Ecology and conserva/on of the endangered Clanwilliam Sandfish (Labeo seeberi) in the Olifants-Doring river system, South Africa

Cerrilla, Cecilia

Ecology and conserva/on of the endangered Clanwilliam Sandfish (Labeo seeberi) in the Olifants-Doring river system, South Africa

Thesis / Dissertation

2026

Publisher

University of Cape Town

Department

Department of Biological Sciences

Faculty

Faculty of Science

Abstract

Freshwater ecosystems, though dispropor4onally rich in biodiversity, are the most endangered globally. Vertebrate popula4on declines in fresh waters are outpacing those on land, with fishes facing par4cularly high ex4nc4on rates. In South Africa, freshwater fishes are the most threatened species group, and invasive alien fishes (IAF) pose the greatest threat, followed by ecosystem modifica4ons, like dams and water over-exploita4on. Within the Cape Fold Ecoregion (CFE), itself a hotspot of endemic range-restricted species, lies the Olifants-Doring River system (ODRS), which has the largest number of threatened fish species in southern Africa. The Clanwilliam sandfish (Labeo seeberi; hereaNer ‘sandfish'), a large-bodied cyprinid endemic to the ODRS, migrates annually from the mainstem Doring River into tributaries for spawning. Despite its migratory life history and poten4ally important role in nutrient cycling as the system's only large detri4vore, its ecology has been understudied. Although a major popula4on decline was observed in the laSer half of the 20th century, no comprehensive study has been conducted to understand the full extent of the species' range contrac4on and fragmenta4on, or the corresponding implica4ons for the species' long-term survival. This thesis evaluates the habitat preferences of cri4cal sandfish life stages, tracks distribu4on shiNs over 4me, and assesses the efficacy of an ongoing head-start conserva4on interven4on in a key spawning tributary. Chapter 1 provides a literature review that highlights the global value of freshwater fishes and discusses major threats to freshwater fishes globally and in South Africa. Background is provided on the Olifants-Doring River system, and the ecology, life history, distribu4on and current threats to sandfish are discussed, as is the Biedouw River as a key spawning tributary for sandfish. Finally, the Saving Sandfish Project is introduced, and ra4onale given for the research ques4ons addressed in each chapter. Chapter 2 assesses the habitat requirements (depth, water velocity, substrate size, and cover) of key developmental stages by weigh4ng habitat use data by the rela4ve abundance of available habitat – yielding a measure of true preference. Surveys were conducted at three 500 m reaches in the Biedouw River during the spawning, larval, and juvenile stages. Habitat measures were recorded where sandfish were observed and along evenly spaced transects. Habitat U4lisa4on Curves and Habitat Availability Curves were produced for each variable using Kernel Density Smoothing, and Habitat Preference Curves (HPCs) generated using an adapta4on of the forage ra4o. For each survey, a composite reach-averaged HPC per habitat variable was produced to represent preference over the greater sampling area. Spawning adults exhibited a peak preference for moderate depths (around 18.2 cm), high veloci4es (around 0.61 m/s), and pebble substrate. Larvae preferred the shallowest depths (0 cm), lowest veloci4es (0 m/s), and sand and gravel substrates. Juveniles preferred deeper habitat (around 37.4 cm), very low veloci4es (0 m/s), and sand and gravel substrates. While spawning adults and juveniles apparently preferred open water, and larvae preferred vegeta4ve or rocky shelter, the inherent bias against visually detec4ng fish using shelter requires that these results be interpreted with cau4on. The chapter concludes with a series of management recommenda4ons to ensure appropriate habitat is available for each life stage, including the maintenance of the ecological reserve, implementa4on of strategic water releases into cri4cal nursery pools during the summer months, and removal of non-na4ve plants across the catchment. This chapter contributes to the broader understanding of how life-stage-specific habitat preferences can guide targeted habitat conserva4on and flow management strategies for