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Diversity, Volume 3, Issue 3 (September 2011), Pages 296-546

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Research

Jump to: Review

Open AccessArticle Juvenile Coral Abundance Has Decreased by More Than 50% in Only Three Decades on a Small Caribbean Island
Diversity 2011, 3(3), 296-307; doi:10.3390/d3030296
Received: 30 April 2011 / Revised: 9 June 2011 / Accepted: 13 June 2011 / Published: 27 June 2011
Cited by 17 | PDF Full-text (2401 KB) | HTML Full-text | XML Full-text
Abstract
A comparison of the community structure of juvenile hermatypic corals of 2 to 37 m depth at the fringing reefs of Curaçao between 1975 and 2005 shows a decline of 54.7% in juvenile coral abundance and a shift in species composition. Agaricia species
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A comparison of the community structure of juvenile hermatypic corals of 2 to 37 m depth at the fringing reefs of Curaçao between 1975 and 2005 shows a decline of 54.7% in juvenile coral abundance and a shift in species composition. Agaricia species and Helioseris cucullata, the most common juveniles in 1975, showed the largest decline in juvenile abundance (a 9 and 120 fold decrease in density respectively) with Helioseris cucullata being nearly extirpated locally. In 2005, Porites astreoides contributed most colonies to the juvenile coral community, increasing from 8.2% (in 1975) to 19.9% of the total juvenile community. Between 1975 and 2005, juveniles of brooding species decreased in relative abundance while the abundance of juveniles of broadcast spawning species increased or remained the same. These data illustrate the magnitude of the changes that have occurred in only three decades in the composition of juvenile coral communities. Full article
(This article belongs to the Special Issue Coral Reef Diversity: Climate Change and Coral Reef Degradation)
Open AccessArticle Soil Rhizosphere Microbial Communities and Enzyme Activities under Organic Farming in Alabama
Diversity 2011, 3(3), 308-328; doi:10.3390/d3030308
Received: 22 April 2011 / Revised: 20 June 2011 / Accepted: 27 June 2011 / Published: 19 July 2011
Cited by 15 | PDF Full-text (1213 KB) | HTML Full-text | XML Full-text
Abstract
Evaluation of the soil rhizosphere has been limited by the lack of robust assessments that can explore the vast complex structure and diversity of soil microbial communities. Our objective was to combine fatty acid methyl ester (FAME) and pyrosequencing techniques to evaluate soil
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Evaluation of the soil rhizosphere has been limited by the lack of robust assessments that can explore the vast complex structure and diversity of soil microbial communities. Our objective was to combine fatty acid methyl ester (FAME) and pyrosequencing techniques to evaluate soil microbial community structure and diversity. In addition, we evaluated biogeochemical functionality of the microbial communities via enzymatic activities of nutrient cycling. Samples were taken from a silt loam at 0–10 and 10–20 cm in an organic farm under lettuce (Lactuca sativa), potato (Solanum tuberosum), onion (Allium cepa L), broccoli (Brassica oleracea var. botrytis) and Tall fescue pasture grass (Festuca arundinacea). Several FAMEs (a15:0, i15:0, i15:1, i16:0, a17:0, i17:0, 10Me17:0, cy17:0, 16:1ω5c and 18:1ω9c) varied among the crop rhizospheres. FAME profiles of the soil microbial community under pasture showed a higher fungal:bacterial ratio compared to the soil under lettuce, potato, onion, and broccoli. Soil under potato showed higher sum of fungal FAME indicators compared to broccoli, onion and lettuce. Microbial biomass C and enzyme activities associated with pasture and potato were higher than the other rhizospheres. The lowest soil microbial biomass C and enzyme activities were found under onion. Pyrosequencing revealed significant differences regarding the maximum operational taxonomic units (OTU) at 3% dissimilarity level (roughly corresponding to the bacterial species level) at 0–10 cm (581.7–770.0) compared to 10–20 cm (563.3–727.7) soil depths. The lowest OTUs detected at 0–10 cm were under broccoli (581.7); whereas the lowest OTUs found at 10–20 cm were under potato (563.3). The predominant phyla (85%) in this soil at both depths were Bacteroidetes (i.e., Flavobacteria, Sphingobacteria), and Proteobacteria. Flavobacteriaceae and Xanthomonadaceae were predominant under broccoli. Rhizobiaceae, Hyphomicrobiaceae, and Acidobacteriaceae were more abundant under pasture compared to the cultivated soils under broccoli, potato, onion and lettuce. This study found significant differences in microbial community structure and diversity, and enzyme activities of nutrient cycling in this organic farming system under different rhizospheres, which can have implications in soil health and metabolic functioning, and the yield and nutritional value of each crop. Full article
