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opencc-zeroDec 2018View details →

Multi-decadal shifts in fish community diversity across a dynamic biogeographic transition zone

Aim: A 21-year fisheries-independent monitoring dataset was used to explore fish community diversity across a latitudinal gradient to quantify how diversity has changed and relate those changes in diversity to changes in the abiotic environment. Additionally, this study spans a biogeographic transition zone, providing insight into future species assemblages across regions of relatively high species diversity. Location: Indian River Lagoon, Florida, USA Methods: Spatial and temporal beta diversity was quantified latitudinally with "best derived breaks" determined by using chronological cluster analyses. Multiple indices of alpha diversity were quantified, including species richness, Shannon diversity, Simpson diversity, and Pielou's evenness. AIC model selection and environmental fit tests were performed to link patterns of diversity and species assemblages with the abiotic environment. Results: Evidence of a biogeographic transition zone was supported by data spanning the entire study period; the largest break in species assemblage occurred near 28°N. Fine scale analyses using small and large seine catches were noisier than broad analyses but indicated a northern shift in location of the biogeographic transition zone. Beta-diversity was generally dominated by species turnover/balance versus nestedness/gradient components, implying that changes were driven by species sorting associated with the physical environment. Excluding the summation of all environmental variables, temperature and dissolved oxygen best describe patterns of diversity and species composition. Main Conclusions: Over years less affected by disturbances, large and small seine catch data suggest the fish community assemblage and location of the biogeographic transition zone has shifted 9 km and 21 km to the north. If the trends observed in these years were to continue from 1999 until the year 2100, a 111 km to 243 km shift in fish communities could be expected. Variation in rates of movement based on gear type suggest novel species assemblages could ensue.

opencc-zeroDec 2016View details →

Data from: Terrestrial-focused protected areas are effective for conservation of freshwater fish diversity in Lake Tanganyika

Freshwater protected areas are rarely designed specifically for this purpose and consequently their conservation benefit cannot be guaranteed. Using Lake Tanganyika as a test case we investigated the benefits of terrestrial-focussed protected areas on the alpha and beta taxonomic and functional diversity of the diverse endemic rocky-shore cichlid fishes. Lake Tanganyika has limited protected shorelines and continued human population growth in its catchment, which has potential for negative impacts on habitat quality and key biological processes. We conducted 554 underwater surveys across a gradient of human disturbance including two protected areas, along 180 km of Tanzanian coastline, sampling 70 cichlid species representing a diverse range of life-histories and trophic groups. Alpha diversity was up to 50% lower outside of protected areas, and herbivores appeared most affected. Turnover dominated within-locality variation in beta diversity, but the nestedness component was positively related to human disturbance indicating an increase in generalist species outside of protected areas. Within protected areas the decline in zeta diversity (the expected number of shared species across multiple surveys) was best described by power law functions, which occur when local abundance is predicted by regional abundance; but declined exponentially in unprotected waters indicating a dominance of stochastic assembly. Despite not being designed for the purpose, the protected areas are clearly benefitting cichlid taxonomic and functional diversity within Lake Tanganyika, probably through local reduction in sediment deposition and/or pollution, but as cichlids can be poor dispersers protected area coverage should be expanded to benefit isolated communities.

opencc-zeroJun 2021View details →

eDNA metabarcoding in lakes to quantify influences of landscape features and human activity on aquatic invasive species prevalence and fish community diversity

Aim: Our goal was to use eDNA metabarcoding to characterize fish community diversity, detect aquatic invasive species (AIS), and assess how measures of community (or AIS) diversity are influenced by lake physical and environmental covariates, measures of hydrological connectivity, and human accessibility. Location: Michigan, USA. Methods: eDNA samples collected from 22 lakes were sequenced using two mitochondrial gene regions (12S and 16S rRNA). Metabarcoding data were compared to traditional fisheries survey data for a subset of lakes, and data from all 22 lakes were combined with environmental information to identify significant associations with community diversity and AIS relative abundance. Results: Occupancy modeling indicated that detection probabilities were generally higher with eDNA than traditional fisheries gear. Measures of connectivity with upstream aquatic habitats were positively associated with both AIS relative abundance and fish species diversity. We also demonstrate the use of spatial interpolation methods to map distributions of species diversity and AIS relative abundance within lakes. Conclusions: eDNA metabarcoding methods provided information on the composition and diversity of fish assemblages and the presence of AIS in freshwater lakes that varied greatly in drainage connectivity and anthropogenic development. Our case study identified associations between environmental covariates and fish diversity or AIS relative abundance across lakes. This information is of particular importance given increasing anthropogenic disturbance, invasive species spread, and associated declines in aquatic biodiversity. Incorporating eDNA metabarcoding as a supplement to traditional fisheries surveys will permit managers to identify greater numbers of taxa, including early detection of AIS, with less field effort and fish mortality. Further, eDNA methods may more accurately identify physical and biological features that correlate with diversity and abundance, and allow agencies to more effectively direct AIS management activities.

