Geology topics

Ji X. He

Publications and source records attributed to Ji X. He.

15 recordsLinked to original sources

USGS2025

Assessing fish growth changes under an ecosystem regime shift: The approach of linear mixed-effects modeling with application to Lake Huron lake trout

Linear mixed-effects modeling has been used to characterize fish growth changes over time, but early studies did not fully consider the implicit relationship among the three major factors of fish age, year-class, and sampling year in model development. Our objective is to resolve this issue and develop a linear mixed-effects model to clearly assess how lake trout ( Salvelinus namaycush ) growth has responded to the ecosystem regime shift in Lake Huron. We found that, from the late 1970s through the early 2000s, lake trout weight-at-age in northern Lake Huron had large variation with no apparent temporal trend, whereas the weight-at-age in southern Lake Huron steadily declined but remained larger than that in northern Lake Huron. The difference between northern and southern Lake Huron almost disappeared prior to the 2003 collapse of alewives, which accelerated the weight-at-age declines during the 2000s in both regions. By 2010, lake trout growth had a modest recovery and then stabilized. Our model fitted and explained variation in lake trout weight-at-age between years, regions, and recruitment origins, with the fixed age effect representing the general growth trajectory, the fixed year effect as the year-specific growth index, and the random year-class effect as the cohort-specific growth index.

Lake Huron↗

USGS2025

Comparing year-class strength indices from longitudinal analysis of catch-at-age data with those from catch-curve regression: Application to Lake Huron lake trout

Fish year-class strength (YCS) has been estimated via longitudinal analysis of catch-at-age data and via catch-curve regression, but no study has compared the two approaches. The objective of this study was to compare YCS estimates derived from both approaches applied to catch-at-age data for the lake trout (Salvelinus namaycush) population in the main basin of Lake Huron, one of the Laurentian Great Lakes of North America. YCS was reconstructed for both hatchery-stocked and wild lake trout. Akaike information criterion (AIC) and Bayesian information criterion (BIC) were used to compare 14 linear mixed-effects models for longitudinal analysis of catch-at-age data, and three linear mixed-effects models for catch-curve regression. From the best models based on AIC or BIC comparisons, YCS estimates with year-class as a fixed effect were consistent with those estimated with year-class as a random effect. Patterns and trends in the YCS estimates were also the same or similar between the longitudinal analysis of catch-at-age data approach and the catch-curve regression approach, suggesting that both modeling approaches are applicable to a variety of fish populations. indicating that both approaches provide robust measures of YCS. Potential bias in using the approach of catch-curve regression could be caused by abrupt changes in adult mortality. It is also critical to recognize multiple recruitment origins for using the approach of longitudinal analysis of catch-at-age data.

Lake Huron↗

USGS2024

Reconstructing half a century of coregonine recruitment reveals species-specific dynamics and synchrony across the Laurentian Great Lakes

Understanding how multiple species and populations vary in their recruitment dynamics can elucidate the processes driving recruitment across space and time. Lake Whitefish ( Coregonus clupeaformis ) and Cisco ( C. artedi ) are socioecologically important fishes across their range; however, many Laurentian Great Lakes populations have experienced declining, poor, or sporadic recruitment in recent decades. We integrated catch and age data from 38 long-term surveys across each of the Great Lakes and Lake Simcoe, resulting in a combined time series spanning 1960–2019. We estimated Lake Whitefish and Cisco year-class strength (YCS) in each lake using longitudinal mixed-effects regressions of relative cohort abundance. We subsequently quantified interspecific, spatial, and temporal synchrony in YCS using correlation and dynamic factor analyses. Lake Whitefish YCS was positively spatially synchronous on average, and YCS in all six lakes was elevated during the 1980s–1990s. In contrast, Cisco YCS was sporadic, not spatially synchronous, and highly variable around long-term, lake-specific means. YCS was not synchronous between species in any lake. Collectively, our analyses demonstrate that these species exhibit differential recruitment dynamics that may be regulated by species-specific factors. Results from this study can be leveraged in future research on the causes and consequences of cross-species, cross-basin recruitment variability.

