Scalesia (Asteraceae) is the largest endemic plant genus of the Galápagos archipelago and an example of adaptive radiation. While Scalesia species are highly varied in habit and morphology, most remarkable is their variety of leaf shapes, especially in the differential presence of leaf lobing/serration, a derived trait that evolved multiple times as a likely adaptation to the islands’ hot and dry equatorial climate. Using population-level genomic data from 396 individuals representing all 15 recognized Scalesia species, we characterize this young radiation (around 1 million years ago), and reveal that their substantial morphological divergence and ecological specialization are primarily based on shared genetic variation. To further elucidate the repeated adaptive evolution of leaf lobing in Scalesia, we integrate genomic and leaf morphometric data, with transcriptomes from different developmental stages, and conclude that leaf lobing evolved through diversifying selection. Natural selection occurs independently on different regulators in the pathway controlling the development of adaxial-abaxial leaf polarity, highlighting the importance of the founder populations’ high genetic diversity maintained via allopolyploidy. Finally, our findings have implications for the conservation of Scalesia’s threatened biodiversity, as unexpectedly high intra-specific genetic structure and long-term isolation among populations indicate widespread nascent speciation. This dataset contains files associated with the article. Specifically, it contains code and scripts used to analyse the data, the source data files for the main text and supplementary figures, and the Cytoscape file used for the transcriptomics analysis in the article. It also contains example input and output files to calculate dxy and genome-wide Tajima's D.

<b>Abstract</b><br/><p><em>Scalesia</em> (Asteraceae) is the largest endemic plant genus of the Galápagos archipelago and an example of adaptive radiation. While <em>Scalesia</em> species are highly varied in habit and morphology, most remarkable is their variety of leaf shapes, especially in the differential presence of leaf lobing/serration, a derived trait that evolved multiple times as a likely adaptation to the islands’ hot and dry equatorial climate. Using population-level genomic data from 396 individuals representing all 15 recognized <em>Scalesia</em> species, we characterize this young radiation (around 1 million years ago), and reveal that their substantial morphological divergence and ecological specialization are primarily based on shared genetic variation. To further elucidate the repeated adaptive evolution of leaf lobing in <em>Scalesia</em>, we integrate genomic and leaf morphometric data, with transcriptomes from different developmental stages, and conclude that leaf lobing evolved through diversifying selection. Natural selection occurs independently on different regulators in the pathway controlling the development of adaxial-abaxial leaf polarity, highlighting the importance of the founder populations’ high genetic diversity maintained via allopolyploidy. Finally, our findings have implications for the conservation of <em>Scalesia</em>’s threatened biodiversity, as unexpectedly high intra-specific genetic structure and long-term isolation among populations indicate widespread nascent speciation. This dataset contains files associated with the article. Specifically, it contains code and scripts used to analyse the data, the source data files for the main text and supplementary figures, and the Cytoscape file used for the transcriptomics analysis in the article. It also contains example input and output files to calculate dxy and genome-wide Tajima's D.</p>

Additional file 1: PLSDB matches to 22 plasmids sequence representatives.

Additional file 1: PLSDB matches to 22 plasmids sequence representatives.

Additional file 2: Genome completeness and contamination stats after removal of plasmids sequence.

Additional file 2: Genome completeness and contamination stats after removal of plasmids sequence.

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.

