Non Technical Summary
Freshwater recreational fisheries generate a lot of economic activity in rural areas of New York, and trout are the second most commonly reported type of fish caught. The official state fish in New York is the Brook trout, a beautifully speckled native species prized by anglers. Originally widespread throughout the state, this cold water species is now severely restricted by habitat degradation and the introduction of competing fish species. After more than a century of state management using hatchery-based stocking for fishery enhancement, there are now two sets of genetically distinct brook trout populations, and two ongoing management objectives. Brook trout strains representing the original native diversity are rare and these genetically distinct "heritage" populations are protected from stocking and used as broodstock to restore "reclaimed" waters. Most other stocked waters receive hybrid progeny from annual crosses between a Canadian strain (maintained in NY) and a domesticated hatchery strain, and naturalized (local-breeding) brook trout populations in historically stocked waters hve become genetically homogenized as a result (Hare and VanMaaren in prep.). Conserving heritage trout stocks is expensive and using them for anything more than targeted stocking is impractical because of their poor fitness in hatcheries. Furthermore, only a few heritage strains still exist, each maintained in one or two isolated ponds. Thus, they are vulnerable to anthropogenic accidents (e.g., invasive species release), genetic drift, and environmental change. Currently, conservation of heritage strains is based on a value judgment that native genetic diversity is good, and/or an assumption that some local genetic variation is uniquely adaptive for Adirondack brook trout. With no empirical basis for this prioritization, the increasing costs of protecting heritage strains will become more difficult to justify. In addition, it is possible that Adirondack heritage strains are no longer the best genetic stock to maintain evolutionary capacity in the face of climate change. This study will provide ecologically relevant experimental results on relative fitness of brook trout strains under several stocking contexts in order to inform both conservation priorities and stocking practices.
Animal Health Component
Research Effort Categories
Goals / Objectives
This project will test relative fitness between heritage strains of brook trout and hybrid strains used for stocking, both compared under several stocking contexts to inform conservation priorities and stocking practices.(i) sample existing brook trout populations in the experimental ponds(ii) stock heritage and heritage hybrid fall fingerlings(iii) monitor environmental conditions(iv) sample annually(v) genotype samples for sibship and parentage analysis(vi) estimate relative reproductive success(vii) prepare manuscripts for review and publication
Methods entail six tasks: (i) sample existing brook trout populations in the experimental ponds, (ii) stock heritage and heritage hybrid fall fingerlings, (iii) monitor environmental conditions, (iv) sample annually, (v) genotype samples for sibship and parentage analysis, (vi) estimate RRS.(i) Sampling of the naturalized population will begin in the summer of project year one (2015). Young of the year (YOY) will be caught and released by electrofishing in August to collect fin clips and identify the wild cohort that will be most similar in age to stocked fish. In addition, adults will be sampled in October 2015 with trap nets in each lake, including age-1 potential first time breeders. A fin will be clipped for genetic analysis, sex recorded, and measurements will be recorded for total length and weight. These data and samples are important for building a baseline understanding of genetic variation, number of breeders and distribution of family size in the naturalized population of each lake.(ii) Stocking will be Windfall x Domestic F1 hybrids and pure Windfall heritage fall fingerlings (Age-0 juveniles) obtained from NYSDEC hatcheries in fall 2015. If necessary, juvenile fish culture will occur at the Little Moose Lake Field Station hatchery (D. Josephson). However, this is a last resort because we want the stocked fish to be representative of standard DEC culture practices/environments. Stocked fall fingerlings will have one fin clipped and total length and weight will be recorded. Because the fin clip will allow us to individually identify survivors in later samples, these early phenotypic data will be valuable to test for an association with survival and RRS.(iii) At the three League Club lakes, measurements of pH and ANC will be taken from water collected in summer (July and August) just below the surface at the deepest location in each lake. At that same location temperature and oxygen will be measured at 1 meter intervals from the surface to the bottom of the lake. A baseline of similar water quality data is available for these lakes from previous years including pH, base cation surplus, and inorganic aluminum levels. Locations of groundwater inputs along the study lake shorelines will be inferred using a modeling approach developed to identify areas of groundwater discharge in Adirondack lakes (Stevens 2008).