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Accession numbers of used gene sequences downloaded from GenBank. Asterisks on accession numbers indicate sequences that are not linked to a published journal article. (PDF 67Â kb)

Comparison of estimated node ages of the 19 major clades of Pinus across all applied dating approaches. Boxplots illustrate the estimated node ages across dating approaches and fossil sets for the major clades (a-s illustrated in Fig. 2 ). Whiskers span the 95% highest probability density (HPD), while boxes span the 50% HPD, with the median node age indicated by a vertical bar. The x-axis indicates the geological time in million years. The following abbreviations are used. FBD: fossilized birth-death method using “tip date” approach. FBD age range using “age range” approach. ND: node dating method; l: analyses based on the large fossil set; s: analyses based on the small fossil set; n: narrow log normal calibration priors in ND based on the geological age of the respective fossil; b: broad log normal calibration priors in ND; u: uniform calibration priors. The lower and upper limits of the uniform distribution represent the 2.5% and 97.5% CI levels used for the log-normal priors in the NDb method. (PDF 68 kb)

Settings and output summary of PartitionFinder showing the best partition scheme for the used sequence data in this study. (PDF 30Â kb)

Sequence matrix used for phylogenetic inference. The number of nucleotide base pairs per gene sequence used for each pine species. N in parentheses gives the number of positions in this gene sequence for which the nucleotide pair is undetermined. (PDF 68Â kb)

Sensitivity of the time calibration to single fossil exclusion for the node dating approaches (ND). This test measures the difference in age estimates of the 19 major nodes (a-s, see also Fig. 2) when keeping versus removing single calibration constraints (fossil, labeled on x-axis) at a time. NDns and NDnl are based on narrow prior calibration densities using the small (A) and the large (B) fossil set, respectively. NDbs and NDbl are based on broad prior calibration densities using the small (C) and the large (D) fossil set, respectively. Letters (see Fig. 2 for assignment) indicate nodes with highest deviations. (PDF 125Â kb)

Comparison of estimated node ages of the 19 major clades of Pinus across all applied dating approaches. A: Densities of effect sizes originate from a mixed-effect model and illustrate to what degree the estimated node ages differ among dating approaches (different colors; see legend) and among fossil sets (1. darker colors for the large, 2. brighter colors for the small fossil set; see legend). The 95% confidence intervals of effect sizes are illustrated with a line below the density curves. Non-overlap of these intervals indicates significant difference on node ages among all 19 nodes. B: Boxplots illustrate the estimated node ages across dating approaches and fossil sets for the major clades (a-s illustrated in Fig. 2). Whiskers span the 95% highest probability density (HPD), while boxes span the 50% HPD, with the median node age indicated by a vertical bar. The x-axis indicates the geological time in million years. The following abbreviations are used. FBD: fossilized birth-death method; ND: node dating method; l: analyses based on the large fossil set; s: analyses based on the small fossil set; n: narrow calibration priors in ND based on the geological age of the respective fossil; b: broad calibration priors in ND. (PDF 116Â kb)

Comparison of the effective age prior density against the posterior calibration densities (Bayesian phylogenetic age estimate) for the three dating approaches used (FBD: fossilized birth-death (blue); NDn/b: node dating with narrow (red) and broad (orange) prior distributions; s/l: small (A) and large (B) fossil sets. Boxplots represent the absolute deviation from the 1:1 line, while letters indicate significant differences in absolute deviations at the level of p = 0.05 (based on a paired Wilcox test). (PDF 116 kb)

Comparison of the specified calibration prior in BEAUti (log-transformed) against the effective calibration prior (log-transformed), as estimated without sequence data, and illustrated for all node dating approaches (ND). NDns and NDnl are based on narrow prior calibration densities using the small (A) and the large (B) fossil set, respectively. NDbs and NDbl are based on broad prior calibration densities using the small (C) and the large (D) fossil set, respectively. Labels are only given for fossil constraints with high deviance from the 1:1 line. (PDF 69Â kb)

Overview of fossils used in this study. The following abbreviations and symbols are used: FBD: fossilized birth-death method; ND: node dating method; l: denotes analyses based on the large fossil set; s: denotes analyses based on the small fossil set; n: narrow calibration priors in ND based on the geological age of the respective fossil; b: broad calibration priors in ND. “x” in tables indicates which fossil was used in the different fossil sets. Asterisks on fossil numbers represent those used in the large fossil set only. A: the fossils used for calibration constraints are listed with the minimum age of each fossil listed. Table A1: Summary of fossils used in each fossil set and the geological layer (and the time scale thereof in Ma) in which the fossils were excavated with the corresponding references. Table A2: Specified prior calibration densities used for Bayesian clock methods. Fig. A1: Illustration of taxonomic assignment for each fossil in ND. Fig. A2: Illustration of taxonomic assignments for each fossil in FBD. Red dots indicate fossils that were allowed to be placed anywhere within the corresponding clade. Black dots illustrate fossils that were allowed to be placed anywhere along the indicated branch. B: Descriptions of alternative hypotheses (AH). Table A3: Summary of fossils used in each fossil set of the alternative hypotheses (AH). Fig. A3: Illustration of taxonomic assignment of fossils in the four alternative hypotheses. Fig. A4: Estimated ages by each of the four alternative hypotheses compared to the primary age estimates in Fig. 3. Boxplots illustrate the estimated node ages across dating approaches and fossil sets for the major clades (a-s illustrated in Fig. 2). Whiskers span the 95% highest probability density (HPD), while boxes span the 50% HPD, with the median node age indicated by a vertical bar. The x-axis indicates the geological time in million years. C: Fossil descriptions and justifications ordered by taxonomic groups. Bold-italic font represents those fossils used in the smaller fossil set, while italic font represents those used in the larger fossil set only. (PDF 508 kb)

