Historical Patterns and Drivers of Spatial Changes in Recreational Fishing Activity in Puget Sound,Washington

Small-scale fisheries are the primary users of many coastal fish stocks; yet, spatial and temporal patterns of recreational and subsistence fishing in coastal marine ecosystems are poorly documented. Knowledge about the spatial distribution of fishing activities can inform place-based management that balances species conservation with opportunities for recreation and subsistence. We used a participatory mapping approach to document changes in spatial fishing patterns of 80 boat-based recreational anglers from 1950 to 2010 in Puget Sound, Washington, USA. Hand-drawn fishing areas for salmon, rockfishes, flatfishes, and crabs were digitized and analyzed in a Geographic Information System. We found that recreational fishing has spanned the majority of Puget Sound since the 1950s, with the heaviest use limited to small areas of central and northern Puget Sound. People are still fishing in the same places they were decades ago, with relatively little change in specific locations despite widespread declines in salmon and bottomfish populations during the second half of the 20^th century. While the location of core fishing areas remained consistent, the size of those areas and intensity of use changed over time. The size of fishing areas increased through the 2000s for salmon but declined after the 1970s and 1980s for rockfishes, flatfishes, and crabs. Our results suggest that the spatial extent of recreational bottomfishing increased after the 1960s, when the availability of motorized vessels and advanced fish-finding technologies allowed anglers to expand their scope beyond localized angling from piers and boathouses. Respondents offered a wide range of reasons for shifts in fishing areas over time, reflecting substantial individual variation in motivations and behaviors. Changes in fishing areas were most commonly attributed to changes in residence and declines in target species and least tied to fishery regulations, despite the implementation of at least 25 marine preserves since 1970.     

Limited realized dispersal and introgressive hybridization influence genetic structure and conservation strategies for brown rockfish, <Emphasis Type="Italic">Sebastes auriculatus</Emphasis>

Understanding patterns of connectivity among marine fish populations with demersal adults and pelagic larvae is critical for effective conservation of west coast rockfishes. The brown rockfish (Sebastes auriculatus) occurs in nearshore habitat and is common from northern Baja California, Mexico to northern California, rare off the outer coast of Oregon and Washington and again common in the inland waters of Puget Sound, Washington. Here we examine patterns of microsatellite DNA diversity from throughout the species’ range as an indirect measure of long-term trends in larval dispersal. Genetic divergence was large and highly significant over all populations (F _ST=0.056, P<0.0001), and was significantly correlated with geographic distance when considering coastal populations. The best estimates of mean coastal dispersal distance were on the order of 10 km or less per generation. Diversity was relatively low in the Puget Sound, suggesting that Puget Sound rockfish populations experienced a post-glacial founder effect followed by genetic isolation and low effective population size. Puget Sound individuals appeared to have recent mixed ancestry as a result of introgression with S. maliger and S. caurinus. Genetic isolation of Puget Sound fish provides a basis for consideration as a Distinct Population Segment (DPS) under the provisions of the Endangered Species Act. We recommend that coastal brown rockfish fisheries be managed at regional rather than coast-wide scales, and that design of marine reserve networks considers the surprisingly low realized dispersal distance of some species with high dispersal potential.     

Cooperative research sheds light on population structure and listing status of threatened and endangered rockfish species

Population genetics has increasingly become an important tool for determining appropriate taxonomic units for managing species of conservation interest. Yelloweye rockfish (Sebastes ruberrimus), canary rockfish (S. pinniger) and bocaccio (S. paucispinis) in the inland waterways of Puget Sound (PS), WA, USA were listed under the U.S. Endangered Species Act (ESA) in 2010. These listings relied heavily on evidence from other species that these populations were ‘discrete’ taxonomic units because little information was available for these species in PS. To fill this data gap, we collaborated with recreational fishing communities in PS to collect tissue samples and used population genetics analyses to determine whether samples from PS were genetically differentiated from samples collected from the outer coasts of the U.S. and Canada. Multiple analyses using restriction-site associated DNA sequencing data showed that yelloweye rockfish in PS and British Columbia, Canada were genetically different from coastal populations, while canary rockfish showed no genetic differentiation. These results support hypotheses that the genetic connectivity of rockfish populations is based on interactions between life-history characteristics and oceanographic conditions. These data also support the ESA designation status and the expansion of protected geographical boundaries for yelloweye rockfish but also suggest canary rockfish in PS are not a ‘discrete’ population and may not meet the first criterion of the ESA, as initially assumed. Collaboration among agencies and fishing communities, and cost-efficient genetic analyses provided a framework for collecting and analyzing data essential to the conservation and management of threatened and endangered species.     

