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The Abundance of Large Piscivorous Ferox Trout (Salmo trutta) in Loch Rannoch, Scotland

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Background Ferox Trout are large, long-lived piscivorous Brown Trout ( Salmo trutta ). Due to their exceptionally large size, Ferox Trout are highly sought after by anglers while their life-history strategy, which includes delayed maturation, multiphasic growth and extended longevity, is of interest to ecological and evolutionary modelers. However, despite their recreational and theoretical importance, little is known about the typical abundance of Ferox Trout. Methods To rectify this situation a 16 year angling-based mark-recapture study was conducted on Loch Rannoch, which at 19 km ² is one of the largest lakes in the United Kingdom. Results A hierarchical Bayesian Jolly-Seber analysis of the data suggest that if individual differences in catchability are negligible the population of Ferox Trout in Loch Rannoch in 2009 was approximately 71 fish. The results also suggest that a single, often unaccompanied, highly-experienced angler was able to catch roughly 8% of the available fish on an annual basis. Discussion It is recommended that anglers adopt a precautionary approach and release all trout with a fork length ≥400 mm caught by trolling in Loch Rannoch. There is an urgent need to assess the status of Ferox Trout in other lakes.
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Submitted 11 May 2016
Accepted 3 October 2016
Published 1 November 2016
Corresponding author
Joseph L. Thorley,
joe@poissonconsulting.ca
Academic editor
Céline Audet
Additional Information and
Declarations can be found on
page 9
DOI 10.7717/peerj.2646
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2016 Thorne et al.
Distributed under
Creative Commons CC-BY 4.0
OPEN ACCESS
The abundance of large, piscivorous
Ferox Trout (Salmo trutta) in Loch
Rannoch, Scotland
Alastair Thorne1, Alisdair I. MacDonald1and Joseph L. Thorley2
1Freshwater Laboratory, Marine Scotland, Pitlochry, Scotland
2Poisson Consulting, Nelson, British Columbia, Canada
ABSTRACT
Background. Ferox Trout are large, long-lived piscivorous Brown Trout (Salmo trutta).
Due to their exceptionally large size, Ferox Trout are highly sought after by anglers while
their life-history strategy, which includes delayed maturation, multiphasic growth and
extended longevity, is of interest to ecological and evolutionary modelers. However,
despite their recreational and theoretical importance, little is known about the typical
abundance of Ferox Trout.
Methods. To rectify this situation a 16 year angling-based mark-recapture study was
conducted on Loch Rannoch, which at 19 km2is one of the largest lakes in the
United Kingdom.
Results. A hierarchical Bayesian Jolly-Seber analysis of the data suggest that if individual
differences in catchability are negligible the population of Ferox Trout in Loch Rannoch
in 2009 was approximately 71 fish. The results also suggest that a single, often
unaccompanied, highly-experienced angler was able to catch roughly 8% of the available
fish on an annual basis.
Discussion. It is recommended that anglers adopt a precautionary approach and release
all trout with a fork length 400 mm caught by trolling in Loch Rannoch. There is an
urgent need to assess the status of Ferox Trout in other lakes.
Subjects Aquaculture, Fisheries and Fish Science, Conservation Biology, Ecology, Statistics
Keywords Survival, Hierarchical, Bayesian, Exploitation, Jolly-Seber, Abundance, Ferox Trout,
Brown Trout, Piscivorous
INTRODUCTION
Due to its large size and distinctive appearance, the Ferox Trout was originally considered
its own species, Salmo ferox (Jardine, 1834); an appellation that was lost when all the
forms of Brown Trout were lumped into Salmo trutta. More recently, Duguid, Ferguson &
Prodohl (2006) have demonstrated that Ferox Trout in Lochs Melvin (Ireland), Awe and
Laggan (Scotland) are reproductively isolated and genetically distinct from their sympatric
conspecifics and together form a monophyletic grouping. Based on this evidence, Duguid,
Ferguson & Prodohl (2006) argue that the scientific name S. ferox should be resurrected.
Ferox Trout are characterized by their large size and extended longevity. The British
rod caught record is 14.4 kg (31 lb 12 oz) and the oldest recorded individual was estimated
to be 23 ±1 years of age based on scale annuli (Campbell, 1979). The consensus view is
that Ferox Trout achieve their large size by forgoing spawning until they are big enough
How to cite this article Thorne et al. (2016), The abundance of large, piscivorous Ferox Trout (Salmo trutta) in Loch Rannoch, Scotland.
PeerJ 4:e2646; DOI 10.7717/peerj.2646
to switch to a primarily piscivorous diet at which point they experience an increased
growth rate (Campbell, 1971;Campbell, 1979;Went, 1979). The resultant higher survival
and fecundity is assumed to compensate for the lost spawning opportunities (Mangel,
1996;Mangel & Abrahams, 2001).
Comparative lake studies (Campbell, 1971;Campbell, 1979) and ecological models
(Mangel, 1996;Mangel & Abrahams, 2001) indicate that Ferox Trout require a large
(>1 km2) oligotrophic lake and an abundant population of Arctic Charr (Salvelinus
alpinus). The ecological models also suggest that under such conditions, Ferox Trout should
constitute approximately 5% of the total Brown Trout population (Mangel & Abrahams,
2001). However, there is a lack of robust estimates of the abundance of Ferox Trout or
assessments of the potential for angling to impact individual populations. The reasons
for this knowledge gap were clearly stated by Duguid, Ferguson & Prodohl (2006, p. 90).
One of the main difficulties in attempting a detailed ferox study is obtaining sufficient
specimens. Ferox densities are believed to be low, and their large size and usual
distribution deep in the water column makes angling the only practical way to obtain
fish. Only a small number of ferox, however, are caught from any lake in a single year
even by anglers specializing in ferox capture.
At 19 km2, Loch Rannoch, which is situated in central Scotland, is one of the largest
lakes in the United Kingdom. It was chosen for the current study due to its long history
of producing Ferox Trout (Campbell, 1971;Campbell, 1979). Whether the Ferox Trout
in Loch Rannoch are sufficiently isolated and genetically distinct to be considered a
separate species (Duguid, Ferguson & Prodohl, 2006) is unknown. Consequently, Ferox
Trout were identified based on their large size and capture method—trolled dead baits and
lures (Campbell, 1971;Campbell, 1979;Went, 1979;Grey et al., 2002). As well as Brown and
Ferox Trout, Loch Rannoch also contains three ecologically and morphologically distinct
forms of Arctic charr (Verspoor et al., 2010).
In 1994, the first author (AT)—a highly-experienced ferox angler—began tagging and
releasing all Ferox Trout captured by himself or his boat companion on Loch Rannoch.
He continued this practise for 16 years. The paper uses the resultant dataset to estimate
the abundance of Ferox Trout in Loch Rannoch. Although the current dataset represents a
unique opportunity to better understand the life history of this top-level piscivore, the data
are nonetheless sparse. Consequently, they are analyzed using Bayesian methods which
provide statistically unbiased estimates irrespective of sample size (Kéry & Schaub, 2011;
Royle & Dorazio, 2008).
METHODS
Field site
Loch Rannoch, which is located in Highland Perthshire (Latitude: 56.685 Longitude:
4.321), has a length of 15.1 km, width of 1.8 km and a maximum depth of 134 m. It
is oligotrophic with a stony shoreline and lies in a catchment dominated by mixed relict
deciduous and coniferous woodlands with areas of rough grazing and marginal cultivation.
