DOI: 10.5061/dryad.n8pk0p303
title: Spatial patterns of phylogenetic and species diversity of Fennoscandian vascular plants in protected areas

description: 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.
description: <strong>Generation of sequence
 data:</strong> 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. <strong>Multi-sequence
 Alignment: </strong> 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. 
description: # Spatial patterns of phylogenetic and species diversity of Fennoscandian
 vascular plants in protected areas
 [https://doi.org/10.5061/dryad.n8pk0p303](https://doi.org/10.5061/dryad.n8pk0p303) Author Information Principal Investigator Contact Information Name: Damaris M. Matten Institution: Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU); Trondheim, Norway Email: damaris.m.matten@ntnu.no ## Description of the data and file structure fasta\_file\_of\_newly\_generated\_sequences\_for\_data\_dryad.txt - sequences for all newly generated taxa Fennoscandia\_final\_alignment.fasta - multi-sequence alignment of native Fennoscandian flora