More stories

  • in

    Sensitivity of non-conditional climatic variables to climate-change deep uncertainty using Markov Chain Monte Carlo simulation

    As stated above this study aims to shed light on the deep uncertainties that are associated with the climate change phenomenon. The seasonally-averaged surface air temperature, hereafter simply referred to as temperature, was selected as the non-conditional climatic variable to be monitored within the Karkheh River Basin, Iran, during the baseline period (1975–2005). The CORDEX datasets (RCP 8.5) were employed to make climate-change projections.The first step in the proposed framework is to identify the most suitable theoretical distribution function to represent the stochastic behavior patterns of both historical and climate change data sets. Such identification considered the following theoretical distributions: normal, lognormal, exponential, Weibull, 3-parameter Weibull, extreme value, gamma, logistic, and loglogistic. It is important to note here that the primary strategy in this study is to analyze the data from a numeric standpoint without any presumption about the stochastic structure of the data44. As such, the study would opt for any distribution that is deemed fittest to describe the data. A summary of the fitted distributions to represent the prior distributions and likelihood functions is found in Tables S1 through S4 (see the Appendix). Furthermore, the climate-change period was divided into three mutually exclusive time frames which are short-term (2010–2039), mid-term (2040–2069), and long-term (2070–2099) future to gain a better understanding of the evoluton of future temperature changes.With Bayes’ theorem in mind, a Markov Chain Monte Carlo (MCMC) method was then applied to merge the prior distributions and the likelihood functions and to generate a sample set from the posterior distribution set. After a series of trials-and-errors, the sample size for the MCMC algorithm was set to be 1000 (n = 1000). These generated sample sets were then used to specify the most suitable theoretical pdfs to represent the posterior distribution functions. Figure 3, for instance, illustrates the most appropriate theoretical distribution that could represent the posterior distribution for the Seimareh sub-basin during spring under the short-term period.Figure 3The step-by-step process of computing the posterior pdf: (a) the prior distribution of Seimareh sub-basin during spring and the likelihood function of this sub-basin in the short-term future; (b) the histogram of the generated samples; and (c) the posterior distribution.Full size imageFigure 4 demonstrates the frequency with which each specific theoretical distribution functions was deemed the most suitable to characterize the prior, likelihood, and posterior distributions. Analyzing the fitted pdfs in Fig. 4 reveals an important point about the nature of RCMs’ raw projections. Specifically, the most frequently chosen distribution function for prior and posterior distributions is the 3-parameter Weibull. As for the likelihood function, however, it was the normal distribution that outperformed other available alternatives. Furthermore, the type of selected theoretical distribution for prior and posterior pdfs seems far more diverse compared to those from the likelihood functions. In fact, the likelihood functions were only limited to three types of distributions, most of which are normal distributions. Keep in mind that these functions are the most suitable pdfs that were fitted to the RCMs projected results. The cause behind this notion might be traced back to the nature of RCMs’ projections. RCMs operate at a finer horizontal resolution than GCMs, and thus they provide localized and high-resolution detailed climatic information that can be of importance for many management purposes, especially in regions with complex topography. However, the analyzed data revealed that among the distributions fitted for the likelihood function the normal distribution was found to be the best distribution to describe the data 70% of the time. This could be interpreted as signaling that employing RCMs’ raw projections, especially for regions that have considerable volatility in their climatic variables, should be used with caution, and further adjustment to the raw projected data may be required in some cases. Note that from a statistical standpoint, the normal distribution is not heavy-tailed, and as such, may not be the best way to portray this data. The fact that, in most cases, it has been selected as the best way to portray the stochastic nature of the likelihood function (i.e., RCM’s projections) means that innate characteristics of these data might prevent them to truly represent these types of variables on their own.Figure 4The frequency of using each individual theoretical pdfs as prior, likelihood function, and posterior distributions.Full size imageFigure 5 provides additional information regarding the frequency in which each individual theoretical distributions were deemed suitable to represent the posterior pdfs. While posterior distribution sets are, indeed, the most diverse in terms of the number of different types of distributions, a significant proportion of fitted pdfs (approximately 52%), however, are fitted by the 3-parameter Weibull distribution. Further information regarding the fitted distributions to represent the posterior pdfs is found in Tables S5 to S7 (Appendix).Figure 5The frequency of using different theoretical distributions as posterior pdfs.Full size imageThe computed posterior distribution functions can be interpreted as modified representations of the stochastic behavior of temperature variable concerning the short-term, mid-term, and long-term climate change projections. In that spirit, employing the confidence interval of 95%, the average temperature of the entire basin is depicted in Fig. 6 associated with historical and climate change conditions. Two sets of behavior patterns are observed. The first one is a broad trend in summer. The second pattern describes the rest of the seasons. In summer (Fig. 6b) the presence of a mild, yet, steady positive trend (upward) is detected. Here, one can expect the average temperature of the basin to increase steadily with the passage of time. As for the rest of the seasons, while it seems that the average temperature of the basin would experience a mild drop in the short-term, the temperature would begin to rise with a steady trend with time. In spring (Fig. 6a) and autumn (Fig. 6c) time series, it is projected that the expected average temperature in the basin would eventually surpass those that had been experienced in the baseline condition in the mid-term and long-term future. Concerning winter temperature it is seen in Fig. 6d that it is projected to increase over time. Yet, it has been estimated that it might not reach the observed average temperature of the basin in neither of the expressed time frames. Of course, given the upward trend in the data, this temperature would indeed be reached in a longer timeframe. It is worth noting that these patterns are in line with the idea that the earlier impacts of climate change are to amplify the historical patterns in climatic variables. That is why the data show a slight drop in colder seasons and an uptick in the warmer ones. That is, of course, until eventually, a new climatic equilibrium is reached on a global scale. At this point, the temperature as shown here would start to increase gradually.Figure 6The historical and simulated average temperatures of the entire basin with the 95%confidence interval in (a) spring; (b) summer; (c) autumn; and (d) winter.Full size imageThe other notable implication that can be understood by analyzing Fig. 6 is the variation in the width of the confidence intervals under baseline and climate change conditions. In comparison to the baseline condition, the length of the 95% confidence intervals would dramatically decrease under climate change conditions. This shrinking indicates that the generated results are more densely surrounding the central tendency measure herein chosen as the mean (ÎŒ) of the data. This notion is still in line with the idea that RCM’s projections mostly resemble the stochastic characteristic of normal distributions. A normal distribution is by nature not a heavily-tailed distribution, meaning that it rarely generates tail values. Even though the MCMC framework has mitigated this effect to some extent, they inevitably inherit this stochastic property from the likelihood functions.Again, to truly understand the obtained results here, one must first acknowledge how Bayesian models work. The main idea behind a Bayesian-based framework is to adjust the prior assumptions about a stochastic phenomenon through observed samples. In this case, the prior information represents the historical data, and the likelihood function (i.e., the samples) is obtained from RCM projects. As can be seen here, while RCMs’ projections might be perfectly capable of portraying the normal behavior of a variable under climate change conditions, which is usually sufficient for most lumped evaluation of climate change impact assessments, they might not be suitable to study extreme hydro-climatic events. The main problem with the raw RCM projections is that they follow a normal distribution, which is a symmetric distribution. Figure 4 suggests that while the MCMC framework here is mitigating this impact the final projections inherit this property from the likelihood functions. This simply means that while any RCM-based projection is perfectly suitable to understand the general outline of the climate change impacts, they are not the best option to study extreme events because even by modifying their pdfs, they rarely generate truly extreme values. The average temperatures in all sub-basins under baseline and climate change conditions are summarized in Table 1.Table 1 The average surface air temperature in all sub-basins under baseline and climate change conditions (°C).Full size tableAs for the impact of climate change, it is clear that these data are associated with deep uncertainty; that is, the parameters used to describe the stochastic behavior of a variable may be subjected to some degree of uncertainty. These parameters, ÎŒ for one, may also be represented by a pdf of their own. This study focuses on highlighting this type of deep uncertainty that might interfere with the central tendency measure ÎŒ.The deep uncertainty in this instance dictates that the recorded parameters for each posterior distribution are not deterministic values. While for a given prior distribution and likelihood function the MCMC would lead to a specific type of posterior pdf, the parameters that are used to define this pdf (e.g., ÎŒ), could vary each time the algorithm is used. If this variation is mild, there is more certainty about the nature of the variable’s stochastic behavior pattern (i.e., the posterior distribution function). If it is determined that the parameters are experiencing severe variations then the deep uncertain environment would leave the decision-makers unsure about the variables’ stochastic behavior pattern.With that idea in mind the combination of prior distributions and likelihood functions was executed for 100 times, and in each iteration the mean of 1000 samples was recorded. A theoretical distribution function was then fitted to the recorded values. Naturally, if the recorded values are generally close to one another numerically, the parameters of the computed posterior pdfs are less subjected to deep uncertainty. If, however, these values show significant fluctuation then the deep uncertainty of climate change would impede predictions of the stochastic behavior pattern of temperature. Figure 7, for example, portrays the uncertainty of the computed ÎŒ parameter for Seimareh sub-basin in spring under short-term future condition.Figure 7The uncertainty of the computed ÎŒ parameter for Seimareh sub-basin in spring under short-term future condition demonstrated by (a) a histogram and (b) a probability distribution function.Full size imageFigure 8 demonstrates the number of times each theoretical distribution was chosen to portray the stochastic behavior of the ÎŒ parameter. As can be seen here, the normal and lognormal distributions are the most common pdfs used to describe the variation in the ÎŒ parameter. One should also note the fact that about 65% of the distributions used to describe the future condition are normal distributions. The list of fitted pdfs is summarized in Tables S8 to S10.Figure 8The frequency with which each theoretical distribution was found suitable to describe the stochastic distribution of the ÎŒ parameter.Full size imageTable 2 summarizes the variation in the computed ÎŒ parameter in each given sub-basin. It is seen in Table 2 the 95% confidence interval of the ÎŒ parameter in all cases ranges between ± 0.1 and ± 0.3 °C. In 55% of the cases, this interval was found not to be more than ± 0.1 °C, and, furthermore, in 97% of them the interval was less than ± 0.2 °C. Needless to say, a widened confidence interval for the ÎŒ parameter can only signal that the deep uncertainty has a more pronounced impact on the temperature’s stochastic behavior. As for the case of the spring data set of the Seimareh sub-basin under the short-term condition, or the case of the Gharesou sub-basin’s winter data series under short-term period, the confidence interval for the ÎŒ parameter is estimated to be ± 0.3 °C wide. This indicates that compared to other projected posterior pdfs there is less certainty about the predicted stochastic behavior pattern of temperature variable for these particular cases. As shown in Table 2 in some cases, the variation in the projected ÎŒ temperature’ posterior pdfs is decreasing over time (for a given season over different timeframes). As discussed earlier, this was interpreted as the deep uncertainties of the climate change projections, meaning that lower volatility in this measure indicates that the said variable is less affected by the deep uncertainty of the climate-change phenomenon. This observation is in line with the general belief that, in the near future, the climate change phenomenon is most likely to intensify the historical patterns in climatic variable, but gradually we expect to see an upward trend in temperature in the longer run45. In this case, there is more volatility in the earlier time frames, but as time progresses, this volatility seems to decrease in some cases. This means that the obtained projections are showing less uncertainty about the outline behavior of the parameter for the long-term future as the models that are simulating the climatic behavior under climate change conditions have already reached a new equilibrium by that point.Table 2 The variation in the computed ÎŒ of the temperature’ posterior pdfs.Full size table More

  • in

    The effect of territorial awareness in a three-species cyclic predator–prey model

