missing the boat on freshwater fish conservation in … assessment of freshwater fish in california...

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Missing the boat on freshwater fish conservation in California

Theodore E. Grantham, Department of Environmental Science, Policy, and Management, University

of California Berkeley, Berkeley, California ([email protected])

Kurt A. Fesenmyer, Trout Unlimited, Boise, Idaho ([email protected])

Ryan Peek, Center for Watershed Sciences, University of California Davis, Davis, California

([email protected])

Eric Holmes, Center for Watershed Sciences, University of California Davis, Davis, California

([email protected])

Rebecca M. Quiñones, Center for Watershed Sciences, University of California Davis, Davis, California

([email protected])

Andy Bell, Center for Watershed Sciences, University of California Davis, Davis, California

([email protected])

Nick Santos, Center for Watershed Sciences, University of California Davis, Davis, California

([email protected])

Jeanette K. Howard, The Nature Conservancy, San Francisco, California ([email protected])

Joshua H. Viers, School of Engineering, University of California Merced, Merced, California

([email protected])

Peter B. Moyle, Center for Watershed Sciences and Department of Wildlife, Fish and Conservation

Biology, University of California Davis, Davis, California ([email protected])

Running title: California fish conservation planning

Keywords: systematic conservation planning; fish diversity; freshwater protected areas; Zonation

software; California

Article type: Letter

Number of words in abstract: 148

Number of words in article: 3,147

Number of references: 38

http://dx.doi.org/

http://dx.doi.org/

http://dx.doi.org/


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Number of tables: 0

Corresponding author: Theodore Grantham, Department of Environmental Science, Policy, and

Management, 130 Mulford Hall #3114, Berkeley, California 94720-3114. Phone: (510) 664-4664.

Email: [email protected]


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Abstract Population growth and increasing water-use pressures threaten California’s freshwater ecosystems

and have led many native fishes to the brink of extinction. To guide fish conservation efforts, we

provide the first systematic prioritization of river catchments and identify those that

disproportionately contribute to fish taxonomic diversity. Using high-resolution range maps of

exceptional quality, we also assess the representation of fish taxa within the state’s protected areas

and examine the concordance of high-priority catchments with existing reserves and among distinct

taxonomic groups. Although most of the state’s native fishes are found within protected areas, only

a small proportion of their ranges are represented. Few high-priority catchments occur within

protected areas, suggesting that fish conservation will require active management and targeted river

restoration outside of reserves. These results provide the foundation for systematic freshwater

conservation planning in California and for prioritizing where limited resources are allocated for fish

recovery and protection.

Introduction Worldwide, freshwater ecosystem degradation and loss of freshwater biodiversity and are strongly

linked to human development pressures (Vörösmarty et al. 2010, Limburg et al. 2011). In California,

for example, a rapid decline of freshwater fauna has coincided with economic growth and

widespread modification of freshwater ecosystems by water infrastructure, agriculture and

urbanization (Katz et al. 2013; Moyle et al. 2011). California’s native fishes, most of which are

endemic, are particularly imperiled (Howard et al. 2015a). A recent conservation status assessment

report that 107, or 83%, of native fish taxa risk extinction in the next century if recent trends

continue (Moyle et al. 2011).

Decline of the state’s native fish fauna highlights the failure of past and ongoing management efforts

to protect freshwater biodiversity and ecosystems. This is in spite of the fact that substantial

resources have been invested in fish conservation and recovery programs. Over $2 billion (USD) has

been spent in California on river restoration alone since 1980 (Kondolf et al. 2007), with new billion-

dollar restoration efforts planned and underway in large, highly-degraded systems such as the San

Joaquin River (Pitzer 2011) and Los Angeles River (Zahniser 2015). However, most fish recovery

programs are driven by the federal Endangered Species Act, a powerful legal tool, but one that

promotes piecemeal, river- and species-specific conservation efforts (Viers and Rheinheimer 2011).

Furthermore, within the state’s large network of protected areas, few were designed with the

intention of, or have explicit management plans for, protecting freshwater ecosystems and species.

The current role of, and potential for, protected areas for conserving freshwater biodiversity in

California remains poorly understood. In light of these deficiencies, some have argued that a

strategic, statewide plan for freshwater fish conservation that includes designated priority

catchments for aquatic biodiversity management is warranted (Moyle 2002; Moyle and Yoshiyama

1994). But proposed aquatic management areas have not been adopted by natural resource

agencies and there is no statewide plan to address impending fish extinctions, even though most

native fish taxa (79%) are endemic to the state (Moyle et al. 2002).


