CoChat
Sign Up
Cited by 10Marine and fisheries researchFish Ecology and Management StudiesFish Biology and Ecology Studies

Estimating Common Growth Patterns in Juvenile Chinook Salmon (Oncorhynchus tshawytscha) from Diverse Genetic Stocks and a Large Spatial Extent

Open access
Goertler, Pascale A. L., Scheuerell, Mark D., Simenstad, Charles A., Bottom, Daniel L.·2016·PLOS ONE
DOI 10.1371/journal.pone.0162121PMC PMC5047595
Open this paper in CoChat — free accountOpen PDF

Abstract

Life history variation in Pacific salmon (Oncorhynchus spp.) supports species resilience to natural disturbances and fishery exploitation. Within salmon species, life-history variation often manifests during freshwater and estuarine rearing, as variation in growth. To date, however, characterizing variability in growth patterns within and among individuals has been difficult via conventional sampling methods because of the inability to obtain repeated size measurements. In this study we related otolith microstructures to growth rates of individual juvenile Chinook salmon (O. tshawytscha) from the Columbia River estuary over a two-year period (2010-2012). We used dynamic factor analysis to determine whether there were common patterns in growth rates within juveniles based on their natal region, capture location habitat type, and whether they were wild or of hatchery origin. We identified up to five large-scale trends in juvenile growth rates depending on month and year of capture. We also found that hatchery fish had a narrower range of trend loadings for some capture groups, suggesting that hatchery fish do not express the same breadth of growth variability as wild fish. However, we were unable to resolve a relationship between specific growth patterns and habitat transitions. Our study exemplifies how a relatively new statistical analysis can be applied to dating or aging techniques to summarize individual variation, and characterize aspects of life history diversity.

AI snapshot

Written from the paper’s full text.

TL;DR

Using otolith microstructure and dynamic factor analysis, this study estimated common growth trends among 524 juvenile Chinook salmon from the Columbia River estuary sampled in 2010–2012. It found up to five large-scale growth trends depending on capture month/year, with hatchery fish showing narrower trend-loading ranges in May, but no clear links between growth patterns and genetic stock, capture habitat, or environmental covariates.

Key findings

  • DFA best supported one trend for May 2010, May 2011, July 2010, and July 2011, but three trends for September 2010 and five trends for September 2011; overall, up to five large-scale trends were identified depending on month and year of capture.
  • Hatchery fish in May 2010 had a narrower range of trend loadings (0.53 to −0.29) than wild fish (1 to −0.53), and a similar pattern was seen to a lesser degree in May 2011, suggesting hatchery fish may not express the same breadth of growth variability as wild fish.
  • Growth trends did not clearly align with genetic stock of origin, capture location/habitat type, or habitat transitions; the best-supported covariate matrix was the D matrix with no covariates.
  • Of 524 otoliths used, capture-group sample sizes were May 2010: 128, May 2011: 152, July 2010: 115, July 2011: 100, September 2010: 13, and September 2011: 16; average fork length increased from 53 mm in May to 70 mm in July to 99 mm in September, while the coefficient of variation in fork length decreased from 0.26 in May to 0.17 in July and 0.13 in September.

Methods

  • Juvenile Chinook salmon were collected from an estuary-wide survey in the Columbia River freshwater tidal reaches: 18 sites across six hydrogeomorphic reaches and three habitat types, sampled every other month from March 2010 to March 2012 using beach and pole seines.
  • Genetic stock of origin was assigned using 13 microsatellite loci and ONCOR; out-of-basin stocks and individuals with relative assignment probabilities <0.80 (18% of assignments) were excluded.
  • Otolith microstructure was used to estimate daily growth: 665 otoliths were dissected, 524 highest-confidence samples were analyzed, and otolith width predicted fork length with R² = 0.95; growth time series were averaged over 7-day periods, z-scored, and grouped into six capture month/year groups.
  • Dynamic factor analysis was fit in R with MARSS, comparing 1–5 latent trends per capture group using AICc, and testing four D matrices that included natal tributary and estuary temperature and Columbia River discharge covariates.