    ModelTo investigate the evolution of cyclically competing species with intraspecific interaction which sensitively plays to the territory awareness, we employ the spatial RPS model11,19,20,23. At the microscopic level, the model can be demonstrated on a lattice system, and for convenience, we consider a square lattice of size N with periodic boundary conditions where all sites have von Neumann neighbors. Each site can be occupied by an individual from one of the three species (referred to as A, B, and C, respectively) or left empty(E), and thus the system describes a limited carrying capacity. In addition, to explore the effect of territory awareness on intraspecific interaction, we assume that the given lattice is divided into two areas of the same size which may possibly realize different territorial ranges. Here we simply divide the two regions into the top and bottom halves of the given square lattice. To reflect the territorial awareness on intraspecific interaction, we distribute population in each group into two sub-networks randomly, and denote species (X_1) for the top and (X_2) for the bottom ((X in {A, B, C})) to distinguish the emergence of intraspecific interaction between individuals who lie on different domains. The distribution of all species with respect to the separation of the domain is illustrated in Fig. 1a.Figure 1Schematic diagrams of network structure and the invasion rules among species. (a) Each circle represents a node, and individuals of species A, B, and C are evenly and randomly distributed on each node. To realize territorial awareness, the lattice is divided into two regions of equal size: the top and the bottom where the dashed line indicates the regional boundary. Two genera of the same species are distributed in different regions, and different color markers represent different species types. Nodes without color markers are empty nodes. (b) Interspecific interaction among three species A, B, and C (indicated by three boxes) occurs cyclically with a rate (p_1). A box of each group describes the intraspecific interaction between individuals who belong to different territories where the interaction is regulated by territorial consciousness. Here intraspecific interaction in each group occurs with a rate (k_i cdot p_2) ((i in {A, B, C})).Full size imageUnder the given assumption for the lattice, all the interactions between individuals occur within nearest neighboring sites by the following set of rules (see Fig. 1b):$$begin{aligned}&A_{i}+B_{j}overset{p_{1}}{longrightarrow }A_{i}+E,quad B_{i}+C_{j}overset{p_{1}}{longrightarrow }B_{i}+E,quad C_{i}+A_{j}overset{p_{1}}{longrightarrow }C_{i}+E, end{aligned}$$
    (1)
    $$begin{aligned}&A_{i}+A_{j}overset{k_{A} cdot p_{2}}{longrightarrow }A_{i}+E,mathrm{or},E+A_{j}, quad B_{i}+B_{j}overset{k_{B} cdot p_{2}}{longrightarrow }B_{i}+E,mathrm{or},E+B_{j}, quad C_{i}+C_{j}overset{k_{C} cdot p_{2}}{longrightarrow }C_{i}+E,mathrm{or},E+C_{j},quad ine j, end{aligned}$$
    (2)
    $$begin{aligned}&A_{i}+Eoverset{r}{longrightarrow }A_{i}+A_{i},quad B_{i}+Eoverset{r}{longrightarrow }B_{i}+B_{i},quad C_{i}+Eoverset{r}{longrightarrow }C_{i}+C_{i}, end{aligned}$$
    (3)
    $$begin{aligned}&A_{i}+otimes overset{m}{longrightarrow }otimes +A_{i},quad B_{i}+otimes overset{m}{longrightarrow }otimes +B_{i},quad C_{i}+otimes overset{m}{longrightarrow }otimes +C_{i}, end{aligned}$$
    (4)
    where (i, j=1, 2). The mark (otimes) stands for any species or empty sites. Relation (1) describes interspecific interaction among three species which occurs cyclically with a rate (p_1): (A_{i}) dominates (B_{i}), (B_{i}) dominates (C_{i}), and (C_{i}) dominates (A_{i}) ((i=1, 2)). The defeated individual dies and the site becomes an empty site. Relation (2) demonstrates the intraspecific interaction which will sensitively depend on territorial awareness. Since we assume the intraspecific interaction is related to the territorial consciousness, the rate in each species may be defined by (k_{A} cdot p_{2}), (k_{B} cdot p_{2}), (k_{C} cdot p_{2}) for species A, B, C, respectively, where (p_{2}) is the given rate of interaction, k is the the sensitive parameter to territorial awareness. Similar to previous works, the result of intraspecific interaction eventually results in a death of one individual at random with a 1/2 chance. Relation (3) stands for the reproduction with a rate r which is allowed when an empty site in neighbors is selected, and migration defined by an exchange between two neighboring sites is denoted in Relation (4). Based on the theory of random walks38, it occurs with a rate (m=2MN) where M and N indicate individuals’ mobility and a system size, respectively, as usual to previous works. Thus, an actual time step is defined when each individuals has interacted with others once on average, i.e., N pairwise interactions will occur in one actual time step unit. In order to make an unbiased comparison with previous works15,19,20,21 and for the convenience of interpretations, we assume parameters as (p_{1}=p_{2}=r=1) and (k_{A}=k_{B}=k_{C}=k) (see the Methods for the meanings of specific parameters) in our simulations. Three species are divided into two types to distinguish distributions on different regions: (A_{1,2}), (B_{1,2}), and (C_{1,2}), and randomly distributed initially on a square lattice of size (N= 300 times 300). In addition, in all our simulations, species coexistence refers to the coexistence of (A_i), (B_j), and (C_k) for any combination of (i,,j,,k in left{ 1,,2 right}).Biodiversity under territorial awarenessWe first consider the effect of territorial awareness on species biodiversity. In general, it is well-known that, the spatial RPS game exhibits a transition of survival states from coexistence to extinction (which is presented by the uniform state) as individuals’ mobility increases. The phase transition occurs when M exceed a certain value, referred to as a critical mobility (M_c = (4.5 pm 0.5) times 10^{-4}), which is identified in Ref.11. To address the effect of territorial awareness, we consider two different mobility values (M=1 times 10^{-5}) and (M=1 times 10^{-3}) which eventually yield different survival states: coexistence and extinction, respectively, for different sensitivity parameter k.In general, the total simulation time T in classic spatial RPS games is considered as (T = N) which can yield the extinction for the critical mobility (M_c)11. In this regard, using the time (T=N) may yield different results for species evolution and corresponding survival states due to stochastic events, and such behaviors may be induced by the choice of mobility. In our simulations, since we consider two different mobility values where the one (Fig. 2a–c) is quite lower and the other (Fig. 2d–f) is higher than (M_c), we thus consider different simulation times at (M=1 times 10^{-5}) and (M=1 times 10^{-3}): more than 490, 000 and 180, 000 steps, respectively, to obtain robust features on species survival states. The time dependent evolution of densities are illustrated in Fig. 2 where the top and bottom panels are obtained from simulations with the first 250, 000 and 140, 000 steps, respectively.Figure 2Time dependent evolution of densities in the system for different M and k. Top and bottom panels are obtained with (M=1times 10^{-5}) and (M=1times 10^{-3}), respectively, and the sensitivity parameter k is given by (k=5), 10, and 20 from the left to right in each row. (a–c) Regardless of the choice k, the low mobility still leads species coexistence as usual. (d–f) At high mobility regimes, the system also always exhibit the extinction state.Full size imageEven if different k are considered, the panels in Fig. 2 show features similar to previous works11,14,15,16,18,20: coexistence and extinction for tops and bottoms, respectively. At the low mobility (M=1times 10^{-5}) as shown in Fig. 2a–c, even if the individuals located in different domains in each group disappear, the spatial RPS game eventually exhibits coexistence as k increases since some of individuals in A, B, C are survived. For instance, in our simulations, coexistence can be presented by survival of species (A_1), (B_1), (C_1) (Fig. 2a–b) or (A_2), (B_2), (C_1) (Fig. 2c). Since the typical waiting time for extinction is exponentially increasing to the size N at low mobility11, there will be extinction and eventually only one species will dominate the system after extremely long times. Thus, within the finite time steps, one type of each species will disappear slowly with the increase of k and the system exhibits coexistence.On the other hand, the high mobility (M=1times 10^{-3}) leads the extinction and only one species dominate the whole domain. As shown in Fig. 2d–f, the extinction that is defined by the two types of the species disappear occurs and the only one species finally dominate the system [e.g., (C_2), (B_2), and (C_1) for (k=5), 10, and 20, respectively]. In this case, the increase in k has little effect on the disappearance of one of the species, but has a tendency to accelerate the complete extinction of the second species. Take Fig. 2d for example, when species (A_2), (B_1) and (B_2) became extinct, (A_1), (C_1) and (C_2) is left in the system, the density of (A_1) in the system had an absolute advantage, while (C_1) and (C_2) had intraspecific interaction. Since the intensity of intraspecific interaction sensitive to territorial awareness was greater than that of interspecific interaction, the interaction was mainly intraspecific interaction between (C_1) and (C_2), then (C_1) was defeated into extinction, (C_2) preyed on the only specie (A_2) remaining in the system and eventually occupied the whole system. As k value affects the intraspecific interaction intensity, it determines the waiting time for the extinction of two species in the system. For example, we found that the larger the k value is, the shorter the waiting time for the extinction of two species is, as shown in Fig. 2e–f. But this is only the observation result of a single simulation. Due to the randomness of the simulation, this phenomenon needs further verification, so we give specific results about the effect of k value on the average extinction time in the next section. Due to stochastic events during Monte-Carlo simulations, the combination of survival species for coexistence and extinction at the final step can be different, but the such states at two mobility regimes will be still maintained. Fig. 2 may impose the follows: territorial awareness on intraspecific interaction can eventually yield similar feature to previous works in a broad aspect, but the composition of the surviving species type for each state may vary.Average extinction time versus territorial awarenessWhile survival states in both cases are consistent with previous works on the effects of species migration in Fig. 2, we found an interesting feature that the evolutionary time when some type of species disappear is changed depending on k. To be concrete, at (M=1 times 10^{-5}), we found that one type of each species (A_1), (B_1), (C_1) (Fig. 2a) will eventually coexist while their companion species (A_2), (B_2), (C_2) are extinct as t exceeds (t approx 50{,}000). As k is increasing, the time point when one genus of each species disappears shows an increasing pattern as presented in Fig. 2b,c. The opposite trend can be captured at high mobility (M=1 times 10^{-3}), that is, the increase of k seems to shorten the evolution time of two species extinction in the system. Based on these observations, we may assume that the critical time for such disappearance phenomena has a certain relationship with k and the relation may differ to the choice of M.To answer the issue, we measure the average extinction time T. In classic RPS games, traditionally, the extinction state on spatially extended systems has been identified by the uniform state that only one species dominates whole domain11,14,15,16,18,20. As shown in Fig. 2a–c which ultimately describe a coexistence state in a finite time, however, any one of type in each species disappeared and the time associated with the phenomena is changed by the strength of k. In a slightly different aspect to the classic meaning of extinction, we here define the average extinction time T with respect to the regime of mobility: (a) the evolutionary time when one genus of each species disappears for low mobility and (b) the time when two of the three species disappear completely for high mobility. In this consideration, for both given cases of M in Fig. 2, the average extinction time T in each k is measured from 30 independent realizations and presented in Fig. 3.Figure 3The average extinction time T as a function of the territorial sensitive parameter k. (a) Two cases of fixed mobility in territorial sensitive intraspecific interaction. For low mobility (M=1times 10^{-5}), the time T which is measured by detecting the time when one genus of each species disappears tends to increase with the increase of k, i.e., the high sensitivity of territorial awareness has the effect of delaying the waiting time for extinction. Similarly, it can be seen that at high mobility (M=1times 10^{-3}), an increase in k value will also delay the waiting time for extinction, but the effect is much more gentle. (b) At low mobility value (M=1times 10^{-5}), traditional intraspecific interaction (i.e., intraspecific interaction among all individuals of the same species, regardless of territorial residence) was compared with territorial sensitive intraspecific interaction. Here, for the traditional case, k represents intraspecific interaction intensity, and the running time of the simulation is 810, 000 steps. In the case that the final steady state has not occurred before the end of the simulation, we take the maximum time step ((t=810{,}000)) as the extinction time T value, which causes the blue line to become gentle when (k >14). Compared with the traditional situation, the intraspecific interaction affected by territorial awareness significantly reduced the average extinction time, that is, accelerated the damage of species diversity in the system. The results were averaged from 30 independent simulations, and error bars (using standard errors, which defined as the sample standard deviation divided by the square root of the number of samples) are shown in the figure.Full size imageAs shown in Fig. 3a, we find clearly that the average extinction time is obviously affected by the strength of sensitivity coefficient k, especially, when the mobility is low. When species has no consciousness on territories ((k=0)), the system becomes exactly the classic RPS model11 since intraspecific interaction is undefined, and the waiting time T generally tends to increase exponentially to the choice of M. However, our simulation shows the T is approximately measured at (T=110{,}000) at (k=0). Traditionally, it is well known that the average waiting time for extinction in the classic RPS game is taken (T=N) near the critical mobility regime ((M approx M_c)), and the coexistence duration is exponentially increasing as M decreases from (M_c). Within this knowledge, our simulation results may seem inconsistent with the general concept of extinction time. In our model, however, the definition of extinction is different at the low mobility regime, and the change into a single RPS system as one genus of each individual disappears may have a similar meaning to the previous definition of extinction in some sense, the above result can be said to be reasonable.The important point is actually addressed for (k >0). In this case, species can allow intraspecific interaction and the strength of intraspecific interaction is also increasing since the territorial awareness is intensified. As a result, it is found that the average extinction time T shows a tendency to gradually increase with the increase of k at (M=1 times 10^{-5}). In addition, this trend can also be observed at (M = 1 times 10^{-3}), but it is more gradual. To investigate whether the tendency to prolong the waiting time for extinction time at low migration rates is caused by territorial awareness or the existence of intraspecific interaction, we compared traditional intraspecific interaction (i.e., intraspecific interaction among all individuals of the same species, regardless of territorial residence, which equivalent to removing the condition (ine j) from Relation (2)) with territorial-sensitive intraspecific interaction in our model, the results are shown in Fig. 3b. We found that in the presence of intraspecific interaction, the average extinction time increased with the intensity of intraspecific interaction. Specifically, the stronger the intraspecific interaction, the slower the loss of species diversity. However, compared with the traditional situation, intraspecific interaction influenced by territorial consciousness controlled the delay of extinction to a certain extent. Even if our simulations have been carried on for two specific M, it is obvious that the territorial awareness can affect the average extinction time, and we suggest that a strong sense of territoriality can also delay species extinction and lead to long-term coexistence of systems at low mobility regimes, although the introduction of territoriality leads to faster damage to species diversity than is traditionally the case, while it does not affect significantly on the extinction time and the biodiversity (which eventually appears as extinction) at high mobility regimes.Evolution of the interface between territoriesFrom the investigation on the average extinction time in Fig. 3, we know that the territorial awareness can affect not only species survival but also the maintenance period of survival states. Here, we may wonder why the territorial awareness can affect the waiting time to extinction. In order to investigate such an issue, we observe evolution of the spatial system, in particular invasion between species near the border on two territories, i.e., the evolution of the interface. To capture the phenomena in detail, we consider pattern formations associated with the given two mobility values at the initial state of the evolution (e.g. (t=1000)) which are represented in Fig. 4.Figure 4The typical snapshots of evolution on patterns at (t=1000) for different k: 0.5 for (a) and (e), 2 for (b) and (f), 10 for (c) and (g), and 20 for (d) and (h), where the mobility is considered as (M = 1times 10^{-5}) for tops and (M=1 times 10^{-3}) for bottoms. Different colors correspond to different species types, as shown in Figs. 1 and 2, with white indicating vacancy. As k increases, the invasion among species between two territories occurs more gradually, and such phenomena are clearly observed for the high mobility as shown in the panel (h).Full size imageThe top and bottom panels in Fig. 4 exhibit spatial patterns for the low and high mobility values, respectively. For (M=1 times 10^{-5}), when the value k is small such as (k=0.5) (see Fig. 4a), interspecific interaction can occur more frequently than intraspecific interaction among all pairwise reactions (1)–(4). The system can exhibit similar pattern formations to the classic RPS game11. Three species, even if they are distinguished into six subgroups, are spirally entangled with clearly exhibiting spiral waves which are appeared in both two territories. Since the given lattice has periodic boundaries, species in both territories can migrate to the other region each other, but such migration is weak because the normalized probability for migration (Relation (4)) is small at the low mobility. Thus, when the system exhibits coexistence, it may be possible to predict that the top and bottom territories present dominance of species (X_1) and (X_2) ((X in {A, B, C})), respectively, while our simulations only present spatial patterns at the first 1,000 steps which may be too short to lead phase transitions.We also find that the spiral-wave patterns are getting to fuzzy as k increases. In particular, such fuzzy patterns are conspicuous near the boundary between the two territories at the large k (see Fig. 4c,d). The increase of k directly means the intensification of intraspecific interaction, and according to the setting on the initial distribution of population, intraspecific interaction will have many chances to occur in the vicinity of the boundary than near the top and bottom periodic boundaries. Frequent intraspecific interaction can provide as many chances to allow reproduction as possible, and high intraspecific interaction rate can dominate on pairwise invasions than interspecific interaction.In the vicinity of the border between two territories, the occurrence of intraspecific interaction is observed more prominently at (M=1 times 10^{-3}), and such features are clear as k increases. To be concrete, compared with figures among Fig. 4e–h, we found that empty sites are produced near the border and their presence is clear for high strength k such as 10 and 20 (Fig. 4g–h). In this case, the two domains appear to be more clearly divided and each domain is dominated by a single RPS system. Each single RPS system shows extinction state (only one genus survives) at high mobility, and eventually shows extinction state through interspecific or intraspecific interaction depending on the type of surviving genus. This is in good agreement with the results we obtained in Fig. 2. However, it can be seen from Fig. 3 that the time for each domain system to reach extinction at high mobility is very short compared to that at low mobility, and this has no relation with the degree of territorial awareness in interspecific interaction.From our simulations, we find that: the relationship between territorial awareness and the average extinction time is particularly prominent at the low mobility, and the likelihood of intraspecific interaction is relatively high near territorial boundaries. Under these considerations, we may expect a new relationship between the delay of the extinction time and boundary of two territories. To uncover this veil, we try to quantify a width for occurrence of intraspecific interaction near the border between two area with respect to the territorial awareness. Specifically, we give each node on a two-dimensional grid a coordinate, defined by its row and column position. For each column (j=1,ldots ,L), calculate the interface width, defined as I:$$begin{aligned} I_{j}= {left{ begin{array}{ll} P(1,j)-P(2,j),&{}quad text {if } P(1,j) >P(2,j)\ 0,&{}quad text {if } P(1,j) More

