Ahemad Sade’s research while affiliated with Queen Elizabeth Hospital, Kota Kinabalu, Malaysia and other places

Simple Summary One-third of shark and ray species are threatened due to overfishing, but a lack of information on each species makes conservation decisions difficult. To address this issue, we conducted a study to identify the different species of sharks and rays in Malaysian waters using DNA barcoding of the CO1 gene, which is akin to DNA fingerprinting for species. We collected 175 individuals between June 2015 and June 2022, randomly selecting up to six specimens from each species. We successfully generated DNA barcodes for 67 species, belonging to 44 genera, 20 families, and 11 orders. Accurate species identification will improve species-specific catch landing data and accelerate the identification of use and illegal trade in Malaysia. Abstract The data provided in this article are partial fragments of the Cytochrome c oxidase subunit 1 mitochondrial gene (CO1) sequences of 175 tissues sampled from sharks and batoids collected from Malaysian waters, from June 2015 to June 2022. The barcoding was done randomly for six specimens from each species, so as to authenticate the code. We generated barcodes for 67 different species in 20 families and 11 orders. DNA was extracted from the tissue samples following the Chelex protocols and amplified by polymerase chain reaction (PCR) using the barcoding universal primers FishF2 and FishR2. A total of 654 base pairs (bp) of barcode CO1 gene from 175 samples were sequenced and analysed. The genetic sequences were blasted into the NCBI GenBank and Barcode of Life Data System (BOLD). A review of the blast search confirmed that there were 68 valid species of sharks and batoids that occurred in Malaysian waters. We provided the data of the COI gene mid-point rooting phylogenetic relation trees and analysed the genetic distances among infra-class and order, intra-species, inter-specific, inter-genus, inter-familiar, and inter-order. We confirmed the addition of Squalus edmundsi, Carcharhinus amboinensis, Alopias superciliosus, and Myliobatis hamlyni as new records for Malaysia. The establishment of a comprehensive CO1 database for sharks and batoids will help facilitate the rapid monitoring and assessment of elasmobranch fisheries using environmental DNA methods.

The coastal waters of the Malaysian state of Sabah are frequently affected by harmful algal blooms (HABs) mainly caused by Pyrodinium bahamense var. compressum and Margalefidinium polykrikoides, that have negative impacts on the aquaculture industry and human health. The project aims to develop a Public Information Map using ArcGIS to increase the effectiveness of sharing and communication of HAB information among relevant stakeholders and the community. The Department of Fisheries Sabah (DOFS) also participated in the project and knowledge transfer was done through a two-day on-line training. The output of the project are WebApps called MyRedTides. Altogether, two WebApps were developed: 1) cell density of P. bahamense and M. polykrikoides and 2) paralytic shellfish poisoning (PSP), i.e., toxin concentration of various coastal locations in Sabah. The developed WebApps contain useful information to the users such as the species responsible, recent, and previous HAB cases, as well as providing a platform for the sharing and exchange of information. Nevertheless, the use of this online WebApps as an early warning system is still at the preliminary stage because the acceptance and reaction of the stakeholders and local communities need to be evaluated. This is important to ensure that the HAB information is handled in the most effective manner.

The region of Eastern Sabah, Malaysia, harbours a rich diversity of eucheumatoid (i.e. Kappaphycus and Eucheuma spp.) algae. The global cultivation of this group of red algae has generally been increasing over the last five decades to respond to worldwide demand in carrageenans. Yet, the industry relies on a handful of clonally propagated individuals; hence the diverse populations of eucheumatoids in Eastern Sabah, Malaysia are widely regarded as potential source of novel germplasm useful for marker-assisted breeding. Based on an unprecedented depth of sampling of previously surveyed areas, this study was undertaken to determine the specific and intraspecific diversity of wild eucheumatoids in the Eastern Sabah region. Six eucheumatoid populations were haphazardly sampled, yielding 195 specimens. Using our previously established methods, the cox2–3 spacer (332 bp) and cox1 (1,407 bp) genetic markers were sequenced and analysed. Our data confirm that eucheumatoids in this area are extremely diverse: four eucheumatoid species in total were encountered and up to three different species coexist in each location surveyed; across all species, 17 novel haplotypes were uncovered. Importantly, we also found that the populations at the six sites investigated were highly differentiated, suggesting that nearby islands may also harbour distinct populations and more unknown haplotypes. Our findings also identified several cox2–3 spacer farmed haplotypes of K. alvarezii (haplotype 3, SWAG) and K. striatus (haplotype 89), suggesting that escapees from farms reproduce in the wild and may potentially compete with the indigenous eucheumatoid population in East Malaysia. These results highlight a need to extend genetic surveys to other islands for discovering novel diversity and to extend the coverage of conservation policies. They also stress the importance of Malaysia acting now to develop its own cultivars by tapping into the country’s rich natural diversity, as well as assessing the risks of bioinvasion to the natural population via long-term biodiversity assessments.