opencc-zeroDec 2016View details →

Data from: Increasing the fish diversity of the Triassic faunas of Gondwana: a new redfieldiiform (Actinopterygii) from the Middle Triassic of Argentina and its palaeobiogeographical implications

A new actinopterygian, Calaichthys tehul gen. et sp. nov. is described on the basis of a few, well-preserved specimens from the Anisian Cerro de Las Cabras Formation, Cuyo Basin in Mendoza Province. The new genus shows a combination of primitive characters (e.g. deep posterior region of the maxilla contacting the preopercle, a suspensorium backwardly oriented) and more advanced characters (e.g. distally segmented fin rays, hemiheterocercal caudal fin) and is thus considered to be a 'subholostean' fish. The new taxon is assigned to Redfieldiiformes on the basis of its single branchiostegal plate-like ray, a median gular plate, pectoral fins with stout, stiff, mainly non-segmented and distally branched fin rays, long and robust fringing fulcra in all fins, basal fulcra bordering both lobes of the caudal fin, and opposite dorsal and anal fins. Calaichthys is characterized by a combination of characters some of which are unique among redfieldiiforms (i.e. strongly ornamented but thin scales with a serrated posterior margin, smooth skull roof bones, extrascapulars with a bifid posterior margin, three suborbital bones, a hatchet-shaped preopercle, rectangular and slender opercle, deep mouth gape, entopterygoid and ectopterygoid with small pointed teeth disposed in several series, unornamented rostral bone, massive pectoral fins and delicate dorsal, pelvic and anal fins). Calaichthys provides novel information about the anatomy of redfieldiiforms, in particular in relation with the fins and associated scaly elements, as well as the scale morphology and their disposition over the body. Our work confirms for the first time that redfieldiiforms occur in South America. Redfieldiiforms seem to have originated in Gondwana and shown two diversity peaks: in the Anisian and the Carnian. Calaichthys is coeval with those redfieldiiforms of the Middle Triassic (Anisian) of Africa and Australia dwelling in ephemeral lakes.

opencc-zeroDec 2012View details →

Data from: A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents

Introduction: The PCR-based analysis of homologous genes has become one of the most powerful approaches for species detection and identification, particularly with the recent availability of Next Generation Sequencing platforms (NGS) making it possible to identify species composition from a broad range of environmental samples. Identifying species from these samples relies on the ability to match sequences with reference barcodes for taxonomic identification. Unfortunately, most studies of environmental samples have targeted ribosomal markers, despite the fact that the mitochondrial Cytochrome c Oxidase subunit I gene (COI) is by far the most widely available sequence region in public reference libraries. This is largely because the available versatile ("universal") COI primers target the 658 barcoding region, whose size is considered too large for many NGS applications. Moreover, traditional barcoding primers are known to be poorly conserved across some taxonomic groups. Results: We first design a new PCR primer within the highly variable mitochondrial COI region, the "mlCOIintF" primer. We then show that this newly designed forward primer combined with the "jgHCO2198" reverse primer to target a 313 bp fragment performs well across metazoan diversity, with higher success rates than versatile primer sets traditionally used for DNA barcoding (i.e. LCO1490/HCO2198). Finally, we demonstrate how the shorter COI fragment coupled with an efficient bioinformatics pipeline can be used to characterize species diversity from environmental samples by pyrosequencing. We examine the gut contents of three species of planktivorous and benthivorous coral reef fish (family: Apogonidae and Holocentridae). After the removal of dubious COI sequences, we obtained a total of 334 prey Operational Taxonomic Units (OTUs) belonging to 14 phyla from 16 fish guts. Of these, 52.5% matched a reference barcode (>98% sequence similarity) and an additional 32% could be assigned to a higher taxonomic level using Bayesian assignment. Conclusions: The molecular analysis of gut contents targeting the 313 COI fragment using the newly designed mlCOIintF primer in combination with the jgHCO2198 primer offers enormous promise for metazoan metabarcoding studies. We believe that this primer set will be a valuable asset for a range of applications from large-scale biodiversity assessments to food web studies.