Murray & Pullar (1904) provide a more complete description of its physical characteristics.
Thorne et al. (2016), PeerJ, DOI 10.7717/peerj.2646 2/12
Figure 1 Map of Ferox Trout Caught by Angling on Loch Rannoch between 1994 and 2009. The 69 ini-
tial captures are indicated by black circles and the 11 inter-annual recaptures by red triangles. Consecutive
recaptures of the same individual are linked by black lines. The coordinates are for UTM Zone 30N (EPSG
32630). Map data from Land Cover of Scotland data, MLURI 1993.
Loch Rannoch is part of the Tummel Valley Hydro Electric generation complex and has
been a hydroelectric reservoir since 1928, when Rannoch Power Station began to receive
water from Loch Ericht. A low barrage at the eastern end of the loch limits the change in
water level to a maximum of 2.74 m.
As well as Brown and Ferox Trout, the loch contains at least seven other species of fish:
Arctic Charr, Atlantic Salmon (Salmo salar), Pike (Esox lucius), Perch (Perca fluviatilis),
Eels (Anguilla anguilla), Three-Spined Sticklebacks (Gasterosteus aculeatus) and Minnows
(Phoxinus phoxinus).
Fish capture and tagging
Between 1994 and 2009, AT tagged and released all Ferox Trout captured by himself or
his boat companion while angling on Loch Rannoch (Fig. 1). In the absence of any genetic
data, a Ferox Trout was deemed to be any member of the Brown trout species complex
that was caught by trolling with a fork length 400 mm. A fork length of 400 mm was
chosen as this is considered to be the upper length threshold for the inferred switch to
piscivory (Campbell, 1971;Campbell, 1979). All the fish were caught during the angling
season (March 15 to October 6) by licensed anglers using permitted angling methods.
The research was conducted within the framework of the UK 1986 Animals Scientific
Procedures Act.
The Ferox Trout were angled by trolling mounted dead baits and lures behind a boat at
differing depths and speeds (Greer, 1995). The dead baits (usually Brown Trout or Arctic
Charr) were mounted to impart fish-like movement. An echo sounder was used to search
the contours of the loch bottom for drop-offs and likely fish holding areas and to ascertain
fishing depth. Typically, one entire circuit of the loch’s shoreline excluding the shallow
west end, which has an area of 3 km2, was undertaken on each visit.
Hooked fish were played with care and netted directly into a large tank of water before
being carefully unhooked. The fish was then transferred into a large fine-mesh keep net
(net pen), on the shore closest to the point of capture, where it was allowed to recover
before processing. After recovering, the fish was removed from the keep net and placed
in a tank containing water and anesthetic (0.05% aqueous solution of 2-pheoxyethanol).
When the fish was sufficiently sedated its fork length and wet mass were obtained. The
adipose fin was then clipped to aid in the identification of recaptures. In addition, all but
Thorne et al. (2016), PeerJ, DOI 10.7717/peerj.2646 3/12
Table 1 Initial captures and subsequent recaptures of Angled Loch Rannoch Ferox Trout by year.
Captures Year 95 96 97 98 99 00 01 02 03 04 05 06 07 08 09
7 1994 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0
6 1995 0 0 0 0 0 0 0 0 0 0 0 0 0 0
5 1996 0 0 0 0 0 0 0 0 0 0 0 0 0
2 1997 0 0 0 0 0 0 0 0 0 0 0 0
5 1998 0 0 0 1 0 0 0 1 0 0 0
2 1999 0 0 0 0 0 0 0 0 0 0
12 2000 0 1 1 0 0 0 0 0 0
6 2001 1 0 1 1 0 0 0 0
3 2002 0 0 0 0 0 0 0
4 2003 0 0 0 0 0 0
2 2004 0 0 0 0 0
2 2005 0 1 0 1
1 2006 0 0 0
1 2007 0 0
2 2008 0
9 2009
one fish (F63) was externally tagged using a Carlin, dart or anchor tag. The tags included
the text ‘‘REWARD’’ and a telephone number for reporting. The reward value which was
not printed on the tag was five British pounds. The type of tag used depended on which
type was available at the time. After tagging, the fish was returned to the keep net to recover
and then released from the shore. The entire procedure typically took less than 30 min.
The capture location was estimated using a 1:5,000 map.
Five anglers, including AIM, accompanied AT on one or more occasions. On average
AT spent 10 days boat angling per year for approximately 10 h per day while fishing three
rods although detailed logs of angling effort were not kept. The boat, outboard, rods, reels,
line type and dead bait set-up remained constant throughout the study.
Statistical analysis
Fish
Two fish (F53 and F58), which were both recaught once, were excluded from the study
because they had a deformed spine and jaw, respectively. After the further exclusion of four
intra-annual recaptures, the data set contained information on 80 encounters involving 69
different Ferox Trout (Table 1); seven of which were recaught in at least one subsequent
year.
Hierarchical Bayesian model
The abundance, annual survival and probability of (re)capture were estimated from
the mark-recapture data using a hierarchical Bayesian Jolly-Seber (JS) model (Kéry &
Schaub, 2011). The model was the superpopulation implementation of Schwarz & Arnason
(1996) in the form of a state-space model with data augmentation (Kéry & Schaub, 2011).
Based on preliminary analyses the augmented data set was fixed at 1,000 (genuine and
Thorne et al. (2016), PeerJ, DOI 10.7717/peerj.2646 4/12
pseudo-) individuals. The zero-inflation of the augmented data set was modeled as an
inclusion probability (ψ). Due to the sparsity of data, the annual survival (S) and the
probability of (re)capture (p) were assumed to be constant. The only remaining primary
parameter was the probability of an individual recruiting to the population at the start of
the first year (ρ1). The prior probability distributions for ψ,S,pand ρ1were all uniform
distributions between zero and one. The hierarchical Bayesian JS state-space model made
the following assumptions:
1. Every individual in the population had the same constant probability of
(re)capture (p).
2. Every individual in the population had the same constant probability of surviving (S).
3. Previously captured individuals were correctly identified.
4. The number of individuals recruiting to the population at the start of each year (B)
remained constant.
5. Sampling is instantaneous.
Parameter estimates
The posterior distributions of the parameters were estimated using a Monte Carlo Markov
Chain (MCMC) algorithm. To guard against non-convergence of the MCMC process, five
chains were run, starting at randomly selected initial values. Each chain was run for at least
105iterations with the first half of the chains discarded for burn-in followed by further
thinning to leave at least 10,000 samples. Convergence was confirmed by ensuring that the
Brooks-Gelman–Rubin convergence diagnostic was ˆ
R1.05 for each of the parameters
in the model (Brooks & Gelman, 1998;Kéry & Schaub, 2011). The reported point estimates
are the mean and the 95% credible intervals (CRIs) are the 2.5 and 97.5% quantiles
(Gelman, 2014).
Software
The analyses were performed using R version 3.3.1 (R Core Team, 2015), JAGS 4.2.0
(Plummer, 2003) and the ranmrdata and ranmr R packages, which were developed
specifically for this paper. Article S1 provides instructions on how to download the
packages and replicate the analysis.
