Ecological Archives --D1

Walter Durka and Stefan G. Michalski. 2012. Daphne: a dated phylogeny of a large European flora for phylogenetically informed ecological analyses. Ecology 93:2297. http://dx.doi.org/10.1890/12-0743.1

INTRODUCTION

All extant species are connected by a common phylogeny often represented by an evolutionary tree. The common evolutionary history among species can lead to a degree of similarity of traits and life history characteristics among related species, and are statistically not independent (Felsenstein 1985, Harvey and Pagel 1991). In turn, trait provisions may affect ecological performance of a particular species and thus can have imprints on community structure.

Consequently the phylogenetic relationships have to be taken into account when a comparative approach is used for the analysis of, e.g., trait correlations, trait evolution, trait based ecological processes, or community assembly. Various approaches of phylogenetically informed comparative analyses of trait evolution have been developed, like phylogenetically independent contrasts (PICS) (Felsenstein 1985, Purvis and Rambaut 1995, Pagel 1999), or phylogenetic general least squares (PGLS) regression (Revell 2010). Similarly, the phylogenetic structure of communities and niches are important current research fields (Webb et al. 2002, Strauss et al. 2006) and several tools for their analysis are available (Webb et al. 2008, Kembel et al. 2010).

Despite major progress in unravelling the phylogenetic tree of life by methods of molecular systematics and barcoding initiatives (e.g., http://tolweb.org, http://www.iplantcollaborative.org/), most phylogenies are far from being comprehensive, even for well studied floras like the European vascular plants.

Previously, we compiled a phylogenetic tree for the German flora (Durka 2002). However, this earlier version suffered from a number of drawbacks. First, for a number of families, evolutionary relationships were far from sufficiently resolved. Second, the tree provided topological information only, i.e., unit branch lengths throughout the tree, thus essentially reducing the distance between species to the number of nodes separating them. Such a pure topology has been found useful (e.g., Prinzing et al. 2001, 2002, Gerhold et al. 2011) and quantitative estimates for evolutionary divergence among species have been derived alternatively (Grafen 1989 e.g., Zhu et al. 2010). Still, a phylogeny of the vascular plants including both, state-of-the-art topology and branch length information is highly demanded.

Here, we present a comprehensive, dated phylogeny of a large European flora comprising the vascular plants of the British Isles, Germany, the Netherlands and Switzerland, totalling 4685 species. The phylogeny was built by manually grafting subtrees on a family backbone topology, dating of nodes and finally calculating an ultrametric tree. For details on species, topology and node dating, see below, Metadata, II.B.

METADATA

CLASS I. DATA SET DESCRIPTORS

A. Data set identity:

Title: Daphne - a dated phylogeny of a large European flora for phylogenetically informed ecological analyses

B. Data set identification code:

Suggested data set identification code: Daphne_01

C. Data set description

1. Principal Investigators:

Walter Durka, Helmholtz Centre for Environmental Research – UFZ, Department of Community Ecology (BZF), Theodor-Lieser-Str. 4, D-06120 Halle, Germany

Stefan G. Michalski, Helmholtz Centre for Environmental Research – UFZ, Department of Community Ecology (BZF), Theodor-Lieser-Str. 4, D-06120 Halle, Germany

Abstract: This data set represents a comprehensive, dated phylogeny of a large European flora comprising the vascular plants of the British Isles, Germany, the Netherlands, and Switzerland, totalling 4685 species. The phylogeny thus encompasses all species in the trait databases BIOLFLOR, PLANTATT, and BioBase 2003. The topology of the phylogenetic tree is based on a backbone family phylogeny of the Angiosperm Phylogeny Group III. Subsequently, partial phylogenetic subtrees derived from a total of 518 recent molecular studies were manually pruned onto the backbone tree, using multi-gene consensus topologies if possible. Similarly, 1103 internal nodes and the root node were dated based on 261 recent studies. Finally, an ultrametric tree was calculated by placing undated nodes evenly between dated nodes. The phylogeny provides a reference data set for comparative analyses of trait correlations, trait evolution, trait based ecological processes, community assembly, or other phylogenetically informed analyses across a large taxon of European plant species. It can readily be used in phylogenetic analysis tools like ape, phytools, picante, or MESQUITE.

D. Key words: BIOLFLOR; British flora; German flora; macroecology; Netherlands flora; phylogeny; PLANTATT; supertree; Swiss flora; vascular plants.

CLASS II. RESEARCH ORIGIN DESCRIPTORS

A. Overall project description

Identity: Plant species phylogeny for phylogenetically informed ecological analyses

Originator: W. Durka and S.G. Michalski

Period of Study: 2011–2012

Objectives: Phylogenetically informed macroecological analyses rely on phylogenetic hypotheses. We developed a comprehensive phylogeny for a large European flora based on topologies and dated nodes derived largely from molecular studies.

