Philippa Kaur

Figure 1 presents the track of the eight-month cruise, and Table 1 provides the detail of the legs and dates. On a routine basis R/V Hesperides sailed at an average speed of 11 knots from around 3 pm to 4 am (local time). The vessel arrived on station at around 4 am daily to carry out sampling operations at a fixed point for about 11 hours.Fig. 1Cruise track and integrated backscatter at different stations (NASC, daytime 200 to 1000 m).Full size imageTable 1 Dates and starting points of the 7 legs of the Malaspina cruise.Full size tableAcoustic measurements were carried out continuously using a Simrad EK60 echosounder), operating at 38 and 120 kHz (7° beamwidth transducers) with a ping rate of 0.5 Hz. Unfortunately, the 120 kHz failed during the first leg of the cruise and only 38 kHz data were collected. Echosounder observations were recorded down to 1000 m depth. The echosounder files are in the proprietary Simrad raw format and can be read by various softwares (e.g., LSSS, Echoview, Sonar5, MATECHO, ESP3, echopype, pyEcholab). GPS locations and calibration constants are imbedded in each file.Additionally, daytime data integrated over 2 m vertical bins from 200 to 1000 m depth are provided as Nautical Area Scattering Coefficient (NASC). Each “voxel” is the average of all cleaned and validated data recorded over that depth range, in a time period starting 8 hours before the start of the station (defined as start of the CTD cast) and ending 8 hours after the start of the station, with only data recorded in the period between 1 hour after local sunrise and 1 hour prior to local sunset accepted (i.e., during local daytime hours, but removing crepuscular periods when vertical migration of biota is strong). The relatively long interval over which data were accepted around each station was chosen since the station sampling resulted in noisy acoustic data,, a long interval was therefore chosen to ensure valid data on all stations.Finally, summaries of per station daytime and nighttime acoustic data (omitting data recorded within 1 hour of sunrise and sunset) are provided. The data fields in this file are station date, latitude and longitude, and per day and night average NASC 200–1000 m, average NASC 0–1000, weighted mean depth (WMD) of NASC 200–1000 m, migration amplitude, NASC day-to-night ratio and migration ratio. More

We analyse weekly reported counts of suspected and confirmed human cases and deaths attributed to LF (as defined in Supplementary Table 1), between 1 January 2012 and 30 December 2019, from across the entire of Nigeria. The weekly counts were reported from 774 LGAs in 36 Federal states and the Federal Capital Territory, under Integrated Disease Surveillance and Response (IDSR) protocols, and collated by the NCDC. All suspected cases, confirmed cases and deaths from notifiable infectious diseases (including viral haemorrhagic fevers; VHFs) are reported weekly to the LGA Disease Surveillance and Notification Officer (DSNO) and State Epidemiologist (SE). IDSR routine data on priority diseases are collected from inpatient and outpatient registers in health facilities, and forwarded to each LGA’s DSNO using SMS or paper form. Subsequently, individual LGA DSNOs collate and forward the data to their respective SE, also by SMS and paper form, for weekly and monthly reporting respectively to NCDC. From mid-2017 onwards, data entry in 18 states has been conducted using a mobile phone-based electronic reporting system called mSERS, with the data entered using a customised Excel spreadsheet that is used to manually key into NCDC-compatible spreadsheets. Data from this surveillance regime (WERs) were collated by epidemiologists at NCDC throughout the period 2012 to March 2018 (Supplementary Fig. 1).Throughout the study period, within-country LF surveillance and response has been strengthened under NCDC coordination2,20,33. LGAs are now required to notify immediately any suspected case to the state-level, which in turn reports to NCDC within 24 h, and also sends a cumulative weekly report of all reported cases. A dedicated, multi-sectoral NCDC LF TWG was set up in 2016 with the responsibility of coordinating all LF preparedness and response activities across states. Further capacity building occurred in 2017 to 2019, with the opening of three additional LF diagnostic laboratories in Abuja (Federal Capital Territory), Abakaliki (Ebonyi state) and Owo (Ondo state) (to a total of five; Fig. 2) and the rollout of intensive country-wide training on surveillance, clinical case management and diagnosis. We note that, due to the rapid expansion in a test capacity, the definition of a suspected case in our data has subtly changed over the surveillance period: from 2012 to 2016, suspected cases include probable cases that were not lab-tested, whereas from 2017 to 2019, all suspected cases were tested and confirmed to be negative.In addition to the WERs data, since 2017 LF case reporting data has also been collated by the LF TWG and used to inform the weekly NCDC LF Situation Reports (SitRep data; https://ncdc.gov.ng/diseases/sitreps). This regime includes post hoc follow-ups to ensure more accurate case counts, so our analyses use WER-derived case data from 2012 to 2016, and SitRep-derived case data from 2017 to 2019 (see Fig. 1 for full time series). A visual comparison of the data from each separate time series, including the overlap period (2017 to March 2018) is provided in Supplementary