Laurentian Great Lakes↗

USGS2023

Longitudinal analyses of catch-at-age data for reconstructing year-class strength, with an application to lake trout (Salvelinus namaycush) in the main basin of Lake Huron

We investigated using longitudinal models to reconstruct year-class strength (YCS) from catch-at-age data, with an example application to lake trout ( Salvelinus namaycush ) in the main basin of Lake Huron. The best model structure depended on the age range used for model implementation. The YCS trajectory from the full age range (3–30 years) was similar to the trajectory from a narrow age range that approximated the age of recruitment to the fishing gears (5–7 years), but YCS estimates from the full age range included additional variations due to time-dependent selectivity and mortality. When using ages younger or older than the likely ages of recruitment, YCS estimates did not represent recruitment abundances and were also biased by trends in age-specific selectivity and mortality across years. Longitudinal YCS estimates are likely more robust than single-age recruitment indices, which are often subject to interannual changes in catchability and selectivity. Our findings provide guidance for future applications of the longitudinal YCS reconstruction that in turn may inform and supplement more comprehensive research and management programs for understanding fish recruitment dynamics.

Lake Huron↗

USGS2023

A generalized application of the catch-curve regression with comparisons of adult mortality and year-class strength between hatchery-stocked and wild-reared lake trout in US waters of Lake Huron

The recently developed approach to estimating the instantaneous total mortality of coded-wire-tagged lake trout ( Salvelinus namaycush ) is generally applicable to catch-at-age data. We further formalized the technique to objectively incorporate the year-class and year effects into the model structure of catch-curve regression. We used this new method to compare adult mortality and year-class strength between the hatchery-stocked and wild-reared lake trout in US waters of Lake Huron, one of the Laurentian Great Lakes. Model comparisons showed no difference in adult mortality between the hatchery-stocked and wild-reared lake trout. Based on 95% confidence intervals, the estimate of adult mortality using the simple catch-curve regression with average number-at-age was not statistically different from the estimate using the linear mixed model with individual number-at-age of multiple year-classes and sampling years. The linear mixed model, however, also quantified lake trout year-class strength and indicated that since 2003, the increases in recruitment of wild-reared lake trout did not fully compensate for the rapid declines in recruitment of hatchery-stocked lake trout in Lake Huron.

Lake Huron↗

USGS2022

Estimating catch curve mortality based on relative return rates of coded wire tagged lake trout in US waters of Lake Huron

We estimated total mortality using catch curves based on relative return rates (RRs) of coded wire tagged lake trout ( Salvelinus namaycush ) in US waters of Lake Huron. RR was calculated as age-specific CPUE per million of fish stocked. Annual mortality for the late 1990s through early 2000s was estimated as 38% from the 1991–1995 year classes, with an effective age range of 5–10 years, and then was estimated as 24% for the post-2000 period from the 1996–2009 year classes. The two estimates from simple catch curve regressions based on average RR at age values were the same as from a mixed model with individual RR values from all stocking events. These two estimates were also comparable to the findings from statistical catch-at-age assessments with fundamentally different assumptions. Our approach is not constrained by the assumption that the expected recruitment is a constant over time and thus has the advantage to use multiple observations on each age from multiple cohorts. Our approach has broad applicability to aquatic ecosystems in which multiple mark-and-release events of fish stocking have been implemented.

Michigan↗

USGS2020

Dynamics of lake trout production in the main basin of Lake Huron

To inform lake trout (Salvelinus namaycush) fishery management in Lake Huron that has undergone rapid ecosystem changes, we quantified lake trout production dynamics by coupling age-structured stock assessment and fish bioenergetics models. Our approach revealed the connection between piscivore production and prey consumption, included growth compensation to reproduction losses, and allowed comparisons between long-term dynamics of fishery harvests and fish production. We found that despite the collapse of alewives, a major non-native pelagic prey fish, lake trout production appeared to be sustainable. To a certain degree, the effect of recent recruitment declines on lake trout production was offset by release of harvest pressure from subadult lake trout, and reduction of fishing and sea lamprey induced mortality on adult lake trout. Evidence for sustainability also included the finding that no changes in average ratios of annual production to beginning-of-the-year biomass. Juvenile P:B ratio remained as high as 2.1. The effect of growth declines on adult and subadult production was offset by reduction in population mortality. Body growth and condition did not continue to decline when lake trout became more and more reliant on round goby as food, and the dynamics of total consumption of prey fish continued to be recipient controlled.

