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    Using citizen science to test for acoustic niche partitioning in frogs

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    Reply to: Conclusions of low extinction risk for most species of reef-building corals are premature

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    Modelling the emergence dynamics of the western corn rootworm beetle (Diabrotica virgifera virgifera)

    Let (y_{itk}) denote the WCR count observed for trap i in week t in year k, and assume it to follow a Poisson distribution with parameter (mu _{itk})$$begin{aligned} y_{itk} | mu _{itk}, sim Poisson(mu _{itk}) end{aligned}$$
    (1)
    The intensity parameter (mu _{itk}) represents the rate of emergence for a given time period. Instead of allowing it to depend purely on time t, a phenological variable of growing degree days (GDD) is used, as warmer temperatures are required for WCR development25,26,27,28. GDDs reflect the heat accumulation and are defined as an integral of warmth above a base temperature after a given start date:$$begin{aligned} GDD = int (T(t)-T_{base})dt. end{aligned}$$
    (2)
    The above integral can be approximated by$$begin{aligned} GDD = max left( frac{T_{max} – T_{min}}{2} – T_{base}, 0 right) . end{aligned}$$
    (3)
    Here (T_{min}) is the minimum daily temperature, (T_{max}) is the maximum daily temperature, and (T_{base}) is a set base temperature. In this study, the base temperature was set to (10,^{circ })C, and the starting date was the beginning of April, which marks the start of the growing season in Austria.The rate of cumulative emergence of the WCR beetle can be described by a Gompertz function. The Gompertz function is a sigmoidal function which describes growth as being slowest at the beginning and the end of a given period and is defined as$$begin{aligned} f(z_t) = alpha exp (-beta exp (-gamma z_t)). end{aligned}$$
    (4)
    where (alpha) is the upper asymptote, (beta) is a relative starting value, (gamma) is a growth rate coefficient which affects the slope, and (z_t) are the cumulative growing degree days. In this study, one can consider the asymptote as proxy to the saturation level of WCR population growth. Lower values of (beta) suggest an earlier first emergence in the season, while lower values of (gamma) indicate a longer emergence period. To investigate whether there is an association between climate variables and the emergence dynamics, the Gompertz curve parameters were assumed to linearly depend on climate covariates. In this regression modelling framework, a spatially correlated residual structure can be added in either (alpha), (beta), and/or (gamma) if there is evidence to do so.To reflect the nature of the emergence dynamics and to preserve the shape of the increasing Gompertz curve, the parameters of the model were restricted to positive values such that (alpha >0), (beta >0), and (gamma >0). The time at inflection or period of highest growth can be obtained by solving Eq. (4) for the value of t at which the concavity of the function changes. The time at inflection is described as:$$begin{aligned} T_z^* = frac{log (beta )}{gamma } end{aligned}$$
    (5)
    The Gompertz function describes cumulative emergence. Thus to describe the marginal emergence rate, the derivative of the Gompertz function can be used instead. Consequently, as the WCR trapping data consisted of weekly counts, the rate of emergence (mu _{itk}) is better described by the log of the derivative of the Gompertz function$$begin{aligned} log (mu _{itk}) = log (alpha _{ik}) + log (gamma _{ik}) + log (beta _{ik}) + gamma _i z_{itk} – beta _{ik} exp (-gamma z_{itk}). end{aligned}$$
    (6)
    The parameters (alpha _{ik}), (beta _{ik}) and (gamma _{ik}) are site and year specific such that:$$begin{aligned}&alpha _{ik} sim N(mu _{alpha _{ik}}, tau _{alpha }) end{aligned}$$
    (7)
    $$begin{aligned}&gamma _{ik} sim N(mu _{gamma _{ik}}, tau _{gamma }) end{aligned}$$
    (8)
    $$begin{aligned}&beta _{ik} sim N(mu _{beta _{ik}}, tau _{beta }). end{aligned}$$
    (9)
    Here, (tau _{alpha }), (tau _{beta }), and (tau _{gamma }) are the precision (inverse variance) parameters of the prior distributions for (alpha), (beta) and (gamma) respectively. Moreover, the means of the distributions (mu _{alpha _{ik}}), (mu _{beta _{ik}}), and (mu _{gamma _{ik}}) can be expressed as functions of known covariates:$$begin{aligned} mu _{alpha _{ik}}= & {} a_{0} + {mathbf {w}}^T X_{alpha _{ik}}, end{aligned}$$
    (10)
    $$begin{aligned} mu _{beta _{ik}}= & {} b_{0}, end{aligned}$$
    (11)
    $$begin{aligned} mu _{gamma _{ik}}= & {} g_{0} + {mathbf {u}}^T X_{gamma _{ik}}. end{aligned}$$
    (12)
    Here (a_{0}) is the intercept, ({mathbf {w}}) is a vector of the regression coefficients, and (X_{alpha _{ik}}) are the location and year specific covariates. The predictors used in the regression of (mu _{alpha _{ik}}) are the average winter temperature, the precipitation sum during winter, the year, the percentage of the agricultural area per Austrian municipality used for cultivating maize crops (maize), and the corresponding centred coordinates of the trap locations; x, y, and their functions (x^2), (y^2), and xy. The parameter (g_{0}) is the intercept for the regression of (mu _{gamma _{ik}}), and u is the corresponding regression coefficient. The predictor used for (mu _{gamma _ik}) is the average yearly spring temperature.The intercepts and regression coefficients ((mathbf {w}) and (mathbf {u})) were given non-informative normal priors N(0, 0.01). The precision parameters (tau _{alpha }), (tau _{beta }) and (tau _{gamma }) were assigned prior distributions Gamma(0.01, 0.01).The model was fitted using WinBUGS through the R2WinBUGS package in R29,30,31. The model was run for 20000 iterations, with a burn-in of 10000 iterations, and a thinning rate of five. Convergence was determined by visual assessments of trace plots and marginal posterior densities. More

