Optimization of an amplicon sequencing-based microsatellite panel and protocol for stock identification and kinship inference of lake trout (Salvelinus namaycush).

Kinship-based methods of population assessment such as close-kin mark-recapture require accurate and efficient genotyping methods capable of resolving complex relationships among kin. Inference of such relationships can be difficult using biallelic loci due to the large number of markers required to obtain the necessary power. Sequencing-based microsatellite panels offer an efficient alternative, combining high polymorphism with efficient next-generation methods. Here we construct, optimize, and test one such panel for lake trout (Salvelinus namaycush) using a combination of previously-published loci adapted for sequencing and de novo loci mined from a genome assembly. We performed three rounds of primer optimization, yielding a final panel of 131 loci, followed by testing with two different levels of PCR multiplexing (all primers in one or two groups) and two different reaction volumes (5 and 10 µL). Our results showed that the use of the largest multiplex and smallest reaction volume did not substantially change results, allowing significant cost and time savings. To test panel accuracy, we used both a set of 153 known-origin samples from origins of management interest and a series of hatchery crosses representing nine families with parent-offspring, half-sibling, and largely-unrelated pairs. Our results indicate that sequencing-based microsatellite panels can efficiently and accurately provide the information required for a population genetics analyses including population assignment, calculation of between-population F ST, and kinship-based population estimation techniques. Such techniques are seeing increasing applications for a wide range of taxa; our findings should provide insight and guidance for the development of the necessary molecular resources.

Diel activity of newly metamorphosed juvenile sea lamprey (Petromyzon marinus).

Timing of activity, especially for juvenile anadromous fishes undertaking long migrations can be critical for survival. River-resident larval sea lamprey metamorphose into juveniles and migrate from their larval stream habitats in fall through spring, but diel timing of this migratory behavior is not well understood. Diel activity was determined for newly metamorphosed sea lamprey using day/night net sampling and passive integrated transponder (PIT) telemetry in two natural streams and PIT telemetry in an artificial stream. Downstream migration was primarily nocturnal in all studies. All but one of 372 sea lamprey were captured during night sampling in the day/night net collections and all detections (N = 56) for the in-stream PIT telemetry occurred within a few hours after sunset. Most (81% of 48) tagged lamprey moved downstream during the first night following release and moved at speeds consistent with observed water velocities. During long-term observation of behavior in the artificial stream most sea lamprey movement occurred during the night with limited occurrence of movement during daylight hours. Understanding seasonal and diel timing of downstream migration behavior may allow more effective management of sea lamprey for both conservation and control.

Temporal constraints on the potential role of fry odors as cues of past reproductive success for spawning lake trout.

Deciding where to reproduce is a major challenge for most animals. Many select habitats based upon cues of successful reproduction by conspecifics, such as the presence of offspring from past reproductive events. For example, some fishes select spawning habitat following odors released by juveniles whose rearing habitat overlaps with spawning habitat. However, juveniles may emigrate before adults begin to search for spawning habitat; hence, the efficacy of juvenile cues could be constrained by degradation or dissipation rates. In lake trout (Salvelinus namaycush), odors deposited by the previous year's offspring have been hypothesized to guide adults to spawning reefs. However, in most extant populations, lake trout fry emigrate from spawning reefs during the spring and adults spawn during the fall. Therefore, we postulated that the role of fry odors in guiding habitat selection might be constrained by the time between fry emigration and adult spawning. Time course chemical, physiological, and behavioral assays indicated that the odors deposited by fry likely degrade or dissipate before adults select spawning habitats. Furthermore, fry feces did not attract wild lake trout to constructed spawning reefs in Lake Huron. Taken together, our results indicate fry odors are unlikely to act as cues for lake trout searching for spawning reefs in populations whose juveniles emigrate before the spawning season, and underscore the importance of environmental constraints on social cues.