  • in

    Behavioural traits of rainbow trout and brown trout may help explain their differing invasion success and impacts

    1.Holway, D. A. & Suarez, A. V. Animal behavior: An essential component of invasion biology. TREE 14, 328–330 (1999).CAS 
    PubMed 

    Google Scholar 
    2.Chapple, D. G., Simmonds, S. M. & Wong, B. B. M. Can behavioral and personality traits influence the success of unintentional species introductions? Trends Ecol. Evol. 27, 57–64 (2012).PubMed 

    Google Scholar 
    3.Weis, J. & Sol, D. Behaviour and the Invasion Process. in Biological Invasions and Animal Behaviour 5–116 (Cambridge University Press, 2016).4.Cote, J., Fogarty, S., Weinersmith, K., Brodin, T. & Sih, A. Personality traits and dispersal tendency in the invasive mosquitofish (Gambusia affinis). Proc. R. Soc. B Biol. Sci. 277, 1571–1579 (2010).
    Google Scholar 
    5.Myles-Gonzalez, E., Burness, G., Yavno, S., Rooke, A. & Fox, M. G. To boldly go where no goby has gone before: Boldness, dispersal tendency, and metabolism at the invasion front. Behav. Ecol. 26, 1083–1090 (2015).
    Google Scholar 
    6.Mutascio, H. E., Pittman, S. E. & Zollner, P. A. Investigating movement behavior of invasive Burmese pythons on a shy–bold continuum using individual-based modeling. Perspect. Ecol. Conserv. 15, 25–31 (2017).
    Google Scholar 
    7.Chuang, A. Living Life on the Edge: The Role of Invasion Processes in Shaping Personalities in a Non-Native Spider Species (The University of Tennessee, Knoxville, 2019). https://doi.org/10.1017/CBO9781107415324.004.Book 

    Google Scholar 
    8.Blackburn, T. M. et al. A proposed unified framework for biological invasions. Trends Ecol. Evol. 26, 333–339 (2011).PubMed 

    Google Scholar 
    9.Pintor, L. M., Sih, A. & Kerby, J. L. Behavioral correlations provide a mechanism for explaining high invader densities and increased impacts on native prey. Ecology 90, 581–587 (2009).PubMed 

    Google Scholar 
    10.Petren, K. & Case, T. J. An experimental demonstration of exploitation competition in an ongoing invasion. Ecology 77, 118–132 (1996).
    Google Scholar 
    11.Wright, T. F., Eberhard, J. R., Hobson, E. A., Avery, M. L. & Russello, M. A. Behavioral flexibility and species invasions: The adaptive flexibility hypothesis. Ethol. Ecol. Evol. 22, 393–404 (2010).
    Google Scholar 
    12.Dick, J. T. A. Role of behaviour in biological invasions and species distributions; lessons from interactions between the invasive Gammarus pulex and the native G. duebeni (Crustacea: Amphipoda). Contrib. Zool. 77, 91–98 (2008).
    Google Scholar 
    13.Dick, J. T. A. et al. Invader Relative Impact Potential: A new metric to understand and predict the ecological impacts of existing, emerging and future invasive alien species. J. Appl. Ecol. 54, 1259–1267 (2017).
    Google Scholar 
    14.Dick, J. T. A., Elwood, R. W. & Montgomery, W. I. The behavioural basis of a species replacement: differential aggresssion and predation between the introduced Gammarus pulex and the native G. duebeni celticus (Amphipoda). Behav. Ecol. Sociobiol. 37, 393–398 (1995).
    Google Scholar 
    15.Dick, J. T. A. et al. Ecological impacts of an invasive predator explained and predicted by comparative functional responses. Biol. Invasions 15, 837–846 (2013).
    Google Scholar 
    16.Dick, J. T. A. et al. Advancing impact prediction and hypothesis testing in invasion ecology using a comparative functional response approach. Biol. Invasions 16, 735–753 (2014).
    Google Scholar 
    17.Iacarella, J. C., Dick, J. T. A. & Ricciardi, A. A spatio-temporal contrast of the predatory impact of an invasive freshwater crustacean. Divers. Distrib. 21, 803–812 (2015).
    Google Scholar 
    18.Toscano, B. J. & Griffen, B. D. Trait-mediated functional responses: Predator behavioural type mediates prey consumption. J. Anim. Ecol. 83, 1469–1477 (2014).PubMed 

    Google Scholar 
    19.MacCrimmon, H. R. World distribution of rainbow trout (Salmo gairdneri): further observations. J. Fish. Res. Board Canada 28, 663–704 (1971).
    Google Scholar 
    20.MacCrimmon, H. R., Marshall, T. L. & Gots, B. L. World distribution of brown trout, Salmo trutta: further observations. J. Fish. Res. Board Canada 27, 811–818 (1970).
    Google Scholar 
    21.Crawford, S. S. & Muir, A. M. Global introductions of salmon and trout in the genus Oncorhynchus: 1870–2007. Rev. Fish Biol. Fish. 18, 313–344 (2008).
    Google Scholar 
    22.Crowl, T. A., Townsend, C. R. & Mcintosh, A. R. The impact of introduced brown and rainbow trout on native fish: The case of Australasia. Rev. Fish Biol. Fish. 241, 217–241 (1992).
    Google Scholar 
    23.Hasegawa, K. Invasions of rainbow trout and brown trout in Japan: A comparison of invasiveness and impact on native species. Ecol. Freshw. Fish 29, 419–428 (2020).
    Google Scholar 
    24.Cambray, J. A. The global impact of alien trout species—A review; with reference to their impact in South Africa. African J. Aquat. Sci. 28, 61–67 (2003).
    Google Scholar 
    25.Dunham, J. B., Wheeler, A. & Rosenberger, A. Assessing the consequences of nonnative trout in headwater ecosystems in western North America. Fisheries 29, 37–41 (2004).
    Google Scholar 
    26.Fausch, K. D., Taniguchi, Y., Nakano, S., Grossman, G. D. & Townsend, C. R. Flood disturbance regimes influence rainbow trout invasion success among five holarctic regions. Ecol. Appl. 11, 1438–1455 (2001).
    Google Scholar 
    27.Anderson, R. M. & Nehring, R. B. Effects of a catch-and-release regulation on a wild trout population in Colorado and its acceptance by Anglers. North Am. J. Fish. Manag. 4, 257–265 (1984).
    Google Scholar 
    28.Young, K. A. et al. A trial of two trouts: Comparing the impacts of rainbow and brown trout on a native galaxiid. Anim. Conserv. 13, 399–410 (2010).
    Google Scholar 
    29.Conrad, J. L., Weinersmith, K. L., Brodin, T., Saltz, J. B. & Sih, A. Behavioural syndromes in fishes: A review with implications for ecology and fisheries management. J. Fish Biol. 78, 395–435 (2011).CAS 
    PubMed 

    Google Scholar 
    30.Mowles, S. L., Cotton, P. A. & Briffa, M. Consistent crustaceans: The identification of stable behavioural syndromes in hermit crabs. Behav. Ecol. Sociobiol. 66, 1087–1094 (2012).
    Google Scholar 
    31.Sih, A., Bell, A. & Johnson, J. C. Behavioral syndromes: An ecological and evolutionary overview. Trends Ecol. Evol. 19, 372–378 (2004).PubMed 

    Google Scholar 
    32.Bell, A. M. Behavioural differences between individuals and two populations of stickleback (Gasterosteus aculeatus). J. Evol. Biol. 18, 464–473 (2005).CAS 
    PubMed 

    Google Scholar 
    33.Bourne, G. R. & Sammons, A. J. Boldness, aggression and exploration: evidence for a behavioural syndrome in male pentamorphic livebearing fish, Poecilia parae. AACL Bioflux 1, 39–50 (2008).
    Google Scholar 
    34.Lukas, J. et al. Consistent behavioral syndrome across seasons in an invasive freshwater fish. Front. Ecol. Evol. 8, 466 (2021).ADS 

    Google Scholar 
    35.Gjedrem, T., Gjþen, H. M. & Gjerde, B. Genetic origin of Norwegian farmed Atlantic salmon. Aquaculture 98, 41–50 (1991).
    Google Scholar 
    36.Huntingford, F. & Adams, C. Behavioural syndromes in farmed fish: Implications for production and welfare. Behaviour 142, 1207–1221 (2005).
    Google Scholar 
    37.Alvarez, D. & Nicieza, A. G. Predator avoidance behaviour in wild and hatchery-reared brown trout : The role of experience and domestication. J. Fish Biol. 63, 1565–1577. https://doi.org/10.1046/j.1095-8649.2003.00267.x (2003).Article 

    Google Scholar 
    38.Geffroy, B. et al. Evolutionary dynamics in the anthropocene: Life history and intensity of human contact shape antipredator responses. PLoS Biol. 18, 1–17 (2020).
    Google Scholar 
    39.Lincoln, R. F. & Scott, A. P. Production of all-female triploid rainbow trout. Aquaculture 30, 375–380 (1983).
    Google Scholar 
    40.Maxime, V. The physiology of triploid fish: Current knowledge and comparisons with diploid fish. Fish Fish. 9, 67–78 (2008).
    Google Scholar 
    41.Chatterji, R., Longley, D., Sandford, D., Roberts, D. & Stubbing, D. Performance of stocked triploid and diploid brown trout and their effects on wild brown trout in UK rivers. (2008).42.Benfey, T. J. The physiology and behavior of triploid fishes. Rev. Fish. Sci. 7, 39–67 (1999).
    Google Scholar 
    43.Carter, C. G. et al. Food consumption, feeding behaviour, and growth of triploid and diploid Atlantic salmon, Salmo salar L., parr.. Can. J. Zool. 72, 609–617 (1994).
    Google Scholar 
    44.Weber, G. M., Hostuttler, M. A., Cleveland, B. M. & Leeds, T. D. Growth performance comparison of intercross-triploid, induced triploid, and diploid rainbow trout. Aquaculture 433, 85–93 (2014).
    Google Scholar 
    45.Øverli, Ø., Pottinger, T. G., Carrick, T. R., Øverli, E. & Winberg, S. Differences in behaviour between rainbow trout selected for high- and low-stress responsiveness. J. Exp. Biol. 205, 391–395 (2002).PubMed 

    Google Scholar 
    46.Sadoul, B., Leguen, I., Colson, V., Friggens, N. C. & Prunet, P. A multivariate analysis using physiology and behavior to characterize robustness in two isogenic lines of rainbow trout exposed to a confinement stress. Physiol. Behav. 140, 139–147 (2015).CAS 
    PubMed 

    Google Scholar 
    47.Adriaenssens, B. & Johnsson, J. I. Learning and context-specific exploration behaviour in hatchery and wild brown trout. Appl. Anim. Behav. Sci. 132, 90–99 (2011).
    Google Scholar 
    48.NĂ€slund, J. & Johnsson, J. I. State-dependent behavior and alternative behavioral strategies in brown trout (Salmo trutta L.) fry. Behav. Ecol. Sociobiol. 70, 2111–2125 (2016).PubMed 
    PubMed Central 

    Google Scholar 
    49.Mortensen, E. Density-dependent mortality of trout fry (Salmo trutta L.) and its relationship to the management of small streams. J. Fish Biol. 11, 613–617 (1977).
    Google Scholar 
    50.Armstrong, J. D. & Nislow, K. H. Critical habitat during the transition from maternal provisioning in freshwater fish, with emphasis on Atlantic salmon (Salmo salar) and brown trout (Salmo trutta). J. Zool. 269, 403–413 (2006).
    Google Scholar 
    51.Walsh, R. N. & Cummins, R. A. The open-field test: A critical review. Psychol. Bull. 83, 482–504 (1976).CAS 
    PubMed 

    Google Scholar 
    52.Adriaenssens, B. & Johnsson, J. I. Shy trout grow faster: Exploring links between personality and fitness-related traits in the wild. Behav. Ecol. 22, 135–143 (2010).
    Google Scholar 
    53.Sneddon, L. U. The bold and the shy: Individual differences in rainbow trout. J. Fish Biol. 62, 971–975 (2003).
    Google Scholar 
    54.Adriaenssens, B. Individual variation in behaviour: personality and performance of brown trout in the wild (University of Gothenburg, 2010).55.Elias, A., Thrower, F. & Nichols, K. M. Rainbow trout personality: Individual behavioural variation in juvenile Oncorhynchus mykiss. Behaviour 155, 205–230 (2018).
    Google Scholar 
    56.Dick, J. T. A. et al. Functional responses can unify invasion ecology. Biol. Invasions 19, 1667–1672 (2017).
    Google Scholar 
    57.Sloman, K. A., Metcalfe, N. B., Taylor, A. C. & Gilmour, K. M. Plasma cortisol concentrations before and after social stress in rainbow trout and brown trout. Physiol. Biochem. Zool. 74, 383–389 (2001).CAS 
    PubMed 

    Google Scholar 
    58.Sadoul, B., Blumstein, D. T., Alfonso, S. & Geffroy, B. Human protection drives the emergence of a new coping style in animals. PLoS Biol. 19, 1–11 (2021).
    Google Scholar 
    59.Campbell, J. M., Carter, P. A., Wheeler, P. A. & Thorgaard, G. H. Aggressive behavior, brain size and domestication in clonal rainbow trout lines. Behav. Genet. 45, 245–254 (2015).PubMed 