Limitations

  • The paper states that otolith samples were an opportunistic subsample of a larger study, not consistent over space or time, and no capture group represented all 18 sampling sites; September capture groups also had the smallest sample sizes and longest growth time series, which could affect DFA results because it models random walks.
  • The paper states that the best-supported covariate matrix had no covariates, so the authors were unable to relate individuals, genetic groups, or trends to specific environmental variables in the estuary or natal tributaries, and could not assign particular attributes to evidence of estuarine rearing.
  • The paper states that DFA results may be too complex for categorizing life history types and may not be practical for identifying management targets due to complexity and time-intensive laboratory and statistical techniques; evident from the text, excluding out-of-basin stocks and assignments <0.80 means the analyzed fish are a subset of the total catch, which may limit generalization to the full juvenile assemblage.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1371/journal.pone.0162121

Cites

62 of 62 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

9 of 40 cited sources checked · 6 supported · 0 flagged · accuracy not yet measured

  • Findingown data

    Dynamic factor analysis identified up to five large-scale trends in juvenile Chinook salmon growth rates, with the number of trends depending on month and year of capture.

    “We identified up to five large-scale trends in juvenile growth rates depending on month and year of capture.”
    • Also stated in: § Dynamic Factor Analysis · plain
      “The growth trajectories of juvenile Chinook salmon in capture groups May 2010, May 2011, July 2010, and July 2011 were best explained by one trend. However, juvenile Chinook salmon were best described by three and five trends, respectively in capture groups September 2010 and September 2011.”
    Quote in the paperSubstantial claim
    • The authors state this as an assumption: Otolith reader observation error is equal for all fish.
    • The authors state this as an assumption: Latent trends follow a random walk with process innovations distributed as a multivariate normal with mean-vector zero and an identity variance-covariance.
  • Findingown data

    Hatchery marked fish in May 2010 and to a lesser degree May 2011 capture groups had a narrower range of trend loading values than wild fish.

    “We also found that hatchery fish had a narrower range of trend loadings for some capture groups”
    • Also stated in: § Dynamic Factor Analysis · plain
      “However, hatchery marked fish in May 2010 and to a lesser degree May 2011 capture groups had a narrower range of trend loading values (i.e. in May 2010 loadings ranged from 0.53 to -0.29 for hatchery fish and 1 to -0.53 for wild fish).”
    Quote in the paperSubstantial claim
    • The authors state this as an assumption: Otolith reader observation error is equal for all fish.
    • The authors state this as an assumption: Latent trends follow a random walk with process innovations distributed as a multivariate normal with mean-vector zero and an identity variance-covariance.
  • Findingnone given

    The study was unable to resolve a relationship between specific growth patterns and habitat transitions.

    “However, we were unable to resolve a relationship between specific growth patterns and habitat transitions.”
    Quote in the paperSubstantial claim
    • The authors state this as an assumption: Otolith reader observation error is equal for all fish.
    • The authors state this as an assumption: Latent trends follow a random walk with process innovations distributed as a multivariate normal with mean-vector zero and an identity variance-covariance.
  • Findingown data

    Associations to genetic assignment to stock of origin, capture location, and hatchery/wild origin were limited.

    “However associations to their genetic assignment to stock of origin, capture location and hatchery/wild origin were limited.”
    Quote in the paperSubstantial claim
    • The authors state this as an assumption: Otolith reader observation error is equal for all fish.
    • The authors state this as an assumption: Latent trends follow a random walk with process innovations distributed as a multivariate normal with mean-vector zero and an identity variance-covariance.
  • Findingown data

    Hatchery fish in May capture periods had a smaller range of DFA trend loadings.

    “but operated within a smaller range of loading values”
    • Also stated in: § Discussion · plain
      “but the marked hatchery fish did have a smaller range of trend loadings from the DFA analysis in May capture periods”
    Quote in the paperSubstantial claim
  • Classified as probably not a substantial claim. 28
  • May combine two claims. 29
  • The quote only partly states this claim. 1

  • Classified as probably not a substantial claim.

    Premisecitation

    A central dogma in salmon ecology and management often constrains juvenile life history diversity to ocean type and stream type juveniles, denoting whether individuals out-migrate to the ocean before or after their first year of life.

    “A central dogma in salmon ecology and management often constrains juvenile life history diversity to ocean type and stream type juveniles, denoting whether individuals out-migrate to the ocean before or after their first year of life [7, 8].”
    Quote in the paperSubstantial claim2 of 2 sources checked
    • cites [7] MC Healey, 1983, Coastwide distribution and ocean migration patterns of stream and ocean type Chinook salmon, <italic>Oncorhynchus tshawytscha</italic>, Can. Field Nat source

      The Discussion (page unavailable) treats stream- and ocean-type Chinook as two life-history types, and the Ocean Distribution section distinguishes recently emerged ocean-type fry migrants from stream-type smolts. These passages support the two-type distinction and differing freshwater residence, but do not establish that salmon ecology or management treats it as a ‘central dogma’ that constrains recognition of juvenile diversity. (LLM, conf=0.83)