Open AccessArticle Species Richness and Community Structure on a High Latitude Reef: Implications for Conservation and Management
Diversity 2011, 3(3), 329-355; doi:10.3390/d3030329
Received: 19 April 2011 / Revised: 12 July 2011 / Accepted: 13 July 2011 / Published: 19 July 2011
Cited by 6 | PDF Full-text (1596 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
In spite of the wealth of research on the Great Barrier Reef, few detailed biodiversity assessments of its inshore coral communities have been conducted. Effective conservation and management of marine ecosystems begins with fine-scale biophysical assessments focused on diversity and the architectural species
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In spite of the wealth of research on the Great Barrier Reef, few detailed biodiversity assessments of its inshore coral communities have been conducted. Effective conservation and management of marine ecosystems begins with fine-scale biophysical assessments focused on diversity and the architectural species that build the structural framework of the reef. In this study, we investigate key coral diversity and environmental attributes of an inshore reef system surrounding the Keppel Bay Islands near Rockhampton in Central Queensland, Australia, and assess their implications for conservation and management. The Keppels has much higher coral diversity than previously found. The average species richness for the 19 study sites was ~40 with representatives from 68% of the ~244 species previously described for the southern Great Barrier Reef. Using scleractinian coral species richness, taxonomic distinctiveness and coral cover as the main criteria, we found that five out of 19 sites had particularly high conservation value. A further site was also considered to be of relatively high value. Corals at this site were taxonomically distinct from the others (representatives of two families were found here but not at other sites) and a wide range of functionally diverse taxa were present. This site was associated with more stressful conditions such as high temperatures and turbidity. Highly diverse coral communities or biodiversity ‘hotspots’ and taxonomically distinct reefs may act as insurance policies for climatic disturbance, much like Noah’s Arks for reefs. While improving water quality and limiting anthropogenic impacts are clearly important management initiatives to improve the long-term outlook for inshore reefs, identifying, mapping and protecting these coastal ‘refugia’ may be the key for ensuring their regeneration against catastrophic climatic disturbance in the meantime. Full article
(This article belongs to the Special Issue Coral Reef Diversity: Climate Change and Coral Reef Degradation)
Open AccessArticle Infection Dynamics Vary between Symbiodinium Types and Cell Surface Treatments during Establishment of Endosymbiosis with Coral Larvae
Diversity 2011, 3(3), 356-374; doi:10.3390/d3030356
Received: 12 July 2011 / Accepted: 18 July 2011 / Published: 19 July 2011
Cited by 8 | PDF Full-text (540 KB) | HTML Full-text | XML Full-text
Abstract
Symbioses between microbes and higher organisms underpin high diversity in many ecosystems, including coral reefs, however mechanisms underlying the early establishment of symbioses remain unclear. Here we examine the roles of Symbiodinium type and cell surface recognition in the establishment of algal endosymbiosis
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Symbioses between microbes and higher organisms underpin high diversity in many ecosystems, including coral reefs, however mechanisms underlying the early establishment of symbioses remain unclear. Here we examine the roles of Symbiodinium type and cell surface recognition in the establishment of algal endosymbiosis in the reef-building coral, Acropora tenuis. We found 20–70% higher infection success (proportion of larvae infected) and five-fold higher Symbiodinium abundance in larvae exposed to ITS-1 type C1 compared to ITS-1 type D in the first 96 h following exposure. The highest abundance of Symbiodinium within larvae occurred when C1-type cells were treated with enzymes that modified the 40–100 kD glycome, including glycoproteins and long chain starch residues. Our finding of declining densities of Symbiodinium C1 through time in the presence of intact cell surface molecules supports a role for cell surface recognition molecules in controlling post-phagocytosis processes, leading to rejection of some Symbiodinium types in early ontogeny. Reductions in the densities of unmodified C1 symbionts after 96 h, in contrast to increases in D symbionts may suggest the early initiation of a winnowing process contributing to the establishment of Symbiodinium D as the dominant type in one-month old juveniles of A. tenuis. Full article
