Restoring Intertidal Boulder‐Fields as Habitat for “Specialist” and “Generalist” Animals

Restoration is important in urban areas where habitat destruction is greatest. It incorporates many levels of intervention, with creation of new habitat the most extreme form. Most research on habitat creation has been terrestrial, or in marine habitats dominated by large structuring biota, such as mangroves. Intertidal boulder‐fields in urban areas are vulnerable to disturbances and habitat loss, which adversely affect numerous habitat specialists. This study describes experiments in which quarried stones were used to create new habitat outside natural boulder‐fields as a practical approach to restoring habitat. Colonization by specialist fauna and by common algae and invertebrates was measured for a year after deployment. Despite sessile assemblages on new boulders differing from those on natural boulders, common and rare animals rapidly colonized the new habitat. There was no clear succession, but colonization was variable and patchy at all scales examined, although diversities and abundances of some species in this novel habitat matched those of natural boulders within a few months. Rare and common animals generally colonized the new habitat as adults moving in from surrounding areas. Creating new boulder‐fields using quarried rocks is a successful approach to restoration and conservation of fauna where natural boulder‐fields are threatened.     

Spatial and Temporal Considerations in Restoring Habitat for Wildlife

An accumulated body of theory and empirical evidence suggests that habitat selection by animals is a scale‐dependent, hierarchical process. Hierarchy theory predicts that habitat suitability is influenced by the interaction of factors at multiple spatial scales from the microsite to the landscape and that higher‐order factors impose constraints at lower levels. For instance, large‐scale factors such as landscape context may make a site unsuitable for a species even if the vegetation structure and composition are appropriate. In addition, the spatial arrangement of habitat elements at all scales must be considered when planning restoration efforts. For example, the presence of snags does not ensure that the site will be suitable for snag‐dependent species. The size, age, and spacing of snags and their juxtaposition to other habitat elements must also be considered. Finally, all habitats are dynamic, and therefore the ecological processes that contribute to those dynamics must be maintained or suitable substitutes included in the recovery plan. When considering restoring habitat for wildlife, we recommend that managers: (1) identify the wildlife species they want to target for restoration efforts, (2) consider the size and landscape context of the restoration site and whether it is appropriate for the target species, (3) identify the habitat elements that are necessary for the target species, (4) develop a strategy for restoring those elements and the ecological processes that maintain them, and (5) implement a long‐term monitoring program to gauge the success of the restoration efforts.     

Habitat split as a driver of disease in amphibians

Anthropogenic habitat disturbance is fundamentally altering patterns of disease transmission and immunity across the vertebrate tree of life. Most studies linking anthropogenic habitat change and disease focus on habitat loss and fragmentation, but these processes often lead to a third process that is equally important: habitat split. Defined as spatial separation between the multiple classes of natural habitat that many vertebrate species require to complete their life cycles, habitat split has been linked to population declines in vertebrates, e.g. amphibians breeding in lowland aquatic habitats and overwintering in fragments of upland terrestrial vegetation. Here, we link habitat split to enhanced disease risk in amphibians (i) by reviewing the biotic and abiotic forces shaping elements of immunity and (ii) through a spatially oriented field study focused on tropical frogs. We propose a framework to investigate mechanisms by which habitat split influences disease risk in amphibians, focusing on three broad host factors linked to immunity: (i) composition of symbiotic microbial communities, (ii) immunogenetic variation, and (iii) stress hormone levels. Our review highlights the potential for habitat split to contribute to host-associated microbiome dysbiosis, reductions in immunogenetic repertoire, and chronic stress, that often facilitate pathogenic infections and disease in amphibians and other classes of vertebrates. We highlight that targeted habitat-restoration strategies aiming to connect multiple classes of natural habitats (e.g. terrestrial–freshwater, terrestrial–marine, marine–freshwater) could enhance priming of the vertebrate immune system through repeated low-load exposure to enzootic pathogens and reduced stress-induced immunosuppression.     