RESULTS
Fish
The (re)captured fish varied from 400 to 825 mm in length and from 0.62 to 7.41 kg
in mass (Fig. 2). Although two large recaptures appeared to senesce (as evidenced by a
decline in mass with increasing length), there was no obvious effect of previous capture
on body condition (Fig. 2). Tag loss was only recorded for one of the individuals: F21
on its second recapture eight years after it was initially tagged. F21 was identified from
photographs of its melanophore constellations (Figs. S1S3). F13 and F45 were recaught
by non-participatory anglers. F45 was released. Both recapture events were excluded from
the data, plots and analyses.
Thorne et al. (2016), PeerJ, DOI 10.7717/peerj.2646 5/12
Figure 2 Mass-length scatterplot for Ferox Trout Caught by Angling. The 69 initial captures are indi-
cated by black circles and the 11 inter-annual recaptures by red triangles. Consecutive recaptures of the
same individual are linked by black lines.
Parameter estimates
The Bayesian JS mark-recapture model estimated the annual survival (S) to be 0.74
(95% CRI 0.57–0.89) and the annual probability of capture by the primary author or
his companion (p) to be 0.08 (95% CRI 0.03–0.16). The inclusion parameter (ψ) was
estimated to be 0.42 (95% CRI 0.23–0.76) while the probability of recruiting at the start of
the first year (ρ1) was 0.26 (95% CRI 0.13–0.44). The number of individuals recruiting to
the population annually (B) was 21 individuals (95% CRI 11–37). The abundance estimate
was 111 individuals (95% CRI 39–248) in 1994 and 71 individuals (95% CRI 30 –148) in
2009 (Fig. 3).
Model adequacy
The Bayesian p-value on the posterior predictive check was 0.31 which indicates that
the distribution of the number of encounters (captures and recaptures) each year was
consistent with the assumed constant capture efficiency.
DISCUSSION
Abundance
The JS mark-recapture model estimated that the population of Ferox Trout in Loch
Rannoch declined from 111 individuals in 1994 to just 71 individuals in 2009. Whether
Thorne et al. (2016), PeerJ, DOI 10.7717/peerj.2646 6/12
Figure 3 Loch Rannoch Ferox Trout abundance estimates by year. The solid line indicates the point es-
timates and the dotted lines the 95% credible intervals.
or not the abundance estimates are accurate depends in part on the extent to which the
assumption of a constant capture probability is met. The assumption can be violated
in two ways: the capture probability can vary among years or it can vary among fish.
Variation among years can introduce an artificial trend in the abundance estimates across
the course of the study while variation among fish can cause the abundance to be over or
underestimated depending on whether any individual differences are fixed (Biro, 2013) or
learnt (Askey et al., 2006), respectively. Although angling logs were not kept the posterior
predictive check, which compared the number of predicted versus observed encounters,
statistically confirmed the relative constancy of pamong years. Nevertheless, individual
Ferox Trout may still have differed in their vulnerability to capture by angling. As is the
case for many mark-recapture studies the reliance on a single capture method and the
relatively low number of encounters means it is not possible to determine the presence or
form of any individual differences (Biro, 2013).
If the individual differences in catchability are negligible, the abundance estimates are
unbiased and by 2009 the Ferox Trout were present at a density of just 0.044 fish.ha1when
the shallow west end is excluded (Engstrom-Heg, 1986). For comparison, Johnston et al.
(2007) estimated that the density of large piscivorous Bull Trout (Salvelinus confluentus) in
the 6.5 km Lower Kananaskis Lake, Alberta, was 0.093 fish.ha1when being overexploited.
In response to a zero-harvest regulation, the density of large Bull Trout in Lower Kannaskis
Thorne et al. (2016), PeerJ, DOI 10.7717/peerj.2646 7/12
Lake increased to over 2.6 fish.ha1in less than a decade. The higher density of Bull Trout in
Lower Kananaskis Lake could reflect differences in lake productivity or life-history strategy.
The annual interval mortality estimate (1S) of 0.26 includes handling and tagging by
the primary author and his companion as well as natural mortality and fishing mortality
by all other anglers on the loch. As all fish recovered well and were only adipose clipped
and marked with a single external tag, it is likely that handling and tagging effects were
small. Furthermore, despite the offer of a reward only two fish were reported to have been
recaught by a member of the public which suggests that the exploitation rate by other
anglers on the loch was low. Consequently, if individual differences in catchability are
negligible, 26% is probably only a moderate overestimate of the natural mortality rate.
For comparison, Johnston et al. (2007) estimated the equilibrium natural mortality rate for
adult Bull Trout in Lower Kananaskis Lake to be around 27%.
Management and conservation implications
A concern for any small salmonid population is that the loss of genetic variation results in
loss of adaptive potential or inbreeding depression (Wang, Hard & Utter, 2002). Although
the levels at which the low genetic variation results in population-level consequences are
difficult to predict (Vincenzi et al., 2010), the rate at which genetic variation is being lost can
be calculated from the effective population size (Ne) (Wright, 1931;Wright, 1978). Due to
their mating systems and life-histories, the Neof most salmonid populations is considered
to be around 25% of the spawning population size (Allendorf et al., 1997;McElhaney et al.,
2000). Thus, even if all the adult Ferox Trout in Loch Rannoch spawn in each year then
this suggests that if individual differences in catchability are negligible the Nein 2009 was
just eight. The low effective population size is concerning because an Ne50 is needed
to minimize inbreeding effects and an Ne500 is required to retain long-term adaptive
potential (Allendorf et al., 1997).
Whether or not the Ferox Trout in Loch Rannoch are at risk of inbreeding depression
partly depends on the extent to which they are reproductively isolated from the other
Brown Trout in the loch. If they, like the Ferox Trout in Lochs Melvin, Awe and Laggan,
are sufficiently isolated and genetically distinct to be considered a separate species (Duguid,
Ferguson & Prodohl, 2006) then inbreeding is likely occurring. Alternatively, if the Ferox
Trout in Loch Rannoch are simply Brown Trout adopting an alternative life-history
strategy, then the effective population size is a function of the total number of Brown Trout
spawners and inbreeding is not an issue.
Nonetheless, even if the Ferox Trout in Loch Rannoch are not genetically isolated, a
sustained high exploitation rate could result in adaptive change. Mangel and Abrahams’
Mangel & Abrahams (2001) individual-based model predicted that the proportion of the
population adopting the ferox life-history strategy is affected by mortality with high
size-independent mortality being associated with no or few Ferox Trout. The explanation
is straightforward; with increasing mortality the chances of benefiting from delayed
maturation diminish. The potentially high catchability suggests that in the absence of catch
and release even small amounts of angler effort could produce sufficient fishing mortality
to select against the ferox adaptation (Hard et al., 2008).
Thorne et al. (2016), PeerJ, DOI 10.7717/peerj.2646 8/12
Given the concerns associated with a potentially high exploitation rate on a long-lived,
late-maturing population it is recommended that anglers adopt a conservative approach
and release all trout longer than 400 mm caught by trolling in Loch Rannoch. There is an
urgent need to assess the status of Ferox Trout in other lakes.
ACKNOWLEDGEMENTS
We thank the Loch Rannoch Conservation Association for approving the study; C and J
Monkton for allowing access to the loch and providing a mooring; PJ Bacon, RA Duguid,
R Greer, RL Irvine, IA Malcom and AF Youngson for feedback on earlier drafts and
S Vincenzi and two other anonymous reviewers for their helpful comments. We particularly
thank the Ferox85 group members who assisted the study.
ADDITIONAL INFORMATION AND DECLARATIONS
Funding
The study was partially funded by Poisson Consulting Ltd. in the form of a salary for Joseph
Thorley. The funders had no role in study design, data collection and analysis, decision to
publish, or preparation of the manuscript.