(This article belongs to the Special Issue Coral Reef Diversity: Climate Change and Coral Reef Degradation)
Open AccessArticle Genetic Risk Assessment of a Threatened Remnant Population of Hairy Prairie-Clover (Dalea villosa var. villosa) in the Canadian Prairie
Diversity 2011, 3(3), 375-389; doi:10.3390/d3030375
Received: 4 June 2011 / Revised: 13 July 2011 / Accepted: 28 July 2011 / Published: 8 August 2011
Cited by 1 | PDF Full-text (654 KB) | HTML Full-text | XML Full-text
Abstract
Hairy prairie-clover [Dalea villosa (Nutt.) Spreng. var. villosa] is a threatened Canadian wildflower. To facilitate the efforts of conserving this threatened plant, amplified fragment length polymorphism (AFLP) technique was applied to assess genetic diversity in a remnant hairy prairie-clover population
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Hairy prairie-clover [Dalea villosa (Nutt.) Spreng. var. villosa] is a threatened Canadian wildflower. To facilitate the efforts of conserving this threatened plant, amplified fragment length polymorphism (AFLP) technique was applied to assess genetic diversity in a remnant hairy prairie-clover population in the Canadian Prairie. Three AFLP primer pairs were employed to genotype 610 individual plants from the population and 15 plants from a North Dakota composite population, and 100 polymorphic AFLP bands were analyzed. The assayed plants displayed 23% AFLP variation present between the remnant population and the North Dakota composite population, but maintained a high level (91%) of AFLP variation within patches of the remnant population. The individual genetic distinctiveness measured by average AFLP dissimilarity was positively associated with latitude and negatively with elevation. The among-patch AFLP variation was significantly related to inter-patch distance, indicating local genetic differentiation within the remnant population. However, the proportions of within-patch AFLP variation were not associated with any patch characteristics assessed (i.e., patch size, perimeter, nearest neighbor distance, mean inter-patch distance). No fine-scale genetic structure was found within three large patches, suggesting little genetic correlations present for plants five meters apart. Some genetically distinctive and diverse patches were also identified. These findings indicate that the genetic risk of the remnant hairy prairie-clover population in the Canadian Prairie is low. Full article
Open AccessArticle No Evidence for Temporal Variation in a Cryptic Species Community of Freshwater Amphipods of the Hyalella azteca Species Complex
Diversity 2011, 3(3), 390-404; doi:10.3390/d3030390
Received: 30 June 2011 / Accepted: 27 July 2011 / Published: 8 August 2011
Cited by 8 | PDF Full-text (613 KB) | HTML Full-text | XML Full-text
Abstract
The co-occurrence of cryptic species of Hyalella amphipods is a challenge to our traditional views of how species assemble. Since these species have similar morphologies, it is not evident that they have developed phenotypic differences that would allow them to occupy different ecological
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The co-occurrence of cryptic species of Hyalella amphipods is a challenge to our traditional views of how species assemble. Since these species have similar morphologies, it is not evident that they have developed phenotypic differences that would allow them to occupy different ecological niches. We examined the structure of a community of Hyalella amphipods in the littoral zone of a boreal lake to verify if temporal variation was present in relative abundances. Morphological and molecular analyses using the mitochondrial cytochrome c oxidase I (COI) gene enabled us to detect three cryptic species at the study site. No temporal variation was observed in the community, as one cryptic species was always more abundant than the two others. The relative abundances of each species in the community appeared constant at least for the open-water season, both for adult and juvenile amphipods. Niche differences are still to be found among these species, but it is suggested that migration from nearby sites may be an important factor explaining the species co-occurrence. Full article
(This article belongs to the Special Issue Spatial and Temporal Benthic Diversity Patterns)