Fig. 1, and all statistical models considered random intercepts for the different surveillance regimes. Where other studies of recent Nigeria LF incidence have been more spatially and temporally restricted34,35, the extended monitoring period and fine spatial granularity of these data provide the opportunity for a detailed empirical perspective on the local drivers of LF at a country-wide scale and their relationship to changes in reporting effort.Recent trends in LF surveillance in NigeriaWe visualised temporal and seasonal trends in suspected and confirmed LF cases within and between years, for both surveillance datasets. Weekly case counts were aggregated to country-level and visualised as both annual case accumulation curves, and aggregated weekly case totals (Fig. 1 and Supplementary Fig. 1). We also mapped annual counts of suspected and confirmed cases across Nigeria at the LGA-level to examine spatial changes in reporting over the surveillance period (Fig. 2). State and LGA shapefiles used for modelling and mapping were obtained from Humanitarian Data Exchange under a CC-BY-IGO license (https://data.humdata.org/dataset/nga-administrative-boundaries).Analyses of aggregated district data are sensitive to differences in scale and shape of aggregation (the modifiable areal unit problem; MAUP36), and LGA geographical areas in Nigeria are highly skewed and vary over >3 orders of magnitude (median 713 km2, mean 1175 km2, range 4–11,255 km2). We therefore also aggregated all LGAs across Nigeria into 130 composite districts with a more even distribution of geographical areas, using distance-based hierarchical clustering on LGA centroids (implemented using hclust in R), with the constraint that each new cluster must contain only LGAs from within the same state (to preserve potentially important state-level differences in surveillance regime). Weekly and annual suspected and confirmed LF case totals were then calculated for each aggregated district. We used these spatially aggregated districts to test for the effects of scale on spatial drivers of LF occurrence and incidence.Statistical analysisWe analysed the full case time series (Fig. 1) to characterise the spatiotemporal incidence and drivers of LF in Nigeria, while controlling for year-on-year increases and expansions of surveillance effort. We firstly modelled annual LF occurrence and incidence at a country-wide scale, to identify the spatial, climatic and socio-ecological correlates of disease risk across Nigeria. Secondly, we modelled seasonal and temporal trends in weekly LF incidence within hyperendemic areas in the north and south of Nigeria, to identify the seasonal climatic conditions associated with LF risk dynamics and evaluate the scope for forecasting. All data processing and modelling was conducted in R v.3.4.1 with the packages R-INLA v.20.03.1737, raster v.3.4.1338 and velox v0.2.039. Statistical modelling was conducted using hierarchical regression in a Bayesian inference framework (integrated nested Laplace approximation (INLA)), which provides fast, stable and accurate posterior approximation for complex, spatially and temporally-structured regression models37,40, and has been shown to outperform alternative methods for modelling environmental phenomena with evidence of spatially biased reporting41.Processing climatic and socio-ecological covariatesWe collated geospatial data on socio-ecological and climatic factors that are hypothesised to influence either M. natalensis distribution and population ecology (rainfall, temperature and vegetation patterns), frequency and mode of human–rodent contact (poverty and improved housing prevalence), both of the above (agricultural and urban land cover) or likelihood of LF reporting (travel time to nearest laboratory with LF diagnostic capacity and travel time to nearest hospital). For each LGA we extracted the mean value for each covariate across the LGA polygon. The full suite of covariates tested across all analyses, data sources and associated hypotheses are described in Supplementary Table 5.We collated climate data spanning the full monitoring period and up until the date of analysis (July 2011 to January 2021). We obtained daily precipitation rasters for Africa42 from the Climate Hazards Infrared Precipitation with Stations (CHIRPS) project; this dataset is based on combining sparse weather station data with satellite observations and interpolation techniques, and is designed to support hydrologic forecasts in areas with poor weather station coverage (such as tropical West Africa)42. A recent study ground-truthing against weather station data showed that CHIRPS provides greater overall accuracy than other gridded precipitation products in Nigeria43. Air temperature daily minimum and maximum rasters were obtained from NOAA and were also averaged to calculate daily mean temperature. EVI, a measure of vegetation quality, was obtained from processing 16-day composite layers from NASA (National Aeronautics and Space Administration) (excluding all grid cells with unreliable observations due to cloud cover and linearly interpolating between observations to give daily values; Supplementary Table 5).We derived several spatial bioclimatic variables to capture conditions across the full monitoring period (Jan 2012 to Dec 2019): mean precipitation of the driest annual month, mean precipitation of the wettest annual month, precipitation seasonality (coefficient of variation), annual mean air temperature, air temperature seasonality, annual mean EVI and EVI seasonality. We also calculated monthly total precipitation, 3-month SPI44, average daily mean (Tmean), minimum (Tmin) and maximum (Tmax) temperature and EVI variables at sequential time lags prior to reporting week for seasonal modelling (described below in Temporal drivers). SPI is a standardised measure of drought or wetness conditions relative to the historical average conditions for a given period of the year. SPI was calculated within a rolling 3-month window across the full 40-year historical CHIRPS rainfall time series (1981–2020) using the R package SPEI v.1.744.We accessed annual human population rasters at 100 m resolution from WorldPop. We accessed the proportion of the population living in poverty in 2010 ( More

