Use of environmental DNA to detect Eastern Sand Darter (Ammocrypta pellucida Putnam, 1863) in large Laurentian Great Lakes embayments

A single-species environmental DNA (eDNA) method was developed to sample for a small, benthic rare species, Eastern Sand Darter (Ammocrypta pellucida Putnam, 1863) in two large Lake Ontario embayments. Summer water sampling allowed for: (a) surveys of habitats (Wellers Bay) where traditional fish sampling gear could not be used; and, (b) a comparison between eDNA and seining-based detection probabilities at known occupied habitats (West Lake). In 2018, replicate (n = 3) 1 L water samples were collected from 90 Wellers Bay sites and 71 West Lake sites. A site-occupancy model, a hierarchical logistic regression model, was fitted to determine site occupancy, sample occupancy (presence of Eastern Sand Darter DNA in a water sample) and probability of detection (p) based on replicate quantitative polymerase chain reaction (qPCR) results for each water sample. Eastern Sand Darter was detected at 10 West Lake sites, but not from Wellers Bay. Mean site occupancy was 0.31 (0.12–0.70; 95% CLs), mean sample occupancy was 0.28 (0.09–0.58; 95% CLs), and mean detection probability in a subsample (i.e., successful qPCR amplification) given it was present was 0.40 (0.25–0.55; 95% CLs). While the eDNA method successfully detected Eastern Sand Darter from known occupied areas in West Lake, it was not more effective for assessing local site occupancy than traditional sampling methods, such as the seine.     

Three years of experience in biomanipulating a small eutrophic lake: Lago di Candia (Northern Italy)

Results obtained from a step by step approach to the biomanipulation of a natural lacustrine environment (Lago di Candia, Northern Italy) are presented. Since the diversion of the municipal sewage of the small town of Candia, runoff and precipitation have been the sole contributors of nutrient to the lake. Fish population is mainly characterized by rudd (Scardinius erythrophthalmus) overstocking and by a low density of large-mouth-bass (Micropterus salmoides) and pike (Esox lucius). During 1986 about 12t of rudd (1–2 year old) were removed from the lake. Considering 1986 as ‘control year’, average Secchi disc transparency improved from 2.3 m in 1986 to 3.3 m in 1988; phytoplankton biovolume decreased from 114 to 58 mm³ l⁻¹ but zooplankton biovolume increased from 8 to 11.5 mm³ l⁻¹. The results achieved show that a grodual biomanipulation treatment can have a satisfactory outcome, and has the advantage of not producing catastrophic situations either in the biotic or in the abiotic compartments of the lake.     

Changes in the Georgian Bay fish community,with special reference to lake trout (Salvelinus namaycush) rehabilitation

We describe and explain some of the changes in the fish community as reflected by the catches of the commercial fishery, and evaluate the efforts to restore the trout (Salvelinus spp.) in Georgian Bay. The changes in the fish community were caused in part by excessive fishing for lake trout (S. namaycush), lake whitefish (Coregonus clupeaformis) and deepwater ciscoes (Coregonus spp.), and the introduction of new species such as sea lamprey (Petromyzon marinus), alewife (Alosa pseudoharengus), rainbow smelt (Osmerus mordax) and salmonids (Oncorhynchus spp.). The most striking changes were the near extinction of the lake trout, reductions in lake herring (Coregonus artedii), deepwater ciscoes and lake whitefish, and the increase in abundance of smelt and alewife. In an effort to replace the loss of yield from the cold-water habitat, a fast growing and early maturing hybrid trout (splake [S. namaycush × S. fontinalis]) and its backcross to lake trout were selectively bred for stocking in Georgian Bay. Splake did poorly because of low survival immediately after planting. The survival of backcross after planting was better, but adult mortality was still high. Adult survival of backcross improved considerably after restrictions were placed on the commercial fishery in 1984. The first naturally produced backcross larvae were collected in 1985.     

Southernmost distribution limit for endangered Peladillas (Aplochiton taeniatus) and non-native coho salmon (Oncorhynchus kisutch) coexisting within the Cape Horn biosphere reserve,Chile

The Cape Horn Biosphere Reserve, one of the last wild areas of the planet, is not exempt from the pressures of global change, such as non-native species introductions. During 2018 and 2019 we studied the Róbalo river basin in order to update the diversity and distribution of fishes. Here, we report for the first time the native and endangered “Peladillas” Aplochiton taeniatus and the non-native coho salmon Oncorhynchus kisutch. The coexistence of native and non-native fishes poses a challenge for the management and conservation of aquatic biota from the Cape Horn Biosphere Reserve.     

