Geology topics

B. H. Letcher

Publications and source records attributed to B. H. Letcher.

At least 19 recordsLinked to original sources

USGS2011

GONe: Software for estimating effective population size in species with generational overlap

GONe is a user‐friendly, Windows‐based program for estimating effective size (N e ) in populations with overlapping generations. It uses the Jorde–Ryman modification to the temporal method to account for age structure in populations. This method requires estimates of age‐specific survival and birth rate and allele frequencies measured in two or more consecutive cohorts. Allele frequencies are acquired by reading in genotypic data from files formatted for either GENEPOP or TEMPOFS. For each interval between consecutive cohorts, Ne is estimated at each locus and over all loci. Furthermore, Ne estimates are output for three different genetic drift estimators ( F s , F c and F k ). Confidence intervals are derived from a chi‐square distribution with degrees of freedom equal to the number of independent alleles. GONe has been validated over a wide range of Ne values, and for scenarios where survival and birth rates differ between sexes, sex ratios are unequal and reproductive variances differ.

Molecular Ecology Resources↗

USGS2011

Variation in local abundance and species richness of stream fishes in relation to dispersal barriers: Implications for management and conservation

1.Barriers to immigration, all else being equal, should in principle depress local abundance and reduce local species richness. These issues are particularly relevant to stream-dwelling species when improperly designed road crossings act as barriers to migration with potential impacts on the viability of upstream populations. However, because abundance and richness are highly spatially and temporally heterogeneous and the relative importance of immigration on demography is uncertain, population- and community-level effects can be difficult to detect. 2.In this study, we tested the effects of potential barriers to upstream movements on the local abundance and species richness of a diverse assemblage of resident stream fishes in the Monongahela National Forest, West Virginia, U.S.A. Fishes were sampled using simple standard techniques above- and below road crossings that were either likely or unlikely to be barriers to upstream fish movements (based on physical dimensions of the crossing). We predicted that abundance of resident fishes would be lower in the upstream sections of streams with predicted impassable barriers, that the strength of the effect would vary among species and that variable effects on abundance would translate into lower species richness. 3.Supporting these predictions, the statistical model that best accounted for variation in abundance and species richness included a significant interaction between location (upstream or downstream of crossing) and type (passable or impassable crossing). Stream sections located above predicated impassable culverts had fewer than half the number of species and less than half the total fish abundance, while stream sections above and below passable culverts had essentially equivalent richness and abundance. 4.Our results are consistent with the importance of immigration and population connectivity to local abundance and species richness of stream fishes. In turn, these results suggest that when measured at appropriate scales (multiple streams within catchments), with simple protocols amenable to use by management agencies, differences in local abundance and species richness may serve as indicators of the extent to which road crossings are barriers to fish movement and help determine whether road-crossing improvements have restored connectivity to stream fish populations and communities. Published 2011. This article is a US Government work and is in the public domain in the USA.

Freshwater Biology↗

USGS2011

A model for estimating passive integrated transponder (PIT) tag antenna efficiencies for interval-specific emigration rates

Our goal was to understand movement and its interaction with survival for populations of stream salmonids at long-term study sites in the northeastern United States by employing passive integrated transponder (PIT) tags and associated technology. Although our PIT tag antenna arrays spanned the stream channel (at most flows) and were continuously operated, we are aware that aspects of fish behavior, environmental characteristics, and electronic limitations influenced our ability to detect 100% of the emigration from our stream site. Therefore, we required antenna efficiency estimates to adjust observed emigration rates. We obtained such estimates by testing a full-scale physical model of our PIT tag antenna array in a laboratory setting. From the physical model, we developed a statistical model that we used to predict efficiency in the field. The factors most important for predicting efficiency were external radio frequency signal and tag type. For most sampling intervals, there was concordance between the predicted and observed efficiencies, which allowed us to estimate the true emigration rate for our field populations of tagged salmonids. One caveat is that the model's utility may depend on its ability to characterize external radio frequency signals accurately. Another important consideration is the trade-off between the volume of data necessary to model efficiency accurately and the difficulty of storing and manipulating large amounts of data.