Phototactic behaviourThe optimization results of the proposed behavioural setup allowed the phototactic behaviour of the studied D. magna clone and the effects of FK treatment on this behaviour to be monitored and quantified. Furthermore, the effects of the FKs were evident only upon light exposure, were more apparent after a short (5 min) acclimation to light and were tightly regulated by the light intensity. The above-mentioned factors agree with previous studies, which found a marked positive phototactism of clone P132,8528 and that the effects of the FKs become consistent after 5 min of light exposure28. Moreover, it has also been reported that light intensity controls anti-predatory defences in Daphnia29.The effects of the pharmacological treatments were consistent for GABAergic and muscarinic cholinergic compounds across two or three identical non-consecutive experiments performed over more than one year. Consistency of the toxicological results and, in particular, of the behavioural responses should be compulsory in toxicological studies to increase the credibility and robustness of the findings30,31. Agonists of these two neurotransmitter receptors (DZP, PILO) and the antagonist of the GABA receptor (PICRO) affected the induction of the phototactic behavioural changes (i.e., interfered with fish recognition). The receptor agonists DZP and PILO counteracted the negative phototactism evoked by the FKs, whereas PICRO enhanced the effect of the FKs, increasing the negative phototactism. None of the three applied substances when applied alone induced anti-predatory fish phototactic behaviour, indicating that these compounds interfered with the FK sensorial pathway. Alternatively, the muscarinic cholinergic antagonist SCOP interfered with phototaxis itself, almost completely abolishing the positive phototactic behaviour of the studied clone under both control and FK conditions. This indicates that the muscarinic cholinergic signalling pathway could potentially be a major regulator of anti-predatory fish phototactic behaviour. In D. pulex and D. galeata, the formation of neck teeth or helmets in response to predatory kairomones released by invertebrate predators has been related to a series of biological reactions that involve kairomone perception and neuronal signals, which are converted into endocrine signals and subsequently induce changes in the expression of morphogenetic factors32,33. We previously showed that DZP, PILO, PICRO and SCOP were neuroactive in D. magna, affecting sensitization and/or habituation motile responses to repetitive light stimuli34; thus, it is likely that these compounds disrupted neurological signalling pathways related to the phototactism shifts caused by FK perception or to the phototaxis itself.Little is known about how phototaxis is neuronally coded. In D. pulex, both in silico and experimental works have shown that histaminergic neurons may mediate phototactic responses to UV irradiation12. By using histamine immunohistochemistry, the previous authors labelled putative photoreceptors in the compound eye and neuronal projections from these cells to the brain. The D. pulex genome also has a putative Drosophila orthologue of histidine decarboxylase (the rate-limiting biosynthetic enzyme for histamine), as well as two putative histamine-gated chloride channels (hclA and hclB orthologues). Exposure of D. magna to cimetidine, an H2 receptor antagonist known to block both hclA and hclB in D. melanogaster, inhibited the negative phototactic responses of these orthologues to UV irradiation. In another study, it was found that short-day photoperiods induced a significant increase in light-avoidance behaviours relative to controls and increased glutamate signalling, which is a critical pathway in arthropod light-avoidance behaviour35. It has also been reported that a group of serotonergic cells located in the protocerebrum probably control phototactic behaviour16. Notably, the perception of predatory kairomones and neuronal and cellular wiring is largely unknown in Daphnia2. For example, the receptors that detect invertebrate cues from Notonecta in D. longicephala were shown to be located on the first antennae, from which neurites extend into the deutocerebrum of the brain. However, key olfactory neuronal structures, such as olfactory glomeruli in the deutocerebrum, were not found2.Our results obtained for DZP, an agonist of the GABAA receptor, agree with those of Weiss et al.11, who found that co-exposure to FKs and exogenous GABA ameliorated life history changes to FKs in a D. pulex clone, whereas co-exposure with the GABAA antagonist PICRO did not have any effect. The ineffectiveness