Open AccessArticle Diversity, Stand Characteristics and Spatial Aggregation of Tree Species in a Bangladesh Forest Ecosystem
Diversity 2011, 3(3), 453-465; doi:10.3390/d3030453
Received: 11 May 2011 / Revised: 27 July 2011 / Accepted: 9 August 2011 / Published: 16 August 2011
Cited by 1 | PDF Full-text (24994 KB) | HTML Full-text | XML Full-text
Abstract
Assessing biodiversity and the spatial structures of forest ecosystems are important for forestry and nature conservation. However, tropical forests of Bangladesh are only sparsely investigated. Here we determined biodiversity (alpha, beta and gamma), spatial species turnover and stand characteristics of one of the
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Assessing biodiversity and the spatial structures of forest ecosystems are important for forestry and nature conservation. However, tropical forests of Bangladesh are only sparsely investigated. Here we determined biodiversity (alpha, beta and gamma), spatial species turnover and stand characteristics of one of the few remnant tropical forests in Bangladesh. Two differently protected areas of Satchari forest were compared. We recorded tree species composition, in a systematic plot design, measured diameter at breast height for each individual tree (to assess basal area), and calculated decay in similarity of tree species composition with geographical distance. The distance-decay was assessed separately for the whole study area and for two subsamples from Satchari National Park and Satchari Reserve Forest. Satchari National Park (strictly protected) had, despite its smaller area, a higher Alpha and Gamma diversity, but a lower Beta diversity than Satchari Reserve Forest. Variation in species composition was not significant between the two differently protected areas. Basal area increased significantly with protection status although tree individuals were of equal size in both areas. Plots in the Reserve Forest were associated with higher species turnover than in the National Park. We suggest anthropogenic disturbance, which occurs in the less strictly protected Reserve Forest, is the main driver for the detected spatial heterogeneity in species composition. Full article
Open AccessArticle Raiding the Coral Nurseries?
Diversity 2011, 3(3), 466-482; doi:10.3390/d3030466
Received: 28 June 2011 / Revised: 25 July 2011 / Accepted: 26 July 2011 / Published: 24 August 2011
Cited by 3 | PDF Full-text (459 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
A recent shift in the pattern of commercial harvest in the Keppel Island region of the southern inshore Great Barrier Reef raises concern about the depletion of a number of relatively rare restricted range taxa. The shift appears to be driven by demand
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A recent shift in the pattern of commercial harvest in the Keppel Island region of the southern inshore Great Barrier Reef raises concern about the depletion of a number of relatively rare restricted range taxa. The shift appears to be driven by demand from the United States (US) for corals for domestic aquaria. Data from the annual status reports from the Queensland Coral Fishery were compared with export trade data to the US from the Convention on International Trade in Endangered Species (CITES). Evidence was found of recent increases in the harvest of species from the Mussidae family (Acanthastrea spp.) which appears to be largely driven by demand from the US. On present trends, the industry runs the risk of localized depletion of Blastomussa and Scolymia; evidenced by an increase in the harvest of small specimens and the trend of decreasing harvest despite a concurrent increase in demand. Considering their relatively high sediment tolerance compared to other reef-building species, and the current lack of information about their functional role in reef stability, the trend raises concerns about the impact of the harvest on local coral communities. The recent shift in harvest patterns could have impacts on slow-growing species by allowing harvest beyond the rate of population regeneration. In light of these factors, combined with the value of such species to local tourism, a commercial coral fishery based on uncommon but highly sought-after species may not be ecologically sustainable or economically viable in the Keppels. Full article
(This article belongs to the Special Issue Coral Reef Diversity: Climate Change and Coral Reef Degradation)
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Open AccessArticle Greater Genetic Diversity in Spatially Restricted Coral Reef Fishes Suggests Secondary Contact among Differentiated Lineages
Diversity 2011, 3(3), 483-502; doi:10.3390/d3030483
