DOI: 10.5061/dryad.1g1jwstxh
title: Bushmeat yields, species extinction rates and ecosystem-level impacts of bushmeat harvesting as predicted by the Madingley General Ecosystem Model

description: The datasets contain data generated using the
 Madingley General Ecosystem Model for experiments decribed in the paper:
 "T. Barychka, G.M.Mace and D.W.Purves (2021) The Madingley General
 Ecosystem Model predicts bushmeat yields, species extinction rates and
 ecosystem-level impacts of bushmeat harvesting. Oikos." The Madingley
 General Ecosystem Model was used to generate predictions
 of bushmeat yields, extinction rates and broader ecosystem
 impacts for a range of harvesting intensities of duiker-sized endothermic
 herbivores. Duiker antelope (such as Cephalophus callipygus and
 Cephalophus dorsalis) are the most heavily hunted species in sub-Saharan
 Africa, contributing 34%-95% of all bushmeat in the Congo
 Basin. In the Madingley, the harvested group was described as
 "Heterotroph – Herbivore – Terrestrial – Mobile – Iteroparous–
 Endotherm", with adult bodymasses of 13-21 kg and juvenile
 bodymasses of &gt;100 g. Harvesting period was set at 30
 years (n =30). In the first experiment, we used the Madingley
 model to predict bushmeat yields ("Harvested
 Biomasses") and extinction rates ("Density") from
 harvesting duiker-sized herbivores using proportional harvesting strategy,
 with harvest rates ranging from 0 to 0.90. These were compared to the
 estimates of bushmeat yields and survival probabilities for two
 duiker antelope species (Cephalophus callipygus and Cephalophus dorsalis)
 from conventional single-species Beverton-Holt model.  In the
 second experiment, we used the Madingley model to generate data on the
 state ("State") of the harvested ecosystem. The datasets
 contain estimates of biomasses, abundances, adult and juvenile
 bodymasses, etc. of the harvested duiker-sized herbivores as well
 as unharvested herbivores, omnivores and carnivores present in
 the simulated ecosystem. In the paper we focused on abundances;
 however, other estimates e.g., adult
 bodymasses can be used to conduct further studies
 on the effects of harvesting in tropical ecosystems. Main results
 of the experiments are that: 1) the Madingley model gave
 estimates for optimal harvesting rate, and extinction rate, that were
 qualitatively and quantitatively similar to the estimates from
 conventional single-species Beverton-Holt model; 2) the Madingley
 model predicted a background local extinction probability for the target
 species of at least 10%; 3) at medium and high levels of harvesting of
 duiker-sized herbivores, the Madingley model predicted
  statistically significant, but moderate, reductions in the
 densities of the targeted functional group; increases in small-bodied
 herbivores; decreases in large-bodied carnivores; and minimal
 ecosystem-level impacts overall.
description: <strong>Harvesting</strong> In the
 Madingley model, a 100-year 'burn-in' (no harvesting, 30
 replicates) followed by a 30-year harvesting period was run to produce
 estimates of the following: for each functional group
 (carnivore/omnivore/herbivore), the number of surviving animal cohorts,
 abundances, biomass and adult body masses. <br> We used a constant
 proportional harvesting policy, where each year a proportion of animals
 were targeted. This harvest rate remained constant for the duration of
 harvesting period. Experiments were replicated 30 times at each harvest
 rate, with harvest rate ranging from 0 (no harvest) to 0.90 in discrete
 steps of 0.05 (smaller steps for survival probability). Harvesting was
 applied from year 1 onwards (no harvesting took place in year
 0). <strong>Target Group</strong>
 We simulated harvesting strategies for animals similar to duiker
 antelope <em>Cephalophus callipygus </em>and
 <em>Cephalophus dorsalis</em>. We set up harvesting in the
 Madingley model to target terrestrial herbivorous endotherms, described
 using the following categorical traits: ‘Heterotroph – Herbivore –
 Terrestrial – Mobile – Iteroparous– Endotherm’. This definition was
 further narrowed using two continuous traits: adult body mass (13-21
 kg) and juvenile body mass (&gt;100 g).
 <strong>Location</strong> Our
 experimental site was simulated in the Madingley model on a 1° × 1°
 geographic grid cell (111.32 × 110.57 km) centred on 1°S, 15°E; the
 coordinates were selected to fall within the known duiker range in the
 tropical forests of the Republic of Congo. For the purposes of this study,
 no inter-cell migration was modelled, i.e. no animals were allowed from
 outside the experimental area.
 <strong>Extinction</strong> The
 rate of extinction of duiker-like animals in the Madingley model was
 estimated at each time step. Extinction was defined when the total
 density of animals that matched the definition of duiker-like fell below
 0.1 animals km−2 during  a simulation run.
 <strong>Ecosystem response</strong>
 The ecosystem-level information was recorded in the Madingley at
 each time step, such as, for each functional group, adult body masses,
 animal biomasses and<br> abundances. Overall, the ecosystem-level
 response to harvesting was analysed as follows. First, each cohort’s
 functional group was identified as being a herbivore, omnivore or
 carnivore. Individuals were also allocated into a body mass bin ranging
 from the smallest body mass (10^−3 to 10^−2 g) to the largest bin
 (10^6–10^7 g). Total abundances were then calculated for each functional
 group in each body mass bin and logged (on log10 scale). Changes in
 abundances were calculated by subtracting total animal abundances under
 one of the four harvesting regimes (20%, 50%, 70% and 90% of duiker-like
 population harvested) to total animal abundances without
 harvesting. All data processing and analysis were
 carried out in R ver. 3.6.3.
description: For Yields use 'HarvestedBiomasses' data.
 For Survival Probability use 'Density' data.
 For Ecosystem Impacts use 'State' files.
 In each file, 'Set' refers to order in which files were
 created (3 sets, 10 replicates each); 6-digits number gives the date of
 the simulation; 'DL' stands for duiker-like harvesting;
 non-integer (e.g. 0.30) represents harvest rate (between 0 and 0.90) and
 final integer (e.g. 4) stands for the replicate number (0 to 9).