Marine moult migration of the freshwater Scaly‐sided Merganser Mergus squamatus revealed by stable isotopes and geolocators

Scaly‐sided Mergansers Mergus squamatus breed on freshwater rivers in far eastern Russia, Korea and China, wintering in similar habitats in China and Korea, but nothing was known of their moulting habitat. To investigate the moult strategies of this species, we combined wing feather stable isotope ratios (males and females) with geolocator data (nesting females) to establish major habitat types (freshwater, brackish or saltwater) used by both sexes during wing moult. Although most Scaly‐sided Mergansers of both sexes probably moult on freshwater, some males and non‐breeding and failed breeding females appeared to undertake moult migration to brackish and marine waters. Given the previous lack of any surveys of coastal or estuarine waters for this species during the moult period, these findings suggest important survey needs for the effective conservation of the species during the flightless moult period.     

Restoration for variability: emergence of the habitat diversity paradigm in terrestrial ecosystem restoration

Ecosystem restoration implies focusing on multiple trophic levels and ecosystem functioning, yet higher trophic levels, that is, animals, are less frequently targeted by restoration than plants. Habitat diversity, the spatial heterogeneity between and within habitat patches in a landscape, is a well‐known driver of species diversity, and offers possible ways to increase species diversity at multiple trophic levels. We argue that habitat diversity is central in whole‐ecosystem restoration as we review its importance, provide a practical definition for its components, and propose ways to target it in restoration. Restoration targeting habitat diversity is used commonly in aquatic ecosystems, mostly to increase the physical diversity of habitats, meant to provide more niches available to a higher number of animal species. To facilitate the uptake of habitat diversity in terrestrial ecosystem restoration, we distinguish between compositional and structural habitat diversity, because different animal groups will respond to different aspects of habitat diversity. We also propose four methods to increase habitat diversity: varying the starting conditions to obtain divergent successional pathways, emulating natural disturbances, establishing keystone structures, and applying ecosystem engineer species. We provide two case studies to illustrate how these components and methods can be incorporated in restoration. We conclude that targeting habitat diversity is a promising way to restore habitats for a multitude of species of animals and plants, and that it should become mainstream in restoration ecology and practice. We encourage the restoration community to consider compositional and structural habitat diversity and to specifically target habitat diversity in ecosystem restoration.     

Reintroduction of freshwater macroinvertebrates: challenges and opportunities

Species reintroductions – the translocation of individuals to areas in which a species has been extirpated with the aim of re‐establishing a self‐sustaining population – have become a widespread practice in conservation biology. Reintroduction projects have tended to focus on terrestrial vertebrates and, to a lesser extent, fishes. Much less effort has been devoted to the reintroduction of invertebrates into restored freshwater habitats. Yet, reintroductions may improve restoration outcomes in regions where impoverished regional species pools limit the self‐recolonisation of restored freshwaters. We review the available literature on macroinvertebrate reintroductions, focusing on identifying the intrinsic and extrinsic factors that determine their success or failure. Our study reveals that freshwater macroinvertebrate reintroductions remain rare, are often published in the grey literature and, of the attempts made, approximately one‐third fail. We identify life‐cycle complexity and remaining stressors as the two factors most likely to affect reintroduction success, illustrating the unique challenges of freshwater macroinvertebrate reintroductions. Consideration of these factors by managers during the planning process and proper documentation – even if a project fails – may increase the likelihood of successful outcomes in future reintroduction attempts of freshwater macroinvertebrates.     

Pulmonate phylogeny based on 28S rRNA gene sequences: a framework for discussing habitat transitions and character transformation

Pulmonate snails occupy a wide range of marine, estuarine, freshwater and terrestrial environments. Non-terrestrial forms are supposed to be basal in pulmonate evolution but the group's phylogeny is not well resolved either morphologically or on the basis of available DNA sequence data. The lack of a robust phylogeny makes it difficult to understand character polarization and habitat transformation in pulmonates. We have investigated pulmonate relationships using 27 new sequences of 28S rRNA from pulmonates and outgroups, augmented with data from GenBank. The complete alignments comprised about 3.8kb. Maximum parsimony, maximum likelihood and Bayesian analyses of alignments generated under different assumptions are reported. Complete alignments appear to have a degree of substitution saturation so where there is conflict between hypothesised relationships more weight is given to analyses where regions of random similarity are excluded and which are not affected by this complication. Monophyly of the five main pulmonate groups was robustly supported in almost all analyses. The marine group Amphiboloidea and the freshwater Glacidorbidae are the most basal. The remaining pulmonates (Siphonariidae, Hygrophila and Eupulmonata) form a moderately-supported monophyletic group in all analyses bar one probably affected by saturation of substitutions. Siphonariidae, a predominantly marine and intertidal family, and Eupulmonata (mainly terrestrial with marine, estuarine and freshwater species) form a strongly supported clade that is the sister group to Hygrophila (freshwater). Multiple colonizations of freshwater and terrestrial habitats by pulmonate snails are suggested. No analyses strongly support the possibility of habitat reversions. The colonizations of freshwater by Hygrophila and of land by Stylommatophora were apparently phylogenetically independent although it cannot yet be excluded that there were transient terrestrial phases in the history of the former group or freshwater phases in the latter.     

