Bird Survey Around Mida Creek

Study Extent

The Kenyan coast was once a large continuous forest called the Northern Zanzibar-Inhambane coastal forest mosaic, of which Arabuko-Sokoke Forest is the largest remainder of today. Extensively studied, this forest is an area of high endemism and was therefore gazetted as a National Park in the late 1980s. Since then, it has benefited from a hard protection from deforestation and human influence. However, the surrounding habitat has been strongly affected by human and agricultural extensions on what used to be forest land. On the other side of our study area, Mida Creek is a 580 ha tidal marine multi-habitat ecosystem fringed with a diverse assemblage of mangrove species (Ceriops tagal, Rhizophora rnucronata, Bruguiera gyrnnorrhiza, Avicennia marina, Sonneratia alba and Xylocarpus benadirensis). Surveys in this area allow us to study the distribution and abundance of common species not necessarily restricted to a specific habitat (such as forest or mangrove), as well as their association with certain habitats. The transects were defined to cover all habitat types between Arabuko-Sokoke Forest, Mida Creek and the coast. They were designed such that the habitat remains relatively homogeneous during each 1hr survey (i.e. along the forest edge or mangrove edge). In addition, each survey starts and finishes near a main road to facilitate access and early start (6am). See for a map of the transects.

Sampling

Each survey is performed by 2 persons. Each survey is designed to last 1 hour, covering a transect of 1km. During a survey, each bird species seen and/or heard is recorded once upon the first encounter (i.e., no count data, just presence/absence) The data is collected with the Birdlasser app, allowing to record the GPS location of the observer at the moment of the observation (i.e., not the bird), the exact time of observation (date and hour) as well as any additional comment. Surveys can be paused if interrupted due to heavy rain or interaction with land owners, for instance. This information is recorded in the dynamicProperties and eventRemarks columns in events. Surveys are performed in clusters of 4, starting at 6am up to 10am. Some remote transects (e.g. Kiperwe Island) required more time, thus surveys were performed until 12pm. The Birdlasser data is then exported in CSV format, collected on A Rocha infrastructure and available at /data/birdlasser_files.

Quality Control

Quality control is performed in the Rmarkdown script Processe2GBIF.rmd (https://a-rocha-kenya.github.io/Bird-Survey-Around-Mida-Creek/Process2GBIF.html). Protocol: Surveys were discarded if the protocol was not properly followed. This happened mainly at the beginning, before the guides were fully trained. We also deleted surveys when the rain lasted longer than 30 minutes. Spatial error: Phone GPS errors or sightings entered later at wrong locations were manually identified by plotting all sightings on a map. These locations were interpolated linearly between the surrounding sightings of the same survey. The column georeferenceVerificationStatus indicates if such interpolation was performed and georeferenceRemarks provides the original coordinate. Species list: All species recorded were manually verified by Raphaël Nussbaumer, Colin Jackson and checked with the guides by Kirao Lennox. The spreadsheet species_lists_validation.xlsx(https://github.com/A-Rocha-Kenya/Bird-Survey-Around-Mida-Creek/blob/main/data/species_lists_validation.xlsx) was used to record the status (see table below) of each species. In general, each specie was either validated or flagged with an error code. Some errors could be corrected by providing the Equivalent specieID (e.g., taxonomic issue).

Method steps

1. All the processing steps from the original Birdlasser datafile to the GBIF formatted file are described in the Rmarkdown script Process2GBIF.rmd (https://a-rocha-kenya.github.io/Bird-Survey-Around-Mida-Creek/Process2GBIF.html).

We record all birds seen (Aves sp.) at the species level (with the exception of the Hybrid Lovebird Agapornis fischeri x personatus). We use the taxonomy from the Checklist of the Birds of Kenya (5th Edition) (https://github.com/A-Rocha-Kenya/Birds-of-Kenya) (ISBN: 9966-761-37-3) for the scientificName and vernacularName. The taxonID and taxonRank are taken from the eBird/Clements Checklist of Birds of the World: v2019 (https://www.birds.cornell.edu/clementschecklist/download/). See section Sampling Description for explanations on how the taxons were initially recorded in the field and later filtered and matched to these taxonomy lists. Our dataset contains 217 unique species belonging to 64 families.

1. Aves
   common name: Bird rank: class

The surveys were performed between Arabuko-Sokoke Forest and Mida Creek, on the coast of Kenya. See for more information about the spatial extent of the dataset and a map of the transects at https://github.com/A-Rocha-Kenya/Bird-Survey-Around-Mida-Creek/blob/main/data/transects.geojson