations varied widely and reflect the differential influences of historical demography, microevolutionary processes and anthropogenic factors across the species' range. Sequential reductions of diversity with latitude among formerly glaciated rivers are consistent with stepwise postglacial colonization and successive population founder events. Weak differentiation among U.S. iteroparous populations may be a consequence of human-mediated gene flow, while weak differentiation among semelparous populations probably reflects natural gene flow. Evidence for an effect of reproductive strategy on population structure suggests an important role for environmental variation and suggests that the factors that are responsible for shaping American shad life history patterns may also influence population genetic structure.

opencc-zeroDec 2017View details →

Data from: Standing genetic diversity and selection at functional gene loci are associated with differential invasion success in two non-native fish species

Invasive species are expected to experience a unique combination of high genetic drift due to demographic factors while also experiencing strong selective pressures. The paradigm that reduced genetic diversity should limit the evolutionary potential of invasive species and thus their potential for range expansion has received little empirical support, possibly due to the choice of genetic markers. Our goal was to test for effects of genetic drift and selection at functional genetic markers as they relate to the invasion success of two paired invasive goby species, one widespread (successful) and one with limited range expansion (less successful). We genotyped fish using two marker types: single nucleotide polymorphisms (SNPs) in known-function, protein-coding genes and microsatellites to contrast the effects of neutral genetic processes. We identified reduced allelic variation in the invaded range for the less-successful tubenose goby. SNPs putatively under selection were responsible for the observed differences in population structure between marker types for round goby (successful) but not tubenose goby (less successful). A higher proportion of functional loci experienced divergent selection for round goby, suggesting increased evolutionary potential in invaded ranges may be associated with round goby's greater invasion success. Genes involved in thermal tolerance were divergent for round goby populations but not tubenose goby, consistent with the hypothesis that invasion success for fish in temperate regions is influenced by capacity for thermal tolerance. Our results highlight the need to incorporate functional genetic markers in studies to better assess evolutionary potential for the improved conservation and management of species.

opencc-zeroJul 2021View details →

Data: Diversity-production relationships of fish communities in freshwater stream ecosystems

Ecological relationships between species richness and biomass production are increasingly thought to be pervasive across the globe. Yet diversity-production relationships have not been explored extensively for freshwater fish communities even though fisheries production provides key services to humans. Our aim was to evaluate the diversity-production relationship for fish communities inhabiting freshwater streams across the Appalachian Mountain range and examine how diversity-production relationships varied across streams possessing different thermal signatures. Our study area included 25 freshwater stream ecosystems spanning from Vermont to North Carolina in the United States. Twenty sites were located in Maryland south to Tennessee and North Carolina while five additional higher latitude sites were sampled in Massachusetts and Maine. We sampled 25 study streams from June to September 2012 and collected fish population information to calculate biomass, species richness, Shannon diversity index, and annual production for each fish community. Linear mixed models were used to analyze the relationship between diversity indices and total community production. We also compared diversity and production relationships across other taxa. Across all streams, community fish production, biomass and P/B ratios ranged 0.15-6.79 g m2 y1, 0.61-0.73 g m-2, and 0.21-1.07 y-1, respectively. Species richness had a significant positive effect (p = 0.012) on community fish production, while accounting for the thermal signature of the streams as a random effect and other habitat covariates. Shannon diversity index did not have a significant effect (p = 0.101) on community production. The diversity-production relationship observed for stream fish communities was similar to other studies but demonstrated one of the highest slopes. Our results demonstrate that effects of biodiversity resonate to influence the production of fishes; thus, management of fisheries is more closely coupled to biodiversity than previously thought.

opencc-zeroJul 2021View details →

Data: Diversity of fish parasites of the Penzhina River (Kamchatka Krai, Russia)

The study of the fauna of fish parasites helps to understand the ways of formation of ichthyofauna and obtain a more complete knowledge of the biodiversity of the aquatic ecosystem as a whole. Parasitologically, the Penzhina River, one of the largest and most inaccessible rivers in the Russian Far East, remained poorly studied for a long time. Penzhina is characterized by an unusually extended mouth area, its estuary is distinguished by extremely high tides, up to 13.0 m, which is the highest tide in Russia. Rich ichthyofauna (21 species of fish and cyclostomes) and a variety of hydrological conditions favor the formation of a diverse fauna of fish parasites in the Penzhina River. The published parasitological data was still fragmentary and concerned few host species, so it is significantly broadened by the authors' findings and observations. The paper provides information on 122 species of fish parasites in the lower reaches and estuary of the Penzhina River, and Penzhinskaya Bay.

opencc-by-4.0Jul 2021View details →

Data: Use of environmental DNA in assessment of fish functional and phylogenetic diversity

