Jason A. Coombs

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.

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.

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...

Robust estimates of environmental effects on population vital rates: an integrated capture–recapture model of seasonal brook trout growth, survival and movement in a stream network

Modelling the effects of environmental change on populations is a key challenge for ecologists, particularly as the pace of change increases. Currently, modelling efforts are limited by difficulties in establishing robust relationships between environmental drivers and population responses. We developed an integrated capture-recapture state-space model to estimate the effects of two key environmental drivers (stream flow and temperature) on demographic rates (body growth, movement and survival) using a long-term (11 years), high-resolution (individually tagged, sampled seasonally) data set of brook trout (Salvelinus fontinalis) from four sites in a stream network. Our integrated model provides an effective context within which to estimate environmental driver effects because it takes full advantage of data by estimating (latent) state values for missing observations, because it propagates uncertainty among model components and because it accounts for the major demographic rates and interactions that contribute to annual survival. We found that stream flow and temperature had strong effects on brook trout demography. Some effects, such as reduction in survival associated with low stream flow and high temperature during the summer season, were consistent across sites and age classes, suggesting that they may serve as robust indicators of vulnerability to environmental change. Other survival effects varied across ages, sites and seasons, indicating that flow and temperature may not be the primary drivers of survival in those cases. Flow and temperature also affected body growth rates; these responses were consistent across sites but differed dramatically between age classes and seasons. Finally, we found that tributary and mainstem sites responded differently to variation in flow and temperature. Annual survival (combination of survival and body growth across seasons) was insensitive to body growth and was most sensitive to flow (positive) and temperature (negative) in the summer and fall. These observations, combined with our ability to estimate the occurrence, magnitude and direction of fish movement between these habitat types, indicated that heterogeneity in response may provide a mechanism providing potential resilience to environmental change. Given that the challenges we faced in our study are likely to be common to many intensive data sets, the integrated modelling approach could be generally applicable and useful.

pedagog: software for simulating eco-evolutionary population dynamics.

pedagog is a Windows program that can be used to determine power for, and validate inferences drawn from, eco‐evolutionary studies. It models dynamics of multiple populations and their interactions through individual‐based simulations while simultaneously recording genotype, pedigree and trait information at the individual level. pedagog also allows for specification of heritable traits, natural and sexual selection acting upon those traits, population sampling schemes and incorporation of genetic and demographic errors into the output. Overall, parameters can be specified for genetic diversity, demographics, mating design, genetic and demographic errors, individual growth models, trait heritability and selection, and output formatting. Demographic parameters can be either age or function based, and all parameters can be drawn from 12 statistical distributions where appropriate. Simulation results can be automatically formatted for 57 existing software programs to facilitate postsimulation analyses. pedagog is freely available for download at https://bcrc.bio.umass.edu/pedigreesoftware/.

Maintenance of phenotypic variation: repeatability, heritability and size-dependent processes in a wild brook trout population.

Phenotypic variation in body size can result from within‐cohort variation in birth dates, among‐individual growth variation and size‐selective processes. We explore the relative effects of these processes on the maintenance of wide observed body size variation in stream‐dwelling brook trout (Salvelinus fontinalis). Based on the analyses of multiple recaptures of individual fish, it appears that size distributions are largely determined by the maintenance of early size variation. We found no evidence for size‐dependent compensatory growth (which would reduce size variation) and found no indication that size‐dependent survival substantially influenced body size distributions. Depensatory growth (faster growth by larger individuals) reinforced early size variation, but was relatively strong only during the first sampling interval (age‐0, fall). Maternal decisions on the timing and location of spawning could have a major influence on early, and as our results suggest, later (>age‐0) size distributions. If this is the case, our estimates of heritability of body size (body length = 0.25) will be dominated by processes that generate and maintain early size differences. As a result, evolutionary responses to environmental change that are mediated by body size may be largely expressed via changes in the timing and location of reproduction.

