Research Articles (Biodiversity and Conservation Biology)

Permanent URI for this collectionhttps://hdl.handle.net/10566/35

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Infection by Cardiodectes bellottii (Copepoda: Pennellidae) on Lampanyctodes hectoris (Actinopterygii: Myctophidae) in the southern Benguela Current upwelling ecosystem
(National Inquiry Services Centre Ltd, 2026) van der Lingen, Carl David; Shongwe, Thembeka; Reed, Cecile C.
Hector’s lanternfish Lampanyctodes hectoris is an abundant mesopelagic fish found in the Benguela Current marine ecosystem and is frequently parasitised by the copepod Cardiodectes bellottii. This parasite is relatively large compared with its fish host, and negative impacts of its infection on other lanternfishes have been reported. We examined 1 800 L. hectoris sampled over a wide spatio-temporal range in the southern Benguela to document C. bellottii infection indices in this lanternfish species, and we compare selected biological characteristics of infected and uninfected fish. Infection prevalence showed spatio-temporal variability, with an overall mean of 20.7% (95% confidence limits: 18.9–22.6%; 373/1 800 fish). This is the highest reported infection prevalence by C. bellottii among five lanternfish species for which large sample sizes (of >500 fish) were processed. We found that infection (i) significantly reduced female host weight-at-length but not that of male hosts; (ii) significantly reduced female but not male gonadosomatic index; and (iii) had no significant effect on length frequency distributions. Cardiodectes bellottii infection in L. hectoris does not appear to increase host mortality but can reduce both somatic and/or gonadal growth, and hence reproductive success. These findings suggest that the productivity and population dynamics of L. hectoris in the southern Benguela may be partly driven by infections by this parasitic copepod.
Intra- and interannual changes in siphonophore assemblages over the Transkei shelf, South Africa
(Elsevier Ltd, 2026) Moodaley, Dylan; Thibault, Delphine; Gibbons, Mark J.
As one of the world's strongest western boundary currents, the Agulhas Current plays a significant role in global and regional climate, yet its impact on local shelf processes is not fully understood. Recent oceanographic studies conducted over the Transkei Shelf in 2017, reveal pronounced seasonal impacts of The Current on the dynamics of shelf circulation that are reflected by phytoplankton communities. We extend that investigation here to look at mesoscale coupling with the zooplankton (using siphonophores), anticipating seasonal and cross-shelf changes that mirror the bio-physical environment. We also compare these data with historic information from the same region (collected in 1990/1991), anticipating little interannual change given the wide-ranging nature of most siphonophores. The structure of regional siphonophore assemblages in 2017 was strongly influenced by season, latitude and depth: offshore waters were characterized by high numbers of species, low abundances, and a relative homogeneity in numerical composition, perhaps typical of Tropical Surface Waters. Shelf assemblages were of higher abundance but lower richness, as well as a greater heterogeneity in numerical composition that reflected the upwelling of diverse water masses onto the shelf. Persistent upwelling off Port Alfred and between Capes Padrone and Recife were characterized by high densities of Muggiaea atlantica, regardless of water source. As expected, siphonophore assemblages between 1990/1991 and 2017 did not change in structure, and indeed the cross-shelf pattern was maintained during both surveys. Our results highlight the value of siphonophores as indicators of water masses and emphasise the role they can play in understanding the stability of marine ecosystems over time.
Acoustic remote sensing with deep learning enables non-invasive estimation of seabird nest density
(Elsevier B.V., 2026) Ludynia, Katrin; Terranova, Francesca; Todaro, Lorenzo
Passive Acoustic Monitoring (PAM) is increasingly used as a non-invasive tool for biodiversity monitoring, particularly for species breeding in habitats where visual surveys are difficult or biased. The Critically Endangered African Penguin ( Spheniscus demersus ) is a highly vocal, burrow-nesting colonial seabird, making it an ideal species for evaluating whether soundscape data can be translated into reliable estimates of nest density. We deployed Autonomous Recording Units at multiple sampling points at the Stony Point Penguin Colony, South Africa, over two consecutive breeding seasons (2024 and 2025), capturing soundscapes spanning different nest densities and environmental conditions. We developed an automated detector for Ecstatic Display Songs (EDS), the species' territorial song, using a Convolutional Neural Network trained on a multi-source dataset from both in situ and ex situ recordings. The detector achieved high recall and precision, supporting the use of heterogeneous training datasets for reliable detection. To link vocal activity to nest density, we derived, for each sampling point, an index based on the maximum number of EDS detections across 30-min recordings and modelled its relationship with active nest counts using Generalized Additive Models. The index reliably predicted nest density, but the relationship was nonlinear: nest density rose as vocal activity increased before plateauing at higher levels. The model trained on 2024 data generalized well to independent 2025 data. Together, these results show that, up to intermediate densities, nest density can be reliably estimated from passive acoustic recordings alone. This approach requires no observer presence and is applicable to large-scale, long-term seabird monitoring.
