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Many populations of freshwater fishes are threatened with losses, and increasingly, the release of hatchery individuals is one strategy being implemented to support wild populations. However, stocking of hatchery individuals may pose long‐term threats to wild populations, particularly if genetic interactions occur between wild and hatchery individuals. One highly prized sport fish that has been heavily stocked throughout its range is the brook trout (Salvelinus fontinalis). In Nova Scotia, Canada, hatchery brook trout have been stocked since the early 1900s, and despite continued stocking efforts, populations have suffered declines in recent decades. Before this study, the genetic structure of brook trout populations in the province was unknown; however, given the potential negative consequences associated with hatchery stocking, it is possible that hatchery programs have adversely affected the genetic integrity of wild populations. To assess the influence of hatchery supplementation on wild populations, we genotyped wild brook trout from 12 river systems and hatchery brook trout from two major hatcheries using 100 microsatellite loci. Genetic analyses of wild trout revealed extensive population genetic structure among and within river systems and significant isolation‐by‐distance. Hatchery stocks were genetically distinct from wild populations, and most populations showed limited to no evidence of hatchery introgression (

Many fishes express high levels of intraspecific variability, often linked to resource partitioning. Several studies show that a species' evolutionary trajectory of adaptive divergence can undergo reversals caused by changes in its environment. Such a reversal in neutral genetic and morphological variation among lake trout Salvelinus namaycush ecomorphs appears to be underway in Lake Superior. However, a water depth gradient in neutral genetic divergence was found to be associated with intraspecific diversity in the lake. To investigate patterns of adaptive immunogenetic variation among lake trout ecomorphs, we used Illumina high-throughput sequencing. The population's genetic structure of the major histocompatibility complex (MHC Class IIβ exon 2) and 18 microsatellite loci were compared to disentangle neutral and selective processes at a small geographic scale. Both MHC and microsatellite variation were partitioned more by water depth stratum than by ecomorph. Several metrics showed strong clustering by water depth in MHC alleles, but not microsatellites. We report a 75% increase in the number of MHC alleles shared between the predominant shallow and deep water ecomorphs since a previous lake trout MHC study at the same locale (c. 1990s data). This result is consistent with the reverse speciation hypothesis, although adaptive MHC polymorphisms persist along an ecological gradient. Finally, results suggested that the lake trout have multiple copies of the MHC II locus consistent with a historic genomic duplication event. Our findings indicated that conservation approaches for this species could focus on managing various ecological habitats by depth, in addition to regulating the fisheries specific to ecomorphs.

Depth is usually considered the main driver of Lake Trout intraspecific diversity across lakes in North America. Given that Great Bear Lake is one of the largest and deepest freshwater systems in North America, we predicted that Lake Trout intraspecific diversity to be organized along a depth axis within this system. Thus, we investigated whether a deep-water morph of Lake Trout co-existed with four shallow-water morphs previously described in Great Bear Lake. Morphology, neutral genetic variation, isotopic niches, and life-history traits of Lake Trout across depths (0-150 m) were compared among morphs. Due to the propensity of Lake Trout with high levels of morphological diversity to occupy multiple habitat niches, a novel multivariate grouping method using a suite of composite variables was applied in addition to two other commonly used grouping methods to classify individuals. Depth alone did not explain Lake Trout diversity in Great Bear Lake; a distinct fifth deep-water morph was not found. Rather, Lake Trout diversity followed an ecological continuum, with some evidence for adaptation to local conditions in deep-water habitat. Overall, trout caught from deep-water showed low levels of genetic and phenotypic differentiation from shallow-water trout, and displayed higher lipid content (C:N ratio) and occupied a higher trophic level that suggested an potential increase of piscivory (including cannibalism) than the previously described four morphs. Why phenotypic divergence between shallow- and deep-water Lake Trout was low is unknown, especially when the potential for phenotypic variation should be high in deep and large Great Bear Lake. Given that variation in complexity of freshwater environments has dramatic consequences for divergence, variation in the complexity in Great Bear Lake (i.e., shallow being more complex than deep), may explain the observed dichotomy in the expression of intraspecific phenotypic diversity between shallow- vs. deep-water habitats. The ambiguity surrounding mechanisms driving divergence of Lake Trout in Great Bear Lake should be seen as reflective of the highly variable nature of ecological opportunity and divergent natural selection itself.

In this study, we investigated the relative influence of habitat variables on the decision by Sterna dougallii (Roseate Tern) parents to move from (movers) or to stay at (stayers) the nest after chick hatch. At Country Island, NS, Canada, 75% of the 21 Roseate Tern breeding pairs in this study were movers. Using a model-selection approach, we found that the chicks were more likely to be moved from nest sites in cobble beach habitat with low vegetation height and high nest densities of congener terns. However, differences in reproductive parameters among movers and stayers were not statistically significant. Though we could not establish whether moving the chicks or staying were adaptive strategies, we provide firm evidence that Roseate Tern chicks are moved to areas of lower tern densities. Chicks move further away from other terns as they age, perhaps as a mechanism to avoid kleptoparasitism as their nutritional requirements increase. Based on our findings, Roseate Terns appear more likely to re...

Little is known about how a 70% loss of native forests has affected the genetic connectivity of remnant bird populations in New Zealand. We use the common and widely distributed New Zealand Bellbird Anthornis melanura as an indicator species of population connectivity for well-flighted birds. Using eight microsatellite loci, we identified five main genetic populations in the North Island, South Island, sub-Antarctic Auckland Islands and two small remnant island populations adjacent to a large region of avian extirpations in northern North Island. Only one remnant island population, on a 30-year-old conservation reserve at Tiritiri Matangi, displayed a clear signature of recent genetic bottleneck. The 7% migration rate at Tiritiri Matangi indicates that bottlenecks can be maintained despite habitat rehabilitation, possibly through behavioural barriers to gene flow. Adjacent to the same extirpation zone, Bellbirds on the Poor Knights Islands were found to have low genetic diversity and low re-colonization potential. Two gaps concordant with deforestation patterns separated the Kapiti Coast of southern North Island from populations to both the north and the south. In summary, we identified linked avian habitats, as well as isolated and inbred populations and suggest that Bellbirds are good re-colonizers. We emphasize the importance of genetic studies that assess animal dispersal among newly rehabilitated habitat patches.

All examples of lake charr (Salvelinus namaycush) diversity occur within the largest, deepest lakes of North America (i.e. > 2000 km2). We report here Rush Lake (1.3 km2) as the first example of a small lake with two lake charr morphs (lean and huronicus). Morphology, diet, life history, and genetics were examined to demonstrate the existence of morphs and determine the potential influence of evolutionary processes that led to their formation or maintenance. Results showed that the huronicus morph, caught in deep-water, had a deeper body, smaller head and jaws, higher eye position, greater buoyancy, and deeper peduncle than the shallow-water lean morph. Huronicus grew slower to a smaller adult size, and had an older mean age than the lean morph. Genetic comparisons showed low genetic divergence between morphs, indicating incomplete reproductive isolation. Phenotypic plasticity and differences in habitat use between deep and shallow waters associated with variation in foraging opportunities seems to have been sufficient to maintain the two morphs, demonstrating their important roles in resource polymorphism. Rush Lake expands previous explanations for lake charr intraspecific diversity, from large to small lakes and from reproductive isolation to the presence of gene flow associated with strong ecological drivers.

We describe eight novel microsatellite loci for the tui, Prosthemadera novaeseelandiae, and the cross-amplification of six polymorphic loci developed for the bellbird (Anthornis melanura). Fifty tui samples from Tawharanui Regional Park, New Zealand, were genotyped using the 14 loci described. Numbers of alleles ranged from 3 to 16. Observed and expected heterozygosities ranged between 0.180–0.940 and 0.237–0.878, respectively. There was no evidence of linkage disequilibrium. One locus (Ame-22) significantly deviated from Hardy–Weinberg Equilibrium. This study highlights the benefits of long-repeat microsatellites in minimising scoring errors. These are the first microsatellites to be developed for the tui and also provide potential markers for studying other honeyeaters throughout the Austro-Papuan region.

SUMMARYUnderstanding the origin of invasive parasites and ecological transmission barriers on the distribution of mosquito-borne pathogens is enriched by molecular phylogenetic approaches now that large databases are becoming available. Here we assess the biogeographical relationships among haemosporidian blood parasites and an avian host, the New Zealand bellbird (Meliphagidae, Anthornis melanura). Four Plasmodium haplotypes were identified among 93 infected bellbirds (693 screened) using nested PCR of a mitochondrial DNA cytochrome b gene fragment. The most common lineage, LIN1 (11%), is confined to northern New Zealand and falls within a known clade of Plasmodium (subgenus Novyella) sp. infecting Australian meliphagids. LIN1 differs within that clade by 4 9% sequence divergence suggestive of an endemic lineage to New Zealand. The most widespread lineage, LIN2 (2%), is an exact match with a global cosmopolitan (P. elongatum GRW06). Two rare lineages, LIN3 and LIN4 are less abundant, geographically restricted within New Zealand and have P. (Novyella) sp. (AFTRU08) and P. relictum (LINOLI01) documented from Africa. For the first time, we provide invaluable information on possible rates of entry of invading parasites in New Zealand and their distribution from temperate to cold environments.