PedAgree: software to quantify error and assess accuracy and congruence for genetically reconstructed pedigree relationships

PedAgree is software for rapid comparison of genetically reconstructed pedigrees (RP’s). Its two primary functions are (1) to assess accuracy of a RP by comparing it to a known pedigree, and (2) to measure congruence between two RP’s. The accuracy function is used to assist in determining confidence for a RP. The congruence function is used to determine the level of agreement between two RP’s. This function determines which links within the RP’s are identical, and thus more likely to be correct. Congruence assessment between RP’s generated by sibship reconstruction (SR) and parentage assignment (PA) programs allows for implementation of the sibship constraint method. This method has been shown to increase assigned parentage accuracy by up to 53%, and to be robust to dataset characteristics that reduce conventional PA accuracies. PedAgree can compare output produced by seven SR and twelve PA programs, and is freely available for download at https://bcrc.bio.umass.edu/pedigreesoftware/.

Effective number of breeders provides a link between interannual variation in stream flow and individual reproductive contribution in a stream salmonid

The effective number of breeders that give rise to a cohort (Nb) is a promising metric for genetic monitoring of species with overlapping generations; however, more work is needed to understand factors that contribute to variation in this measure in natural populations. We tested hypotheses related to interannual variation in Nb in two long‐term studies of brook trout populations. We found no supporting evidence for our initial hypothesis that N^b reflects N^c (defined as the number of adults in a population at the time of reproduction). N^b was stable relative to N^C and did not follow trends in abundance (one stream negative, the other positive). We used stream flow estimates to test the alternative hypothesis that environmental factors constrain Nb. We observed an intermediate optimum autumn stream flow for both N^b (R2 = 0.73, P = 0.02) and full‐sibling family evenness (R2 = 0.77, P = 0.01) in one population and a negative correlation between autumn stream flow and full‐sib family evenness in the other population (r = −0.95, P = 0.02). Evidence for greater reproductive skew at the lowest and highest autumn flow was consistent with suboptimal conditions at flow extremes. A series of additional tests provided no supporting evidence for a related hypothesis that density‐dependent reproductive success was responsible for the lack of relationship between Nb and NC (so‐called genetic compensation). This work provides evidence that Nb is a useful metric of population‐specific individual reproductive contribution for genetic monitoring across populations and the link we provide between stream flow and Nb could be used to help predict population resilience to environmental change.

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

GONe is a user‐friendly, Windows‐based program for estimating effective size (Ne) 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 (Fs, Fc and Fk). 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. GONe is freely available for download at https://bcrc.bio.umass.edu/pedigreesoftware/.

Experimental test of genetic rescue in isolated populations of brook trout

Genetic rescue is an increasingly considered conservation measure to address genetic erosion associated with habitat loss and fragmentation. The resulting gene flow from facilitating migration may improve fitness and adaptive potential, but is not without risks (e.g., outbreeding depression). Here, we conducted a test of genetic rescue by translocating ten (five of each sex) brook trout (Salvelinus fontinalis) from a single source to four nearby and isolated stream populations. To control for the demographic contribution of translocated individuals, ten resident individuals (five of each sex) were removed from each recipient population. Prior to the introduction of translocated individuals, the two smallest above‐barrier populations had substantially lower genetic diversity, and all populations had reduced effective number of breeders relative to adjacent below‐barrier populations. In the first reproductive bout following translocation, 31 of 40 (78%) translocated individuals reproduced successfully. Translocated individuals contributed to more families than expected under random mating and generally produced larger full‐sibling families. We observed relatively high (>20%) introgression in three of the four recipient populations. The translocations increased genetic diversity of recipient populations by 45% in allelic richness and 25% in expected heterozygosity. Additionally, strong evidence of hybrid vigour was observed through significantly larger body sizes of hybrid offspring relative to resident offspring in all recipient populations. Continued monitoring of these populations will test for negative fitness effects beyond the first generation. However, these results provide much‐needed experimental data to inform the potential effectiveness of genetic rescue‐motivated translocations.