The effects of age,sex, and habitat on body size and shape of the blackstripe topminnow,Fundulus notatus (Cyprinodontiformes: Fundulidae) (Rafinesque 1820)

Lake and stream habitats pose a variety of challenges to fishes due to differences in variables such as water velocity, habitat structure, prey community, and predator community. These differences can cause divergent selection on body size and/or shape. Here, we measured sex, age, length, and eight different morphological traits of the blackstripe topminnow, Fundulus notatus, from 19 lake and stream populations across four river drainages in central Illinois. Our goal was to determine whether size and shape differed consistently between lake and stream habitats across drainages. We also considered the effects of age and sex as they may affect size and morphology. We found large differences in body size of age 1 topminnows where stream fish were generally larger than lake fish. Body shape mainly varied as a function of sex. Adult male topminnows had larger morphological traits (with the exception of body width) than females, in particular longer dorsal and anal base lengths. Subtle effects of habitat were present. Stream fish had a longer dorsal fin base than lake fish. These phenotypic patterns may be the result of genetic and/or environmental variation. As these lakes are human‐made, the observed differences, if genetic, would have had to occur relatively rapidly (within about 100 years). © 2013 The Linnean Society of London     

Mechanosensory based orienting behaviors in fluvial and lacustrine populations of mottled sculpin ( Cottus bairdi )

We compared prey-orienting and rheotactic behaviors in a fluvial (Coweeta Creek) and lacustrine (Lake Michigan) population of mottled sculpin. Blinded sculpin from both populations exhibited unconditioned, mechanosensory based rheotaxis to low velocity flows. Whereas Lake Michigan sculpin generally showed increasing levels of positive rheotaxis to increasing velocities, Coweeta Creek sculpin show varying levels of positive rheotaxis at low to intermediate velocities and often reduced positive rheotaxis or even negative rheotaxis at the highest velocities (12?cm?s^?1). Blinded Lake Michigan, but not Coweeta Creek mottled sculpin exhibited an orienting response to a small (3?mm diameter) artificial prey (50?Hz vibrating sphere). In conclusion, the two populations differed in the strength and polarity of the rheotactic response at higher velocities and in their responsiveness to mechanosensory cues from epibenthic prey sources. These behavioral differences have most likely arisen from different learning experiences in different habitats and from the greater importance of visual cues to the Coweeta Creek mottled sculpin and mechanosensory cues to Lake Michigan mottled sculpin in the sensory guidance of orienting behaviors.     

Mechanosensory based orienting behaviors in fluvial and lacustrine populations of mottled sculpin (Cottus bairdi)

We compared prey-orienting and rheotactic behaviors in a fluvial (Coweeta Creek) and lacustrine (Lake Michigan) population of mottled sculpin. Blinded sculpin from both populations exhibited unconditioned, mechanosensory based rheotaxis to low velocity flows. Whereas Lake Michigan sculpin generally showed increasing levels of positive rheotaxis to increasing velocities, Coweeta Creek sculpin show varying levels of positive rheotaxis at low to intermediate velocities and often reduced positive rheotaxis or even negative rheotaxis at the highest velocities (12 cm s^-1). Blinded Lake Michigan, but not Coweeta Creek mottled sculpin exhibited an orienting response to a small (3 mm diameter) artificial prey (50 Hz vibrating sphere). In conclusion, the two populations differed in the strength and polarity of the rheotactic response at higher velocities and in their responsiveness to mechanosensory cues from epibenthic prey sources. These behavioral differences have most likely arisen from different learning experiences in different habitats and from the greater importance of visual cues to the Coweeta Creek mottled sculpin and mechanosensory cues to Lake Michigan mottled sculpin in the sensory guidance of orienting behaviors.     