The trophic ecology of 12 mesopelagic fish species in the northern Benguela Current ecosystem contributes to species coexistence
(National Inquiry Services Centre Ltd, 2026) Zacarias, Lourenço; van der Lingen, Carl David; Gibbons, Mark J.
Mesopelagic fishes are abundant and play an important role, even if incompletely understood, in the ecology and functioning of the global ocean. Mesopelagic fishes are predominantly carnivorous, and assemblages may comprise species that feed on similar zooplankton resources. Yet, their species diversity remains generally high. This study examined the trophic ecology of 12 of the most common mesopelagic fish species found in the northern Benguela Current ecosystem in an effort to understand interactions between species. Integrating morphometric traits, stomach content analysis, and stable isotope values revealed complex, multidimensional niche partitioning within the mesopelagic assemblage. Though morphological similarities suggested potential competition, systematic gape-size analysis demonstrated a clear scaling relationship with prey-size spectra, providing a mechanical basis for resource partitioning. Stomach content analysis confirmed this partitioning, with species-specific preferences for distinct zooplankton groups. These dietary differences were reflected in stable isotope biplots of carbon and nitrogen, which delineated a clear trophic hierarchy. By combining these three methodologies, our study indicates that coexistence is achieved through a synergy of morphological specialisation and trophic positioning, rather than spatial segregation alone.
Seasonal windows of opportunity: exploratory trawling for mesopelagic fishes off South Africa’s west coast
(National Inquiry Services Centre Ltd, 2026) Coetzee, Janet C
Shortages of fishmeal and fish oil and the resultant high prices for these products have intensified commercial interest for potentially harvesting mesopelagic fishes. Data from an exploratory pelagic trawl programme off South Africa’s west coast in 2010/2011 and 2017–2019, largely targeting Hector’s lanternfish Lampanyctodes hectoris, were analysed to investigate drivers of catch per unit effort (CPUE) and to explore operational constraints of a dedicated mesopelagic trawl fishery. Across trips, the mean catch was ∼64 (SE = 5.3) tonnes (t) d-1 and CPUE was 2.7 (SE = 0.2) t h-1, but with high variability. Month was the dominant driver of CPUE, with an elevated CPUE in only 3–4 months of the year. Diel differences (day, night, dawn or dusk), towing speed, fishing depth and bottom depth showed no consistent effects. Catches of mesopelagic fishes were concentrated near the 200-m isobath between Lambert’s Bay and Cape Town, close to the existing fishmeal factories at St Helena Bay. A simple benchmark against local trips made by anchovy purse-seiners indicated comparatively higher trip-level catch rates for anchovy Engraulis encrasicolus (mean ∼157 t d-1) and highlighted throughput and cost disadvantages for a dedicated mesopelagic trawl fishery. The fishmeal and fish oil yield was seasonal, peaking in late summer or autumn and not aligned with the peak in CPUE, negatively impacting the economic viability of this prospective fishery.