migratory freshwater fishes. In Chapter 3, historical and current sandfish occurrence and abundance records are used to evaluate shiNs in distribu4on since 1936 and inform future management of the species. Historical records gathered from the Freshwater Biodiversity Informa4on System (FBIS) and the grey literature were used to construct decadal distribu4on maps from the 1930s onwards. Data from previous fish surveys in the ODRS conducted in 2001, 2011, and 2013 were obtained and u4lised to generate sandfish distribu4on and abundance maps over the last two decades. In October 2021, a large fyke net was used to resample 10 ODF survey sites along the Doring mainstem. In March-April 2022, five tributaries of the Doring River with historical sandfish records (Gif, Kransgat, Biedouw, Tra-Tra, and Matjies Rivers) were sampled with smaller fyke nets. Captured fish were iden4fied and a subsample measured (total length). Data were also obtained from Oorlogskloof Nature Reserve (ONR) personnel following their semi-annual survey of the Oorlogskloof River gorge in March 2022. The 2021 and 2022 surveys were compared with historical data to determine differences in species composi4on and size classes present. Sandfish size distribu4ons at mainstem sites were also compared with those from past ODF mainstem catches. Finally, the species' current total area of occupancy (AOO) was calculated and mapped, and its distribu4on assessed for overlap with protected areas to evaluate the level of protec4on currently afforded to the species. Sandfish were found across the Olifants River mainstem between the 1930s and 1970s, with records confined to the reach below Bulshoek Dam in the 1980s. Sandfish have not been recorded from the Olifants River system since. Since the onset of fish surveys in the Doring River system in the 1980s, sandfish have been recorded in the Doring mainstem and in the Gif, Brandewyn, Oorlogskloof-Koebee, Kransgat, Biedouw, Tra-Tra, and Matjies Rivers. While the upper reaches of the Doring appear to be a mainstem stronghold, the lack of subadults indicate that recruitment is likely func4onally absent. Non-na4ve fishes comprised 83% of mainstem catches by abundance, dominated by bluegill (Lepomis macrochirus) and black basses (Micropterus spp.) Two novel invaders were recorded for the first 4me in the Doring River system: common carp (Cyprinus carpio) and Mozambique 4lapia (Oreochromis mossambicus), with banded 4lapia (Tilapia sparrmanii) also present in low numbers. Sandfish were present in five of the 10 mainstem sites surveyed in 2021. Between 91.1 – 99.7% of catches in the Matjies, Biedouw, Kransgat and Oorlogskloof Rivers consisted of na4ve fishes, as did 72.6% of the catch in the Gif River and 0.3% in the Tra-Tra. Non-na4ve fishes present in the tributaries included L. macrochirus, M. punctulatus, M. dolomieu, and T. sparrmanii. The highest densi4es of sandfish were found in the Kransgat and Oorlogskloof Rivers. Sandfish sampled in tributaries were smaller in size, on average, than mainstem fish, although those sampled from the Koebee more closely approximated the mainstem average. The Gif, Matjies, Kransgat, and Oorlogskloof Rivers hosted moderate to high numbers of small and intermediate size classes. The conserva4ve AOO es4mate was 7.86 km2, covering 36 sub-quaternary catchments in the Doring River system and spanning 430.2 river-kilometres. Catchment overlap with protected areas was generally low (12.8%) and mostly concentrated around the Matjies River. Management recommenda4ons deriving from these results include the iden4fica4on of tributaries where flow augmenta4on or IAF eradica4on efforts may be most effec4ve for sandfish recovery, the establishment of stewardship agreements with private landowners where rivers fall outside of protected areas, and the expansion of na4ve fish refugia in tributaries. The chapter concludes by iden4fying several research gaps that could posi4vely inform future management of the species. These findings highlight the importance of long-term monitoring for mi4ga4ng threats and iden4fying opportuni4es for interven4on. Chapter 4 evaluates the efficacy of head-star4ng efforts in the Biedouw River aimed at increasing juvenile survival to reduce ex4nc4on risk. Juvenile sandfish were rescued from drying pools in the Biedouw