Abstract: We generated a dated phylogeny of a large European flora comprising the vascular plants of the British Isles, Germany, the Netherlands, and Switzerland, totalling 4685 species. The phylogeny was built by manually grafting subtrees on a family backbone topology, dating of nodes and finally calculating an ultrametric tree.

Sources of funding: Helmholtz Centre for environmental Research-UFZ, Theodor-Lieser-Str. 4, 06120 Halle, Germany.

B. Specific subproject description

1. Species included

The phylogeny comprises a major part of the Flora of Central and Northwestern Europe. We included all vascular plant species of Germany as encompassed in the BIOLFLOR database (3657 spp., Klotz et al. 2002, Kühn et al. 2004), all species of the PLANTATT database representing a large fraction of the species of the British Isles (1825 spp., Hill et al. 2004), all species of the Netherlands as listed in BioBase 2003 (1897 spp., Centraal Bureau voor de Statistiek 1997, 2003) and all species from Switzerland (3133 spp., Aeschimann and Heitz 2005). We did not include subspecies and hybrids listed in the respective sources.

In total, the phylogeny encompasses 4685 plant species in 166 families. Of these, about 600 are partial or putative apomicts: Ranunculus auricomus agg. (49 spp.), Rubus fruticosus agg. (301 spp.), Alchemilla vulgaris agg. (31 spp.), Oenothera biennis agg. (46 spp.), Limonium binvervosum group (10 spp.), Hieracium subgen. Pilosella (77 spp.), Hieracium subgen. Hieracium (76 spp.).

For those species added to the original BIOLFLOR data set, we retained the nomenclature of the different source databases. Thus the current list does neither intend to present a reference taxonomy nor a reference nomenclature, but rather a practical compromise between the various original treatments. A list of synonyms of the different sources and the current phylogeny is provided as separate document DaPhnE_01_Synonymy.txt.

Aggregate taxa (e.g., "Achillea millefolium agg.") have generally been treated as names for nodes in the phylogeny which are followed by the final tips of s.str. or taxa within the aggregates. If such aggregate taxa are to be used, they have to be synonymized with one of the respective tip taxa (e.g., "Achillea millefolium agg." à "Achillea millefolium"). However, two exceptions were made where we added two common and widely used aggregate species as extra taxa in tip-position: "Ranunculus auricomus" and "Rubus fruticosus".

2. Tree topology

The tree topology was build by manually grafting partial phylogenetic subtrees on a backbone family tree. The family tree was based on Smith et al. 2006 and Qiu et al. 2007 for the basal lineages of vascular plants and ferns and on the phylogeny of the Angiosperm Phylogeny Group III (APG III 2009) for the spermatophytes. The latter was refined for families within Lamiales based on Schäferhoff et al. 2010 and Ruscaceae were included in Asparagaceae (Chase et al. 2009, Kim et al. 2010). Phylogenetic relationships within families were assembled from a total of 518 published molecular phylogenetic studies (DaPhnE_01_reference_list.txt, DaPhnE_01_nodes_with_references.txt). In these studies, multi-gene consensus topologies were used if available. Conflicting topologies within and among studies were resolved to the best of our knowledge or were treated as polytomies. Overall, 429 out of a total of 463 genera (93%) and 2598 of the 4685 species (55.5 %) were covered by the source phylogenies. However, for families/genera with only 1–2 genera/species we did not necessarily look up phylogenetic information as the topology is clear in these cases. Considering additionally that approximately 600 species are apomicts, the proportion of species are matched by molecular phylogenetic analyses amounts to about 65% of the non-apomictic species. For species that were not included in the molecular phylogenies available, we considered their affiliation to traditional systematic taxa of tribes, subtribes, genera, subgenera, sections, subsections, series or aggregates to assign them into the respective clades.

3. Dating and branch lengths

Internal nodes of the topological tree were dated based on an extensive literature survey on published ages of the respective branching events. If multiple values were available for single nodes, the mean age between maximum and minimum reported values was used. For the root node and for 1103 of the in total 3345 internal nodes we obtained ages from a total of 261 published studies and additional resources (www.timetree.org, accessed between August 2011 and March 2012). An ultrametric tree was created from the supertree topology by distributing nodes without dating information evenly between dated nodes using the bladj package of PHYLOCOM (Webb et al. 2008). References for dated nodes are given in two separate tab-delimited documents (DaPhnE_01_reference_list.txt, DaPhnE_01_nodes_with_references.txt).

