Ecology

Dataset of beneficial plantsI collated a species-level dataset of plant benefits (presence/absence data) starting from the information gathered by Kleunen et al.32. These authors extracted data from the WEP database (National Plant Germplasm System GRIN-GLOBAL; https://npgsweb.ars-grin.gov/gringlobal/taxon/taxonomysearcheco.aspx, Accessed 7 Jan 2016), which is based on the book by Wiersema and León20. Their dataset included 84 categories and subcategories of plant benefits pertaining human and animal nutrition, materials, fuels, medicine, useful poisons, social and environmental benefits. Subcategories of benefits, which often included very few records, were merged here into 25 standard and major categories following the guidelines in the Economic Botany Data Collection Standard33 as in Molina-Venegas et al.13, namely ornamental plants, soil improvers, hedging/shelter, human food, human-food additives, vertebrate food, invertebrate food, fuelwood, charcoal, other biofuels, timber, cane/stems, fibres, tannins/dyestuffs, beads, gums/resins, lipids, waxes, essential oils/scents, latex/rubber, medicines, invertebrate poison, vertebrate poison, smoking materials/drugs and symbolic/inspirational plants (Fig. 1). A few records (n = 93) that could not be assigned to any of the above categories were disregarded, and so was the category ‘gene source’ because unlike other benefits, any species is intrinsically a potential gene donor and hence there is not a clear link between the benefit and species features. Note that this is not to say that preserving genetic diversity, which indeed is the underlying message of this research, is a meaningless goal. Infraspecific taxa were collapsed at the species level, and the very few fern taxa in the original database32 were excluded. In total, I gathered 15,834 plant-benefit records sorted in a matrix of 25 types of benefits and 9521 species of seed plants. Most species (83.74%) provided only one or two benefits representing 62.83% of the records in the dataset, and the maximum number of benefits per species was 10 (only three species). Although the WEP database is the largest species-level database on plant benefits32, it does not claim to be comprehensive20. Yet, the size of the dataset I gathered here represented 76.19% of the total seed-plant genus-level records collated for the same types of benefits in a more comprehensive survey by Molina-Venegas et al.13 that based on Mabberley’s Plant-book34. Moreover, the total number of records per category (at the genus-level) strongly correlated between the datasets (Pearson r = 0.94, p  More

