Better understanding of human attitudes towards sharks is essential to foster support for shark c... more Better understanding of human attitudes towards sharks is essential to foster support for shark conservation. Here, a quantitative multivariate approach was used to analyse data from questionnaire-based surveys of public attitudes towards sharks in the Galapagos Marine Reserve to identify some of the most influential socio-economic factors, emotions and beliefs that shape those attitudes. The aesthetic value of sharks, their environmental role, and their perceived dangerousness had the greatest influence on attitudes. However, attitudes also varied according to the gender, occupation, and residency status of respondents. Knowledge and experience with sharks had a moderate influence on attitudes, while behavioural responses, such as tolerance and support for the protection of sharks, showed strong correlations with attitudes. Therefore, it is recommended that efforts to promote positive attitudes and behaviours towards sharks should use strategies that encourage support for shark conservation policies by targeting the most influential emotions and beliefs held by the public.
This is an open access article under the terms of the Creative Commons Attribution License, which... more This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
The essence of the generalised multivariate Behrens-Fisher problem (BFP) is how to test the null ... more The essence of the generalised multivariate Behrens-Fisher problem (BFP) is how to test the null hypothesis of equality of mean vectors for two or more populations when their dispersion matrices differ. Solutions to the BFP usually assume variables are multivariate normal and do not handle high-dimensional data. In ecology, species' count data are often highdimensional, non-normal and heterogeneous. Also, interest lies in analysing compositional dissimilarities among whole communities in non-Euclidean (semi-metric or non-metric) multivariate space. Hence, dissimilarity-based tests by permutation (e.g., PERMANOVA, ANOSIM) are used to detect differences among groups of multivariate samples. Such tests are not robust, however, to heterogeneity of dispersions in the space of the chosen dissimilarity measure, most conspicuously for unbalanced designs. Here, we propose a modification to the PERMANOVA test statistic, coupled with either permutation or bootstrap resampling methods, as a solution to the BFP for dissimilarity-based tests. Empirical simulations demonstrate that the type I error remains close to nominal significance levels under classical scenarios known to cause problems for the unmodified test. Furthermore, the permutation approach is found to be more powerful than the (more conservative) bootstrap for detecting changes in community structure for real ecological datasets. The utility of the approach is shown through analysis of 809 species of benthic soft-sediment invertebrates from 101 sites in five areas spanning 1960 km along the Norwegian continental shelf, based on the Jaccard dissimilarity measure.
The potential effectiveness of marine protected areas (MPAs) as a conservation tool for large sha... more The potential effectiveness of marine protected areas (MPAs) as a conservation tool for large sharks has been questioned due to the limited spatial extent of most MPAs in contrast to the complex life history and high mobility of many sharks. Here we evaluated the movement dynamics of a highly migratory apex predatory shark (tiger shark Galeocerdo cuvier) at the Galapagos Marine Reserve (GMR). Using data from satellite tracking passive acoustic telemetry, and stereo baited remote underwater video, we estimated residency, activity spaces, site fidelity, distributional abundances and migration patterns from the GMR and in relation to nesting beaches of green sea turtles (Chelonia mydas), a seasonally abundant and predictable prey source for large tiger sharks. Tiger sharks exhibited a high degree of philopatry, with 93% of the total satellite-tracked time across all individuals occurring within the GMR. Large sharks (> 200 cm TL) concentrated their movements in front of the two most...
Marine ecosystems are difficult to sample quantitatively at increasing depth. Hence, few studies ... more Marine ecosystems are difficult to sample quantitatively at increasing depth. Hence, few studies attempt to measure patterns of beta diversity for ecological communities in the deep sea. Here we (i) present and quantify large-scale gradients in fish community structure along depth and latitude gradients of the New Zealand EEZ, (ii) obtain rigorous quantitative estimates of these depth (50-1200 m) and latitudinal effects (29.15-50.91°S) and their interaction, and (iii) explicitly model how latitudinal beta diversity of fishes varies with depth. The sampling design was highly structured, replicated and stratified for latitude and depth, using data obtained from 345 standardised baited remote underwater stereo-video deployments. Results showed that gradients in fish community structure along depth and latitude were strong and interactive in New Zealand waters; latitudinal variation in fish communities progressively decreased with depth following an exponential decay (r (2) = 0.96), rev...
Tropical bird assemblages display patterns of high alpha and beta diversity and, as tropical bird... more Tropical bird assemblages display patterns of high alpha and beta diversity and, as tropical birds exhibit strong habitat specificity, their spatial distributions are generally assumed to be driven primarily by environmental heterogeneity and interspecific interactions. However, spatial distributions of some Amazonian forest birds are also often restricted by large rivers and other large-scale topographic features, suggesting that dispersal limitation may also play a role in driving species' turnover. In this study, we evaluated the effects of environmental characteristics, topographic and spatial variables on variation in local assemblage structure and diversity of birds in an old-growth forest in central Amazonia. Birds were mist-netted in 72 plots distributed systematically across a 10,000 ha reserve in each of three years. Alpha diversity remained stable through time, but species composition changed. Spatial variation in bird-assemblage structure was significantly related to...
