Source: CORNELL UNIVERSITY submitted to
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
Funding Source
Reporting Frequency
Accession No.
Grant No.
Project No.
Proposal No.
Multistate No.
Program Code
Project Start Date
Oct 1, 2014
Project End Date
Sep 30, 2017
Grant Year
Project Director
Hare, MA.
Recipient Organization
Performing Department
Natural Resources
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

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
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
Project Methods
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.

Progress 10/01/14 to 09/30/17

Target Audience:The two main stakeholders (target audiences) are New York State Department of Environmental Conservation (NYSDEC) and their angling constituencies (for public lakes) and private landowners (fishing clubs, League Club specifically). Contact with stakeholders primarily has been for coordination and updates to date. For example, a coordination meeting with NYSDEC occurred Feb. 10 2016, at the NY Chapter meeting of the American Fisheries Society. The stocked experimental ponds are privately held by The League Club, so they also are an important target audience reached through annual updates provided at the Adirondack Research Forum, League Club, Old Forge, NY. Changes/Problems:The original objectives included collaborative experiments working with NYSDEC to sample heritage fish that had been stocked in two "reclaimed" Adirondack ponds, where the only fish population is stocked after restoring suitable pH. The motivation was to test relative reproductive success of heritage vs heritage x domestic F1 hybrids in a context where there were no pre-existing trout at the time of stocking. Unfortunately, sampling efforts at these ponds failed to capture any brook trout, suggesting that stocked strains did not survive or are doing so at very low abundance. We were successful with our objectives in League Club ponds where stocking was on top of pre-existing fish populations. These ponds provide a relevant ecological context for our studies, but have less direct relevance to NYSDEC management goals wherein heritage strains are mostly used for stocking reclaimed ponds. What opportunities for training and professional development has the project provided?In both the laboratory and field, technician staff were trained in the procedures needed to adequately support the study design and maintain data quality. How have the results been disseminated to communities of interest?Symposium presentation by Matt Hare at New York Chapter American Fisheries Society meeting Feb. 10 2016.Symposium: "Building Resiliency into Fish Management Plans to Sustain Fisheries". Hare title: "Managing for Evolutionary Resilience". Adirondack Research Forum, Old Forge, NY, March 2017 with scientists, students and NYSDEC staff in attendance:"Relative reproductive success of heritage and hybrid brook trout strains stocked in Adirondack lakes" presented by Matt Hare. A presentation of updated results is planned for ARF March 2018. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

