DOI: 10.5061/dryad.n5tb2rc4k
title: Extirpated species in Berlin, dates of last detections, habitats, and number of Berlin’s inhabitants

description: Species loss is highly scale-dependent, following the species-area
 relationship. We analysed spatio-temporal patterns of species’ extirpation
 on a multitaxonomic level using Berlin, the capital city of Germany.
 Berlin is one of the largest cities in Europe and has experienced a strong
 urbanisation trend since the late 19th century. We expected species’
 extirpation to be exceptionally high due to the long history of
 urbanisation. Analysing regional Red Lists of Threatened Plants, Animals,
 and Fungi of Berlin (covering 9498 species), we found that 16 % of species
 were extirpated, a rate 5.9 times higher than at the German scale, and
 47.1 times higher than at the European scale. Species’ extirpation in
 Berlin is comparable to that of another German city with a similarly broad
 taxonomic coverage, but much higher than in regional areas with less human
 impact. The documentation of species’ extirpation started in the 18th
 century and is well documented for the 19th and 20th centuries. We found
 an average annual extirpation of 3.6 species in the 19th century, 9.6
 species in the 20th century, and the same number of extirpated species as
 in the 19th century were documented in the 21th century, despite the much
 shorter time period. Our results showed that species’ extirpation is
 higher at small than on large spatial scales, and might be negatively
 influenced by urbanisation, with different effects on different taxonomic
 groups and habitats. Over time, we found that species’ extirpation is
 highest during periods of high human alterations and is negatively
 affected by the number of people living in the city. But, there is still a
 lack of data to decouple the size of the area and the human impact of
 urbanisation. However, cities might be suitable systems for studying
 species’ extirpation processes due to their small scale and human impact.
description: <strong>Data extraction</strong>:
 To determine the proportion of extirpated species for Germany, we
 manually summarised the numbers of species classified in category 0
 ‘extinct or extirpated’ and calculated the percentage in relation to the
 total number of species listed in the Red Lists of Threatened Species for
 Germany, taken from the website of the Red List Centre of Germany (Rote
 Liste Zentrum, 2024a). For Berlin, we used the 37 current Red Lists of
 Threatened Plants, Animals, and Fungi from the city-state of Berlin,
 covering the years from 2004 to 2023, taken from the official capital city
 portal of the Berlin Senate Department for Mobility, Transport, Climate
 Protection and Environment (SenMVKU, 2024a; see overview of Berlin Red
 Lists used in Table 1). We extracted all species that are listed as
 extinct/extirpated, i.e. classified in category 0, and additionally, if
 available, the date of the last record of the species in Berlin. The Red
 List of macrofungi of the order Boletales by Schmidt (2017) was not
 included in our study, as this Red List has only been compiled once in the
 frame of a pilot project and therefore lacks the category 0 ‘extinct or
 extirpated’. We used Python, version 3.7.9 (Van Rossum and Drake, 2009),
 the Python libraries Pandas (McKinney et al., 2010), and Camelot-py,
 version 0.11.0 (Vinayak Meta, 2023) in Jupyter Lab, version 4.0.6 (Project
 Jupyter, 2016) notebooks. In the first step, we created a metadata table
 of the Red Lists of Berlin to keep track of the extraction process,
 maintain the source reference links, and store summarised data from each
 Red List pdf file. At the extraction of each file, a data row was added to
 the metadata table which was updated throughout the rest of the process.
 In the second step, we identified the page range for extraction for each
 extracted Red List file. The extraction mechanism for each Red List file
 depended on the printed table layout. We extracted tables with lined rows
 with the Lattice parsing method (Camelot-py, 2024a), and tables with
 alternating-coloured rows with the Stream method (Camelot-py, 2024b). For
 proofing the consistency of extraction, we used the Camelot-py accuracy
 report along with the Pandas data frame shape property (Pandas, 2024).