Grant Disclosures
The following grant information was disclosed by the authors:
Poisson Consulting Ltd.
Competing Interests
Alastair Thorne and Alasdair MacDonald are members of Ferox85, an informal organization
dedicated to understanding Ferox Trout biology and management. Joseph Thorley is
employed by Poisson Consulting Ltd. to provide independent analytic services for a wide
variety of government agencies, corporations and conservation organizations on a range
of different species and issues.
Author Contributions
Alastair Thorne and Alisdair I. MacDonald conceived and designed the experiments,
performed the experiments, reviewed drafts of the paper.
Joseph L. Thorley analyzed the data, wrote the paper, prepared figures and/or tables.
Animal Ethics
The following information was supplied relating to ethical approvals (i.e., approving body
and any reference numbers):
All the fish were caught during the angling season (March 15 to October 6) by
licensed anglers using permitted angling methods. The research was conducted within
the framework of the UK 1986 Animals Scientific Procedures Act.
Thorne et al. (2016), PeerJ, DOI 10.7717/peerj.2646 9/12
Data Availability
The following information was supplied regarding data availability:
ranmrdata R data package:
10.5281/zenodo.51110,
https://github.com/Poissonconsulting/ranmrdata;
ranmr R analysis package:
10.5281/zenodo.51274,
https://github.com/Poissonconsulting/ranmr.
Supplemental Information
Supplemental information for this article can be found online at http://dx.doi.org/10.7717/
peerj.2646#supplemental-information.
REFERENCES
Allendorf FW, Bayles D, Bottom DL, Currens KP, Frissell CA, Hankin D, Lichatowich
JA, Nehlsen W, Trotter PC, Williams TH. 1997. Prioritizing Pacific salmon stocks
for conservation. Conservation Biology 11(1):140–152
DOI 10.1046/j.1523-1739.1997.95248.x.
Askey PJ, Richards SA, Post JR, Parkinson EA. 2006. Linking angling catch rates and fish
learning under catch-and-release regulations. North American Journal of Fisheries
Management 26(4):1020–1029 DOI 10.1577/M06-035.1.
Biro PA. 2013. Are most samples of animals systematically biased? Consistent individual
trait differences bias samples despite random sampling. Oecologia 171(2):339–345
DOI 10.1007/s00442-012-2426-5.
Brooks S, Gelman A. 1998. General methods for monitoring convergence of iterative
simulations. Journal of Computational and Graphical Statistics 7(4):434–455.
Campbell RN. 1971. The growth of brown trout Salmo trutta L. in northern Scottish
lochs with special reference to the improvement of fisheries. Journal of Fish Biology
3(1):1–28 DOI 10.1111/j.1095-8649.1971.tb05902.x.
Campbell RN. 1979. Ferox trout, Salmo trutta L., and charr, Salvelinus alpinus (L.), in
Scottish lochs. Journal of Fish Biology 14(1):1–29
DOI 10.1111/j.1095-8649.1979.tb03491.x.
Duguid RA, Ferguson A, Prodohl P. 2006. Reproductive isolation and genetic differen-
tiation of ferox trout from sympatric brown trout in Loch Awe and Loch Laggan,
Scotland. Journal of Fish Biology 69:89–114 DOI 10.1111/j.1095-8649.2006.01118.x.
Engstrom-Heg R. 1986. Interaction of area with catchability indices used in analyz-
ing inland recreational fisheries. Transactions of the American Fisheries Society
115(6):818–822 DOI 10.1577/1548-8659(1986)115<818:IOAWCI>2.0.CO;2.
Gelman A. 2014. Bayesian data analysis. 3rd edition. Boca Raton: Chapman & Hall/CRC
Texts in Statistical Science, CRC Press.
Greer R. 1995. Ferox trout and Arctic charr. Shrewsbury: Swan Hill.
Thorne et al. (2016), PeerJ, DOI 10.7717/peerj.2646 10/12
Grey J, Thackeray SJ, Jones RI, Shine A. 2002. Ferox trout (Salmo trutta) as ‘Russian
dolls’: complementary gut content and stable isotope analyses of the Loch Ness food-
web. Freshwater Biology 47(7):1235–1243 DOI 10.1046/j.1365-2427.2002.00838.x.
Hard JJ, Gross MR, Heino M, Hilborn R, Kope RG, Law R, Reynolds JD. 2008. Evo-
lutionary consequences of fishing and their implications for salmon. Evolutionary
Applications 1(2):388–408 DOI 10.1111/j.1752-4571.2008.00020.x.
Jardine W. 1834. Observations upon the Salmonidae met with during an excursion to the
north-west of Sutherlandshire. Edinburgh New Philosophical Journal 18:46–58.
Johnston FD, Post JR, Mushens CJ, Stelfox JD, Paul AJ, Lajeunesse B. 2007. The
demography of recovery of an overexploited bull trout, Salvelinus confluentus,
population. Canadian Journal of Fisheries and Aquatic Sciences 64(1):113–126
DOI 10.1139/f06-172.
Kéry M, Schaub M. 2011. Bayesian population analysis using WinBUGS: a hierarchical
perspective. Boston: Academic Press.
Mangel M. 1996. Life history invariants, age at maturity and the ferox trout. Evolutionary
Ecology 10(3):249–263 DOI 10.1007/BF01237683.
Mangel M, Abrahams MV. 2001. Age and longevity in fish, with consideration of the
ferox trout. Experimental Gerontology 36(4–6):765–790
DOI 10.1016/S0531-5565(00)00240-0.
McElhaney P, Ruckleshaus M, Ford M, Wainright T, Bjorkstedt E. 2000. Viable
salmonid populations and the recovery of evolutionarily significant units. Seattle:
Northwest Fisheries Science Center.
Murray J, Pullar L. 1904. Bathymetrical survey of the fresh-water lochs of Scotland.
Scottish Geographical Magazine 20(1):1–47 DOI 10.1080/14702540408554614.
Plummer M. 2003. JAGS: a program for analysis of Bayesian graphical models using
Gibbs sampling. In: Hornik K, Leisch F, Zeileis A, eds. Proceedings of the 3rd
international workshop on distributed statistical computing (DSC 2003). Vienna,
Austria.
R Core Team. 2015. R: a language and environment for statistical computing. Vienna: R
Foundation for Statistical Computing. Available at https:// www.R- project.org/ .
Royle JA, Dorazio RM. 2008. Hierarchical modeling and inference in ecology: the analysis
of data from populations, metapopulations and communities. London: Elsevier/Aca-
demic Press.
Schwarz C, Arnason A. 1996. A general method for the analysis of capture-recapture in
open populations. Biometrics 52:860–873 DOI 10.2307/2533048.
Verspoor E, Knox D, Greer R, Hammar J. 2010. Mitochondrial DNA variation in
Arctic charr (Salvelinus alpinus (L.)) morphs from Loch Rannoch, Scotland:
evidence for allopatric and peripatric divergence. Hydrobiologia 650(1):117–131
DOI 10.1007/s10750-010-0106-1.
Vincenzi S, Crivelli AJ, Jesenšek D, De Leo GA. 2010. The management of small, isolated
salmonid populations: do we have to fix it if it ain’t broken? Animal Conservation
13(1):21–23 DOI 10.1111/j.1469-1795.2009.00292.x.