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Systematic conservation planning offers a structured framework for guiding a statewide

conservation strategy for freshwater biodiversity and ecosystems (Margules and Pressey 2000; Nel

et al. 2009). Tools for terrestrial and marine protected area planning have been adapted to

freshwater systems over time, taking into account the unique directional connectivity of river

systems and recognizing the catchment as a fundamental spatial unit for freshwater ecosystem

management (Abell et al. 2007; Linke et al. 2011). In this study, we provide the first systematic

conservation assessment of freshwater fish in California to identify catchments that contribute

disproportionately to taxonomic diversity in the region. A new statewide database of freshwater fish

distributions of exceptional quality (Howard et al. 2015a; Santos et al. 2014) enables our analysis.

First, we use a spatial conservation prioritization approach to delineate catchments that maximize

representation of fish diversity. Our dataset of historical and current fish distributions also provides

an opportunity to perform the first examination of how catchment priorities change over time in

response to range shifts and local extirpations of taxa. Next, we examine representation of native

fish taxa within the state’s protected areas to assess the potential of existing reserves to support fish

conservation. We also quantify the spatial concordance of high-priority catchments among different

taxonomic groups and with the existing protected area network. Together, these analyses provide

the foundation for strategic freshwater fish conservation planning in California.

Methods California native fish range mapping

We used the geospatial database and mapping software system PISCES (http://pisces.ucdavis.edu/)

to estimate the historical and current range of freshwater fish taxa in California. PISCES is designed

to aggregate and convert diverse spatial data from third-party sources to range maps at the

Hydrologic Unit Code 12 (HUC12) catchment scale (NRCS 2014). The data are compiled from expert-

informed range maps and approximately 300,000 records of native and non-native fishes from

accounts in primary and gray literature (Santos et al. 2014). All imported data are quality-controlled

by taxonomic experts to generate best estimates of historical and current ranges of California’s 129

native fish taxa (Appendix S1). Observations of fish prior to 1975 were used to estimate historical

taxa ranges, even though significant changes in California’s freshwater ecosystems had already

occurred by this time. This year was selected as a historical baseline because it is when the first

systematic evaluation of California’s fish fauna was performed (Moyle 1976) and represents the

beginning of the era of rapid decline in fish population status in California (Moyle et al. 2011).

Catchment prioritization for fish conservation

We identified catchments that optimize representation of native fish taxa based on their historical

and current distributions using the conservation planning software Zonation (version 3.1.11,

Conservation Biology Informatics Group 2014). Zonation is a publically available decision-support

system designed for use in systematic conservation planning (Moilanen et al. 2008). It applies a

complementarity-based algorithm to occurrence data to rank catchments according to their

representation of species. The priority ranking is implemented by iteratively removing map units

associated with the smallest marginal loss of conservation value, calculated from the total and

remaining species representation within a study area. We used the core-area algorithm in Zonation


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(Moilanen 2012) that builds an optimal reserve network by retaining map units which capture the

greatest proportion of rare species. We specifically examined the “proportion” output, which

identifies the minimum proportion of each taxon’s range remaining for each step of the map unit

removal process. Thus, we were able to delineate an optimal configuration of map units (HUC12

catchments) that capture minimum proportions taxa ranges.

Zonation’s directed connectivity module was used to represent hydrologic connectivity among

catchments. The module applies a penalty for removing interconnected catchments and therefore

favors solutions that preserve contiguous river basins, as opposed to isolated catchments (Moilanen

et al. 2008). The penalty for fragmenting connected catchments is dependent on user-defined

response functions of the target taxa (Appendices S1 and S2). To account for the effect of dams on

river network connectivity, each catchment with a large dam (USACE 2010) on the mainstem river

was manually bisected and the catchment connectivity matrix was modified to treat all catchments

below dams as headwaters (i.e., no upstream contributing catchments). Conservation priority areas

based on current fish occurrence data were evaluated using the dam-fragmented river network.

Historical fish priority areas were evaluated using the unaltered hydrologic landscape.

To account for major differences in life history and range occupancy of California’s native fish fauna,

we partitioned fish taxa into the three groups: anadromous, range-restricted, and wide-ranging

(Appendix S1). Fish taxa that historically occupied 25 or fewer HUC12 catchments were considered

“range-restricted” (< 24,000 km2), while non-anadromous taxa in the “wide-ranging” group occurred

in more than 25 HUC12 catchments. The threshold was determined by plotting the number of

catchments historically occupied by each taxon and visually identifying a natural break in the

distribution. For each group, we identified high priority catchments (i.e., those which maximized

representation of taxa) according to their historical and current ranges. We then calculated the

difference in each catchment’s historical and current ranking to determine whether it has increased

or decreased in conservation importance. Additional methodological details of Zonation

implementation are provided as supplementary material (Appendix S2).