Received: 30 June 2011 / Revised: 1 September 2011 / Accepted: 2 September 2011 / Published: 14 September 2011
Cited by 6 | PDF Full-text (1285 KB) | HTML Full-text | XML Full-text
Abstract
The maintenance of genetic diversity is a central goal of conservation. It is the raw material for evolutionary change and if lost, can accelerate extinction of species. According to theory, total genetic diversity should be less in species with restricted ranges and in
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The maintenance of genetic diversity is a central goal of conservation. It is the raw material for evolutionary change and if lost, can accelerate extinction of species. According to theory, total genetic diversity should be less in species with restricted ranges and in populations on the margins of distributional ranges, making such species or populations more vulnerable to environmental perturbations. Using mtDNA and nuclear Inter Simple Sequence Repeat (ISSR) data we investigated how the genetic diversity and structure of three con-generic species pairs of coral reef fishes (Pomacentridae) was related to species’ range size and position of populations within these ranges. Estimates of genetic structure did not differ significantly among species, but mtDNA and nucDNA genetic diversities were up to 10 times greater in spatially restricted species compared to their widespread congeners. In two of the three species pairs, the distribution of genetic variation indicated secondary contact among differentiated lineages in the spatially restricted species. In contrast, the widespread species displayed a typical signature of population expansion suggesting recent genetic bottlenecks, possibly associated with the (re) colonization of the Great Barrier Reef. These results indicate that historical processes, involving hybridization and founder effects, possibly associated with Pleistocene sea level fluctuations, have differentially influenced the widespread and spatially restricted coral reef damselfish species studied here. Full article
(This article belongs to the Special Issue Coral Reef Diversity: Climate Change and Coral Reef Degradation)
Open AccessArticle Forest Biodiversity Assessment in Relic Ecosystem: Monitoring and Management Practice Implications
Diversity 2011, 3(3), 531-546; doi:10.3390/d3030531
Received: 6 July 2011 / Revised: 25 August 2011 / Accepted: 7 September 2011 / Published: 21 September 2011
PDF Full-text (829 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The remnants of old-growth cedar forests in Lebanon are currently protected since they are taken to represent relic ecosystems sheltering many endemic, rare and endangered species. However, it is not always obvious how “natural” these forest relics are, and how the past use,
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The remnants of old-growth cedar forests in Lebanon are currently protected since they are taken to represent relic ecosystems sheltering many endemic, rare and endangered species. However, it is not always obvious how “natural” these forest relics are, and how the past use, conservation and management history have affected their current structural properties and species community composition. Even though Integrated Monitoring Programs have been initiated and developed, they are not being implemented effectively. The present research studied the effect of forest stand structure and the impacts of the anthropogenic activities effects on forest composition and floristic richness in four cedar forests in Lebanon. Horizontal and vertical structure was assessed by relying on the measurement of the physical characteristics and status of cedar trees including diversity and similarity indices. Two hundred and seventeen flora species were identified, among which 51 species were found to have biogeographical specificity and peculiar traits. The species composition seems not to be correlated with stand age structure; however, the occurrence of multiple age cedar stands favors floristic richness and variability in species composition as observed in one of the stands where the variation in diversity indices was high. In conclusion; to conserve biodiversity across landscapes, it is necessary to maintain a collection of stands of different vertical structure; an effect produced both by natural and anthropogenic disturbances since they both create a mosaic of different aged succession stands. Full article
(This article belongs to the Special Issue Biodiversity, Conservation and Ecosystem Management)

Review

Jump to: Research

Open AccessReview Novel Genetic Diversity Through Somatic Mutations: Fuel for Adaptation of Reef Corals?