Lake Huron↗

USGS2017

Asynchrony in the inter-annual recruitment of lake whitefish Coregonus clupeaformis in the Great Lakes region

Spatially separated fish populations may display synchrony in annual recruitment if the factors that drive recruitment success, particularly abiotic factors such as temperature, are synchronised across broad spatial scales. We examined inter-annual variation in recruitment among lake whitefish ( Coregonus clupeaformis ) populations in lakes Huron, Michigan and Superior using fishery-dependent and -independent data from 1971 to 2014. Relative year-class strength (RYCS) was calculated from catch-curve residuals for each year class across multiple sampling years. Pairwise comparison of RYCS among datasets revealed no significant associations either within or between lakes, suggesting that recruitment of lake whitefish is spatially asynchronous. There was no consistent correlation between pairwise agreement and the distance between datasets, and models to estimate the spatial scale of recruitment synchrony did not fit well to these data. This suggests that inter-annual recruitment variation of lake whitefish is asynchronous across broad spatial scales in the Great Lakes. While our method primarily evaluated year-to-year recruitment variation, it is plausible that recruitment of lake whitefish varies at coarser temporal scales (e.g. decadal). Nonetheless, our findings differ from research on some other Coregonus species and suggest that local biotic or density-dependent factors may contribute strongly to lake whitefish recruitment rather than inter-annual variability in broad-scale abiotic factors.

Great Lakes↗

USGS2016

Age and growth of round gobies in Lake Huron: Implications for food web dynamics

Although the round goby ( Neogobius melanostomus ) has become established throughout the Laurentian Great Lakes, information is scarce on spatial variation in round goby growth between and within lakes. Based on a sample of 754 specimens captured in 2014, age, growth, and mortality of round gobies at four locations in Lake Huron were assessed via otolith analysis. Total length ( TL ) of round gobies ranged from 44 to 111 mm for Saginaw Bay, from 45 to 115 mm for Rockport, from 50 to 123 mm for Hammond Bay, and from 51 to 118 mm for Thunder Bay. Estimated ages of round gobies ranged from 2 to 5 years for Saginaw Bay, from 2 to 6 years for Rockport, and from 2 to 7 years for Hammond Bay and Thunder Bay. Sex-specific, body–otolith relationships were used to back-calculate total lengths at age, which were then fitted to von Bertalanffy growth models. For each sex, round goby growth showed significant spatial variation among the four locations within Lake Huron. At all four locations in Lake Huron, males grew significantly faster than females and attained a larger asymptotic length than females. Annual mortality rate estimates were high (62 to 85%), based on catch-curve analysis, suggesting that round gobies may be under predatory control in Lake Huron.

Michigan↗

USGS2016

Reply to comments by Riley and Dunlop on He et al. (2015)

He et al. (2015) described piscivory patterns in the main basin of Lake Huron 1984-2010, during which there was also a pattern of stepwise declines in the abundance of dominant prey fish species. The approach of He et al. (2015) was to couple age-structured stock assessment and fish bioenergetics models to estimate prey fish consumption, and to compare these patterns with prey fish biomass from a bottom trawl survey. Riley and Dunlop (2015) were highly critical of the methods and conclusions reached by He et al. (2015). They claimed that we incorrectly interpreted the bottom trawl survey data, and did not account for uncertainty. We respond to these and other criticisms below, which we find do not undermine our findings.

Canadian Journal of Fisheries and Aquatic Sciences↗

USGS2015

Coupling age-structured stock assessment and fish bioenergetics models: a system of time-varying models for quantifying piscivory patterns during the rapid trophic shift in the main basin of Lake Huron

We quantified piscivory patterns in the main basin of Lake Huron during 1984–2010 and found that the biomass transfer from prey fish to piscivores remained consistently high despite the rapid major trophic shift in the food webs. We coupled age-structured stock assessment models and fish bioenergetics models for lake trout ( Salvelinus namaycush ), Chinook salmon ( Oncorhynchus tshawytscha ), walleye ( Sander vitreus ), and lake whitefish ( Coregonus clupeaformis ). The model system also included time-varying parameters or variables of growth, length–mass relations, maturity schedules, energy density, and diets. These time-varying models reflected the dynamic connections that a fish cohort responded to year-to-year ecosystem changes at different ages and body sizes. We found that the ratio of annual predation by lake trout, Chinook salmon, and walleye combined with the biomass indices of age-1 and older alewives ( Alosa pseudoharengus ) and rainbow smelt ( Osmerus mordax ) increased more than tenfold during 1987–2010, and such increases in predation pressure were structured by relatively stable biomass of the three piscivores and stepwise declines in the biomass of alewives and rainbow smelt. The piscivore stability was supported by the use of alternative energy pathways and changes in relative composition of the three piscivores. In addition, lake whitefish became a new piscivore by feeding on round goby ( Neogobius melanostomus ). Their total fish consumption rivaled that of the other piscivores combined, although fish were still a modest proportion of their diet. Overall, the use of alternative energy pathways by piscivores allowed the increases in predation pressure on dominant diet species.