Hindlimb and pelvic girdle reduction with associated skeletal changes in the South African limb-reduced skink Scelotes Fitzinger, 1826
(Taylor and Francis Ltd, 2026) Wilson, Brian; Hendricks, Martin; Zhao, Zhongning; Heideman, Neil
We used stained specimens to describe hindlimb and pelvic girdle reduction in a skeletal morphocline of Scelotes species, a South African scincine group, as well as how the two processes are interrelated. The findings reflect the generally varied nature of the evolutionary pathways to a limbless serpentine form among lacertilians, which presumably reflect the interplay between selective and developmental processes. The relationship between hindlimb and pelvic girdle degeneration in terms of onset, process concurrency and patterns was clarified but its applicability to lacertilians in general will have to be verified. Substantial increases in presacral vertebra counts were responsible for the increase in body length of the species. Our phylogenetic analyses suggest that Scelotes most likely descended from a limbless ancestor, with extant digit-bearing species reflecting secondary gains and subsequent losses. Forelimb and hindlimb evolution were decoupled: forelimb change was concentrated among few states (0, 3, 5) with dominant 0↔3 shifts, while hindlimbs were more labile and clustered into intermediate (3), low (1–2) and extreme (0 or 5) states, implying stepwise, multi-pathway transitions driven by developmental modularity, selective (fossorial) pressures, and constraints. Further confirmation of these findings is required by investigating the evolutionary process in the remainder of the Scelotes species, and in lacertilians in general.
Ambrosia beetle invasions are structured by inbreeding, intraspecific hybridization, and bridgeheads
(Oxford University Press, 2026) Huisamen, Elizabeth J; Schmidt, Thomas L; Terblanche, John S
When invasive populations establish in regions far from their origin, they may accumulate deleterious mutations that limit population viability and later expansion. Invasions stemming from such bridgehead populations may experience further sequential bottlenecks. However, deleterious mutations can be masked or eliminated when populations outbreed with other lineages. Here, we analyze global invasions of a species complex of persistently inbreeding ambrosia beetles, using genomic data (n = 247) from invasive populations in Africa, North America, and Australia, and from native populations in Asia. We mostly focus on one species of this complex (Euwallacea fornicatus), which poses a severe threat to tree species worldwide and is rapidly expanding its global range. We uncover a single lineage of this species across California, South Africa, and Western Australia, involving an invasive bridgehead and containing almost no nuclear genetic variation. In South Africa, we identify a second lineage that has repeatedly hybridized with the first lineage. Genetic patterns in the native range indicate that such opportunistic outbreeding may be common. Despite lacking nuclear variation, the first lineage contained two CO1 haplotypes that were also observed in every hybrid lineage, pointing to heteroplasmy and possible hybrid origins of this lineage. Native populations had fewer missense mutations than invasive populations, indicating that opportunistic outbreeding may help purge fixed deleterious mutations when local lineage diversity is high. These findings highlight the importance of outbreeding even when inbreeding is common, and they demonstrate the biosecurity threat posed by subsequent gene flow into invasive populations.
Full life cycle cultivation of three local kelp species (Ecklonia maxima, Laminaria pallida and Macrocystis pyrifera) in an aquaculture setting in Small Bay of Saldanha Bay, South Africa
(Springer Science and Business Media B.V., 2026) Botes, Lizeth; Schalkwyk, Musadiq; Moosa, Waqeefah
Seaweed farming is a growing global industry with significant potential for environmental and economic benefits. While East and Southeast Asian countries dominate current production, interest and investment in kelp farming are expanding to other regions, including Africa. In South Africa limited information is available on the cultivation potential of the three local west coast kelp species Ecklonia maxima, Laminaria pallida and Macrocystis pyrifera. This study was conducted as part of the South African Kelp Farming Project (SA KFP) and is the first full life cycle cultivation of the three species in an aquacul ture setting over the same 8-month period in Africa. All three kelp species were grown in the hatchery/nursery to ~ 1 cm in 49 days (at 15 ℃, a 16 h L:8 h D photoperiod, GeO2 in the first two weeks, half strength PES from the second week onward, spore concentration of 2000 spores mL−1 for E. maxima and L. pallida, and 5000 spores mL−1 for M. pyrifera). To overcome sedimentation and biofouling pressure at the grow-out site, an at-sea weaning step was introduced where juvenile sporophytes were grown for ~ 2 weeks to 2.0–2.5 cm. Results of the 6-month grow-out period demonstrated that all three species can be cultivated in an aquaculture setting but that a good understanding of the spatiotemporal variations in environmental and biological factors at any particular site is critical before full-scale operations are attempted. The methodologies used in this study provide a foundation from which a kelp farming industry in South Africa could potentially develop and improve on.
Can hydroponic fodder be used to fill the seasonal fodder gap for pastoral livestock in Namaqualand, South Africa?
