BackgroundSalmonids are regarded as 4R derivative species, having experienced 4 whole genome duplication events in their ancestry. Many duplicated chromosome regions still share extensive homology with one another which is maintained primarily through male-based homeologous chromosome pairings during meiosis. The formation of quadrivalents during meiosis leads to pseudolinkage. This phenomenon is more prevalent within 5 of the 12 ancestral teleost linkage groups in salmonids.ResultsWe constructed a genetic linkage map for brook charr and used this in combination with the genetic map from Arctic charr, to make comparisons with the genetic map of rainbow trout. Although not all chromosome arms are currently mapped, some homologous chromosome rearrangements were evident between Arctic charr and brook charr. Notably, 10 chromosome arms in brook charr representing 5 metacentric chromosomes in Arctic charr have undergone rearrangements. Three metacentrics have one arm translocated and fused with another chromosome arm in brook charr to a make a new metacentrics while two metacentrics are represented by 4 acrocentric pairs in brook charr. In two cases (i.e., BC-4 and BC-16), an apparent polymorphism was observed with the identification of both a putative metacentric structure (similar to metacentric AC-4 = BC-4 and a joining of acrocentric AC-16 + one arm of AC-28 = BC-16), as well as two separate acrocentric linkage groups evident in the mapping parents. Forty-six of the expected 50 karyotypic arms could be inter-generically assigned. SEX in brook charr (BC-4) was localized to the same homologous linkage group region as in Arctic charr (AC-4). The homeologous affinities detected in the two charr species facilitated the identification of 20 (expected number = 25) shared syntenic regions with rainbow trout, although it is likely that some of these regions were partial or overlapping arm regions.ConclusionsInter-generic comparisons among 2 species of charr (genus Salvelinus) and a trout (genus Oncorhynchus) have identified that linkage group arm arrangements are largely retained among these species. Previous studies have revealed that up to 7 regions of high duplicate marker retention occur between Salmo species (i.e., Atlantic salmon and brown trout) and rainbow trout, with 5 of these regions exhibiting higher levels of pseudolinkage. Pseudolinkage was detected in the charr species (i.e., BC-1/21, AC-12/27, AC-6/23, = RT-2p/29q, RT-12p/16p, and RT-27p/31p, respectively) consistent with three of the five 'salmonid-specific' pseudolinkage regions. Chromosome arms with the highest number of duplicated markers in rainbow trout are the linkage group arms with the highest retention of duplicated markers in both charr species.

We investigated the response of the invertebrate drift to the regulated peaking Magpie River under experimental sub-hourly changes in flow conditions. Benthic invertebrates were also quantified upstream of invertebrate drift sampling sites in order to examine the propensity of nearby invertebrates to drift under hydropeaking cycles. To provide an understanding of the natural patterns of drift in relation to changes in discharge, the proximate natural Batchawana River was similarly sampled. Increased discharge was associated with higher drift densities and greater particulate organic matter in the Magpie River. At the family level, multiple drift responses were observed suggesting that ecological traits and behaviors drive drift response to changes in discharge. The drift densities of some invertebrates varied in proportion to discharge; whereas, other invertebrates in the drift decreased to pre-peaking levels shortly after peak discharge was reached, with some invertebrates exhibiting a secondary peak in density as discharge returned to pre-peaking levels. Although average drift densities were comparable between the two rivers, drift density on the natural Batchawana River was much more stable than that of the Magpie River. Changes in drift density associated with flow manipulation likely impact feeding patterns and behavior of drift feeding fish.

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Long-term monitoring of the food web of a regulated hydropeaking river was conducted to assess if previously documented effects of changing ramping rates (RRs) were maintained with the addition of 6 years of data. Using carbon and nitrogen stable isotope analyses, we hypothesized that: (1) macroinvertebrates and fish inhabiting areas below peaking hydrodams would be higher in δ 15 N and lower in δ 13 C due to increased flow velocity and the influence of light respired dissolved inorganic carbon, relative to those sampled from areas with a natural flow regime; (2) the increase in δ 15 N of macroinvertebrates would lead a shorter food web length in the regulated river, but δ 13 C and niche width would be similar between the restricted and unrestricted RR periods (i.e., the BACI analysis); and (3) isotopic metrics (e.g., δ 13 C, δ 15 N, niche width [SEA B ], and food chain length [Δ 15 N]) would correlate with variations in flow characteristics through time. Consistent with previous analysis conducted over a shorter time period, a shift toward higher δ 15 N values was observedfor both fish and invertebrates, but, contrarily, only invertebrates (not fish) had a lower δ 13 C value downstream of the dam. Over the long term, the before-aftercontrol-impact analysis found no effect of RRs on any of the food web metrics, implying that the change in operation did not affect the river food web. However, analysis of the time series data indicated that flow metrics and trophic metrics were often correlated, including a negative effect of RR (invertebrates) and discharge (fish) on food chain length. This study illustrates the difficulty in detecting changes in food web structure and function under changing flow regime influenced by natural and anthropogenic effects. As such, this study highlights the need for considering large spatial and temporal scales to differentiate between confounding effects of climate, natural variability, and altered flow regimes on food webs in regulated rivers. KEYWORDScarbon and nitrogen isotopic niche, flow, hydropeaking, regulated rivers, stable isotopes