opencc-zeroDec 2012View details →

Data from: Water level fluctuations and metapopulation dynamics as drivers of genetic diversity in populations of three Tanganyikan cichlid fish species

Understanding how genetic variation is generated and maintained in natural populations, and how this process unfolds in a changing environment, remains a central issue in biological research. In this work, we analyzed patterns of genetic diversity from several populations of three cichlid species from Lake Tanganyika in parallel, using the mitochondrial DNA control region. We sampled populations inhabiting the littoral rocky habitats in both very deep, and very shallow areas of the lake. We hypothesized that the former would constitute relatively older, more stable and genetically more diverse populations, because they should have been less severely affected by the well-documented episodes of dramatic water level fluctuations. In agreement with our predictions, populations of all three species sampled in very shallow shorelines showed traces of stronger population growth than populations of the same species inhabiting deep shorelines. However, contrary to our working hypothesis, we found a significant trend towards increased genetic diversity in the younger, demographically less stable populations inhabiting shallow areas, in comparison to the older and more stable populations inhabiting the deep shorelines. We interpret this finding as the result of the establishment of metapopulation dynamics in the former shorelines, by the frequent perturbation and reshuffling of individuals between populations due to the lake level fluctuations. The repeated succession of periods of allopatric separation and secondary contact is likely to have further increased the rapid pace of speciation in lacustrine cichlids.

opencc-zeroDec 2018View details →

Data from: Biogeography of functional trait diversity in the Taiwanese reef fish fauna

The richness of Taiwanese reef fish species is inversely correlated to latitude as a direct consequence of the abiotic environment and its effects on benthic habitats. However, to date, no studies have investigated the variations in the diversity of traits (FD) linked with the role of these fishes in the ecosystem. FD is usually considered more sensitive than species richness in detecting early changes in response to disturbances, and therefore could serve as an indicator of ecological resilience to environmental changes. Here, we aim to characterize FD in the Taiwanese reef fish fauna and to document its regional variations. Six traits were used to categorize the 1,484 reef fish species occurring in four environmentally contrasted regions around Taiwan. The number of unique trait combinations (FEs), their richness (FRic), their redundancy (FR), their over-redundancy (FOR), and their vulnerability (FV) were compared among these regions. Overall, 416 FEs were identified. Their number decreased from south to north in step with regional species richness but FRic remained similar among regions. FR and FOR were higher to the south. At the local scale, variations in FEs and FRic are in concordance with the worldwide pattern of FD. High-latitude, impoverished fish assemblages, offer a range of trait combinations similar to diversified tropical assemblages. Increasing diversity in the latter mainly contributes to raising FR and supports already over-redundant entities. High vulnerability makes many combinations highly sensitive to species loss, and was higher at intermediate latitudes when using a fine resolution in trait categories. It suggests that the loss of FEs may first be characterized by an increase in their vulnerability, a pattern that could have been overlooked in previous global scale analyses. Overall, this study provides new insights into reef fish trait biogeography with potential ramifications for ecosystem functioning.

opencc-zeroDec 2013View details →

Data from: Diversity and disparity through time in the adaptive radiation of Antarctic notothenioid fishes

According to theory, adaptive radiation is triggered by ecological opportunity that can arise through the colonization of new habitats, the extinction of antagonists or the origin of key innovations. In the course of an adaptive radiation, diversification and morphological evolution are expected to slow down after an initial phase of rapid adaptation to vacant ecological niches, followed by speciation. Such 'early bursts' of diversification are thought to occur because niche space becomes increasingly filled over time. The diversification of Antarctic notothenioid fishes into over 120 species has become one of the prime examples of adaptive radiation in the marine realm and has likely been triggered by an evolutionary key innovation in the form of the emergence of antifreeze glycoproteins. Here, we test, using a novel time-calibrated phylogeny of 49 species and five traits that characterize notothenioid body size and shape as well as buoyancy adaptations and habitat preferences, whether the notothenioid adaptive radiation is compatible with an early burst scenario. Extensive Bayesian model comparison shows that phylogenetic age estimates are highly dependent on model choice and that models with unlinked gene trees are generally better supported and result in younger age estimates. We find strong evidence for elevated diversification rates in Antarctic notothenioids compared to outgroups, yet no sign of rate heterogeneity in the course of the radiation, except that the notothenioid family Artedidraconidae appears to show secondarily elevated diversification rates. We further observe an early burst in trophic morphology, suggesting that the notothenioid radiation proceeds in stages similar to other prominent examples of adaptive radiation.

