Historical baselines and a century of change in the demersal fish assemblages on South Africa's Agulhas Bank

Accurate interpretation of recent variability observed in fish populations, species compositions, distribution ranges or ecological indicators, depends on knowledge of their past dynamics and historical states. The onset of systematic fisheries data collection typically lagged decades or even centuries behind modern fishing exploits. As a consequence, pre-disturbed reference points and descriptions of subsequent change are rarely available. A remarkably detailed set of historical trawl survey data from South Africa provided such a rare opportunity. Government-funded exploration of the Agulhas Bank fishery potential resulted in meticulously-documented trawl survey data from 1897-1904, when prior human impacts on those resources were negligible. Although they used less effective technology, the information recorded and methods used were similar to modern surveys. This thesis investigated change in demersal fish fauna of the Agulhas Bank and documents comparisons between historical trawl surveys and modern re-enactments at the same locations. In comparing trawl survey catches over multiple decades or among different periods, unquantified changes in fishing power pose a key challenge. The shape, size, materials, mesh sizes and speed at which trawl nets are dragged, interact with the behaviour, size and shape of fish, influencing fishing performance. To accurately compare current catch rates with those of historical trawl surveys, the same trawl gear and methods were carefully replicated in repeat surveys at three sites. An investigation of literature and photographs of the original vessel and equipment were conducted to support the construction of a replica 'Granton' otter trawl net. The net was composed of Manila hemp with a headline length of 27 m (90 ft) and was attached to flat wooden trawl boards. The historical towing speed was estimated as 1.34 m s⁻¹ (2.6 knots). Three parts of the shallow Agulhas Bank that were surveyed 111 years prior, were re-surveyed in 2015. Species composition was contrasted between the historical and re-survey periods by way of unconstrained ordination, permutational multivariate analysis of variance and tests of the homogeneity of multivariate group dispersions. Taxa discerning between periods were identified with similarity percentage analyses. Changes of standardised catch between periods were tested for 27 taxa, using a non-parametric bootstrap approach. Proportions among size-classes, recorded for three taxa, were tested using Fisher's exact test. Results revealed a substantially transformed demersal catch assemblage, where the period effect explained almost half of the measured variance among samples. These changes included the disappearance or heavy depletion of kob (Argyrosomus spp., absent in re-surveys), panga (Pterogymnus laniarius; 2.4% of historical catch abundance) and east coast sole (Austroglossus pectoralis; 4.6% of historical catch abundance), which had jointly contributed 70-84% of historical catch composition. Average re-survey catches were largely made up of gurnards (Chelidonichthys spp.; 3 792% of historical abundance), horse mackerel (Trachurus trachurus; 4 738% of historical abundance), spiny dogfish (Squalus spp.; 3 121% of historical abundance), hake (Merluccius capensis; 558% of historical abundance) and white sea catfish (Galeichthys feliceps; 13 863% of historical abundance). Analysis of available length information confirmed the expectation that fish sizes (specifically M. capensis and A. pectoralis) had declined. This implies that comparisons by weight would be more severe for declined abundances and less severe for those that increased, relative to contrasts of numerical abundance. Habitat preferences as well as geographic and depth distribution appeared to separate the taxa that increased from those that declined. These factors, together with reproductive and growth characteristics, as well as indirect trophic impacts, likely shaped the responses of demersal fauna to fishing and other human impacts during the 111 years between trawl surveys. An assessment of distribution changes of 44 common demersal taxa was undertaken. These analyses were restricted to the last 30 years of trawl survey data as the units and spatio-temporal resolution of prior data were incompatible. Standardised catches were used from annual spring and autumn south coast trawl surveys conducted by the government fisheries department. Geostatistical delta-generalised linear mixed models were used to predict species distribution functions, which were used to calculate annual estimates of latitude/longitude centres of gravity and effective areas occupied by each population. Average trends over the study period (1986-2016) were assessed using a Bayesian state-space model. Of nine species found to have a trend in average location, six moved westward or south-westward, while three moved eastward or north-eastward. Two species showed a trend of contracting spatial extent and one showed an expansion. Across the entire assemblage combined, there was a significant contraction in extent and a westward shift in average location. These assemblage-wide average trends are interpreted to be driven by climate forcing. Fishing impacts are expected to have contributed to the eastward movement in centre of gravity for kob, lesser sandshark (Rhinobatos annulatus) and white stumpnose (Rhabdosargus globiceps). Interpretation of these distribution shifts is hampered by a lack of knowledge on subsurface hydrographic trends on the Agulhas Bank, which is identified as a research priority. My research revealed substantial change in demersal fish communities on South Africa's Agulhas Bank and adds novel insight to the history underlying current states of demersal ecosystems. Valuable additions include a) documentation of the extent to which demersal assemblages have transformed during the last century at three representative inshore sites; b) estimates of current abundances relative to pre-disturbed baselines at those sites, which c) highlights drastic local depletion for certain taxa and d) reveals substantial abundance increases of certain species during the post-industrial fishing period; e) novel evidence of distribution trends in south coast demersal species; and f) identification of trends in the average distribution of the demersal fish assemblage, suspected to be climate-forced. Long-term comparisons, using minimally-disturbed baselines, revealed drastic transformation of the fish assemblage during a century of industrialisation, which points to trawling-induced alteration of benthic habitats and substantial changes in ecosystem structure. Besides the provision of novel historical context for current and future studies and decision-making, this work counters the erosive nature of shifting baselines in South Africa's marine environment

