Trevor J. Willis

CANONICAL ANALYSIS OF PRINCIPAL COORDINATES: A USEFUL METHOD OF CONSTRAINED ORDINATION FOR ECOLOGY

A flexible method is needed for constrained ordination on the basis of any distance or dissimilarity measure, which will display a cloud of multivariate points by reference to a specific a priori hypothesis. We suggest the use of principal coordinate analysis (PCO, metric MDS), followed by either a canonical discriminant analysis (CDA, when the hypothesis concerns groups) or a canonical correlation analysis (CCorA, when the hypothesis concerns relationships with environmental or other variables), to provide a flexible and meaningful constrained ordination of ecological species abundance data. Called “CAP” for “Canonical Analysis of Principal coordinates,” this method will allow a constrained ordination to be done on the basis of any distance or dissimilarity measure. We describe CAP in detail, including how it can uncover patterns that are masked in an unconstrained MDS ordination. Canonical tests using permutations are also given, and we show how the method can be used (1) to place a new observation into...

Global conservation outcomes depend on marine protected areas with five key features

In line with global targets agreed under the Convention on Biological Diversity, the number of marine protected areas (MPAs) is increasing rapidly, yet socio-economic benefits generated by MPAs remain difficult to predict and under debate. MPAs often fail to reach their full potential as a consequence of factors such as illegal harvesting, regulations that legally allow detrimental harvesting, or emigration of animals outside boundaries because of continuous habitat or inadequate size of reserve. Here we show that the conservation benefits of 87 MPAs investigated worldwide increase exponentially with the accumulation of five key features: no take, well enforced, old (>10 years), large (>100 km2), and isolated by deep water or sand. Using effective MPAs with four or five key features as an unfished standard, comparisons of underwater survey data from effective MPAs with predictions based on survey data from fished coasts indicate that total fish biomass has declined about two-thirds from historical baselines as a result of fishing. Effective MPAs also had twice as many large (>250 mm total length) fish species per transect, five times more large fish biomass, and fourteen times more shark biomass than fished areas. Most (59%) of the MPAs studied had only one or two key features and were not ecologically distinguishable from fished sites. Our results show that global conservation targets based on area alone will not optimize protection of marine biodiversity. More emphasis is needed on better MPA design, durable management and compliance to ensure that MPAs achieve their desired conservation value.

A baited underwater video system for the determination of relative density of carnivorous reef fish

Estimates of the relative density of fishes form the basis of many marine ecological studies as well as the assessment of effects of fishing or pollution. Plasticity in the behavioural response of large reef fishes to SCUBA divers means that commonly used underwater visual census (UVC) techniques do not always provide reliable estimates of relative density. The paper describes the system configuration, deployment methods, testing and use of a remotely deployed baited underwater video (BUV) system for the survey of carnivorous reef fishes (snapper, Pagrus auratus and blue cod,Parapercis colias) in marine reserves of northern New Zealand. Concurrent UVC and BUV surveys inside and outside a marine reserve showed that, whereas UVC detected few snapper in either area (resulting in little confidence in statistically significant results), BUV demonstrated significant differences in relative density. Conversely, blue cod were found to occur at significantly higher densities within the reserve by UVC, but not by BUV. The provision of accurate estimates of fish size (<20 mm error) from video footage also illustrated differences in size structure between protected and fished populations. The data suggest that a combination of survey techniques is likely to be necessary where multispecies assemblages are being assessed.

Integrating abundance and functional traits reveals new global hotspots of fish diversity