      Experimental — accuracy not yet measured
    • cites [8] Dawley EM (1986) Migrational Characteristics, Biological Observations, and Relative Survival of Juvenile Salmonids Entering the Columbia River Estuary, 1966–1983, 1985 Final Report of Research. National Oceanic and Atmospheric Administration 1984BP39652. source

      The Analysis section distinguishes yearling from subyearling Chinook salmon migrants, supporting the age-based part of the claim. The Conclusions section also says wild Chinook salmon have diverse migration timing and age structure. Our copy does not describe an ocean-type/stream-type classification or say that it is a central dogma constraining how juvenile diversity is understood; page numbers were not provided for these passages. (LLM, conf=0.79)

      Experimental — accuracy not yet measured

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Spatial variation in the freshwater and estuarine environment decreases variation in juvenile survival over time, contributing to the portfolio effect.

    “However, spatial variation in the freshwater and estuarine environment also decreases variation in juvenile survival over time, contributing to the “portfolio effect” [5, 6].”
    Quote in the paperNot a substantial claim1 of 2 sources checked
    • cites [5] JT Thorson, 2014, Spatial variation buffers temporal fluctuations in early juvenile survival for and endangered Pacific salmon, J. Anim. Ecol source
    • cites [6] AM Sturrock, 2015, Reconstructing the migratory behavior and long-term survivorship of juvenile Chinook salmon under contrasting hydrologic regimes, PLoS ONE source

      The Introduction says that asynchronous salmon populations can stabilize the stock complex through a portfolio effect, and the Discussion (Management implications) says juvenile life-history diversity likely buffers variation. Neither passage establishes that spatial variation specifically in freshwater and estuarine environments decreases variation in juvenile survival over time. Page numbers are not provided in our copy. (LLM, conf=0.84)

      Experimental — accuracy not yet measured

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    The portfolio effect may convey resilience in variable environments and stabilize abundance to help sustain healthy fisheries.

    “This so-called “portfolio effect” may convey resilience in variable environments and stabilize abundance to help sustain healthy fisheries [1, 2].”
    Quote in the paperNot a substantial claim1 of 2 sources checked
    • cites [1] R Hilborn, 2003, Biocomplexity and Fisheries Sustainability, P. Natl. Acad. Sci. USA source
    • cites [2] DE Schindler, 2010, Population diversity and the portfolio effect in an exploited species, Nature source

  • Classified as probably not a substantial claim.

    Premisecitation

    Growth is a common metric for juvenile fish habitat quality.

    “We specifically focus on growth, which is a common metric for juvenile fish habitat quality [20–23], and varies between different types of nursery habitats for juvenile fish [24–27].”
    Quote in the paperSubstantial claim4 of 4 sources checked
    • cites [20] SM Sogard, 1992, Variability in growth rates of juvenile fishes in different estuarine habitats, Mar. Ecol. Prog. Ser source
    • cites [21] KW Able, 1999, Habitat quality for shallow water fishes in an urban estuary: the effects of man-made structures on growth, Mar. Ecol. Prog. Ser source
    • cites [22] L Meng, 2000, Using winter flounder growth rates to assess habitat quality in Rhode Island’s coastal lagoons, Mar. Ecol. Prog. Ser source
    • cites [23] AMD Necaise, 2005, Estuarine habitat evaluation measured by growth of juvenile summer flounder, <italic>Paralichthys dentatus</italic>, in a North Carolina estuary, Mar. Ecol. Prog. Ser source

  • Classified as probably not a substantial claim.

    Premisecitation

    Growth varies between different types of nursery habitats for juvenile fish.

    “We specifically focus on growth, which is a common metric for juvenile fish habitat quality [20–23], and varies between different types of nursery habitats for juvenile fish [24–27].”
    Quote in the paperSubstantial claim1 of 4 sources checked
    • cites [24] M Kjelson, 1981, Life history of fall run juvenile Chinook salmon <italic>Oncrhynchus tshaytscha</italic> in the Sacramento-San Joaquin estuary California USA source
    • cites [25] JD Neilson, 1985, Estuarine growth of juvenile Chinook salmon (<italic>Oncorhynchus tshawytscha</italic>) as inferred from otolith microstructure, Can. J. Fish. Aquat. Sci source
    • cites [26] DR Gundrson, 1990, Patterns of Estuarine use by juvenile English Sole (<italic>Parophrys vetulus</italic>) and Dungeness crab (<italic>Cancer magister</italic>), Estuaries source
    • cites [27] MW Beck, 2001, The identification, conservation and management of estuarine and marine nurseries for fish and invertebrates, BioScience source

  • May combine two claims.