Many large, fishery-targeted predatory species have attained very high relative densities as a di... more Many large, fishery-targeted predatory species have attained very high relative densities as a direct result of protection by no-take marine reserves. Indirect effects, via interactions with targeted species, may also occur for species that are not themselves targeted by fishing. In some temperate rocky reef ecosystems, indirect effects have caused profound changes in community structure, notably the restoration of predator-urchin-macroalgae trophic cascades. Yet, indirect effects on small benthic reef fishes remain poorly understood, perhaps because of behavioral associations with complex, refuge-providing habitats. Few, if any, studies have evaluated any potential effects of marine reserves on habitat associations in small benthic fishes. We surveyed densities of small benthic fishes, including some endemic species of triplefin (Tripterygiidae), along with fine-scale habitat features in kelp forests on rocky reefs in and around multiple marine reserves in northern New Zealand over...
Multivariate data in ecological applications most often occur in the form of counts of species ab... more Multivariate data in ecological applications most often occur in the form of counts of species abundances in assemblages, where each species is a variable. These data do not generally conform to traditional statistical assumptions, and so special approaches and methods are needed in this context. Statisticians need to be informed about these special problems with ecological data. In addition, the rationale for complex experimental designs that is a trademark of most ecological studies needs to be well understood by applied statisticians in this area. On the other hand, successful approaches for teaching ecologists about the use of multivariate statistics include sticking to the conceptual, rather than the mathematical. I provide here an overview of the methods that have helped teaching across these two disciplines, including a general approach for the use of novel non-parametric methods in the analysis of ecological community data.
The nature of the combined effects of copper and zinc depends on species and the particular respo... more The nature of the combined effects of copper and zinc depends on species and the particular response variable being examined.
Journal of Statistical Computation and Simulation, Oct 29, 2010
Several permutation strategies are often possible for tests of individual terms in analysis-of-va... more Several permutation strategies are often possible for tests of individual terms in analysis-of-variance (ANOVA) designs. These include restricted permutations, permutation of whole groups of units, permutation of some form of residuals or some combination of these. It is unclear, especially for complex designs involving random factors, mixed models or nested hierarchies, just which permutation strategy should be used for any
The physical and chemical nature of a substratum's surface, including the presence of dissolved c... more The physical and chemical nature of a substratum's surface, including the presence of dissolved compounds or a bacterial film, may induce the settlement of invertebrate larvae. Based on previous observations of (1) enhanced recruitment of Sydney rock oysters (Saccostrea commercialis) on concrete surfaces and (2) high alkalinity at the surface of concrete due to the leaching of calcium hydroxide (Ca(OH)*) from the cement, experiments were designed to test the hypothesis that a surface containing Ca(OH), enhances settlement of oysters. The effect of a biofilm on settlement of Sydney rock oysters was also tested. The results obtained from the field experiment differed slightly from those obtained in the laboratory. In both the laboratory and the field, Ca(OH)2 had a positive effect on settlement. No significant effect of a biofilm on settlement on concrete substrata was observed in either experiment; a positive effect of a biofilm on substrata made with sand only or on sandstone was seen in both the laboratory and the field. For the substrata made with Ca(OH)2 and sand, however, the effect of a biofilm was positive in the field but negative in the lab. Although the results from the lab and field experiments were similar, the discrepancy was crucial in accepting or rejecting one of the hypotheses under test. The results of the study demonstrated that (1) the effects of a biofilm on settlement vary with the substratum and (2) these oysters can respond to a chemical cue (Ca(OH)*) in the field. The ecological implications of the ability of larvae to select a habitat in response to chemical cues are discussed.
