Page last updated 13/10/2017

ClimGrim database

This MSAccess database was set up to facilitate analysis of data relevant to our (Grimm & Denk, 2012) critical re-evaluation of the so-called "co-existence approach" (CA) by Mosbrugger & Utescher (1997), which is considered by some as a "robust" (Utescher et al., 2014) standard to reconstruct palaeoclimate (for Eurasia except Japan) despite of fundamental problems inherent to the application of this method (both in theory and practise; Utescher et al., 2014; Grimm et al., 2016; Grimm & Potts, 2016) and – so far (July 2016) – the lack of any meaningful validation of the basic method and data (cf. Mosbrugger & Utescher, 1997; Grimm & Denk, 2012; Utescher et al., 2014).

The current version (0.2.1) includes Köppen signatures for over 900 species/genera and MAT ('mean annual temperature') tolerances of various taxa used as "nearest living relatives" (NLRs) in CA studies as recorded in the online version of the Palaeoflora database by October 2011. In addition, it lists also the (often markedly different) MAT tolerances of these NLRs and further taxa based on the monographic works of Thompson et al. (1999a, 1999b, 2001, 2006) for North America and Fang et al. (2009) for China, which have been complemented by other sources (annotated in the database; cf. Grimm and Denk, 2012). Additional annotations to some of the taxa include details about their geographic (and altitudinal) distribution and information relevant to the estimation of MAT tolerances.

Time line

26/05/2015 Major update to version 0.2.1 — Complemented Köppen signatures for Fagales (now including also tropical-subtropical taxa and few modifications of taxa already in the database), added species sets for Celtis, Elaeagnus, Ulmus, and Zelkova (Fagales/Rosales present at the Lavanttal locality, Austria; Grímsson et al., 2016)

28/03/2014 Minor update of version 0.2 (28/03/2014) — Added Köppen signatures for most species of Betulaceae increasing total number of covered species (potential modern analogues of fossil taxa) to 588.

30/11/2012 Update to Version 0.2; including Köppen signatures for potential NLRs as implemented and used in Denk et al. (2013).

The database provided here is a copy of a working database, and naturally will be subject to changes, in irregular time intervals. It comes without any warranty (like all palaeoclimate reconstructions using fossil plant assemblages).

Everybody is welcomed to use this database, but if so, please be so kind as to cite Grimm & Denk (2012) for climate data and Denk et al. (2013) for Köppen signatures. Please feel free to contact me in case you have questions, suggestions for corrections or improvements, or any other request regarding this database.

The current version is 0.2.1

Download the zipped (compressed) current version (c. 2.4 MB) here. The deflated database will be about 97 MB large, you'll need MS Access 2003 or higher-compatible program to use the database.

Older versions: v. 0.2 v. 0.1

References
Denk, T., Grimm, G.W., Grímsson, F., Zetter, R., 2013. Evidence from "Köppen signatures" of fossil plant assemblages for effective heat transport of Gulf Stream to subarctic North Atlantic during Miocene cooling. Biogeosciences 10, 7927–7942.
Fang, J., Wang, Z., Tang, Z., 2009. Atlas of Woody Plants in China. Volumes 1 to 3 and index. Higher Education Press, Beijing.
Grimm, G.W., Denk, T., 2012. Reliability and resolution of the coexistence approach – a revalidation using modern-day data. Rev. Palaeobot. Palynol. 172, 33–47
Grimm, G.W., Potts, A., 2016. Fallacies and fantasies: the theoretical underpinnings of the Coexistence Approach for palaeoclimate reconstruction. Climates of the Past 12: 611–622.
Grimm G.W., Bouchal, J.M., Denk T., Potts A.J. 2016. Fables and foibles: a critical analysis of the Palaeoflora database and the Coexistence approach for palaeoclimate reconstruction. Rev. Palaeobot. Palynol. 233, 216–235 (2015 preprint @ bioRxiv, doi: 10.1101/016378)
Grímsson, F., Grimm, G.W., Meller, B., Bouchal J.M., Zetter, R., 2016. Combined LM and SEM study of the middle Miocene (Sarmatian) palynoflora from the Lavanttal Basin, Austria: Part IV. Magnoliophyta 2 - Fagales to Rosales Grana 55, 101–163
Mosbrugger, V., Utescher, T., 1997. The coexistence approach - a method for quantitative reconstructions of Tertiary terrestrial palaeoclimate data using plant fossils. Palaeogeogr. Palaeoclimat. Palaeoecol. 134, 61–86.
Thompson, R.S., Anderson, K.H., Bartlein, P.J., 1999a. Atlas of relations between climatic parameters and distribution of important trees and shrubs in North America — Hardwoods. U.S. Geol. Survey Prof. Paper 1650–B, 1–423.
Thompson, R.S., Anderson, K.H., Bartlein, P.J., 1999b. Atlas of relations between climatic parameters and distributions of important trees and shrubs in North America — Introduction and Conifers. U.S. Geol. Survey Prof. Paper 1650–A, 1–269.
Thompson, R.S., Anderson, K.H., Bartlein, P.J., 2001. Atlas of relations between climatic parameters and distributions of important trees and shrubs in North America — Additional conifers, hardwoods, and monocots. U.S. Geol. Survey Prof. Paper 1650–C, 1–386.
Thompson, R.S., Anderson, K.H., Strickland, L.E., Shafer, S.L.,Pelltier, R.T., Bartlein, P.J., 2006. Atlas of Relations Between Climatic Parameters and Distributions of Important Trees and Shrubs in North America—Alaska Species and Ecoregions. U.S. Geol. Survey Prof. Paper 1650-D, 1–342.
Utescher, T., Bruch, A.A., Erdei, B., François, L., Ivanov, D., Jacques, F.M.B., Kern, A.K., Liu, Y-S., