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Article

Machine Learning and Its Applications in Studying the Geographical Distribution of Ants

by
Shan Chen
1 and
Yuanzhao Ding
2,*
1
Faculty of Education, Southwest University, No. 2 Tiansheng Road, Beibei District, Chongqing 400715, China
2
School of Geography and the Environment, University of Oxford, South Parks Road, Oxford OX1 3QY, UK
*
Author to whom correspondence should be addressed.
Diversity 2022, 14(9), 706; https://doi.org/10.3390/d14090706
Submission received: 20 May 2022 / Revised: 23 August 2022 / Accepted: 24 August 2022 / Published: 26 August 2022
(This article belongs to the Section Biodiversity Conservation)
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Abstract

:
Traditional species distribution modelling relies on the links between species and their environments, but often such information is unavailable or unreliable. The objective of our research is to take a machine learning (ML) approach to estimate ant species richness in data-poor countries based on published data on the broader distribution of described ant species. ML is a novel black box method that does not consider functional links between species and their environment. Its prediction accuracy is limited only by the quality and quantity of species records data. ML modelling is applied to calculate the global distribution of ant species richness and achieves 71.78% (decision tree), 70.62% (random forest), 71.09% (logistic regression), and 75.18% (neural network) testing accuracy. The results show that in some West African countries, the species predicted by ML are 1.99 times as many as the species currently recorded. These West African countries have many ant species but lack observational data, and policymakers may be overlooking areas that require protection.

1. Introduction

The distribution of species richness is an essential research field in biodiversity conservation. Based on a species’ response to environmental factors, scientists generally employ species distribution modelling (SDM) [1,2]. SDM is a numerical tool that links species observation with environmental estimations [3,4]. Typically, SDM consists of five steps: (1) environmental data and species data, including climate and presence/absence; (2) model structure, meaning model algorithm selection, and specification; (3) model calibration and model fitting; (4) model validation, including verification of the model’s performance; and (5) model projection, suggesting predictions under different scenarios [3,4,5]. Normally, SDM uses three approaches: correlative models (statistical links between spatial data and distribution of species richness), process-based models (mechanistic links between the functional traits of organisms and their environments), and hybrid models [6]. However, these methods have limitations: for example, process-based mechanistic models are built on existing links that lead to bias and they cannot guarantee an accurate outcome [6,7,8].
To decrease the effect of links and bias, scientists consider using novel “black box” machine learning (ML) methods to make predictions about the distribution of species richness based on field data [9]. ML specialises in processing massive continual and categorical data to acquire accurate prediction results [10,11,12,13]. It has been applied with complex modelling skills to correctly solve undiscovered nonlinear relationships by working with massive and intractable variables in animal science [14,15]. ML has also been confirmed to be an effective tool for predicting animal distribution, including avian [16], mosquito [17], fish [18], and great grey shrike [19]. Since ML uses high-quality and extensive data, its accuracy would overcome the disadvantages associated with SDM and discover more unknown links between the functional traits of organisms and their environments (Table 1). Therefore, ML is an intelligent, rapid, and accurate method that has great potential for use in predicting the distribution of species richness.
To examine the application of ML methods in the distribution of species richness, we select ants as the object of this paper for the following reasons. First, this is a global-scale study, and ants are widely distributed in most countries [27,28]. Second, ants are small and difficult to capture, causing databases to vary widely from country to country [29]. Third, more than 14,000 classified species of ants exist, and scientists can assess comprehensive databases of these insects [30]. Fourth, ants are an ecologically dominant faunal group globally [31,32]. Finally, ants greatly impact humans, such as by suppressing pest populations in the soil or providing biological control for citrus cultivation [33,34]. Kass et al. applied ML with high resolution (20 km) to predict ant distribution in comparison with the distribution of vertebrate groups globally. They suggested that landscape conservation would benefit both vertebrate and invertebrate groups because the existence of these animals relies heavily on certain environmental conditions [35]. Kass et al.’s study inspired us to further explore ant distribution, specifically in West African countries since these countries have been recognised to have a scarcity of ant species, and in these countries, it is difficult to obtain observational information. Moreover, we introduced some new variables (e.g., temperature, precipitation, forest area, GDP per capita, and human development index) to ascertain which factors influence ant distribution the most [36,37,38,39,40,41], as well as to utilise the neural network method to make predictions. Numerous studies have addressed the distribution of ants geographically through fieldwork and observation [42,43,44,45]. However, these data are mostly from developed rather than underdeveloped countries [46,47]. Consequently, scientists are often confused about whether or not a given species exists in an underdeveloped country. In such cases, policymakers occasionally equate situations in which data are missing with the absence of a given species when they designate protected areas [48].
The objective of our research is to take an ML approach to estimate species richness in data-poor countries based on published data on the broader distribution of described ant species. The specific aims are (1) to compile the number of described species and total species records for all countries. It is important to note that our study deals with described species only, and does not take into account differences among countries in numbers of undescribed species; (2) to correlate these with environmental and socioeconomic factors (e.g., temperature, precipitation, forest area, GDP per capita, human development index); (3) to use ML to estimate the likely number of described species in each country; and (4) to map the discrepancy between the number of recorded species and the number of likely species [49].

2. Material and Methods

The ML method followed the previous studies with minor modifications [50,51,52]. It captured linear and nonlinear patterns via mathematical expressions. Briefly, ML involved three steps: (1) collecting data, (2) using the data to train the model, and (3) applying the model to predict the species richness (Figure 1).
First, the ant database was constructed using AntWiki (https://www.antwiki.org, accessed on 1 May 2022) and with 33,655 records and labelled with four distribution categories: “Uncertain”, “Introduced”, “Likely”, and “Present” [53]. The environmental data were obtained from governmental websites and the WorldClim database (https://www.worldclim.org/, accessed on 1 May 2022) [54,55]. The temperature data came from the Global Temperature and World Bank databases [56,57]. The precipitation data came from the Global Precipitation Climatology Centre and World Bank databases [57,58]. The forest data came from the World Bank database [57]. “Temperature”, “Precipitation”, and “Forest area” were the data that most directly affected the environment and the distribution of species richness. The GDP per capita data were obtained from the International Monetary Fund [59] and World Bank databases [57]. The human development index was a composite index of life expectancy, education, and income from the human development report of the United Nations Development Programme [60].
Second, the model input the dataset with 33,655 records. Of the data set, 80% was used to train the model and the remaining 20% was used for testing. Then the model was trained based on supervised learning, in which a function was learned based on input–output pairs [26]. Unless otherwise stated, we trained the ML via the following environment: Python 3.7.1 (Python Software Foundation, Wilmington, DE, USA), Scikit-learn 0.20.0, Graphviz 0.8.4, Numpy 1.15.3, Pandas 0.23.4, Matplotlib 3.0.1, and SciPy 1.1.0 [61,62]. The coding library was based on Scikit-learn (Sklearn), Keras, Pandas, and Matplotlib. Four ML methods for calculation were decision tree [63,64], random forest [65,66], logistic regression [64], and neural network [9]. ML methods were based on previous studies with default methods in the Scikit-learn module [21,22,23]. For the neural network, there were 100 hidden layers in total [67], and each layer had 100 nodes [68]. The maximum number of iterations was 50. The activation function was the rectified linear unit (“relu”). The solver for the neural network algorithm was Adam optimisation (“adam”). The Python coding was obtained from GitHub with minor modifications (Tables S2–S6; permissions under MIT license) [21,22,23].
Third, after the model was trained, we examined the training accuracy and testing accuracy. Furthermore, we applied the ML model to make predictions on the data in unknown areas. For the convenience of calculation, the distribution of species richness was quantified and standardised using a distribution index. The distribution index was the ratio of the total likely number of species and all known ant species in a certain country with a value from 0 (the lowest number of the documented species) to 1 (the highest possible number of the observed species). All countries all over the world were finally calculated to a value from 0 to 1. According to the number for each country, the global distribution index of ants was visualised using the software Heatmapper, Canada (http://www.heatmapper.ca/, accessed on 1 May 2022) [69].

3. Results

3.1. Observation Data Analysis

The “present” category had the most common category of data, accounting for approximately 60–70% of all data (Figure 2). The amount of data on the distribution of species richness varied greatly among the different countries (Figure 2). A large amount of the observed data on the distribution of species richness was from Argentina, China, Brazil, Mexico, and the United States. In this case, the number of described species has been comprehensively documented. There were few observed data on species occurrence in Niger, Mauritania, Mali, Chad, and Bhutan. For example, Mauritania had records for only 15 native species, whereas neighbouring Algeria (with a similar landscape and area) had records for 339 native species (https://antmaps.org/).

3.2. Observation versus Prediction via ML

The neural network achieved the best overall accuracy in the training (75.77%) and testing (75.18%; Table 2). As a result, we applied the neural network for next-step analysis.
In the temperature analysis, we found that there were two peaks above the annual average temperature, 7 °C and 25 °C. In the precipitation analysis, most species of ants were observed in the range of approximately 700 mm to 2000 mm of annual precipitation (see Figure 3a,b). The data showed that most species of ants were distributed between warm and humid regions. In the forest area analysis, most ant species were observed in countries with 30% to 60% of the forest area and 0.65 to 0.95 of the human development index (see Figure 3c,d). This indicates that developed countries with high vegetation coverage contribute positively to the distribution of species richness. The prediction frequency (see Figure 3e–h) showed a similar pattern to the observation frequency from the overall data structure.
From the correlation heatmap analysis (see Figure 4), the main factors affecting observation frequency were “Forest area” (+0.13), “GDP per capita” (+0.23), and “Human development index” (+0.21). These results suggest that the natural environment (forest area) plays an important role in the distribution of species richness. A higher GDP per capita and human development index may lead to an adequate food supply, leading to higher ant population development. In feature importance analysis, we ranked all features affecting the predictions “GDP per capita” (0.546), “Human development index” (0.309), “Temperature” (0.090), “Precipitation” (0.034), and “Forest area” (0.022). These results suggest that economic factors may play a more important role in the distribution of species richness than environmental factors (Figure S2).
We also found that observation and prediction showed a correlation of +0.2. This result showed that there was a weak positive correlation between the predicted results and the observed results. In the distribution of these species, ants may actually exist in some areas but lack observed data.
When we carefully checked the test results of the neural network, the predicted result of 25,301 was consistent with the observed result in a total dataset of 33,655 (see Table 3). Of the 20,659 “presented” species in the observation, 17,896 were accurately predicted (see Table 3). From a global perspective, the predicted result was roughly consistent with the observed result and the accuracy was good. However, the deviation was large when we paid attention to a country or a small area.
The distribution of observed species richness is mapped in Figure 5a, and the full dataset is provided in Supplementary Materials Figure S1. These figures show that the United States has a high number of observed species, which indicates the privilege of research support and favourable conditions for research in the United States. On the contrary, few species have been observed in some countries in West Africa, which suggests that these underdeveloped countries have not received enough research support in the past due to their fragile economic status and instability [35]. Both the observed species richness and the ML-predicted results capture a lot of variations among countries. Most countries present little difference between observation and ML prediction, and this is a special case in Europe (Figure 5b). However, a few countries in West Africa show a large difference between observation and ML prediction.

4. Discussion

4.1. Distribution of Species Richness in Data-Poor Countries

One specific aim of this study is to use ML to estimate the likely number of described species in each country by overcoming the limitations of low sampling intensity in underdeveloped countries. Upon examining the global distribution of species richness, we found significant differences between the observed data and the ML prediction results in certain countries.
Specifically, this paper carefully examined several countries with the smallest observed index. Five of these countries were in West Africa, two were in Central Africa, two were in West Asia, one was in South Asia, and one was in South America. In these countries, the predicted index was much higher than the observed index. The observed data for these countries were highly suspicious, as very few species were observed (Table 4). We believe that this suspicion was probably due to insufficient observational fieldwork rather than a lack of species richness [70].
Based on the above analysis, we suggest that scientists and policymakers should not underestimate the distribution of species richness in underdeveloped countries due to a lack of observational data. In some data-poor countries in West Africa in particular, scientists have naturally considered the existence of very few species, and policymakers have ignored these areas when formulating conservation plans [71]. When observation data are insufficient, ML prediction has a wide application and can provide effective suggestions for policymakers to determine areas requiring protection [72,73].
ML will always show a little discrepancy between observed and predicted richness in island states such as Australia (and indeed North America), and also in regions of very low ant diversity such as in the boreal zone. We acknowledge that our analysis considers described species only, and that very many undescribed ant species are known to occur. However, the proportion of undescribed species is likely to be higher in underdeveloped countries, which would further accentuate the influence of socioeconomic status on documented patterns of ant diversity.