opencc-zeroDec 2019View details →

Data from: Small population size and low genomic diversity have no effect on fitness in experimental translocations of a wild fish

Little empirical work in nature has quantified how wild populations with varying effective population sizes and genetic diversity perform when exposed to a gradient of ecologically important environmental conditions. To achieve this, juvenile brook trout from 12 isolated populations or closed metapopulations that differ substantially in population size and genetic diversity were transplanted to previously fishless ponds spanning a wide gradient of ecologically important variables. We evaluated the effect of genome-wide variation, effective population size (Ne), pond habitat, and initial body size on two fitness correlates (survival and growth). Genetic variables had little effect on either fitness correlate, which were determined primarily by habitat (pond temperature, depth, and pH) and initial body size. These results suggest that some vertebrate populations with low genomic diversity, low Ne and long-term isolation can represent important sources of variation and be capable of maintaining fitness in, and ultimately persisting and adapting to, changing environments. Our results also reinforce the paramount importance of improving available habitat and slowing habitat degradation for species conservation.

opencc-zeroDec 2018View details →

Data from: Diversity patterns of native and exotic fish species suggest homogenization processes, but partly fail to highlight extinction threats

Exotic species are a major threat to biodiversity and have modified native communities worldwide. Invasion processes have been extensively studied, but studies on species richness and beta diversity patterns of exotic and native species are rare. We investigate such patterns among exotic and native fish communities in upland and lowland rivers to explore their relationship with environmental drivers. Location: Northern Italy. Exotic and native fish beta diversity patterns were investigated separately in lowland and upland sites using Local Contribution to Beta Diversity (LCBD) and Species Contribution to Beta Diversity (SCBD) analyses. To examine the main environmental variables affecting the LCBD, a Boosted Regression Trees (BRT) method was used. Community dispersion among and within stream orders was investigated with the PERMDISP test. In lowland sites, exotic species richness was higher than native species richness, especially in large rivers and drainage canals. An opposite trend was found in upland sites, where native species richness was higher than exotic species richness, especially in large rivers. No clear LCBD patterns were found along stream orders in the lowland, whereas higher stream orders in the upland showed the highest LCBD. Its patterns in upland and lowland sites were related with a number of factors, such as total suspended solids and total phosphorus. Community dispersion among stream orders did not show a relationship with environmental heterogeneity. SCBD values were positively correlated with species occupancy in the study area and native species showed higher SCBD values than exotic species only in the uplands. Main conclusions: Large rivers in the uplands are important in maintaining native fish diversity and should be protected against invasive fish. In contrast, most lowland rivers have suffered from biological homogenization. Some rare native species can show low contribution to beta diversity, but still need conservation actions due to their risk of local extinction.

opencc-zeroDec 2017View details →

Data from: Body shape diversity in Triassic‒Early Cretaceous neopterygian fishes: sustained holostean disparity and predominantly gradual increases in teleost phenotypic variety

Comprising Holostei and Teleostei, the ~32,000 species of neopterygian fishes are anatomically disparate and represent the dominant group of aquatic vertebrates today. However, the pattern by which teleosts rose to represent almost all of this diversity, while their holostean sister group dwindled to 8 extant species and two broad morphologies, is poorly constrained. A geometric morphometric approach was taken to generate a morphospace from over 400 fossil taxa, representing almost all articulated neopterygian taxa known from the first 150 million years—roughly 60%—of history (Triassic‒Early Cretaceous). Patterns of morphospace occupancy and disparity are examined in order to: assess evidence for a phenotypically 'dominant' holostean phase; evaluate whether expansions in teleost phenotypic variety are predominantly abrupt or gradual, including assessment of whether apomorphy-defined teleosts are as morphologically conservative as typically assumed; compare diversification in crown and stem teleosts. The systematic affinities of dapediiforms and pycnodontiforms, two extinct neopterygian clades of uncertain phylogenetic placement, significantly impact patterns of morphological diversification. For instance, alternative placements dictate whether or not holosteans possessed statistically higher disparity than teleosts in the Late Triassic and Jurassic. Despite this ambiguity, all scenarios agree that holosteans do not exhibit a decline in disparity during the Early Triassic‒Early Cretaceous interval, but instead maintain their Toarcian‒Callovian variety until the end of the Early Cretaceous without substantial further expansions. After a conservative Induan‒Carnian phase, teleosts colonize (and persistently occupy) novel regions of morphospace in a predominantly gradual manner until the Hauterivian, after which expansions are rare. Furthermore, apomorphy-defined teleosts possess greater phenotypic variety than typically assumed. Comparison of crown and stem teleost partial disparity indicates that, despite substantial expansion in crown teleosts between the Late Jurassic and earliest Cretaceous, stem teleosts remained important long-term contributors to overall teleost disparity during this time.