Species richness has dominated our view of global biodiversity patterns for centuries. The dominance of this paradigm is reflected in the focus by ecologists and conservation managers on richness and associated occurrence-based measures for understanding drivers of broad-scale diversity patterns and as a biological basis for management. However, this is changing rapidly, as it is now recognized that not only the number of species but the species present, their phenotypes and the number of individuals of each species are critical in determining the nature and strength of the relationships between species diversity and a range of ecological functions (such as biomass production and nutrient cycling). Integrating these measures should provide a more relevant representation of global biodiversity patterns in terms of ecological functions than that provided by simple species counts. Here we provide comparisons of a traditional global biodiversity distribution measure based on richness with metrics that incorporate species abundances and functional traits. We use data from standardized quantitative surveys of 2,473 marine reef fish species at 1,844 sites, spanning 133 degrees of latitude from all ocean basins, to identify new diversity hotspots in some temperate regions and the tropical eastern Pacific Ocean. These relate to high diversity of functional traits amongst individuals in the community (calculated using Rao’s Q), and differ from previously reported patterns in functional diversity and richness for terrestrial animals, which emphasize species-rich tropical regions only. There is a global trend for greater evenness in the number of individuals of each species, across the reef fish species observed at sites (‘community evenness’), at higher latitudes. This contributes to the distribution of functional diversity hotspots and contrasts with well-known latitudinal gradients in richness. Our findings suggest that the contribution of species diversity to a range of ecosystem functions varies over large scales, and imply that in tropical regions, which have higher numbers of species, each species contributes proportionally less to community-level ecological processes on average than species in temperate regions. Metrics of ecological function usefully complement metrics of species diversity in conservation management, including when identifying planning priorities and when tracking changes to biodiversity values.

Burdens of evidence and the benefits of marine reserves: putting Descartes before des horse?

An extensive literature has appeared since 1990 on the study of ‘no-take’ marine reserves and their potential to make significant contributions to the conservation and management of fisheries, especially in tropical environments (see Polunin 1990; Roberts & Polunin 1991; DeMartini 1993; Roberts 1997; Allison et al. 1998; Guenette et al. 1998). The literature describes many potential benefits of marine reserves to fisheries, including increases in spawner-biomass-per-recruit and increases in larval supply from protecting ‘source’ populations (Jennings 2000). The important word here is ‘potential’. Some claims made by advocates of marine reserves might be regarded as optimistic, whereas critics of reserves might sometimes have been unduly harsh. Conservation goals for marine reserves are often poorly defined, and differences of opinion regarding the efficacy of reserves for fulfilling any of their stated goals can frequently be attributed to a lack of good information with which to predict their effects. Here, we critically examine the literature from 1990–2001 to determine (1) the relative effort put into empirical and theoretical approaches to predict reserve effects, and (2) the quality of empirical evidence available to support theoretical predictions. It is not the purpose of this article to single out particular studies for criticism (although this is sometimes inevitable to provide examples), nor to draw conclusions concerning the efficacy of marine reserves.

Evidence for long-term site fidelity of snapper (Pagrus auratus) within a marine reserve

Abstract Increases in the density of exploited species on unfished reefs logically implies that some individuals are at least temporarily resident, or show fidelity to a particular area. We tagged snapper (Pagrus auratus (Bloch & Schneider 1801)) in the Leigh Marine Reserve, New Zealand using visible implant fluorescent elastomer tags, recoverable by diver visual sightings without the need to recapture the fish. Batch tagging of snapper (n = 907) was done during an angling survey in June and December 1996, and individually coded tags were implanted by divers (n = 117) in January 1999. Snapper tagged during both programmes were recovered on irregular intervals from 1997 to 2000. There were 71 recoveries of batch tags within 500 m of their tagging sites, and these recoveries were still being made >3 years after tagging: Of individually coded fish, 49 (42%) were seen, sometimes repeatedly over several months, close to their respective tagging sites. These observations included snapper as small as 23 cm fork length, contradicting the commonly held impression that only large snapper take up long‐term residency on reefs. This preliminary evidence suggests that some snapper exhibit site fidelity to areas only a few hundred metres wide, and in the absence of fishing may occupy the same area for years.

Reflecting on the next generation of models for community-based natural resources management

Community-based natural resource management (CBNRM) has been a pervasive paradigm in conservation circles for three decades. Despite many potentially attractive attributes it has been extensively critiqued from both ecological and sociological perspectives with respect to theory and practice (for example Leach et al. 1999; Berkes 2004; Fabricius et al. 2004; Blaikie 2006). Nonetheless, many successful examples exist, although an equal number have seemingly not met expectations. Is this because of poor implementation or rather a generally flawed model? If the criteria and conditions for success are so onerous that relatively few projects or situations are likely to qualify, what then is the value of the model? The questions thus become: how and what can we learn from the past theory and practice to develop a new generation of flexible, locally responsive and implementable CBNRM models, and what are likely to be the attributes of such models?

