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Scientists and resource managers increasingly use Markdown-based tools to create reproducible reports and manuscripts. These workflows allow people to use standardized methods that are more reproducible, efficient, and transparent than other standard office tools. We present a Quarto template and demonstrate how this template may be used for a journal, the Journal of Fish and Wildlife Management , in our article. This template may also be readily adapted to other journals that use Microsoft Word-based workflows and for other product types such as annual reports. We also provide a high-level overview of Quarto and other Markdown-based workflows as part of the document. Lastly, we provide examples of some features of the Quarto publishing system that may be helpful for authors when customizing Quarto templates for specific journal formatting requirements and other product types.
Management of threatened and endangered species would seem to be a perfect context for adaptive management. Many of the decisions are recurrent and plagued by uncertainty, exactly the conditions that warrant an adaptive approach. But although the potential of adaptive management in these settings has been extolled, there are limited applications in practice. The impediments to practical implementation are manifold and include semantic confusion, institutional inertia, misperceptions about the suitability and utility, and a lack of guiding examples. In this special section of the Journal of Fish and Wildlife Management , we hope to reinvigorate the appropriate application of adaptive management for threatened and endangered species by framing such management in a decision-analytical context, clarifying misperceptions, classifying the types of decisions that might be amenable to an adaptive approach, and providing three fully developed case studies. In this overview paper, I define terms, review the past application of adaptive management, challenge perceived hurdles, and set the stage for the case studies which follow.
Several surveys have documented the increasing population size and geographic distribution of Eastern Population greater sandhill cranes Grus canadensis tabida since the 1960s. Sport hunting of this population of sandhill cranes started in 2012 following the provisions of the Eastern Population Sandhill Crane Management Plan. However, there are currently no published estimates of Eastern Population sandhill crane survival rate that can be used to inform harvest management. As part of two studies of Eastern Population sandhill crane migration, we deployed solar-powered global positioning system platform transmitting terminals on Eastern Population sandhill cranes ( n = 42) at key concentration areas from 2009 to 2012. We estimated an annual survival rate for Eastern Population sandhill cranes from data resulting from monitoring these cranes by using the known-fates model in the MARK program. Estimated annual survival rate for adult Eastern Population sandhill cranes was 0.950 (95% confidence interval = 0.885–0.979) during December 2009–August 2014. All fatalities ( n = 5) occurred after spring migration in late spring and early summer. We were unable to determine cause of death for crane fatalities in our study. Our survival rate estimate will be useful when combined with other population parameters such as the population index derived from the U.S. Fish and Wildlife Service fall survey, harvest, and recruitment rates to assess the effects of harvest on population size and trend and evaluate the effectiveness of management strategies.
Recent records of mountain lions Puma concolor and concurrent declines in desert bighorn sheep Ovis canadensis mexicana on Kofa National Wildlife Refuge in Arizona, United States, have prompted investigations to estimate the number of mountain lions occurring there. We performed noninvasive genetic analyses and identified species, individuals, and sex from scat samples collected from the Kofa and Castle Dome Mountains. From 105 scats collected, we identified a minimum of 11 individual mountain lions. These individuals consisted of six males, two females and three of unknown sex. Three of the 11 mountain lions were identified multiple times over the study period. These estimates supplement previously recorded information on mountain lions in an area where they were historically considered only transient. We demonstrate that noninvasive genetic techniques, especially when used in conjunction with camera-trap and radiocollaring methods, can provide additional and reliable information to wildlife managers, particularly on secretive species like the mountain lion.
