BackgroundDNA barcoding aims to provide an efficient method for species-level identifications using an array of species specific molecular tags derived from the 5′ region of the mitochondrial cytochrome c oxidase I (COI) gene. The efficiency of the method hinges on the degree of sequence divergence among species and species-level identifications are relatively straightforward when the average genetic distance among individuals within a species does not exceed the average genetic distance between sister species. Fishes constitute a highly diverse group of vertebrates that exhibit deep phenotypic changes during development. In this context, the identification of fish species is challenging and DNA barcoding provide new perspectives in ecology and systematics of fishes. Here we examined the degree to which DNA barcoding discriminate freshwater fish species from the well-known Canadian fauna, which currently encompasses nearly 200 species, some which are of high economic value like salmons and sturgeons.Methodology/Principal FindingsWe bi-directionally sequenced the standard 652 bp “barcode” region of COI for 1360 individuals belonging to 190 of the 203 Canadian freshwater fish species (95%). Most species were represented by multiple individuals (7.6 on average), the majority of which were retained as voucher specimens. The average genetic distance was 27 fold higher between species than within species, as K2P distance estimates averaged 8.3% among congeners and only 0.3% among concpecifics. However, shared polymorphism between sister-species was detected in 15 species (8% of the cases). The distribution of K2P distance between individuals and species overlapped and identifications were only possible to species group using DNA barcodes in these cases. Conversely, deep hidden genetic divergence was revealed within two species, suggesting the presence of cryptic species.Conclusions/SignificanceThe present study evidenced that freshwater fish species can be efficiently identified through the use of DNA barcoding, especially the species complex of small-sized species, and that the present COI library can be used for subsequent applications in ecology and systematics.

Summer water temperatures are rising in many river systems in North America, and this warming trend is projected to intensify in the coming decades. Cold-water fish may alleviate thermal stress in summer by aggregating in discrete cold-water plumes that provide thermal refuge from high ambient river temperatures. Reliance on cold-water thermal refugia is expected to increase in a warming climate, and many river reaches already lack suitable thermal refugia as a result of an absence of thermal diversity. A comprehensive fish management strategy could proactively address this imminent threat to cold-water fish populations across North America by preserving existing thermal refugia, augmenting thermal anomalies to improve performance as refugia, and creating new thermal refugia in uniformly warm river reaches. We provide practical recommendations on how these measures can be accomplished based on insight derived from recent research focused on the Miramichi River, New Brunswick. Opportunities include limiting land use change, construction aggregate extraction (e.g. sand and gravel pits), and groundwater pumping/consumption. Existing thermal anomalies can be enhanced by controlling advective thermal mixing between cold-water tributaries and the river mainstem flow, installing riparian shading, and adding temporary structures for protection from avian predators. New refugia can be created by temporarily pumping groundwater to discrete points within the river during periods of thermal stress. These concepts are discussed in the context of a comprehensive thermal refugia management strategy. Copyright

Spawning areas selected by brook trout (Salvelinus fontinalis) displayed variable relationships to discharging groundwater across geologic regions. In Canadian Shield waters, spawning was associated with areas of distinct, discharging groundwater. The specific mechanism of selection could not be determined. Groundwater did not appear to influence the selection of individual redd sites within these discharge areas. Competition among females for the opportunity to spawn in a limited area defined by the discharging groundwater appeared to control the selection of redd sites. In southwestern Ontario streams, discharging groundwater was prominent throughout areas of spawning both at redds and at adjacent, nonspawning substrates (≤7 m). Consequently, relationships between groundwater and spawning site selection were ambiguous. On the unglaciated plateau of central Pennsylvania, no groundwater was observed in redds or nonspawning substrates in streams. Brook trout management programmes must consider these groundwater relationships and therefore the impact of land use on groundwater quality and quantity.