opencc-zeroDec 2015View details →

Data from: Speciation and the latitudinal diversity gradient: insights from the global distribution of endemic fish

The nearly universal pattern that species richness increases from the poles to the equator (the latitudinal diversity gradient [LDG]) has been of intense interest since its discovery by early natural-history explorers. Among the many hypotheses proposed to explain the LDG, latitudinal variation in (1) productivity, (2) time and area available for diversification, and (3) speciation and/or extinction rates have recently received the most attention. Because tropical regions are older and were formerly more widespread, these factors are often intertwined, hampering efforts to distinguish their relative contributions to the LDG. Here we examine the global distribution of endemic lake fishes to determine how lake age, area, and latitude each affect the probability of speciation and the extent of diversification occurring within a lake. We analyzed the distribution of endemic fishes worldwide (1,933 species and subspecies from 47 families in 2,746 lakes) and find that the probability of a lake containing an endemic species and the total number of endemics per lake increase with lake age and area and decrease with latitude. Moreover, the geographic locations of endemics in 34 of 41 families are found at lower latitudes than those of nonendemics. We propose that the greater diversification of fish at low latitudes may be driven in part by ecological opportunities promoted by tropical climates and by the coevolution of species interactions.

FIGURE 4 in Brachyhypopomus gauderio, new species, a new example of underestimated species diversity of electric fishes in the southern South America (Gymnotiformes: Hypopomidae)

FIGURE 4. Map of southern Brazil, Uruguay, Argentina and Paraguay with the distribution of Brachyhypopomus gauderio. Squares represent non-type specimens. Empty circle represents the type locality.

FIGURE 3. A in Brachyhypopomus gauderio, new species, a new example of underestimated species diversity of electric fishes in the southern South America (Gymnotiformes: Hypopomidae)

FIGURE 3. A: Female of Brachyhypopomus gauderio (paratype UFRGS 8933, 101.6 mm LEA); B: Sexually dimorphic caudal filament of a mature male of Brachyhypopomus gauderio (paratype MZUSP 100308, 139.6 mm LEA, caudal filament length 44.8 mm).

FIGURE 2 in Brachyhypopomus gauderio, new species, a new example of underestimated species diversity of electric fishes in the southern South America (Gymnotiformes: Hypopomidae)

FIGURE 2. Head of the Holotype (MCP 43280, male, 149.0 mm LEA) of Brachyhypopomus gauderio, Palmares do Sul, Rio Grande do Sul, Brazil.

FIGURE 1 in Brachyhypopomus gauderio, new species, a new example of underestimated species diversity of electric fishes in the southern South America (Gymnotiformes: Hypopomidae)

FIGURE 1. Holotype (MCP 43280, male, 149.0 mm LEA) of Brachyhypopomus gauderio, Palmares do Sul, Rio Grande do Sul, Brazil.

FIGURE 5 in Brachyhypopomus gauderio, new species, a new example of underestimated species diversity of electric fishes in the southern South America (Gymnotiformes: Hypopomidae)

FIGURE 5. Typical habitat of Brachyhypopomus gauderio; flooded area near Arroio dos Ratos creek, Charqueadas, Rio Grande do Sul, Brazil.

opennotspecifiedDec 2016View details →

FIGURE 6. Serrapinnus kriegi, UFRGS 20135, 20.2 in Inventory of the freshwater fishes from a densely collected area in South America — a case study of the current knowledge of Neotropical fish diversity

FIGURE 6. Serrapinnus kriegi, UFRGS 20135, 20.2 mm SL, rio Ibicuí, tributary of the rio Uruguay; new record for the state of Rio Grande do Sul.

opennotspecifiedDec 2016View details →

FIGURE 14 in Inventory of the freshwater fishes from a densely collected area in South America — a case study of the current knowledge of Neotropical fish diversity

FIGURE 14. Approximate localities of collection of expeditions made in the second half of the XIX Century and beginning of XX Century in Rio Grande do Sul State: Reinhold F. Hensel (1863-1866, pink); Emperor Dom Pedro II (1865-1866, red); Herman von Ihering (1880-1892, blue); Herbert H. Smith (1882, green); John D. Haseman (1909, yellow); Ernst Garbe (1914, black); Herman Kleerekoper (1941, white).