Aim In this study, we explored spatial patterns of phylogenetic diversity (PD) and endemism in the flora of Norway and tested hypothesized post‐glacial environmental drivers of PD, including temperature, precipitation, edaphic factors and time since glacial retreat. Location Norway. Taxon Vascular plants (Trachaeophyta). Methods We produced a multi‐locus maximum‐likelihood (ML) phylogeny using a combination of newly produced DNA sequences from herbarium specimens and sequences available from public repositories. We combined the phylogeny with species occurrence data to estimate PD and phylogenetic endemism across Norway, using a spatial randomization to judge statistical significance. We used multiple‐model inference to identify environmental variables that contributed the most to the patterns of PD. Finally, we estimated phylogenetic turnover and used this to identify Norwegian plant assemblages in terms of composition and evolutionary history. Results Our ML phylogeny contained 87% of all currently described native Norwegian vascular plants. Assemblages were phylogenetically overdispersed in warmer and wetter regions of Norway, as well as in regions with a longer post‐glacial history. In cold and dry regions, plant assemblages were phylogenetically clustered, and characterized by neo‐endemism, while the mild and wet regions were characterized by both paleo‐ and neo‐endemism. PD was positively correlated with summer temperature and habitat heterogeneity, and peaked in the southeast of Norway. Main conclusions Both contemporary ecological factors (climate and habitat heterogeneity), and post‐glacial history seem to have shaped the phylogenetic structure of the flora of Norway. The flora in the far north of Norway appear to be a result of recent diversification while the coastal regions are assemblages of deeper lineages. Our results suggest that there is an evolutionary signal in the distribution of the Norwegian vascular flora.

Methods: We produced a multi-locus Maximum Likelihood (ML) phylogeny using a combination of newly produced DNA sequences from herbarium specimens and sequences available from public repositories. We combined the phylogeny with species occurrence data to estimate phylogenetic diversity and phylogenetic endemism across Norway, using a spatial randomization to judge statistical significance. We used multiple-model inference to identify environmental variables that contributed the most to the patterns of phylogenetic diversity. Finally, we estimated phylogenetic turnover and used this to identify Norwegian plant assemblages in terms of composition and evolutionary history. Results: Our ML phylogeny contained 87% of all currently described native Norwegian vascular plants. Assemblages were phylogenetically overdispersed in warmer and wetter regions of Norway, as well as in regions with a longer post-glacial history. In cold and dry regions, plant assemblages were phylogenetically clustered, and characterised by neo-endemism, while the mild and wet regions were characterised by both paleo- and neo-endemism. Phylogenetic diversity was positively correlated with summer temperature and habitat heterogeneity, and peaked in the southeast of Norway. Main conclusions: Both contemporary ecological factors (climate and habitat heterogeneity), and post-glacial history seem to have shaped the phylogenetic structure of the flora of Norway. The flora in the far north of Norway appear to be a result of recent diversification while the coastal regions are assemblages of deeper lineages. Our results suggest that there is an evolutionary signal in the distribution of the Norwegian vascular flora.

Abstract: Aim: In this study, we explored spatial patterns of phylogenetic diversity and endemism in the flora of Norway and tested hypothesized post-glacial environmental drivers of phylogenetic diversity, including temperature, precipitation, edaphic factors, and time since glacial retreat. Location: Norway. Taxon: Vascular plants (Trachaeophyta). Methods: We produced a multi-locus Maximum Likelihood (ML) phylogeny using a combination of newly produced DNA sequences from herbarium specimens and sequences available from public repositories. We combined the phylogeny with species occurrence data to estimate phylogenetic diversity and phylogenetic endemism across Norway, using a spatial randomization to judge statistical significance. We used multiple-model inference to identify environmental variables that contributed the most to the patterns of phylogenetic diversity. Finally, we estimated phylogenetic turnover and used this to identify Norwegian plant assemblages in terms of composition and evolutionary history. Results: Our ML phylogeny contained 87% of all currently described native Norwegian vascular plants. Assemblages were phylogenetically overdispersed in warmer and wetter regions of Norway, as well as in regions with a longer post-glacial history. In cold and dry regions, plant assemblages were phylogenetically clustered, and characterised by neo-endemism, while the mild and wet regions were characterised by both paleo- and neo-endemism. Phylogenetic diversity was positively correlated with summer temperature and habitat heterogeneity, and peaked in the southeast of Norway. Main conclusions: Both contemporary ecological factors (climate and habitat heterogeneity), and post-glacial history seem to have shaped the phylogenetic structure of the flora of Norway. The flora in the far north of Norway appear to be a result of recent diversification while the coastal regions are assemblages of deeper lineages. Our results suggest that there is an evolutionary signal in the distribution of the Norwegian vascular flora.