River and relocated to six off-stream reservoirs to be reared to a larger size in 2020, 2021, 2022, and 2023. They were released back into the wild in 2021, 2022, and 2023. Most (90%) head-started fish were PIT-tagged prior to release. A passive PIT-tag detec4on antenna was deployed near the mouth of the Biedouw River in 2022 and 2023 to assess return rates during the annual migra4on. Mortality during rescues, growth and survival in the reservoir environment, and return rates rela4ve to wild run size were evaluated as measures of the programme's success. A generalised linear mixed model (GLMM) was used to evaluate the influence of several condi4ons at release on the probability of fish returning in 2022 and 2023. A total of 36,104 juvenile sandfish were rescued. The mortality rate of sandfish during the rescue process from 2021-2023 was 0.69%. Growth rate in the reservoir environment varied by reservoir and season, with most growth occurring between the months of November and March. Between 2021 and 2023, 2,829 sandfish were recaptured from reservoirs and released to the wild, ranging in size from 98 – 325 mm TL. Aner one year, the es4mated survival rate at Enjo Reservoir was 67.9% (95% CI: 38.5 – 97.3%). Seventy-seven tagged fish were detected by the PIT tag antenna in 2021, as were 221 fish in 2022, corresponding to return rates of 7.7% and 16.4%, respec4vely. Seventy of the fish detected in 2022 were returning for the second consecu4ve year, indica4ng a minimum survival rate of 90.9% for these fish in the wild between their first and second year post-release. Ninety-eight (9.9%) of the 2021 release cohort deferred their first migra4on to 2023, indica4ng that annual return rate may be dependent on inter-annual environmental varia4on, and that subsequent-year return rates may be higher than first-year return rates. The return of 221 unique fish detected in 2023 represents a minimum 123% increase in run size compared to the 180 wild sandfish observed migra4ng in 2021 during a comprehensive visual survey. The GLMM predicted that for every cen4metre increase in size at release, the odds of return increased by 11.0% (p < 0.001). Fish released aNer the migra4on were predicted to have a 90.4% lower chance of return than those released during the migra4on (p < 0.001). The 4ming of PIT tag detec4ons was also used to evaluate the environmental cues to migra4on onset, which were preceded by flood events. Addi4onally, observa4ons of spawning events were temporally linked to water temperature and flow data recorded by a submerged Levelogger to define the range of temperatures and discharges at which sandfish spawned in 2021 and 2022. Spawning appeared to take place as high flows subsided and water temperatures increased in spring. During spawning events, water temperature and discharge varied between 14.3 and 20.7 °C and 0.14 to 0.38 m3/s, respec4vely. This research will posi4vely inform future conserva4on efforts for sandfish and serves as a model for the conserva4on of freshwater fishes where there is an imminent risk of ex4nc4on by demonstra4ng the effec4veness of head-star4ng as a popula4on augmenta4on tool. Chapter 5 presents the overarching conclusions gleaned from this thesis, with a par4cular focus on management recommenda4ons and future opportuni4es for research. This study demonstrated clear niche differen4a4on between three sandfish life stages, mapped temporal distribu4on shiNs, and evaluated a pioneering head-start interven4on programme as part of an evidence-based conserva4on approach for the species. These results highlight the importance of maintaining natural heterogeneity across the river networks sandfish rely on, iden4fied loca4ons to priori4se for different conserva4on ac4ons, and provided insight into the factors that are most likely to maximise the impact of sandfish popula4on augmenta4on efforts. Moreover, the insights gained into the species' ecology, including environmental cues to migra4on and spawning, will inform the ongoing recovery efforts for the species. The thesis concludes with promising avenues for future research. Overall, this thesis advances the field of conserva4on biology by integra4ng ecological research and applied interven4ons, providing a framework applicable to other imperilled freshwater species facing similar threats.