Three Arctic marine fishes Icelus spatula, Aspidophoroides olrikii and Leptoclinus maculatus have been identified as target species for investigating the effects of ocean warming on population patterns in high-latitude marine habitats around Canada. In preparation for this research, we have resolved whole mitochondrial genome sequences of 16 384, 17 200 and 16 384 bp for each species, respectively. GC content for each species was 47.5%, 44.2% and 45.3%, respectively. Mitogenome gene composition included 13 protein-encoding genes, 2 rRNA and 22 tRNA genes, for I. spatula and L. maculatus, consistent with other teleosts. Only 20 tRNA genes were annotated for A. olrikii, because tRNA-Pro and tRNA-Thr are poorly characterized and aberrantly located in this species.

In eastern Canada during the early 1990s, a shift in the distribution of Capelin (Mallotus villosus) resulted in a prolonged absence (at least 8 years) of the preferred prey for the Atlantic Puffin (Fratercula arctica) breeding at Gannet Islands, Labrador. It has been documented that there is no suitable alternative prey to Capelin in the northwest Atlantic for seabirds, thus these extreme changes in food supply may have negative effects on reproduction and adult survivorship. In this study, foraging behavior, chick growth and productivity of Atlantic Puffins at the Gannet Islands, Labrador during 1996-1998 were compared to data in a study undertaken in 1981-1983, prior to the decline in Capelin abundance. It was confirmed that the dramatic change in Capelin abundance was reflected in chick diet as Atlantic Puffin chicks received 50-70% (by mass) less Capelin in 1996-1998 than in 1981-1983. Hatch dates did not differ among decades and breeding success, chick wing growth and fledge mass were unaff...

We compared nestling diet and growth, breeding phenology, breeding success, and adult mass of Atlantic Puffins (Fratercula arctica) between two seabird colonies adjacent to ocean habitat with presumed high and low capelin (Mallotus villosus) abundance in 1996–1998. We hypothesized that puffins at their colony at Gannet Islands, Labrador, where capelin were scarce, would exhibit lower reproductive performance than at Gull Island, Witless Bay, where capelin were abundant. Historically, capelin comprised approximately 60%–95% of the chick diet biomass at both colonies. In the late 1990s, puffin chicks at the Gannet Islands received 3%–24% capelin (by mass), which was 39%–97% less than was received at Gull Island. Postlarval sandlance (Ammodytes sp.) comprised up to 49% (by mass) of the chick diet at the Gannet Islands. Hatching success and fledge success estimates at the Gannet Islands in 1997–1998 were statistically similar to those at Gull Island in 1998. Fledge mass (expressed as percentage of adult mass) was similar between Gannet Islands (69%) and Gull Island (68%). The high interyear variability in chick diet at both colonies and the low variation in breeding performance during our study suggest that Atlantic Puffins in Labrador are resilient to large-scale prey-base changes.

DNA barcode sequences were developed from 557 mesopelagic and upper bathypelagic teleost specimens collected in waters off Atlantic Canada. Confident morphological identifications were available for 366 specimens, of 118 species and 93 genera, which yielded 328 haplotypes. Five of the species were novel to the Barcode of Life Database (BOLD). Most of the 118 species conformed to expectations of monophyly and the presence of a “barcode gap”, though some known weaknesses in existing taxonomy were confirmed and a deficiency in published keys was revealed. Of the specimens for which no firm morphological identification was available, 156 were successfully identified to species, and a further 11 to genus, using their barcode sequences and a combination of distance- and character-based methods. The remaining 24 specimens were from species for which no reference barcode is yet available or else ones confused by apparent misidentification of publicly available sequences in BOLD. Addition of the new sequences to those previously in BOLD contributed support to recent taxonomic revisions of Chiasmodon and Poromitra, while it also revealed 18 cases of potential cryptic speciation. Most of the latter appear to result from genetic divergence among populations in different ocean basins, while the general lack of strong horizontal environmental gradients within the deep sea has allowed morphology to be conserved. Other examples of divergence appear to distinguish individuals living under the sub-tropical gyre of the North Atlantic from those under that ocean’s sub-polar gyre. In contrast, the available sequences for two myctophid species, Benthosema glaciale and Notoscopelus elongatus, showed genetic structuring on finer geographic scales. The observed structure was not consistent with recent suggestions that “resident” populations of myctophids can maintain allopatry despite the mixing of ocean waters. Rather, it indicates that the very rapid speciation characteristic of the Myctophidae is both on-going and detectable using barcodes.