Retention and in situ detectability of visible implant fluorescent elastomer (VIFE) tags in Pagrus auratus (Sparidae)

This paper assesses the potential effec- tiveness of the visible implant fluorescent elastomer (VIFE) tagging system for identifying groups of snapper {Pagrus auratus: Sparidae) in the field. Retention rate after surface tagging longline-caught fish was 93% over a 2-week period, with no mortality attributable to tagging. Incidence of fin or scale infection did not differ between tagged and control fish. A protocol for tagging snapper underwater was also developed. This technique caused less stress to the fish than remote fishing methods, but was labour intensive when large sample sizes were required. Orange VIFE tags were visible to divers at ranges of up to 6 m in water visibility of 8-10 m, when exposed to light frequencies capable of inducing fluorescent emissions. Red, green, and yellow tags were only identifiable at shorter ranges, depending on ambient light levels and direction. The range of tag detection increased with increasing water clarity. We suggest that VIFE tagging has better retention rates and is less intrusive compared with previously employed externally readable tags. Because tags are identifiable in situ without the necessity of recapture, this method has potentially wide-ranging applications in fish ecology and behavioural studies for adult as well as juvenile fishes.

Morphometric and meristic comparison of orange roughy (Hoplostethus atlanticus: Trachichthyidae) from the Puysegur Bank and Lord Howe Rise, New Zealand, and its implications for stock structure

Significant morphological differences were found between orange roughy, Hoplostethus atlanticus, caught in 1993 on the Puysegur Bank and those caught on the Lord Howe Rise, New Zealand. A total of 17 separate body measurements and counts were taken from each fish. Treating the sexes separately, significant differences were found between sites when linear relations between eight particular body measures and standard length were compared. The eight measures indicating differences in shape were head length, snout length, orbit diameter, maxilla width, premaxilla length, caudal peduncle, gill raker count, and anal fin count. Discriminant functions were used to compare sites and sexes, and these permitted a >90% success rate in distinguishing fish from the two sites. A discriminant function could not be found which successfully separated two separate tows made on the Puysegur Bank, indicating that phenotypic differences do not vary as much within a site as they do between sites. All analyses made suggested that fish from the two different areas had different body shapes. Morphological differences, such as those found in the current investigation, could only arise if the fish populations from the two areas were relatively discrete. There may be some movement of fish between areas, quite possibly enough to bring about relative genetic homogeneity, but clearly there is insufficient to prevent the two populations from differing phenotypically. These differences suggest that morphometric analysis may be a useful tool for distinguishing New Zealand orange roughy stocks.

Recolonisation and recruitment of fishes to intertidal rockpools at Wellington, New Zealand

SynopsisA study of recolonisation of rockpools by intertidal fishes on the Wellington south coast, New Zealand, found the assemblage to be resilient and seasonally stable. A total of 26 species from nine families were recorded, dominated by the Tripterygiidae (triplefins) and Gobiesocidae (clingfishes). A pattern of alternating species dominance occurred, with the triplefinsBellapiscis medius andForsterygion lapillum being numerically dominant in summer, but becoming less common in winter and replaced as dominants by the clingfishesTrachelochismus pinnulatus andGastroscyphus hectoris. Juvenile recruits of eleven species occurred in the samples from spring to early summer, however only the aforementioned four species recruit to the intertidal zone in large numbers. The speed of rockpool recolonisation by fishes after extractive sampling is seasonally dependent, being quicker in the summer than winter. In general, recolonisation takes at least one month, but probably fewer than three. While stochastic factors influence assemblage composition in the short term, overall regulation of the fish assemblage of rockpools appears to be primarily deterministic, resulting in an essentially predictable taxonomic structure.