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    Persistence of the invasive bird-parasitic fly Philornis downsi over the host interbreeding period in the Galapagos Islands

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    Ant Lasius niger joining one-way trails go against the flow

    Ant experimentsAnt coloniesSeven colonies of the garden ant L. niger collected from the Soka University and a nearby park were used in this study (Extended Data Table S1). They were placed in plastic cases (35 × 25 × 6 cm). Water was provided ad libitum. They were fed a sucrose solution, and were starved for 2–5 days before the start of the experiment. The colonies were queen-less colonies with 200–700 workers. Aqueous sucrose solution was used as a food resource (bait) in the experiments. The laboratory room where the experiments were performed and the ant colonies were kept was maintained at a temperature of 25–27 °C and a humidity of 60–70%. Artificial lights were also installed in this room.ApparatusWe used an apparatus, called “the main apparatus,” with two paths from the nest to the feeding site (length: 30 cm, width: 2 cm, height: 12 cm for the outward path and 15 cm for the return path) (Fig. 1). This apparatus could separate the outward path (bridge) from the inward path (bridge). Here, the outward path refers to that taken by ants from the nest to the feeding site, whereas the inward path refers to the path taken by ants from the feeding site to the nest.Figure 1The main apparatus used in the three experiments (the main experiment and the comparison experiments 1 and 2). Nests are connected to the experimental apparatus by a slope. In the main experiment, on the outward path, there is ant traffic from the nest to the feeding site on a pheromone trail, and on the inward path, there is ant traffic from the feeding site to the nest on a pheromone trail. In the comparison experiment 1, only a pheromone trail is present on both the outward and inward paths. In the comparison experiment 2, no pheromone trail or ant traffic is present on both the outward and inward paths.Full size imageTwo important features of this apparatus were as follows: firstly, it allowed ants to only enter the outward path from the nest. A rat-guard structure at the end of the inward path prevented the ants on the outward path from entering the inward path (Extended Data Fig. S1A). Secondly, we installed a vertical structure at the end of the outward path (height: 4 cm). After climbing the vertical structure, ants were not allowed to return to the outward path (Extended Data Fig. S1B). Moreover, we installed partitions on the feeding site, which also prevented ants from returning to the outward path after reaching the feeding site (Extended Data Fig. S1C). After entering the feeding site, ants had to pass through a narrow gap (width: 0.5 cm) created by the partition. No visual cues were offered as the apparatus was surrounded on all four sides by plastic walls.In this experiment, we made another apparatus for a single ant (target ant), which would be joining the ant trail on the main bridges (Extended Data Fig. S2). This apparatus, called “the confluence device,” was a detachable device that could be connected at right angles to the outward and inward bridges of the main apparatus. To connect this device to the outward bridge, we made the confluence path of this device under the inward bridge of the main apparatus, since the outward bridge was lower than the inward bridge. Thus, we made a slope on the outward confluence path connected to the outward bridge of the main apparatus. Further, because placing the ants directly on the sidewalk sometimes caused them to fall off the sidewalk owing to panic, we constructed a free space and a wall (height: 5 cm) in the middle of the confluence device on which the ants were placed calmly. Owing to this modification, we could let each target ant calm down and then access the main bridge whenever they wanted to. The apparatus used in this experiment was made of white plastic plates.Pheromone trail with ant trafficThis main experiment was limited to once a day for each colony. A sucrose solution was dripped into the feeding site. Target ants, which were walking on a plastic case as foragers, had been moved from their nests to another case immediately before a trail of (nontarget) ants was formed. Thus, dozens of ants were moved in advance to the case to be used as target ants. Subsequently, a trail of (nontarget) ants was formed from the nest to the main apparatus. Considering that it took some time for the ants that had finished foraging and returned to the nest to recruit their mates, the ants were left for approximately 40 min to an hour until