Understanding spatial variation in biodiversity along environmental gradients is a central theme ... more Understanding spatial variation in biodiversity along environmental gradients is a central theme in ecology. Differences in species compositional turnover among sites (beta diversity) occurring along gradients are often used to infer variation in the processes structuring communities. Here, we show that sampling alone predicts changes in beta diversity caused simply by changes in the sizes of species pools. For example,
Canadian Journal of Fisheries and Aquatic Sciences, 2001
The most appropriate strategy to be used to create a permutation distribution for tests of indivi... more The most appropriate strategy to be used to create a permutation distribution for tests of individual terms in complex experimental designs is currently unclear. There are often many possibilities, including restricted permutation or permutation of some form of residuals. This paper provides a summary of recent empirical and theoretical results concerning available methods and gives recommendations for their use in univariate and multivariate applications. The focus of the paper is on complex designs in analysis of variance and multiple regression (i.e., linear models). The assumption of exchangeability required for a permutation test is assured by random allocation of treatments to units in experimental work. For observational data, exchangeability is tantamount to the assumption of independent and identically distributed errors under a null hypothesis. For partial regression, the method of permutation of residuals under a reduced model has been shown to provide the best test. For analysis of variance, one must first identify exchangeable units by considering expected mean squares. Then, one may generally produce either (i) an exact test by restricting permutations or (ii) an approximate test by permuting raw data or some form of residuals. The latter can provide a more powerful test in many situations. Résumé : La stratégie la plus appropriée pour générer une distribution de permutation en vue de tester les termes individuels d'un plan expérimental complexe n'est pas évidente à l'heure actuelle. Il y a souvent plusieurs options, dont la permutation restreinte et la permutation d'une quelconque forme des résiduels. On trouvera ici un résumé d'informations récentes empiriques et théoriques sur les méthodes disponibles, ainsi que des recommandations pour leur utilisation dans des applications unidimensionnelles et multidimensionnelles. L'emphase est mise sur les plans complexes d'analyse de variance et de régression multiple (i.e. les modèles linéaires). Dans un travail expérimental, la supposition d'échangeabilité requise pour un test par permutation est assurée par l'assignation au hasard à des unités des divers traitements. Dans le cas d'observations, l'échangeabilité équivaut à supposer que les erreurs, dans une hypothèse nulle, sont indépendantes et distribuées de façon identique. Pour la régression partielle, la méthode de permutation des résiduels dans un modèle réduit s'est avérée la meilleure. Pour l'analyse de variance, il faut d'abord identifier les unités échangeables à l'examen des carrés moyens attendus. Ensuite, il est généralement possible de produire (i) un test exact en restreignant les permutations ou alors (ii) un test approximatif en permutant les données brutes ou une forme quelconque des résiduels. Cette dernière méthode fournit, dans plusieurs situations, un test plus puissant.
Natural heterogeneity in ecological parameters, like population abundance, is more widely recogni... more Natural heterogeneity in ecological parameters, like population abundance, is more widely recognized and investigated than variability in the processes that control these parameters. Experimental ecologists have focused mainly on the mean intensity of predictor variables and have largely ignored the potential to manipulate variances in processes, which can be considered explicitly in experimental designs to explore variation in causal mechanisms. In the present study, the effect of the temporal variance of disturbance on the diversity of marine assemblages was tested in a field experiment replicated at two sites on the northeast coast of New Zealand. Fouling communities grown on artificial settlement substrata experienced disturbance regimes that differed in their inherent levels of temporal variability and timing of disturbance events, while disturbance intensity was identical across all levels. Additionally, undisturbed assemblages were used as controls. After 150 days of experimental duration, the assemblages were then compared with regard to their species richness, abundance and structure. The disturbance effectively reduced the average total cover of the assemblages, but no consistent effect of variability in the disturbance regime on the assemblages was detected. The results of this study were corroborated by the outcomes from simultaneous replicate experiments carried out in each of eight different biogeographical regions around the world.
Isolation of wildlife into fragmented populations as a consequence of anthropogenic-mediated envi... more Isolation of wildlife into fragmented populations as a consequence of anthropogenic-mediated environmental change may alter host-pathogen relationships. Our understanding of some of the epidemiological features of infectious disease in vulnerable populations can be enhanced by the use of commensal bacteria as a proxy for invasive pathogens in natural ecosystems. The distinctive population structure of a well-described meta-population of a New Zealand endangered flightless bird, the takahe (Porphyrio hochstetteri), provided a unique opportunity to investigate the influence of host isolation on enteric microbial diversity. The genomic epidemiology of a prevalent rail-associated endemic commensal bacterium was explored using core genome and ribosomal multilocus sequence typing (rMLST) of 70 Campylobacter sp. nova 1 isolated from one third of the takahe population resident in multiple locations. While there was evidence of recombination between lineages, bacterial divergence appears to have occurred and multivariate analysis of 52 rMLST genes revealed location-associated differentiation of C. sp. nova 1 sequence types. Our results indicate that fragmentation and anthropogenic manipulation of populations can influence host-microbial relationships, with potential implications for niche adaptation and the evolution of micro-organisms in remote environments. This study provides a novel framework in which to explore the complex genomic epidemiology of micro-organisms in wildlife populations.
1. Exploitation of living marine resources has resulted in major changes to populations of target... more 1. Exploitation of living marine resources has resulted in major changes to populations of targeted species and functional groups of large-bodied species in the ocean. However, the effects of overfishing and collapse of large top predators on the broad-scale biodiversity of oceanic ecosystems remain largely unexplored. 2. Populations of the Atlantic cod (Gadus morhua) were overfished and several collapsed in the early 1990s across Atlantic Canada, providing a unique opportunity to study potential ecosystem-level effects of the reduction of a dominant predator on fish biodiversity, and to identify how such effects might interact with other environmental factors, such as changes in climate, over time. 3. We combined causal modelling with model selection and multimodel inference to analyse 41 years of fishery-independent survey data (1970-2010) and quantify ecosystem-level effects of overfishing and climate variation on the biodiversity of fishes across a broad area (172 000 km 2) of the Scotian Shelf. 4. We found that alpha and beta diversity increased with decreases in cod occurrence; fish communities were less homogeneous and more variable in systems where cod no longer dominated. These effects were most pronounced in the colder northeastern parts of the Scotian Shelf. 5. Our results provide strong evidence that intensive harvesting (and collapse) of marine apex predators can have large impacts on biodiversity, with far-reaching consequences for ecological stability across an entire ecosystem.