Ecological effects of reduced nutrient loading (oligotrophication) on lakes: an introduction

1. The variable ecological response of lakes to reduced nutrient loading (oligotrophication) at sites in Europe and North America was discussed at a workshop held in Silkeborg (Denmark) in January 2003. Studies of lake oligotrophication were presented based on both long‐term monitoring and data generated by palaeolimnological methods. 2. This introduction to the special issue provides short summaries of a series of the papers presented and their limnological context. Results show that the majority of lakes had approached a new equilibrium of phosphorus (P) and nitrogen (N) concentrations 10–15 years (P) and 0–5 years (N) after a major reduction in loading, irrespective of hydraulic retention time. Phytoplankton biomass decreased and a shift towards meso‐oligotrophic species dominance occurred. The fish responded surprisingly fast to the loading reduction in most lakes. As a result, the percentage of piscivores increased and total fish biomass declined markedly, which may explain an increase in the body size of cladocerans and an increase in the zooplankton to phytoplankton biomass ratio seen in many of the lakes. 3. Monitoring has in general been initiated after the effects of eutrophication became apparent. In this context palaeolimnological techniques become very useful because they allow limnologists to extend time scales of coverage and to define restoration targets and baseline conditions. Moreover, lake sediments pre‐dating anthropogenic disturbance can be used to examine ecological response to, for instance, climate variability, allowing problems associated with multiple stressors to be addressed. 4. It is concluded that there is a great need for a synthetic, holistic approach to studying lake oligotrophication, combining multiple techniques of palaeolimnological sediment analysis with detailed but temporally limited long‐term monitoring of chemical and biological variables. This is important, not least to assess future responses to nutrient loading reductions, as global warming will interact with a range of external stressors and ultimately affect lake management strategies to deal with the resultant feedbacks.     

Identification of a novel member in the family Albulidae (bonefishes)

A novel Caribbean species Albula sp. cf. vulpes in the family Albulidae (bonefishes) was diagnosed through genetic and morphometric study. Phylogenies derived from 16S rRNA sequences revealed deeply separated lineages among Caribbean bonefishes. Mitochondrial DNA sequence divergences indicated a separation between 3·0 and 5·2 million years before present (b.p.). Cytochrome b phylogenies further supported the classification of A. sp. cf. vulpes as a novel albulid. Morphological variability revealed several differences between A. sp. cf. vulpes and other Caribbean species. A microsatellite library was developed to discern hybridization rates among the species. Microsatellite analyses revealed low levels of hybridization between some members in the complex. One instance of backcrossing was found between A. vulpes×A. sp. B and a pure A. sp. B, indicating that hybrids may have reduced fitness or may be reproductively isolated due to temporal–spatial spawning habitat differences.     

Modelling roach (Rutilus rutilus) microhabitat using linear and nonlinear techniques

• 1 Multiple linear regression (MLR), generalised additive models (GAM) and artificial neural networks (ANN), were used to define young of the year (0+) roach (Rutilus rutilus) microhabitat and to predict its abundance.
• 2 0+ Roach and nine environmental variables were sampled using point abundance sampling by electrofishing in the littoral area of Lake Pareloup (France) during summer 1997. Eight of these variables were used to set up the models after log₁₀ (x+ 1) transformation of the dependent variable (0+ roach density). Model training and testing were performed on independent subsets of the whole data matrix containing 306 records.
• 3 The predictive quality of the models was estimated using the determination coefficient between observed and estimated values of roach densities. The best models were provided by ANN, with a correlation coefficient (r) of 0.83 in the training procedure and 0.62 in the testing procedure. GAM and MLR gave lower prediction in the training set (r = 0.53 for GAM and r = 0.32 for MLR) and in the testing set (r = 0.48 for GAM and r = 0.43 for MLR). In the same way, samples without fish were reliably predicted by ANN whereas GAM and MLR predicted absence unreliably.
• 4 ANN sensitivity analysis of the eight environmental variables in the models revealed that 0+ roach distribution was mainly influenced by five variables: depth, distance from the bank, local slope of the bottom and percentage of mud and flooded vegetation cover. The nonlinear influence of these variables on 0+ roach distribution was clearly shown using nonparametric lowess smoothing procedures.
• 5 Non‐linear modelling methods, such as GAM and ANN, were able to define 0+ fish microhabitat precisely and to provide insight into 0+ roach distribution and abundance in the littoral zone of a large reservoir. The results showed that in lakes, 0+ roach microhabitat is influenced by a complex combination of several environmental variables acting mainly in a nonlinear way.