    Findingown data

    In both years, fish size variability in May (coefficient of variation in fork length = 0.26) was greater than July (cv = 0.17) and September (cv = 0.13).

    “In both years, fish size variability in May (coefficient of variation in fork length = 0.26) was greater than July (cv = 0.17) and September (cv = 0.13).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Positive loadings to the three September 2010 trends were 43%, 55%, and 88% for trend one (type three with decreased growth), two (increasing type), and three (type three with increased growth), respectively.

    “positively loadings were 43%, 55% and 88% for trend one (type three with decreased growth), two (increasing type) and three (type three with increased growth), respectively”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    In general, three major patterns were identified: increased growth over time, decreased growth over time, and one extreme period of increased or decreased growth between emergence and capture in the freshwater tidal estuary.

    “In general, we identified three major patterns: (1) increased growth over time, (2) decreased growth over time, and (3) one extreme period of increased or decreased growth between emergence and capture in the freshwater tidal estuary.”
    Quote in the paperSubstantial claim
    • The authors state this as an assumption: Otolith reader observation error is equal for all fish.
    • The authors state this as an assumption: Latent trends follow a random walk with process innovations distributed as a multivariate normal with mean-vector zero and an identity variance-covariance.

  • May combine two claims.

    Findingown data

    Juvenile salmon captured in September were the oldest fish in the study and also exhibited more DFA trends than those captured in May or July.

    “Juvenile salmon captured in September were the oldest fish in our study and also exhibited more DFA trends than those captured in May or July”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Juvenile Chinook salmon were best described by three and five trends, respectively, in capture groups September 2010 and September 2011.

    “However, juvenile Chinook salmon were best described by three and five trends, respectively in capture groups September 2010 and September 2011.”
    Quote in the paperNot a substantial claim
    • The authors state this as an assumption: Otolith reader observation error is equal for all fish.
    • The authors state this as an assumption: Latent trends follow a random walk with process innovations distributed as a multivariate normal with mean-vector zero and an identity variance-covariance.

  • May combine two claims.

    Findingown data

    July 2011 exhibited a decreasing pattern, similar to July 2010.

    “July 2011 exhibited a decreasing pattern, similar to July 2010”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    In May 2010, the DFA trend was an increasing pattern, with 73% of fish loading positively.

    “May 2010 exhibited an increasing pattern, with the majority of the fish loading positively (73%)”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    73% of fish loaded positively to the May 2011 trend, with some particularly extreme positive loadings in fish captured in reach D.

    “73% of the fish loaded positively to this trend, with some particularly extreme positive loadings in fish captured in reach D”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Some individuals within a capture group positively or negatively loaded to a single trend as well as (in September) loaded to several trends.

    “For example, some individuals within a capture group positively or negatively loaded to a single trend as well as (in the case of individuals captured in September) loaded to several trends”
    Quote in the paperSubstantial claim

  • May combine two claims. The quote only partly states this claim.

    Findingown data

    Regional stocks and capture location did not display divergent growth histories or consistent growth patterns.

    “Regional stocks and capture location did not display divergent growth histories”
    • Also stated in: § Discussion · plain
      “Regional stocks and capture habitat did not display consistent growth patterns”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    July 2010 displayed a decreasing pattern, with 69% of fish loading positively.

    “July 2010 displayed a decreasing pattern, with the majority of the fish loading positively (69%)”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Fish captured in September 2011 were best represented by five trends, which can be described by all three pattern types.

    “Fish captured in September 2011 were best represented by five trends, which can be described by all three pattern types”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The September 2010 capture group was best represented by three trends, two of which were pattern type three and one of which was an increasing pattern.

    “The September 2010 capture group was best represented by three trends, two of which were pattern type three and one of which was an increasing pattern”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    82% of fish in the July 2011 capture period loaded positively to this trend, with hatchery (34%) and wild fish loading similarly.

    “82% of the fish in the July 2011 capture period loaded positively to this trend, with hatchery (34%) and wild fish loading similarly”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Findingown data

    Of the 524 otoliths used for growth time series, the largest sample sizes among capture groups were in May (2010: 128, 2011: 152) and July (2010: 115, 2011: 100), with September having much smaller sample sizes (2010: 13, 2011: 16).

    “Of the 524 otoliths used for growth time series, the largest sample sizes among capture groups were in May (2010: 128, 2011: 152) and July (2010: 115, 2011: 100), with September having much smaller sample sizes (2010: 13, 2011: 16).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    All fish in September 2011 loaded to more than one trend, with 47% loading to all five trends.

    “All fish loaded to more than one trend with close to half the fish loading to all five trends (47%)”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    No one capture group represented all eighteen sampling sites.