    Google Scholar 
    60.Berejikian, B. A., Mathews, S. B. & Quinn, T. P. Effects of hatchery and wild ancestry and rearing environments on the development of agonistic behavior in steelhead trout (Oncorhynchus mykiss) fry. Can. J. Fish. Aquat. Sci. 53, 2004–2014 (1996).
    Google Scholar 
    61.Laverty, C. et al. Assessing the ecological impacts of invasive species based on their functional responses and abundances. Biol. Invasions 19, 1653–1665 (2017).
    Google Scholar 
    62.Alexander, M. E., Dick, J. T. A., Weyl, O. L. F., Robinson, T. B. & Richardson, D. M. Existing and emerging high impact invasive species are characterized by higher functional responses than natives. Biol. Lett. 10, 20130946 (2014).PubMed 
    PubMed Central 

    Google Scholar 
    63.Dickey, J. W. E., Cuthbert, R. N., Steffen, G. T., Dick, J. T. A. & Briski, E. Sea freshening may drive the ecological impacts of emerging and existing invasive non-native species. Divers. Distrib. 27, 144–156 (2021).
    Google Scholar 
    64.Sadler, J., Pankhurst, P. M. & King, H. R. High prevalence of skeletal deformity and reduced gill surface area in triploid Atlantic salmon (Salmo salar L.). Aquaculture 198, 369–386 (2001).
    Google Scholar 
    65.Benfey, T. J. & Biron, M. Acute stress response in triploid rainbow trout (Oncorhynchus mykiss) and brook trout (Salvelinus fontinalis). Aquaculture 184, 167–176 (2000).CAS 

    Google Scholar 
    66.Sadler, J., Pankhurst, N. W., Pankhurst, P. M. & King, H. Physiological stress responses to confinement in diploid and triploid Atlantic salmon. J. Fish Biol. 56, 506–518 (2000).
    Google Scholar 
    67.Berrebi, P., Splendiani, A., Palm, S. & Berna, R. Genetic diversity of domestic brown trout stocks in Europe. Aquaculture 544, 737043 (2021).CAS 

    Google Scholar 
    68.Gross, R., Lulla, P. & Paaver, T. Genetic variability and differentiation of rainbow trout (Oncorhynchus mykiss) strains in northern and Eastern Europe. Aquaculture 272, 139–146 (2007).
    Google Scholar 
    69.Whelan, K. Assessing and mitigating the impact of a major rainbow trout escape on the wild salmon and trout populations of the Mourne river system, Northern Ireland. (2017).70.Shelton, J. et al. Temperature mediates the impact of non-native rainbow trout on native freshwater fishes in South Africa’s Cape Fold Ecoregion. Biol. Invasions 20, 2927–2944 (2018).
    Google Scholar 
    71.Michelangeli, M. et al. Sex-dependent personality in two invasive species of mosquitofish. Biol. Invasions 22, 1353–1364 (2020).
    Google Scholar 
    72.Friard, O. & Gamba, M. BORIS: A free, versatile open-source event-logging software for video/audio coding and live observations. Methods Ecol. Evol. 7, 1325–1330 (2016).
    Google Scholar 
    73.R Core Team. R: A language and environment for statistical computing. (2018).74.RStudio Team. RStudio Team (2020). RStudio: Integrated Development for R. RStudio, PBC, Boston, MA. http://www.rstudio.com/. 2019 (2020).75.Zuur, A. F., Ieno, E. N., Walker, N. J., Saveliev, A. A. & Smith, G. M. Mixed effects models and extensions in ecology with R. Springer https://doi.org/10.1086/648138 (2008).Article 
    MATH 

    Google Scholar 
    76.Bates, D., MĂ€chler, M., Bolker, B. M. & Walker, S. C. Fitting linear mixed-effects models using lme4. J. Stat. Softw. 67, 18637 (2015).
    Google Scholar 
    77.Wickham, H., François, R., Henry, L. & MĂŒller, K. dplyr: A Grammar of Data Manipulation. R package version. Media https://doi.org/10.1007/978-0-387-98141-3 (2019).Article 

    Google Scholar 
    78.Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer-Verlag, 2016).MATH 

    Google Scholar 
    79.Barton, K. MuMIn: Multi-Model Inference. 2020 (2020).80.Lenth, R., Singmann, H., Love, J., Buerkner, P. & Herve, M. emmeans: estimated marginal means, aka least-squares means. R package version 1.5.2-1 (2020).81.Pritchard, D. frair: tools for functional response analysis. R package version 0.0.100 (2017).82.Juliano, S. A. Predation and functional response curves. in Design and Analysis of Ecological Experiments (eds. Scheiner, S. & Gurevitch, J.) Chapter 10 (2001).83.Rogers, D. Random search and insect population models. J. Anim. Ecol. 41, 369–383 (1972).
    Google Scholar 
    84.Bolker, B. M. Rogers random predator equation: extensions and estimation by numerical integration. 1–20 (2012). More

  • in

    Ecological niche modeling predicting the potential distribution of African horse sickness virus from 2020 to 2060

    1.MacLachlan, N. J. & Guthrie, A. J. Re-emergence of bluetongue, African horse sickness, and other Orbivirus diseases. Vet. Res. 41, 35 (2010).Article 

    Google Scholar 
    2.Zientara, S., Weyer, C. T. & Lecollinet, S. African horse sickness. OIE Revue Sci. Tech. 34, 315–327 (2015).CAS 
    Article 

    Google Scholar 
    3.Ayelet, G. et al. Outbreak investigation and molecular characterization of African horse sickness virus circulating in selected areas of Ethiopia. Acta Trop. 127, 91–96 (2013).Article 

    Google Scholar 
    4.Diarra, M. et al. Spatial distribution modelling of Culicoides (Diptera: Ceratopogonidae) biting midges, potential vectors of African horse sickness and bluetongue viruses in Senegal. Parasit. Vectors 11, 1–15 (2018).Article 

    Google Scholar 
    5.Karamalla, S. T. et al. Sero-epidemioloical survey on African horse sickness virus among horses in Khartoum State, Central Sudan. BMC Vet. Res. 14, 1–6 (2018).Article 

    Google Scholar 
    6.Escobar, L. E. Ecological Niche modeling: An introduction for veterinarians and epidemiologists. Front. Vet. Sci. 7, 519059. https://doi.org/10.3389/fvets.2020.519059 (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    7.Okely, M., Anan, R., Gad-Allah, S. & Samy, A. M. Mapping the environmental suitability of etiological agent and tick vectors of Crimean-Congo hemorrhagic fever. Acta Trop. 203, 105319 (2020).CAS 
    Article 

    Google Scholar 
    8.Chavy, A. et al. Ecological niche modelling for predicting the risk of cutaneous leishmaniasis in the Neotropical moist forest biome. PLoS Negl. Trop. Diseases 13, e0007629 (2019).Article 

    Google Scholar 
    9.Sloyer, K. E. et al. Ecological niche modeling the potential geographic distribution of four Culicoides species of veterinary significance in Florida, USA. PLoS ONE 14, e0206648 (2019).CAS 
    Article 

    Google Scholar 
    10.Fick, S. E. & Hijmans, R. J. WorldClim 2: new 1-km spatial resolution climate surfaces for global land areas. Int. J. Climatol. 37, 4302–4315 (2017).Article 

    Google Scholar 
    11.Cao, Z., Jin, Y., Shen, T., Xu, F. & Li, Y. Risk factors and distribution for peste des petits ruminants (PPR) in Mainland China. Small Rumin. Res. 162, 12–16 (2018).Article 

    Google Scholar 
    12.Naimi, B. & AraĂșjo, M. B. sdm: a reproducible and extensible R platform for species distribution modelling. Ecography 39, 368–375 (2016).Article 

    Google Scholar 
    13.Naimi, B., Hamm, N. A. S., Groen, T. A., Skidmore, A. K. & Toxopeus, A. G. Where is positional uncertainty a problem for species distribution modelling. undefined 37, 191–203 (2014).
    Google Scholar 
    14.R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, (2020).15.Thuiller, W., Lafourcade, B., Engler, R. & AraĂșjo, M. B. BIOMOD—a platform for ensemble forecasting of species distributions. Ecography 32, 369–373 (2009).Article 

    Google Scholar 
    16.AraĂșjo, M. B. & New, M. Ensemble forecasting of species distributions. Trends Ecol. Evol. 22, 42–47 (2007).Article 

    Google Scholar 
    17.Uusitalo, R. et al. Predicting spatial patterns of sindbis virus (Sinv) infection risk in finland using vector, host and environmental data. Int. J. Environ. Res. Public Health 18, 7064 (2021).Article 

    Google Scholar 
    18.Raffini, F. et al. From nucleotides to satellite imagery: Approaches to identify and manage the invasive pathogen Xylella fastidiosa and its insect vectors in Europe. Sustainability (Switzerland) 12, 4508 (2020).CAS 
    Article 

    Google Scholar 
    19.Phillips, S. B., Aneja, V. P., Kang, D. & Arya, S. P. Maximum entropy modeling of species geographic distributions. Ecol. Model. 190, 231–259 (2006).Article 

    Google Scholar 
    20.Barbet-Massin, M., Jiguet, F., Albert, C. H. & Thuiller, W. Selecting pseudo-absences for species distribution models: how, where and how many?. Methods Ecol. Evol. 3, 327–338 (2012).Article 

    Google Scholar 
    21.Hernåndez-Urcera, J., Murillo, F. J., Regueira, M., Cabanellas-Reboredo, M. & Planas, M. Preferential habitats prediction in syngnathids using species distribution models. Marine Environ. Res. 172, 105488 (2021).Article 

    Google Scholar 
    22.Smeraldo, S. et al. Generalists yet different: distributional responses to climate change may vary in opportunistic bat species sharing similar ecological traits. Mammal Rev. 51, 571–584 (2021).Article 

    Google Scholar 
    23.Thomson, A. M. et al. RCP4.5: A pathway for stabilization of radiative forcing by 2100. Clim. Change 109, 77–94 (2011).ADS 
    CAS 
    Article 

    Google Scholar 
    24.QGIS Development Team. QGIS Geographic Information System. Open-Source Geospatial Foundation Project. (2020).25.Ramirez-Reyes, C. et al. Embracing ensemble species distribution models to inform at-risk species status assessments. J. Fish Wildl. Manag. 12, 98–111 (2021).Article 

    Google Scholar 
    26.Stephenson, F. et al. Presence-only habitat suitability models for vulnerable marine ecosystem indicator taxa in the South Pacific have reached their predictive limit. ICES J. Mar. Sci. 78, 2830–2843 (2021).Article 

    Google Scholar 
    27.Zhu, G., Fan, J. & Peterson, A. T. Cautions in weighting individual ecological niche models in ensemble forecasting. Ecol. Modelling 448, 109502 (2021).Article 

    Google Scholar 
    28.Leta, S. et al. Modeling the global distribution of Culicoides imicola: an Ensemble approach. Sci. Rep. 9, 1–9 (2019).ADS 
    CAS 
    Article 

    Google Scholar 
    29.Onyango, M. G. et al. Delineation of the population genetic structure of Culicoides imicola in East and South Africa. Parasit. Vectors 8, 660 (2015).Article 

    Google Scholar 
    30.Carpenter, S., Mellor, P. S., Fall, A. G., Garros, C. & Venter, G. J. African horse sickness virus: history. Transm. Curr. Status. 62, 343–358. https://doi.org/10.1146/annurev-ento-031616-035010 (2017).CAS 
    Article 

    Google Scholar 
    31.Carpenter, S., Mellor, P. S., Fall, A. G., Garros, C. & Venter, G. J. African Horse Sickness Virus: History, Transmission, and Current Status. Annu. Rev. Entomol. 62, 343–358 (2017).CAS 
    Article 

    Google Scholar 
    32.Fall, M. et al. Culicoides (Diptera: Ceratopogonidae) midges, the vectors of African horse sickness virus—a host/vector contact study in the Niayes area of Senegal. Parasit. Vectors 8, 1–13 (2015).Article 

    Google Scholar 
    33.Mellor, P. S. Epizootiology and vectors of African horse sickness virus. Comp. Immunol. Microbiol. Infect. Dis. 17, 287–296 (1994).CAS 
    Article 

    Google Scholar 
    34.Wu, X., Lu, Y., Zhou, S., Chen, L. & Xu, B. Impact of climate change on human infectious diseases: Empirical evidence and human adaptation. Environ. Int. 86, 14–23 (2016).Article 

    Google Scholar 
    35.Nosrat, C. et al. Impact of recent climate extremes on mosquito-borne disease transmission in Kenya. PLOS Negl. Trop. Diseases 15, e0009182 (2021).CAS 
    Article 

    Google Scholar 
    36.Abiodun, G. J., Maharaj, R., Witbooi, P. & Okosun, K. O. Modelling the influence of temperature and rainfall on the population dynamics of Anopheles arabiensis. Malar. J. 15, 1–15 (2016).Article 

    Google Scholar  More

  • in

    Parallel evolution of urban–rural clines in melanism in a widespread mammal

    1.Angel, S. et al. The dimensions of global urban expansion: Estimates and projections for all countries, 2000–2050. Prog. Plan. 75, 53–107 (2011).
    Google Scholar 
    2.Grimm, N. B. et al. Global change and the ecology of cities. Science 319, 756–760 (2008).ADS 
    CAS 
    PubMed 

    Google Scholar 
    3.McKinney, M. L. Urbanization as a major cause of biotic homogenization. Biol. Conserv. 127, 247–260 (2006).
    Google Scholar 
    4.Groffman, P. M. et al. Ecological homogenization of urban USA. Front. Ecol. Environ. 12, 74–81 (2014).
    Google Scholar 
    5.Bolnick, D. I. et al. (Non)Parallel evolution. Annu. Rev. Ecol. Evol. Syst. 49, 303–330 (2018).
    Google Scholar 
    6.Donihue, C. M. & Lambert, M. R. Adaptive evolution in urban ecosystems. Ambio 44, 194–203 (2015).PubMed 

    Google Scholar 
    7.Johnson, M. T. J. & Munshi-South, J. Evolution of life in urban environments. Science 358, eaam8327 (2017).
    Google Scholar 
    8.Rivkin, L. R. et al. A roadmap for urban evolutionary ecology. Evol. Appl. 12, 384–398 (2019).PubMed 

    Google Scholar 
    9.Santangelo, J. S. et al. Urban environments as a framework to study parallel evolution. In Urban Evolutionary Biology (eds Szulkin, M. et al.) (Oxford University Press, 2020).
    Google Scholar 
    10.Cosentino, B. J., Moore, J.-D., Karraker, N. E., Ouellet, M. & Gibbs, J. P. Evolutionary response to global change: Climate and land use interact to shape color polymorphism in a woodland salamander. Ecol. Evol. 7, 5426–5434 (2017).PubMed 
    PubMed Central 