     

The diet of native and invasive fish species along the eastern Mediterranean coast (Osteichthyes)

The opening of the Suez Canal in 1869 enabled the invasion of more than 100 alien fish species into the Mediterranean. The aim of the present study was to compare the diet of native and alien fish species and to identify possibly shared food resources. We examined the diet composition of 13 of the most abundant fish species (6 alien, 7 native) on shallow soft bottom off southern Israel. All 13 species are omnivorous/carnivorous. The native fish exhibited a wider diversity of food types than the aliens. Alien fish prey upon and are preyed by native species as well as by other alien fish. A high level of diet overlap was found among some species, the aliens Saurida lessepsianus and Scomberomorus commerson overlapped with the native Synodus saurus; and the alien Nemipterus randalli with the native species Pagrus caeruleostictus, Lithognathus mormyrus and Pagellus erythrinus. The identified diet overlap is discussed, and the possibility of competitive interactions between these species is considered.     

Carp (Cyprinus carpio) as a powerful invader in Australian waterways

1. The invasion of carp (Cyprinus carpio L.) in Australia illustrates how quickly an introduced fish species can spread and dominate fish communities. This species has become the most abundant large freshwater fish in south‐east Australia, now distributed over more than 1 million km². 2. Carp exhibit most of the traits predicted for a successful invasive fish species. In addition, degradation of aquatic environments in south‐east Australia has given them a relative advantage over native species. 3. Derivation of relative measures of 13 species‐specific attributes allowed a quantitative comparison between carp and abundant native fish species across five major Australian drainage divisions. In four of six geographical regions analysed, carp differed clearly from native species in their behaviour, resource use and population dynamics. 4. Climate matching was used to predict future range expansion of carp in Australia. All Australian surface waters appear to be climatically suitable for carp. 5. This assessment strongly reinforces the need for immediate management of carp in Australia to include targeted control of human‐assisted dispersal, such as use of carp as bait by anglers, distribution to new locations by anglers and the use of the ‘Koi’ strain in the aquarium industry. 6. Given their historical spread, dispersal mechanisms and ecological requirements, the expansion of carp across most of the remainder of Australia is to be expected.     

The Effects of Stocking and Removal of a Nonnative Salmonid on the Plankton of an Alpine Lake

Bighorn Lake, a fishless alpine lake, was stocked with nonnative brook trout, Salvelinus fontinalis, in 1965 and 1966. The newly introduced trout rapidly eliminated the large crustaceans Hesperodiaptomus arcticus and Daphnia middendorffiana from the plankton. In July 1997, we began to remove the fish using gill nets. The population comprised 261 fish that averaged 214 g in wet weight and 273 mm in fork length. Thereafter, zooplankton abundance increased within weeks. Early increases were caused by the maturation of Diacyclops bicuspidatus, few of which reached copepodid stages before the removal of the fish because of fish predation. Daphnia middendorffiana, absent when fish were present, reappeared in 1998. Hesperodiaptomus arcticus, which had been eliminated by the stocked fish, did not return. The proportion of large zooplankton increased after fish removal, but their overall biomass did not change. Algal biomass was low and variable throughout the 1990s and correlated with water temperature but not with nutrient concentrations or grazer densities. Diatoms were the most abundant algal taxon in the lake, followed by Dinophyceae. Chrysophyceans and cryptophyceans were eliminated after the fish were removed. Chlorophyll a concentrations were unaffected. Gill netting is a viable fish eradication technique for smaller (less than 10 ha), shallow (less than 10 m deep) lakes that lack habitable inflows and outflows or other sensitive species. Further work is required to define appropriate removal methods for larger lakes and watersheds. Received 30 May 2000; Accepted 14 November 2000.     

Zooplankton in a quasi-stable phase in an endorheic lake (Lake Chilwa,Malawi)

Lake Chilwa, a fairly large, turbid, brackish and very shallow endorheic lake in Malawi, Central Africa, dried up completely in 1968 and filled up again in the following wet season. Compared with the zooplankton in the drying, filling and post-filling phases (1966–1971), differences in their composition, density, distribution and reproduction were found in 1975–1976, a year when the lake was 1–2 metres deeper. This situation is discussed in relation to environmental factors, fish predation and the supply of detritus from the surrounding Typha swamp, to illustrate the relative stability of the zooplankton populations in periods between lake recessions.University of Malawi     

Inbreeding, outbreeding and environmental effects on genetic diversity in 46 walleye (Sander vitreus) populations