Hagfishes from New Zealand are reviewed and a phylogeny proposed using morphological and genetic ... more Hagfishes from New Zealand are reviewed and a phylogeny proposed using morphological and genetic data (DNA sequences of cytochrome c oxidase subunit I gene, COI, and the small subunit RNA, 16S). Eptatretus cryptus sp. nov. was previously confused with Eptatretus cirrhatus (Forster in Bloch & Schneider, 1801) because of their similar morphology, and is found from the Three Kings Islands to Stewart Island and in the eastern part of the Chatham Rise (at depths of 96-922 m). Eptatretus poicilus sp. nov. is endemic to the Three Kings Islands, where it is common and associated with soft sediment and deep-sea coral-sponge habitats (114-842 m). Neomyxine caesiovitta sp. nov. is a slender hagfish found along the east coast of the North Island south to the Chatham Rise (430-1083 m). A neotype is erected for E. cirrhatus (type locality: Breaksea Sound, Fiordland), occurring widely in New Zealand coastal, shelf, and slope waters (1-922 m), but not at the Three Kings Islands. Eptatetrus goliath Mincarone & Stewart, 2006, Neomyxine biniplicata (Richardson & Jowett, 1951), and Nemamyxine elongata Richardson, 1958 are further described using additional material. Rubicundus eos (Fernholm, 1991) is still only known from the holotype (type locality: Challenger Plateau). Genetic results showed that the New Zealand Eptatretus species form a monophyletic group within the subfamily Eptatretinae, indicating likely speciation from a single common ancestor within the area. Eptatretus poicilus sp. nov. is the sister species of E. cirrhatus, and E. cryptus sp. nov. is closely associated with the clade formed by these two species. Eptatretus goliath is most closely associated with Eptatretus minor Fernholm & Hubbs, 1981 (Gulf of Mexico), these two species basally diverging within New Zealand hagfishes. The endemic genus Neomyxine forms a well-supported monophyletic group of as yet uncertain position within the phylogenetic tree. A key to the New Zealand hagfishes, fresh colour photographs, distribution maps, and in situ video recordings are presented.
Evaluating the effects of marine reserves on exploited species can be challenging because they oc... more Evaluating the effects of marine reserves on exploited species can be challenging because they occur within a context of natural spatial and temporal variation at many scales. For rigorous inferences to be made, such evaluations require monitoring programmes that are replicated at appropriate scales. We analysed monitoring data of snapper Pagrus auratus (Sparidae) in northeastern New Zealand, comprised of counts from baited-underwater-video surveys from inside and outside 3 marine reserves. Surveys were replicated at many levels, including areas inside and outside of marine reserves at 3 locations in 2 seasons, over a period of up to 14 yr, in an unbalanced design. The Bayesian modelling approach allowed the use of some familiar aspects of ANOVA, including mixed models of fixed and random effects, hierarchically nested structures, and variance decomposition, while allowing for overdispersion and excess zeros in the counts. Model selection and estimates of variance components revealed that protection by marine reserves was by far the strongest measured source of variation for relative densities of legal-sized snapper. The size of the effect varied across years among the 3 reserves, with relative densities between 7 and 20 times greater in reserves than in nearby areas. Other than the reserve effect, the temporal factors of season and year were generally more important than the spatial factors at explaining variation in counts. In particular, overall relative densities were ~2 to 3 times greater in autumn than in spring for legal-sized snapper, although the seasonal effect was also variable among locations and years. We consider that the Bayesian generalised linear mixed modelling approach, as used here, provides an extremely useful and flexible tool for estimating the effects of management actions and comparing them directly with other sources of spatial and temporal variation in natural systems.
We examined relationships between stable isotopes of carbon (delta(13)C) and oxygen (delta(18)O) ... more We examined relationships between stable isotopes of carbon (delta(13)C) and oxygen (delta(18)O) in tree rings of Callitris columellaris F. Muell in the semi-arid Pilbara region of north-western Australia. To test the hypothesis that stomatal control of photosynthesis decreases during drier periods, we developed delta(13)C and delta(18)O chronologies spanning 1919-1999, and used a permutation regression approach to relate a 21-year running correlation between delta(13)C and delta(18)O to rainfall and temperature at Marble Bar and our study site. The relationship between delta(13)C and delta(18)O switched from being always negative before 1955 to being consistently positive after 1976, suggesting an increase in stomatal control of photosynthesis in recent decades. Changes in the delta(13)C-delta(18)O relationship reflected changes in rainfall, which has increased in the region by 30% since 1976. The correlation between delta(13)C and delta(18)O was positively related to the 21-year r...