Genetic Evidence of Postglacial Population Expansion in Puget Sound Rockfish (Sebastes emphaeus)

Several rockfish species (genus Sebastes) along the northeastern Pacific Ocean have rapidly declined in abundance owing in part to overfishing. A striking exception is the dwarf-like Puget Sound rockfish Sebastes emphaeus, whose densities have increased by several orders of magnitude over the last several decades. To describe their genetic structure, we sequenced 395 bp from the mitochondrial control region of 128 S. emphaeus adults from 5 locations spanning approximately 120 km of the Northwest Straits of Washington state. We detected no significant genetic differentiation among these populations and substantial genetic variation within populations, a pattern that may indicate high levels of ongoing gene flow. Preliminary data from 2 microsatellite loci are also consistent with panmixia. The mtDNA sequences also suggest that Puget Sound rockfish populations have expanded substantially since the retreat of Pleistocene glaciers made habitat in Puget Sound region available approximately 12,000 years ago.     

Dispersal of a nearshore marine fish connects marine reserves and adjacent fished areas along an open coast

Marine species with pelagic larvae typically exhibit little population structure, suggesting long‐distance dispersal and high gene flow. Directly quantifying dispersal of marine fishes is challenging but important, particularly for the design of marine protected areas (MPAs). Here, we studied kelp rockfish (Sebastes atrovirens) sampled along ~25 km of coastline in a boundary current‐dominated ecosystem and used genetic parentage analysis to identify dispersal events and characterize them, because the distance between sedentary parents and their settled offspring is the lifetime dispersal distance. Large sample sizes and intensive sampling are critical for increasing the likelihood of detecting parent–offspring matches in such systems and we sampled more than 6,000 kelp rockfish and analysed them with a powerful set of 96 microhaplotype markers. We identified eight parent–offspring pairs with high confidence, including two juvenile fish that were born inside MPAs and dispersed to areas outside MPAs, and four fish born in MPAs that dispersed to nearby MPAs. Additionally, we identified 25 full‐sibling pairs, which occurred throughout the sampling area and included all possible combinations of inferred dispersal trajectories. Intriguingly, these included two pairs of young‐of‐the‐year siblings with one member each sampled in consecutive years. These sibling pairs suggest monogamy, either intentional or accidental, which has not been previously demonstrated in rockfishes. This study provides the first direct observation of larval dispersal events in a current‐dominated ecosystem and direct evidence that larvae produced within MPAs are exported both to neighbouring MPAs and to proximate areas where harvest is allowed.     

Habitat-based submersible assessment of macro-invertebrate and groundfish assemblages at Heceta Bank, Oregon, from 1988 to 1990

Exploitation of groundfish off the U.S. Pacific coast reached maximum levels during the 1990s, resulting in severe declines in at least nine species of groundfish. From 1988 to 1990, we used the 2-man submersible Delta to make 42 dives and run replicate visual belt transects at six stations ranging from 67-360 m in depth at Heceta Bank on the outer continental shelf of Oregon. We identified four major habitats and associated benthic macroinvertebrate and groundfish assemblages: (1) shallow rock ridges and large boulders (< 100 m deep) dominated by basket stars, juvenile rockfishes, yelloweye rockfish, and lingcod; (2) mid-depth small boulder-cobbles (100-150 m) dominated by crinoids, brittle stars, rosethorn, pygmy/Puget sound, and canary rockfishes; (3) deep cobble (150-200 m) dominated by crinoids, brittle stars and various small rockfish species, and (4) deep mud slope (> 200 m) dominated by fragile urchins, sea cucumbers, shortspine thornyhead, and flatfishes. Although substantial interannual variation in groundfish abundance among seafloor types was evident in the 12 most abundant and/or commercially important fish taxa sampled, high variance resulted in statistically significant differences among years only in juvenile rockfishes. These data provide a baseline for future comparisons exploring long-term change this continental-shelf ecosystem.     

