The dataset contains 412 records of Diptera species from the families Limoniidae, Pediciidae and Tipulidae, collected between 2003 to 2019 in Portugal, including the Azores and Madeira archipelagos (Ferreira et al., 2021; Oosterbroek et al., 2020; Starý, 2014). Specimens have been identified to species or subspecies level, in a total of 83 species representing 58% of the Craneflies known for Portugal. Specimens were captured during fieldwork directed specifically for the sampling of Diptera using different methodologies and the majority was stored in 96% ethanol. A tissue sample, usually a leg, was collected from each individual, from which DNA was extracted. The DNA barcoding of these specimens was conducted within the InBIO Barcoding Initiative (IBI), funded by the EnvMetaGen and PORBIOTA projects. The dataset “DNA barcodes of Portuguese Diptera 02 - Limoniidae, Pediciidae and Tipulidae” is part of a group of Diptera datasets published by IBI, the first of which, “The InBIO Barcoding Initiative Database: Diptera 01” (https://doi.org/10.15468/q1bvt3) has already been made available through GBIF. DNA barcode sequences were deposited in BOLD (Barcode of Life Data System) and GenBank databases. All DNA extracts are deposited in the IBI collection at the CIBIO (Research Center in Biodiversity and Genetic Resources).

The data presented here comes from samples collected as part of one recent research project (MACDIV), which aimed to understand the drivers of community assembly in Macaronesian islands. We applied the sampling protocol COBRA (Conservation Oriented Biodiversity Rapid Assessment, Cardoso 2009) in twelve 50 m x 50 m native forest plots in the Madeira Island, five dry plots in Madeira Island and five dry plots in Porto Santo Island to assess the diversity of spiders species. Through this publication we contribute to the knowledge of the arachnofauna of the Madeira archipelago, and more specifically, to that of the islands of Madeira and Porto Santo. Of the 87 species and 18 morphospecies (undescribed) collected, 34 were endemic, 26 native non-endemic, 22 introduced and 23 species of unknown origin. Although most of the species had been previously recorded on both islands, 21 species are new records for Madeira island and 32 new for Porto Santo (33 for the whole archipelago).

This checklist includes, as rigorously as possible, all the known terrestrial and freshwater, i.e. insular, fungi, plants and animals of the Madeira and Selvagens archipelagos with the indication of their known presence on the islands of Madeira, Porto Santo, Desertas and Selvagens. It results from the collaborative work of many taxonomists from different Portuguese and foreign institutions (about 90 taxonomists), under the editorial coordination of the Azorean Biodiversity Group (http://www.gba.uac.pt). The total estimated number of terrestrial species and subspecies in the Madeira and Selvagens archipelagos was about 7,571 (7,452 species and 421 subspecies). Fungi and plants represent about 42% of the terrestrial diversity. However, animals dominate, arthropods being the majority (51%) of all recorded taxa. The total number of endemic species and subspecies from the Madeira and Selvagens archipelagos is about 1,419 (1,286 species and 182 subspecies), which represents 19% of the overall species diversity. The animal Phyla are the most diverse in endemic taxa, namely Mollusca (210) and Arthropoda (979), comprising about 84% of the Madeiran endemics. The percentage of endemism within Mollusca is particularly remarkable, reaching 71%. Within vascular plants there are 154 endemic species and subspecies (13% of the overall plant species diversity) while the remaining higher taxonomic groups are less diverse in terms of endemic forms: Fungi – 36 (5%); Lichens – 12 (2%); Bryophytes – 11 (2%); vertebrates 15 (24%).