Effects of Flow Restoration and Exotic Species Removal on Recovery of Native Fish: Lessons from a Dam Decommissioning

Flow diversion and invasive species are two major threats to freshwater ecosystems, threats that restoration efforts attempt to redress. Yet, few restoration projects monitor whether removal of these threats improve target characteristics of the ecosystem. Fewer still have an appropriate experimental design from which causal inferences can be drawn as to the relative merits of removing exotic fish, restoring flow, or both. We used a dam decommissioning in Fossil Creek, Arizona, to compare responses of native fish to exotic fish removal and flow restoration, using a before‐after‐control‐impact design with three impact treatments: flow restoration alone where exotics had not been present, flow restoration and exotic fish removal, and flow restoration where exotics remain and a control reach that was unaffected by restoration actions. We show that removal of exotic fish dramatically increased native fish abundance. Flow restoration also increased native fish abundance, but the effect was smaller than that from removing exotics. Flow restoration had no effect where exotic fish remained, although it may have had other benefits to the ecosystem. The cost to restore flow ($12 million) was considerably higher than that to eradicate exotics ($1.1 million). The long‐term influence of flow restoration could increase, as travertine dams grow and re‐shape the creek increasing habitat for native fish. But in the 2‐year period considered here, the return on investment for extirpating exotics far exceeded that from flow restoration. Projects aimed to restore native fish by restoring flow should also consider the additional investment required to eradicate exotic fish.     

Freshwater Habitat Restoration Actions in the Pacific Northwest: A Decade's Investment in Habitat Improvement

Across the Pacific Northwest (PNW), both public and private agents are working to improve riverine habitat for a variety of reasons, including improving conditions for threatened and endangered salmon. These projects are moving forward with little or no knowledge of specific linkages between restoration actions and the responses of target species. Targeted effectiveness monitoring of these actions is required to redress this lack of mechanistic understanding, but such monitoring depends on detailed restoration information—that is, implementation monitoring. This article describes the process of assembling a database of restoration projects intended to improve stream and river habitat throughout the PNW. We designed the database specifically to address the needs of regional monitoring programs that evaluate the effectiveness of restoration actions. The database currently contains spatially referenced, project‐level data on over 23,000 restoration actions initiated at over 35,000 locations in the last 15 years (98% of projects report start or end dates between 1991 and 2005) in the states of Washington, Oregon, Idaho, and Montana. Data sources included federal, state, local, nongovernmental organization, and tribal contributors. The process of database production identified difficulties in the design of regional project tracking systems. The technical design issues range from low‐level information such as what defines a project or a location to high‐level issues that include data validation and legalities of interagency data sharing. The completed database will inform efficient monitoring design, effectiveness assessments, and restoration project planning.     

Migration strategy and pathogen risk: non‐breeding distribution drives malaria prevalence in migratory waders