Distribution, Habitat, and Behavior of Rockfishes, Sebastes spp., in Nearshore Waters of Southeastern Alaska: Observations From a Remotely Operated Vehicle

We examined distribution, habitat, and behavior of rockfishes, Sebastes spp., with a remotely operated vehicle (ROV) in coastal waters <90m deep of southeastern Alaska from 1998 to 2000. We identified black, S. melanops, canary, S. pinniger, China, S. nebulosus, copper, S. caurinus, dusky, S. ciliatus, harlequin, S. variegatus, Puget Sound, S. emphaeus, quillback, S. maliger, redstripe, S. proriger, rosethorn, S. helvomaculatus, silvergray, S. brevispinis, tiger, S. nigrocinctus, yelloweye, S. ruberrimus, and yellowtail, S. flavidus, rockfish. Quillback and dusky rockfish were the most widely distributed species, China and harlequin rockfish were the least widely distributed species. Species richness was greater at sites on or near the outer coast than at sites in more inside, sheltered waters. Most (>75%) observations of rockfish were over complex bottoms of boulder and rock or in vertical bedrock wall habitats. Few rockfish were observed over soft bottoms with no relief. Median depth of observation was 30m for black, copper, dusky, and yellowtail rockfish and >30m for all other species. Median temperature of observation ranged from 6.1°C for harlequin rockfish to 9.4°C for black rockfish. Size of fish was positively correlated (p 0.036) with depth for dusky, quillback, and yelloweye rockfish. Species often observed alone were China (67%), copper (46%), quillback (46%), and rosethorn (43%) rockfish. Most (70%) observations of harlequin, Puget Sound, silvergray, tiger, and yelloweye rockfish were in mixed species assemblages. When first observed, the behavior of most rockfish species was swimming or hovering. Notable exceptions were China, harlequin, rosethorn, and tiger rockfish; 33–57% were resting on bottom or in a hole or crevice.     

Subsurface behavior of bottlenose dolphins (Tursiops truncatus) interacting with fish trawl nets in northwestern Australia: Implications for bycatch mitigation

Most studies of delphinid‐trawler interactions have documented the surface behavior of dolphins feeding on discarded bycatch, but not their subsurface behavior around demersal trawl gear. Using video cameras mounted inside trawl nets, we recorded the subsurface behavior of common bottlenose dolphins (Tursiops truncatus) in a demersal fish trawl fishery in northwestern Australia. Footage from 36 trawls across the fishery was analyzed to determine the extent of dolphin‐gear interactions and the behavior of dolphins inside the nets. Interaction rates were high, with dolphins present inside and outside the nets during 29 and 34 trawls, respectively, and for up to 99% of the trawl duration. The proportion of foraging behaviors exhibited inside the nets was higher than the proportions of traveling and socializing behaviors. Twenty‐nine individuals were identified inside the net, seven of which returned repeatedly within and between trawls and fishing trips, but were observed primarily in the same localized areas in which they were first recorded. Our results suggest that entering trawl nets may be a frequently occurring, yet specialized behavior exhibited by a small subset of trawler‐associated dolphins. We propose that gear modifications, not spatial or temporal adjustments to fishing effort, have the greatest potential to reduce dolphin bycatch.     

Parallel signatures of selection in temporally isolated lineages of pink salmon

Studying the effect of similar environments on diverse genetic backgrounds has long been a goal of evolutionary biologists with studies typically relying on experimental approaches. Pink salmon, a highly abundant and widely ranging salmonid, provide a naturally occurring opportunity to study the effects of similar environments on divergent genetic backgrounds due to a strict two‐year semelparous life history. The species is composed of two reproductively isolated lineages with overlapping ranges that share the same spawning and rearing environments in alternate years. We used restriction‐site‐associated DNA (RAD) sequencing to discover and genotype approximately 8000 SNP loci in three population pairs of even‐ and odd‐year pink salmon along a latitudinal gradient in North America. We found greater differentiation within the odd‐year than within the even‐year lineage and greater differentiation in the southern pair from Puget Sound than in the northern Alaskan population pairs. We identified 15 SNPs reflecting signatures of parallel selection using both a differentiation‐based method (BAYESCAN) and an environmental correlation method (BAYENV). These SNPs represent genomic regions that may be particularly informative in understanding adaptive evolution in pink salmon and exploring how differing genetic backgrounds within a species respond to selection from the same natural environment.     

An experimental study of the habitat preferences and movement patterns of copper,quillback, and brown rockfishes (Sebastes spp.)

