Benjamin H. Letcher

Alternative life histories shape brain gene expression profiles in males of the same population

Atlantic salmon (Salmo salar) undergo spectacular marine migrations before homing to spawn in natal rivers. However, males that grow fastest early in life can adopt an alternative ‘sneaker’ tactic by maturing earlier at greatly reduced size without leaving freshwater. While the ultimate evolutionary causes have been well studied, virtually nothing is known about the molecular bases of this developmental plasticity. We investigate the nature and extent of coordinated molecular changes that accompany such a fundamental transformation by comparing the brain transcription profiles of wild mature sneaker males to age-matched immature males (future large anadromous males) and immature females. Of the ca. 3000 genes surveyed, 15% are differentially expressed in the brains of the two male types. These genes are involved in a wide range of processes, including growth, reproduction and neural plasticity. Interestingly, despite the potential for wide variation in gene expression profiles among individuals sampled in nature, consistent patterns of gene expression were found for individuals of the same reproductive tactic. Notably, gene expression patterns in immature males were different both from immature females and sneakers, indicating that delayed maturation and sea migration by immature males, the ‘default’ life cycle, may actually result from an active inhibition of development into a sneaker.

Population response to habitat fragmentation in a stream-dwelling brook trout population

Fragmentation can strongly influence population persistence and expression of life-history strategies in spatially-structured populations. In this study, we directly estimated size-specific dispersal, growth, and survival of stream-dwelling brook trout in a stream network with connected and naturally-isolated tributaries. We used multiple-generation, individual-based data to develop and parameterize a size-class and location-based population projection model, allowing us to test effects of fragmentation on population dynamics at local (i.e., subpopulation) and system-wide (i.e., metapopulation) scales, and to identify demographic rates which influence the persistence of isolated and fragmented populations. In the naturally-isolated tributary, persistence was associated with higher early juvenile survival (∼45% greater), shorter generation time (one-half) and strong selection against large body size compared to the open system, resulting in a stage-distribution skewed towards younger, smaller fish. Simulating barriers to upstream migration into two currently-connected tributary populations caused rapid (2–6 generations) local extinction. These local extinctions in turn increased the likelihood of system-wide extinction, as tributaries could no longer function as population sources. Extinction could be prevented in the open system if sufficient immigrants from downstream areas were available, but the influx of individuals necessary to counteract fragmentation effects was high (7–46% of the total population annually). In the absence of sufficient immigration, a demographic change (higher early survival characteristic of the isolated tributary) was also sufficient to rescue the population from fragmentation, suggesting that the observed differences in size distributions between the naturally-isolated and open system may reflect an evolutionary response to isolation. Combined with strong genetic divergence between the isolated tributary and open system, these results suggest that local adaptation can ‘rescue’ isolated populations, particularly in one-dimensional stream networks where both natural and anthropogenically-mediated isolation is common. However, whether rescue will occur before extinction depends critically on the race between adaptation and reduced survival in response to fragmentation.

Remote monitoring of fish in small streams: A unified approach using PIT tags

Abstract Accurate assessments of fish populations are often limited by re-observation or recapture events. Since the early 1990s, passive integrated transponders (PIT tags) have been used to understand the biology of many fish species. Until recently, PIT applications in small streams have been limited to physical recapture events. To maximize recapture probability, we constructed PIT antenna arrays in small streams to remotely detect individual fish. Experiences from two different laboratories (three case studies) allowed us to develop a unified approach to applying PIT technology for enhancing data assessments. Information on equipment, its installation, tag considerations, and array construction is provided. Theoretical and practical definitions are introduced to standardize metrics for assessing detection efficiency. We demonstrate how certain conditions (stream discharge, vibration, and ambient radio frequency noise) affect the detection efficiency and suggest that by monitoring these conditions, exp...

Tag Retention and Survival of Age-0 Atlantic Salmon following Surgical Implantation with Passive Integrated Transponder Tags

Abstract We evaluated an alternative to using hypodermic needles to implant passive integrated transponder (PIT) tags in the body cavities of juvenile salmonids. We used surgical techniques to place PIT tags into the body cavities of 3,037 age-0 Atlantic salmon Salmo salar and then held fish under hatchery conditions for 9 months. Tag retention was 99.8% (six fish lost tags), and survival was 94.3% (174 fish died) after controlling for initial mortality (0.7%). A single tagger was able to tag 80–100 fish per hour. Surgically implanting PIT tags into the body cavities of age-0 Atlantic salmon proved to be a viable alternative to using hypodermic needles.

Distance, flow and PCR inhibition: eDNA dynamics in two headwater streams.