    “Additionally, no one capture group represented all eighteen sampling sites (Table 3).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingcitation

    There was no detectable relationship between estuarine growth or life-time growth trends with stock of origin.

    “as there was no detectable relationship between estuarine growth [53] or life-time growth trends with stock of origin”
    • Also stated in: § Discussion · hedged
      “Despite this within-stock of origin variability in the catch data, we do not see a clear relationship with stock of origin and the growth trends produced from the DFA analysis”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [53] PAL Goertler, 2016, Estuarine Habitat and Demographic Factors Affect Juvenile Chinook (<italic>Oncorhynchus tshawytscha</italic>) Growth Variability in a Large Freshwater Tidal Estuary, Estuar. Coast source

  • May combine two claims.

    Study design and conductown data

    For 25% of the fish, each reader provided a second growth time series estimate and had the exact same level of precision, therefore the readers were concluded to be interchangeable.

    “For 25% of the fish, each reader provided a second growth time series estimate, and had the exact same level of precision therefore we concluded they were interchangeable.”
    Quote in the paperSubstantial claim
    • The authors state this as an assumption: Otolith reader observation error is equal for all fish.

  • Classified as probably not a substantial claim.

    Premisecitation

    Five was chosen as the maximum number of trends because that was the number of juvenile Chinook salmon life history types described by Reimers.

    “We chose five as the maximum number of trends because that was the number of juvenile Chinook salmon life history types described by Reimers [9].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [9] PE Reimers, 1973, The length of residence of juvenile fall Chinook salmon in Sixes River Oregon, Research Reports of the Fish Commission of Oregon

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    DFA has been used previously to identify patterns in abundance and productivity of adult salmon.

    “DFA has been used previously to identify patterns in abundance and productivity of adult salmon [18, 19], but we are unaware of any applications to juvenile salmon or individual dating or aging techniques, such as daily growth estimates derived from otolith microstructure.”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [18] MM Stachura, 2013, Oceanographic influences on patterns in North Pacific salmon abundance, Can. J. Fish. Aquat. Sci source
    • cites [19] J Ohlberger, Population coherence and environmental impacts across spatial scales: a case study of Chinook salmon, Ecosphere

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    In a conservation context, genetic and phenotypic diversity (e.g. life history diversity) is considered one of four important aspects for maintaining viable populations.

    “In a conservation context, genetic and phenotypic diversity (e.g. life history diversity) is considered one of four important aspects for maintaining viable populations [3, 4].”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [3] McElhany P, Ruckelshaus MH, Ford MJ, Wainwright TC, Bjorkstedt EP (2000) Viable salmonid populations and the recovery of evolutionarily significant units. NOAA Tech. Memo. NMFS-NWFSC-42, U.S. Department of Commerce.
    • cites [4] MH Ruckelshaus, 2002, The Pacific salmon wars: what science brings to the challenge of recovering species, Annu. Rev. Ecol. Syst source

  • Probably not a substantial claim: may not pass S2 (checkable), S4 (based).

    Interpretationnone given

    A narrow focus on timing and size at migration offers no direct measure of salmon performance.

    “Additionally, a narrow focus on timing and size at migration offers no direct measure of salmon performance.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    The otolith chemical markers (e.g., Sr and Ca) most widely used to indicate fish entry into salt water are not limited by fish size, but provide no information about salmon rearing histories in the freshwater tidal reaches of estuaries.

    “The otolith chemical markers (e.g., Sr and Ca) most widely used to indicate fish entry into salt water are not limited by fish size, but provide no information about salmon rearing histories in the freshwater tidal reaches of estuaries [12].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [12] GE Bath, 2000, Strontium and barium update in aragonitic otoliths of marine fish, Geochemica Et Cosmochimica Acta source

  • Classified as probably not a substantial claim.

    Study design and conductnone given

    Only the highest rated samples (N = 524) were used for further analysis.

    “A relative index of reader confidence (1–5) was recorded for every otolith age estimate and only the highest rated samples (N = 524) were used for further analysis.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Study design and conductreasoning

    To ensure overall stock assignment accuracy in the data used for the DFA, juveniles with relative assignment probabilities < 0.80 were excluded (18% of the individual assignments determined from the total catch).

    “To ensure overall stock assignment accuracy in the data used for the DFA, we excluded juveniles with relative assignment probabilities < 0.80 (18% of the individual assignments determined from the total catch).”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Premisecitation

    DFA is a multivariate time series method that seeks to explain the variance in n time series with a linear combination of m hidden random walks where n >> m.