Thorne et al. (2016), PeerJ, DOI 10.7717/peerj.2646 11/12
Wang S, Hard J, Utter F. 2002. Salmonid inbreeding: a review. Reviews in Fish Biology
and Fisheries 11:301–319 DOI 10.1023/A:1021330500365.
Went AEJ. 1979. ‘Ferox’ trout, Salmo trutta L. of Loughs Mask and Corrib. Journal of Fish
Biology 15(3):255–262 DOI 10.1111/j.1095-8649.1979.tb03606.x.
Wright S. 1931. Evolution in Mendelian populations. Genetics 16(2):97–159.
Wright S. 1978. Evolution and the genetics of populations: a treatise in four volumes. Vol. 4,
variability within and among natural populations. Chicago: University of Chicago
Press.
Thorne et al. (2016), PeerJ, DOI 10.7717/peerj.2646 12/12
... Trout were captured by angling to undertake radio tagging so that fish could be subsequently tracked to spawning streams. Trout were classified as ferox based on their coloration, size and capture method (Campbell, 1979;Thorne et al., 2016;Went, 1979). Most ferox had a distinctive coloration, being heavily marked with large dark spots on the flanks over a background of gold (Campbell, 1979).Trout were captured by angling using trolled dead bait, normally roach, behind a moving boat. ...
... Corrib and Mask, the overall ferox stock is likely to be small relative to the sympatric brown trout population. Thorne et al. (2016) noted that a concern for any small salmonid population is that the loss of genetic variation results in loss of adaptive potential or inbreeding depression (Wang et al., 2002). They commented that even if the ferox trout in Loch Rannoch are not genetically isolated, a sustained high exploitation rate could result in adaptive change. ...
... Hughes et al. (2016b) demonstrated that parentally acquired dominance-related differences driving the maintenance of the ferox life history type is inherited from one generation to the next. They commented that ferox trout are rare (Duguid et al., 2006), live in low densities in the wild (Thorne et al., 2016) and are highly sought after by recreational anglers. These findings have implications for the management of this rare life history type. ...
Article
Ferox trout are large, long‐lived, piscivorous trout normally found in deep lakes; they are highly prized by trophy anglers. Lough Corrib and Lough Mask, western Ireland, have recorded the majority of Irish specimen ferox trout since angling records began. Little was known regarding the spawning location of ferox trout relative to sympatric brown trout, and a radio telemetry study was initiated in both catchments in 2005. Over the period 2005–2009, 79 ferox were captured by angling and radio tagged in Lough Corrib, while 55 ferox were tagged in Lough Mask. Manual and helicopter tracking were carried out on all spawning streams entering both lakes over the autumn / winter period to detect tagged fish. Overall, 37 radio tagged trout (46.8%) were detected in Lough Corrib streams and 21 tagged trout (38.2%) were recorded from Lough Mask streams. Results from radio tracking indicate that the majority (92%) of ferox trout tagged in Lough Corrib spawned in a single spawning stream, the Cong river, while the majority (76%) of ferox trout tagged in Lough Mask spawned in the Cong canal and Cong river. These results suggest that these streams are most likely the principle spawning locations of ferox trout in both lakes.. The occurrence of ferox trout predominantly in single spawning rivers in both catchments highlights the vulnerability of the study ferox populations. As a result of these findings, conservation measures were introduced for ferox trout in both catchments. This article is protected by copyright. All rights reserved.
... For example, Arctic charr (Salvelinus alpinus) have repeatedly evolved sympatric forms of zooplanktivores and piscivores on multiple continents [15,16], including Iceland's Lake Thingvallavatn (e.g., [17]). Additionally, a large and piscivorous form of brown trout ("Ferox" trout; Salmo trutta) occurs throughout Ireland and Scotland [18,19]. A variety of divergent life-history patterns can be found in populations across the native range of O. mykiss, including migration patterns (resident vs. anadromous), habitat type (lake vs. stream), and diet (piscivory vs. insectivory) [20]. ...
... The 20 most divergent windows (representing the most divergent 0.10% of all windows) all had F ST estimates > 0.609, and were spread across 13 chromosomes (Additional file 1: Table S2). To examine whether selection or recombination was driving signals of high genetic differentiation, we compared patterns of within-population nucleotide diversity ( π ) to absolute differentiation (d xy ) across four bins 19,512 in total, between all pairs of rainbow trout groups. Orange represents Blackwater insectivores-Kootenay Lake piscivores, blue is Blackwater insectivores-Kootenay Lake insectivores, and red is Kootenay Lake insectivores-Kootenay Lake piscivores. ...
Article
Full-text available
Background Identifying ecologically significant phenotypic traits and the genomic mechanisms that underly them are crucial steps in understanding traits associated with population divergence. We used genome-wide data to identify genomic regions associated with key traits that distinguish two ecomorphs of rainbow trout ( Oncorhynchus mykiss )—insectivores and piscivores—that coexist for the non-breeding portion of the year in Kootenay Lake, southeastern British Columbia. “Gerrards” are large-bodied, rapidly growing piscivores with high metabolic rates that spawn north of Kootenay Lake in the Lardeau River, in contrast to the insectivorous populations that are on average smaller in body size, with lower growth and metabolic rates, mainly forage on aquatic insects, and spawn in tributaries immediately surrounding Kootenay Lake. We used pool-seq data representing ~ 60% of the genome and 80 fish per population to assess the level of genomic divergence between ecomorphs and to identify and interrogate loci that may play functional or selective roles in their divergence. Results Genomic divergence was high between sympatric insectivores and piscivores ( $$F_{\text{ST}}$$ F ST = 0.188), and in fact higher than between insectivorous populations from Kootenay Lake and the Blackwater River ( $$F_{\text{ST}}$$ F ST = 0.159) that are > 500 km apart. A window-based $$F_{\text{ST}}$$ F ST analysis did not reveal “islands” of genomic differentiation; however, the window with highest $$F_{\text{ST}}$$ F ST estimate did include a gene associated with insulin secretion. Although we explored the use of the “Local score” approach to identify genomic outlier regions, this method was ultimately not used because simulations revealed a high false discovery rate (~ 20%). Gene ontology (GO) analysis identified several growth processes as enriched in genes occurring in the ~ 200 most divergent genomic windows, indicating many loci of small effect involved in growth and growth-related metabolic processes are associated with the divergence of these ecomorphs. Conclusion Our results reveal a high degree of genomic differentiation between piscivorous and insectivorous populations and indicate that the large body piscivorous phenotype is likely not due to one or a few loci of large effect. Rather, the piscivore phenotype may be controlled by several loci of small effect, thus highlighting the power of whole-genome resequencing in identifying genomic regions underlying population-level phenotypic divergences.
... The most common foraging strategy among this latter group is to feed on littoral zoobenthos [38] yet in some large, deep and oligotrophic lakes adfluvial potamodrous brown trout may exhibit a relatively rare piscivorous life history [39][40][41][42]. Although piscivorous life histories have also evolved in other salmonid species, they are typically found in very low abundances within populations compared to other sympatric life history forms [30,34,[43][44][45][46]. This rare life history, colloquially referred to as a "ferox" life history (hereafter ferox trout), manifests predominantly in the occupation of the pelagic lacustrine habitat and piscivorous trophic niche [42,[47][48][49]. ...