Diversity 2011, 3(3), 405-423; doi:10.3390/d3030405
Received: 15 June 2011 / Revised: 26 July 2011 / Accepted: 27 July 2011 / Published: 12 August 2011
Cited by 33 | PDF Full-text (1022 KB) | HTML Full-text | XML Full-text
Abstract
Adaptation of reef corals to climate change is an issue of much debate, and often viewed as too slow a process to be of relevance over decadal time scales. This notion is based on the long sexual generation times typical for some coral
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Adaptation of reef corals to climate change is an issue of much debate, and often viewed as too slow a process to be of relevance over decadal time scales. This notion is based on the long sexual generation times typical for some coral species. However, the importance of somatic mutations during asexual reproduction and growth on evolution and adaptation (i.e., cell lineage selection) is rarely considered. Here we review the existing literature on cell lineage selection and show that the scope for somatic mutations to arise in the coral animal and associated Symbiodinium is large. For example, we estimate that ~100 million somatic mutations can arise within a branching Acropora coral colony of average size. Similarly, the large population sizes and rapid turn-over times of in hospite Symbiodinium likely result in considerable numbers of somatic mutations. While the fate of new mutations depends on many factors, including ploidy level and force and direction of selection, we argue that they likely play a key role in the evolution of reef corals. Full article
(This article belongs to the Special Issue Coral Reef Diversity: Climate Change and Coral Reef Degradation)
Open AccessReview Changes in Biodiversity and Functioning of Reef Fish Assemblages following Coral Bleaching and Coral Loss
Diversity 2011, 3(3), 424-452; doi:10.3390/d3030424
Received: 30 June 2011 / Revised: 2 August 2011 / Accepted: 3 August 2011 / Published: 12 August 2011
Cited by 39 | PDF Full-text (594 KB) | HTML Full-text | XML Full-text
Abstract
Coral reef ecosystems are increasingly subject to severe, large-scale disturbances caused by climate change (e.g., coral bleaching) and other more direct anthropogenic impacts. Many of these disturbances cause coral loss and corresponding changes in habitat structure, which has further important effects on abundance
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Coral reef ecosystems are increasingly subject to severe, large-scale disturbances caused by climate change (e.g., coral bleaching) and other more direct anthropogenic impacts. Many of these disturbances cause coral loss and corresponding changes in habitat structure, which has further important effects on abundance and diversity of coral reef fishes. Declines in the abundance and diversity of coral reef fishes are of considerable concern, given the potential loss of ecosystem function. This study explored the effects of coral loss, recorded in studies conducted throughout the world, on the diversity of fishes and also on individual responses of fishes within different functional groups. Extensive (>60%) coral loss almost invariably led to declines in fish diversity. Moreover, most fishes declined in abundance following acute disturbances that caused >10% declines in local coral cover. Response diversity, which is considered critical in maintaining ecosystem function and promoting resilience, was very low for corallivores, but was much higher for herbivores, omnivores and carnivores. Sustained and ongoing climate change thus poses a significant threat to coral reef ecosystems and diversity hotspots are no less susceptible to projected changes in diversity and function. Full article
(This article belongs to the Special Issue Coral Reef Diversity: Climate Change and Coral Reef Degradation)
Open AccessReview Frogs, Fish and Forestry: An Integrated Watershed Network Paradigm Conserves Biodiversity and Ecological Services
Diversity 2011, 3(3), 503-530; doi:10.3390/d3030503
Received: 4 August 2011 / Revised: 31 August 2011 / Accepted: 1 September 2011 / Published: 15 September 2011
Cited by 5 | PDF Full-text (3154 KB) | HTML Full-text | XML Full-text
Abstract
Successfully addressing the multitude of stresses influencing forest catchments, their native biota, and the vital ecological services they provide humanity will require adapting an integrated view that incorporates the full range of natural and anthropogenic disturbances acting on these landscapes and their embedded
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Successfully addressing the multitude of stresses influencing forest catchments, their native biota, and the vital ecological services they provide humanity will require adapting an integrated view that incorporates the full range of natural and anthropogenic disturbances acting on these landscapes and their embedded fluvial networks. The concepts of dendritic networks, disturbance domains, the stream continuum, and hydrologic connectivity can facilitate this integration. Managing catchments based on these combined concepts would better maintain all the components of watersheds and the interacting processes that comprise their ecological integrity. To examine these ideas, I review riparian protection regulations in the Pacific Northwest of the United States, regulations considered by many to be among the best available, and evaluate their ability to protect headwater amphibians. I present evidence for the inadequacy of these rules to maintain robust populations of these amphibians, and discuss the implications of these shortcomings for downstream-dwelling coho salmon. Emphasizing headwaters (1st to 3rd-order channels), I discuss disturbance regimes and how differences in their fluvial and geomorphic processes determine the structuring of channels, their internal environments, and the composition of the resident biota. I examine amphibian dependence on specific channel attributes, and discuss links between their abundances, altered attribute states, and natural and anthropogenic disturbances. Using these examples, I discuss the limitations of current protections to maintain key attributes necessary to support robust populations of headwater amphibians, and via hydrologic connectivity, many downstream organisms. I propose that the goal of maintaining whole catchment biodiversity and ecological services could be improved by managing watersheds based on integrating science-based network organizing concepts and evaluating and adjusting outcomes with a suite of responsive bio-indicators. Full article
(This article belongs to the Special Issue Biodiversity, Conservation and Ecosystem Management)
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