    Google Scholar 
    11.Koprowski, J. L., Munroe, K. E. & Edelman, A. J. Gray not grey: Ecology of Sciurus carolinensis in their native range in North America. In Grey Squirrels: Ecology and Management of an Invasive Species in Europe (eds Shuttleworth, C. M. et al.) (European Squirrel Initiative, 2016).
    Google Scholar 
    12.McRobie, H., Thomas, A. & Kelly, J. The genetic basis of melanism in the gray squirrel (Sciurus carolinensis). J. Hered. 100, 709–714 (2009).CAS 
    PubMed 

    Google Scholar 
    13.Gibbs, J. P., Buff, M. F. & Cosentino, B. J. The biological system: Urban wildlife, adaptation and evolution: Urbanization as a driver of contemporary evolution in gray squirrels (Sciurus carolinensis). In Understanding Urban Ecology (eds Hall, M. A. & Balogh, S.) (Springer, 2019).
    Google Scholar 
    14.Lehtinen, R. M. et al. Dispatches form the neighborhood watch: Using citizen science and field survey data to document color morph frequency in space and time. Ecol. Evol. 10, 1526–1538 (2020).PubMed 
    PubMed Central 

    Google Scholar 
    15.Perlut, N. G. Long-distance dispersal by eastern gray squirrels in suburban habitats. Northeast. Nat. 27, 195–200 (2020).
    Google Scholar 
    16.Goheen, J. R., Swihart, R. K., Gehring, T. M. & Miller, M. S. Forces structuring tree squirrel communities in landscapes fragmented by agriculture: Species differences in perceptions of forest connectivity and carrying capacity. Oikos 102, 95–103 (2003).
    Google Scholar 
    17.Ducharme, M. B., Larochelle, J. & Richard, D. Thermogenic capacity in gray and black morphs of the gray squirrel, Sciurus carolinensis. Physiol. Zool. 62, 1273–1292 (1989).
    Google Scholar 
    18.Linnen, C. R. & Hoekstra, H. E. Measuring natural selection on genotypes and phenotypes in the wild. Cold Spring Harb. Symp. Quant. Biol. 74, 155–168 (2010).PubMed Central 

    Google Scholar 
    19.Campbell-Staton, S. C. et al. Parallel selection on thermal physiology facilitates repeated adaptation of city lizards to urban heat islands. Nat. Ecol. Evol. 4, 652–658 (2020).PubMed 

    Google Scholar 
    20.Reid, N. M. et al. The genomic landscape of rapid repeated evolutionary adaptation to toxic pollution in wild fish. Science 354, 1305–1308 (2016).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    21.Bowers, M. A. & Breland, B. Foraging of gray squirrels on an urban-rural gradient: Use of the GUD to assess anthropogenic impact. Ecol. Appl. 6, 1135–1142 (1996).
    Google Scholar 
    22.McCleery, R. A., Lopez, R. R., Silvy, N. J. & Gallant, D. L. Fox squirrel survival in urban and rural environments. J. Wildl. Manage. 72, 133–137 (2008).
    Google Scholar 
    23.Benson, E. The urbanization of the eastern gray squirrel in the United States. J. Am. Hist. 100, 691–710 (2013).
    Google Scholar 
    24.Leveau, L. United colours of the city: A review about urbanization impact on animal colours. Austral Ecol. 46, 670–679 (2021).
    Google Scholar 
    25.Ducrest, A.-L., Keller, L. & Roulin, A. Pleiotropy in the melanocortin system, coloration, and behavioural syndromes. Trends Ecol. Evol. 23, 502–510 (2008).PubMed 

    Google Scholar 
    26.Stothart, M. R. & Newman, A. E. M. Shades of grey: Host phenotype dependent effect of urbanization on the bacterial microbiome of a wild mammal. Anim. Microbiome. 3, 46 (2021).PubMed 
    PubMed Central 

    Google Scholar 
    27.VasemĂ€gi, A. The adaptive hypothesis of clinal variation revisited: Single-locus clines as a result of spatially restricted gene flow. Genetics 173, 2411–2414 (2006).PubMed 
    PubMed Central 

    Google Scholar 
    28.Merrick, M. J., Evans, K. L. & Bertolino, S. Urban grey squirrel ecology, associated impacts, and management challenges. In Grey Squirrels: Ecology and Management of an Invasive Species in Europe (eds Shuttleworth, C. M. et al.) (European Squirrel Initiative, 2016).
    Google Scholar 
    29.Chipman, R., Slate, D., Rupprecht, C. & Mendoza, M. Downside risk of wildlife translocation. In Towards the Elimination of Rabies in Eurasia (eds Dodet, B. et al.) (Dev. Biol Basel, Karger, 2008).
    Google Scholar 
    30.Allen, D. L. Michigan Fox Squirrel Management (Michigan Department of Conservation, 1943).
    Google Scholar 
    31.Schorger, A. W. Squirrels in early Wisconsin. Trans. Wis. Acad. Sci. Arts Lett. 39, 195–247 (1949).
    Google Scholar 
    32.Robertson, G. I. Distribution of Color Morphs of Sciurus carolinensis in Eastern North America (University of Western Ontario, 1973).
    Google Scholar 
    33.MacCleery, D. W. American Forests: A History of Resiliency and Recovery (Forest History Society, 2011).
    Google Scholar 
    34.Foster, D. R. et al. Wildlands and Woodlands: A Vision for the New England Landscape (Harvard University Press, 2010).
    Google Scholar 
    35.Thompson, R. T., Carpenter, D. N., Cogbill, C. V. & Foster, D. R. Four centuries of change in northeastern United States forests. PLoS ONE 8(9), e72540 (2013).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    36.Lambert, M. R. et al. Adaptive evolution in cities: Progress and misconceptions. Trends Ecol. Evol. 36, 239–257 (2021).PubMed 

    Google Scholar 
    37.Farquhar, D. N. Some Aspects of Thermoregulation as Related to the Geographic Distribution of the Northern Melanic Phase of the Grey Squirrel (York University, 1974).
    Google Scholar 
    38.Innes, S. & Lavigne, D. M. Comparative energetics of coat colour polymorphs in the eastern gray squirrel Sciurus carolinensis. Can. J. Zool. 57, 585–592 (1979).
    Google Scholar 
    39.Santangelo, J. S. et al. Predicting the strength of urban-rural clines in a Mendelian polymorphism along a latitudinal gradient. Evol. Lett. 4, 212–225 (2020).PubMed 
    PubMed Central 

    Google Scholar 
    40.Fidino, M. et al. Landscape-scale differences among cities alter common species’ responses to urbanization. Ecol. Appl. 31, e02253 (2021).PubMed 

    Google Scholar 
    41.Dickinson, J. L., Zuckerberg, B. & Bonter, D. N. Citizen science as an ecological research tool: Challenges and benefits. Annu. Rev. Ecol. Evol. Syst. 41, 149–172 (2010).
    Google Scholar 
    42.Alberti, M. Global urban signatures of phenotypic change in animal and plant populations. Proc. Natl. Acad. Sci. U.S.A. 114, 8951–8956 (2017).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    43.United States Census Bureau. 2019 TIGER/Line Shapefiles (machine-readable data files) https://www2.census.gov/geo/tiger/TIGER2019/UAC/ (2019).44.XX. Statistics Canada. Population Centre Boundary File, Census year 2016 https://www150.statcan.gc.ca/n1/en/catalogue/92-166-X (2017).45.Aiello-Lammens, M. E. et al. spThin: An R package for spatial thinning of species occurrence records for use in ecological niche models. Ecography 38, 541–545 (2015).
    Google Scholar 
    46.R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. (2020).47.Brown de Colstoun, E. C. et al. Documentation for the Global Man-made Impervious Surface (GMIS) Dataset from Landsat (NASA Socioeconomic Data and Applications Center, 2017).
    Google Scholar 
    48.Steele, M. A. & Koprowski, J. L. North American Tree Squirrels (Smithsonian Books, 2001).
    Google Scholar 
    49.Hansen, M. C. et al. High-resolution global maps of 21st-century forest cover change. Science 342, 850–853 (2013).ADS 
    CAS 
    PubMed 

    Google Scholar 
    50.Fick, S. E. & Hijmans, R. J. WorldClim 2: New 1km spatial resolution climate surfaces for global land areas. Int. J. Climatol. 37, 4302–4315 (2017).
    Google Scholar 
    51.Hijmans, R. L. raster: Geographic data analysis and modeling. R package version 3.3–13. https://CRAN.R-project.org/package=raster (2020).52.Baston, D. exactextractr: Fast extraction from raster datasets using polygons. R package version 0.5.1. https://CRAN.R-project.org/package=exactextractr (2020).53.Harrison, X. A. et al. A brief introduction to mixed effects modelling and multi-model inference in ecology. PeerJ 6, e4794 (2018).PubMed 
    PubMed Central 

    Google Scholar 
    54.Bates, D., Maechler, M., Bolker, B. & Walker, S. Fitting linear mixed-effects models using lme4. J. Stat. Softw. 67, 1–48 (2015).
    Google Scholar 
    55.Gelman, A. & Su, Y. arm: Data analysis using regression and multilevel/hierarchical models. R package version 1.11–2. https://CRAN.R-project.org/package=arm (2020).56.Gelman, A. & Hill, J. Data Analysis Using Regression and Multilevel/Hierarchical Models (Cambridge University Press, 2007).
    Google Scholar 
    57.Crase, B., Liedloff, A. C. & Wintle, B. A. A new method for dealing with residual spatial autocorrelation in species distribution models. Ecography 35, 879–888 (2012).
    Google Scholar 
    58.Bivand, R. S. & Wong, D. W. S. Comparing implementations of global and local indicators of spatial association. TEST 27, 716–748 (2018).MathSciNet 
    MATH 

    Google Scholar 
    59.Bardos, D. C., Guillera-Arroita, G. & Wintle, B. A. Valid auto-models for spatially autocorrelated occupancy and abundance data. Methods Ecol. Evol. 6, 1137–1149 (2015).
    Google Scholar  More

  • in

    Poaching of protected wolves fluctuated seasonally and with non-wolf hunting

    Time-to-event models for wild animals generally model exposure of individuals to natural conditions that may affect the risk of mortality and disappearance. Most models neglect to consider seasons of high human activity that may affect such risks, or interactions between endpoint hazards (reflected in incidences) that may illuminate ecology. For many large carnivores, which suffer from low natural mortality yet are also subject to high risk of anthropogenic mortality and poaching, seasons of anthropogenic activity may be as important as natural ones in mediating cause-specific mortality and disappearance.Importantly, such anthropogenic seasons of higher mortality need not be specific to the animals being studied, especially if the species is controversial and much mortality illegal: our anthropogenic seasons consist of state hunting and hounding seasons for species other than wolves (i.e., deer or bear hunting, and hounding; not wolf hunting), but that mediate human activity on the landscape during those seasons. Our results support the hypothesis that increases in poaching risk during hunting seasons may be attributable to the surge of individuals with inclination to poach on the landscape14,18,29. Alternatively, it could also suggest enhanced criminal activity of a few poachers during the same periods. We temper this increase in poaching risk by establishing snow cover as a major environmental factor strongly associated with poaching. Moreover, our time-to-event analyses illuminate how to evaluate the effects that such anthropogenic seasons may have on risk of mortality and disappearance of monitored animals throughout their lifetime, and how considering such seasons may elucidate the mechanisms behind anthropogenic mortality and disappearance.Additionally, our analysis period precedes and completely excludes any established public wolf hunting seasons. Hence, our modeled anthropogenic seasons represent the periods of most relevant anthropogenic activity for wolves, as hypothesized by other studies14,29,33 and suggested by social science studies on inclinations to poach self-reported by both deer hunters and bear hunters, as well as acceptance of poaching by hunters and farmers30,31,32.Our analyses show increases in the hazard of disappearances of collared wolves (LTF) relative to the baseline period (which excludes environmental and anthropogenic risks) for all seasons. The highest hazard of LTF occurs during the snow season, whereas increases in hazard are lower (and similar) for the two seasons that included hounding and hunting. LTF may experience changes in hazard due to changes in the hazard of any/all of its components: migration, collar failure, or cryptic poaching.Constant and steep increases in LTF hazard throughout a wolf’s lifetime suggests mechanisms other than migration regulating LTF hazard, given migration for adults is most frequent by yearlings and younger adults, around 1.5 to 2.2 years34,35,36. Moreover, only migration out of state would end monitoring, not routine extraterritorial movements of radio-collared wolves. That our seasonal LTF curves depict the cumulative hazards more than doubling beyond those t generally associated with dispersal (~ t  More

  • in

    Vertical stratification of insect abundance and species richness in an Amazonian tropical forest

    1.Nakamura, A. et al. Forests and their canopies: Achievements and horizons in canopy science. Trends Ecol. Evol. 32, 438–451 (2017).PubMed 

    Google Scholar 
    2.Scheffers, B. R. et al. Microhabitats reduce animal’s exposure to climate extremes. Glob. Change Biol. 20, 495–503 (2014).ADS 

    Google Scholar 
    3.Lefsky, M. A. et al. Estimates of forest canopy height and aboveground biomass using ICESat. Geophys. Res. Lett. 32, L22S02 (2005).
    Google Scholar 
    4.Ellwood, M. D. F. & Foster, W. A. Doubling the estimate of invertebrate biomass in a rainforest canopy. Nature 429, 549–551 (2004).ADS 
    CAS 
    PubMed 

    Google Scholar 
    5.Dial, R. et al. Arthropod abundance, canopy structure, and microclimate in a Bornean lowland tropical rain forest. Biotropica 38, 643–652 (2006).
    Google Scholar 
    6.Valencia, R. et al. High tree alpha-diversity in Amazonian Ecuador. Biodivers. Conserv. 3, 21–28 (1994).
    Google Scholar 
    7.Stone, M. J. et al. Edge effects and beta diversity in ground and canopy beetle communities of fragmented subtropical forest. PLoS ONE 13, e0193369 (2018).PubMed 
    PubMed Central 

    Google Scholar 
    8.Nadkarni, N. M. Diversity of species and interactions in the upper tree canopy of forest ecosystems. Am. Zool. 34, 70–78 (1994).
    Google Scholar 
    9.Stanton, D. E. et al. Rapid nitrogen fixation by canopy microbiome in tropical forest determined by both phosphorus and molybdenum. Ecology 100(9), e02795 (2019).PubMed 