(Taylor and Francis Ltd., 2026) Kekaya, Imanathi; Samuels, Igshaan; Cupido, Clement; Müller, Francuois
Livestock production in Namaqualand’s semi-arid rangelands is constrained by seasonal fluctuations in forage quality and water scarcity. This study evaluates (1) the seasonal nutrient changes of available natural veld forages and their capacity to sustain livestock across different rainfall regions, and (2) the potential of hydroponically grown barley fodder as a supplemental feed resource. Forage samples from Steinkopf communal rangelands revealed significant (p < 0.05) seasonal decline in crude protein concentration (13.9% to 5.8%) from the wet season to the dry season, with energy concentrations insufficient for livestock requirements. Concurrently, hydroponic trials using four water sources (borehole, municipal, distilled, and nutrient solution) demonstrated that barley fodder produced a high protein content (14.2%–18.8%) but with a limited energy value. While hydroponic fodder cannot fully replace natural forage, it effectively mitigates dry-season protein deficiencies. Strategic integration of hydroponics with mineral supplementation is recommended to enhance livestock productivity, especially in water-limited agropastoral systems.
Grazing management systems across biomes and land tenure in South Africa
(Taylor and Francis Ltd., 2026) Ntombela, Khululiwe Primrose; Samuels, Igshaan; Finca, Andiswa; Letsoalo, Ngoako Lucas
Grazing management in South Africa often distinguishes between rotational and continuous grazing. However, due to the country’s complexity and diversity of rangelands and land tenure, there is a need for a detailed and nuanced understanding of grazing management practices beyond these dualistic descriptions. This research aimed to describe grazing management practices of livestock farmers with different land tenure in five South African biomes. A case study approach with descriptive analysis was used for the study. A total of 66 interview responses were summarised from the Grassland, Savanna, Nama-Karoo, Succulent Karoo and Albany Thicket biomes. Twelve grazing management systems were identified, with herding, the 3-camp rotation and group camp approach as the main implemented systems across biomes and land tenure. These grazing management systems were associated with increased rangeland resting periods, reduced selective grazing and livestock protection. Intensive and technological grazing systems were practised on private farms, while traditional grazing systems were mainly practised on land reform and communal lands. The study recommends that South African agricultural policies and programme development need to take into consideration the complexity of rangelands, land tenure and grazing management systems in order to improve the sustainability of agricultural production in the country
Molecular phylogenetics of Thymelaeaceae-Thymelaeoideae: resolving the paraphyly of Gnidia and a new monophyletic generic classification for the group
(John Wiley and Sons Inc, 2026) Olaniyan, Oluwayemisi; Boatwright, James; Magee, Anthony; Manning, John C; van der Bank, Michelle
Earlier phylogenetic analyses of the family Thymelaeaceae using combined plastid (matK, rbcL, rps16, trnL-F) and nuclear (ITS) regions showed that the African-Malagasy genus Gnidia was extensively polyphyletic in relation to the southern African genera Lachnaea, Passerina and Struthiola, as well as to other Southern Hemisphere genera such as Drapetes, Kelleria and Pimelea. We present here a robust and well-sampled phylogenetic analysis of the subfamily Thymelaeoideae, with sampling in Gnidia increased to 76% of the species, to better resolve the polyphyly of the genus. Our analysis retrieved seven lineages of Gnidia nested in four independent evolutionary clades within the “Gnidia group” of the subfamily Thymelaeoideae. We analysed the options available for re-circumscribing Gnidia as a monophyletic genus, with secondary considerations of nomenclatural stability, phylogenetic and biogeographic information, and ease of identification. The option that we present retains the traditionally recognized genera Drapetes, Kelleria, Lachnaea, Passerina, Pimelea and Struthiola through the recognition of six lineages of Gnidia at the generic level. We propose that Gnidia be retained as a monotypic genus, including only the type of the genus name G. pinifolia. We reinstate the four previously recognized genera Basutica, Craspedostoma, Gnidiopsis and Thymelina and recognize the two new genera Epichroxantha and Phidia for the remaining two lineages of continental African Gnidia for which no names were available, plus the monotypic Zacharia for an anomalous Malagasy species that was previously excluded from Lasiosiphon. A taxonomic key and descriptions are provided for the genera in the “Gnidia group”. We also provide the necessary new combinations for names of Gnidia species now transferred to other genera.