4. DaPhnE phylogeny

The phylogeny with branch lengths scaled in million years, is available in Newick format as DaPhnE_01.tre. As such it is readable by standard tree viewers such as DENDROSCOPE Huson et al. 2007 and phylogenetic analysis tools, e.g., ape (Paradis 2006), phytools (Revell 2012) or picante (Kembel et al. 2010) for the R environment (R Development Core Team 2009) or MESQUITE (Maddison and Maddison 2011). Internal node names are either numbered (e.g., N36) or named (e.g., Asteraceae) to identify clades. Node names correspond to the names given in DaPhnE_01_nodes_with_references.txt.

CLASS III. DATA SET STATUS AND ACCESSIBILITY

A. Status

Latest update: 2012

Latest Archive date: 2012

Metadata status: Metadata are complete and are stored with the data (see B. below).

Data verification:Data were checked during entry

B. Accessibility

Storage location and medium: All digital data and metadata are stored on the Principle Investigators´ computers and on computer hard drives at the Helmholtz Centre for environmental Research-UFZ.

Contact persons:

Walter Durka, Helmholtz Centre for Environmental Research – UFZ, Department of Community Ecology (BZF), Theodor-Lieser-Str. 4, D-06120 Halle, Germany, email [email protected];

Stefan G. Michalski, Helmholtz Centre for Environmental Research – UFZ, Department of Community Ecology (BZF), Theodor-Lieser-Str. 4, D-06120 Halle, Germany, email [email protected]

Copyright restrictions: None, the data is freely available for scientific use.

Proprietary restrictions: None, the authors would appreciate notification when and how data are used.

a. Release date: July, 16th, 2012

b. Citation: This paper

CLASS IV. DATA STRUCTURAL DESCRIPTORS

A. Data set file: Data set is downloadable as a single archive, DaPhnE_01.zip. This file contains 4 data files described below.

IV.A.1 Data file name: DaPhnE_01_Synonymy.txt

This file is a tab-delimited ASCII file containing the list of the binomials used by the German, British, the Netherlands, and Swiss source databases and the respective binomials used in DaPhnE. Additionally, genus, family and if appropriate, the includeing aggregate is given as seperate column.

Header information:

IV.A.2 Data file name: DaPhnE_01.tre

This file is an ASCII file of the phylogeny in Newick format (http://evolution.genetics.washington.edu/phylip/newicktree.html)

IV.A.3 Data file name: DaPhnE_01_nodes_with_references.txt

This file is a tab-delimited ASCII file containing 1212 lines listing nodes with either a reference for the partial phylogenies used to construct the supertree or to the node ages. References are numbered and full bibliography is provided as a second file.

IV.A.4 Data file name: DaPhnE_01_reference_list.txt

This file is a tab-delimited ASCII file containing 738 references for phylogenies and node dates given in DaPhnE_01_nodes_with_references.txt.

LITERATURE CITED

Aeschimann, D., and C. Heitz. 2005. Index synomymique de la Flore de Suisse [http://www.crsf.ch/?page=download]. CRSF, Geneve.

APG III. 2009. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Botanical Journal of the Linnean Society 161:105–121.

Centraal Bureau voor de Statistiek. 1997. BioBase 1997, Register biodiversiteit, CD-Rom, Voorburg/Heerlen, the Netherlands.

Centraal Bureau voor de Statistiek. 2003. BioBase 2003, Register biodiversiteit, CD-Rom [http://www.cbs.nl/nl-NL/menu/methoden/classificaties/overzicht/namenlijsten-planten-dieren/default.htm], Voorburg/Heerlen, the Netherlands.

Chase, M. W., J. L. Reveal, and M. F. Fay. 2009. A subfamilial classification for the expanded asparagalean families Amaryllidaceae, Asparagaceae and Xanthorrhoeaceae. Botanical Journal of the Linnean Society 161:132–136.

Durka, W. 2002. Phylogenie der Farn- und Blütenpflanzen Deutschlands. Pages 75–91 in S. Klotz, I. Kühn, and W. Durka, editors. BIOLFLOR - Eine Datenbank mit biologisch-ökologischen Merkmalen zur Flora von Deutschland, Bonn, Germany.

Felsenstein, J. 1985. Phylogenies and the comparative method. American Naturalist 125:1–15.

Gerhold, P., M. Partel, O. Tackenberg, S. M. Hennekens, I. Bartish, J. H. J. Schaminee, A. J. F. Fergus, W. A. Ozinga, and A. Prinzing. 2011. Phylogenetically Poor Plant Communities Receive More Alien Species, Which More Easily Coexist with Natives. American Naturalist 177:668–680.

Grafen, A. 1989. The phylogenetic regression. Philosophical Transactions of the Royal Society London B 326:119–156.