    Google Scholar 
    10.Basset, Y. et al. (eds) Arthropods of Tropical Forests. Spatio-Temporal Dynamics and Resource Use in the Canopy (Cambridge University Press, 2003).
    Google Scholar 
    11.Schowalter, T. D. et al. Post-hurricane successional dynamics in abundance and diversity of canopy arthropods in a tropical rainforest. Environ. Entomol. 46, 11–20 (2017).CAS 
    PubMed 

    Google Scholar 
    12.Silva, R. R. & Brandão, C. R. F. Morphological patterns and community organization in leaf-litter ant assemblages. Ecol. Monogr. 80, 107–124 (2010).
    Google Scholar 
    13.McCaig, T., Sam, L., Nakamura, L. & Stork, N. E. Is insect vertical distribution in rainforests better explained by distance from the canopy top or distance from the ground?. Biodivers. Conserv. 29, 1081–1103 (2020).
    Google Scholar 
    14.Floren, A. & Linsenmair, K. E. The influence of anthropogenic disturbances on the structure of arboreal arthropod communities. Plant Ecol. 153, 153–167 (2001).
    Google Scholar 
    15.Adis, J. et al. Canopy fogging of an overstory tree—Recommendations for standardization. Ecotropica 4, 93–97 (1998).
    Google Scholar 
    16.Bar-Ness, Y. D. et al. Sampling forest canopy arthropod biodiversity with three novel minimal-cost trap designs. Aust. J. Entomol. 51, 12–21. https://doi.org/10.1111/j.1440-6055.2011.00836.x (2012).Article 

    Google Scholar 
    17.Erwin, T. L. Canopy arthropod biodiversity: A chronology of sampling techniques and results. Rev. Peru. Entomol. 2, 71–77 (1990).
    Google Scholar 
    18.Floren, A. Sampling arthropods from the canopy by insecticidal knockdown. In Manual on Field Recording Techniques and Protocols for All Taxa Biodiversity Inventories, Part 1 Vol. 8 (eds Eymann, J., Degref, J., HĂ€user, C. et al.) 158–172 (ABC Taxa, 2010).
    Google Scholar 
    19.Leather, S. R. (ed.) Insect Sampling in Forest Ecosystems (Blackwell Science, 2005).
    Google Scholar 
    20.Lowman, M., Moffett, M. & Rinker, H. B. A new technique for taxonomic and ecological sampling in rain forest canopies. Selbyana 14, 75–79 (1993).
    Google Scholar 
    21.Lowman, M. D., Kitching, R. L. & Carruthers, G. Arthropod sampling in Australian subtropical rain forest: How accurate are some of the more common techniques?. Selbyana 17, 36–42 (1996).
    Google Scholar 
    22.Lowman, M. D., Schowalter, T. D. & Franklin, J. F. Methods in Forest Canopy Research (University of California Press, 2012).
    Google Scholar 
    23.Majer, J. D. & Recher, H. F. Invertebrate communities on Western Australian eucalypts—A comparison of branch clipping and chemical knockdown procedures. Aust. J. Ecol. 13, 269–278. https://doi.org/10.1111/j.1442-9993.1988.tb00974.x (1988).Article 

    Google Scholar 
    24.Ozanne, C. M. P. Techniques and methods for sampling canopy insects. In Insect Sampling in forest ecosystems (ed. Leather, S. R.) 146–165 (Blackwell, 2005).
    Google Scholar 
    25.Paarmann, W. & Stork, N. E. Canopy fogging, a method of collecting living insects for investigation of life history strategies. J. Nat. Hist. 21, 563–566. https://doi.org/10.1080/00222938700770341 (1987).Article 

    Google Scholar 
    26.Parker, G. G., Smith, A. P. & Hogan, K. P. Access to the upper forest canopy with a large tower crane. Bioscience 42, 664–670. https://doi.org/10.2307/1312172 (1992).Article 

    Google Scholar 
    27.Skvarla, M. J., Larson, J. L., Fisher, J. R. & Dowling, A. P. G. A review of terrestrial and canopy malaise traps. Ann. Entomol. Soc. Am. 114(1), 27–47. https://doi.org/10.1093/aesa/saaa044 (2021).Article 

    Google Scholar 
    28.Stork, N. E. Australian tropical forest canopy crane: New tools for new frontiers. Aust. Ecol. 32, 4–9. https://doi.org/10.1111/j.1442-9993.2007.01740.x (2007).Article 

    Google Scholar 
    29.Basset, Y. et al. IBISCA-Panama, a large-scale study of arthropod beta-diversity and vertical stratification in a lowland rainforest: Rationale, study sites and field protocols. Bull. Inst. R. Sci. Nat. Belg. Entomol. 77, 39–69 (2007).
    Google Scholar 
    30.Basset, Y., Cizek, L. & CuĂ©noud, P. Arthropod diversity in a tropical forest. Science 338, 1481–1484. https://doi.org/10.1126/science.1226727 (2012).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    31.Kitching, R. L. et al. The biodiversity of arthropods from Australian rainforest canopies: General introduction, methods, sites and ordinal results. Aust. J. Ecol. 18, 181–191. https://doi.org/10.1111/j.1442-9993.1993.tb00442.x (1993).Article 

    Google Scholar 
    32.Lindo, Z. & Winchester, N. N. Oribatid mite communities and foliar litter decomposition in canopy suspended soils and forest floor habitats of western red cedar forests, Vancouver Island, Canada. Soil Biol. Biochem. 39, 2957–2966. https://doi.org/10.1016/j.soilbio.2007.06.009 (2007).CAS 
    Article 

    Google Scholar 
    33.Schowalter, T. D. Canopy arthropod communities in relation to forest age and alternative harvest practices in western Oregon. For. Ecol. Manage 78, 115–125 (1995).
    Google Scholar 
    34.Southwood, T. R. E., Moran, V. C. & Kennedy, C. E. J. The assessment of arboreal insect fauna: Comparisons of knockdown sampling and faunal lists. Ecol. Entomol. 7, 331–340. https://doi.org/10.1111/j.1365-2311.1982.tb00674.x (1982).Article 

    Google Scholar 
    35.Stork, N. E. Guild structure of arthropods from Bornean rain forest trees. Ecol. Entomol. 12, 69–80. https://doi.org/10.1111/j.1365-2311.1987.tb00986.x (1987).Article 

    Google Scholar 
    36.Stork, N. E. et al. (eds) Canopy Arthropods (Chapman & Hall, 1997).
    Google Scholar 
    37.DeVries, P. J. Stratification of fruit-feeding nymphalid butterflies in a Costa Rican rain forest. J. Res. Lepid. 26, 98–108 (1988).ADS 

    Google Scholar 
    38.Hill, C. J., Gillison, A. N. & Jones, R. E. The spatial distribution of rain forest butterflies at three sites in North Queensland, Australia. J. Trop. Ecol. 8, 37–46 (1992).
    Google Scholar 
    39.Medina, M. C., Robbins, R. K. & Lamas, G. Vertical stratification of flight by Ithomiinae butterflies (Lepidoptera: Nymphalidae) at Pakitza, Manu National Park, Peru. In Manu—The Biodiversity of Southeastern Peru (eds Wilson, D. E. & Sandoval, A.) 211–216 (Smithsonian Institution, 1996).
    Google Scholar 
    40.DeVries, P. J., Murray, D. & Lande, R. Species diversity in vertical, horizontal, and temporal dimensions of a fruitfeeding butterfly community in an Ecuadorian rainforest. Biol. J. Linn. Soc. 62, 343–364. https://doi.org/10.1111/j.1095-8312.1997.tb01630.x (1997).Article 

    Google Scholar 
    41.DeVries, P. J., Murray, D. & Lande, R. Species diversity in vertical, horizontal, and temporal dimensions of a fruit-feeding butterfly community in an Ecuadorian rain forest. Biol. J. Linn. Soc. 62, 343–364 (1997).
    Google Scholar 
    42.Beccaloni, G. W. Vertical stratification of ithomiine butterfly (Nymphalidae: Ithomiinae) mimicry complexes: The relationship between adult flight height and larval host-plant height. Biol. J. Linn. Soc. 62, 313–341 (1997).
    Google Scholar 
    43.Schulze, C. H., Linsenmair, K. E. & Fiedler, K. Understorey versus canopy: Patterns of vertical stratification and diversity among Lepidoptera in a Bornean Rain Forest. Plant Ecol. 153, 133–152. https://doi.org/10.1023/A:1017589711553 (2001).Article 

    Google Scholar 
    44.Fordyce, J. A. & DeVries, P. J. A tale of two communities: Eotropical butterfly assemblages show higher beta diversity in the canopy compared to the understory. Oecologia 181, 235–243. https://doi.org/10.1007/s00442-016-3562-0 (2016).ADS 
    Article 
    PubMed 

    Google Scholar 
    45.Santos, J. P., Iserhard, C. A., Carreira, J. Y. O. & Freitas, A. V. L. Monitoring fruit-feeding butterfly assemblages in two vertical strata in seasonal Atlantic Forest: Temporal species turnover is lower in the canopy. J. Trop. Ecol. 33(5), 345–355 (2017).
    Google Scholar 
    46.Lourido, G. M., Motta, C. S., Graça, M. B. & Rafael, J. A. Diversity patterns of hawkmoths (Lepidoptera: Sphingidae) in the canopy of an ombrophilous forest in Central Amazon, Brazil. Acta Amazon. 48, 117–125 (2018).
    Google Scholar 
    47.Araujo, P. F., Freitas, A. V. L., Gonçalves, G. A. S. & Ribeiro, D. B. Vertical stratification on a small scale: The distribution of fruit-feeding butterflies in a semi-deciduous Atlantic forest in Brazil. Stud. Neotrop. Fauna Environ. 56, 10–39 (2021).
    Google Scholar 
    48.Charles, E. & Basset, Y. Vertical stratification of leaf-beetle assemblages (Coleoptera: Chrysomelidae) in two forest types in Panama. J. Trop. Ecol. 21, 329–336. https://doi.org/10.1017/S0266467405002300 (2005).Article 

    Google Scholar 
    49.Grimbacher, P. S. & Stork, N. E. Vertical stratification of feeding guilds and body size in beetle assemblages from an Australian tropical rainforest. Aust. Ecol. 32, 77–85. https://doi.org/10.1111/j.1442-9993.2007.01735.x (2007).Article 

    Google Scholar 
    50.Floren, A. & Schmidl, J. (eds) Canopy Arthropod Research in Europe: Basic and Applied Studies from the High Frontier (Bioform Entomology & Equipment, 2008).
    Google Scholar 
    51.Stork, N. E. et al. Vertical stratification of beetles in tropical rainforests as sampled by light traps in North Queensland, Australia. Austral Ecol. 41(2), 168–178 (2015).
    Google Scholar 
    52.Tregidgo, D. J., Qie, L., Barlow, J., Sodhi, N. S. & Lee-Hong, L. S. Vertical stratification responses of an arboreal dung beetle species to tropical forest fragmentation in Malaysia. Biotropica 42, 521–552 (2010).
    Google Scholar 
    53.Davis, A. J., Sutton, S. L. & Brendell, M. J. D. Vertical distribution of beetles in a tropical rainforest in Sulawesi: The role of the canopy in contributing to Biodiversity. Sepilok Bull. 13 & 14, 59–83 (2011).
    Google Scholar 
    54.Heatwole, H. Changes in ant assemblages across an arctic treeline. Rev d’Entomol du Quebec 34, 10–22 (1989).
    Google Scholar 
    55.Roubik, D. W. Tropical pollinators in the canopy and understory: Field data and theory for stratum “preferences”. J. Ins. Behav. 6, 659–673. https://doi.org/10.1007/BF01201668 (1993).Article 

    Google Scholar 
    56.Longino, J. T. & Colwell, R. K. Biodiversity assessment using structured inventory: Capturing the ant fauna of a tropical rain forest. Ecol. Appl. 7, 1263–1277. https://doi.org/10.1890/1051-0761(1997)007[1263:BAUSIC]2.0.CO;2 (1997).Article 

    Google Scholar 
    57.Vance, A. C. C., Smith, S. M., Malcolm, J. R., Huber, J. & Bellocq, M. I. Differences between forest type and vertical strata in the diversity and composition of hymenopteran families and mymarid genera in Northeastern Temperate Forests. Environ. Entomol. 36, 1073–1083. https://doi.org/10.1603/0046-225X(2007)36[1073:DBFTAV]2.0.CO;2 (2007).CAS 
    Article 
    PubMed 

    Google Scholar 
    58.Hernández-Flores, J. et al. Effect of forest disturbance on ant (Hymenoptera: Formicidae) diversity in a Mexican tropical dry forest canopy. Insect Conserv. Diver. 14(3), 393–402. https://doi.org/10.1111/icad.12466 (2020).Article 

    Google Scholar 
    59.Roberts, H. R. Arboreal Orthoptera in the rain forest of Costa Rica collected with insecticide: A report on the grasshoppers (Acrididae) including new species. Proc. Acad. Nat. Sci. Phila. 125, 46–66 (1973).
    Google Scholar 
    60.Rodgers, D. J. & Kitching, R. L. Vertical stratification of rainforest collembolan (Collembola: Insecta) assemblages: Description of ecological patterns and hypotheses concerning their generation. Ecography 21, 392–400. https://doi.org/10.1111/j.1600-0587.1998.tb00404.x (1998).Article 

    Google Scholar 
    61.Krab, E. J., Oorsprong, H., Berg, M. P. & Cornelissen, J. H. C. Turning northern peatlands upside down: Disentangling microclimate and substrate quality effects on vertical distribution of Collembola. Funct. Ecol. 24, 1362–1369. https://doi.org/10.1111/j.1365-2435.2010.01754.x (2010).Article 

    Google Scholar 
    62.Coots, C., Lambdin, P., Grant, J., Rhea, R. & Mockford, E. Vertical stratification and co-occurrence patterns of the psocoptera community associated with Eastern Hemlock, Tsuga canadensis (L.) Carriùre, in the Southern Appalachians. Forests 3, 127–136. https://doi.org/10.3390/f3010127 (2012).Article 

    Google Scholar 
    63.Wardhaugh, C. W. et al. Vertical stratification in the spatial distribution of the beech scale insect (Ultracoelostoma assimile) in Nothofagus tree canopies in New Zealand. Ecol. Entomol. 31, 185–195 (2006).
    Google Scholar 
    64.Brown, B. V. et al. Comprehensive inventory of true flies (Diptera) at a tropical site. Commun. Biol. 1, 1–8 (2018).ADS 