Better understanding of human attitudes towards sharks is essential to foster support for shark c... more Better understanding of human attitudes towards sharks is essential to foster support for shark conservation. Here, a quantitative multivariate approach was used to analyse data from questionnaire-based surveys of public attitudes towards sharks in the Galapagos Marine Reserve to identify some of the most influential socio-economic factors, emotions and beliefs that shape those attitudes. The aesthetic value of sharks, their environmental role, and their perceived dangerousness had the greatest influence on attitudes. However, attitudes also varied according to the gender, occupation, and residency status of respondents. Knowledge and experience with sharks had a moderate influence on attitudes, while behavioural responses, such as tolerance and support for the protection of sharks, showed strong correlations with attitudes. Therefore, it is recommended that efforts to promote positive attitudes and behaviours towards sharks should use strategies that encourage support for shark conservation policies by targeting the most influential emotions and beliefs held by the public.
This is an open access article under the terms of the Creative Commons Attribution License, which... more This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
The essence of the generalised multivariate Behrens-Fisher problem (BFP) is how to test the null ... more The essence of the generalised multivariate Behrens-Fisher problem (BFP) is how to test the null hypothesis of equality of mean vectors for two or more populations when their dispersion matrices differ. Solutions to the BFP usually assume variables are multivariate normal and do not handle high-dimensional data. In ecology, species' count data are often highdimensional, non-normal and heterogeneous. Also, interest lies in analysing compositional dissimilarities among whole communities in non-Euclidean (semi-metric or non-metric) multivariate space. Hence, dissimilarity-based tests by permutation (e.g., PERMANOVA, ANOSIM) are used to detect differences among groups of multivariate samples. Such tests are not robust, however, to heterogeneity of dispersions in the space of the chosen dissimilarity measure, most conspicuously for unbalanced designs. Here, we propose a modification to the PERMANOVA test statistic, coupled with either permutation or bootstrap resampling methods, as a solution to the BFP for dissimilarity-based tests. Empirical simulations demonstrate that the type I error remains close to nominal significance levels under classical scenarios known to cause problems for the unmodified test. Furthermore, the permutation approach is found to be more powerful than the (more conservative) bootstrap for detecting changes in community structure for real ecological datasets. The utility of the approach is shown through analysis of 809 species of benthic soft-sediment invertebrates from 101 sites in five areas spanning 1960 km along the Norwegian continental shelf, based on the Jaccard dissimilarity measure.
The potential effectiveness of marine protected areas (MPAs) as a conservation tool for large sha... more The potential effectiveness of marine protected areas (MPAs) as a conservation tool for large sharks has been questioned due to the limited spatial extent of most MPAs in contrast to the complex life history and high mobility of many sharks. Here we evaluated the movement dynamics of a highly migratory apex predatory shark (tiger shark Galeocerdo cuvier) at the Galapagos Marine Reserve (GMR). Using data from satellite tracking passive acoustic telemetry, and stereo baited remote underwater video, we estimated residency, activity spaces, site fidelity, distributional abundances and migration patterns from the GMR and in relation to nesting beaches of green sea turtles (Chelonia mydas), a seasonally abundant and predictable prey source for large tiger sharks. Tiger sharks exhibited a high degree of philopatry, with 93% of the total satellite-tracked time across all individuals occurring within the GMR. Large sharks (> 200 cm TL) concentrated their movements in front of the two most...
Marine ecosystems are difficult to sample quantitatively at increasing depth. Hence, few studies ... more Marine ecosystems are difficult to sample quantitatively at increasing depth. Hence, few studies attempt to measure patterns of beta diversity for ecological communities in the deep sea. Here we (i) present and quantify large-scale gradients in fish community structure along depth and latitude gradients of the New Zealand EEZ, (ii) obtain rigorous quantitative estimates of these depth (50-1200 m) and latitudinal effects (29.15-50.91°S) and their interaction, and (iii) explicitly model how latitudinal beta diversity of fishes varies with depth. The sampling design was highly structured, replicated and stratified for latitude and depth, using data obtained from 345 standardised baited remote underwater stereo-video deployments. Results showed that gradients in fish community structure along depth and latitude were strong and interactive in New Zealand waters; latitudinal variation in fish communities progressively decreased with depth following an exponential decay (r (2) = 0.96), rev...
Tropical bird assemblages display patterns of high alpha and beta diversity and, as tropical bird... more Tropical bird assemblages display patterns of high alpha and beta diversity and, as tropical birds exhibit strong habitat specificity, their spatial distributions are generally assumed to be driven primarily by environmental heterogeneity and interspecific interactions. However, spatial distributions of some Amazonian forest birds are also often restricted by large rivers and other large-scale topographic features, suggesting that dispersal limitation may also play a role in driving species' turnover. In this study, we evaluated the effects of environmental characteristics, topographic and spatial variables on variation in local assemblage structure and diversity of birds in an old-growth forest in central Amazonia. Birds were mist-netted in 72 plots distributed systematically across a 10,000 ha reserve in each of three years. Alpha diversity remained stable through time, but species composition changed. Spatial variation in bird-assemblage structure was significantly related to...