Challenges, pitfalls, and potential solutions in assessing status and trends of spheniscus penguins
(Frontiers Media SA, 2026) Barham, Peter J; Balza, Ulises; Ampuero-Merino, Lyanne; Arce, Paulina; Boersma, P. Dee
Reliable, up-to-date assessments of population status and trends are essential for effective conservation. For the four Spheniscus penguin species, these are often undermined by methodological and logistical constraints due to their unique breeding ecology (e.g., burrow nesting and asynchronous breeding). As a result, no single survey method is universally applicable across the genus. Moreover, uneven sampling effort, inconsistent survey protocols, and variable data quality across countries and research groups further obscure true demographic patterns and complicate interpretations across species and regions. In consequence, population trends for these species—among the world's most threatened seabirds—are frequently uncertain or contradictory, limiting our ability to propose effective management actions. Here, we summarize the current challenges faced by researchers working across the ranges of Humboldt, African, Magellanic, and Galápagos penguins. We discuss pitfalls associated with extrapolating from non-representative colonies, integrating disparate data types, and interpreting trends in the context of climate-driven variability and threats. Finally, we propose a suite of solutions to strengthen future assessments and improve consistency and accuracy. Overall, we aim to chart a collaborative path toward more robust, comparable, and effective conservation assessments for these penguins as well as other seabirds.
Bulbine alooides (Asphodelaceae), a revision of a misunderstood succulent from the Western Cape
(British Cactus and Succulent Society, 2026) van Jaarsvelc, Ernst J.; Tribble, Derek V
Several species of Bulbine resemble an Aloe. This paper clarifies over a century of confusion surrounding application of the name Bulbine alooides, first published by Linnaeus as Anthericum alooides. It is a perennial leaf succulent from the Little Karoo region of South Africa. A very different, deciduous, tuberous species to which this name has been applied in recent decades is given a new name, Bulbine neo-nutans. A key is provided for identification that includes other broad-leaved Bulbines from sur-rounding areas. Three synonyms are reallocated. The fieldwork sheds new light on historical literature.
Regional mesopelagic fish assemblages in the Indian Ocean and Bay of Bengal, and their relationships to hydrographic characteristics
(National Inquiry Services Centre Ltd, 2026) Chacate, Osvaldo Ernesto; Coetzee, Janet; Gibbons, Mark
Mesopelagic fish often dominate the micronekton in the mesopelagic zone. Despite their ecological importance, information about their diversity, distribution and abundance in some areas of the Indian Ocean remains patchy and incomplete. Using data collected from three acoustic/trawl surveys spanning the western (WIO), central (CIO) and eastern (EIO) Indian Ocean regions in 2018, we investigated the composition and structure of the fish assemblages that were sampled using different pelagic trawl types, namely Macrozooplankton and Multpelt, which targeted the deep scattering layer (DSL) and shallow scattering layer (SSL). We assessed the structure of mesopelagic assemblages across the region at the level of genus and family, and analysed relationships between the samples with concurrently collected hydrographic data using multivariate statistics. Mesopelagic fish taxonomic richness varied across the region, as follows: WIO–68 genera (13 unique), 34 families (4); CIO–48 genera (6), 35 families (5); and EIO–86 genera (26), 44 families (9). Although there was a pronounced difference in the structure of the assemblages by survey region, gear type and time of day (and many interactions between these), the assemblages were significantly impacted by water temperature, dissolved oxygen and aspects of the chlorophyll a environment— which varied across the sampled areas. Intriguingly, the spatial patterns (and diversity) observed when the mesopelagic fish assemblages were examined at the genus level were likewise reflected when the data were analysed at the family level. The implications of these results are discussed.