of PICRO on the modulation of FK effects in D. pulex found by Weiss et al.11 might indicate species differences resulting from different receptor amino acid sequences. For example, GABAA receptor subtypes with a single amino acid replacement make the Drosophila GABAA receptor PICRO-insensitive36. Indeed, in crustaceans, lobster GABAA receptors were also found to be insensitive to PICRO37. There is also the possibility that FK-mediated changes in phototactic behaviour and life history traits may be controlled by different mechanisms6.Reported information on the modulatory effects of cholinergic compounds on anti-predatory defences in Daphnia is limited to invertebrate predatory cues, which, according to previous studies, should be regulated by neurological mechanisms distinct from those of fish2,11. Our results showed that the neurological cholinergic mechanisms that modulate induced defence responses against invertebrate predators or that mimic these responses are also able to do the same for fish predation but in the opposite way. Physostigmine and carbaryl, which are acetylcholinesterase inhibitors that increase acetylcholine receptor activity, enhanced and mimicked, respectively, the morphogenetic effects of invertebrate kairomones in several Daphnia species11,21,23. Conversely, atropine, which is a muscarinic acetylcholine receptor (AChR) inhibitor like SCOP, diminished neck tooth formation in D. pulex11,21. In our study, SCOP alone abolished the positive phototactism of the studied clone, which mimicked the effects of the FKs. Conversely, PILO, which is a muscarine AChR agonist, ameliorates the phototactic responses to FKs.The nicotinic AChR agonists (NICO, IMI) and antagonist (MEC) only marginally affected the phototactic responses to the FKs. This indicates that muscarinic cholinergic signalling but not nicotinic signalling is involved in phototaxis/phototactic behaviour. It is therefore possible that both FK and SCOP treatment, through inhibition of muscarinic cholinesterase receptor activity, diminished the positive phototaxis of the studied clone, and PILO activation of these receptors ameliorated the effects of the FKs. In insects, neurons that connect olfactory inputs to higher-order brain areas that coordinate behavioural responses are thought to be under cholinergic control38.In general, GABA is known to have inhibitory functions. It has been proposed that the continuous activation of the GABAergic neuronal pathway by endogenous GABA without predatory cues prevents life history shifts11, which in our case would be the transition from positive to negative phototaxis. FKs and PICRO relieve inhibition, which can be re-established by the experimental application of GABAA receptor agonists such as DZP or GABA itself. Our results and those of Weiss et al.11 agree with the previous argument.Equi-effective mixtures of the tested agonists and antagonists had similar effects on D. magna responses to FKs as the single mixture compound treatments did, indicating that the joint effects of agonists and antagonists of the GABAergic and cholinergic signalling pathways can act cooperatively and probably independently, modulating the effects of FKs. This is in line with other findings that showed that key ecophysiological responses in Daphnia are regulated by several signalling receptor pathways, which likely ensures more robust control. This is the case for the storage lipid dynamics associated with moulting and reproduction39.The involvement of additional neurotransmitter signalling pathways, such as the serotonergic pathway, can also be taken into consideration despite being less consistent. Agonists of the serotonin receptor (such as serotonin) or treatments that increase serotonin levels (such as fluoxetine) ameliorated the effects of the FKs in only one experiment, but treatments that decreased serotonin, such as PCPA, increased the effects of the FKs in two out of the three experiments. Previously, we reported that serotonin activity in the brains of D. magna increased with algae food levels, and thus, the effects of fluoxetine on the enhancement of brain serotonin levels could only be observed under limited food conditions24. This indicates that the high levels of food used in our experiments probably prevented fluoxetine from increasing the already high serotonin levels in the central nervous system. Interestingly, inducible fish kairomone changes in phototactic behaviour in Daphnia increased with food level40, which is probably related to high levels of serotonin. On the other hand, the effects of PCPA, which decreases serotonin concentrations26, are unlikely to be modulated by food since this drug inhibits tryptophan hydrolase, the serotonin synthesis rate-limiting enzyme in D. magna41. This is apparently the case in our study.Neurophysiological stimulation experiments with dopaminergic/adrenergic agonists and antagonists were inconclusive since in only one out of two experiments the dopaminergic agonist APO diminish negative phototaxis after FK exposure. We also did not find any effects from the glutamatergic agonists and antagonists on phototactism. This could be related to the low stability of dopaminergic compounds in water and the reported small effects of glutaminergic compounds on the Daphnia motile response to light34.Consistent failure of the tested antihistaminergic drugs to modulate phototactism to visible light disagrees with previous findings that discovered that these drugs