Protected areas assessment

The U.S. Geological Survey’s (USGS) Protected Areas Dataset was used to identify and map existing

protected areas that may support fish conservation (USGS 2015, Figure 1). The dataset classifies

protected areas according to management intent for biodiversity conservation: Class 1 protected

areas are managed for biodiversity and disturbance events are either mimicked or allowed to

proceed without intervention; Class 2 areas are managed for biodiversity but disturbance events are

suppressed; Class 3 areas are managed for multiple uses, which may include mining, logging, and

recreational vehicle access; and Class 4 areas have no known mandate for biodiversity protection.

We first evaluated the degree of concordance between protected areas and fish taxa ranges. Next,

we calculated the total area of Class 1 and 2 protected lands and identified the highest-priority

catchments from the Zonation analysis that occupy an equivalent area. These catchments represent

a hypothetical, alternative configuration of protected lands that would optimize representation of

native fishes. Finally, we applied Zonation’s mask module to delineate priority catchments while


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accounting for existing protected areas. This module forces the optimization algorithm to remove

catchments within protected areas last, providing a solution that efficiently leverages existing

protected lands for native fish conservation.

Results Historical priority catchments for native fish conservation

Historically, anadromous fishes occupied all coastal catchments and extended hundreds of

kilometers inland in the north coast region and Sacramento-San Joaquin River basin (Figure 2A).

Areas with the highest richness of anadromous taxa were the Sacramento River and Klamath River

basins. Range-restricted taxa historically occurred in discrete zones in the state’s southeastern xeric

region, southern and northern California coast, and northeastern corner of the state. Wide-range

taxa occurred throughout most of the state, with the exception of xeric regions in the southeast and

high elevation zones of the Sierra Nevada.

Since 1975, five fish taxa have been extirpated (Appendix S1) and the total range of native fish taxa

has contracted slightly (7%) from approximately 280,000 km2 to 260,000 km2. Range contractions

are more sizable at the group level, with reductions in occupied area of 35% and 40% for

anadromous and range-restricted taxa, respectively. Local extirpations of anadromous taxa are

concentrated along the coast in northern-central California and in tributaries to the Sacramento and

San Joaquin Rivers (Figure 2B), especially in areas where fish passage has been blocked by major

dams (e.g., Shasta Dam on the Sacramento River). Extirpation of range-restricted taxa has been

greatest in the Owens River basin; for wide-ranging taxa, extirpations have primarily occurred in the

Central Valley, most notably in the San Joaquin River basin where at least six taxa have been lost,

representing approximately two-thirds of the historical assemblage in that system.

Priority catchments for native fish conservation

For the current distribution of native fishes, priority catchments for the three taxa groups occur in

distinct regions of the state (Figure 3A). High-ranking catchments for anadromous taxa include the

Sacramento River, lower Klamath River, and several coastal basins along the northern coast. Priority

catchments for range-restricted taxa include natural lakes supporting unique endemic fish fauna

such as Goose Lake and Eagle Lake (in northeastern California), Clear Lake (north of San Francisco

Bay), and Lake Tahoe. High-ranking basins for range-restricted taxa also include geographically

isolated systems in the state’s xeric region, including the Owens River, Amargosa River, and Salton

Sea. High-ranking basins for the wide-ranging group included the entire Klamath River, Pit River,

Sacramento-San Joaquin Delta, and several small rivers draining the eastern slope of the Sierra

Nevada.

A comparison of catchment rankings from historical (Appendix S3) to current time (Figure 3A)

illustrates where catchments have decreased or increased in importance (Figure 3B). The ranking of

catchments decreased in many areas of the state, primarily due to the local extirpation of fish taxa,

whereas some catchments increased in priority, indicating that they are locations where taxa with

contracted ranges have persisted. For anadromous taxa, locations that were more important


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historically occur above dams which block passage and extirpated runs of salmon, steelhead, and

sturgeon; locations which have increased in importance include the portions of the southern coast

and scattered catchments in the north coast and Central Valley regions. For range-restricted taxa,

locations which were more important historically occur in the vicinity of the Russian, Kern, Owens,

and Colorado river basins; locations which are now more important include portions of the lower

Klamath, Pit, and Santa Clara river basins. For wide-ranging taxa, locations which were more

important historically include the San Joaquin River basin and coastal rivers on the south coast;

tributaries to the Sacramento River on the west slope of the Sierra Nevada have become more

important.