Observed degradation of aquatic systems at Big Stone National Wildlife Refuge, located in west-central Minnesota, have been associated with sediment-laden inflows from riverine systems. To support management, a study was conducted during 2013–2014 with overall goals of characterizing the aquatic invertebrate and vegetation communities of the Big Stone National Wildlife Refuge and exploring relations between these communities and various water-quality parameters. Sample sites were located along an observed vegetation gradient and assigned to three predetermined habitat zones for comparison purposes: upstream, transition, and downstream. Of the 12 species of aquatic vegetation that were identified, invasive narrowleaf cattail Typha angustifolia dominated the upstream zone (observed at .90% of sample locations), coontail Ceratophyllum demersum and narrowleaf cattail were most common in the transition zone (collected or observed at 100 and 83% of sample locations, respectively), and coontail and narrowleaf pondweed Potamogeton strictifolius were most common in the downstream zone collected at 100 and 64% of sample locations, respectively). Measured values for the water-quality parameters varied among dates, reflecting the continually fluctuating nature of riverine systems. Based on general observations across sample dates, turbidity and dissolved oxygen concentrations were greatest in the upstream zone sample sites, while oxidation-reduction potential was greatest in the downstream zone sites. There were 115 unique aquatic invertebrate taxa identified to varying levels of taxonomic resolution. Results suggested that there were overall differences in invertebrate biomass among the sample dates, but that there were no strong trends among the sample zones. Aquatic invertebrates and vegetation communities, along with the water-quality parameters, varied temporally and showed irregular relations among the sample zones. These general observations emphasize the importance of temporally and spatially intensive sampling to account for natural variation. Moreover, short- and long-term streamflow and water-level information obtained for this study demonstrated substantial variability that must be considered when conducting biotic inventories and monitoring water quality, as well as when using such data to assess management options. Periodic monitoring of wetlands and associated streamflows, along with sediment loads and water quality of inflows, should allow Big Stone National Wildlife Refuge staff to identify habitat degradation and potential contributing factors, and to develop strategies to achieve specific management objectives and goals.
Northern pintail Anas acuta (hereafter, pintail) populations have declined substantially throughout the western US since the 1970s, largely as a result of converting wetlands to cropland. Managed wetlands have been developed throughout the San Francisco Bay estuaries to provide wildlife habitat, particularly for waterfowl. Many of these areas were historically tidal baylands and plans are underway to remove dikes and restore tidal action. The relationship between tidal baylands and waterfowl populations is poorly understood. Our objective was to provide information on selection and avoidance of managed and tidal marshland by pintails. During 1991–1993 and 1998–2000, we radio-marked and relocated 330 female pintails (relocations, n =11,574) at Suisun Marsh, the largest brackish water estuary within San Francisco Bay, to estimate resource selection functions during the nonbreeding months (winter). Using a distance-based modeling approach, we calculated selection functions for different ecological communities (e.g., tidal baylands) and investigated variation explained by time of day (day or night hours) to account for differences in pintail behavior (i.e., foraging vs. roosting). We found strong evidence for selection of managed wetlands. Pintails also avoided tidal marshes and bays and channels. We did not detect differences in selection function between day and night hours for managed wetlands but the degree of avoidance of other habitats varied by time of day. We also found that areas subjected to tidal action did not influence the selection of immediately adjacent managed wetlands. If current management goals include providing habitat for wintering waterfowl populations, particularly pintail, then we recommend wildlife managers focus tidal restoration on areas that are not currently managed wetland and/or improve conditions in areas of managed wetlands to increase local carrying capacities
Adaptive management is a form of structured decision making designed to guide management of natural resource systems when their behaviors are uncertain. Where decision making can be replicated across units of a landscape, learning can be accelerated, and biological processes can be understood in a larger spatial context. Broad-based partnerships among land management agencies, exemplified by Landscape Conservation Cooperatives (conservation partnerships created through the U.S. Department of the Interior), are potentially ideal environments for implementing spatially structured adaptive management programs.
Management objectives for long-lived species are difficult to define because many taxa have delayed maturity and variable recruitment. White Sturgeon Acipenser transmontanus is an example of a species with a complex life history that complicates long-term status monitoring and establishment of management objectives. Historically, White Sturgeon in the Sacramento–San Joaquin River basin have been monitored by tracking the abundance of age-15 individuals as outlined by the Central Valley Project Improvement Act. However, infrequent recruitment complicates progress toward Central Valley Project Improvement Act management objectives because abundance of a single cohort fails to represent overall population trends. By using a Leslie population matrix, we demonstrate that the probability of reaching the Central Valley Project Improvement Act objective of 11,000 age-15 White Sturgeon is highly unlikely. We propose an alternative metric of 155,000 adults, which better represents overall population trends of White Sturgeon in the Sacramento–San Joaquin River basin, can be efficiently monitored, and can support both the goal of the Central Valley Project Improvement Act and management objectives.