Transactions of the American Fisheries Society↗

USGS2011

Early discrimination of Atlantic salmon smolt age: Time course of the relative effectiveness of body size and shape

The goal of this study was to test the relative effectiveness of morphological measurements and body size in predicting the smolt age of Atlantic salmon Salmo salar and to determine the time course of body size and shape differences between smolt ages. Analyses were conducted on age-0 to age-2 fish that were stocked as fry in the West Brook, Massachusetts and on laboratory-raised age-0 to age-1 fish. Using both body size and shape, we could partition the age-0 fish collected during fall into future early or late smolts, although the predictive ability of body shape was somewhat weaker than that of body size, especially in the laboratory. Classification success averaged 81% (size) and 79% (shape) in the field and 85% (size) and 73% (shape) in the laboratory. Despite differences in smolt age between the field and the laboratory, the relative timing of growth rate differences between future early and late smolts was similar in the field and the laboratory and peaked at 50-60% of development from fry to smolt. While body shape differed between early and late smolts well before smoltification, it did not improve classification based on size alone.

Transactions of the American Fisheries Society↗

USGS2011

Thermal marking of Atlantic salmon otoliths

By exposing fry of Atlantic salmon Salmo salar to various temperature regimes, we determined conditions required to produce a readable thermal otolith mark. Marks were quantified by using a darkness index that represented the number of times darker the mark was than the background. Minimum requirements for a strong mark were 1 d at a relatively warm premark temperature of 9°C and 8 h at a lower marking temperature (1°C). Temperature decreases of 4°C (from 5°C to 1°C) resulted in strong marks if fish were held at the premark temperature for 4 d and at the marking temperature for at least 24 h.

Vermont↗

USGS2010

Determining the effects of dams on subdaily variation in river flows at a whole-basin scale

River regulation can alter the frequency and magnitude of subdaily flow variations causing major impacts on ecological structure and function. We developed an approach to quantify subdaily flow variation for multiple sites across a large watershed to assess the potential impacts of different dam operations (flood control, run-of-river hydropower and peaking hydropower) on natural communities. We used hourly flow data over a 9-year period from 30 stream gages throughout the Connecticut River basin to calculate four metrics of subdaily flow variation and to compare sites downstream of dams with unregulated sites. Our objectives were to (1) determine the temporal scale of data needed to characterize subdaily variability; (2) compare the frequency of days with high subdaily flow variation downstream of dams and unregulated sites; (3) analyse the magnitude of subdaily variation at all sites and (4) identify individual sites that had subdaily variation significantly higher than unregulated locations. We found that estimates of flow variability based on daily mean flow data were not sufficient to characterize subdaily flow patterns. Alteration of subdaily flows was evident in the number of days natural ranges of variability were exceeded, rather than in the magnitude of subdaily variation, suggesting that all rivers may exhibit highly variable subdaily flows, but altered rivers exhibit this variability more frequently. Peaking hydropower facilities had the most highly altered subdaily flows; however, we observed significantly altered ranges of subdaily variability downstream of some flood-control and run-of-river hydropower dams. Our analysis can be used to identify situations where dam operating procedures could be modified to reduce the level of hydrologic alteration. ?? 2009 John Wiley & Sons, Ltd.

River Research and Applications↗

USGS2009

Ecology of stream fish: Insights gained from an individual-based approach to juvenile Atlantic salmon

Using data from an ongoing study of juvenile Atlantic salmon growth and survival in tributaries of the Connecticut River, USA, we compare standard population-level approaches to those focusing on individuals. We highlight the potential benefits of resampling individually tagged stream fish as compared to standard approaches. Specifically we focus on growth, survival, movements and population estimation. The advantages of estimating sizes and growth rates from individual size trajectories include obtaining growth histories and the ability to perform retrospective analysis of the consequences of different life-history strategies. An example might be the patterns of growth leading to either early maturity or migration. Resampling known individuals is the only way we know to chart both short-term and long-term movements and to assign growth and mortality consequences to such movements. Finally, individual-level data permit robust estimation of survival and density/abundance using methods such as Cormack/Jolly-Seber. The results indicate that population estimates were about 10% lower using individual data than using population data, that survival from sample to sample was typically >90%, that the majority of recaptured fish did not move during the summer, that growth was rapid during spring and most fish lost mass during the summer and that growth trajectories for maturing and non-maturing fish showed substantially different patterns. An individual-based approach to stream fish ecology provides the opportunity to explore the mechanisms responsible for population-level patterns but comes at the cost of significant field effort. Tradeoffs between increased data resolution and the effort required to obtain the data must be considered before undertaking individual-based field studies of stream fishes.