... The estimated admixture proportions showed that admixture from ferox into benthivorous brown trout was on average significantly stronger (81.7%) than vice versa (53.6%). Inferred effective population sizes (Ne) of benthivorous brown trout (1146 individuals) were approximately 3 times higher compared to ferox trout (393), which is expected based on the rarity of ferox trout [42,46] or could also be due to the difference in generation time between ferox trout and benthivorous brown trout [50][51][52]. Detailed estimates and confidence intervals for all estimated parameters are given in Table 3 and Figure 3. ...
Article
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Identifying the genetic basis underlying phenotypic divergence and reproductive isolation is a longstanding problem in evolutionary biology. Genetic signals of adaptation and reproductive isolation are often confounded by a wide range of factors, such as variation in demographic history or genomic features. Brown trout (Salmo trutta) in the Loch Maree catchment, Scotland, exhibit reproductively isolated divergent life history morphs, including a rare piscivorous (ferox) life history form displaying larger body size, greater longevity and delayed maturation compared to sympatric benthivorous brown trout. Using a dataset of 16,066 SNPs, we analyzed the evolutionary history and genetic architecture underlying this divergence. We found that ferox trout and benthivorous brown trout most likely evolved after recent secondary contact of two distinct glacial lineages, and identified 33 genomic outlier windows across the genome, of which several have most likely formed through selection. We further identified twelve candidate genes and biological pathways related to growth, development and immune response potentially underpinning the observed phenotypic differences. The identification of clear genomic signals divergent between life history phenotypes and potentially linked to reproductive isolation, through size assortative mating, as well as the identification of the underlying demographic history, highlights the power of genomic studies of young species pairs for understanding the factors shaping genetic differentiation
... Some ferox populations have been shown to have small population sizes (Thorne et al., 2016) making them particularly vulnerable to extinction through stochastic demographic changes (Goodman, 1987). Age at maturity has also been identified as a major positive correlate of risk status (Parent & Schriml, 1995), (Muhlfeld et al., 2019). ...
Article
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Salmonid (Salmonidae) sympatric diversity is the co-occurrence, in a lake or river, of two or more reproductively isolated populations/subpopulations, or phenotypes resulting from phenotypic plasticity. Sympatric populations can arise through allopatric and/ or sympatric evolution. Subsequently, allopatric lineages can occur in sympatry due to independent colonisation and/or through anthropogenic introduction. Sympatric divergence is often driven by feeding opportunities, with populations segregating as planktivorous, benthivorous and piscivorous ecotypes ("trophic polymorphism"), and further segregation occurring by feeding depth and body size. Subpopulations evolve by natal homing where a water has two or more discrete spawning areas, often resulting in phenotypically and ecologically cryptic sympatry. Most known sympatric populations/phenotypes in trout of the genus Salmo (Eurasian trout aka brown trout) involve sympatric piscivorous (ferox) and lifetime invertivorous trout. Segregation on the benthic-limnetic axis has been poorly studied in Eurasian trout compared with other salmonids but is likely commoner than currently described. While three sympa-tric populations/species of Eurasian trout are recognised from Lake Ohrid (Albania/ North Macedonia), limited ecological information is available and there are only two lakes with three or four sympatric populations with described benthic, limnetic and piscivorous trophic segregation: Lough Melvin (Ireland) and Loch Laidon (Scotland), the latter having the only identified case of a sympatric profundal benthic feeding populations, possibly due to the absence of Arctic charr (Salvelinus alpinus) in the lake. Many thousands of waters are yet to be examined. Some sympatric populations are extinct, and others are vulnerable with conservation action being urgently required. This should ideally be based on populations/conservation units, but the lack of recognition of intraspecific units in most legislations in the native Eurasian trout range necessitates a pragmatic approach, with species classification, where appropriate, based on integrative taxonomy. Some sympatric populations clearly merit species status and should be formally classified as such if a valid previous name is not available. K E Y W O R D S conservation units, ecotype, ferox, genetic markers, integrative taxonomy, Salmonidae This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
... They are known to occupy small core home ranges (Guzzo et al. 2016); therefore, potential predation by a pike was defined as repeated consecutive detections between an adjacent group of receivers over at least 1 day, followed by repeated detections at one receiver until the end of the detection stream, indicating that the tag was likely passed by the predator (Weinz et al. 2020). There are additional species of predatory fish in Loch Lomond including Perca fluviatilis Linnaeus 1758 (perch) and piscivorous brown trout (Ferox trout), Salmo trutta Linnaeus 1758; however, predation of smolts by these species were assumed to be inconsequential in this study since perch in Scottish lakes have been reported to feed almost completely on benthic and planktonic invertebrates, and the abundance of Ferox trout in Scottish lakes is extremely low (Thorpe 1977;Thorne et al. 2016). ...
Article
Full-text available
The Atlantic salmon, Salmo salar Linnaeus 1758, is a charismatic, anadromous species that has faced dramatic declines throughout its range. There is currently a lack of information on the effect of free-standing bodies of water on a key life event, sea migration, for the species. This study extends our understanding in this area by combining acoustic telemetry with a correlated random walk model to try to examine potential morphological and behavioural factors that differentiate successful from unsuccessful migrants through Scotland’s largest lake. Consistent with other studies, we found that smolts experienced a high rate of mortality in the lake (~ 43%), with approximately 14% potentially predated upon by birds and 4% by Northern pike. Migration speed in the lake was slow (the mean minimum movement speed between centres of activity was 0.13 m/s), and pathways frequently deviated away from the outlet river. There was no evidence of a morphological or behavioural trait or migratory pathway that distinguished successful from unsuccessful smolts. This suggests that migration movement direction in the main body of Loch Lomond appeared to be random. This was further supported by the output of a correlated random walk model which closely resembled the pathway and migration speed and distance patterns displayed by successful migrants. However, once successful smolts came within ~2 km of the lake exit, a high proportion remained in this region prior to entering the River Leven. We suggest that this “goldilocks zone” is where directional cues become apparent to migrating fish. Future studies should combine random walk models with environmental variables to determine if external factors are driving the apparently random movement patterns exhibited by smolts in lakes.
... In addition to planktivory and benthivory, piscivory may add to variation: known to be present in several of the study lakes, piscivorous ferox trout characteristically possess disproportionately long heads, and males often show a pronounced kype (Campbell, 1979). However, the impact of individuals upon morphology at a population level is likely to be small: ferox in Scottish lakes are both relatively rare and typically much larger than the samples studied here (Campbell, 1979;Duguid et al., 2006;Thorne et al., 2016). Even if the average tends towards exploitation of the littoral, the presence of other specialist foragers would account for wide morphological variance. ...
Article
The fragmented, heterogeneous and relatively depauperate ecosystems of recently glaciated lakes present contrasting ecological opportunities for resident fish. Across a species, local adaptation may induce diverse and distinct phenotypic responses to various selection pressures. We tested for intraspecific phenotypic structuring by population in a common native lake-dwelling fish species across a medium-scale geographic region with considerable variation in lake types. We investigated potential lake-characteristic drivers of trophic morphology. Using geometric morphometric techniques, we quantified the head shapes of 759 adult brown trout (Salmo trutta L.) from 28 lakes and reservoirs across Scotland. Multivariate statistical analyses showed that almost all populations differed from one another. Trout from larger and deeper lakes had deeper, but shorter heads, and smaller eyes. Higher elevation lakes were associated with fish with shorter heads and jaws. Within-population shape variation also differed by population, and was positively correlated with lake surface area and depth. Trout within reservoirs differed subtly from those in natural lakes, having larger eyes, shorter jaws and greater variability. This study documents an extraordinary morphological variation between and within populations of brown trout, and demonstrates the role of the extrinsic environment in driving phenotypic structuring over a medium-scale and varied geographic area.