We describe 12 new microsatellite loci for the Korimako (New Zealand Bellbird), Anthornis melanura. The loci include 9 tetranucleotide loci, 2 pentanucleotide loci and one hexanucleotide locus. We characterized these loci in a sample from Tiritiri Matangi Island and found 2–8 alleles per locus, observed and expected heterozygosities ranged from 0.21–0.74 to 0.25–0.72 respectively. One locus was out of Hardy–Weinburg equilibrium and no evidence of linkage disequilibrium among loci was found.

This is the first documented incident of River Otter (Lutra canadensis) feeding on Common Goldeneye (Bucephala clangula) in a little studied region, southern Labrador. Our observations were made during spring staging when waterfowl aggregate at open water sites in frozen lakes and rivers, locally known as ashkui. We suggest that otters and raptors opportunistically forage on staging waterfowl at ashkui.

North America's northern lakes are undergoing major changes. Lake Superior is the coldest and northernmost of the Laurentian Great Lakes. Here, we present an extension of a long-term data set that monitors genetic and phenotypic diversity of lake trout Salvelinus namaycush in Lake Superior. Hypotheses were investigated pertaining to loss of genetic diversity and genetic homogenization among three lake trout ecomorphs in Lake Superior during their recovery several decades after a major fishery collapse in the early 1960s. Comparison of a contemporary (2004–2013) microsatellite DNA data set to a previously published, post-collapse recovery period data set (1995–1999) indicated substantive losses in genetic diversity. Allelic richness decreased by 5.7%, 12.3%, and 6.8% at Isle Royale, Stannard Rock, and Klondike Reef, respectively. A 60.7% reduction in genetic distance among ecomorphs since the 1990s was detected. Comparisons with a third data set of samples collected during the fishery collapse (1959) indicated an overall 18.2% loss in allelic richness at Isle Royale. The amount of introgression among ecomorphs has likely increased over time. Apparent losses in genetic diversity could be a consequence of historical fishery harvests (early 1900s) exacerbated by intensive stocking (1950s–1980s) and invasions of non-native species (1960s–1990s). Overlap in foraging and breeding areas may have contributed to increasing levels of hybridization among ecomorphs. Knowledge of these processes will help to identify impediments and strategies for the maintenance of lake trout biodiversity in northern Great Lakes, and their re-establishment in the Laurentian Great Lakes.

Background Adaptive radiation involving a colonizing phenotype that rapidly evolves into at least one other ecological variant, or ecotype, has been observed in a variety of freshwater fishes in post-glacial environments. However, few studies consider how phenotypic traits vary with regard to neutral genetic partitioning along ecological gradients. Here, we present the first detailed investigation of lake trout Salvelinus namaycush that considers variation as a cline rather than discriminatory among ecotypes. Genetic and phenotypic traits organized along common ecological gradients of water depth and geographic distance provide important insights into diversification processes in a lake with high levels of human disturbance from over-fishing. Results Four putative lake trout ecotypes could not be distinguished using population genetic methods, despite morphological differences. Neutral genetic partitioning in lake trout was stronger along a gradient of water depth, than by locality or ecotype. Contemporary genetic migration patterns were consistent with isolation-by-depth. Historical gene flow patterns indicated colonization from shallow to deep water. Comparison of phenotypic (Pst) and neutral genetic variation (Fst) revealed that morphological traits related to swimming performance (e.g., buoyancy, pelvic fin length) departed more strongly from neutral expectations along a depth gradient than craniofacial feeding traits. Elevated phenotypic variance with increasing water depth in pelvic fin length indicated possible ongoing character release and diversification. Finally, differences in early growth rate and asymptotic fish length across depth strata may be associated with limiting factors attributable to cold deep-water environments. Conclusion We provide evidence of reductions in gene flow and divergent natural selection associated with water depth in Lake Superior. Such information is relevant for documenting intraspecific biodiversity in the largest freshwater lake in the world for a species that recently lost considerable genetic diversity and is now in recovery. Unknown is whether observed patterns are a result of an early stage of incipient speciation, gene flow-selection equilibrium, or reverse speciation causing formerly divergent ecotypes to collapse into a single gene pool. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0788-8) contains supplementary material, which is available to authorized users.