Studies have shown that cultivars of the carrageenophytes Kappaphycus and Eucheuma are clones of a limited number of strains originally domesticated from wild populations. For the development and selection of new cultivars, it is important that a comprehensive record of available variants exists. This study was conducted to provide up-to-date analysis and compilation of the current state of cultivars as the last list of cultivars was compiled nearly a decade ago. The present study analyzed the cox2–3 spacer and cox1 (1356 bp) genetic diversity of cultivars collected from 2019 to 2020 from the east coast of Sabah where the seaweed farms are concentrated. These data were compared with cultivars reported from 2010 to 2012 to assess changes, if any, to the gene pool of farmed eucheumatoid in Malaysia. Kappaphycus alvarezii, K. striatus, and K. malesianus are currently cultivated while Eucheuma denticulatum is no longer an important cultivar compared to a decade ago, probably due to its lower price. Analysis of the cox2–3 spacer revealed a new haplotype, LBT10, and, by including published GenBank data, a further four previously unnamed haplotypes were recognized from Sabah. This study confirms that there is a limited gene pool within cultivars in Malaysia and suggests the need for new or genetically diverse cultivars which can adapt to a changing environment, to ensure a more sustainable carrageenan industry.

This study evaluated on-farm implementation and effectiveness of Malaysian seaweed aquaculture policies and regulations that applied the biosecurity concept. The knowledge-attitude-practice (KAP) survey tool was utilised to assess the effectiveness of the biosecurity measures adopted by seaweed stakeholders, including 67 seaweed farmers and ten government extension officers, who were located in the three most productive seaweed producing regions. The KAP results indicated a disconnection between the implementation of biosecurity measures in national policy and uptake by practising farmers. Although farmer’s biosecurity knowledge and attitude scores were fair (55.7–64.1%), implementation of practices was poor (36.1–40.6%). The survey data highlighted that a low educational level, combined with the temporary nature of employment in the seaweed sector, contributes to the lower KAP scores. Extension officers are also limited in their ability to support farmers in implementing good biosecurity practices due to their moderate knowledge (57.9%), despite having a good attitude towards biosecurity (76.9%). The implementation of national seaweed policies including biosecurity prevention, and mitigation measures, remains weak due to the limited understanding and ability of the stakeholders to carry out farm risks. By identifying some forthwith gaps, this work highlights where short-term improvements and longer-term goals could be introduced. This study also highlights the importance of translating biosecurity policy into on-the-ground knowledge and stresses the need for economic support to enable a more significant impact in the upstream level of the seaweed aquaculture industry.

We characterized the genetic diversity, phylogeography, and demography of Tor sp. (Cyprinidae) from Sabah, Malaysian Borneo, by examining nucleotide variation in the D-loop region of the mtDNA. Sequence analysis of 18 populations (N = 173) yielded 35 unique mtDNA haplotypes with mean haplotype and nucleotide diversity of 0.833 and 0.023, respectively. Phylogenetic reconstructions using Bayesian, neighbor-joining, and maximum parsimony methods, as well as haplotype network, revealed four well-defined clades, namely, the eastern, central, northwestern, and southwestern clades, which corresponded to evolutionarily significant units (ESUs). These ESUs were estimated to have become separated since the late Miocene to Pliocene era (between 5 and 1 million years ago), with the central highlands of Sabah Crocker Trusmadi Range (CTR) constituting the main barrier to genetic exchange between clades. Analysis of molecular variance (AMOVA) and pairwise genetic differentiation showed significant population structuring (Φct = 0.575–1.000, p < 0.05). We further identified eight major groups of river systems harboring reproductively isolated Tor subpopulations. Neutrality statistics and Bayesian skyline plots (BSP) suggested constant population size over time for most Tor populations. Tor sp. in Sabah is comprised of four ESUs (eastern, central, northwestern, and southwestern ESUs), and that each ESU can be compartmentalized into 1–4 MUs. Due to isolation by distance, the highest number of MU occurs in the low-elevation drainages of Eastern Sabah, which is the largest in terms of land area. The evidence provided by this study supports the hypothesis that the four ESU represent genetically distinct subpopulations of Tor and highlight the urgent need for the in situ conservation of these subpopulations.