Predation on juvenile native fish by introduced rainbow trout Oncorhynchus mykiss and brown trout Salmo trutta is considered a significant threat to the persistence of endangered humpback chub Gila cypha in the Colorado River in Grand Canyon. Diet studies of rainbow and brown trout in Glen and Grand canyons indicate that these species eat native fish, but impacts are difficult to assess because predation vulnerability is highly variable depending on the physical conditions under which the predation interactions take place. We conducted laboratory experiments to evaluate how short-term predation vulnerability of juvenile humpback chub changes in response to changes in turbidity. In overnight laboratory trials, we exposed hatchery-reared juvenile humpback chub and bonytail Gila elegans (a surrogate for humpback chub) to adult rainbow and brown trout at turbidities ranging from 0 to 1,000 formazin nephlometric units. We found that turbidity as low as 25 formazin nephlometric units significantly reduced predation vulnerability of bonytail to rainbow trout and led to a 36% mean increase in survival (24–60%, 95% CI) compared to trials conducted in clear water. Predation vulnerability of bonytail to brown trout at 25 formazin nephlometric units also decreased with increasing turbidity and resulted in a 25% increase in survival on average (17–32%, 95% CI). Understanding the effects of predation by trout on endangered humpback chub is important when evaluating management options aimed at preservation of native fishes in Grand Canyon National Park. This research suggests that relatively small changes in turbidity may be sufficient to alter predation dynamics of trout on humpback chub in the mainstem Colorado River and that turbidity manipulation may warrant further investigation as a fisheries management tool.
The National Wildlife Refuge System (Refuge System) is a collection of public lands maintained by the U.S. Fish and Wildlife Service for migratory birds and other wildlife. Wetlands on individual National Wildlife Refuges (Refuges) may be at risk of increased sedimentation because of land use and water management practices. Increased sedimentation can reduce wetland habitat quality by altering hydrologic function, degrading water quality, and inhibiting growth of vegetation and invertebrates. On Refuges negatively affected by increased sedimentation, managers have to address complex questions about how to best remediate and mitigate the negative effects. The best way to account for these complexities is often not clear. On other Refuges, managers may not know whether sedimentation is a problem. Decision makers in the Refuge System may need to allocate resources to studying which Refuges could be at risk. Such analyses would help them understand where to direct support for managing increased sedimentation. In this paper, we summarize a case study demonstrating the use of decision-analytic tools in the development of a sedimentation management plan for Agassiz National Wildlife Refuge, Minnesota. Using what we learned from that process, we surveyed other Refuges in U.S. Fish and Wildlife Service Region 3 (an area encompassing the states of Illinois, Indiana, Iowa, Ohio, Michigan, Minnesota, Missouri, and Wisconsin) and Region 6 (an area encompassing the states of Colorado, Kansas, Montana, Nebraska, North Dakota, South Dakota, Utah, and Wyoming) about whether they experience sediment-related impacts to management. Our results show that cases of management being negatively affected by increased sedimentation are not isolated. We suggest that the Refuge System conduct a comprehensive and systematic assessment of increased sedimentation among Refuges to understand the importance of sedimentation in context with other management problems that Refuges face. The results of such an assessment could guide how the Refuge System allocates resources to studying and managing widespread stressors.
Riverine catostomids can show a wide range of interspecific variation in life-history characteristics. Understanding these differences is an important consideration in evaluating the sensitivity of these fishes to disturbance and in formulating effective conservation strategies, particularly when dealing with an assemblage consisting of multiple species within a watershed. We collected Apalachicola redhorse Moxostoma n. sp. cf. poecilurum ( n = 125), spotted sucker Minytrema melanops ( n = 94), and quillback Carpiodes cyprinus ( n = 94) to determine age, growth, and reproductive biology of spawning catostomids in the Apalachicola River, Florida, during 2007. Quillback was the smallest in total length at age; longest-lived; most fecund; and produced the smallest eggs. Apalachicola redhorse was the largest in body size; had an intermediate life span; and produced the fewest yet largest eggs. Spotted sucker was more similar to Apalachicola redhorse in most characteristics. Growth during ages 1-3 in all three species seemed to be negatively related to the proportion of observations of extreme flow, both high (Q 90 ) and low (Q 10 ), per year and a positive response in growth rate to high flows (>Q 75 but < Q 90 ). However, Apalachicola redhorse and spotted sucker growth was more sensitive to flow conditions than that of quillback. Our results suggest the life histories and ecological response of Apalachicola River catostomids to flow regulation are important components for developing strategies that incorporate the needs of these fishery resources into an ecosystem-based management approach.