Genetic diversity is recognized as an important population attribute for both conservation and evolutionary purposes; however, the functional relationships between the environment, genetic diversity, and fitness-related traits are poorly understood. We examined relationships between selected lake parameters and population genetic diversity measures in 46 walleye (Sander vitreus) populations across the province of Ontario, Canada, and then tested for relationships between six life history traits (in three categories: growth, reproductive investment, and mortality) that are closely related to fitness, and genetic diversity measures (heterozygosity, d2, and Wright's inbreeding coefficient). Positive relationships were observed between lake surface area, growing degree days, number of species, and hatchery supplementation versus genetic diversity. Walleye early growth rate was the only life history trait significantly correlated with population heterozygosity in both males and females. The relationship between FIS and male early growth rate was negative and significant (P < 0.01) and marginally nonsignificant for females (P = 0.06), consistent with inbreeding depression effects. Only one significant relationship was observed for d2: female early growth rate (P < 0.05). Stepwise regression models showed that surface area and heterozygosity had a significant effect on female early growth rate, while hatchery supplementation, surface area and heterozygosity had a significant effect on male early growth rate. The strong relationship between lake parameters, such as surface area, and hatchery supplementation, versus genetic diversity suggests inbreeding and outbreeding in some of the populations; however, the weak relationships between genetic diversity and life history traits indicate that inbreeding and outbreeding depression are not yet seriously impacting Ontario walleye populations.     

Threatened fishes of the world: <Emphasis Type="Italic">Notropis boucardi</Emphasis> (Günther 1868) (Cyprinidae)

Synopsis We present a short communication on an endangered freshwater fish species from central Mexico, Notropis boucardi, to be published in the threatened fishes of the world series.     

Identification of weakfish Cynoscion (Gill) in the Bay of Panama with RFLP markers

A molecular approach, polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP), was developed to identify the planktonic larvae of Cynoscion species. Species-specific mitochondrial DNA markers were developed using three restriction endonucleases ( Dde I, Hae III and Hin fI). These markers permitted the accurate discrimination of the five Cynoscion species in the Bay of Panama.     

Rampant drift in artificially fragmented populations of the endangered tidewater goby (Eucyclogobius newberryi)

Habitat fragmentation and its genetic consequences are a critically important issue in evaluating the evolutionary penalties of human habitat modification. Here, we examine the genetic structure and diversity in naturally subdivided and artificially fragmented populations of the endangered tidewater goby (Eucyclogobius newberryi), a small fish restricted to discrete coastal lagoons and estuaries in California, USA. We use five naturally fragmented coastal populations from a 300‐ km spatial scale as a standard to assess migration and drift relative to eight artificially fragmented bay populations from a 30‐ km spatial scale. Using nine microsatellite loci in 621 individuals, and a 522‐base fragment of mitochondrial DNA control region from 103 individuals, we found striking differences in the relative influences of migration and drift on genetic variation at these two scales. Overall, the artificially fragmented populations exhibited a consistent pattern of higher genetic differentiation and significantly lower genetic diversity relative to the naturally fragmented populations. Thus, even in a species characterized by habitat isolation and subdivision, further artificial fragmentation appears to result in substantial population genetic consequences and may not be sustainable.     

Proteomic Analysis of the Lake Trout (Salvelinus namaycush) Liver Identifies Proteins from Evolutionarily Close and ‐Distant Fish Relatives

Lake trout are used as bioindicators for toxics exposure in the Great Lakes ecosystem. Here the first lake trout (Salvelinus namaycush) liver proteomics study is performed and searched against specific databases: (NCBI and UniProtKB) Salvelinus, Salmonidae, Actinopterygii, and Oncorhynchus mykiss, and the more distant relative, Danio rerio. In the biological replicate 1 (BR1), technical replicate 1 (TR1), (BR1TR1), a large number of lake trout liver proteins are not in the Salvelinus protein database, suggesting that lake trout liver proteins have homology to some proteins from the Salmonidae family and Actinopterygii class, and to Oncorhynchus mykiss and Danio rerio, two more highly studied fish. In the NCBI search, 4194 proteins are identified: 3069 proteins in Actinopterygii, 1617 in Salmonidae, 68 in Salvelinus, 568 in Oncorhynchus mykiss, and 946 in Danio rerio protein databases. Similar results are observed in the UniProtKB searches of BR1RT1, as well as in a technical replicate (BR1TR2), and then in a second biological replicate experiment, with two technical replicates (BR2TR1 and BR2TR2). This study opens the possibility of identifying evolutionary relationships (i.e., adaptive mutations) between various groups (i.e., zebrafish, rainbow trout, Salmonidae, Salvelinus and lake trout) through evolutionary proteomics. Data are available via the PRIDE Q2 (PXD011924).