    Google Scholar 
    65.Borkent, A. et al. Remarkable fly (Diptera) diversity in a patch of Costa Rican cloud forest: Why inventory is a vital science. Zootaxa 4402, 53–90 (2018).PubMed 

    Google Scholar 
    66.Hebert, P. D. N. et al. Counting animal species with DNA barcodes: Canadian insects. Philos. Trans. R. Soc. Lond. Ser. B. 371, 20150333 (2016).
    Google Scholar 
    67.Basset, Y. et al. Arthropod distribution in a tropical rainforest: Tackling a four dimensional puzzle. PLoS ONE 10, e0144110 (2015).PubMed 
    PubMed Central 

    Google Scholar 
    68.MacArthur, R. H. Population ecology of some warblers of northeastern coniferous forests. Ecology 39, 599–619 (1958).
    Google Scholar 
    69.Higuchi, N. et al. Governos locais amazÎnicos e as questÔes climåticas globais 103 (INPA/edição dos autores, 2009).
    Google Scholar 
    70.Brown, B. V. Malaise trap catches and the crisis in Neotropical dipterology. Am. Entomol. 51, 180–183 (2005).
    Google Scholar 
    71.Gressitt, J. L. & Gressitt, M. K. An improved Malaise trap. Pacific Insects 4, 87–90 (1962).
    Google Scholar 
    72.van Achterberg, K. Can Townes type Malaise traps be improved? Some recent developments. Entomologische Berichten 69, 129–135 (2009).
    Google Scholar 
    73.R Core Team (2018). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. (Accessed 20 October 2021); https://www.R-project.org/.
    74.Konietschke, F. (2011). nparcomp: nparcomp-package. R package version 1.0-1. (Accessed 20 October 2021); http://CRAN.R-project.org/package=nparcomp75.Alboukadel Kassambara (2020). ggpubr: ‘ggplot2’ Based Publication Ready Plots. R package version 0.3.0. (Accessed 20 October 2021); https://CRAN.R-project.org/package=ggpubr76.Watson, J. E. M. et al. The exceptional value of intact forest ecosystems. Nat. Ecol. Evol. 2, 599–610 (2018).PubMed 

    Google Scholar 
    77.Gibson, L. et al. Primary forests are irreplaceable for sustaining tropical biodiversity. Nature 478, 378–381 (2011).ADS 
    CAS 
    PubMed 

    Google Scholar 
    78.Qin, Y. et al. Improved estimates of forest cover and loss in the Brazilian Amazon in 2000–2017. Nat. Sustain. 2, 764–772 (2019).
    Google Scholar 
    79.Gardner, T. A. et al. Predicting the uncertain future of tropical forest species in a data vacuum. Biotropica 39, 25–30 (2007).
    Google Scholar  More

  • in

    Species delimitation and mitonuclear discordance within a species complex of biting midges

    1.De Queiroz, K. Species concepts and species delimitation. Syst. Biol. 56, 879–886. https://doi.org/10.1080/10635150701701083 (2007).Article 
    PubMed 

    Google Scholar 
    2.Coyne, J. A. & Orr, H. A. Speciation (Sinauer Associates Inc, 2004).
    Google Scholar 
    3.Endler, J. A. Gene flow and population differentiation: studies of clines suggest that differentiation along environmental gradients may be independent of gene flow. Science 179, 243–250 (1973).CAS 
    PubMed 
    ADS 

    Google Scholar 
    4.Mayr, E. Systematics and the Origin of Species, from the Viewpoint of a Zoologist (Harvard University Press, 1999).
    Google Scholar 
    5.Richardson, J. L., Urban, M. C., Bolnick, D. I. & Skelly, D. K. Microgeographic adaptation and the spatial scale of evolution. Trends Ecol. Evol. 29, 165–176 (2014).PubMed 

    Google Scholar 
    6.Nosil, P. Ernst Mayr and the integration of geographic and ecological factors in speciation. Biol. J. Lin. Soc. 95, 26–46 (2008).
    Google Scholar 
    7.Kisel, Y. & Barraclough, T. G. Speciation has a spatial scale that depends on levels of gene flow. Am. Nat. 175, 316–334 (2010).PubMed 

    Google Scholar 
    8.Leliaert, F. et al. DNA-based species delimitation in algae. Eur. J. Phycol. 49, 179–196 (2014).
    Google Scholar 
    9.Carstens, B. C., Pelletier, T. A., Reid, N. M. & Satler, J. D. How to fail at species delimitation. Mol. Ecol. 22, 4369–4383 (2013).PubMed 

    Google Scholar 
    10.Schlick-Steiner, B. C. et al. Integrative taxonomy: a multisource approach to exploring biodiversity. Annu. Rev. Entomol. 55, 421–438 (2010).CAS 
    PubMed 

    Google Scholar 
    11.Capblancq, T., MavĂĄrez, J., Rioux, D. & DesprĂ©s, L. Speciation with gene flow: evidence from a complex of alpine butterflies (Coenonympha, Satyridae). Ecol. Evol. 9, 6444–6457 (2019).PubMed 
    PubMed Central 

    Google Scholar 
    12.Pedraza-Marrón, C. d. R. et al. Genomics overrules mitochondrial DNA, siding with morphology on a controversial case of species delimitation. Proc. R. Soc. B 286, 20182924 (2019).PubMed 
    PubMed Central 

    Google Scholar 
    13.Hinojosa, J. C. et al. A mirage of cryptic species: genomics uncover striking mitonuclear discordance in the butterfly Thymelicus sylvestris. Mol. Ecol. 28, 3857–3868 (2019).PubMed 

    Google Scholar 
    14.Nygren, A. et al. A mega-cryptic species complex hidden among one of the most common annelids in the North East Atlantic. PLoS ONE 13, e0198356 (2018).PubMed 
    PubMed Central 

    Google Scholar 
    15.Thielsch, A., Knell, A., Mohammadyari, A., Petrusek, A. & Schwenk, K. Divergent clades or cryptic species? Mito-nuclear discordance in a Daphnia species complex. BMC Evol. Biol. 17, 1–9 (2017).
    Google Scholar 
    16.Eyer, P. A. & Hefetz, A. Cytonuclear incongruences hamper species delimitation in the socially polymorphic desert ants of the Cataglyphis albicans group in Israel. J. Evol. Biol. 31, 1828–1842 (2018).CAS 
    PubMed 

    Google Scholar 
    17.Borkent, A. Biology of Disease Vectors. 2nd edn, i–xxiii + 1–785 (Elsevier Academic Press, 2004).18.Mellor, P., Boorman, J. & Baylis, M. Culicoides biting midges: their role as arbovirus vectors. Annu. Rev. Entomol. 45, 307–340 (2000).CAS 
    PubMed 

    Google Scholar 
    19.Rushton, J. & Lyons, N. Economic impact of Bluetongue: a review of the effects on production. Veterinaria italiana 51, 401–406 (2015).PubMed 

    Google Scholar 
    20.Tabachnick, W. J. Culicoides vriipennis and Bluetongue-Virus eidemiology in the United States. Annu. Rev. Entomol. 41, 23–43. https://doi.org/10.1146/annurev.en.41.010196.000323 (1996).CAS 
    Article 
    PubMed 

    Google Scholar 
    21.Wirth, W. W. & Jones, R. H. The North American Subspecies of Culicoides variipennis (Diptera, Heleidae). U. S. Dep. Agric. Tech. Bull 1170, 1–35 (1957).
    Google Scholar 
    22.Holbrook, F. R. et al. Sympatry in the Culicoides variipennis Complex (Diptera: Ceratopogonidae): a Taxonomic Reassessment. J. Med. Entomol. 37, 65–76. https://doi.org/10.1603/0022-2585-37.1.65 (2000).CAS 
    Article 
    PubMed 

    Google Scholar 
    23.Hopken, M. W. Pathogen Vectors at the Wildlife-Livestock Interface: Molecular Approaches to Elucidating Culicoides (Diptera: Ceratopogonidae) Biology (University of Colorado, 2016).
    Google Scholar 
    24.Shults, P. A Study of the Taxonomy, Ecology, and Systematics of Culicoides Species (Diptera: Ceratopogonidae) Including those Associated with Deer Breeding Facilities in Southeast Texas (Texas A&M University, 2015).
    Google Scholar 
    25.Velten, R. K. & Mullens, B. A. Field morphological variation and laboratory hybridization of Culicoides variipennis sonorensis and C. v. occidentalis (Diptera:Ceratopogonidae) in southern California. J. Med. Entomol. 34, 277–284 (1997).CAS 
    PubMed 

    Google Scholar 
    26.Fontaine, M. C. et al. Extensive introgression in a malaria vector species complex revealed by phylogenomics. Science 347, 1258522 (2015).PubMed 

    Google Scholar 
    27.Bolnick, D. I. & Otto, S. P. The magnitude of local adaptation under genotype-dependent dispersal. Ecol. Evol. 3, 4722–4735 (2013).PubMed 
    PubMed Central 

    Google Scholar 
    28.Slatkin, M. Isolation by distance in equilibrium and non-equilibrium populations. Evolution 47, 264–279 (1993).PubMed 

    Google Scholar 
    29.Pante, E. et al. Species are hypotheses: avoid connectivity assessments based on pillars of sand. Mol. Ecol. 24, 525–544 (2015).PubMed 

    Google Scholar 
    30.Jacquet, S. et al. Colonization of the Mediterranean basin by the vector biting midge species Culicoides imicola: an old story. Mol. Ecol. 24, 5707–5725. https://doi.org/10.1111/mec.13422 (2015).CAS 
    Article 
    PubMed 

    Google Scholar 
    31.Onyango, M. G. et al. Genotyping of whole genome amplified reduced representation libraries reveals a cryptic population of Culicoides brevitarsis in the Northern Territory, Australia. BMC Genomics 17, 769. https://doi.org/10.1186/s12864-016-3124-1 (2016).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    32.Onyango, M. G. et al. Delineation of the population genetic structure of Culicoides imicola in East and South Africa. Parasit. Vectors 8, 660. https://doi.org/10.1186/s13071-015-1277-4 (2015).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    33.Mignotte, A. et al. High dispersal capacity of Culicoides obsoletus (Diptera: Ceratopogonidae), vector of bluetongue and Schmallenberg viruses, revealed by landscape genetic analyses. Parasit. Vectors 14, 1–14 (2021).
    Google Scholar 
    34.Sanders, C. J. & Carpenter, S. Assessment of an immunomarking technique for the study of dispersal of Culicoides biting midges. Infect. Genet. Evol. 28, 583–587 (2014).PubMed 

    Google Scholar 
    35.Kluiters, G., Swales, H. & Baylis, M. Local dispersal of palaearctic Culicoides biting midges estimated by mark-release-recapture. Parasit. Vectors 8, 86 (2015).PubMed 
    PubMed Central 

    Google Scholar 
    36.Ducheyne, E. et al. Quantifying the wind dispersal of Culicoides species in Greece and Bulgaria. Geospat. Health 10, 177–189 (2007).
    Google Scholar 
    37.Purse, B. V. et al. Climate change and the recent emergence of bluetongue in Europe. Nat. Rev. Microbiol. 3, 171–181 (2005).CAS 
    PubMed 

    Google Scholar 
    38.Jacquet, S. et al. Range expansion of the Bluetongue vector, Culicoides imicola, in continental France likely due to rare wind-transport events. Sci. Rep. https://doi.org/10.1038/srep27247 (2016).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    39.Rundle, H. D. & Nosil, P. Ecological speciation. Ecol. Lett. 8, 336–352 (2005).
    Google Scholar 
    40.Wang, I. J. & Bradburd, G. S. Isolation by environment. Mol. Ecol. 23, 5649–5662 (2014).PubMed 

    Google Scholar 
    41.Shults, P. A Study of Culicoides Biting Midges in the Subgenus Monoculicoides: Population Genetics, Taxonomy, Systematics, and Control. Ph.D. thesis, Texas A&M University (2021).42.Jewiss-Gaines, A., Barelli, L. & Hunter, F. F. First records of Culicoides sonorensis (Diptera: Ceratopogonidae), a known vector of bluetongue virus, Southern Ontario. J. Med. Entomol. 54, 757–762. https://doi.org/10.1093/jme/tjw215 (2017).CAS 
    Article 
    PubMed 

    Google Scholar 
    43.Chan, K. M. & Levin, S. A. Leaky prezygotic isolation and porous genomes: rapid introgression of maternally inherited DNA. Evolution 59, 720–729 (2005).CAS 
    PubMed 

    Google Scholar 
    44.Harrison, R. G. Hybrid zones: windows on evolutionary process. Oxf. Surv. Evol. Biol. 7, 69–128 (1990).
    Google Scholar 
    45.Harrison, R. G. Animal mitochondrial DNA as a genetic marker in population and evolutionary biology. Trends Ecol. Evol. 4, 6–11 (1989).CAS 
    PubMed 

    Google Scholar 
    46.DesprĂ©s, L. One, Two or More Species? Mitonuclear Discordance and Species Delimitation. Molecular ecology 28(17), 3845–3847 (2019).PubMed 

    Google Scholar 
    47.Janes, J. K. et al. The K= 2 conundrum. Mol. Ecol. 26, 3594–3602 (2017).PubMed 

    Google Scholar 
    48.De Meester, L., Vanoverbeke, J., Kilsdonk, L. J. & Urban, M. C. Evolving perspectives on monopolization and priority effects. Trends Ecol. Evol. 31, 136–146 (2016).PubMed 

    Google Scholar 
    49.Ballard, J. W. O., Chernoff, B. & James, A. C. Divergence of mitochondrial DNA is not corroborated by nuclear DNA, morphology, or behavior in Drosophila simulans. Evolution 56, 527–545 (2002).PubMed 

    Google Scholar 
    50.Behura, S., Sahu, S., Mohan, M. & Nair, S. Wolbachia in the Asian rice gall midge, Orseolia oryzae (Wood-Mason): Correlation between host mitotypes and infection status. Insect Mol. Biol. 10, 163–171 (2001).CAS 
    PubMed 

    Google Scholar 
    51.Covey, H. et al. Cryptic Wolbachia (Rickettsiales: Rickettsiaceae) detection and prevalence in Culicoides (Diptera: Ceratopogonidae) midge populations in the United States. J. Med. Entomol. 57, 1262–1269. https://doi.org/10.1093/jme/tjaa003 (2020).Article 
    PubMed 