 After initial data cleaning for consistent column counts and missing data,
 we filtered the data for species in category 0 only. We collated data
 frames together and exported them as a CSV file. In a further step, we
 proofread whether the filtered data was tallied with the summary tables,
 given in each Red List. Finally, we cleaned each Red List table to contain
 the species, the current hazard level (category 0), the date of the
 species’ last detection in Berlin, and the reference (codes and data
 available at: Github, 2023). When no date of last detection was given for
 a species, we contacted the authors of the respective Red Lists and/or
 used former Red Lists to find information on species’ last detections
 (Burger et al., 1998; Saure et al., 1998; 1999; Braasch et al., 2000;
 Saure, 2000). Determination of the recording time windows of the Berlin
 Red Lists We determined the time windows, the Berlin Red Lists look back
 on, from their methodologies. If the information was missing in the
 current Red Lists, we consulted the previous version (see all detailed
 time windows of the earliest assessments with references in Table B2 in
 Appendix B). <br><strong>Data
 classification</strong>: For the analyses of the
 percentage of species in the different hazard levels, we used the German
 Red List categories as described in detail by Saure and Schwarz (2005) and
 Ludwig et al. (2009). These are: Prewarning list, endangered (category 3),
 highly endangered (category 2), threatened by extinction or extirpation
 (category 1), and extinct or extirpated (category 0). To determine the
 number of indigenous unthreatened species in each Red List, we subtracted
 the number of species in the five categories and the number of
 non-indigenous species (neobiota) from the total number of species in each
 Red List. For further analyses, we pooled the taxonomic groups of the 37
 Red Lists into more broadly defined taxonomic groups: Plants, lichens,
 fungi, algae, mammals, birds, amphibians, reptiles, fish and lampreys,
 molluscs, and arthropods (see categorisation in Table 1). We categorised
 slime fungi (Myxomycetes including Ceratiomyxomycetes) as ‘fungi’, even
 though they are more closely related to animals because slime fungi are
 traditionally studied by mycologists (Schmidt and Täglich, 2023). We
 classified ‘lichens’ in a separate category, rather than in ‘fungi’, as
 they are a symbiotic community of fungi and algae (Krause et al., 2017).
 For analyses of the percentage of extirpated species of each pooled
 taxonomic group, we set the number of extirpated species in relation to
 the sum of the number of unthreatened species, species in the prewarning
 list, and species in the categories one to three. We further categorised
 the extirpated species according to the habitats in which they occurred.
 We therefore categorised terrestrial species as ‘terrestrial’ and aquatic
 species as ‘aquatic’. Amphibians and dragonflies have life stages in both,
 terrestrial and aquatic habitats, and were categorised as
 ‘terrestrial/aquatic’. We also categorised plants and mosses as
 ‘terrestrial/aquatic’ if they depend on wetlands (see all habitat
 categories for each species in Table C1 in Appendix C). The available data
 considering the species’ last detection in Berlin ranked from a specific
 year, over a period of time up to a century. If a year of last detection
 was given with the auxiliary ‘around’ or ‘circa’, we used for further
 analyses the given year for temporal classification. If a year of last
 detection was given with the auxiliary ‘before’ or ‘after’, we assumed
 that the nearest year of last detection was given and categorised the
 species in the respective century. In this case, we used the species for
 temporal analyses by centuries only, not across years. If only a timeframe
 was given as the date of last detection, we used the respective species
 for temporal analyses between centuries, only. We further classified all
 of the extirpated species in centuries, in which species were lastly
 detected: 17th century (1601-1700); 18th century (1701-1800); 19th century
 (1801-1900); 20th century (1901-2000); 21th century (2001-now) (see all
 data on species’ last detection in Table C1 in Appendix C). For analyses
 of the effects of the number of inhabitants on species’ extirpation in
 Berlin, we used species that went extirpated between the years 1920 and
 2012, because of Berlin’s was expanded to ‘Groß-Berlin’ in 1920 (Buesch
 and Haus, 1987), roughly corresponding to the cities’ current area.
 Therefore, we included the number of Berlin’s inhabitants for every year a
 species was last detected (Statistische Jahrbücher der Stadt Berlin, 1920,
 1924-1998, 2000; see all data on the number of inhabitants for each year
 of species’ last detection in Table C1 in Appendix C).
 Materials and Methods from Keinath et al. (2024): 'High
 levels of species’ extirpation in an urban environment – A case study from
 Berlin, Germany, covering 1700-2023'.
description: # Extirpated species in Berlin, dates of last detections, habitats, and
 number of Berlin’s inhabitants
 [https://doi.org/10.5061/dryad.n5tb2rc4k](https://doi.org/10.5061/dryad.n5tb2rc4k) #### **Description of the data and file structure** Data on extirpated species (category 0) in Berlin, Germany, their dates of last detections, habitats, and the number of Berlin’s inhabitants used in Keinath et al. 2024 ‘High levels of species’ extirpation in an urban environment – A case study from Berlin, Germany, covering 1700-2023’. Data were extracted from 37 Red Lists of Threatened Species from the federal state Berlin, Germany. **Sharing/Access information** Links to codes developed and used for extracting extirpated species from the Berlin Red Lists of Threatened Species: [https://github.com/Zzzhenya/Berlin-red-list ](https://github.com/Zzzhenya/Berlin-red-list) Links to the used Red Lists of Threatened Species from the federal state of Berlin, Germany: [https://www.berlin.de/sen/uvk/natur-und-gruen/naturschutz/artenschutz/artenlisten-rote-listen/](https://www.berlin.de/sen/uvk/natur-und-gruen/naturschutz/artenschutz/artenlisten-rote-listen/) Missing data code- NA