What was accomplished under these goals? For the 3 League Club lakes (Chandler, Deer, Lower Sylvan), goals i - vi have been accomplished: i) All three lakes adults were sampled in 2015. This represents the pre-experiment genetic composition of brook trout. ii) Little Tupper heritage strain and F1 hybrid Windfall x Domestic fish were stocked into all three ponds in September 2015. Equal numbers of each strain were stocked into each pond, and number of fish per pond was determined by pond size. iii) Environmental and water quality conditions were monitored in all three lakes iv) Sampling of adult fish occurred in 2015 and 2016. Young of the year (YOY) fish were sampled from all three lakes in 2016-17. v) DNA was extracted and 12 microsatellite markers genotyped from all stocked and wild fish samples (1705 fish) vi) Relative reproductive success estimates required a minimum of two years for stocked fish to mature, making 2017 YOY samples crucial for testing. In the two lakes with sufficient YOY samples (130 in Lower Sylvan and 113 in Chambers) we had high power to distinguish offspring from stocked fish and found no evidence of them among sampled YOY. However, a conservative parentage analysis, using a stringent statistical threshold to minimize false positives, showed that some 2017 YOY were produced by fish that were sampled as wild juveniles in 2015. Thus, wild fish were reproducing within two years, but no reproduction was detectable from the stocked strains. This suggests that relative reproductive success of stocked strains is lower than the wild fish, but with two important caveats: (1) If stocked fish experienced enough mortality after stocking that they represented a small fraction of breeders then our methods would not be able to detect their reproduction. (2) Another possibility is that stocked fish take longer to mature so that a comparison at age 2 is not representative of later reproductive output. We are seeking funds to sample additional years to test this hypothesis. Either way, the current data do not allow any estimation of relative reproductive success between the two stocked strains. Table summarizing project samples and their genetic diversity including allelic richness [AR(20)] normalized for a sample size n=20, expected heterozygosity (exp. H), effective number of breeders contributing to a cohort based on linkage disequilibrium (NeB). "fing." = fingerling juveniles" Stocking strains Date N Age AR(20) exp.H NeB (95% CI) Little Tupper 9/15/15 415 fing. 4.62 0.587 33.6 (28 - 43) Windfall x Domestic 9/15/15 415 fing. 4.74 0.641 13.2 (11 - 15) Source Lake Chambers Lake 2015 51 YOY 4.23 0.623 15.5 (12.1 - 19.9) Chambers Lake 2015 37 adults 6.21 0.730 Chambers Lake 2016 53 YOY 4.34 0.608 7.2 (5.2 - 9.1) Chambers Lake 2016 34 adults 5.64 0.665 Chambers Lake 2017 113 YOY 4.83 0.650 10.8 (9.3 - 12.3) Deer Lake 2015 3 YOY - - - Deer Lake 2015 32 adults 5.29 0.694 Deer Lake 2016 24 YOY 4.76 0.680 9.5 (6.9 - 13.1) Deer Lake 2016 40 adults 5.72 0.723 Deer Lake 2017 6 YOY - - - Lower Sylvan Pond 2015 150 YOY 5.70 0.706 14.8 (13.4 - 16.4) Lower Sylvan Pond 2015 41 adults 6.11 0.731 Lower Sylvan Pond 2016 139 YOY 5.57 0.723 17.6 (15.8 - 19.6) Lower Sylvan Pond 2016 22 adults 6.33 0.733 Lower Sylvan Pond 2017 130 YOY 5.52 0.694 21.6 (19.1 - 24.3) Total 1705 These summary statistics show, as expected, that single cohort YOY allelic richness is slightly below the adults because not all adults breed in any particular year. The three experimental lakes all have similarly small effective number of breeders with some of the highest values in the smallest pond, Lower Sylvan (16 acres as opposed to 26-33 acres for the other two). We also collaborated with NYSDEC to apply objectives i - vi to two isolated Adirondack ponds recently reclaimed and stocked by NYSDEC. Unfortunately, sampling by NYSDEC in Hawk and Lyon ponds in 2016 yielded no brook trout. This may mean that stocked fish did not survive, or their density was too low to be sampled.


    Progress 10/01/15 to 09/30/16

    Target Audience:The two main stakeholders (target audiences)are NYSDEC and their angling constituencies (for public lakes) and private landowners (fishing clubs, League Club specifically). Contact with stakeholders has only been for coordination and updates because the project has not proceeded long enough to have results. For example, a coordination meeting with NYSDEC occurred Feb. 102016, at the NY Chapter meeting of the American Fisheries Society. Changes/Problems:No major changes are warranted but larger sample sizes from the field will be attempted. What opportunities for training and professional development has the project provided? Nothing Reported How have the results been disseminated to communities of interest?The stocked fish are not expected to reproduce until 2017, so the major goal of the project, to measure relative reproductive success, will not be possible until we obtain and analyze 2017 young of the year samples. Nothing disseminated. What do you plan to do during the next reporting period to accomplish the goals?Collect young of the year from all three lakes and continue with goals v, vi and vii (i.e., estimate relative reproductive success). In addition, collections will be attempted again from DEC lakes Hawk and Lyon.