Synopsis A study was designed to test whether habitat association affects the movement patterns and habitat preferences of copper, quillback, and brown rockfishes. Resighting of tagged rockfishes (512 tagged rockfishes and 726 resightings) from July 1986 through June 1988 indicated that home ranges, movements from reefs, and tendency to return from experimental displacement (up to 8.0 km) were significantly different on the three habitat types compared. On high relief rocky reefs, rockfishes maintained small home ranges (most within 30 m²) and displayed strong reef fidelity that was not affected by season; no off-reef movement was detected and rockfishes generally returned from displacements. On artificial reefs, rockfishes also maintained small home ranges (most within 30 m²), however, there were pronounced seasonal habitat preferences. In the summer, artificial reefs become less suitable; considerable off-reef movement occurred and rockfish did not return from displacements. In contrast, during fall and winter, rockfishes remained on artificial reefs and returned from displacements. On low relief rocky reefs, rockfishes maintained considerably larger home ranges (most within 400 m² and some up to 1500 m²) and habitat use was strongly affected by season; rockfishes only inhabited low relief reefs in the summer and only returned from displacements in the summer coincident when peak algal cover. In addition, there was substantial movement between artificial reefs and adjacent low relief reefs; many rockfishes leave artificial reefs in the summer, move to low relief reefs, and return to artificial reefs in the fall when kelp disappears on low relief reefs. Through habitat assessment, movement in response to habitat quality, and ability to home, these rockfish maintain a flexible behavior for optimal habitat use.     

Recent trends in paralytic shellfish toxins in Puget Sound,relationships to climate,and capacity for prediction of toxic events

Temporal and spatial trends in paralytic shellfish toxins (PSTs) in Puget Sound shellfish and their relationships with climate are investigated using long-term monitoring data since 1957. Data are selected for trend analyses based on the sensitivity of shellfish species to PSTs and their depuration rates, and the frequency of sample collection at individual sites. These criteria limit the analyses to the shellfish species Mytilus edulis at 20 sites from 1993 to 2007. Blue mussel toxicity is highly variable, but typically exceeds the regulatory limit for human consumption from July to November annually, with most closures occurring early in fall. Using blue mussel data only, we find no robust evidence to suggest that the frequency, magnitude, duration, or geographic scope of PST events in Puget Sound increased between 1993 and 2007. However, there is a significant basin-wide trend for closures to occur earlier in the year. There are no significant correlations between annual indices of mussel toxicity and aspects of the local and large-scale climate. Case studies of daily variations in local environmental factors leading up to exceptionally toxic events identify a combination of conditions that generally precedes most closures from 1993 to 2007. These results suggest that periods of warm air and water temperatures and low streamflow on sub-seasonal timescales may facilitate toxin accumulation in mussels. No relationships were found between water residence times in the surface layer and either streamflow or mussel toxicity. Recommendations are made for future monitoring to improve forecasting of PST risks in Puget Sound, an important region for recreational, commercial, and tribal subsistence shellfish harvesting.     

Growth,reproduction, and age at maturity of Lessa’s butterfly ray Gymnura lessae in the northern Gulf of Mexico

Environmental Biology of Fishes - In the northern Gulf of Mexico, batoids are caught as bycatch in the shrimp trawl fishery and targeted by recreational bowfishers. The vulnerability of these...     

Design and test of a grid to reduce bycatch in the longfin inshore squid (Doryteuthis pealeii) trawl fishery

A species separation grid was tested for a squid trawl to reduce finfish bycatch in the Nantucket Sound longfin inshore squid (Doryteuthis pealeii) fishery in southern New England, USA. The experimental trawl with a grid significantly reduces bycatch of summer flounder (Paralichthys dentatus) (76.4%, p < .001), black sea bass (Centropristis striata) (71.7%, p = .001), smooth dogfish (Mustelus canis) (86.0%, p < .001), and total bycatch (69.2%, p < .001) when compared to a conventional trawl. The catch rate of scup (Stenotomus chrysops) is 40.2% less than in the experimental trawl, but this difference is not statistically significant (p = .258). However, the experimental trawl also reduces targeted squid capture by 47.5% (p < .001), which is commercially unacceptable. Length analysis indicates no size effect on the retention for squid between the trawl with a grid (experimental) and the one without a grid (control), but the experimental trawl significantly reduces larger scup (>27 cm FL) and larger black sea bass (>37 cm TL), and all summer flounder size‐classes. Therefore, this grid design may not be a suitable bycatch reduction device for the Nantucket Sound squid trawl fishery, and further work is needed to understand squid behavior within a trawl to develop a successful bycatch reduction strategy for the New England longfin inshore squid fishery.     

Some data on the distribution,occurrence, and biology of rockfish of the genus <Emphasis Type="Italic">Sebastes</Emphasis> (Sebastidae) off the western coast of Sakhalin

Results of trawl surveys performed by SakhNIRO in Tatar Strait in the end of the 1970s and 1990s, as well as in the beginning of the current century, made it possible to clarify former concepts of rockfish species of the genus Sebastes dwelling off the western coast of Sakhalin, specific features of their distribution, and some aspects of biology. According to specified data, the number of rockfish species in the area of western Sakhalin attains ten.     