Many large, fishery-targeted predatory species have attained very high relative densities as a di... more Many large, fishery-targeted predatory species have attained very high relative densities as a direct result of protection by no-take marine reserves. Indirect effects, via interactions with targeted species, may also occur for species that are not themselves targeted by fishing. In some temperate rocky reef ecosystems, indirect effects have caused profound changes in community structure, notably the restoration of predator-urchin-macroalgae trophic cascades. Yet, indirect effects on small benthic reef fishes remain poorly understood, perhaps because of behavioral associations with complex, refuge-providing habitats. Few, if any, studies have evaluated any potential effects of marine reserves on habitat associations in small benthic fishes. We surveyed densities of small benthic fishes, including some endemic species of triplefin (Tripterygiidae), along with fine-scale habitat features in kelp forests on rocky reefs in and around multiple marine reserves in northern New Zealand over...
Multivariate data in ecological applications most often occur in the form of counts of species ab... more Multivariate data in ecological applications most often occur in the form of counts of species abundances in assemblages, where each species is a variable. These data do not generally conform to traditional statistical assumptions, and so special approaches and methods are needed in this context. Statisticians need to be informed about these special problems with ecological data. In addition, the rationale for complex experimental designs that is a trademark of most ecological studies needs to be well understood by applied statisticians in this area. On the other hand, successful approaches for teaching ecologists about the use of multivariate statistics include sticking to the conceptual, rather than the mathematical. I provide here an overview of the methods that have helped teaching across these two disciplines, including a general approach for the use of novel non-parametric methods in the analysis of ecological community data.
The nature of the combined effects of copper and zinc depends on species and the particular respo... more The nature of the combined effects of copper and zinc depends on species and the particular response variable being examined.
Journal of Statistical Computation and Simulation, Oct 29, 2010
Several permutation strategies are often possible for tests of individual terms in analysis-of-va... more Several permutation strategies are often possible for tests of individual terms in analysis-of-variance (ANOVA) designs. These include restricted permutations, permutation of whole groups of units, permutation of some form of residuals or some combination of these. It is unclear, especially for complex designs involving random factors, mixed models or nested hierarchies, just which permutation strategy should be used for any
The physical and chemical nature of a substratum's surface, including the presence of dissolved c... more The physical and chemical nature of a substratum's surface, including the presence of dissolved compounds or a bacterial film, may induce the settlement of invertebrate larvae. Based on previous observations of (1) enhanced recruitment of Sydney rock oysters (Saccostrea commercialis) on concrete surfaces and (2) high alkalinity at the surface of concrete due to the leaching of calcium hydroxide (Ca(OH)*) from the cement, experiments were designed to test the hypothesis that a surface containing Ca(OH), enhances settlement of oysters. The effect of a biofilm on settlement of Sydney rock oysters was also tested. The results obtained from the field experiment differed slightly from those obtained in the laboratory. In both the laboratory and the field, Ca(OH)2 had a positive effect on settlement. No significant effect of a biofilm on settlement on concrete substrata was observed in either experiment; a positive effect of a biofilm on substrata made with sand only or on sandstone was seen in both the laboratory and the field. For the substrata made with Ca(OH)2 and sand, however, the effect of a biofilm was positive in the field but negative in the lab. Although the results from the lab and field experiments were similar, the discrepancy was crucial in accepting or rejecting one of the hypotheses under test. The results of the study demonstrated that (1) the effects of a biofilm on settlement vary with the substratum and (2) these oysters can respond to a chemical cue (Ca(OH)*) in the field. The ecological implications of the ability of larvae to select a habitat in response to chemical cues are discussed.