    What was accomplished under these goals? Collections were attempted in Hawk and Lyon ponds by NYSDEC in 2016 with no success. This may mean that stocked fish have not survived or, if their density is low or their habitat restricted in the pond, existing populations could have been missed. Collections will be attempted again in 2017. For the 3 League Club lakes (Chandler, Deer, Lower Sylvan), goals i - v have been accomplished: i) Adult and young of the year fish were sampled from all three lakes in 2015 ii) Little Tupper heritage strain and F1 hybrid Windfall x Domestic fish were stocked into all three ponds in September 2015 iii) Environmental and water quality conditions have been monitored in all three lakes iv) Adult and young of the year fish were sampled from all three lakes in 2016 v) DNA has been extracted and genotypedfrom stocked fish and wild fish samples (1123 out of 1456 total so far). A summary of genetic patterns in the following table includes allelic richness [AR(20)]normalized for a sample size n=20, expected heterozygosity (exp. H), effective number of breeders contributing to a cohort based on linkage disequilibrium (NeB-LD) and coancestry (NeB-CoAn). Ranges are 95% confidence limits. "fing." = fingerling juveniles Stocking strains Date N Age AR(20) exp.H NeB - LD NeB - CoAn Little tupper 9/15/15 217 fing. 4.76 0.584 31.9 (27.8 - 36.5) 38.4 (6.4 - 98.5) Windfall x Domestic 9/15/15 280 fing. 4.76 0.637 12.5 (11.0 - 14.0) 10.9 (6.2 - 16.9) Source Lake Chambers Lake 8/21/15 51 YOY 4.44 0.648 15.3 (11.9 - 19.7) 13.2 (5.7 - 23.8) Chambers Lake 10/8/15 37 adults 6.33 0.732 Chambers Lake 7/27/16 53 YOY 4.56 0.623 6.7 (4.1 - 8.7) 5.5 (3.1 - 8.6) Chambers Lake 10/3/16 34 adults 5.95 0.685 Deer Lake 8/20/15 3 YOY - - - - Deer Lake 10/14/15 32 adults 5.31 0.686 Deer Lake 7/28/16 24 YOY 4.74 0.675 8.9 (6.3 - 12.7) 4.2 (2.5 - 6.2) Deer Lake 10/5/16 40 adults 5.67 0.710 Lower Sylvan Pond 7/27/15 150 YOY 5.57 0.696 14.5 (12.9 - 16.2) 6.7 (4.0 - 10.0) Lower Sylvan Pond 10/14/15 41 adults 6.00 0.721 Lower Sylvan Pond 7/26/16 139 YOY 5.45 0.714 17.4 (15.3 - 19.6) 9.3 (6.9 - 12.1) Lower Sylvan Pond 10/2016 22 adults 6.45 0.728


      Progress 10/01/14 to 09/30/15

      Target Audience:During the first year of this study our activities have been focused on sample acquisition, so there have been no directed efforts to reach a particular audience. Changes/Problems:Stocking in League Club ponds was proposed to beWindfall x Domestic F1 hybrids and pure Little Tupper heritage strain. We obtained Windfall x Domestic F1 hybridfall fingerlings from the NYSDEC and they did not have pure Windfallfish available to pair with them in our stocking. Instead, they providedLittle Tupper heritage strain fall fingerlings. This heritage strain has natal watersin the same drainage as Windfall strain and shows a high level of genetic similarity to Windfall compared with other heritage strains. Thus, it is a suitable alternative for the experiments. Sampling of Lyon pond fish was proposed to commence in 2015 but the NYSDEC estimated that reproduction of stocked fish probably had not begun, so sampling was postponed until 2016. Hawk pond is not expected to have reproduction until 2017. What opportunities for training and professional development has the project provided? Nothing Reported How have the results been disseminated to communities of interest? Nothing Reported What do you plan to do during the next reporting period to accomplish the goals?During the second year our focus will be on specific aims iv and v, as well as continued environmental monitoring (aim iii).

      What was accomplished under these goals? During the first year of this project we accomplished specific aims i, ii and iii in the League Club ponds. No monitoring or sampling has been accomplished yet in the NYSDEC-stocked Lyon and Hawk ponds.In the League Club, 830 fall fingerlings were stocked into three ponds to initiate the experimental comparison between hatchery-produced F1 hybrids vs. pure heritage strain stocked fish.Fin clips were collected from the following samples (YOY = young of year; "Windfall" and "Little Tupper" are heritage strains, "Domestic" is the NYSDEC hatchery strain used for stocking in the Adirondacks): wild fish: Site Date N Description Chambers Lake 8/21/15 51 YOY from tributaries Chambers Lake 10/8/15 37 adults Deer Lake 8/20/15 3 YOY from tributaries Deer Lake 9/4/15 32 adults Lower Sylvan Pond 8/20/15 150 YOY from tributary Lower Sylvan Pond 10/5/15 41 adults Upper Sylvan Pond 10/2/15 45 adults Stocked fingerlings: Chambers Lake 9/15/15 130 Windfall x Domestic Chambers Lake 9/15/15 130 Little tupper Deer Lake 9/15/15 165 Windfall x Domestic Deer Lake 9/15/15 165 Little tupper Lower Sylvan Pond 9/14/15 120 Windfall x Domestic Lower Sylvan Pond 9/14/15 120 Little tupper