    “DFA is a multivariate time series method that seeks to explain the variance in n time series with a linear combination of m hidden random walks where n >> m [15].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [15] AF Zuur, 2003, Estimating common trends in multivariate time series using dynamic factor analysis, Environmetrics source

  • Classified as probably not a substantial claim.

    Premisecitation

    To use otolith growth as a proxy for juvenile Chinook salmon growth, there must be a strong relationship between fish size and otolith size.

    “To use otolith growth as a proxy for juvenile Chinook salmon growth, there must be a strong relationship between fish size and otolith size [47].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [47] SE Campana, 1985, Microstructure of fish otoliths, Can. J. Fish. Aquat. Sci source

  • Probably not a substantial claim: may not pass S2 (checkable).

    Interpretationreasoning

    By oversimplifying descriptions of juvenile life history, researchers may be ignoring other critical indicators of phenotypic diversity that are important to population resilience and long-term salmon conservation.

    “By oversimplifying our descriptions of juvenile life history we may be ignoring other critical indicators of phenotypic diversity that are important to population resilience and long-term salmon conservation.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Premisecitation

    Summarizing variability over weeks is a common practice in otolith microstructure to incorporate growth variation and decrease the influence of edge effects.

    “Summarizing variability over weeks is a common practice in otolith microstructure to incorporate growth variation and decrease the influence of edge effects [48, 49].”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [48] MJ Bradford, 1997, Individual variation in dispersal behaviour of newly emerged Chinook salmon (<italic>Oncorhynchus tshawytscha</italic>) from the upper Fraser River, British Columbia, Can. J. Fish. Aquat. Sci source
    • cites [49] JA Miller, 2013, Disentangling bottom-up and top-down effects on survival during early ocean residence in a population of Chinook salmon (<italic>Oncorhynchus tshawytscha</italic>), Can. J. Fish. Aquat. Sci source

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductown data

    Of the 665 otoliths dissected, approximately 5% (27) were lost due to damage during processing and 23 otoliths were determined to be vatritic and therefore unusable.

    “Of the 665 otoliths dissected, approximately 5% (27) were lost due to damage during processing and 23 otoliths were determined to be vatritic, and therefore unusable.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S2 (checkable).

    Interpretationown data

    The study exemplifies how a relatively new statistical analysis can be applied to dating or aging techniques to summarize individual variation, and characterize aspects of life history diversity.

    “Our study exemplifies how a relatively new statistical analysis can be applied to dating or aging techniques to summarize individual variation, and characterize aspects of life history diversity.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    Wild juvenile salmon life history diversity, especially estuarine entrance and residency, can be difficult to document, and juvenile salmon life history diversity is not often integrated into resilience studies.

    “Wild juvenile salmon life history diversity, especially estuarine entrance and residency can be difficult to document, and juvenile salmon life history diversity is not often integrated into resilience studies [5].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [5] JT Thorson, 2014, Spatial variation buffers temporal fluctuations in early juvenile survival for and endangered Pacific salmon, J. Anim. Ecol source

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Distinct changes in growth have been used to describe habitat changes in juvenile Chinook salmon.

    “Furthermore, distinct changes in growth have been used to describe habitat changes in juvenile Chinook salmon [25, 28].”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [25] JD Neilson, 1985, Estuarine growth of juvenile Chinook salmon (<italic>Oncorhynchus tshawytscha</italic>) as inferred from otolith microstructure, Can. J. Fish. Aquat. Sci source
    • cites [28] SE Campana, 1990, How reliable are growth back-calculations based on otoliths, Can. J. Fish. Aquat. Sci source

  • May combine two claims.

    Study design and conductreasoning

    The fish retained for otolith analysis were opportunistically collected during several Columbia River estuary projects and therefore are not consistent over space or time.

    “These fish were opportunistically collected during several Columbia River estuary projects and therefore are not consistent over space or time (Table 3, S1 Fig).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Sampling lower in the Columbia River estuary has shown that hatchery-produced fish have limited variation in timing and abundance.

    “Sampling lower in the Columbia River estuary has shown that hatchery-produced fish have limited variation in timing and abundance [66]”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [66] LA Weitkamp, 2012, Seasonal and interannual variation in juvenile salmonids and associated fish assemblage in open waters of the lower Columbia River estuary, Fish. B-NOAA

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Interpretationreasoning

    Three and five DFA trends described in September as opposed to a single trend in May and July in both years may suggest increased diversity in juveniles which remained in freshwater through the fall or greater individual variation as fish age.