Harvey, P. H., and M. D. Pagel. 1991. The comparative method in evolutionary biology. Oxford University Press, Oxford, UK.

Hill, M. O., C. D. Preston, and D. B. Roy. 2004. PLANTATT - Attributes of British and Irish Plants: Status, size, life history, geography and habitats. Updated version downloaded 2011 from http://www.brc.ac.uk/downloads/PLANTATT_19_Nov_08.zip. NERC, Cambridgeshire.

Huson, D., D. Richter, C. Rausch, T. Dezulian, M. Franz, and R. Rupp. 2007. Dendroscope: An interactive viewer for large phylogenetic trees. BMC Bioinformatics 8:460.

Kembel, S. W., P. D. Cowan, M. R. Helmus, W. K. Cornwell, H. Morlon, D. D. Ackerly, S. P. Blomberg, and C. O. Webb. 2010. Picante: R tools for integrating phylogenies and ecology. Bioinformatics 26:1463–1464.

Kim, J. H., D. K. Kim, F. Forest, M. F. Fay, and M. W. Chase. 2010. Molecular phylogenetics of Ruscaceae sensu lato and related families (Asparagales) based on plastid and nuclear DNA sequences. Annals of Botany 106:775–790.

Klotz, S., I. Kühn, and W. Durka. 2002. BIOLFLOR - Eine Datenbank mit biologisch-ökologischen Merkmalen zur Flora von Deutschland.in S. Klotz, I. Kühn, and W. Durka, editors. Landwirtschaftsverlag, Bonn, Germany.

Kühn, I., W. Durka, and S. Klotz. 2004. BiolFlor - a new plant-trait database as a tool for plant invasion ecology. Diversity and Distributions 10:363–365.

Maddison, W. P., and D. R. Maddison. 2011. Mesquite: a modular system for evolutionary analysis. Version 2.75 http://mesquiteproject.org.

Pagel, M. 1999. Inferring the historical patterns of biological evolution. Nature 401:877–884.

Paradis, E. 2006. Analysis of Phylogenetics and Evolution with R. Springer, New York, New York, USA.

Prinzing, A., W. Durka, S. Klotz, and R. Brandl. 2001. The niche of higher plants: evidence for phylogenetic conservatism. Proceedings of the Royal Society of London Series B-Biological Sciences 268:2383–2389.

Prinzing, A., W. Durka, S. Klotz, and R. Brandl. 2002. Geographic variability of ecological niches of plant species: are competition and stress relevant? Ecography 25:721–729.

Purvis, A., and A. Rambaut. 1995. Comparative analysis by independent contrasts (CAIC) - an Apple-Macintosh application for analyzing comparative data. Computer Applications In The Biosciences 11:247–251.

Qiu, Y. L., L. B. Li, B. Wang, Z. D. Chen, O. Dombrovska, J. Lee, L. Kent, R. Q. Li, R. W. Jobson, T. A. Hendry, D. W. Taylor, C. M. Testa, and M. Ambros. 2007. A nonflowering land plant phylogeny inferred from nucleotide sequences of seven chloroplast, mitochondrial, and nuclear genes. International Journal of Plant Sciences 168:691–708.

R Development Core Team. 2009. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org.

Revell, L. J. 2010. Phylogenetic signal and linear regression on species data. Methods in Ecology and Evolution 1:319–329.

Revell, L. J. 2012. phytools: an R package for phylogenetic comparative biology (and other things). Methods in Ecology and Evolution 3:217–223.

Schäferhoff, B., A. Fleischmann, E. Fischer, D. C. Albach, T. Borsch, G. Heubl, and K. F. Müller. 2010. Towards resolving Lamiales relationships: insights from rapidly evolving chloroplast sequences. BMC Evolutionary Biology 10.

Smith, A. R., K. M. Pryer, E. Schuettpelz, P. Korall, H. Schneider, and P. C. Wolf. 2006. A classification for extant ferns. Taxon 55:705–731.

Strauss, S. Y., C. O. Webb, and N. Salamin. 2006. Exotic taxa less related to native species are more invasive. Proceedings of the National Academy of Sciences of the United States of America 103:5841–5845.

Webb, C. O., D. D. Ackerly, and S. W. Kembel. 2008. Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics 24:2098–2100.

Webb, C. O., D. D. Ackerly, M. A. McPeek, and M. J. Donoghue. 2002. Phylogenies and community ecology. Annual Review of Ecology and Systematics 33:475–505.

Zhu, Y., R. T. W. Siegwolf, W. Durka, and C. Körner. 2010. Phylogenetically balanced evidence for structural and carbon isotope responses in plants along elevational gradients. Oecologia 162:853–863.

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