Plant localities
Based on historical data availability for plants in Denmark (see Finderup Nielsen et al. 2019), we chose 11 focal localities in which reasonably thorough surveys had been conducted 1835-1915 (Fig. 2). These varied in size (range: 1.2-55.2 km2) and habitat composition but generally had high habitat heterogeneity (Supplementary Information S1).
Plant data
We retrieved historical presence-only data for the selected sites from published literature and from unpublished diary notes (Supplementary Information S2). We aimed for thorough, unbiased species lists for well-defined, well-investigated areas sampled by distinguished botanists. These were supplemented with stray records from somewhat earlier and later times but still representing the state of ecosystems before the industrialization of agri- and silviculture. Thus, occurrences spanned 1790-1947 with a mode 1835-1915, and many of the later records being rediscoveries of species already known from the site.
For these localities, we retrieved current (1992-2023) presence-only vascular plant species data from two databases: A national atlas database (Atlas Flora Danica (AFD) 1992-2014 (Hartvig 2015)) and GBIF (1992-2023). We used data with geographic uncertainty < 1 km (99% of the data). For both current and historical data, we aligned taxonomy, aggregated subspecies and varieties to species level, omitted genus-level records and hybrids, and merged species lists, omitting duplicates. Aggregated taxa were constructed due to changes in species circumscription between the 19th century and now: Carex muricata group (C. spicata, C. pairaei, C. divulsa), Glyceria fluitans+G. notata+G. declinata; Malva neglecta+M. pusilla, Nuphar lutea+N. pumila; Polypodium vulgare+P. interjectum; Rorippa nasturtium+R. microphylla; Rosa tomentosa+R. sherardii. Agrostis canina+A. vinealis, Dryopteris dilatata+ D. expansa+D. carthusiana.
The final current plant list had 1307 species, while the historical list had 888 species, including aggregated taxa.
Butterfly data
Butterfly localities matched plant localities, except two localities with no historical records (Pamhule Skov and Jonstrup Vang), i.e. nine localities were used (Supplementary Information S1).
Historical and current butterfly presence/absence data were based on all existing databases (www.naturbasen.dk, www.arter.dk, ADD database (Atlas of Danish Butterflies), Bugbase (https://lepidoptera.dk/), Zoological Museum of Copenhagen collections, Danish Ornithological Society database (https://dofbasen.dk/), various private 20th century collections, and extensive field work (Bjerregård et al. 2023) and aggregated temporally to three time periods: 1900-1949, 1950-1999, and 2000-2019. There were many indications that historical data had false negative records of species that were historically too common to be considered “noteworthy”, but which have since then declined in occupancy. Thus, for sedentary species (according to Eskildsen et al. 2015), large and stable populations of a species at a given locality during the later time periods was assumed as evidence of presence also in earlier time periods (n = 91 occurrences; Supplementary Information S3). In particular, this was applied to sites, for which historical data came from single excursion reports, giving a seasonal bias. For mobile species, no changes were made. Conversely, stray finds in single years of mobile species were considered false positives and removed (n = 52 occurrences; Supplementary Information S3). The final data comprised 72 butterfly species.
To interpret temporal changes in butterfly communities within localities and relate them to changes in land use, we retrieved data on butterfly host plant distribution for the 72 species in our study from Eskildsen et al. (2015). Habitat openness preference for each species was extracted from the species’ habitat description in Stoltze (1996) and categorized into four classes: open, forest-grassland ecotone, woodland, and habitat generalist.
Bird data
For the avifauna, we analyzed traits of nationally increasing (winners) and declining (losers) Danish breeding bird species from 1800-2018. Meltofte et al. (2021) listed 123 species showing clear trends, either increasing or decreasing (Table 1 in Meltofte et al. 2021, Supplementary Information S4). We used the AVONET database (Tobias et al. 2022) to characterize each species’ properties, including habitat preference, vegetation structure, migration, trophic level, and maximum latitude of range (Supplementary Information S5).
We excluded marine and aquatic bird species from our terrestrial ecosystem study, resulting in 105 species (Supplementary Information S4).
Environmental and land-use data
Ellenberg indicator values (Hill et al. 1999) for nutrients (N), soil moisture (F), light (L) and soil pH (R) were available for 970 of 1298 current species (75%) and 787 of 884 historical species (89%). Similarly, Grime’s life strategy indicators for competition (C), stress (S) and disturbance (R) (Grime et al. 1989) were recoded as numeric values for each species following Ejrnæs & Bruun (2000). Species’ grazing/mowing affinity was retrieved from Tyler et al. (2021) (Supplementary Information S6). Mean and standard deviation Ellenberg, mean CSR and mean Tyler’s grazing/mowing affinity were calculated based on species lists for each locality in each time period.
We estimated current and historical habitat diversity within localities using species-habitat affiliations from the Biolflor database (Kühn et al. 2004). For each period and locality, we calculated the number of habitats represented by the plant species list for the specific locality, focusing on natural habitats relevant to Denmark (Supplementary Information S7). Alpine habitats and highly modified agroecosystems were excluded. To account for differences in locality size and sampling effort (number of observed species), habitat diversity was adjusted by dividing the number of habitats with the log transformed number of species in each locality.