Massachusetts↗

USGS2009

Gene-expression signatures of Atlantic salmon's plastic life cycle

How genomic expression differs as a function of life history variation is largely unknown. Atlantic salmon exhibits extreme alternative life histories. We defined the gene-expression signatures of wild-caught salmon at two different life stages by comparing the brain expression profiles of mature sneaker males and immature males, and early migrants and late migrants. In addition to life-stage-specific signatures, we discovered a surprisingly large gene set that was differentially regulated-at similar magnitudes, yet in opposite direction-in both life history transitions. We suggest that this co-variation is not a consequence of many independent cellular and molecular switches in the same direction but rather represents the molecular equivalent of a physiological shift orchestrated by one or very few master regulators. ?? 2009 Elsevier Inc. All rights reserved.

General and Comparative Endocrinology↗

USGS2009

Atlantic salmon (Salmo salar) smolt production: the relative importance of survival and body growth

The complex life history of Atlantic salmon (Salmo salar) coupled with interacting abiotic and biotic factors leads to extreme demographic variability across the species' range. Our goal was to evaluate the relative importance of survival and body growth in determining smolt production across space and time. We used passive integrated transponder tags and capture-mark-recapture analyses to estimate survival, emigration, and growth for six cohorts of presmolt Atlantic salmon in two streams (three cohorts per stream) in New England, USA. We observed remarkable among-cohort consistency in mean monthly survival during a 17-month period from age-0+ autumn to age-2+ spring yet high variability in monthly survival over shorter time intervals (seasons). Despite this latter variability, survival did not translate into amongcohort differences in proportions of age-2+ versus age-3+ smolts. Alternatively, the high variability across seasons and cohorts in mean individual growth rate did lead to differences in within-cohort proportions of age-2+ versus age-3+ smolts (regardless of stream). We conclude that in our two small study streams, variability in growth and size impacted smolt age and, ultimately, smolt production. Density-dependent effects on growth at the scale of the entire study site represent a possible mechanism underlying our observations.

Canadian Journal of Fisheries and Aquatic Sciences↗

USGS2008

Movement patterns and study area boundaries: Influences on survival estimation in capture-mark-recapture studies

The inability to account for the availability of individuals in the study area during capture-mark-recapture (CMR) studies and the resultant confounding of parameter estimates can make correct interpretation of CMR model parameter estimates difficult. Although important advances based on the Cormack-Jolly-Seber (CJS) model have resulted in estimators of true survival that work by unconfounding either death or recapture probability from availability for capture in the study area, these methods rely on the researcher's ability to select a method that is correctly matched to emigration patterns in the population. If incorrect assumptions regarding site fidelity (non-movement) are made, it may be difficult or impossible as well as costly to change the study design once the incorrect assumption is discovered. Subtleties in characteristics of movement (e.g. life history-dependent emigration, nomads vs territory holders) can lead to mixtures in the probability of being available for capture among members of the same population. The result of these mixtures may be only a partial unconfounding of emigration from other CMR model parameters. Biologically-based differences in individual movement can combine with constraints on study design to further complicate the problem. Because of the intricacies of movement and its interaction with other parameters in CMR models, quantification of and solutions to these problems are needed. Based on our work with stream-dwelling populations of Atlantic salmon Salmo salar, we used a simulation approach to evaluate existing CMR models under various mixtures of movement probabilities. The Barker joint data model provided unbiased estimates of true survival under all conditions tested. The CJS and robust design models provided similarly unbiased estimates of true survival but only when emigration information could be incorporated directly into individual encounter histories. For the robust design model, Markovian emigration (future availability for capture depends on an individual's current location) was a difficult emigration pattern to detect unless survival and especially recapture probability were high. Additionally, when local movement was high relative to study area boundaries and movement became more diffuse (e.g. a random walk), local movement and permanent emigration were difficult to distinguish and had consequences for correctly interpreting the survival parameter being estimated (apparent survival vs true survival). ?? 2008 The Authors.