Bioregions in marine environments: Combining Biological and Environmental Data for Management and Scientific Understanding

Bioregions are important tools for understanding and managing natural resources. Bioregions should describe locations of relatively homogenous assemblages of species occur, enabling managers to better regulate activities that might affect these assemblages. Many existing bioregionalization approaches, which rely on expert-derived, Delphic comparisons or environmental surrogates, do not explicitly include observed biological data in such analyses. We highlight that, for bioregionalizations to be useful and reliable for systems scientists and managers, the bioregionalizations need to be based on biological data; to include an easily understood assessment of uncertainty, preferably in a spatial format matching the bioregions; and to be scientifically transparent and reproducible. Statistical models provide a scientifically robust, transparent, and interpretable approach for ensuring that bioregions are formed on the basis of observed biological and physical data. Using statistically derived bioregions provides a repeatable framework for the spatial representation of biodiversity at multiple spatial scales. This results in better-informed management decisions and biodiversity conservation outcomes.Peer reviewe

Transdisciplinarity in transformative ocean governance research—reflections of early career researchers

This paper interrogates the concept of transdisciplinarity, both theoretically and practically, from a perspective of early career researchers (ECRs) in transformative ocean governance research. Aiming to advance research methodologies for future complex sustainability challenges, the paper seeks to illuminate some common uncertainties and challenges surrounding transdisciplinarity from a marine science perspective. Following a literature review on transdisciplinary research, workshops, and a series of surveys, we determine that transdisciplinarity appears to be a concept in search of definition, and that there is a need to explore transdisciplinarity specifically from an ocean research perspective. The paper discusses a number of challenges experienced by ECRs in conducting transdisciplinary research and provides recommendations for both ECRs wishing to undertake more equitable transdisciplinary research and for the UN Decade for Ocean Science to support ECRs in this endeavour (Figure 1). Based on our findings, we interrogate the role of non-academic collaborators in transdisciplinary research and argue that future transdisciplinarity will need to address power imbalances in existing research methods to achieve knowledge co-production, as opposed to knowledge integration

Criminology or Zemiology? Yes, please! on the refusal of choice between false alternatives

Buried deep within the zemiological movement and its supportive literature is the implicit assumption that the word zemia, the organising concept around which zemiology is built, simply represents ‘the Greek word for harm’. This interpretation has supported numerous drives to ‘move beyond criminology’ and erect strict borders between the study of crime and harm. However, a deeper, albeit still rather brief, exploration of zemia reveals that it possesses a broader range of meaning than that commonly afforded to it. By beginning to unpick zemia’s semantic genealogy, it appears that the conventional use of the word to support the imposition of false alternatives between criminology and zemiology is untenable. Accordingly, this chapter attempts to foreground a more integrated approach to the study of crime and harm