Scientific understanding of biodiversity dynamics, resulting from past climate oscillations and projections of future changes in biodiversity, has advanced over the past decade. Little is known about how these responses, past or future, are spatially connected. Analyzing the spatial variability in biodiversity provides insight into how climate change affects the accumulation of diversity across space. Here, we evaluate the spatial variation of phylogenetic diversity of European seed plants among neighboring sites and assess the effects of past rapid climate changes during the Quaternary on these patterns. Our work shows a marked homogenization in phylogenetic diversity across Central and Northern Europe linked to high climate change velocity and large distances to refugia. Our results suggest that the future projected loss in evolutionary heritage may be even more dramatic, as homogenization in response to rapid climate change has occurred among sites across large landscapes, leaving a legacy that has lasted for millennia., Nature Communications, 11 (1), ISSN:2041-1723

Overview of fossils used in this study. The following abbreviations and symbols are used: FBD: fossilized birth-death method; ND: node dating method; l: denotes analyses based on the large fossil set; s: denotes analyses based on the small fossil set; n: narrow calibration priors in ND based on the geological age of the respective fossil; b: broad calibration priors in ND. “x” in tables indicates which fossil was used in the different fossil sets. Asterisks on fossil numbers represent those used in the large fossil set only. A: the fossils used for calibration constraints are listed with the minimum age of each fossil listed. Table A1: Summary of fossils used in each fossil set and the geological layer (and the time scale thereof in Ma) in which the fossils were excavated with the corresponding references. Table A2: Specified prior calibration densities used for Bayesian clock methods. Fig. A1: Illustration of taxonomic assignment for each fossil in ND. Fig. A2: Illustration of taxonomic assignments for each fossil in FBD. Red dots indicate fossils that were allowed to be placed anywhere within the corresponding clade. Black dots illustrate fossils that were allowed to be placed anywhere along the indicated branch. B: Descriptions of alternative hypotheses (AH). Table A3: Summary of fossils used in each fossil set of the alternative hypotheses (AH). Fig. A3: Illustration of taxonomic assignment of fossils in the four alternative hypotheses. Fig. A4: Estimated ages by each of the four alternative hypotheses compared to the primary age estimates in Fig. 3. Boxplots illustrate the estimated node ages across dating approaches and fossil sets for the major clades (a-s illustrated in Fig. 2). Whiskers span the 95% highest probability density (HPD), while boxes span the 50% HPD, with the median node age indicated by a vertical bar. The x-axis indicates the geological time in million years. C: Fossil descriptions and justifications ordered by taxonomic groups. Bold-italic font represents those fossils used in the smaller fossil set, while italic font represents those used in the larger fossil set only. (PDF 508 kb)

BackgroundThe taxonomy of the genus Pinus is widely accepted and a well-resolved phylogeny based on entire plastome sequences exists. However, there is a large discrepancy in estimated divergence times of major pine clades among existing studies mainly due to differences in fossil placement and dating methods used. We currently lack a dated molecular pine phylogeny that makes full usage of the rich fossil record in pines. This study is the first to estimate the divergence dates of pines based on a large number of fossils (21) evenly distributed across all major clades in combination with applying the most novel dating method.ResultsWe present a range of molecular phylogenetic trees of Pinus generated within a Bayesian framework using both the novel fossilized birth-death and the traditional node dating method with different fossil sets. We find the origin of pines likely to be up to 30 Myr older (Early Cretaceous) than inferred in most previous studies (Late Cretaceous) and propose generally older divergence times for major clades within Pinus than previously thought. Our age estimates vary significantly between the different dating approaches but the results generally agree on older divergence times. We present a revised list of 21 fossils that are suitable to use in dating or comparative analyses of pines.ConclusionsAn accurate timescale for the divergence times in pines is essential if we are to link diversification processes and functional adaptation of this genus to geological events or to changing climates. Next to older divergence times in Pinus, our results indicate that node age estimates in pines depend on dating approaches and fossil sets used due to different inherent characteristics of dating approaches. Our set of dated phylogenetic trees of pines presented herein provide the basis to account for uncertainties in age estimations when applying comparative phylogenetic methods, which will improve our understanding of the evolutionary and ecological history in pines.