There is relatively low concordance among priority catchments for the three fish taxa groups (Figure

4). The greatest concordance is between anadromous and wide-ranging (AN-WR) and range-

restricted and wide-ranging (RR-WR) groups. For example, there is approximately 50% overlap of

catchments that capture at least 20% of the ranges of anadromous and wide-ranging group taxa. The

least concordance among priority catchments is between the wide-ranging and range-restricted

groups (WR-RR) and anadromous and range-restricted groups (AN-RR). For these group pairs, less

than 10% of high-priority catchment area is shared.

Representation of native fish taxa within protected areas

The protected area database includes 44,600 km2 of Class 1 and 52,500 km2 of Class 2 lands, which

are primarily managed for biodiversity conservation (USGS 2015). There are 101,200 km2 of Class 3

lands and 24,500 km2 of Class 4 lands (Figure 1). To evaluate representation of fish diversity within

protected areas, we calculated the spatial overlap of Class 1 and 2 protected areas (hereafter,

protected areas) with the ranges of individual fish taxa and with the three fish groups. Nearly all

native fish taxa (119 of 122) occur within protected areas, but for many taxa (n=51), less than 10% of

their extant range is represented (Appendix S1). At the group level (Figure 5 inset table), 12% of the

current range of anadromous taxa and of wide-ranging taxa occurs within protected areas. A greater

proportion (20%) of the range of range-restricted taxa occurs within protected areas.

Optimal configuration of protected areas for fish conservation

To assess how an alternative reserve network could better represent fish biodiversity in California,

we selected the highest priority catchments on the landscape that occupied a similar area to

protected areas (97,100 km2; Figure 5). Catchments within the optimal, hypothetical configuration of

protected areas are found along the coast and on the state’s major rivers, including the Pit, Klamath,

Russian, Sacramento/San Joaquin, and Owens Rivers. This optimal reserve network would represent

all of the state’s fish taxa and capture at least 35% of the range of each anadromous taxon, 31% of

the range of each range-restricted taxon, and 20% of the range of each wide-ranging taxon.

Finally, to consider how the existing reserve network could be leveraged in a systematic

conservation approach, catchments within protected areas were forced into the Zonation solution

and the prioritization analysis was re-run to rank remaining catchments (Appendix S4). For

anadromous taxa, catchments in interior coastal northern California and coastal central and

southern California become more important when accounting for protected areas. For range-


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restricted taxa, scattered catchments in the northeastern portion of the state and eastern slopes of

the Sierra Nevada become more important. Catchments for wide-ranging taxa are more important in

tributaries to the Sacramento River, Kern River basin, and coastal tributaries.

Discussion Based on our analysis of freshwater fish representation and protected public lands, an opportunity

for statewide fish conservation through protected area planning in California has been missed.

Although most of the state’s taxa occur in catchments that at are least partially protected, a

relatively small proportion of their range is represented. Furthermore, protected areas include few

of the catchments disproportionately representative of fish diversity, suggesting that their utility for

conserving the state’s native fish fauna is limited. These findings are consistent with a national

assessment by Lawrence et al. (2011), who found that National Parks of the United States

represented much of the nation’s fish diversity, but missed a significant number of endemic and

imperiled species.

Our analyses distinguish areas where focused efforts to conserve fish within the protected area

network is warranted and where conservation outside of the network should be directed. Fish

conservation will continue to be a challenge within protected areas because of conflicting uses

within their boundaries (Nel et al. 2007) as well as vulnerability to external anthropogenic influences

(Abell et al. 2007; Dudgeon et al. 2006). Conservation outside of protected areas will face even

greater challenges, such as the restoration of environmental flows in rivers affected by dams and

diversions (Grantham et al. 2014).

Our results also highlight catchments that may be appropriate targets for restoration. Contraction of

taxa ranges and extirpation of some taxa over the past 40 years has substantially changed the

location of priority catchments. For example, priority catchments for anadromous taxa have shifted

towards the coast and northward due to the widespread construction of dams in the state’s interior

and urbanization in the south. The importance of large river basins, including the Colorado and San

Joaquin River, has also declined due to local extirpations or extinctions. However, these and other

historically important catchments may be suitable targets for restoration if environmental conditions

that once supported a diverse assemblage of native freshwater fishes can be restored.