Environmental DNA (eDNA) detection has emerged as a powerful tool for monitoring aquatic organisms, but much remains unknown about the dynamics of aquatic eDNA over a range of environmental conditions. DNA concentrations in streams and rivers will depend not only on the equilibrium between DNA entering the water and DNA leaving the system through degradation, but also on downstream transport. To improve understanding of the dynamics of eDNA concentration in lotic systems, we introduced caged trout into two fishless headwater streams and took eDNA samples at evenly spaced downstream intervals. This was repeated 18 times from mid‐summer through autumn, over flows ranging from approximately 1–96 L/s. We used quantitative PCR to relate DNA copy number to distance from source. We found that regardless of flow, there were detectable levels of DNA at 239.5 m. The main effect of flow on eDNA counts was in opposite directions in the two streams. At the lowest flows, eDNA counts were highest close to the source and quickly trailed off over distance. At the highest flows, DNA counts were relatively low both near and far from the source. Biomass was positively related to eDNA copy number in both streams. A combination of cell settling, turbulence and dilution effects is probably responsible for our observations. Additionally, during high leaf deposition periods, the presence of inhibitors resulted in no amplification for high copy number samples in the absence of an inhibition‐releasing strategy, demonstrating the necessity to carefully consider inhibition in eDNA analysis.

create: a software to create input files from diploid genotypic data for 52 genetic software programs

create is a Windows program for the creation of new and conversion of existing data input files for 52 genetic data analysis software programs. Programs are grouped into areas of sibship reconstruction, parentage assignment, genetic data analysis, and specialized applications. create is able to read in data from text, Microsoft Excel and Access sources and allows the user to specify columns containing individual and population identifiers, birth and death data, sex data, relationship information, and spatial location data. creates only constraints on source data are that one individual is contained in one row, and the genotypic data is contiguous. create is available for download at http://www.lsc.usgs.gov/CAFL/Ecology/Software.html.

Fine‐scale population structure and riverscape genetics of brook trout (Salvelinus fontinalis) distributed continuously along headwater channel networks

Linear and heterogeneous habitat makes headwater stream networks an ideal ecosystem in which to test the influence of environmental factors on spatial genetic patterns of obligatory aquatic species. We investigated fine‐scale population structure and influence of stream habitat on individual‐level genetic differentiation in brook trout (Salvelinus fontinalis) by genotyping eight microsatellite loci in 740 individuals in two headwater channel networks (7.7 and 4.4 km) in Connecticut, USA. A weak but statistically significant isolation‐by‐distance pattern was common in both sites. In the field, many tagged individuals were recaptured in the same 50‐m reaches within a single field season (summer to fall). One study site was characterized with a hierarchical population structure, where seasonal barriers (natural falls of 1.5–2.5 m in height during summer base‐flow condition) greatly reduced gene flow and perceptible spatial patterns emerged because of the presence of tributaries, each with a group of genetically distinguishable individuals. Genetic differentiation increased when pairs of individuals were separated by high stream gradient (steep channel slope) or warm stream temperature in this site, although the evidence of their influence was equivocal. In a second site, evidence for genetic clusters was weak at best, but genetic differentiation between individuals was positively correlated with number of tributary confluences. We concluded that the population‐level movement of brook trout was limited in the study headwater stream networks, resulting in the fine‐scale population structure (genetic clusters and clines) even at distances of a few kilometres, and gene flow was mitigated by ‘riverscape’ variables, particularly by physical barriers, waterway distance (i.e. isolation‐by‐distance) and the presence of tributaries.

Size-dependent survival of brook trout Salvelinus fontinalis in summer: effects of water temperature and stream flow

A 5 year individual-based data set was used to estimate size-specific survival rates in a wild brook trout Salvelinus fontinalis population in a stream network encompassing a mainstem and three tributaries (1.5-6 m wetted width), western Massachusetts, U.S.A. The relationships between survival in summer and temperature and flow metrics derived from continuous monitoring data were then tested. Increased summer temperatures significantly reduced summer survival rates for S. fontinalis in almost all size classes in all four sites throughout the network. In contrast, extreme low summer flows reduced survival of large fish, but only in small tributaries, and had no significant effects on fish in smaller size classes in any location. These results provide direct evidence of a link between season-specific survival and environmental factors likely to be affected by climate change and have important consequences for the management of both habitats and populations.

Survival of Stream-Dwelling Atlantic Salmon: Effects of Life History Variation, Season, and Age

Abstract To determine seasonal and age-class variation in the abundance and survival of Atlantic salmon Salmo salar, we conducted multiple samplings of individually tagged juveniles in a small stream (West Brook, Massachusetts). We also estimated the differences in survival and probability of smolting for mature and immature parr. Survival was approximately twofold lower during winter as compared with summer and was higher for fish in their first winter than for fish in their second winter. Parr maturation rates were high (50% of all fish) and peaked in September. The estimated numbers of mature and immature fish were equal for the March samples preceding the smolt run, indicating no overall differences in survival between mature and immature fish during stream residence. Age-2 mature fish were one-third as likely to smolt as immature fish, however, resulting in survival probabilities (from March to smoltification) of 0.22 for mature fish and 0.61 for immature fish. Approximately one-third of the fish cap...

Dispersal and Within-Stream Spatial Population Structure of Brook Trout Revealed by Pedigree Reconstruction Analysis

Abstract Spatial patterns of spawning and early dispersal have important implications for the population dynamics of stream-dwelling salmonids, but the limitations of marking technology have made it difficult to measure these processes in wild populations. We used microsatellite DNA markers and sibship and parentage analyses to follow the dispersal, spatial distribution, and distribution of reproductive success in a small, isolated western Virginia population of brook trout Salvelinus fontinalis at 4, 16, and 28 months after fry emergence. For the 2004 year-class (high-recruitment cohort), we identified 180 full-sibling families representing individual spawning events. Offspring were unevenly distributed across families, with 16% of the families accounting for 50% of the offspring and 53% of the families being represented by fewer than three individuals. However, a large proportion of adults had some successful reproduction. Spatial and family size distributions at 4 months after emergence were similar be...