inst/ms/annotated-bib.md

In seananderson/metafolio: Metapopulation Simulations for Conserving Salmon Through Portfolio Optimization

% Annotated Bibliography for Salmon Portfolios Paper % Sean Anderson % June 2013

Broad topics

Biocomplexity: @elmqvist2003 - Mechanisms generating asynchrony: filter and response diversity - The need for prioritization and existing schemes - Existing and well-used salmon simulations - Climate impacts on salmon - At risk status of P NW salmon

What a metapopulation is and evidence an implications for salmon: @gilpin1991,

Notes

@allendorf1997

• Propose a ranking scheme for prioritizing Pacific salmon stocks based on both

• PVA and biological consequences of extinction

@baguette2004

• Basically, we need to loosen up on "classical metapopulation theory" for it to be useful. Classical definition is rare and maybe not always applicable to conservation or empirical work

@battin2007

• Climate change will have big impact on freshwater salmon habitat; restoration and protection of habitat therefore critical. Great uncertainty inherent and management approaches must deal with this (as ours does). Maintaining genetic and life-history diversity is one approach.

@cariveau2013

• detected response diversity but didn't lead to stability of ecosystem services for pollinators

@colwell1998

• The first paper to use the term "biocomplexity". (Plenary transcript from AIBS.)

@cooper1999

• Dangerous to ignore metapopulation structure of salmon metapopulations

@crozier2008

• Any "further decline in fitness significantly threatens" the persistence of Snake River spring/summer Chinook

• Thermal response diversity possible via differences in behaviour to reduce heat exposure (they cite Berman and Quinn 1991, Togersen et al. 1991, Goniea et al. 2006)

• Salmon life-history diversity is 2 part: (1) phenotypic plasticity to environment and (2) location adaptation throughout lifecycle. "Life-history diversity in salmon reflects a combination of phenotypic plasticity in response to variable environmental conditions (Hutchings 2004) and local adaptation throughout the life cycle, across the complete suite of life history, morphological, physiological, and behavioural traits (Ricker 1972; Groot and Margolis 1991; Taylor 1991; Quinn 2005)."

"Local adaptation is facilitated by strong natal homing that limits gene flow between populations in different selective environments."

• Earlier migration over last century for Chinook and sockeye in Columbia over last century.

• Fitness effects of warmer water - various - behaviour inhibition, disease, reduced growth and development, increased energetic costs (they cite McCullough 1999 and Materna 2001, which are reviews).

• Great review of expected evolutionary responses of salmon to climate change: "we emphasize the interacting and cumulative effects of climate change across the life cycle"

• In N Pacific Ocean warming impacts on salmon habitat: (1) rising temperature of upper ocean - increased stratification, (2) wind pattern changes, which affect upwelling of nutrients, (3) ocean acidification, which will impact plankton and those trophically linked.

• Main climate influence in freshwater: (1) changes in snow melt timing, (2) greater hydrologic extremes (droughts and floods more extreme), (3) higher temperatures of streams and watershed in general.

• Thermal diversity possible through disease resistance diversity with increased temperature.

@denboer1968

• Life history diversity reduces extinction risk and reduces risk of low productivity with strong environment

@donato2002

• much of salmon rearing habitat in (Snake River?) already exceeds optimal temperatures for salmonids

@eliason2011

• Thermal tolerance or limits vary within sockeye salmon populations (by stock) according to historical environmental conditions cardiorespiratory physiology varies at the population level among Fraser River sockeye salmon and relates to historical environmental conditions encountered while migrating

@elmqvist2003

• Defines response diversity; states that it's important to resilience; provides "adaptive capacity"

@fahrig2003 (highly cited \~2100)

• A (massive) review of the effects of habitat fragmentation on biodiversity. Habitat loss -> "large, consistently negative effects on biodiversity". Fragmentation -> weaker effects, could be positive or negative. So, measure these separately.

"Habitat fragmentation is usually defined as a landscape-scale process involving both habitat loss and the breaking apart of habitat."

@gilpin1991

• The book that set off metapopulation biology

@haight2008

• Ideal design of reserves depends on "emigration, dispersal mortality, and probabilities of movement between reserves"

@hilborn2003

• Maintenance of biocomplexity (a diversity of life-history strategies) an important component of long-term sustainability

• specifically, they show that not all sockeye in Bristol Bay respond similarly to the environment. And, fishing causes less variability than natural processes.

We believe that long-term sustainability is derived in large part from complementary patterns of productivity in different stock components; It would seem prudent to try to prevent loss of such stock components, including those that appear, at present, to be unproductive. biocomplexity

@hindar2004

• Need to consider genetic effects of harvesting both at local and metapopulation level The genetic consequences of harvesting need to be assessed both at the levels of local populations and the metapopulation.

@hodgson2002

• Climate change impact on salmon; temperatures already approach lethal limits in XX.

@isaak2003

• Salmon metapopulations become more synchronized at low abundance; risk of simultaneous extirpations increases

• Important to not only focus on maintaining large subpopulations but also on desynchronizing subpopulations

• Dispersal unlikely to strongly affect population dynamics unless abundance really low where it can synchronize

Papers to get:

"Studies on a wide range of animal taxa have addressed the topic of spatial synchrony (see reviews by Bjornstad et al. (1999) and Koenig (1999)). Almost invariably, these studies document a negative relationship between correlation in a population parameter — typically abundance — and the geo- graphic distance separating populations. At short distances, dispersal of individuals between populations is believed to be a primary synchronizing factor (Sutcliffe et al. 1997; Ranta et al. 1997), but correlated environments also synchronize population dynamics and may act over greater distances (Heino et al. 1997). Local factors, such as density dependence, heterogeneities in habitats, or small-scale stochastic events, can override or decrease the importance of synchronizing agents and result in population asynchronies (Haydon and Steen 1997; Kendall et al. 2000)."