Interannual variability in Indian Ocean surface waters and tuna-environment relationships : filling the gaps with a coupled bio-physical ocean model

Study of the Indian Ocean has lagged behind that of the Atlantic and Pacific, with large knowledge gaps remaining in our understanding of regional or basin-scale controls on productivity and higher trophic levels. A lack of in situ data, especially for mid and upper trophic-level organisms, has commonly limited to small spatiotemporal scales, investigations into environmental control of biological systems. These data gaps are increasingly being filled by coupled bio-physical ocean models. Throughout this thesis, outputs from such a coupled ocean model (NEMO-PISCES) were employed to provide hindcast (1961-2001) records of three-dimensional environmental fields in the Indian Ocean

Indian Ocean Dipole and El Niño/Southern Oscillation impacts on regional chlorophyll anomalies in the Indian Ocean

International audienceThe Indian Ocean Dipole (IOD) and the El Niño/Southern Oscillation (ENSO) are independent climate modes, which frequently co-occur, driving significant inter-annual changes within the Indian Ocean. We use a four-decade hindcast from a coupled biophysical ocean general circulation model, to disentangle patterns of chlorophyll anomalies driven by these two climate modes. Comparisons with remotely sensed records show that the simulation competently reproduces the chlorophyll seasonal cycle, as well as open-ocean anomalies during the 1997/1998 ENSO and IOD event. Results suggest that anomalous surface and euphotic-layer chlorophyll blooms in the eastern equatorial Indian Ocean in fall, and southern Bay of Bengal in winter, are primarily related to IOD forcing. A negative influence of IOD on chlorophyll concentrations is shown in a region around the southern tip of India in fall. IOD also depresses depth-integrated chlorophyll in the 5-10 • S thermocline ridge region , yet the signal is negligible in surface chlorophyll. The only investigated region where ENSO has a greater influence on chlorophyll than does IOD, is in the Somalia upwelling region , where it causes a decrease in fall and winter chlorophyll by reducing local upwelling winds. Yet unlike most other regions examined, the combined explanatory power of IOD and ENSO in predicting depth-integrated chlorophyll anomalies is relatively low in this region, suggestive that other drivers are important there. We show that the chlorophyll impact of climate indices is frequently asymmetric, with a general tendency for larger positive than negative chlorophyll anomalies. Our results suggest that ENSO and IOD cause significant and predictable regional re-organisation of chlorophyll via their influence on near-surface oceanogra-phy. Resolving the details of these effects should improve our understanding, and eventually gain predictability, of interan-nual changes in Indian Ocean productivity, fisheries, ecosystems and carbon budgets

Taking state of biodiversity reporting into the information age – A South African perspective

South Africa’s National Biodiversity Assessment (NBA) is the primary tool for monitoring and reporting on the state of biodiversity, with a focus on spatial information and key indicators. The NBA distills information that informs policies and strategies, meets national and international reporting requirements, and helps prioritize limited resources for managing and conserving biodiversity. The three previous versions of the NBA (2004, 2011 and 2018) are in the form of detailed thematic technical reports and a synthesis report, served on a simple, static web page. Selected spatial products from the report are available via a dedicated web platform (http://nba.sanbi.org.za/). While all methods and data are clearly described in the technical reports, most of the underlying analyses are inaccessible, lacking reproducibility and transparency. This makes iterative updates to indicators or metrics challenging and inefficient, complicates version control, and exacerbates the risk of capacity, knowledge and data loss during staff turnover. To move the assessment process into the information age we aim to develop well documented and reproducible workflows, and to serve the indicators and their accompanying synthesis on an interactive web platform that facilitates uptake. Achieving these aims will deliver efficiency, greater transparency and trust in future NBA products and will strengthen communication and engagement with the content by the many different users of those products. While these visions will not be realized overnight, the skills and systems required to achieve them can be adaptively built towards an improved NBA that better serves the needs of our society

Data from: Persistence of distinctive morphotypes in the native range of the CITES-listed Aldabra giant tortoise