Abstract Assessing the impact of global changes and protection effectiveness is a key step in monitoring marine fishes. Most traditional census methods are demanding or destructive. Nondisturbing and nonlethal approaches based on video and environmental DNA are alternatives to underwater visual census or fishing. However, their ability to detect multiple biodiversity factors beyond traditional taxonomic diversity is still unknown. For bony fishes and elasmobranchs, we compared the performance of eDNA metabarcoding and long-term remote video to assess species’ phylogenetic and functional diversity. We used 10 eDNA samples from 30 L of water each and 25 hours of underwater videos over 4 days on Malpelo Island (pacific coast of Colombia), a remote marine protected area. Metabarcoding of eDNA detected 66% more molecular operational taxonomic units (MOTUs) than video. We found 66 and 43 functional entities with a single eDNA marker and videos, respectively, and higher functional richness for eDNA than videos. Despite gaps in genetic reference databases, eDNA also detected a higher fish phylogenetic diversity than videos; accumulation curves showed how 1 eDNA transect detected as much phylogenetic diversity as 25 hours of video. Environmental DNA metabarcoding can be used to affordably, efficiently, and accurately census biodiversity factors in marine systems. Although taxonomic assignments are still limited by species coverage in genetic reference databases, use of MOTUs highlights the potential of eDNA metabarcoding once reference databases have expanded. Methods We sampled around the Sanctuary of Fauna and Flora in Malpelo, a remote oceanic island 490 km off the Colombia in the eastern tropical Pacific (Fig. 1), for 4 days (25-28 March 2018) at 1 site (El Arrecife). Malpelo is surrounded by deep water and fishing activities are prohibited in the surrounding 8,757 km2 (Edgar et al. 2011). The reef ecosystem around the island is influenced by major oceanic currents (Rodríguez-Rubio et al. 2003) and local upwelling, and the benthos is bare rock with low coral cover (Quimbayo et al. 2017). Malpelo Island is one of the most pristine and vulnerable reef ecosystems in the tropical eastern Pacific. Fish biomass and biodiversity are high (>250 vertebrates species) and provide a baseline for undisturbed assemblages in this marine province (Quimbayo et al. 2017). We deployed 1 long-duration remote underwater video system (RUV) (Extrem-Vision, Rivesaltes, France) that films up to 12 hours (screenshots in Appendix S1). The camera was 40 cm above the seafloor (13 m deep, 04.00600°, -81.60433°) and had a 90° field of view in which benthic and pelagic areas were recorded over 10 m2. Resolution was 1920 x 1080 pixels, and 30 frames/second were shot. Recording occurred on 25 (day and night) and 28 March (day) (Fig 1c). Cameras filmed 24 hours and 50 minutes of video. At night 2 dive lights illuminated the camera’s view. A Hero 5 (GoPro, San Mateo, California) was mounted on top the RUVs to film in the opposite direction for the first 2 hours of deployment of each daylight recording. Three hours and 30 minutes were recorded with the GoPros. During video recordings, we sampled eDNA above the camera in round surface transects. We did 5 identical transects at different times, corresponding to 10 samples (i.e., eDNA filters) (Fig. 1) because we collected 2 samples/transect. Transects sampled from a boat, and we pumped 30 L of water/sampled. We used an Athena peristaltic pump (Proactive Environmental Products, Bradenton, Florida) (nominal flow 1.0 L/minute) on each side of the boat to filter water through a VigiDNA 0.20 μm cross-flow filtration capsule (SPYGEN, le Bourget du Lac, France). To avoid contamination, we used only disposable sterile tubing and gloves for each filtration capsule. Immediately after filtration, the filter units were filled with CL1 Conservation buffer (SPYGEN, le Bourget du Lac, France) and stored at room temperature (20-25° C) for 5.5 months until DNA extraction. For video processing, two frames/second were extracted from all videos. Fishes were identified at the lowest taxonomic level possible, following Fishbase taxonomy (Froese & Pauly 2000), by trained personnel, who recorded the first occurrence of each species in each of the videos (i.e., number of individuals per species was not recorded). Usage Notes * eDNA Pre and post-processed eDNA metabarcoding data for the three markers used in the study (teleo, chon, vert01) alongside metadata.  * Videos  Recording of each fish species' first occurence.  Please see the README.md file for more information on the files.

opencc-zeroOct 2021View details →

Rise and fall of †Pycnodontiformes: Diversity, competition and extinction of a successful fish clade