a permanent ant trail was formed. It was difficult to form an ant trail immediately after the start of the experiment since no foraging pheromones could be produced in the first foraging trip on the outward path and since experienced foraging ants may make foraging pheromones on the outward path2,21,22. The target ants were allowed to enter bridges of the main apparatus after the establishment of a permanent ant trail. At that time, trails of individual target ants were started. Target ants were allowed to join at right angles to the path on the apparatus, one by one from the confluence device. Individual target ants were allowed to enter the main apparatus at four different points: (1) Left-Left (LL), located at the left side of the center of the outward path. The outward path was on the left side, whereas the inward path was on the right side for the experimenter when seen from the nest. (2) Left–Right (LR), located at the right side of the center of the outward path. (3) and (4) Right-Left (RL) and Right-Right (RR), located at the left and right sides of the center of the inward path, respectively (Fig. 2). We had set these four points to check if target ants tended to turn their body to a certain direction when entering the main bridges, regardless of the movement direction of the other ants. A video camera (Panasonic, AVCHD 30fps) was used to record the migration of ants to the feeding site or nest. Videos were taken from above, and target ants were used only once.Figure 2Four joining points (LL, LR, RL, and RR) and the confluence device (joining device). The confluence (joining) device was connected at right angles to the center of the outward and inward bridges of the main apparatus. Here, the LR version is shown as an example.Full size imageThe goal lines were set at 15 cm from the center of the main paths. We checked the side (nest side or feeding site side) from which a target ant passed the goal line.Pheromone trail with no ant trafficThis comparison experiment 1 was limited to once a day for each colony. Dozens of ants were moved in advance to another case to be used as target ants in a similar manner to the main experiment. The (nontarget) ants were left for about 40 min to an hour until a permanent ant trail was formed. Subsequently, we removed all the ants from the device. Then, target ants were allowed to enter on the side path one by one. In this case, we left the bait in place to control this experiment under the same condition as the main experiment. As the pheromone trail was created on the outward path as well as on the inward path, it was the only decision-making factor for the ants to join at the main path (outward/inward paths). We checked the side (nest side or feeding site side) from which a target ant passed the goal line in a similar manner to the main experiment.No pheromone trail or ant trafficThis comparison experiment 2 was limited to once a day for each colony. Dozens of ants were moved in advance to another case to be used as target ants in a similar manner to the main experiment. This experiment was conducted to investigate ant behavior under the following two conditions: (1) no ant trails and (2) no pheromones trails. The bait was in place in the same manner. We checked the side (nest side or feeding site side) from which a target ant passed the goal line in a similar manner to the main experiment. After each trial (the target ant passed the goal line), we wiped the apparatus with ethanol solution before the next target ant was allowed to enter the main paths.AnalysisThe goal lines were set at 15 cm from the center of the main paths. We checked which goal side the target ants reached the goal line on each trial. A reverse run referred to the goal to the nest on the outward path and the goal to the feeding site on the inward path. A normal run referred to the goal to the feeding site on the outward path and the goal to the nest on the inward path.In some cases of the main experiment, foraging (nontarget) ants that could not reach the feeding site on their outward path or could not return to the nest on their inward path would be against the ant flows. On the outward path, we considered that the ants conducted a “reverse flow” if the position of their heads was on the nest side compared with the position of their stomach. If not, we defined that the ants conducted a “normal flow” (Extended Data Fig. S3). On the inward path, we defined that the ants conducted a “reverse flow” if the position of their head was on the feeding site side compared with the position of their stomach. If not, we defined that the ants conducted a “normal flow” (Extended Data Fig. S3). We focused on the target ants that came in contact with ants with normal flow. Therefore, if an ant with reverse flow was located within 10 cm of the target ant, that trial was excluded from the analysis.Furthermore, we also evaluated if target ants coming in contact with foraging (nontarget) ants immediately after entering the trail would affect the goal choice. Therefore, we conducted an analysis focusing on the contact using the data from the main experiment. We examined whether or not the target ant made contact with other foraging ants until it passed a point 2 cm from the center of the path. As already mentioned, if the target ant came in contact with another ant moving against the normal flow