Genome-wide markers reveal differentiation between and within the cryptic sister species,sunset and vermilion rockfish

The vermilion rockfish complex, which consists of the cryptic sister species vermilion and sunset rockfish, is one of the most valuable recreational fisheries on the U.S. West Coast. These species are currently managed as a single complex, and because of uncertainty surrounding the relative contribution of each species within existing data sources, the stock status of each species is not fully known. A reliable and cost-effective method is needed to disentangle these species that will allow for the development of abundance indices, life history profiles, and catch histories that may potentially support species-specific stock assessments. Using restriction-site associated DNA sequence (RADseq) markers we generated 10,003 polymorphic loci to characterize the vermilion rockfish complex. PCA and Bayesian clustering approaches based on these loci clearly distinguished between sunset and vermilion rockfishes and identified hybrid individuals. These loci included 203 highly differentiated (F_ST?≥?0.99) single nucleotide polymorphisms, which we consider candidates in the planned development of a diagnostic assay capable of distinguishing between these cryptic species. In addition to clearly delineating to species, subsets of the interspecific markers allowed for insight into intraspecific differentiation in both species. Population genetic analyses for sunset rockfish identified two weakly divergent genetic groups with similar levels of genetic diversity. Vermilion rockfish, however, were characterized by three distinct genetic groups with much stronger signals of differentiation and significantly different genetic diversities. Collectively, these data will contribute to well-informed, species-specific management strategies to protect this valuable species complex.

     

GENETIC DIFFERENTIATION AMONG POPULATIONS OF THE PLANKTONIC MARINE DIATOM DITYLUM BRIGHTWELLII (BACILLARIOPHYCEAE)1

Population genetic structure was determined for the planktonic diatom Ditylum brightwellii (West) Grunow in two connected estuaries—Puget Sound and the Strait of Juan de Fuca (WA, USA). Three genetically distinct populations were detected that were characterized by different microsatellite allele distributions and unique alleles. Isolates from the two most genetically diverged populations displayed identical full‐length 18S rDNA sequences suggesting that either a single or two recently diverged species were sampled. The extent of genetic differentiation between populations was not correlated with distance between water samples or time between sampling. Instead, distinct populations were associated with different estuaries. In Puget Sound waters, one population was detected three times over the course of 28 months. Cells from this population were likely maintained inside Puget Sound over long periods through water recirculation within the Sound. In Strait of Juan de Fuca waters, two additional populations were detected. Maximum growth rates of Puget Sound isolates were significantly different from Strait of Juan de Fuca isolates, indicating that populations were composed of cells with different physiological capabilities. The genetic and physiological differentiation observed between populations from intermixing estuaries suggested that genetic exchange between populations was restricted through differential selection. Despite the potential for widespread dispersal in planktonic organisms, it appears that populations with distinct genetic and physiological characteristics can be maintained over long time periods through a combination of hydrology and differential selection.     

Microsatellite markers for the heavily exploited canary (Sebastes pinniger) and other rockfish species

The isolation and characterization of nine polymorphic microsatellite loci (eight tetranucleotide and one dinucleotide) from the canary rockfish Sebastes pinniger are described. Polymorphism at these loci revealed from six to 28 alleles, with expected heterozygosities ranging between 0.42 and 0.88, enabling high‐resolution genetic population structure investigation for this overfished species in the northeastern Pacific. They also amplify in 13 other congeneric species, providing highly variable loci for research on other rockfishes.     

Metagenomic Profiling of Microbial Composition and Antibiotic Resistance Determinants in Puget Sound