(iv) The 2015 sampling effort, both YOY and adults, will be repeated in 2016, the first year when age-1 stocked males could contribute to mating. In 2017 all sampling effort will be focused on YOY. Young of the year samples will be 600 per year (200 per lake) and adult samples will total 300 for each of the two years they are collected (100 per lake).(v) Eleven microsatellite loci will be genotyped in all fin clip samples to inform a combined sibship and parentage analysis. The eleven loci have an average of 9.3 (4 - 17) alleles per locus, average expected heterozygosity of 0.62, average genotyping error rate of 0.73%, and few deviations from Hardy Weinberg in heritage and stocked brook trout pond populations (Hare and Van Maaren in prep). This array of markers includes seven out of eight loci used for parentage analysis to track brook trout dispersal within and among Connecticut streams (Kanno et al.) and CT streams (Hudy et al. 2010). In the latter study eight microsatellite loci showed a parentage accuracy rate of 95.2% when inferred families contained at least three individuals. High confidence in sibship inferences and parentage assignments is anticipated with the use of eleven loci and because the lake populations contain three genetically distinct groups of breeders; (1) naturalized Temiscamie x Domestic, (2) stocked Windfall x Domestic, and (3) stocked pure Windfall heritage. Progeny may be from matings within any of these groups or between any two groups. In the final year-three sample of YOY for this project (2017), the pond pedigrees will mostly contain F1 progeny from stocked fish that bred for the first time in 2016, but may contain some F2 or backcross progeny if stocked males breed in 2015, the year they will be stocked.Sibship and parentage analyses will utilize COLONY 2.5 (Jones and Wang 2010; Wang 2012). This program uses maximum likelihood to infer sibship groups and one or both parents given genotypes for progeny and at least some genotypes from prospective parents. It out-performs other tools by taking into account the entire inferred pedigree, rather than doing exclusion analyses or likelihood ratio tests with pairs or trios of individuals (Harrison et al. 2013). Power is increased with more loci and higher allelic diversities, and when prospective parents are of known sex (true for naturalized population here, but not for stocked fish) and when a higher proportion of prospective parents are sampled (true for stocked fish, but probably not for wild populations). After stocked fall fingerlings and wild samples are genotyped, allele frequencies of the three groups will be used to conduct simulations for estimating power in sibship and parentage analyses and testing sensitivity to parameters (Wang 2013). Sibship reconstruction will be attempted assuming different mating strategies in each lake, and the mating strategy that maximizes the likelihood of the genotype data will be used. The mating strategies will include both-sexes monogamous, both-sexes polygamous, or one-sex monogamous and the other-sex polygamous.(vi) Parentage results and Hardy Weinberg genotype proportions in 2017 YOY will be used to test the null hypothesis that mating was random among the three groups. Based on inferred full-sib family sizes, the distribution of reproductive contributions will be plotted separately for wild males and females, and for all (unsexed) parents from stocked groups. Group contributions will be quantified as the number of progeny sampled from parents in each group, relative to the number of possible parents for the group. The relative parentage contributions of the strain groups (relative reproductive success, RRS) will be analyzed as a Poisson variable (counts of progeny per family) with generalized linear models (GLMs) to test for the effect of parental fish strain, lake, and sex. Covariates will include growth rate (estimated for any recaptures among stocked or wild fish).The lakes also will be compared with respect to contemporary effective population size (Ne) inferred using sibship assignments as implemented in COLONY (Wang 2009). This method of estimating Ne is ideal in this context because it does not assume random mating, but only that a random sample is analyzed from a single cohort. Effective population size is an index that scales with the strength of genetic drift. Because strong genetic drift undermines the efficacy of selection, Ne provides a useful relative measure of adaptive capacity (Hare et al. 2010).Because heterosis effects tend to vary by family (Crespel et al. 2012) and the same parents are not being used to produce heritage x Domestic versus pure heritage fish for stocking, there is no way to explicitly quantify heterosis effects in this proposed study. Nonetheless, we will test for an association between genomic heterozygosity, as measured by microsatellites, and growth rate, survivorship and RRS.