Pathogen exposure has been suggested as one of the factors shaping the myriad of migration strategies observed in nature. Two hypotheses relate migration strategies to pathogen infection: the ‘avoiding the tropics hypothesis’ predicts that pathogen prevalence and transmission increase with decreasing non‐breeding (wintering) latitude, while the “habitat selection hypothesis” predicts lower pathogen prevalence in marine than in freshwater habitats. We tested these scarcely investigated hypotheses by screening wintering and resident wading shorebirds (Charadriiformes) for avian malaria blood parasites (Plasmodium and Haemoproteus spp.) along a latitudinal gradient in Australia. We sequenced infections to determine if wintering migrants share malaria parasites with local shorebird residents, and we combined prevalence results with published data in a global comparative analysis. Avian malaria prevalence in Australian waders was 3.56% and some parasite lineages were shared between wintering migrants and residents, suggesting active transmission at wintering sites. In the global dataset, avian malaria prevalence was highest during winter and increased with decreasing wintering latitude, after controlling for phylogeny. The latitudinal gradient was stronger for waders that use marine and freshwater habitats (marine + freshwater) than for marine‐restricted species. Marine + freshwater wader species also showed higher overall avian malaria parasite prevalence than marine‐restricted species. By combining datasets in a global comparative analysis, we provide empirical evidence that migratory waders avoiding the tropics during the non‐breeding season experience a decreased risk of malaria parasite infection. We also find global support for the hypothesis that marine‐restricted shorebirds experience lower parasite pressures than shorebirds that also use freshwater habitats. Our study indicates that pathogen transmission may be an important driver of site selection for non‐breeding migrants, a finding that contributes new knowledge to our understanding of how migration strategies evolve.     

Comparison of potential increases in juvenile salmonid rearing habitat capacity among alternative restoration scenarios,Trinity River,California

River restoration plans often propose multiple rehabilitation actions to address key habitat impairments, but they rarely attempt to quantify the potential benefits of alternative sets of actions for targeted biota. We use geomorphic and biological analyses to estimate restoration potential under three alternative scenarios for a 64‐km section of the Trinity River, California, between the North Fork Trinity River and Lewiston Dam, which is the focus of habitat rehabilitation efforts under the Trinity River Restoration Program. The three scenarios are (1) increasing habitat quality by wood additions and alcove construction, (2) increasing habitat quantity by increasing sinuosity and side‐channel length, and (3) increasing both habitat quality and quantity. For each scenario, we used existing stream habitat and juvenile salmonid data from previous studies to estimate potential improvements in fry or pre‐smolt production. The potential increase in Oncorhynchus tshawytscha (Chinook salmon) and O. mykiss (steelhead) fry rearing capacity was 62 and 67%, respectively, for Scenario 1 (increasing habitat quality), and 36 and 44% for Scenario 2 (increasing habitat quantity). Only the most optimistic Scenario 3 (increasing both habitat quality and quantity) more than doubles potential juvenile salmonid production (112% increase in Chinook fry capacity and 107% increase in steelhead fry capacity). These quantitative predictions are useful in developing realistic restoration targets and evaluating whether proposed restoration actions can achieve the aims of a restoration program.     

Plant Species Redundancy and the Restoration of Faunal Habitat: Lessons from Plant‐Dwelling Bugs

Restoring disturbed lands is essential for conserving biodiversity. In floristically diverse regions, restoring all plant species following anthropogenic disturbance is financially costly and it is unknown if this can be achieved. However, re‐creating faunal habitat may not require reinstating all plant species if there is a high degree of redundancy. Here, we assess whether there is redundancy among a subset of native plant species chosen to restore fauna habitat following a severe disturbance. Additionally, we determine if reestablished plants support similar faunal assemblages as the same plant species in less disturbed forest. We sampled plant‐dwelling Hemiptera from 1,800 plants across 16 species. We found 190 species of Hemiptera, with most plant species in the forest having distinct hemipteran assemblages. Returning these plant species to areas undergoing restoration reinstated 145 hemipteran species, including the dominant species. Recalcitrant plant species (difficult to propagate and reestablish in restored areas) had different hemipteran assemblages from all other species. There was only one plant species that did not have a distinct assemblage and thus was considered redundant. We conclude that there is little redundancy in this study. For plant‐dwelling Hemiptera (with good powers of dispersal) to recolonize restored areas, restoration efforts will need to reinstate at least 13 of the 16 species of host plant of appropriate age and structure. Consequently, to meet the goal of restoring fauna habitat when there is no knowledge of which plant species are redundant, restoration projects should aim to reinstate all plant species present in less disturbed reference areas.     