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Dissolved oxygen modelThe dissolved oxygen in this model had a number of interactions to consider. Oxygen consumption through the processes of both respiration and nitrification. On the other hand, the water receives oxygen through water agitation as it is pumped through the system and from the oxygen generator. Oxygen is added to the water by oxygen generator and flow aeration (Fig. 1).Figure 1Dissolved oxygen model.Full size imageThe required oxygen supplementation is a sum of the pervious components as follows:$$ DO_{FR} + DO_{B} + DO_{N} = DO_{sup } + DO_{PF} $$
(1)
where DOFR is the dissolved oxygen consumption through fish respiration, g O2 m−3 h−1. DOB is the dissolved oxygen consumption through the biofilter, g O2 m−3 h−1. DON is the dissolved oxygen consumption through nitrification, g O2 m−3 h−1. DOPF is the dissolved oxygen addition through pipe flow, g O2 m−3 h−1. DOsup is the required oxygen supplementation (oxygen generator), g O2 m−3 h−1.The rate of change in DO concentration in fish tank:$$ frac{dDO}{{dt}} = DO_{FR} + DO_{B} + DO_{N} – DO_{PF} $$
(2)
where (frac{dDO}{{dt}}) is the rate of change in DO concentration during the time interval, g O2 m−3 h−1. dt is the rate of change in the time interval, hAfter calculating oxygen concentration for each element at each time step, the net oxygen change is then added to or subtracted from the previous time step`s oxygen concentration. DO concentrations can be calculated at any time (t) as:$$ DO_{t} = DO_{t – 1} + left( {frac{dDO}{{dt}} cdot dt} right) $$
(3)
where DOt is the DO concentration (g m−3) at time t. DOt−1 is the DO concentration (g m−3) at time t−1.The rate of oxygen consumption through fish respiration can be calculated on water temperature and average fish weight. This calculation is shown in the following equation10:$$ FR = 2014.45 + 2.75W – 165.2T + 0.007W^{2} + 3.93T^{2} – 0.21WT $$
(4)
$$ DO_{FR} = frac{FR times SD}{{1000}} $$
(5)
where FR is rate of oxygen consumption through fish respiration, mg O2 kg−1 fish. h−1. W is average of individual fish mass, g. T is water temperature, °C. SD is the stocking density of fish, kg m−3.The correlation coefficient for the equation was 0.99. Data used in preparing the equation ranged from 20 to 200 g for fish weight and from 24 to 32 °C.The rate of oxygen consumption through nitrification is calculated in terms of Total Ammonia Nitrogen (TAN) that is converted from ammonia to nitrate. The rate found in the literature is 4.57 g O2 g−1 TAN6.The oxygen consumption in nitrification process can be calculated as11:$$ DO_{N} = 4.57 times K_{NR} times {{{text{Nr}}} mathord{left/ {vphantom {{{text{Nr}}} {text{V}}}} right. kern-nulldelimiterspace} {text{V}}} $$
(6)
$$ K_{NR} = 0.1left( {1.08} right)^{{left( {T – 20} right)}} $$
(7)
$$ Nr = frac{{0.03 times F_{r} times W times N_{F} }}{24 times 1000} $$
(8)
where KNR is the coefficient of nitrification. Nr is the nitrification rate, g TAN h−1. Fr is the feeding ratio, % of body fish day−1. NF is the number of fish. V is the water volume, m3.The feeding ratio can be calculated as the following equation:$$ F_{r} = 17.02 times e^{{left[ {{raise0.7exhbox{${left( {ln W + 1.14} right)^{2} }$} !mathord{left/ {vphantom {{left( {ln W + 1.14} right)^{2} } { – 19.52}}}right.kern-nulldelimiterspace} !lower0.7exhbox{${ – 19.52}$}}} right]}} $$
(9)
The bacteria in the biofilter are a second source of oxygen consumption. Lawson explains that the biofilter oxygen demand is approximated 2.3 times the BOD5 production rate of fish6. The oxygen consumption of the biofilter is calculated using following equation:$$ DO_{B} = frac{{(2.3)left( {BOD_{5} } right)left( {W_{n} } right)}}{{left( V right)left( {24} right)left( {1000} right)}} $$
(10)
where BOD5 is average unfiltered BOD5 excretion rate, 2160 mg O2 kg−1 fish day−1. Wn is biomass, kg fish.The water pumping cycle was a source of oxygen addition to the system. The amount of oxygen addition through the water pumping cycle was calculated on an hourly basis. The method of calculating aeration from a pipe is detailed by12:$$ DO_{PF} = frac{PC times f times E times OTR}{V} $$
(11)
where PC is pump cycle length, h. f is pumping frequency, h−1. E is efficiency, %. OTR is oxygen transfer rate, g O2 h−1.This model sums the DOFR, DOB, DON, and DOPF to determine the supplemental DO demand in kg h−1. This number can be used to estimate the oxygen consumption if pure oxygen transfers system is used.Fish growth modelFish growth is affected by environmental and physical factors, such as water temperature, dissolved oxygen, unionized ammonia, photoperiod, fish stocking density, food availability, and food quality.In order to calculate the fish growth rate (g day−1) for individual fish, the following model was used13 as it includes the main environmental factors influencing fish growth. These factors are temperature, dissolved oxygen and unionized ammonia.$$ FGR = left( {0.2919 , tau , kappa , delta , varphi , h , f , W^{m} } right) – K.W^{n} $$
(12)
Where FGR is the fish growth rate, g day−1. τ is the temperature factor (0  > τ  к  δ  φ  ƒ  More

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