Understanding the extent of morphological variation in the wild population of Aldabra giant tortoises is important for conservation, as morphological variation in captive populations has been interpreted as evidence for lingering genes from extinct tortoise lineages. If true, this could impact reintroduction programmes in the region. The population of giant tortoises on Aldabra Atoll is subdivided and distributed around several islands. Although pronounced morphological variation was recorded in the late 1960s, it was thought to be a temporary phenomenon. Early researchers also raised concerns over the future of the population, which was perceived to have exceeded its carrying capacity. We analyzed monthly monitoring data from 12 transects spanning a recent 15-year period (1998–2012) during which animals from four subpopulations were counted, measured, and sexed. In addition, we analyzed survival data from individuals first tagged during the early 1970s. The population is stable with no sign of significant decline. Subpopulations differ in density, but these differences are mostly due to differences in the prevailing vegetation type. However, subpopulations differ greatly in both the size of animals and the degree of sexual dimorphism. Comparisons with historical data reveal that phenotypic differences among the subpopulations of tortoises on Aldabra have been apparent for the last 50 years with no sign of diminishing. We conclude that the giant tortoise population on Aldabra is subject to varying ecological selection pressures, giving rise to stable morphotypes in discrete subpopulations. We suggest therefore that (1) the presence of morphological differences among captive Aldabra tortoises does not alone provide convincing evidence of genes from other extinct species; and (2) Aldabra serves as an important example of how conservation and management in situ can add to the scientific value of populations and perhaps enable them to better adapt to future ecological pressures

Transdisciplinarity in transformative ocean governance research - reflections of early career researchers

This paper interrogates the concept of transdisciplinarity, both theoretically and practically, from a perspective of early career researchers (ECRs) in transformative ocean governance research. Aiming to advance research methodologies for future complex sustainability challenges, the paper seeks to illuminate some common uncertainties and challenges surrounding transdisciplinarity from a marine science perspective. Following a literature review on transdisciplinary research, workshops, and a series of surveys, we determine that transdisciplinarity appears to be a concept in search of definition, and that there is a need to explore transdisciplinarity specifically from an ocean research perspective. The paper discusses a number of challenges experienced by ECRs in conducting transdisciplinary research and provides recommendations for both ECRs wishing to undertake more equitable transdisciplinary research and for the UN Decade for Ocean Science to support ECRs in this endeavour (Figure 1). Based on our findings, we interrogate the role of non-academic collaborators in transdisciplinary research and argue that future transdisciplinarity will need to address power imbalances in existing research methods to achieve knowledge co-production, as opposed to knowledge integration

Data from: Persistence of distinctive morphotypes in the native range of the CITES-listed Aldabra giant tortoise

Understanding the extent of morphological variation in the wild population of Aldabra giant tortoises is important for conservation, as morphological variation in captive populations has been interpreted as evidence for lingering genes from extinct tortoise lineages. If true, this could impact reintroduction programmes in the region. The population of giant tortoises on Aldabra Atoll is subdivided and distributed around several islands. Although pronounced morphological variation was recorded in the late 1960s, it was thought to be a temporary phenomenon. Early researchers also raised concerns over the future of the population, which was perceived to have exceeded its carrying capacity. We analyzed monthly monitoring data from 12 transects spanning a recent 15-year period (1998–2012) during which animals from four subpopulations were counted, measured, and sexed. In addition, we analyzed survival data from individuals first tagged during the early 1970s. The population is stable with no sign of significant decline. Subpopulations differ in density, but these differences are mostly due to differences in the prevailing vegetation type. However, subpopulations differ greatly in both the size of animals and the degree of sexual dimorphism. Comparisons with historical data reveal that phenotypic differences among the subpopulations of tortoises on Aldabra have been apparent for the last 50 years with no sign of diminishing. We conclude that the giant tortoise population on Aldabra is subject to varying ecological selection pressures, giving rise to stable morphotypes in discrete subpopulations. We suggest therefore that (1) the presence of morphological differences among captive Aldabra tortoises does not alone provide convincing evidence of genes from other extinct species; and (2) Aldabra serves as an important example of how conservation and management in situ can add to the scientific value of populations and perhaps enable them to better adapt to future ecological pressures