of the ant trail, this contact was excluded from the counts. Moreover, we also excluded cases in which the body of target ants was on a point 2 cm from the center of the path by visual evaluation. Thus, we examined the goal choice of target ants by focusing on whether or not they came in contact with other ants immediately after joining the main bridges.We also conducted a preliminary experiment using a single path apparatus to investigate bi-directional trail behaviour. Please see the Extended Data File S1.Model descriptionThe models were coded using the C programming language. The model description follows the Overview, Design concepts, and Details protocol23,24.PurposeThe purpose of the model was to examine the mechanistic understanding of our findings. We adopted an action of target agents obtained from our ant experiments and compared it with another action of target agents on a trail that was contrary to the fact. To be more precise, target agents were allowed to obey an alignment rule in which they tended to move in the same direction with other agents. We named the former model as the reverse-rule model and the latter model as the alignment-rule model. By doing so, we could find the significance of our findings from ant experiments.Entities, state variables, and scalesWe developed two different models (reverse-rule model and alignment-rule model) that included two types of entities: agents and cells. The agent has the state variable Navigational state, which has two values: Navigational state = {wandering, foraging}. The cell has the state variable Pheromone; this value represents the amount of pheromones in each cell. We used a 2D lattice field and set a straight bridge with 61 cells × 5 cell sizes. We also set goal lines at x-coordinate =  − 30 and 30. If the agents reached coordinates satisfying their x-coordinate =  − 30 or 30, they were removed from the system. If the agents reached y-axis boundaries, their movement direction was restricted. Each trial continued until the target agent reached one of the two goal lines. However, trials were forcibly finished if the target agent never reached any goal line by t = 500-time steps. In total, we conducted 1000 trials.Process overview and schedulingAt the beginning of each trial, an artificial target ant (Navigational state = wandering) was introduced at the center of an artificial simulation field. Foraging agents (Navigational state = foraging) were randomly distributed on the simulation field in advance.Agents on the simulation field selected one direction from two directions (+ x and − x) on each time step and updated their positions. Briefly, an agent at coordinate (x, y) selected one direction from two directions (+ x and − x) and updated its position with one of the three coordinates—(x − 1, y), (x − 1, y + 1), or (x − 1, y − 1)—if it selected the − x direction, or—(x + 1, y), (x + 1, y + 1), or (x + 1, y − 1)—if it selected the + x direction by scanning pheromones on these three coordinates. For example, if an agent at coordinate (0, 2) decided to move in + x direction at one time, the position of this agent was replaced with one of (1, 3), (1, 2) and (1, 1) from (0, 2) by scanning pheromones on these three coordinates. The target agent selected the − x/ + x direction with equal probability on each time step until it met the foragers. In contrast, foraging agents tended to decide to move in the − x direction on each time step with a high probability and therefore they tended to select the − x direction for position updating. Foraging agents deposited pheromones before leaving the current cell (see submodel entitled “Position updating” and submodel entitled “Pheromone updating”). In contrast, the target agents did not deposit pheromones.Using above submodels, artificial ants sometimes met other agents. If the target agent (Navigational state = wandering) met the foragers (Navigational state = foraging), the target agent tended to select one direction from two directions (+ x and − x) on each time step thereafter with a high probability, which was dependent on which direction the met foragers came from. More strictly, in the reverse-rule model, the target agent tended to move in an opposite direction from the foragers if it met the foragers coming from the opposite direction. On the contrary, the target agent in the alignment-rule model tended to move in the same direction with foragers if it met the foragers moving in the same direction (see submodel entitled “The interaction between the target agent and foragers”). For example, in the reverse-rule model, if the target agent at coordinate (x, y), whose previous coordinate was (x − 1, y), met the forager coming from the opposite direction, whose previous coordinate was (x + 1, y), the target agent decided to move in + x direction on each time step thereafter with a high probability until similar events occurred.Design conceptThe mean goal time was the emergent property of the model. Sensing was important as the agents scanned the pheromone concentrations. Stochasticity was used to determine in which direction the agent moved and to select one cell using the pheromone concentrations.InitializationWe set a single agent (target agent) on the coordinate (0, 2) and its Navigational state was set to wandering (Extended Data Fig. S5A). We also set N foraging agents on the bridge