4.2. Further Improvements to ML Models

One of this paper’s goals was to find ML models that can efficiently and accurately predict the global distribution of species richness. To achieve this goal, this paper utilised four popular ML models (i.e., decision tree, random forest, logistic regression, and neural network) [74]. The decision tree, random forest, and logistic regression models achieve fast predictions with around 70% accuracy. In contrast, the neural network model is more flexible. We can adjust the layers, nodes, and other parameters of these models to optimise their algorithms and produce higher prediction accuracy (~75%). Therefore, this paper recommends the use of the neural network to process ML models.
To further improve the ML model, there are three recommendations for the future. First, the present study’s geographic resolution can be improved. Due to limitations in computational capability, we selected countries’ data for calculation. A higher resolution may lead to new findings if a higher resolution of the data (e.g., 5 km × 5 km) can be provided, enabling policymakers to more precisely locate areas that require protection [75,76]. Second, if additional data and factors (such as population migration, vegetation distribution in various regions, and related species in the food chains) can be added to future ML models, more extensive databases and more complex systems can lead to predictions with higher accuracy [77]. Third, by increasing the power of the computation, attempts at prediction can be made using several novel artificial intelligence (AI) methods [78], including classification [79], nearest neighbour [80,81], linear discriminant analysis [82,83], K-means [84,85], hidden Markov [86], and hierarchical planning [87].

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/d14090706/s1, Table S1: Predicted index and observed index in different countries (regions); Table S2: Coding for the machine learning; Table S3: Coding for the data analysis; Table Table S4: Coding for the feature importance; Table S5: Randomised search result of random forest hyperparameter tuning; Table S6: Coding for column drawing; Figure S1: Heatmap to check correlation; Figure S2: Feature importance.

Author Contributions

S.C. worked on the manuscript edition, designed the structure of the paper, and supported on the visualisation. Y.D. conceived of the study, gathered the data, performed the statistical analysis, and prepared the manuscript draft. All authors have read and agreed to the published version of the manuscript.

Funding

This research received no external funding.

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

All data has been included in this study.

Acknowledgments

The authors thank the knowledge and computation support from the School of Geography and the Environment, University of Oxford, United Kingdom.

Conflicts of Interest

The authors declare no conflict of interest.

