The increase in human population, habitat destruction, climate change, invasive species, overexploitation of natural resources and environmental pollution have led to a loss of biodiversity on Earth due to the expansion of the urban, agricultural and mining frontiers. This decline is closely related to the extinction of species, which is a natural process, however it is occurring at a higher rate than the natural. According to predictions, current extinction rates are about a thousand times higher than would be expected from the fossil record, and we could be experiencing an eventual mass extinction (National Geographic Society, 2019)
Species are at risk of extinction for two reasons: loss of habitat and loss of genetic variation (Rutledge, K. et al., 2011).
Habitat loss can occur naturally and through anthropogenic actions. In the case of human activity, housing, industrial, and agricultural development contribute to habitat loss for native organisms (Rutledge, K. et al., 2011).
In the Amazon, one of the regions with the most vegetation in the tropics, trees are cut down to establish livestock systems and urban infrastructure. This activity in the rainforest leads to a reduction in diversity since the treetops are home to vine plants, fungi, insects, birds and mammals. In addition, man, by decreasing his habitat, is more likely to come into contact with poisonous plants and wild animals (Rutledge, K. et al., 2011).
The loss of genetic variation, another key aspect in the decline of biodiversity, also occurs naturally and through human action. Some of these actions are over-harvesting, over-fishing, monocultures and the indiscriminate use of fertilizers and pesticides, which leads to a reduction in populations, and in turn, the number of reproductive couples. With fewer pairs, genetic variation decreases, and thus the capacity to adapt to climate change and disease (Rutledge, K. et al., 2011).
To identify the causes and severity of a species' extinction, the International Union for Conservation of Nature (IUCN) maintains a "Red List of Threatened Species", which classifies information into seven categories: Least Concern, Near Threatened, Vulnerable, Endangered, Critically Endangered, Extinct in the Wild, and Extinct, representing a different level of threat. Species belonging to the threatened or vulnerable categories increase when their population and range decrease (Rutledge, K. et al., 2011).
Colombia is the second most biodiverse country in the world, ranking first in birds and orchids; second in plants, amphibians, butterflies and freshwater fish; third in palms and reptiles; and fourth in mammals. However, about 1,200 species have been identified as threatened according to the criteria of the International Union for Conservation of Nature (IUCN), so there is a need to conduct an analysis of the distribution of these species and ecological niches, to take preventive or corrective measures in the management of these.
Taking into account this problem, the objective of this project is to interconnect the information obtained from satellites of the different space agencies, with digital tools of free use that facilitate the visualization, processing and modeling of data related to the monitoring, conservation of species in danger of extinction.
The continuous analysis of biodiversity is a critical point to know in real time how species are distributed on our planet, so it starts with the search for information in publications of the red books provided by the IUCN and the Humboldt Institute in Colombia in order to identify which endemic species of Colombia are in danger of extinction, which leads to the exploration of public databases that will provide us with information on the presence of the species, as well as climatic variables through satellite images, and then make a cross of this information and identify the ecological niches. In order to evaluate models of species distribution (SDM), two species were chosen as being in danger of extinction in Colombia, one belonging to the animal kingdom Tremarctos ornatus (Spectacled Bear) and the other to the plant kingdom Cariniana pyriformis (Abarco). These two species were selected due to the large number of records found for each one, thus improving the accuracy of the model to be carried out.
- Access to data. Use of information from GBIF, CHELSA (EOSDIS-EARTHDATA-NASA) Use of the rgbif library of R.
- Debugging, structuring and data integration through libraries such as dismo, rgeos, biomod2, raster, among others. All related to spatial data analysis.
- Generation of exploratory visualizations with libraries for data science with R.
- Construction of a machine learning model (Random Forest) as an example of application with R for species distribution modeling Use of the caret library in R.
- Deployment of maps with predicted probabilities for the presence of species.
National Geographic Society. (2019). Conservation. National Geographic
Rutledge, K. et al., 2011. Endangered species. National Geographic
Other References:
https://besjournals.onlinelibrary.wiley.com/doi/10.1111/j.2041-210X.2011.00172.x
https://onlinelibrary.wiley.com/doi/10.1111/aec.12658
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6441032/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6812352/
https://www.car.gov.co/uploads/files/5bd8b7fe8125c.pdf
https://core.ac.uk/download/pdf/11058436.pdf