Understanding spatial variation in biodiversity along environmental gradients is a central theme ... more Understanding spatial variation in biodiversity along environmental gradients is a central theme in ecology. Differences in species compositional turnover among sites (beta diversity) occurring along gradients are often used to infer variation in the processes structuring communities. Here, we show that sampling alone predicts changes in beta diversity caused simply by changes in the sizes of species pools. For example,
Canadian Journal of Fisheries and Aquatic Sciences, 2001
The most appropriate strategy to be used to create a permutation distribution for tests of indivi... more The most appropriate strategy to be used to create a permutation distribution for tests of individual terms in complex experimental designs is currently unclear. There are often many possibilities, including restricted permutation or permutation of some form of residuals. This paper provides a summary of recent empirical and theoretical results concerning available methods and gives recommendations for their use in univariate and multivariate applications. The focus of the paper is on complex designs in analysis of variance and multiple regression (i.e., linear models). The assumption of exchangeability required for a permutation test is assured by random allocation of treatments to units in experimental work. For observational data, exchangeability is tantamount to the assumption of independent and identically distributed errors under a null hypothesis. For partial regression, the method of permutation of residuals under a reduced model has been shown to provide the best test. For analysis of variance, one must first identify exchangeable units by considering expected mean squares. Then, one may generally produce either (i) an exact test by restricting permutations or (ii) an approximate test by permuting raw data or some form of residuals. The latter can provide a more powerful test in many situations. Résumé : La stratégie la plus appropriée pour générer une distribution de permutation en vue de tester les termes individuels d'un plan expérimental complexe n'est pas évidente à l'heure actuelle. Il y a souvent plusieurs options, dont la permutation restreinte et la permutation d'une quelconque forme des résiduels. On trouvera ici un résumé d'informations récentes empiriques et théoriques sur les méthodes disponibles, ainsi que des recommandations pour leur utilisation dans des applications unidimensionnelles et multidimensionnelles. L'emphase est mise sur les plans complexes d'analyse de variance et de régression multiple (i.e. les modèles linéaires). Dans un travail expérimental, la supposition d'échangeabilité requise pour un test par permutation est assurée par l'assignation au hasard à des unités des divers traitements. Dans le cas d'observations, l'échangeabilité équivaut à supposer que les erreurs, dans une hypothèse nulle, sont indépendantes et distribuées de façon identique. Pour la régression partielle, la méthode de permutation des résiduels dans un modèle réduit s'est avérée la meilleure. Pour l'analyse de variance, il faut d'abord identifier les unités échangeables à l'examen des carrés moyens attendus. Ensuite, il est généralement possible de produire (i) un test exact en restreignant les permutations ou alors (ii) un test approximatif en permutant les données brutes ou une forme quelconque des résiduels. Cette dernière méthode fournit, dans plusieurs situations, un test plus puissant.
Natural heterogeneity in ecological parameters, like population abundance, is more widely recogni... more Natural heterogeneity in ecological parameters, like population abundance, is more widely recognized and investigated than variability in the processes that control these parameters. Experimental ecologists have focused mainly on the mean intensity of predictor variables and have largely ignored the potential to manipulate variances in processes, which can be considered explicitly in experimental designs to explore variation in causal mechanisms. In the present study, the effect of the temporal variance of disturbance on the diversity of marine assemblages was tested in a field experiment replicated at two sites on the northeast coast of New Zealand. Fouling communities grown on artificial settlement substrata experienced disturbance regimes that differed in their inherent levels of temporal variability and timing of disturbance events, while disturbance intensity was identical across all levels. Additionally, undisturbed assemblages were used as controls. After 150 days of experimental duration, the assemblages were then compared with regard to their species richness, abundance and structure. The disturbance effectively reduced the average total cover of the assemblages, but no consistent effect of variability in the disturbance regime on the assemblages was detected. The results of this study were corroborated by the outcomes from simultaneous replicate experiments carried out in each of eight different biogeographical regions around the world.
Isolation of wildlife into fragmented populations as a consequence of anthropogenic-mediated envi... more Isolation of wildlife into fragmented populations as a consequence of anthropogenic-mediated environmental change may alter host-pathogen relationships. Our understanding of some of the epidemiological features of infectious disease in vulnerable populations can be enhanced by the use of commensal bacteria as a proxy for invasive pathogens in natural ecosystems. The distinctive population structure of a well-described meta-population of a New Zealand endangered flightless bird, the takahe (Porphyrio hochstetteri), provided a unique opportunity to investigate the influence of host isolation on enteric microbial diversity. The genomic epidemiology of a prevalent rail-associated endemic commensal bacterium was explored using core genome and ribosomal multilocus sequence typing (rMLST) of 70 Campylobacter sp. nova 1 isolated from one third of the takahe population resident in multiple locations. While there was evidence of recombination between lineages, bacterial divergence appears to have occurred and multivariate analysis of 52 rMLST genes revealed location-associated differentiation of C. sp. nova 1 sequence types. Our results indicate that fragmentation and anthropogenic manipulation of populations can influence host-microbial relationships, with potential implications for niche adaptation and the evolution of micro-organisms in remote environments. This study provides a novel framework in which to explore the complex genomic epidemiology of micro-organisms in wildlife populations.
1. Exploitation of living marine resources has resulted in major changes to populations of target... more 1. Exploitation of living marine resources has resulted in major changes to populations of targeted species and functional groups of large-bodied species in the ocean. However, the effects of overfishing and collapse of large top predators on the broad-scale biodiversity of oceanic ecosystems remain largely unexplored. 2. Populations of the Atlantic cod (Gadus morhua) were overfished and several collapsed in the early 1990s across Atlantic Canada, providing a unique opportunity to study potential ecosystem-level effects of the reduction of a dominant predator on fish biodiversity, and to identify how such effects might interact with other environmental factors, such as changes in climate, over time. 3. We combined causal modelling with model selection and multimodel inference to analyse 41 years of fishery-independent survey data (1970-2010) and quantify ecosystem-level effects of overfishing and climate variation on the biodiversity of fishes across a broad area (172 000 km 2) of the Scotian Shelf. 4. We found that alpha and beta diversity increased with decreases in cod occurrence; fish communities were less homogeneous and more variable in systems where cod no longer dominated. These effects were most pronounced in the colder northeastern parts of the Scotian Shelf. 5. Our results provide strong evidence that intensive harvesting (and collapse) of marine apex predators can have large impacts on biodiversity, with far-reaching consequences for ecological stability across an entire ecosystem.