... comm.). While they share the same scientific name as brown trout, they appear to be reproductively isolated and genetically distinct (Thorne et al., 2016). The Clare River is a major contributor of adult trout to Lough Corrib but contains some very large resident trout in its own right. ...
Technical Report
Full-text available
Determining the age of fish is a core tool for fishery scientists. Age determination is essential for knowledge of recruitment frequency and hence population trends and stability. This manual is aimed as a starter for scientists setting out to determine the age of individual Irish fresh water fish, and sets out the methods, from fish in the hand to the measured age, with worked examples of 10 of the common species routinely handled by Inland Fisheries Ireland staff, specifying equipment requirements, nomenclature, and age recording formats.
... Salmo trutta were sampled over a number of years (1966-2014; n = 72) from Loch Awe and Loch Rannoch (1970-2014; n = 111) using Nordic gill nets or a nondestructive, specialised rod and line trolling technique used by experienced anglers (Thorne, MacDonald, & Thorley, 2016). All S. trutta from Loch na Sealga (2013; n = 37) were collected using Nordic gill nets, each comprising 12 mesh sizes ranging from 5 to 50 mm (Appelberg et al., 1995). ...
Article
Full-text available
Large and long‐lived piscivorous brown trout, Salmo trutta, colloquially known as ferox trout, have been described from a number of oligotrophic lakes in Britain and Ireland. The “ferox” life history strategy is associated with accelerated growth following an ontogenetic switch to piscivory and extended longevity (up to 23 years in the UK). Thus, ferox trout often reach much larger sizes and older ages than sympatric lacustrine invertebrate‐feeding trout. Conventional models suggest that S. trutta adopting this life history strategy grow slowly before a size threshold is reached, after which, this gape‐limited predator undergoes a diet switch to a highly nutritional prey source (fish) resulting in a measurable growth acceleration. This conventional model of ferox trout growth was tested by comparing growth trajectories and age structures of ferox trout and sympatric invertebrate‐feeding trout in multiple lake systems in Scotland. In two of the three lakes examined, fish displaying alternative life history strategies, but living in sympatry, exhibited distinctly different growth trajectories. In the third lake, a similar pattern of growth was observed between trophic groups. Piscivorous trout were significantly older than sympatric invertebrate‐feeding trout at all sites, but ultimate body size was greater in only two of three sites. This study demonstrates that there are multiple ontogenetic growth pathways to achieving piscivory in S. trutta and that the adoption of a piscivorous diet may be a factor contributing to the extension of lifespan.
... These results demonstrate that even in less prominent fisheries, catch-and-release practices and conservative regulations can be effective in providing additional angling opportunities. MANAGEMENT BRIEF In this study, most captures by angling at both sites were by relatively few, highly skilled anglers, an observation consistent with other studies (Thorne et al. 2016;van Poorten et al. 2016). Given that postrelease mortality likely declines with increasing angler skill level for Muskellunge (Landsman et al. 2011) and other sport fish species (Meka 2004;Hall et al. 2015), postrelease mortality was assumed to be negligible in this study. ...
Article
Full-text available
Increases in catch‐and‐release practices in addition to angler engagement in management activities to evaluate and improve the trophy potential of Muskellunge Esox masquinongy fisheries have become prevalent in recent decades. An expectation of conservative angling practices and regulations is that released fish can be recaptured by anglers at a later time and potentially at a larger size. Although several studies have evaluated Muskellunge recapture rates, no studies have estimated the number of recaptured Muskellunge relative to the number present in the population. Additionally, few studies have evaluated angling size selectivity and the potential benefits or biases of incorporating those data into traditional Muskellunge assessments. This study evaluated the proportion of Muskellunge that were caught and recaptured relative to the population estimates in two Minnesota water bodies and the potential length‐related bias from angler‐caught fish. Data were obtained from traditional sampling gears (i.e., trap netting, boat electrofishing) and angling by volunteer anglers in the Mississippi and Crow Wing rivers and Baby and Man lakes. Participating anglers captured 11–22% of the population, of which 1–3% were subsequently recaptured at both sites annually. Recaptured fish accounted for 5–16% of the annual catch. At the Mississippi River site, proportionally larger fish were angled compared with the modeled population size structure, whereas angler catch from Baby and Man lakes was similar to the modeled size structure, likely due to the differing techniques used by anglers in the two water bodies. A more thorough understanding of recapture rates and size selectivity may be particularly important when managing a low‐density species as angling pressure and angler involvement in management activities increase.
Preprint
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Background: Identifying ecologically significant phenotypic traits and the genomic mechanisms that underly them are crucial steps in understanding the traits associated with population divergence. We used genome-wide data to identify genomic regions associated with a key trait that distinguishes two ecotypes of rainbow trout (Oncorhynchus mykiss) – insectivores and piscivores – that coexist in Kootenay Lake, southeastern British Columbia, for the non-breeding portion of the year. “Gerrards” are large-bodied (breeding maturity at >60cm) piscivores that spawn ~50km north of Kootenay Lake in the Lardeau River, in contrast to the insectivorous populations that are on average smaller in body size, mainly forage on aquatic insects, and spawn in tributaries immediately surrounding Kootenay Lake. We used pool-seq data covering ~60% of the genome to assess the level of genomic divergence between ecotypes, test for genotype-phenotype associations, and identify loci that may play functional or selective roles in their divergence. Results: Analysis of nearly seven million SNPs provided a genome-wide mean FST estimate of 0.18, indicating a high level of reproductive isolation between populations. The window-based FST analysis did not reveal “islands” of genomic differentiation; however, the window with highest FST estimate did include a gene associated with insulin secretion. Although we explored the use of the “Local score” approach to identify genomic outlier regions, this method was ultimately not used because simulations revealed a high false discovery rate (~20%). Gene Ontology (GO) analysis identified several growth processes as enriched in genes occurring in the ~200 most divergent genomic windows, indicating the importance of genetically-based growth and growth-related metabolic functions in the divergence of these ecotypes. Conclusions: In spite of their sympatric coexistence, a high degree of genomic differentiation separates the populations of piscivores and insectivores, indicating little to no contemporary genetic exchange between ecotypes. Our results further indicate that the large body piscivorous phenotype is likely not due to one or a few loci of large effect, rather it may be controlled by several loci of small effect, thus highlighting the power of whole-genome low-coverage sequencing in phenotypic association studies.
Article
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Many recreational fisheries are subject to varying degrees of catch-and-release fishing through regulations and conservation-minded anglers. Clearly, releasing a proportion of the catch improves conservation of the fishery, yet it is not clear how the released catch contributes to angling quality. If fish change their behavior to lower their individual catchability after they have been caught, then angler catch rates may not be proportional to fish density. Therefore, even catch-and-release fisheries could exhibit poor angling quality if there is sufficiently high angler effort. We tested this idea by experimentally fishing five small lakes that contained rainbow trout Oncorhynchus mykiss in the interior of British Columbia. We found that with sustained effort of 8 angler-hours · d · ha and complete release of the catch, catch rates quickly dropped within 7–10 d. Given the individual capture histories of tagged fish, the most parsimonious catchability model incorporated learning and heterogeneity into intrinsic catchability. The best-fit parameter values suggest that the population contained a group of highly catchable fish that were quickly caught and then learned to avoid hooks. There was a seasonal decrease in catchability that was independent of angling; however, it was not sufficient to explain the data. Our results indicate that catch rates may decline because of high angling effort even when the number of fish remains constant. Therefore, management goals that go beyond conservation issues and attempt to maximize angler satisfaction must account for effort density on a recreational fishery.