Human-health relevant impacts on marine ecosystems are increasing on both spatial and temporal scales. Traditional indicators for environmental health monitoring and microbial risk assessment have relied primarily on single species analyses and have provided only limited spatial and temporal information. More high-throughput, broad-scale approaches to evaluate these impacts are therefore needed to provide a platform for informing public health. This study uses shotgun metagenomics to survey the taxonomic composition and antibiotic resistance determinant content of surface water bacterial communities in the Puget Sound estuary. Metagenomic DNA was collected at six sites in Puget Sound in addition to one wastewater treatment plant (WWTP) that discharges into the Sound and pyrosequenced. A total of ∼550 Mbp (1.4 million reads) were obtained, 22 Mbp of which could be assembled into contigs. While the taxonomic and resistance determinant profiles across the open Sound samples were similar, unique signatures were identified when comparing these profiles across the open Sound, a nearshore marina and WWTP effluent. The open Sound was dominated by α-Proteobacteria (in particular Rhodobacterales sp.), γ-Proteobacteria and Bacteroidetes while the marina and effluent had increased abundances of Actinobacteria, β-Proteobacteria and Firmicutes. There was a significant increase in the antibiotic resistance gene signal from the open Sound to marina to WWTP effluent, suggestive of a potential link to human impacts. Mobile genetic elements associated with environmental and pathogenic bacteria were also differentially abundant across the samples. This study is the first comparative metagenomic survey of Puget Sound and provides baseline data for further assessments of community composition and antibiotic resistance determinants in the environment using next generation sequencing technologies. In addition, these genomic signals of potential human impact can be used to guide initial public health monitoring as well as more targeted and functionally-based investigations.     

Survey augmentation using commercial vessels in the Mid-Atlantic Bight: Sampling density and relative catchability

A series of side‐by‐side tows was conducted between a survey vessel and a commercial vessel in two seasons, spring and fall (autumn), to examine the use of commercial vessels to increase sampling density in trawl‐based stock surveys. Both vessels caught more fish offshore in the spring. The commercial vessel caught more fish than the survey vessel in both seasons. Catches of nearly all species were contagiously distributed in the spring. Most were contagiously distributed in the fall; however, somewhat more species were characterized by random or even distributions. The variance‐to‐mean ratio was consistently higher for most species for commercial vessel catches, regardless of season. As both vessels sampled in the same region at the same time, the increased predilection for the survey vessel to assess the distribution pattern as less patchy than the commercial vessel must accrue from some difference in sampling dynamics rather than variation in species distribution. A simulated decrease in sampling effort from 59 to 30 or 15 hauls increased the variance‐to‐mean ratio. Reduced sampling effort increased the tendency for occasional large catches to vary the estimate of domain biomass. The sampling program included an onshore–offshore gradient in station density. Domain biomass was considerably underestimated with reduced station density for six species characterized by large catches offshore in that portion of the survey domain characterized by low station density. In this study, a factor of two variation in domain biomass became more likely in 40% of species when sampling effort was reduced to 15 hauls from 59. A factor of two in biomass may distinguish a sustainable fishery from one in which a species is overfished. As survey sampling effort in this area was 18 hauls, increasing sample number by inclusion of commercial vessel tows would be advantageous. A regression between paired tows failed to adequately predict catches of one vessel from catches of the other. Standardization of vessel catches by the ratio‐of‐mean catches provided a more realistic comparison because large catches accounted for a significant fraction of domain biomass; however, a single conversion coefficient between boats could not be used for both sampling periods. The underlying impediment in developing a general conversion factor between the two vessels seems to be rooted in the differential in variance‐to‐mean ratios of the catches; this differential exists despite sampling of the same distribution of fish.     

Simulations inform design of regional occupancy‐based monitoring for a sparsely distributed,territorial species

Sparsely distributed species attract conservation concern, but insufficient information on population trends challenges conservation and funding prioritization. Occupancy‐based monitoring is attractive for these species, but appropriate sampling design and inference depend on particulars of the study system. We employed spatially explicit simulations to identify minimum levels of sampling effort for a regional occupancy monitoring study design, using white‐headed woodpeckers (Picoides albolvartus), a sparsely distributed, territorial species threatened by habitat decline and degradation, as a case study. We compared the original design with commonly proposed alternatives with varying targets of inference (i.e., species range, space use, or abundance) and spatial extent of sampling. Sampling effort needed to achieve adequate power to observe a long‐term population trend (≥80% chance to observe a 2% yearly decline over 20 years) with the previously used study design consisted of annually monitoring ≥120 transects using a single‐survey approach or ≥90 transects surveyed twice per year using a repeat‐survey approach. Designs that shifted inference toward finer‐resolution trends in abundance and extended the spatial extent of sampling by shortening transects, employing a single‐survey approach to monitoring, and incorporating a panel design (33% of units surveyed per year) improved power and reduced error in estimating abundance trends. In contrast, efforts to monitor coarse‐scale trends in species range or space use with repeat surveys provided extremely limited statistical power. Synthesis and applications. Sampling resolutions that approximate home range size, spatially extensive sampling, and designs that target inference of abundance trends rather than range dynamics are probably best suited and most feasible for broad‐scale occupancy‐based monitoring of sparsely distributed territorial animal species.