    “Three and five DFA trends described in September as opposed to a single trend in May and July in both years may suggest increased diversity in juveniles which remained in freshwater through the fall or greater individual variation as fish age.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationown data

    Fish captured in 2011 likely encountered different environmental conditions in the estuary due to high discharge in 2011.

    “Fish captured in 2011 likely encountered different environmental conditions in the estuary due to high discharge (Fig 2) in 2011”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationown data

    Growth may be constrained earlier in life and as individual decisions compound over time, growth variability may increase as an individual ages.

    “That is, growth may be constrained earlier in life and as individual decisions compound over time, growth variability may increase as an individual ages”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Premisecitation

    Growth has been shown to be an important indicator for juvenile salmon survival.

    “Although growth has been shown to be an important indicator for juvenile salmon survival [69]”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [69] EJ Duffy, 2011, Rapid growth in the early marine period improves the marine survival of Chinook salmon (<italic>Oncorhynchus tshawytscha</italic>) in Puget Sound, Washington, Can. J. Fish. Aquat. Sci source

  • May combine two claims.

    Interpretationreasoning

    The West Cascade spring-run juveniles show a similar pattern, suggesting at least three estuary rearing or migrating time and size alternatives in lower river spring-run populations.

    “The West Cascade spring-run juveniles show a similar pattern, suggesting at least three estuary rearing or migrating time and size alternatives in lower river spring-run populations”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationreasoning

    The dynamic factor analysis reveals considerable diversity in juvenile Chinook salmon but may not be a practical approach for identifying juvenile life history diversity management targets, due to the complexity of the results and time intensive laboratory and statistical techniques.

    “Finally, the dynamic factor analysis reveals considerable diversity in juvenile Chinook salmon but may not be a practical approach for identifying juvenile life history diversity management targets, due to the complexity of the results and time intensive laboratory and statistical techniques”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S2 (checkable). May combine two claims.

    Interpretationown data

    These results may be too complex for application in categorizing life history types; rather it better describes a continuum.

    “However, these results may be too complex for application in categorizing life history types, rather it better describes a continuum”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Study design and conductown data

    One artifact of being the oldest fish was that September capture groups had the longest growth time series and the smallest sample sizes, and this could have affected the findings due to DFA's method of modeling random walks.

    “However, one artifact of being the oldest fish was that September capture groups had the longest growth time series and the smallest sample sizes (Table 3), and this could have affected our findings due to DFA’s method of modeling random walks.”
    Quote in the paperNot a substantial claim
    • The authors state this as an assumption: Latent trends follow a random walk with process innovations distributed as a multivariate normal with mean-vector zero and an identity variance-covariance.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    All juvenile Chinook salmon examined with otolith microstructure and DFA are considered subyearlings or ocean-type by current fisheries standards for categorizing life history type.

    “In our study, all juvenile Chinook salmon examined with otolith microstructure and DFA are considered subyearlings or ocean-type by current fisheries standards for categorizing life history type [41]”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [41] GE Johnson, 2010, Ecology of juvenile salmon in shallow tidal freshwater habitats of the lower Columbia River, 2007–2010 source

  • Classified as probably not a substantial claim.

    Interpretationown data

    Growth at this individual scale cannot be adequately described by large scale temperature and discharge indices.

    “Finally, the best covariate matrix was the D matrix with no covariates; it may be that growth at this individual scale cannot be adequately described by large scale temperature and discharge indices.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Restoration efforts in the Salmon River estuary have shown that wetland recovery can expand life history variation by allowing a greater expression of estuarine-resident behaviors.

    “Restoration efforts in the Salmon River estuary have shown that wetland recovery can expand life history variation by allowing a greater expression of estuarine-resident behaviors [10]”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [10] DL Bottom, 2005, Patterns of Chinook salmon migration and residency in the Salmon River estuary (Oregon), Estuar. Coastal and Shelf S source
52 of 52

  • The authors state this as an assumption.

    Otolith reader observation error is equal for all fish.

    “We assumed that otolith reader observation error would be equal for all fish, as the reader was blind to the identity of each otolith sample, and therefore all elements along the diagonal of R were unknown, but equal, and all off-diagonal elements were zero.”

  • The authors state this as an assumption.

    Latent trends follow a random walk with process innovations distributed as a multivariate normal with mean-vector zero and an identity variance-covariance.

    “The latent trends at time t (xt) were modeled as a random walk based on the process innovations at time t (wt), which are distributed as a multivariate normal with mean-vector zero and an identity variance-covariance (i.e., all diagonal elements were one with zeroes elsewhere).”

  • The paper relies on this without support.

    No prior applications of DFA to juvenile salmon or individual dating or aging techniques exist.