whose Navigational state was set to foraging. Therefore, N + 1 agents were on the test field at the beginning of each trial. A target agent was the agent k = 0, whereas foraging agents were agents k = 1, 2, …, N. These foragers were randomly distributed on the bridge. Thus, x(k) (in) {n |− 30 ≤ n ≤ 30, n is an integer} and y(k) (in) {n | 0 ≤ n ≤ 4, n is an integer} for k  > 0.Foraging agents were set to move in the -x direction (Direction(k) for k  > 0 = − x). On the other hand, the target agent randomly chose one direction from two directions at the beginning of each trial (Direction(0) was set to + x or − x with equal probability). Herein, Direction(k) can be − x or + x, which implies bias in the movement direction. The parameter prob(k) indicates the probability of moving in Direction(k). The target agent selected the − x/+ x direction with equal probability on each time step until it met the foragers. Therefore, the parameter prob was set to 0.50 for the target ant (prob(0) = 0.50), whereas prob was set to 0.80 for foraging agents (prob(k) = 0.80 for k  > 0). The amount of pheromones on each cell was set to 1 at the beginning of each trial (pheromone(x, y) = 1) and the pheromone evaporation rate q was set to 0.99.The model descriptions are explained using submodels. A Submodel: the interaction between the target agent and foragers causes differences between two rules (the reverse-rule model and the alignment-rule model).SubmodelsSubmodel: the interaction between the target agent and foragersThe parameters Direction(0) and prob(0) were replaced with new ones whenever the following events occurred.In the reverse-rule model, for any agent k (k  > 0),Herein, (xt(k), yt(k)) indicates the x–y-coordinate for the agent k at time t. Furthermore, (xt(0), yt(0)) = (xt(k), yt(k)) means that the target agent and the agent k occupy the same cell at time t while (xt(0) − xt−1(0)) × (xt(k) − xt−1(k)) =  − 1 indicates that the target agent meets the agent k came from the opposite direction. The target agent replaces Direction(0) with an opposite direction from the forager k (see Extended data Fig. S5B).In the alignment-rule model, for any agent k (k  > 0),(xt(0) − xt−1(0)) × (xt(k) − xt−1(k)) = 1 indicates that the target agent meets the agent k came from the same direction. The target agent replaces Direction(0) with a same direction with the forager k (See Extended Data Fig. S5B).In the reverse-rule model, these events are driven from the experimental observations of real ants. Target ants appear to move against the trail and seem to move straight by contacting those other nestmates that come from the opposite direction. Also, target ants seem to select the reverse goal even if physical contact with ant nestmates does not occur immediately after entering the bridge. So, regarding parameter replacements, we did not consider the position at which the target agent met another agent. Note that foraging agents did not change these parameters until the end of each trial. Further, Direction(0) can be replaced with − x from + x and vice versa whenever the target agent meets foragers that come from the opposite direction.In the alignment-rule model, the target agent tends to move in the same direction with other agents. This is contrary to the experimental observations of real ants.Submodel: position updatingFor all k agents (k = 0–N), the movement direction and position updates are shown as follows (Extended Data Fig. S5C);Here, rnt(k) indicates a random number. Thus, rnt(k) (in) [0.00, 1.00].Prob(0) for the target agent is initially set to 0.50. Therefore, the target agent selects one direction from the two (− x and + x) on each time step randomly before the condition described in submodels—the interaction between the target agent and foragers is satisfied. On the other hand, foraging agents select − x direction with a high probability (= Prob(k)) on each time step. After selecting one direction from two (− x and + x), agents scan three cells in the direction of movement. Using pheromone concentrations on those three cells, they update their positions.If agents reach coordinates satisfying their y-coordinate = 4 or 0, those agents update their position by selecting not three but two coordinates since they are located on the edges of the bridge.Submodel: pheromone updatingForaging agents (k  > 0) deposited pheromones on the current cell when leaving that cell.Then, pheromones are evaporated using the evaporation rate q.For each time iteration, these submodels operated in the following order.STEP 1: The interaction between the target agent and foragers.STEP 2: Position updating.STEP 3: Pheromone updating.AnalysisTo check the accuracy of our model, we counted which goal side the target agent entered the goal line from using the reverse-rule model by setting N = 9. If the target agent passed the goal line at x-coordinate =  − 30 (30), we considered that it reached the normal (reverse) goal. Note that trials in which the target agent never reached any goal lines by t = 500 were excluded from this analysis. Furthermore, to investigate the adaptability of the reverse run mechanism, we examined the time until the target agent reached the goal lines using the reverse-rule model and the alignment-rule model. Herein, we set two different conditions with respect to the number of foraging agents (N = 4 and 9). More