Emigration was evaluated for hatchery Chinook salmon ( Oncorhynchus tshawytscha ) microjacks (age-1 mature males) and immature parr (age-1 juveniles, both sexes) released from both a hatchery and a natural stream (fish released as fry). In the hatchery, volitional releases (∼14 to 15 months post-fertilization) to an adjacent river occurred during October–November. The hatchery release was monitored by using an experimental volitional release that diverted fish to a neighboring raceway. Fish captured during the experimental release (range 361–4,321 volitional migrants) were made up of microjacks and immature parr. Microjacks were found only in the migrant samples, averaged 18% (range 0–52%) of all migrants, and were rarely found in non-migrant samples. In comparison, immature parr were common in both the migrant and non-migrant samples. Microjacks were significantly longer (9%), heavier (36%), and had a greater condition factor (16%) than migrant immature parr (P<0.01). In addition, they differed significantly (P<0.01) from non-migrant immature parr; 10% longer, 44% heavier and 14% greater condition factor. In natural streams, microjacks were captured significantly earlier (P<0.01) than immature parr during the late-summer/fall migration and comprised 9–89% of all fish captured. Microjacks have the potential to contribute to natural spawning populations but can also represent a loss of productivity to hatchery programs or create negative effects by introducing non-native genes to wild populations and should be monitored by fishery managers.
Fish and wildlife populations are under unprecedented threats from changes in land use and climate. With increasing threats comes a need for an expanded constituency that can contribute to the public support and financial capital needed for habitat conservation and management. Using an ecosystem services approach can provide a framework for a more holistic accounting of conservation benefits. Our objective here is to provide a greater understanding of the role that taking an ecosystem services approach can have in expanding the public constituency that supports the use of financial capital required to conserve and manage the nation’s natural capital. To demonstrate a methodology and the usefulness of taking an ecosystem services approach when communicating the value of conserving and managing fish and wildlife habitats, we performed an evaluation of U.S. Fish and Wildlife Service-owned Waterfowl Production Areas, National Wildlife Refuges, and easement lands (both wetland and grassland) in Stutsman County, North Dakota. We quantified amphibian habitat, grassland bird habitat, floral resources for pollinators, and carbon storage services under various scenarios of conservation. While we did not include all possible ecosystem services in our model, our case study shows how this process can provide a more complete picture of the collateral benefits of conservation directed primarily toward waterfowl. Using this ecosystem services approach, we documented marked losses in all services modeled if current conservation lands were developed for the production of agricultural crops. By having access to a more complete picture of benefits provided by conservation lands, decision makers can better communicate their value. By garnering greater public support through a more accurate accounting of societal benefits, conservation and management of dwindling natural capital may someday attain the same level of thought and consideration that is put into the conservation and management of the nation’s financial capital.
Conservation efforts to restore historic waterbird distribution and abundance in the Central Valley of California require information on current and historic areas of waterbird habitat. To provide this information, we mapped the area of agricultural fields in the vicinity of the historic Tulare Lake Bed in the Tulare Basin, California, that were treated postharvest with two different flooding regimes that varied in depth and duration of water applied (, 1 cm to 1.5 m water for longer than 1 wk [FLD]; , 1 to 15 cm water for 1 wk or less [IRG]) during August–March 1991–1994 and 2005–2006. We compared our results with published estimates for 1976–1980 and 1981–1987. Area and crops treated postharvest with FLD or IRG flooding differed among years and months. Overall for August through March, weekly area of FLD fields averaged 1,671 ha in 1976–1980 but declined to about half that in later years; the decline was most severe during January–March. Cotton was primarily treated with IRG flooding and comprised 47–95% of the total IRG field area. Other crops were primarily treated with FLD flooding; tomato replaced safflower in 2005–2006. These documented declines since the 1970s in area of FLD fields and changes in crops being flooded postharvest reduce the carrying capacity of the Tulare Basin for waterbirds, a situation that will need to be reversed for restoration of historic waterbird distribution in the Central Valley to be viable. If maintaining agricultural production is a priority and agricultural drainage waters can be disposed of safely, then increasing the extent of FLD grain fields would provide the most benefit for wintering waterbirds; otherwise, restoring and providing adequate water supplies to managed wetlands would most benefit waterbirds
The introduction of exotic species into an environment can introduce great change in the trophic dynamics of native species. This is of even greater concern if the native species is of conservation concern. The giant gartersnake, Thamnophis gigas , an endemic predator of the Central Valley of California and a species of conservation concern at the state and federal levels, has declined as a result of conversion of its once vast wetland habitat to agriculture. Another anthropogenic factor contributing to this snake's changing ecology is the introduction of nonnative prey into the species' habitats. These introductions have resulted in a prey community that is almost completely composed of exotic species and have potential for considerable effects. In order to assess prey preference and selection we performed three sets of behavioral trials on naïve neonates. We examined 1) neonate prey preference in response to olfactory cues of prepared prey extracts, 2) neonate consumption of different live prey items presented simultaneously; and 3) terrestrial feeding behavior and/or latency to successful attack. Results from the olfactory study suggest that native Sierran treefrogs, Pseudacris sierra, are preferred by neonates. Results from consumption trials suggest that neonates are more likely to select frog species than fish species. This is the first study that we are aware of that examines prey selection of this threatened species and serves to inform its conservation and management.