    “DFA has been used previously to identify patterns in abundance and productivity of adult salmon [18, 19], but we are unaware of any applications to juvenile salmon or individual dating or aging techniques, such as daily growth estimates derived from otolith microstructure.”

  • The paper relies on this without support.

    Most tags used to track juvenile salmon movements and habitat use are too large to be used with the smallest size classes of juveniles (e.g., fry < 60mm FL), limiting the breadth of life history types that can be studied.

    “Most tags used to track juvenile salmon movements and habitat use are too large to be used with the smallest size classes of juveniles (e.g., fry < 60mm FL), limiting the breadth of life history types that can be studied.”

  • The paper relies on this without support.

    There is no one optimum phenotype.

    “there is no one optimum phenotype”

  • The paper relies on this without support.

    Many Columbia River Chinook salmon populations are listed as threatened or endangered under the Endangered Species Act.

    “Many of the Columbia River Chinook salmon populations are listed as threatened or endangered on the Endangered Species Act”

  • The paper relies on this without support.

    Few studies incorporate a landscape scale evaluation of habitat performance, and genetic and life history diversity that can be integrated into restoration design.

    “However, few studies incorporate a landscape scale evaluation of habitat performance, and genetic and life history diversity that can be integrated into restoration design.”
7 of 7

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • Nine within-basin stocks claimed, but Table 2 lists seven

    Minor

    The text says nine within-basin regional stocks were identified and points to Table 2, but Table 2 lists only seven stock abbreviations.

1 of 1

Cites

Flagged first, then by citations

Research works printed but not linked: 4

  1. Anderson GO. Variations in estuarine life history diversity of juvenile Chinook salmon based on stable isotope analysis of food web linkages. M.Sc. Thesis, University of Washington. 2006. Available: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://www.lib.washington.edu/engineering/resources/theses" xlink:type="simple">http://www.lib.washington.edu/engineering/resources/theses</ext-link>
  2. DL Bottom, 2005, Salmon at River&apos;s End: The Role of the Estuary in the Decline and Recovery of Columbia River Salmon, NOAA Technical Memorandum NMFS-NWFSC-70, U.S. Department of Commerce
  3. RG Titus, 2004, Use of otolith microstructure to estimate growth rates of juvenile Chinook salmon from a Central Valley, California stock, Am. Fish. S. S, 39, 181
  4. Reimers PE. The length of residence of juvenile fall Chinook salmon in Sixes River, Oregon. M.Sc. Thesis, Oregon State University. 1971. Available: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://hdl.handle.net/1957/6701" xlink:type="simple">http://hdl.handle.net/1957/6701</ext-link>

Cited by

Still being checked.

Related

Authors
Goertler, P. A. L., Scheuerell, M. D., Simenstad, C. A., & Bottom, D. L.
Affiliations
  • University of Washington (US)
  • National Oceanic and Atmospheric Administration (US)
Corresponding author
Goertler, Pascale A. L.
ORCID
Venue
PLOS ONE
Publisher
Public Library of Science (PLoS)
Published
2016-10-03
Volume
11
Issue
10
Pages
e0162121
ISSN
1932-6203 (ISSN-L)
DOI
10.1371/journal.pone.0162121
PMC
PMC5047595
OpenAlex
W2529676796
Cited by
10
References
62
Citations by year
2026: 1 · 2025: 1 · 2024: 2 · 2022: 2 · 2020: 1 · 2019: 1 · 2018: 1 · 2017: 1
FWCI
0.74
Type
journal article
Language
en
Open access
Licence
Locations
  • PLoS ONE (publishedVersion, public-domain)
  • PubMed Central (publishedVersion, public-domain)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • NOAA Institutional Repository (submittedVersion)
Funders
  • National Oceanic and Atmospheric Administration (EST-O10-1)
  • University of Washington School of Aquatic and Fishery Sciences (65-4094)
Topics
  • Physical Sciences › Environmental Science › Global and Planetary Change › Marine and fisheries research
  • Physical Sciences › Environmental Science › Nature and Landscape Conservation › Fish Ecology and Management Studies
  • Life Sciences › Agricultural and Biological Sciences › Aquatic Science › Fish Biology and Ecology Studies
Keywords
Oncorhynchus tshawytscha, juvenile growth rate, otolith microstructure, dynamic factor analysis, life history variation, hatchery-reared fish, wild fish, natal origin, habitat type, Columbia River estuary, fish ageing
MeSH terms
Animals, Ecology, Otolithic Membrane, Salmon, Estuaries

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-27.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-27.

Cited sources are checked by gpt-6-sol.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review