The importance of ecological and behavioural data in studies of hybridisation among marine fishes

Natural hybridisation is a widespread phenomenon, particularly well documented in terrestrial and freshwater ecosystems, where it has been ascribed substantial evolutionary and adaptive relevance. Hybridisation has received comparatively less attention in marine systems, though there has been a recent surge of reported marine hybrids, particularly among corals and fishes. This review summarises the current knowledge of hybridisation in marine fishes, with a focus on ecological and behavioural factors that may play a role in hybridisation processes. Rarity of one or both parental species within the hybrid zone, overlap in habitat use, dietary overlap and the breakdown in assortative mating appear to have a role in facilitating hybridisation. Despite this, most of the recent literature on marine fish hybridisation has a strong genetic focus, with little or no quantitative information about the ecological and behavioural factors that initiate or facilitate hybridisation. Future studies should attempt to gather ecological and behavioural data from hybrid zones, thus teasing out which processes are most relevant to overcoming pre-zygotic barriers to reproductive isolation. Not only will this advance our understanding of the adaptive and evolutionary relevance of hybridisation in marine fishes, but it will also provide unique insights into the maintenance of reproductive isolation and the process of speciation in the marine environment.     

Multiple Interception Pathways for Resource Utilisation and Increased Ecosystem Resilience

Natural ecosystems consist of multiple pathways for resource capture and energy flow. As landscapes become impacted, the diversity of these pathways is reduced and ecosystem health suffers. Efficient resource processing is essential for successful ecosystem restoration and yet little information is available relating the two issues. Disturbances to terrestrial, marine, and freshwater environments have decreased the complexity of such ecosystems thus reducing their resilience to increases in resource loading from anthropogenic sources. The effects of a reduction in the number of pathways are observed in terminal water bodies where increased levels of nutrients are not successfully intercepted beforehand, and conditions often favour a single phytoplankton pathway, resulting in algal blooms. If a suitable number of pathways is restored, significant amounts of resources may be retained, reducing the impacts on downstream ecosystems. The restoration of functional diversity is likely to provide process redundancy and therefore improve ecosystem resilience to further disturbance. This concept provides a more holistic approach to management strategies that may enhance resource interception, while restoring habitat and biological diversity.     

Response of medium‐ and large‐sized terrestrial fauna to corridor restoration along the middle Sacramento River

A fundamental challenge in restoration ecology is to understand when species are expected to colonize newly created habitat. Determining this is important for assessing progress toward restoration goals and, more generally, for gaining insight into ecosystem functioning and dynamics. We studied this question as it relates to mid‐ to large‐sized terrestrial fauna in restored riparian habitats at the Sacramento River National Wildlife Refuge, in northern California. We used camera traps to document use of 16 riparian corridor sites of varying restoration age. Comparisons of species richness (diversity) and visitation frequency (activity) were made across different‐aged sites. We found that predator diversity and activity levels tended to be higher in restored forests than in remnant forests, and that they tended to be highest in young restored forests. This trend persisted when data from variable sampling periods were pooled, although significant differences occurred more often in wet and cold sampling periods. The trend did not always hold for the animal community at large (consisting of both predator and non‐predator species). We conclude that restoration age affects predator diversity and activity levels in restored and remnant floodplain forests, and that predator communities can establish soon after restoration. Our results suggest that restoring natural river processes that promote habitat regeneration may benefit mid‐ to large‐sized terrestrial predators that appear to mostly use early successional habitat.     

Restoring Stream Ecosystems: Lessons from a Midwestern State

Reach‐scale stream restorations are becoming a common approach to repair degraded streams, but the effectiveness of these projects is rarely evaluated or reported. We surveyed governmental, private, and nonprofit organizations in the state of Indiana to determine the frequency and nature of reach‐scale stream restorations in this midwestern U.S. state. For 10 attempted restorations in Indiana, questionnaires and on‐site assessments were used to better evaluate current designs for restoring stream ecosystems. At each restoration site, habitat and water quality were evaluated in restored and unrestored reaches. Our surveys identified commonalities across all restorations, including the type of restoration, project goals, structures installed, and level of monitoring conducted. In general, most restorations were described as stream‐relocation projects that combined riparian and in‐stream enhancements. Fewer than half of the restorations conducted pre‐ or post‐restoration monitoring, and most monitoring involved evaluations of riparian vegetation rather than aquatic variables. On‐site assessments revealed that restored reaches had significantly lower stream widths and greater depths than did upstream unrestored reaches, but riparian canopy cover often was lower in restored than in unrestored reaches. This study provides basic information on midwestern restoration strategies, which is needed to identify strengths and weaknesses in current practices and to better inform future stream restorations.     