Historical land-use categories from 1881 were retrieved at the parish-level using Danmarks Statistik: Statistisk Tabelværks 4de række, Litra C, Nr. 4. Land-use classes were aggregated (Supplementary Information S8) and summarized for each locality based on the areal share of each parish located in a locality. Current land-use categories were aggregated to match historical data categories (Supplementary Information S9) and summarized for each locality based on Basemap 04 (Levin 2022) which is a national map of land use and land cover for Denmark.
Mean current grazing density (kg large herbivore biomass per ha) for each locality was retrieved from the Danish Nature Indicator (Ejrnæs et al. 2021, https://naturindikator.dk/).
Historical grazing densities were estimated from national statistics on horses, cattle and sheep at the parish level in 1864 (Danmarks Statistik: Statistisk Tabelværk ser.3, vol. 3, 1864), recalculated to kg/ha using parish areas overlapping with each locality (Danmarks Statistik: Statistisk Tabelværks 4de række, Litra C, Nr. 4 and Dam 2023) and mean body mass for historically common breeds of cattle, horse and sheep (cattle: Jysk Malkekvæg=350 kg, horses: Frederiksborghest=500 kg, sheep: Dansk Landfår=70 kg). Cattle, horse and sheep were known to graze in most grasslands and forests historically, whereas pigs were disregarded here, as they - by the mid-19th century - were most likely fenced near settlements and no longer roaming freely as pannage pigs. The method assumes that parish-level density is representative for localities and that 1864 livestock mainly fed on wild plants (either grazing or fed locally harvested hay).
Analyses
Plants
We assessed temporal changes in plant species richness by calculating total species richness for each locality. Similarly, we calculated the number of red-listed species (critically endangered, endangered, vulnerable, near threatened, and data deficient) based on the Danish National Red List (www.redlist.au.dk). A few species were matched at subspecies level to retrieve the correct red list category. As a supplement to the red listed species, we used a list of indicator species considered moderately to very sensitive towards habitat changes as defined by Fredshavn et al. (2010). We combined red-listed and indicator species to identify sensitive species lost across localities during the study period. Paired t-tests were employed to compare Ellenberg N, F, L, R and N/R (Andersen et al. 2013) values and Grime C, S, R values between species lost and those remaining in the localities throughout the study period.
Butterflies
To test trends in butterfly species richness per locality for pairs of the three time periods (1900-1949, 1950-1999, and 2000-2019), we used one-tailed, paired t-tests and checked normality with Shapiro-Wilk tests.
We assessed changes in butterfly community composition using nonmetric multidimensional scaling (NMDS) on 72 species across 27 time period-locality combinations using the function metaMDS in the vegan R-package (Oksanen et al. 2017). Dispersion ellipses (0.4 confidence on standard deviations) were drawn for each time period (1900-1949, 1950-1999, and 2000-2019).
We used Mantel test to assess the importance of local environmental variables for butterfly species composition (Legendre & Legendre 1998). A range of dissimilarity matrices were calculated: 1) a species composition dissimilarity matrix based on Sørensen similarity index (only using time periods 1900-1949 and 2000-2019 to match the environmental variables), 2) dissimilarity matrices for Ellenberg L, Ellenberg F, Ellenberg N, Ellenberg R, Grime S, Grime C, Grime R, Biolflor habitat diversity and plant richness based on Euclidean similarity index.
Butterfly species were categorized as winners and losers based on presence/absence of species on each of the localities in two time periods (1900-1949 and 2000-2019) as response variable and ‘time period’ as explanatory variable in a binomial glm. Significant positive estimates indicated winners, while negative estimates indicated losers. The butterfly data set included species found in only a few localities, yet these species are highly important as they may be on the verge of extinction. Because of small sample sizes for some species, we used a significance level of p<0.05 as well as p<0.2 to gain knowledge of the rare species. Differences in ecological traits of winners and losers (p<0.2) were tested using contingency tables for selected traits (host plant distribution and habitat openness) and two-tailed Fischer’s exact test.
Birds
We used contingency tables to test for associations between “species trend” (increasing or decreasing in Table 1 in Meltofte et al. 2021, Supplementary Information S4) and the variables “habitat,” “vegetation structure,” “migration,” and “trophic level”. For the “habitat” variable, two habitats with < 5 species (riverine and rock) were omitted from the analysis. Significance was inferred using two-tailed Fisher's exact tests.
To investigate the potential effect of global warming and northward range shifts in describing bird species trends, we tested for potential differences in “max latitude” between increasing and declining species using the Wilcoxon signed-rank test (Wilcoxon 1945).
Land-use changes
To investigate the potential temporal change in land-use we used paired t-tests on locality mean-values of Ellenberg (L, F, N, R), Grime’s CSR, Tyler’s grazing/mowing affinity, and Biolflor habitat diversity, number of annual plant species and richness of red-listed plant species as well as land-use classes.
All statistical analyses were performed in R version 4.2.2 (R Core team 2022).