    Google Scholar 
    52.PagĂšs, N., Muñoz-Muñoz, F., VerdĂșn, M., Pujol, N. & Talavera, S. First detection of Wolbachia-infected Culicoides (Diptera: Ceratopogonidae) in Europe: Wolbachia and Cardinium infection across Culicoides communities revealed in Spain. Parasit. Vectors 10, 582. https://doi.org/10.1186/s13071-017-2486-9 (2017).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    53.Pilgrim, J. et al. Cardinium symbiosis as a potential confounder of mtDNA based phylogeographic inference in Culicoides imicola (Diptera: Ceratopogonidae), a vector of veterinary viruses. Parasit. Vectors 14, 100. https://doi.org/10.1186/s13071-020-04568-3 (2021).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    54.Hare, M. P. Prospects for nuclear gene phylogeography. Trends Ecol. Evol. 16, 700–706 (2001).
    Google Scholar 
    55.Onyango, M. G. et al. Assessment of population genetic structure in the arbovirus vector midge, Culicoides brevitarsis (Diptera: Ceratopogonidae), using multi-locus DNA microsatellites. Vet. Res. 46, 108. https://doi.org/10.1186/s13567-015-0250-8 (2015).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    56.Fonseca, D. M., Smith, J. L., Kim, H.-C. & Mogi, M. Population genetics of the mosquito Culex pipiens pallens reveals sex-linked asymmetric introgression by Culex quinquefasciatus. Infect. Genet. Evol. 9, 1197–1203 (2009).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    57.Goubert, C., Minard, G., Vieira, C. & Boulesteix, M. Population genetics of the Asian tiger mosquito Aedes albopictus, an invasive vector of human diseases. Heredity 117, 125–134 (2016).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    58.Lehmann, T. et al. Microgeographic structure of Anopheles gambiae in western Kenya based on mtDNA and microsatellite loci. Mol. Ecol. 6, 243–253 (1997).CAS 
    PubMed 

    Google Scholar 
    59.Chapuis, M.-P. & Estoup, A. Microsatellite null alleles and estimation of population differentiation. Mol. Biol. Evol. 24, 621–631. https://doi.org/10.1093/molbev/msl191 (2006).CAS 
    Article 
    PubMed 

    Google Scholar 
    60.Manni, M. et al. Molecular markers for analyses of intraspecific genetic diversity in the Asian Tiger mosquito, Aedes albopictus. Parasit. Vectors 8, 1–11 (2015).
    Google Scholar 
    61.Arntzen, J. W., Jehle, R., Bardakci, F., Burke, T. & Wallis, G. P. Asymmetric viability of reciprocal-cross hybrids between Crested and Marbled Newts (Triturus cristatus and T. marmoratus). Evolution 63, 1191–1202. https://doi.org/10.1111/j.1558-5646.2009.00611.x (2009).Article 
    PubMed 

    Google Scholar 
    62.Gibeaux, R. et al. Paternal chromosome loss and metabolic crisis contribute to hybrid inviability in Xenopus. Nature 553, 337. https://doi.org/10.1038/nature25188 (2018).CAS 
    Article 
    PubMed 
    PubMed Central 
    ADS 

    Google Scholar 
    63.Werren, J. H., Baldo, L. & Clark, M. E. Wolbachia: master manipulators of invertebrate biology. Nat. Rev. Microbiol. 6, 741 (2008).CAS 
    PubMed 

    Google Scholar 
    64.Servedio, M. R. & Kirkpatrick, M. The effects of gene flow on reinforcement. Evolution 51, 1764–1772. https://doi.org/10.1111/j.1558-5646.1997.tb05100.x (1997).Article 
    PubMed 

    Google Scholar 
    65.Howard, D. J. Reinforcement: origin, dynamics, and fate of an evolutionary hypothesis. Hybrid zones and the evolutionary process, 46–69 (1993).66.Yukilevich, R. Asymmetrical patterns of speciation uniquely support reinforcement in Drosophila. Evolution 66, 1430–1446. https://doi.org/10.1111/j.1558-5646.2011.01534.x (2012).Article 
    PubMed 

    Google Scholar 
    67.Downes, J. A. The Culicoides variipennis complex: a necessary re-alignment of nomenclature (Diptera: Ceratopogonidae). Can. Entomol. 110, 63–69 (1978).
    Google Scholar 
    68.Toews, D. P. & Brelsford, A. The biogeography of mitochondrial and nuclear discordance in animals. Mol. Ecol. 21, 3907–3930 (2012).CAS 
    PubMed 

    Google Scholar 
    69.Smith, H. & Mullens, B. A. Seasonal activity, size, and parity of Culicoides occidentalis (Diptera: Ceratopogonidae) in a coastal southern California salt marsh. J. Med. Entomol. 40, 352–355. https://doi.org/10.1603/0022-2585-40.3.352 (2003).Article 
    PubMed 

    Google Scholar 
    70.Linley, J. The effect of salinity on oviposition and egg hatching in Culicoides variipennis sonorensis (Diptera: Ceratopogonidae). J. Am. Mosq. Control Assoc. 2, 79–82 (1986).CAS 
    PubMed 

    Google Scholar 
    71.Gerry, A. C. & Mullens, B. A. Response of Male Culicoides variipennis sonorensis (Diptera: Ceratopogonidae) to carbon dioxide and observations of mating behavior on and near cattle. J. Med. Entomol. 35, 239–244. https://doi.org/10.1093/jmedent/35.3.239 (1998).CAS 
    Article 
    PubMed 

    Google Scholar 
    72.Nolan, D. V. et al. Rapid diagnostic PCR assays for members of the Culicoides obsoletus and Culicoides pulicaris species complexes, implicated vectors of bluetongue virus in Europe. Vet. Microbiol. 124, 82–94 (2007).CAS 
    PubMed 

    Google Scholar 
    73.Sebastiani, F. et al. Molecular differentiation of the Old World Culicoides imicola species complex (Diptera, Ceratopogonidae), inferred using random amplified polymorphic DNA markers. Mol. Ecol. 10, 1773–1786 (2001).CAS 
    PubMed 

    Google Scholar 
    74.Carlson, D. Identification of mosquitoes of Anopheles gambiae species complex A and B by analysis of cuticular components. Science 207, 1089–1091 (1980).CAS 
    PubMed 
    ADS 

    Google Scholar 
    75.Palacios, G. et al. Characterization of the Sandfly fever Naples species complex and description of a new Karimabad species complex (genus Phlebovirus, family Bunyaviridae). J. Gen. Virol. 95, 292 (2014).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    76.Rivas, G., Souza, N. & Peixoto, A. A. Analysis of the activity patterns of two sympatric sandfly siblings of the Lutzomyia longipalpis species complex from Brazil. Med. Vet. Entomol. 22, 288–290 (2008).CAS 
    PubMed 

    Google Scholar 
    77.Wilson, W. C. et al. Current status of bluetongue virus in the Americas. Bluetongue 10, 197–220 (2009).
    Google Scholar 
    78.Allen, S. E. et al. Epizootic Hemorrhagic Disease in White-Tailed Deer, Canada. Emerg. Infect. Dis. 25, 832–834. https://doi.org/10.3201/eid2504.180743 (2019).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    79.McGregor, B. L. et al. Field data implicating Culicoides stellifer and Culicoides venustus (Diptera: Ceratopogonidae) as vectors of epizootic hemorrhagic disease virus. Parasit. Vectors 12, 258. https://doi.org/10.1186/s13071-019-3514-8 (2019).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    80.Shults, P., Ho, A., Martin, E. M., McGregor, B. L. & Vargo, E. L. Genetic diversity of Culicoides stellifer (Diptera: Ceratopogonidae) in the Southeastern United States compared with sequences from Ontario, Canada. J. Med. Entomol. 57, 1324–1327. https://doi.org/10.1093/jme/tjaa025 (2020).CAS 
    Article 
    PubMed 

    Google Scholar 
    81.Mallet, J. Hybridization as an invasion of the genome. Trends Ecol. Evol. 20, 229–237 (2005).PubMed 

    Google Scholar 
    82.Ciota, A. T., Chin, P. A. & Kramer, L. D. The effect of hybridization of Culex pipiens complex mosquitoes on transmission of West Nile virus. Parasit. Vectors 6, 1–4 (2013).
    Google Scholar 
    83.Meiswinkel, R., Gomulski, L., DelĂ©colle, J., Goffredo, M. & Gasperi, G. The taxonomy of Culicoides vector complexes-unfinished business. Vet. Ital. 40, 151–159 (2004).CAS 
    PubMed 

    Google Scholar 
    84.Ewels, P., Magnusson, M., Lundin, S. & KĂ€ller, M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics (Oxford, England) 32, 3047–3048. https://doi.org/10.1093/bioinformatics/btw354 (2016).CAS 
    Article 

    Google Scholar 
    85.Andrews, S. Babraham bioinformatics-FastQC a quality control tool for high throughput sequence data. https://www.bioinformatics.babraham.ac.uk/projects/fastqc (2010).86.Rochette, N. C., Rivera-Colón, A. G. & Catchen, J. M. Stacks 2: Analytical methods for paired-end sequencing improve RADseq-based population genomics. Mol. Ecol. 28, 4737–4754 (2019).CAS 
    PubMed 

    Google Scholar 
    87.Morales-Hojas, R. et al. The genome of the biting midge Culicoides sonorensis and gene expression analyses of vector competence for bluetongue virus. BMC Genomics 19, 624. https://doi.org/10.1186/s12864-018-5014-1 (2018).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    88.Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (Oxford, England) 25, 1754–1760 (2009).CAS 

    Google Scholar 
    89.Pante, E. et al. Use of RAD sequencing for delimiting species. Heredity 114, 450–459 (2015).CAS 
    PubMed 

    Google Scholar 
    90.Benestan, L. M. et al. Conservation genomics of natural and managed populations: building a conceptual and practical framework. Mol. Ecol. 25, 2967–2977 (2016).PubMed 

    Google Scholar 
    91.Lischer, H. E. & Excoffier, L. PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs. Bioinformatics (Oxford, England) 28, 298–299 (2012).CAS 

    Google Scholar 
    92.Pina-Martins, F., Silva, D. N., Fino, J. & Paulo, O. S. Structure_threader: An improved method for automation and parallelization of programs structure, fastStructure and MavericK on multicore CPU systems. Mol. Ecol. Resour. 17, e268–e274 (2017).CAS 
    PubMed 

    Google Scholar 
    93.Raj, A., Stephens, M. & Pritchard, J. K. Variational Inference of Population Structure in Large SNP Datasets. bioRxiv 10, 001073 (2013).
    Google Scholar 
    94.R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.http://www.R-project.org/ (2013).95.Jombart, Thibaut, and Caitlin Collins. A tutorial for discriminant analysis of principal components (DAPC) using adegenet 2.0. 0. London: Imperial College London, MRC Centre for Outbreak Analysis and Modelling (2015).96.Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics (Oxford, England) 30, 1312–1313 (2014).CAS 

    Google Scholar 
    97.LeachĂ©, A. D., Banbury, B. L., Felsenstein, J., De Oca, A.N.-M. & Stamatakis, A. Short tree, long tree, right tree, wrong tree: New acquisition bias corrections for inferring SNP phylogenies. Syst. Biol. 64, 1032–1047 (2015).PubMed 
    PubMed Central 

    Google Scholar 
    98.Pattengale, N. D., Alipour, M., Bininda-Emonds, O. R., Moret, B. M. & Stamatakis, A. How many bootstrap replicates are necessary?. J. Comput. Biol. 17, 337–354 (2010).MathSciNet 
    CAS 
    PubMed 

    Google Scholar 
    99.Trifinopoulos, J., Nguyen, L.-T., von Haeseler, A. & Minh, B. Q. W-IQ-TREE: A fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Res. 44, W232–W235 (2016).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    100.Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K., Von Haeseler, A. & Jermiin, L. S. ModelFinder: Fast model selection for accurate phylogenetic estimates. Nat. Methods 14, 587–589 (2017).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    101.Nguyen, L.-T., Schmidt, H. A., Von Haeseler, A. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2015).CAS 
    PubMed 

    Google Scholar 
    102.Hoang, D. T., Chernomor, O., Von Haeseler, A., Minh, B. Q. & Vinh, L. S. UFBoot2: improving the ultrafast bootstrap approximation. Mol. Biol. Evol. 35, 518–522 (2018).CAS 
    PubMed 

    Google Scholar 
    103.Guindon, S. et al. New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 30. Syst. Biol. 59, 307–321. https://doi.org/10.1093/sysbio/syq010 (2010).CAS 
    Article 
    PubMed 

    Google Scholar 
    104.Rousset, F. genepop’007: a complete re‐implementation of the genepop software for Windows and Linux. Molecular ecology resources 8(1), 103–106 (2008).
    Google Scholar 
    105.Rousset, F. Genetic differentiation between individuals. J Evol Biol 13, 58–62 (2000).
    Google Scholar 
    106.Loiselle, B. A., Sork, V. L., Nason, J. & Graham, C. Spatial genetic structure of a tropical understory shrub, Psychotria officinalis (Rubiaceae). Am. J. Bot. 82, 1420–1425 (1995).
    Google Scholar 
    107.Hardy, O. & Vekemans, X. SPAGeDi 1.5. A program for Spatial Pattern Analysis of Genetic Diversity. User’s manual http://ebe.ulb.ac.be/ebe/SPAGeDi_files/SPAGeDi_1.5_Manual.pdf. UniversitĂ© Libre de Bruxelles, Brussells, Belgium.[Google Scholar] (2015).108.Jay, F., Sjödin, P., Jakobsson, M. & Blum, M. G. Anisotropic isolation by distance: the main orientations of human genetic differentiation. Mol. Biol. Evol. 30, 513–525 (2013).CAS 
    PubMed 

    Google Scholar 
    109.Piry, S. et al. Mapping Averaged Pairwise Information (MAPI): a new exploratory tool to uncover spatial structure. Methods Ecol. Evol. 7, 1463–1475 (2016).
    Google Scholar 
    110.Kearse, M. et al. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics (Oxford, England) 28, 1647–1649. https://doi.org/10.1093/bioinformatics/bts199 (2012).Article 

    Google Scholar 
    111.Hopken, M. W. Pathogen Vectors at The Wildlife-Livestock Interface: Molecular Approaches to Elucidating Culicoides (Diptera: Ceratopogonidae) Ph.D. thesis, Colorado State University (2016).112.Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35, 1547–1549 (2018).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    113.Bandelt, H. J., Forster, P. & Rohl, A. Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. 16, 37–48. https://doi.org/10.1093/oxfordjournals.molbev.a026036 (1999).CAS 
    Article 
    PubMed 

    Google Scholar  More