@kindvall1996

• Habitat heterogeneity can create different responses to the same conditions (for bush cricket metapopulations)

• extinction risk higher in homogeneous habitats

• keyword: environmental filter

@levins1969

• First paper to coin term metapopulation

@levins1970

• Second paper to coin term metapopulation

@liebhold2004

• Spatial synchrony can occur because of:

(1) dispersal between populations (2) Moran effect, (3) trophic interactions with other pops that are synchronous

• shared environment and dispersal more likely for closer populations

@mace1991 (highly cited)

• Define criteria for assessing extinction threat — useful if doing local extinction recording (keyword: extinction risk)

@mcclure2003

• again, Snake River Chinook threatened by any further decline in fitness

@mceacheran2000

• Defines VSP and ESU

@michener2001

• Carefully define biocomplexity; discuss role and future as NSF program

• Define biocomplexity as : "...properties emerging from the interplay of behavioural, biological, chemical, physical, and social interactions that affect, sustain, or are modified by living organisms, including humans."

@mobrand1997

• We need to include more than productivity and capacity when considering salmon performance --- a third dimension of life-history diversity ("through time, space, and life stage") is critical. (Beyond the "bottleneck" approach). This includes connectivity.

@moritz1994 (highly cited; 1870)

• Defines ESU (main first paper to carefully define)

• "significant" refers to historical isolation and therefore has a "distinct potential".

• ESUs mostly relevant for longterm conservation (defining priorities and "setting strategy").

• Defines Management Units (MU s) too. MU s more useful for short-term management... reflect current population structure and short-term management issues.

• "The overriding purpose of defining ESUs to ensure that evolutionary heritage is recognized and protected and that the evolutionary potential inherent across the set of ESUs is maintained." "MU s are the logical unit for population monitoring and demographic study."

@nehlsen1991

• A lot of salmon stocks at risk of extinction in Pacific NW

From Allendorf:

"214 native stocks of Pacific salmon (Oncorhynchus spp.), steelhead (O. mykiss), and coastal cutthroat trout (O. clarki clarki) are at risk of extinction in California, Oregon, Idaho, and Washing- ton (Nehlsen et al. 1991). This list includes 101 stocks at high risk, 58 stocks at moderate risk, and 54 stocks of special concern, along with one stock listed as threatened under the U. S. Endangered Species Act of 1973 (Nehlsen et al. 1991)."

@peterman1998

• Region-level subpopulations react in diverse ways to the environment (shown through survival rates); a combination of freshwater (and less so) marine processes

@quinn1993

• Straying occurs (review). Only consequences are unknown. Straying is quite different from stream to stream, hard to come up with general values. Effect of straying not just amount but also mating and survival success. We can't predict straying well yet.

@quinn2005

• Main pacific salmon reference. One point: Because anadromous salmon pops spend time together in ocean, even if far apart in freshwater experience same environment in ocean, and so correlation may decay less than you'd think with distance

@rahel2013

• Intentionally fragmenting aquatic systems also has benefits … intentional fragmentation may be beneficial when it prevents the spread of nonnative species or exotic diseases, eliminates hybridization between hatchery and wild stocks, or stops individuals from becoming entrapped in sink environment

@ricker1972

• Defines a salmon stock; rivers may have multiple stocks. There can be substantial genetic differences between stocks. Differences between stocks usually have both genetic and environmental components.

Salmon stock definition: "... the fish spawning in a particular lake or stream (or portion of it) at a particular season, which fish to a substantial degree do not interbreed with any group spawning in a different place, or in the same place at a different season"

most of the studied differences between local stocks can and usually do have both a genetic and an environmental basis"

@schindler2008

• Landscape can act as "heterogeneous filter" of climate for salmon populations, need management and policies that are "robust to unknowns" and "responsive to change" It is useful to think of salmon landscapes as heterogeneous filters of climate

@schtickzelle2007

• Anadromous salmon likely fulfil the 3 requirements to be defined as a metapopulation: discrete populations, some asynchrony; some dispersal. Useful concept, but, the concept is rarely used or tested. ...only 0.25% of the papers on conservation and/or management of salmonids list the keyword "metapopulation"

• Main implications of salmon metapopulation dynamics:

• Metapopulation dynamics can influence persistence or collapse (ecological time scale) and

• Evolution and adaptation (evolutionary time scale)

• Dispersal likely just enough to "ensure recolonization of suitable habitat"

• Salmon tend to stray near their natal stream, although not necessarily those closest

@waples1991 (highly cited)

• Defines ESUs (for purposes of salmon for ESA listings) 2 criteria: "substantially reproductively isolated from other conspecific population units" and "represent[s] an important component in the evolutionary legacy of the species"; "isolation does not have to be absolute"

@ando2010

@ando2012

@beacham1989

• Beacham and Murray 1989 (from Crozier et al. 2008 (1) - review): example of thermal tolerance diversity: lower survival of eggs and embryos, and reduced yolk "conversion efficiency" for coastal Chinook salmon than juveniles

@beacham1991

• (from Crozier et al. 2008 (1) review) greater tolerance to warmth for southern BC juvenile Chinook than northern BC pops

To add

@materna2001

• review of effects of warmer water on salmon

Hilborn et al. 2001

Bibliography

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