Protected areas are one of the main strategic means for conserving biodiversity. Yet, the design of protected areas usually neglects phylogenetic diversity, an important diversity measure. In this paper, we assess the phylogenetic diversity and species richness of vascular plants in Fennoscandian protected areas. We evaluate how much species richness and phylogenetic diversity is found within and outside protected areas, and the differences in diversity between different categories of protected areas. We also assess the differences in the diversity-area relationship of the different protected area categories in terms of both species richness and phylogenetic diversity. We build a multi-locus phylogeny of 1,519 native vascular plants of Norway, Sweden, and Finland. We estimate the phylogenetic diversity and species richness by combining the phylogeny with publicly available occurrence data and the currently protected area system of Fennoscandia. Our results indicate that protected areas in Fennoscandia hold more diversity when larger, and that phylogenetic diversity increases faster with area than species richness. We found evidence for more diversity outside of protected areas of the different countries of Fennoscandia than inside of protected areas, but no evidence for diversity differences between areas with different protection status. Hence, our results indicate that the current protected area system in Fennoscandia is no more effective in conserving phylogenetic diversity and species richness of vascular plants than a random selection of localities. Our results also indicate that planning conservation strategies around phylogenetic diversity, rather than species richness, might be more effective in protecting vascular plant diversity.

Generation of sequence data:

We generated 264 new nuclear ribosomal internal transcribed spacer (ITS) sequences from specimens deposited in the herbaria O (Natural History Museum, Oslo) and TRH (NTNU University Museum, Trondheim). DNA extraction, amplification of the ITS region, and Sanger sequencing of the resulting PCR product followed the procedures described by Mienna et al. (2020), with two notable exceptions. Firstly, for all specimens collected before the year 2000, DNA was extracted and prepared for PCR amplification in the NTNU University Museum’s dedicated, UV-sterilised, positively pressurised paleogenomics laboratory facility. Secondly, herbarium specimens yielding degraded DNA extracts, from which we could not amplify the entire ITS region using the primer pair ITS5a/ITS4 (Stanford et al., 2000; White et al., 1990), were subjected to additional attempts amplifying the region in two shorter fragments, targeting ITS1 and ITS2, respectively, using the primer pairs ITS-p2/ITS-p5 and ITS-p3/ITS-p4 (Cheng et al., 2016). The PCR of these two ITS fragments were conducted in 50-μl reaction volumes containing the following components: 5.0 μL template DNA extract, 1.25 units AmpliTaq Gold™ DNA Polymerase, 0.4 mg/mL bovine serum albumin (BSA), 0.2 μM each primer, 1.5 mM MgCl2, 0.25 mM each dNTP, and 1x AmpliTaq PCR Buffer II. The PCR protocol was as follows: 4 min of initial denaturation at 94°C; 40-45 cycles of 30 s at 94°C, 40 s at 55°C, 60 s at 72°C, followed by 10 m final extension at 72°C. PCR products were electrophoresed, and those with a single, appropriately sized band of DNA were chosen for Sanger sequencing at the commercial provider Eurofins Genomics (Germany). We used the same primers for sequencing as we did for the PCR amplification.

Multi-sequence Alignment: 

We obtained the ITS, maturase K (matK) and ribulose-1,5-bisphosphate carboxylase- oxygenase (rbcL) sequences of Norwegian vascular plants from Mienna et al. (2020) and used Matrix Maker (Freyman & Thornhill, Andrew H., 2016/2020) to supplement this dataset with sequence data for additional species from GenBank (Benson et al., 2018), as well as from our own newly generated sequences. We used Mafft Version 7.450 (Katoh & Standley, 2013) to perform an automated alignment of the existing sequences and the 264 newly generated sequences (Table S2). The existing Norwegian three-marker alignment (ITS, matK, and rbcL) was concatenated with the newly generated sequences (ITS) and sequences from Genbank of the Swedish and Finish taxa into a multiple sequence alignment.

Several maximum-likelihood phylogenies were generated using RaxML-HPC v.8 (Stamatakis, 2014) under the GTRGAMMA nucleotide substitution model and using a partition for each of the three loci on the CIPRES Science Gateway (Miller et al., 2010). 1000 bootstrap support replicates were run in each phylogenetic analysis. As in Mienna et al. (2020), we rooted the tree using Pteridophyta. The resulting tree was verified by comparing it to the plant family phylogeny by the Angiosperm Phylogeny Group IV (APG IV, Chase et al., 2016; Stevens, 2001). In cases where an accession was misplaced according to the APG IV phylogeny or genus assignment or occurred on relatively long branches, the alignment was checked for obvious errors in homology inference. After manual correction and removal of highly ambiguously aligned regions, the process was repeated. Accessions that remained problematic were excluded from downstream analyses.