This study provides a foundation for systematic freshwater conservation planning in California. By

delineating catchments that optimize representation of freshwater fishes, focused efforts can be

made to examine their potential to be managed for conservation purposes. Ultimately, identification

of priority catchments for conservation and restoration will require expert validation of results,

congruence with conservation targets for other terrestrial and freshwater taxa (Abell et al. 2011),

and a comprehensive analysis of stressors (sensu Allan et al. 2012), including climate change (Bond

et al. 2014). Dimensions of biodiversity other than taxonomic, such as functional and phylogenic

diversity, should also be considered in defining conservation priorities (e.g., Carvalho et al. 2015;

Maire et al. 2013; Strecker et al. 2011). Such efforts are underway by a multi-institution team of river

scientists and managers (Howard et al. 2015b). Given the threat of climate change and other

anthropogenic stressors, effective freshwater conservation will require a portfolio approach that is


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tailored to regional conditions and opportunities. For example, in the Sierra Nevada, restoration of

meadows and functional environmental flows in managed rivers is likely to increase freshwater

ecosystem resilience (Viers et al. 2013; Yarnell et al. 2010) and is supported by existing

environmental policies (Viers and Rheinheimer 2011). Conversely, catchments of the Sacramento –

San Joaquin Delta are unlikely to emerge as viable conservation priorities without wholesale changes

in environmental policy and management (Luoma et al. 2015).

Long-term degradation of freshwater habitats and acute drought have brought California’s native

freshwater fish fauna to the brink of extinction. A systematic approach to freshwater fish

conservation could greatly improve the likelihood of the persistence of the state’s fishes and other

freshwater-dependent species. Strategic action is required to conserve freshwater fish currently

represented within protected areas and to preserve fish diversity hotspots that primarily occur

outside reserve boundaries. Because priority catchments within and outside reserves are threatened

by climate change and other stressors, conservation will require seeking reconciliation approaches

to create the best possible conditions for freshwater fishes in altered environments (Moyle 2013).

Overall, this study contributes to the ongoing debate in California and elsewhere over how to

manage our water resources in a way that balances human demands with ecosystem needs. While

recognizing that tradeoffs are inevitable, we believe that a systematic approach to freshwater

conservation is the most likely to achieve lasting environmental benefits and is urgently needed in

California.

Acknowledgements We thank Jacob Katz, Michael Kellet, and Steve Goldman. Funding was provided by the S. D. Bechtel,

Jr. Foundation.


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Figures Legends

Figure 1. Study area map with California’s major rivers and lakes and protected area boundaries,

distinguishing areas managed specifically for biodiversity (GAP Class 1 and 2) and those managed for

multiple uses (GAP Class 3 and 4).


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Figure 2. (A) Historical taxa richness in California catchments for anadromous (n = 26), range-

restricted (n = 52), and wide-ranging taxa (n = 51); and (B) losses of taxa from catchments in their

historical range.


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Figure 3. (A) Priority catchments for native fish conservation based the current ranges of

anadromous, range-restricted, and wide-ranging taxa. Catchments rankings indicate the minimum

percentage of the range of each taxon that is represented (e.g., at least 5% of the range of all taxa in

the group are represented by catchments delineated at the “5%” level). Lower panel (B) indicates

change in catchment importance relative to historical priorities.


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Figure 4. Degree of spatial concordance among priority catchments based on current ranges of

anadromous (AN), wide-ranging (WR), and range-restricted (RR) groups. The x-axis indicates the

range representation threshold, defined as the minimum percentage of the range of all group taxa

represented by a set of catchments. The y-axis indicates the concordance among catchments for

each pair of taxa groups at varying range representation thresholds. For example, there is

approximately 50% concordance among catchments that capture at least 20% of the ranges of

anadromous and wide-ranging taxa (AN-WR).


17

Figure 5. Optimal configuration of a hypothetical protected area network for native fish conservation

for three taxa groups. Total area is equivalent to that of the existing GAP Class 1 and 2 protected

areas in California (shown as crosshatch polygons). Inset table indicates the representation of taxa

within the existing protected area network and within the optimal configuration of catchments. The

representation of taxa is reported for the entire range of the taxa group and for the minimum range

of member taxa within each group.


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Supplementary Information Appendix S1. California native fish taxa status, connectivity scores, and range statistics

Appendix S2. Methodological details of Zonation implementation

Appendix S3. Map of priority catchments for native fish conservation based the historical ranges of

anadromous, range-restricted, and wide-ranging taxa

Appendix S4. Maps of catchment prioritization when the existing protected area is included in

Zonation’s optimization solution

Appendix S5. Metadata and tabular results of all Zonation scenarios in .xlsx format

missing the boat on freshwater fish conservation in … assessment of freshwater fish in california...

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