Cost‐effective ecological restoration

Ecological restoration is a multibillion dollar industry critical for improving degraded habitat. However, most restoration is conducted without clearly defined success measures or analysis of costs. Outcomes are influenced by environmental conditions that vary across space and time, yet such variation is rarely considered in restoration planning. Here, we present a cost‐effectiveness analysis of terrestrial restoration methods to determine how practitioners may restore the highest native plant cover per dollar spent. We recorded costs of 120 distinct methods and described success in terms of native versus non‐native plant germination, growth, cover, and density. We assessed effectiveness using a basic, commonly used metric (% native plant cover) and developed an index of cost‐effectiveness (% native cover per dollar spent on restoration). We then evaluated success of multiple methods, given environmental variation across topography and multiple years, and found that the most successful method for restoring high native plant cover is often different from the method that results in the largest area restored per dollar expended, given fixed mitigation budgets. Based on our results, we developed decision‐making trees to guide practitioners through established phases of restoration—site preparation, seeding and planting, and maintenance. We also highlight where additional research could inform restoration practice, such as improved seasonal weather forecasts optimizing allocation of funds in time or valuation practices that include costs of specific outcomes in the collection of in lieu fees.     

Non-native species limit stream restoration benefits for brook trout

Success of stream restoration can be difficult to define because many interacting abiotic and biotic factors across spatio-temporal scales can have measurable effects. Consequently, failure in habitat restoration to achieve targeted biological goals may reflect interactions of habitat restoration with unaccounted risks that have yet to be addressed on the landscape. This is particularly true within invaded landscapes, where habitat restoration can benefit non-native competitors as much as the native fishes for which restoration is designed. We tested for interacting effects of a reach scale habitat restoration effort and non-native trout competition on habitat use by a brook trout (Salvelinus fontinalis) metapopulation within a productive main stem corridor of the Shavers Fork watershed, West Virginia. We used a joint species occupancy model within a BACI sampling design to show that brook trout occupancy of main stem habitat was highest post-restoration within restored sampling reaches, but this benefit to native brook trout was conditional on brown trout (Salmo trutta) not being present within the main stem habitat. Collectively these results indicate that habitat restoration was only beneficial for native brook trout when non-native trout were absent from the restored sampling area. Proactive approaches to restoration will be integral for supporting resilient ecosystems in response to future anthropogenic threats (e.g. climate change), and we have shown that such actions will only be successful if non-native competitors do not also benefit from the restoration actions.     

Macro‐Tidal Salt Marsh Ecosystem Response to Culvert Expansion

The purpose of this paper was to examine the vegetative, sedimentary, nekton and hydrologic conditions pre‐restoration and the initial 2 years post‐restoration at a partially restricted macro‐tidal salt marsh site. Replacement of the culvert increased tidal flow by 88%. This was instrumental in altering the geomorphology of the site, facilitating the creation of new salt marsh pannes, expansion of existing pannes in the mid and high marsh zones, and expansion of the tidal creek network by incorporating relict agricultural ditches. In addition, the increase in area flooded resulted in a significant increase in nekton use, fulfilling the mandate of a federal habitat compensation program to increase and improve the overall availability and accessibility of fish habitat. The restoration of a more natural hydrological regime also resulted in the die‐off of freshwater and terrestrial vegetation along the upland edge of the marsh. Two years post‐restoration, Salicornia europea (glasswort) and Atriplex glabriuscula (marsh orache), were observed growing in these die‐back areas. Similar changes in the vegetation community structure were not observed at the reference site; however, the latter did contain higher species richness. This study represents the first comprehensive, quantitative analysis of ecological response to culvert replacement in a hypertidal ecosystem. These data will contribute to the development of long‐term data sets of pre‐ and post‐restoration, and reference marsh conditions to determine if a marsh is proceeding as expected, and to help with models that are aimed at predicting the response of marshes to tidal restoration at the upper end of the tidal spectrum.