affected phototactism but at much higher doses12.Metabolomic changesThe study of metabolomic changes across the treatments that modulated FK-mediated phototactic changes or altered phototaxis provided further experimental evidence of the involvement of key neurological signalling metabolic pathways. Caution must be exercised, however, since the studied receptor agonist and antagonist drugs do not change the neurotransmitters or their related metabolites. Nevertheless, little is known about how these drugs may affect the Daphnia neuronal metabolome. The cholinergic neurotransmitter system is one of the most important systems that plays a pivotal role in learning and memory in animal species, including D. magna34,42. Whole-body concentrations of acetylcholine decreased in females exposed to FKs and those exposed to SCOP and increased in those exposed to the agonists PILO and DZP. Thus, it is possible to establish a direct link between the decreased levels of acetylcholine and decreased positive phototactism in the studied clone. The results obtained for the GABAergic and serotonergic signalling pathways were less convincing, as FKs alone did not consistently affect the levels of GABA and serotonin. However, co-exposure to FK and the GABAA receptor agonist DZP increased endogenous GABA levels, which is in line with the results reported by Weiss et al.11, who also found that the addition of exogenous GABA ameliorated FK effects. Interestingly, the summarized results depicted in Fig. 4 showed that serotonin levels dereased upon exposure to SCOP, PICRO and PILO but PILO also increase the levels of the serotonin degradation metabolite 5-HIAA. This may indicate that PILO may affect the turnover rather than the levls of serotionin.Previous findings have reported altered responses to light in D. magna individuals lacking serotonin16. Therefore, it is possible to establish a link between the observed marked negative phototactism of females exposed to SCOP and low levels of serotonin.Dopaminergic- and adrenergic-related metabolites deserve special attention, although there is only evidence that dopamine is involved in the proliferation and structural formation of morphological defences in Daphnia for invertebrate kairomones22. In some invertebrates, adrenergic signalling is considered to be absent, and the analogous functions are performed by octopamine43. In our study, fish kairomones and SCOP decreased the levels of dopamine and octopamine, whereas females co-treated with the agonists DZP and PILO and FKs showed relatively high levels of dopamine. In the insect Drosophila melanogaster, which shares many gene signalling pathways with Daphnia44, individuals deficient in dopamine show reduced positive phototactism45. Unfortunately, it is not possible to know whether the observed changes in DA in the whole bodies of D. magna indicate that DA is less used or used in excess. Figure 4 indicates that FK and SCOP reduced both DA and its intermediary metabolite L-DOPA. SCOP also increased the DA degradation metabolite 3-MT and two norepinephrine metabolites/neurotransmitters (NOEM, EPPY) that ultimately depend on DA. This means that FK decreased DA probably decreasing its intermediary metabolite L-DOPA, whereas SCOP decreased DA to a greater extent decreasing its intermediary L-DOPA but also increasing its turnover rate. Our neurophysiological stimulation experiments with dopaminergic active compounds are also not conclusive. This suggests that further research is needed to study the involvement of dopaminergic signalling in the response to fish. Existing studies on adrenergic signalling in daphnids indicated that β-blockers such as propranolol diminish the heart rate46 and motile responses to light27, which are related to the known role of adrenergic signalling that regulates blood pressure47 and other fight-or-flight responses to stress48. Future research is needed to elucidate the involvement of OCT, EPPY and NORM in the phototactic response of D. magna to FKs.In summary, this study provides consistent results that muscarinic cholinergic and GABAergic receptor agonists and antagonists are able to ameliorate or enhance, respectively, the phototactic response of adult females from the studied D. magna clone to FKs. Furthermore, inhibition of the muscarinic acetylcholine receptor by SCOP induced the phototactic response to fish kairomones. This may indicate that muscarinic cholinergic antagonists changed phototaxis, whereas muscarinic cholinergic agonists and GABAergic agonists and antagonists changed the perception of FKs. Serotonergic agonists and antagonists were also able to diminish and increase FK effects, respectively, but only in half of the trials performed. The fact that we could not observe effects from the remaining neuroactive agents (i.e., dopaminergic, histaminergic, glutamatergic) could simply be because they are not relevant for predator-induced anti-phototaxis. The study of neurotransmitters and their related metabolite changes allowed us to identify acetylcholine and GABA as putative key metabolites associated with the observed phototactic modulatory effects of FK and cholinergic and GABAergic compounds. Increased and decreased levels of dopamine in the whole bodies of D. magna were related to positive and negative phototactic behaviours, respectively, but could not be related to neurophysiological studies with the tested dopaminergic drugs. More

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