Food, fuel, or forest? Interrogating the resource nexus dilemma behind deforestation through community-lived experiences in southern Malawi
(Elsevier Ltd, 2026) O'Farrell, Patrick John; Makwinja, Yamikani Harry; Kimengsi, Jude Ndzifon
Local communities are widely blamed for the increasing deforestation in Malawi, primarily due to agricultural expansion and the increased use of biomass energy. Yet, there is limited evidence to understand systemic trade-offs that communities face in their land-use decisions. This study examines the drivers of deforestation in Southern Malawi, focusing on community perceptions and the resource Nexus outcomes related to deforestation. We conducted 25 focus group discussions, 22 key informant interviews, and 271 household interviews across Chikwawa, Blantyre, Mwanza, Mulanje, and Thyolo districts. We also conducted seven expert interviews, facilitated five participatory workshops, and employed ethnographic techniques to gather the lived experiences of community members. The study reveals that (1) socio-economic needs for food, energy and income create a vicious cycle of cropland expansion at the direct expense of forest conservation. (2) Community perceptions identify biomass energy production (index=0.0788) as the main driver of deforestation, followed by cropland expansion (0.0769) and energy poverty (0.0746). (3) The dominance of negative ecological outcomes, followed by economic and political outcomes. The socio-cultural dimension reports the least negative outcomes. Nonetheless, positive outcomes are highest in the socio-cultural dimension, followed by the economic and political dimensions. The least positive outcomes are reported in the ecological dimension. The study empirically shows how community perceptions reshape the Resource Nexus and offers geographically specific policy recommendations. It treats deforestation as both socioeconomic and ecological problem, calling for integrated policies that address livelihood needs and structural drivers in Southern Malawi and similar areas in Sub-Saharan Africa.
High adult mortality of African Penguins Spheniscus demersus in South Africa after 2004 was likely caused by starvation
(Taylor and Francis Ltd., 2025) Sherley, Richard B; Crawford, Robert JM; Shannon, Lynne J; McInnes, Alistair M; Carpenter-Kling, Tegan; Makhado, Azwianewi B
From 2004–2011, following the collapse of sardine Sardinops sagax, a main food for African Penguins Spheniscus demersus, to < 25% of its maximum recorded abundance, survival of penguins breeding at Dassen and Robben islands, north of Cape Town, South Africa decreased markedly. Based on numbers of penguins breeding at the two islands and observed increased levels of mortality, it was estimated that ∼62 000 breeding individuals (∼95% of the birds that elected to breed in 2004) died as a result of food scarcity in this eight-year period. African Penguins moult annually, coming ashore and fasting for 21 days, when they shed and replace all their feathers. Failure to fatten sufficiently to moult, or to regain condition afterwards, results in death. At both islands, annual survival rates of adult penguins, and proportions of breeders that failed to return to their colonies to moult, were significantly related to an index of prey availability developed for the region. Although some adults moulted at a colony to the southeast, where food may have been more plentiful, much of the mortality likely resulted from failure of birds to fatten sufficiently to moult. The fishery exploitation rate of sardines west of Cape Agulhas was consistently above 20% between 2005 and 2010, peaking at 80% in 2006. In 2024, African Penguins were uplisted to Critically Endangered on the IUCN Red List. Management that helps to promote the long-term recovery of sardine biomass in the main foraging areas of African Penguins throughout their annual cycle will be important in securing their future survival.
An assessment of plant taxon richness and habitat distribution of Cape Inland Salt Pans, South Africa
(Elsevier B.V., 2026) Mngomezulu, Nomcebo Treasure; Rajkaran, Anusha; Veldkornet, Dimitri Allastair
Cape Inland Salt Pans (Azi 9) is a distinct vegetation unit in South Africa that is characterised by saline flats, serving as vital habitats, supporting unique biodiversity. Azi9 is different from other inland salt pans as they are remnants of ancient paleolakes. Despite their distinct biodiversity, data on their plant taxa richness and habitat distribution are lacking. This assessed the plant diversity and habitat distribution of Azi 9. Salt pans were visited throughout their distribution, where taxa occurrences were georeferenced, and specimens collected. Habitat composition was mapped using ArcGIS and SA land cover classes. In total, 55 plant taxa from 17 families were recorded, with Amaranthaceae (11 taxa) and Asteraceae (9 taxa) being the most abundant. The Soutvlei, along the southeast coast, had the highest taxa (17), followed by Rocherpan (16) and Yzerfontein salt pan (15). The species, Sporobolus virginicus and Spergularia glandulosa, were the most widely distributed (30% occurrence). There was an 57.9% addition in area and refinement of mapped saline systems from previous maps (8462 ha to 13,365 ha), mainly due to the inclusion of Wadrifsoutpan in the current habitat mapping analysis. Open water and vegetation were the dominant habitat types. Given the increasing environmental pressures on these fragile ecosystems, further research is necessary to ensure long-term preservation.
Do microplastics transfer from lower to higher trophic levels in rocky tidal pools at nature’s valley, South Africa?