Mercury (Hg) concentrations in fish from acidic lakes (pH < 6.0) are typically elevated above those from nearneutral systems. It is unknown whether high biomagnification rates through the supporting food web can explain elevated Hg concentrations in top predators from low pH lakes. To investigate this, we collected yellow perch (Perca flavescens), brown bullhead (Ameiurus nebulosus), banded killifish (Fundulus diaphanous), golden shiner (Notemigonus crysoleucas), and littoral and pelagic invertebrates from four acidic lakes in Kejimkujik National Park and Historic Site (KNPNHS), Nova Scotia, Canada, and analyzed them for total Hg and methyl Hg (MeHg), and d 13 C and d 15 N to determine sources of energy and trophic position, respectively. Mercury biomagnification rates (slopes of log Hg versus d 15 N) varied significantly among the four lakes but did not explain the among-lake differences in perch Hg; these slopes were also within the range published for near-neutral systems. Rather, Hg concentrations in yellow perch (i.e., predatory fish) in KNPNHS were higher in lakes with higher MeHg in lower-trophic-level organisms and suggest that processes influencing Hg uptake at the base of the food web are more important than rates of food web biomagnification for understanding the variation in concentrations of this contaminant among top predators.Résumé : Les concentrations de mercure (Hg) dans les poissons des lacs acides (pH < 6,0) sont typiquement plus élevées que celles des poissons de systèmes près de la neutralité. On ne sait pas si ce sont des taux élevés de bioamplification à travers le réseau alimentaire de support qui peuvent expliquer les concentrations élevées de Hg dans les prédateurs supér-ieurs des lacs à pH bas. Pour étudier la question, nous avons prélevé des perchaudes (Perca flavescens), des barbottes brunes (Ameiurus nebulosus), des fondules barrés (Fundulus diaphanus), des chattes de l'est (Notemigonus crysoleucas), ainsi que des invertébrés littoraux et pélagiques dans quatre lacs acides du parc national et lieu historique national de Kejimkujik (KNPNHS), Nouvelle-É cosse, Canada, et nous avons dosé le Hg total et le méthylmercure (MeHg) et calculé les valeurs de d 13 C et de d 15 N afin de déterminer respectivement les sources d'énergie et la position trophique. Les taux de bioamplification du mercure (pentes de log Hg sur d 15 N) varient significativement entre les quatre lacs, mais n'expliquent pas les différences de Hg chez les perchaudes dans ces différents lacs; ces pentes se retrouvent aussi dans la gamme des pentes publiées pour les lacs près de la neutralité. Au contraire, les concentrations de Hg chez les perchaudes (des poissons prédateurs) dans le KNPNHS sont plus fortes dans les lacs qui ont plus de MeHg dans les organismes de niveau trophique inférieur; cela laisse croire que les processus qui influencent l'incorporation de Hg à la base du réseau alimentaire sont plus importants que les taux de bioamplification dans le réseau alimentaire pour expliquer la variation des concentrations...

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Anthropogenic influences, including climate change, are increasing river temperatures in northern and temperate regions and threatening the thermal habitats of native salmonids. When river temperatures exceed the tolerance levels of brook trout and Atlantic salmon, individuals exhibit behavioural thermoregulation by seeking out cold‐water refugia – often created by tributaries and groundwater discharge. Thermal infrared (TIR) imagery was used to map cold‐water anomalies along a 53 km reach of the Cains River, New Brunswick. Trout and salmon parr did not use all identified thermal anomalies as refugia during higher river temperature periods (>21°C). Most small‐bodied trout (8–30 cm) were observed in 80% of the thermal anomalies sampled. Large‐bodied trout (>35 cm) required a more specific set of physical habitat conditions for suitable refugia, that is, 100% of observed large trout used 30% of the anomalies sampled and required water depths >65 cm within or adjacent to the anomaly. Densities of trout were significantly higher within anomalies compared with areas of ambient river temperature. Salmon parr were less aligned with thermal anomalies at the observed temperatures, that is, 59% were found in 65% of the sampled anomalies; and densities were not significantly different within/ outside anomalies. Salmon parr appeared to aggregate at 27°C, and after several events over 27°C variability in aggregation behaviour was observed – some fish aggregated at 25°C, others did not. We stipulate this is due to variances of thermal fatigue. Habitat suitability curves were developed for velocity, temperature, depth, substrate, and deep water availability to characterize conditions preferred by fish during high‐temperature events. These findings are useful for managers as our climate warms, and can potentially be used as a tool to help conserve and enhance thermal refugia for brook trout and Atlantic salmon in similar systems.

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