Oikos↗

USGS2008

Size and age distributions of Juvenile Connecticut River American shad above Hadley Falls: Influence on outmigration representation and timing

Age- and size-based habitat use and movement patterns of young-of-year American shad in rivers are not well understood. Adult females reach their natal rivers at different times and ascend the river at different rates, which may lead to variation of hatch dates at a single location. Also, shad are serial spawners, so eggs of the same female may be released at different distances from the river mouth. It has long been hypothesized that juvenile shad emigration is a function of size or age, and not necessarily keyed only to a decrease in water temperature during the fall. We seined three sites in the Connecticut River biweekly to collect pre-migrant shad during river residence (spring to fall). During emigration, samples were also collected weekly at two hydroelectric facilities. Otoliths were removed from ???20% of the fish to obtain age and growth rate information. We found increases in length and age over time until late in the season, after which such increases were mostly insigniftlant. Cohorts collected early in the year as pre-migrants were never sampled as migrants later in the year at the hydroelectric projects. Cohorts collected late in the year as migrants were never collected earlier in the year as pre-migrants. Only during a narrow window of time were fish collected as both pre-migrants and migrants. Fish that were hatched later in the season exhibited higher growth rates than fish that were hatched earlier in the season. Copyright ?? 2008 John Wiley & Sons, Ltd.

River Research and Applications↗

USGS2008

Seasonal variation in size-dependent survival of juvenile Atlantic salmon (Salmo salar): Performance of multistate capture-mark-recapture models

We estimated the magnitude and shape of size-dependent survival (SDS) across multiple sampling intervals for two cohorts of stream-dwelling Atlantic salmon (Salmo salar) juveniles using multistate capture-mark-recapture (CMR) models. Simulations designed to test the effectiveness of multistate models for detecting SDS in our system indicated that error in SDS estimates was low and that both time-invariant and time-varying SDS could be detected with sample sizes of >250, average survival of >0.6, and average probability of capture of >0.6, except for cases of very strong SDS. In the field (N ??? 750, survival 0.6-0.8 among sampling intervals, probability of capture 0.6-0.8 among sampling occasions), about one-third of the sampling intervals showed evidence of SDS, with poorer survival of larger fish during the age-2+ autumn and quadratic survival (opposite direction between cohorts) during age-1+ spring. The varying magnitude and shape of SDS among sampling intervals suggest a potential mechanism for the maintenance of the very wide observed size distributions. Estimating SDS using multistate CMR models appears complementary to established approaches, can provide estimates with low error, and can be used to detect intermittent SDS. ?? 2008 NRC Canada.

Canadian Journal of Fisheries and Aquatic Sciences↗

USGS2007

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 tribuory 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 anthropegenically-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.

PLoS ONE↗

USGS2007

An efficient smolt trap for sandy and debris-laden streams

Tripod weir and box traps are traditionally used to capture and enumerate out-migrating salmonid smolts in short-term studies and in streams where temporary or portable traps are the only practical option. Although traditional traps can be effective when conditions are ideal, they are often unable to withstand high-discharge events in streams containing a large amount of debris or sandy substrates. We created a rotary-screw trap and resistance board weir hybrid design that we evaluated along with a tripod weir and box trap, both in a 6.1-m-wide flume and in the field. The new design outperformed the tripod weir in both situations. The tripod weir failed in 10 min in the flume trial, whereas the new design was still operating at the conclusion of an 8-h trial under the same conditions. The new design operated continuously in the field during a high-discharge event that caused the tripod weir to fail. The new design also required less frequent cleaning than the tripod weir. The trap efficiency of the new design was estimated by using passive integrated transponder (PIT) tag antennas and radiotelemetry. The trap was 80% efficient (n = 40) in capturing migrating PIT-tagged individuals detected at an antenna upstream of the trap and 87.5% efficient (n = 48) at recapturing fish that had been tagged and released upstream. With its high efficiency and increased resiliency over the tripod weir, the new trap design will benefit management and research efforts in streams where traditional traps are unsuitable. ?? Copyright by the American Fisheries Society 2007.