(Springer Nature, 2026) du Pree, Cornel Mari; Johnson, Jaime Leigh; Rajkaran, Anusha; Bezuidenhout, Cornelius Carlos; Bouwman, Hindrik; Pieters, Rialet
Microplastics (MPs) are pervasive pollutants in marine ecosystems, yet their transfer across trophic levels in rocky tidal pools (RTPs) remains understudied. We collected and analyzed 239 samples, including seawater, sand, seaweed, and invertebrates representing multiple trophic levels, from RTPs at Nature’s Valley (Indian Ocean). Microplastics were detected in 98% of samples across multiple trophic levels, with mean concentrations ranging from 9 to 56 particles per individual, indicating widespread MP contamination of RTP organisms. These MPs were quantified and categorized by morphotype, color, size, and polymer composition. A total of 7,075 MPs were counted in 160 invertebrates, 60 seaweed fronds, 10 sand samples, and 9 water samples. The polymer composition of 2,350 MPs was separately analyzed using Fourier transform infrared (FT-IR). The MPs were predominantly fibers (96%) composed of polyamide, polypropylene, and polyethylene. The most common colors (>50%) were white and transparent. Morphotype, color, and size distributions show weak evidence of trophic transfer. However, MP polymer compositions showed no discardable correspondence between trophic levels. We therefore found very little evidence of trophic transfer between multiple trophic levels in the RTP organisms we studied. These findings indicate widespread microplastic contamination influenced by complex environmental exposure (such as bleaching and size reductions) and organismal interactions rather than clear trophic transfer pathways. Our study highlights the need for integrated approaches to elucidate MP dynamics in RTP food webs and informs future assessments of ecological risks associated with MP pollution in coastal habitats.
Computationally efficient Bayesian capture–mark–recapture models with transients, applied to survival of hand-reared African Penguins
(British Ecological Society, 2026) Sherley, Richard B.; Christian, Murray; Oosthuizen, W. Chris
Mark–recapture models are the primary framework for estimating demographic parameters in wild organisms. Complex life histories and sampling processes demand complex model formulations, yet these are vulnerable to errors in implementation and unanticipated biases. Simulation is a powerful tool to diagnose potential issues, but as the size of models and data increase, the computational cost of simulation-based model evaluation may discourage its use. A common phenomenon in mark–recapture studies is ‘transients’: the number of individuals that are only captured once exceeds that expected by the model. To avoid biasing survival estimates, transients should be accounted for. Mixture models offer a flexible, extensible and interpretable way to do so, but current implementations of transient mixture models as multievent models can have long runtimes for large datasets. Here, we describe a novel likelihood calculation for transient mixture models, which allows any multistate model with an efficient product-multinomial likelihood to account for transients at negligible extra computational cost. The resulting ‘extended product-multinomial’ (EPM) likelihoods are inferentially equivalent to multievent likelihoods, but faster to fit, often by an order of magnitude or more. A guide to implementation in R and Stan is provided. We illustrate our approach with a case study comparing survival of wild-raised and hand-reared African Penguins Spheniscus demersus. Facilitated by our EPM likelihood, we used simulation to assess our model's ability to disentangle survival differences from confounding factors whilst accounting for trap dependence and transience in the data. Hand-rearing was associated with higher juvenile survival and lower adult survival compared with wild-raised birds.
Phenolic and aldehyde responses of sugarcane and pineapple to sodium chloride and mannitol stress revealed by principal component analysis
(Springer, 2026) Naidoo, Sershen; Quintana-Zaez, Julio César; Lozada, Alberto
Identifying physiological traits that respond to stress is a challenge in plant biotechnology, given the complexity of salinity and water-deficit effects. This study evaluated the usefulness of Principal Component Analysis (PCA) to highlight the most relevant indicators in sugarcane and pineapple cultured in temporary immersion bioreactors (TIBs). Secondary data from previous experiments were used, including shoot multiplication rate, fresh biomass, and biochemical profiles (aldehydes, chlorophylls, carotenoids, and phenolics). PCA reduced dataset dimensionality and emphasized the variables with the greatest contribution to experimental variance, namely soluble phenolics, malondialdehyde, other aldehydes, and cell wall-linked phenolics. These findings confirmed that PCA is a valuable tool to guide breeding programs toward the selection of stress-resilient genotypes.

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