Lake Huron↗

USGS2015

Using time-varying asymptotic length and body condition of top piscivores to indicate ecosystem regime shift in the main basin of Lake Huron: a Bayesian hierarchical modeling approach

We evaluated the ecosystem regime shift in the main basin of Lake Huron that was indicated by the 2003 collapse of alewives, and dramatic declines in Chinook salmon abundance thereafter. We found that the period of 1995-2002 should be considered as the early phase of the final regime shift. We developed two Bayesian hierarchical models to describe time-varying growth based on the von Bertalanffy growth function and the length-mass relationship. We used asymptotic length as an index of growth potential, and predicted body mass at a given length as an index of body condition. Modeling fits to length and body mass at age of lake trout, Chinook salmon, and walleye were excellent. Based on posterior distributions, we evaluated the shifts in among-year geometric means of the growth potential and body condition. For a given top piscivore, one of the two indices responded to the regime shift much earlier than the 2003 collapse of alewives, the other corresponded to the 2003 changes, and which index provided the early signal differed among the three top piscivores.

Lake Huron↗

USGS2014

Lake trout in northern Lake Huron spawn on submerged drumlins

Recent observations of spawning lake trout Salvelinus namaycush near Drummond Island in northern Lake Huron indicate that lake trout use drumlins, landforms created in subglacial environments by the action of ice sheets, as a primary spawning habitat. From these observations, we generated a hypothesis that may in part explain locations chosen by lake trout for spawning. Most salmonines spawn in streams where they rely on streamflows to sort and clean sediments to create good spawning habitat. Flows sufficient to sort larger sediment sizes are generally lacking in lakes, but some glacial bedforms contain large pockets of sorted sediments that can provide the interstitial spaces necessary for lake trout egg incubation, particularly if these bedforms are situated such that lake currents can penetrate these sediments. We hypothesize that sediment inclusions from glacial scavenging and sediment sorting that occurred during the creation of bedforms such as drumlins, end moraines, and eskers create suitable conditions for lake trout egg incubation, particularly where these bedforms interact with lake currents to remove fine sediments. Further, these bedforms may provide high-quality lake trout spawning habitat at many locations in the Great Lakes and may be especially important along the southern edge of the range of the species. A better understanding of the role of glacially-derived bedforms in the creation of lake trout spawning habitat may help develop powerful predictors of lake trout spawning locations, provide insight into the evolution of unique spawning behaviors by lake trout, and aid in lake trout restoration in the Great Lakes.

Michigan↗

USGS2013

Trophic shift, not collapse

Jerald Schnoor’s editorial describes the recent changes in Lake Huron’s aquatic ecosystem as a trophic collapse and attributes this collapse to invasive species dominating energy and nutrient ﬂows in the food web. As state and federal scientists who are closely monitoring Lake Huron’s food web, we believe that the ongoing changes are more accurately characterized as a trophic shift in which benthic pathways have become more prominent. While decreases in abundance have occurred for some species, others are experiencing improved reproduction resulting in the restoration of several important native species.

Environmental Science & Technology↗

USGS2012

Lake trout status in the main basin of Lake Huron, 1973-2010

We developed indices of lake trout Salvelinus namaycush status in the main basin of Lake Huron (1973-2010) to understand increases in the relative abundance of wild year-classes during 1995-2010. Sea lamprey Petromyzon marinus wounds per 100 lake trout declined from 23.63 in 2000 to 5.86-10.64 in 2002-2010. The average age-7 lake trout catch per effort per recruitment (CPE/R; fish•305mof gill net - 1•million stocked yearlings -1 ) increased from 0.56 for the 1973-1990 year-classes to 0.92 for the 1991-2001 year-classes. Total CPE (fish/305 m of gill net) declined from 16.4 fish in 1996 to 4.1 fish in 2010, but the percentage of age-5 and younger lake trout steadily decreased from more than 70% before 1996 to less than 10% by 2009. The modal age in gill-net catches increased from age 5 before 1996 to age 7 by 2005. The average adult CPE increased from 2.8 fish/305 m of gill net during 1978-1995 to 5.34 fish/305 m of gill net during 1996-2010. The 1995-2010 year-classes of wild fish weremore abundant than previous year-classes and were associated with the relatively high adult abundance during 1996-2010. Until the 2002 year-class, there was no decline in age-7 CPE/R; until 2008, there was no decline in adult CPE. Low survival of the 2002 and 2003 year-classes of stocked fish was related to the event of alewife Alosa pseudoharengus population collapse in 2003-2004. Lake trout in the main basin of Lake Huron are undergoing a transition from a hatchery stock to a wild stock, accompanied by an increased uncertainty in delayed recruitment. Future management should pay more attention to the protection of wild recruitment and the abundance of the spawning stock.

Lake Huron↗