Article
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Regulations designed to protect recreational fisheries from overexploitation can fail. Regulations such as size and bag limits restrict harvest by individual anglers but not angler effort and therefore not total harvest. Even when individual harvest limits are set to zero (i.e., catch and release), a combination of hooking mortality and noncompliance may lead to fishing mortality rates that are not sustainable if angling effort is sufficiently high. These assertions were tested and quantified by using simulation experiments on a size- and age-structured model developed for a fishery on an adfluvial bull trout population. The functions and rates describing the biology and fishery were derived from a variety of sources, including published and unpublished information on bull trout and, where such sources were unavailable, from other salmonid species. The model predicts that a 40-cm minimum size limit for harvest would maintain viable populations at an annual effort up to 4 angler-hours · ha−1 · year−1, a 65-cm minimum size limit up to 10 angler-hours · ha−1 · year−1, and a catch-and-release fishery up to 18 angler-hours · ha−1 · year−1. The quality of the fisheries that developed under these three alternative regulations varied substantially with the amount of angler effort imposed. Uncertainty in the minimum population size necessary to ensure sustainability, recruits per unit stock, catchability, hooking mortality rate, and noncompliance rate modifies quantitative predictions, but the qualitative patterns are general. If anglers respond dynamically to variation in the quality of fishing, then the ability of size limit regulations to sustain fisheries is further compromised. The combination of life history and fishery traits such as slow growth, late age at maturity, low fecundity, longevity, and high catchability render adfluvial bull trout particularly susceptible to overfishing, even within relatively narrow bounds of angler effort.
Book
Bayesian statistics has exploded into biology and its sub-disciplines, such as ecology, over the past decade. The free software program WinBUGS and its open-source sister OpenBugs is currently the only flexible and general-purpose program available with which the average ecologist can conduct standard and non-standard Bayesian statistics. Bayesian Population Analysis Using WinBUGS goes right to the heart of the matter by providing ecologists with a comprehensive, yet concise, guide to applying WinBUGS to the types of models that they use most often: linear (LM), generalized linear (GLM), linear mixed (LMM) and generalized linear mixed models (GLMM). Comprehensive and richly-commented examples illustrate a wide range of models that are most relevant to the research of a modern population ecologist. All WinBUGS/OpenBUGS analyses are completely integrated in software R. Includes complete documentation of all R and WinBUGS code required to conduct analyses and shows all the necessary steps from having the data in a text file out of Excel to interpreting and processing the output from WinBUGS in R.
Book
Bayesian statistics has exploded into biology and its sub-disciplines, such as ecology, over the past decade. The free software program WinBUGS and its open-source sister OpenBugs is currently the only flexible and general-purpose program available with which the average ecologist can conduct standard and non-standard Bayesian statistics. Bayesian Population Analysis Using WinBUGS goes right to the heart of the matter by providing ecologists with a comprehensive, yet concise, guide to applying WinBUGS to the types of models that they use most often: linear (LM), generalized linear (GLM), linear mixed (LMM) and generalized linear mixed models (GLMM). Comprehensive and richly-commented examples illustrate a wide range of models that are most relevant to the research of a modern population ecologist. All WinBUGS/OpenBUGS analyses are completely integrated in software R. Includes complete documentation of all R and WinBUGS code required to conduct analyses and shows all the necessary steps from having the data in a text file out of Excel to interpreting and processing the output from WinBUGS in R.
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Over 300 native stocks of Pacific salmon, steelhead, and coastal cutthroat trout (Oncorhynchus spp.) are at risk of extinction in the Pacific Northwest. With only limited resources available for conservation and recovery, prioritization of these stocks may become necessary if meaningful measures are to be implemented. We propose criteria by which prioritization may be guided. First, we rank stocks for risk of extinction, either by population viability analysis or by a set of surrogate measures. Then we rank stocks for biological consequences of extinction, using sets of questions designed to establish the genetic and evolutionary consequences and the ecological consequences if a stock were to become extinct. Together, these rankings allow stocks to be prioritized for a range of possible actions, with those stocks at highest risk and bearing the greatest biological consequences of extinction receiving attention first. Application of the prioritization process to 20 Pacific anadromous salmonid stocks worked as intended, although data limitations are considerable. The process is most likely to work successfully when applied to many stocks on which data exist, when several experts carry out the prioritization, and when the results are peer reviewed.
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We use Bayesian methods to explore fitting the von Bertalanffy length model to tag-recapture data. We consider two popular parameterizations of the von Bertalanffy model. The first models the data relative to age at first capture; the second models in terms of length at first capture. Using data from a rainbow trout Oncorhynchus mykiss study we explore the relationship between the assumptions and resulting inference using posterior predictive checking, cross validation and a simulation study. We find that untestable hierarchical assumptions placed on the nuisance parameters in each model can influence the resulting inference about parameters of interest. Researchers should carefully consider these assumptions when modeling growth from tag-recapture data.
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From 2006 to 2009, we tagged and released 22,202 fish with T-bar anchor tags valued at US$0 to $200 if returned. Our intent was to assess angler tag reporting rates in Idaho and to determine whether reporting rates declined over time or differed between species. A total of 4,643 tags were reported by anglers. Assuming a reporting rate of 100% for $200 tags, weighted mean reporting rates were 54.2% for $0 tags, 69.7% for $10 tags, 91.7% for $50 tags, and 98.9% for $100 tags. By combining $100 and $200 as high-reward tags to increase sample size, nonreward tag-reporting rate was 54.5%. Tag reporting rates varied between groups of species, being highest for harvest-oriented species, both coolwater and warmwater, such as walleye Sander vitreus ($0 = 68.3%), yellow perch Perca flavescens (58.5%), and crappie Pomoxis spp. (59.7%), and lowest for largemouth bass Micropterus salmoides (39.2%). There was little variation in tag-reporting rates over time, weighted means being 53, 56, 50, and 56% from 2006 to 2009, but reporting rate did appear to decline for some species (most notably crappies). There was some evidence of a slight violation of the assumption of independence in tag-reporting, indicated by nonreward tag-reporting rates being marginally higher for anglers reporting both nonreward and reward tags than for those reporting only one or the other (signifying possible batch-reporting of tags). No batch-reporting was evident from differences in reporting rates for households reporting multiple tags compared with those reporting only one tag. Our results suggest that anglers in Idaho reported over half the nonreward tags they encountered, but rates appeared to vary among species, and this knowledge is being used to estimate angler exploitation across Idaho.Received November 22, 2011; accepted April 5, 2012
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We generalize the method proposed by Gelman and Rubin (1992a) for monitoring the convergence of iterative simulations by comparing between and within variances of multiple chains, in order to obtain a family of tests for convergence. We review methods of inference from simulations in older to develop convergence-monitoring summaries that are relevant for the purposes for which the simulations are used. We recommend applying a battery of tests for mixing based on the comparison of inferences from individual sequences and from the mixture of sequences. Finally, we discuss multivariate analogues, for assessing convergence of several parameters simultaneously.