Pycnodontiformes was a successful lineage of primarily marine fishes that broadly diversified during the Mesozoic. They possessed a wide variety of body shapes and were adapted to a broad range of food sources. Two other neopterygian clades possessing similar ecological adaptations in both body morphology (Dapediiformes) and dentition (Ginglymodi) also occurred in Mesozoic seas. Although these groups occupied the same marine ecosystems, the role that competitive exclusion and niche partitioning played in their ability to survive alongside each other remains unknown. Using geometric morphometrics on both the lower jaw (as constraint for feeding adaptation) and body shape (as constraint for habitat adaptation), we show that while dapediiforms and ginglymodians occupy similar lower jaw morphospace, pycnodontiforms are completely separate. Separation also occurs between the clades in body shape so that competition reduction between pycnodontiforms and the other two clades would have resulted in niche partitioning. Competition within pycnodontiforms seemingly was reduced further by evolving different feeding strategies as shown by disparate jaw shapes that also indicate high levels of plasticity. Acanthomorpha was a teleostean clade that evolved later in the Mesozoic and which has been regarded as implicated in driving the pycnodontiforms to extinction. Although they share similar body shapes, no coeval acanthomorphs had similar jaw shapes or dentitions for dealing with hard prey like pycnodontiforms do and so their success being a factor in pycnodontiform extinction is unlikely. Sea surface temperature and eustatic variations also had no impact on pycnodontiform diversity patterns according to our results. Conversely, the occurrence and number of available reefs and hardgrounds as habitats through time seems to be the main factor in pycnodontiform success. Decline in such habitats during the Late Cretaceous and Palaeogene might have had deleterious consequences for pycnodontiform diversity. Acanthomorphs occupied the niches of pycnodontiforms during the terminal phase of their existence.

opencc-zeroMar 2023View details →

Tropicalization of temperate reef fish communities facilitated by urchin grazing and diversity of thermal affinities

Aim: Global declines in structurally complex habitats are reshaping both land and seascapes in directions that affect biological communities' responses to warming. Here, we test whether widespread loss of kelp habitats through sea urchin overgrazing systematically changes sensitivity of fish communities to warming. Location: Global temperate latitudes Time period: Modern Major taxa studied: Fishes Methods: Community thermal affinity shifts related to habitat were assessed by simulating and comparing fish communities from 2,271 surveys across 15 ecoregions. Results: We find that fishes in kelp and urchin barrens differ in realized thermal affinities and range sizes, but only in regions where species pools have high variability in species' thermal affinities. Barrens on warm-temperate reefs host relatively more warm-affinity fish species than neighbouring kelp beds, highlighting acceleration of tropicalization processes facilitated by urchin herbivory. By contrast, proportionally more cool-affinity fishes colonize barrens at high temperate latitudes, contributing to community lags with ocean warming in these regions. Main conclusions: Our findings implicate urchins as drivers of ecological change, in part by affecting biological resilience to warming.

opencc-zeroMay 2023View details →

Global patterns and drivers of beta diversity facets of reef fish faunas

Aim: Exploring the relationships between the different facets of beta diversity and both past and current environmental conditions can unveil the processes that have shaped spatial patterns of biodiversity. In the marine realm, large-scale patterns and processes of beta diversity have been less investigated. Our study aimed to investigate the patterns and drivers of multiple facets of beta diversity and its components, contrasting pairs of reef fish assemblages among marine realms. Location: Tropical reefs. Taxon: Reef fishes. Methods: Based on trait data and phylogenetic relationships for 5,182 tropical reef fish species, we calculated compositional differences between pairs of reef fish assemblages across the Atlantic, Tropical Eastern Pacific (TEP), and Indo-Pacific realms. We also applied a partitioning approach to distinguish between the turnover and nestedness components. We then evaluated the relative importance of several variables related to historical and contemporary environmental conditions in shaping spatial patterns of beta diversity using Constrained Analysis of Principal Coordinates (CAP) models. Results: Both the turnover and nestedness components contributed to total phylogenetic and taxonomic beta diversity in the TEP and Indo-Pacific realms, while the turnover component was found to be more important in the Atlantic realm. In contrast, total trait beta diversity displayed very low values and was primarily explained by the nestedness component. Taxonomic and phylogenetic differences in the composition of tropical reef fish assemblages were influenced by both historical and contemporary factors or solely by historical variables. Main conclusions: Our results suggest that past climate changes and historical contingency left an imprint in the present-day composition of tropical reef fish assemblages. The very low levels of trait beta diversity indicate that reef fish assemblages display similar trait composition even among geographically distant assemblages with contrasting evolutionary histories, which may result from environmental filtering or evolutionary convergence, or the combination of both processes.

publicJun 2019View details →

Data from: Local parasite pressures and host genotype modulate epigenetic diversity in a mixed-mating fish

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