North American Journal of Fisheries Management↗

USGS2007

Growth rate differences between resident native brook trout and non-native brown trout

Between species and across season variation in growth was examined by tagging and recapturing individual brook trout Salvelinus fontinalis and brown trout Salmo trutta across seasons in a small stream (West Brook, Massachusetts, U.S.A.). Detailed information on body size and growth are presented to (1) test whether the two species differed in growth within seasons and (2) characterize the seasonal growth patterns for two age classes of each species. Growth differed between species in nearly half of the season- and age-specific comparisons. When growth differed, non-native brown trout grew faster than native brook trout in all but one comparison. Moreover, species differences were most pronounced when overall growth was high during the spring and early summer. These growth differences resulted in size asymmetries that were sustained over the duration of the study. A literature survey also indicated that non-native salmonids typically grow faster than native salmonids when the two occur in sympatry. Taken together, these results suggest that differences in growth are not uncommon for coexisting native and non-native salmonids. ?? 2007 The Authors.

Journal of Fish Biology↗

USGS2006

Diel and seasonal variation in food habits of Atlantic salmon parr in a small stream

The diel and seasonal food habits of young-of-year (YOY) and post-young-of-year (PYOY) Atlantic salmon ( Salmo salar ) parr were assayed over the course of 11 months in the West Brook, Massachusetts USA. Gut fullness of YOY salmon did not vary significantly among months. PYOY salmon exhibited significant seasonal differences in gut fullness, with peak fullness occurring in the spring and late fall. Significant diel differences in PYOY gut fullness occurred in June and April, with peak fullness always occurring at dawn. Prey composition varied substantially among months. Dominant prey items of PYOY salmon were baetid mayflies in June, July, and August, limnephilid caddisflies in October and November, and ephemerellid mayflies in February and April. Few differences in prey composition between PYOY and YOY salmon were observed. Fish growth was unrelated to prey availability, but gut fullness explained up to 97% of growth variation across seasons. Results suggest that spring and fall are critical periods of feeding for PYOY salmon and that diel feeding intensity shifts seasonally.

Journal of Freshwater Ecology↗

USGS2005

Electroshocking and PIT tagging of juvenile Atlantic salmon: Are there interactive effects on growth and survival?

Electroshocking and tagging of fish with passive integrated transponder (PIT) tags are two commonly used methods for conducting mark-recapture studies in freshwater environments and are frequently used in combination. We conducted an experiment to test for the effects of electroshocking, tagging, and a combination of electroshocking plus tagging on the growth and survival of Atlantic salmon Salmo salar parr. We used five treatments that included the presence or absence of PIT tags and electroshocking at 300 or 500 V plus a control group. Fish were measured, weighed, and electroshocked on four occasions separated by approximately 2-month intervals. The average (??1 SD) fork length was 62.1 ?? 1.9 mm and the average weight was 2.5 ?? 0.3 g at the start of the experiment; at the end of the experiment, length averaged 120.5 ?? 11.6 mm and weight averaged 20.9 ?? 6.1 g. We did not detect any significant effects of electroshocking on growth or survival over the course of the experiment. However, there was evidence that tagging negatively influenced survival over the first interval after initial tagging and that survival was positively correlated with fish size. In addition, tagged fish seemed to suffer a minor depression in growth over the first interval, although differences in size among tagged and untagged fish were nonsignificant throughout the course of the experiment. We suggest that the size at tagging may have a greater effect on survival and growth of small (<80-mm) Atlantic salmon parr than the amount of exposure to electroshocking. ?? Copyright by the American Fisheries Society 2005.

North American Journal of Fisheries Management↗

USGS2005

Interaction of rearing environment and reproductive tactic on gene expression profiles in Atlantic salmon

Organisms that share the same genotype can develop into divergent phenotypes, depending on environmental conditions. In Atlantic salmon, young males of the same age can be found either as sneakers or immature males that are future anadromous fish. Just as the organism-level phenotype varies between divergent male developmental trajectories, brain gene expression is expected to vary as well. We hypothesized that rearing environment can also have an important effect on gene expression in the brain and possibly interact with the reproductive tactic adopted. We tested this hypothesis by comparing brain gene expression profiles of the two male tactics in fish from the same population that were reared in either a natural stream or under laboratory conditions. We found that expression of certain genes was affected by rearing environment only, while others varied between male reproductive tactics independent of rearing environment. Finally, more than half of all genes that showed variable expression varied between the two male tactics only in one environment. Thus, in these fish, very different molecular pathways can give rise to similar macro-phenotypes depending on rearing environment. This result gives important insights into the molecular underpinnings of developmental plasticity in relationship to the environment. ?? 2005 The American Genetic Association.

Conference Paper↗