Hagfishes from New Zealand are reviewed and a phylogeny proposed using morphological and genetic ... more Hagfishes from New Zealand are reviewed and a phylogeny proposed using morphological and genetic data (DNA sequences of cytochrome c oxidase subunit I gene, COI, and the small subunit RNA, 16S). Eptatretus cryptus sp. nov. was previously confused with Eptatretus cirrhatus (Forster in Bloch & Schneider, 1801) because of their similar morphology, and is found from the Three Kings Islands to Stewart Island and in the eastern part of the Chatham Rise (at depths of 96-922 m). Eptatretus poicilus sp. nov. is endemic to the Three Kings Islands, where it is common and associated with soft sediment and deep-sea coral-sponge habitats (114-842 m). Neomyxine caesiovitta sp. nov. is a slender hagfish found along the east coast of the North Island south to the Chatham Rise (430-1083 m). A neotype is erected for E. cirrhatus (type locality: Breaksea Sound, Fiordland), occurring widely in New Zealand coastal, shelf, and slope waters (1-922 m), but not at the Three Kings Islands. Eptatetrus goliath Mincarone & Stewart, 2006, Neomyxine biniplicata (Richardson & Jowett, 1951), and Nemamyxine elongata Richardson, 1958 are further described using additional material. Rubicundus eos (Fernholm, 1991) is still only known from the holotype (type locality: Challenger Plateau). Genetic results showed that the New Zealand Eptatretus species form a monophyletic group within the subfamily Eptatretinae, indicating likely speciation from a single common ancestor within the area. Eptatretus poicilus sp. nov. is the sister species of E. cirrhatus, and E. cryptus sp. nov. is closely associated with the clade formed by these two species. Eptatretus goliath is most closely associated with Eptatretus minor Fernholm & Hubbs, 1981 (Gulf of Mexico), these two species basally diverging within New Zealand hagfishes. The endemic genus Neomyxine forms a well-supported monophyletic group of as yet uncertain position within the phylogenetic tree. A key to the New Zealand hagfishes, fresh colour photographs, distribution maps, and in situ video recordings are presented.
Evaluating the effects of marine reserves on exploited species can be challenging because they oc... more Evaluating the effects of marine reserves on exploited species can be challenging because they occur within a context of natural spatial and temporal variation at many scales. For rigorous inferences to be made, such evaluations require monitoring programmes that are replicated at appropriate scales. We analysed monitoring data of snapper Pagrus auratus (Sparidae) in northeastern New Zealand, comprised of counts from baited-underwater-video surveys from inside and outside 3 marine reserves. Surveys were replicated at many levels, including areas inside and outside of marine reserves at 3 locations in 2 seasons, over a period of up to 14 yr, in an unbalanced design. The Bayesian modelling approach allowed the use of some familiar aspects of ANOVA, including mixed models of fixed and random effects, hierarchically nested structures, and variance decomposition, while allowing for overdispersion and excess zeros in the counts. Model selection and estimates of variance components revealed that protection by marine reserves was by far the strongest measured source of variation for relative densities of legal-sized snapper. The size of the effect varied across years among the 3 reserves, with relative densities between 7 and 20 times greater in reserves than in nearby areas. Other than the reserve effect, the temporal factors of season and year were generally more important than the spatial factors at explaining variation in counts. In particular, overall relative densities were ~2 to 3 times greater in autumn than in spring for legal-sized snapper, although the seasonal effect was also variable among locations and years. We consider that the Bayesian generalised linear mixed modelling approach, as used here, provides an extremely useful and flexible tool for estimating the effects of management actions and comparing them directly with other sources of spatial and temporal variation in natural systems.
We examined relationships between stable isotopes of carbon (delta(13)C) and oxygen (delta(18)O) ... more We examined relationships between stable isotopes of carbon (delta(13)C) and oxygen (delta(18)O) in tree rings of Callitris columellaris F. Muell in the semi-arid Pilbara region of north-western Australia. To test the hypothesis that stomatal control of photosynthesis decreases during drier periods, we developed delta(13)C and delta(18)O chronologies spanning 1919-1999, and used a permutation regression approach to relate a 21-year running correlation between delta(13)C and delta(18)O to rainfall and temperature at Marble Bar and our study site. The relationship between delta(13)C and delta(18)O switched from being always negative before 1955 to being consistently positive after 1976, suggesting an increase in stomatal control of photosynthesis in recent decades. Changes in the delta(13)C-delta(18)O relationship reflected changes in rainfall, which has increased in the region by 30% since 1976. The correlation between delta(13)C and delta(18)O was positively related to the 21-year r...
Uploads
Papers by Marti Anderson