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Figure 1. Framework showing how ML used the experimental data and predicted distribution of species richness in a region that had not yet been investigated. Temperature, precipitation, and forest cover have a significant effect on the distribution of species richness. The socioeconomic factors can affect the intensity of sampling ants.
Figure 1. Framework showing how ML used the experimental data and predicted distribution of species richness in a region that had not yet been investigated. Temperature, precipitation, and forest cover have a significant effect on the distribution of species richness. The socioeconomic factors can affect the intensity of sampling ants.
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Figure 2. Total number of species records for bottom 5 countries and top 5 countries. “Introduced” means a certain species is not native but has been migrated or carried by human activity to that country. “Likely” means the ant species probably exist in that country. “Present” means the ant species has been observed and recorded in that country. “Uncertain” means the ant species has not been confirmed in that country. These are four data categories according to the AntWiki database.
Figure 2. Total number of species records for bottom 5 countries and top 5 countries. “Introduced” means a certain species is not native but has been migrated or carried by human activity to that country. “Likely” means the ant species probably exist in that country. “Present” means the ant species has been observed and recorded in that country. “Uncertain” means the ant species has not been confirmed in that country. These are four data categories according to the AntWiki database.
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Figure 3. Observation frequency (a–d) versus prediction frequency (e–h) of ant distribution. The Y-axis shows the frequency from 0 (the amount of data equal to 0) to 1 (the highest possible amount of data). Coloured areas indicate that the observation frequency (upper Y-axis) and ML prediction frequency (lower Y-axis) of ant distribution are currently present (pink) or likely (blue) or introduced (yellow) or unknown (green) under certain conditions of temperature, precipitation, forest area, and human development index (X-axis).
Figure 3. Observation frequency (a–d) versus prediction frequency (e–h) of ant distribution. The Y-axis shows the frequency from 0 (the amount of data equal to 0) to 1 (the highest possible amount of data). Coloured areas indicate that the observation frequency (upper Y-axis) and ML prediction frequency (lower Y-axis) of ant distribution are currently present (pink) or likely (blue) or introduced (yellow) or unknown (green) under certain conditions of temperature, precipitation, forest area, and human development index (X-axis).
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Figure 4. Heatmap analysis showing the relationship between “Temperature”, “Precipitation”, “Forest area”, “GDP per capita”, “Human development index”, “Observation”, and “Prediction”. The brighter the colour, the stronger the positive correlation between the two data.
Figure 4. Heatmap analysis showing the relationship between “Temperature”, “Precipitation”, “Forest area”, “GDP per capita”, “Human development index”, “Observation”, and “Prediction”. The brighter the colour, the stronger the positive correlation between the two data.
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Figure 5. (a) Distribution index via observation; (b) distribution index via ML prediction; red colour represents areas with a lower distribution of species richness, while green colour represents areas with a higher distribution of species richness; (c) the absolute value of the difference between observation and prediction; dark colour indicates a small difference, while light colour suggests a large difference. The white arrow points to West Africa, an area with a large difference. The data are provided in Supplementary Materials Table S1.
Figure 5. (a) Distribution index via observation; (b) distribution index via ML prediction; red colour represents areas with a lower distribution of species richness, while green colour represents areas with a higher distribution of species richness; (c) the absolute value of the difference between observation and prediction; dark colour indicates a small difference, while light colour suggests a large difference. The white arrow points to West Africa, an area with a large difference. The data are provided in Supplementary Materials Table S1.
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Table
Table 1. Comparison of SDM and ML modelling.
Table 1. Comparison of SDM and ML modelling.
SDMML ModellingReference
RationalUsing computer algorithms to predict the distribution of a species across geographic space based on the environmental dataUsing ML algorithms to predict the distribution of species richness [9,20]
MethodsA correlation model (the link between location data and distribution of species richness), a process model (the link between functional traits of organisms and their environment), and a hybrid modelPredictions based on “black box” models and a complex data matrix[3,4,5,21,22,23,24]
Determinants of accuracyThe accuracy of existing links and assumptionsQuality and quantity of data[3,4,5,21,22,23,24]
AdvantagesA matured method that can perform the predictionsConstructing a model structure conveniently and quickly[9,25]
LimitationsSample selection bias; selection of scale affects prediction resulting in presence-only dataThe “black swan” causing prediction problems in ML[9,25,26]
Table
Table 2. ML training results in comparison among different methods.
Table 2. ML training results in comparison among different methods.
MethodClassifierTraining AccuracyTesting Accuracy
Decision treeDecisionTreeClassifier73.86%71.78%
Random forestRandomForestClassifier73.86%70.62%
Logistic regressionLogisticRegression72.92%71.09%
Neural networkMLPClassifier75.77%75.18%
Table
Table 3. The prediction and observation in the testing set.
Table 3. The prediction and observation in the testing set.
“Uncertain” in Prediction Score: 0“Introduced” in Prediction Score: 1“Likely” in Prediction Score: 2“Present” in Prediction Score: 3Total
“Uncertain” in observation618045835724629457
“Introduced” in observation1613346490730
“Likely” in observation7086011928492809
“Present” in observation194268913217,89620,659
Total89911240172721,69733,655
Table
Table 4. Eleven countries with the smallest observed index. For the observed index and predicted index, 0 means that the number of species is zero, and 1 means the highest possible value of the number of species (all known ant species are found in that country).
Table 4. Eleven countries with the smallest observed index. For the observed index and predicted index, 0 means that the number of species is zero, and 1 means the highest possible value of the number of species (all known ant species are found in that country).
CountryRegionObserved IndexPredicted IndexDifference
MauritaniaWest Africa0.1290.4890.360
NigerWest Africa0.2460.3920.146
Burkina FasoWest Africa0.2730.5580.285
MaliWest Africa0.2760.4980.222
Guinea-BissauWest Africa0.3370.5840.247
Sao Tome and PrincipeCentral Africa0.2630.6950.432
ChadCentral Africa0.2640.4880.224
KuwaitWest Asia0.1790.6310.452
JordanWest Asia0.3020.5560.254
BhutanSouth Asia0.2640.7060.442
ChileSouth America0.1900.5130.323
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Chen, S.; Ding, Y. Machine Learning and Its Applications in Studying the Geographical Distribution of Ants. Diversity 2022, 14, 706. https://doi.org/10.3390/d14090706

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Chen S, Ding Y. Machine Learning and Its Applications in Studying the Geographical Distribution of Ants. Diversity. 2022; 14(9):706. https://doi.org/10.3390/d14090706

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Chen, Shan, and Yuanzhao Ding. 2022. "Machine Learning and Its Applications in Studying the Geographical Distribution of Ants" Diversity 14, no. 9: 706. https://doi.org/10.3390/d14090706

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