Invasive species are a major threat to biodiversity of native fishes in North America. In Atlantic coastal rivers of the United States, large catfishes introduced from the Gulf of Mexico drainages have become established and contributed to native species declines. Flathead Catfish Pylodictis olivaris were introduced to the Chesapeake Bay drainage in the 1960s and 1970s in the James and Potomac river systems in the eastern United States. Diet studies have found James River Flathead Catfish function as apex predators and are known to consume at-risk Alosa spp. To limit further range expansion and impacts to native species, resource management agencies need information on population characteristics to support population assessments and management plan development. Thus, we examined temporal trends in growth rates and estimated total instantaneous mortality for tidal James River Flathead Catfish collected by Virginia Department of Game and Inland Fisheries from 1997 to 2015. Parameters of the von Bertalanffy growth model with length-at-age observations pooled across sampling years were estimated as L ∞ = 1,059 mm, k = 0.231/y, and t 0 = 0.55 y. Flathead Catfish growth differed among sampling years, especially for the years 2007 and 2014, which had the largest sample sizes. However, there were no obvious temporal trends in growth trajectories. James River Flathead Catfish tend to grow much faster than most populations used in development of the relative growth index, but the species is known to grow faster in its nonnative range. Consequently, scientists and managers should use caution when applying growth indices if native and nonnative populations are not expressly considered in development of the index. We estimated total instantaneous mortality as Z = 0.50 and mean natural mortality from six estimators as M = 0.30. A lack of older individuals in the population means that mortality rates may be overestimated as a result of gear selectivity or ongoing maturation of the population. These data provide information to support future work examining the species in the James River and development of population models to evaluate management strategies and management plans.
The effects of a warming climate will alter the hydrological cycles of arid southwestern U.S. reservoirs which primarily support agricultural needs, provide flood control, and generate hydroelectric power while secondarily supporting fish communities and sport fishing opportunities. The success of littoral spawning fishes depends on the timing and variability of water levels. The onset of drought between 2017 and 2018 provided an opportunity to evaluate the timing of hatch dates and relative abundance of young-of-year Largemouth Bass Micropterus salmoides across two water years of varying water temperatures and water levels in a southwestern U.S. reservoir. A retrospective analysis of otoliths in young-of-year Largemouth Bass revealed similar hatch dates in 2017 (14 April–29 May) and 2018 (13 April–28 May) despite differences in water temperature and water level rate of change. Median water temperature during hatch dates was greater in 2017 (median 19.0°C, range 14.3–24.4°C) than 2018 (17.6°C, range 13.5–21.7°C). Water level rate of change during hatch dates in 2017 was positive (+3.1 to +13.1 cm/d), which reflected reservoir filling. In contrast, water level rate of change during hatch dates in 2018 was negative (−8.5 to −0.6 cm/d), which reflected reservoir receding. Relative abundance of young-of-year fish was greater in 2017 (21.7 fish/h) when the reservoir was filling compared with relative abundance in 2018 (6.8 fish/h) when the reservoir was receding. The median growth rate was greater in 2017 (1.02 mm/d) when the reservoir was filling than in 2018 (0.82 mm/d) when the reservoir was receding. Despite differences in water temperature and contrasting reservoir levels between the two water years, the Largemouth Bass population in a southwest U.S. reservoir exhibited similar hatch dates reported for the species in southeastern and northeastern U.S. reservoirs. While water demand in the 21st century may exceed availability, the opportunity exists to collaborate with water managers to benefit Largemouth Bass populations in southwestern reservoirs.