The application of biosecurity in seaweed aquaculture plays an important role in reducing the impact of disease and pest outbreaks. The continuous occurrence of seaweed pests including the macroalgal epiphytes, epi-endophytic filamentous algae and biofilms on Kappaphycus farms may also potentially induce further incidences of the ice-ice syndrome. In this study, on-farm biosecurity management measures were tested on the commercially grown seaweeds Kappaphycus malesianus and Kappaphycus alvarezii during peak ice-ice season at Gallam-Gallam Village, Sabah, Malaysia. The investigation was focused on preventative control measures including the early detection of the ice-ice syndrome and pests through propagule health checks, regular cleaning of the crop thallus and associated long-line ropes and monitoring of the environment. Farm procedures and practices were also assessed in terms of their biosecurity ‘risk’ using the hazard analysis and critical control point (HCCAP) approach. Observations were replicated in two different farm management systems; one system adopted routine biosecurity measures and the other had no biosecurity measures. The results showed that the ice-ice syndrome and pest outbreak was significantly decreased by 60–75% for K. malesianus and 29–71% for K. alvarezii at the farm which adopted the routine biosecurity measures compared with the no biosecurity treatment. The biosecurity measures also significantly improved growth rate and seaweed quality. The infection levels of the epi-endophyte Melanothamnus sp. contributed to the ice-ice syndrome in K. malesianus , whilst the epiphyte coverage was correlated to the ice-ice incidence in K. alvarezii . This study provides the first evidence of biosecurity management measures significantly decreasing the incidence of the ice-ice syndrome and pests on a commercial seaweed farm.

The demersal brown banded bamboo shark Chiloscyllium punctatum is a major component of sharks landed in Malaysia. However, little is known about their population structure and the effect of high fishing pressure on these weak swimming sharks. Both mitochondrial DNA control region (1072 bp) and NADH dehydrogenase subunit 2 (1044 bp) were used to elucidate the genetic structure and connectivity of C. punctatum among five major areas within the Sundaland region. Our findings revealed (i) strong genetic structure with little present day mixing between the major areas, (ii) high intra-population genetic diversity with unique haplotypes, (iii) significant correlation between genetic differentiation and geographical distance coupled with detectable presence of fine scale geographical barriers (i.e. the South China Sea), (iv) historical directional gene flow from the east coast of Peninsular Malaysia towards the west coast and Borneo, and (v) no detectable genetic differentiation along the coastline of east Peninsular Malaysia. Genetic patterns inferred from the mitochondrial DNA loci were consistent with the strong coastal shelf association in this species, the presence of contemporary barriers shaped by benthic features, and limited current-driven egg dispersal. Fine scale population structure of C. punctatum highlights the need to improve genetic understanding for fishery management and conservation of other small-sized sharks.

The eucheumatoids Kappaphycus and Eucheuma are cultivated in tropical or subtropical regions for the production of carrageenan, a hydrocolloid widely used in the food and cosmetic industries. Kappaphycus alvarezii is a highly valued economic crop in the Coral Triangle, with the Philippines, Indonesia and Malaysia ranked among the largest producers. In the absence of measures to mitigate climate change, extreme events including heatwaves, typhoons, severe El Niño and La Niña, are expected to increase in frequency and magnitude. This inadvertently brings adverse effects to the seaweed cultivation industry, especially in the tropics. Temperatures are rapidly reaching the upper limit of biologically tolerable levels and an increase in reports of ice-ice and pest outbreaks is attributable to these shifts of environmental parameters. Nevertheless, few reports on the response of eucheumatoids to a changing environment, in particular global warming, are available. Understanding the responses and possible mechanisms for acclimation to warming is crucial for a sustainable seaweed cultivation industry. Here, the physiological and biochemical responses of K. alvarezii to acute warming indicated that the strain used in the current study is unlikely to survive sudden increases in temperature above 36°C. As temperature increased, the growth rates, photosynthetic performance, phycocolloid quality (carrageenan yield, gel strength and gel viscosity) and pigment content (chlorophyll-a, carotenoid and phycobiliproteins) were reduced while the production of reactive oxygen species increased indicating the occurrence of stress in the seaweeds. This study provides a basis for future work on long term acclimation to elevated temperature and mesocosm-based multivariate studies to identify heat-tolerant strains for sustainable cultivation.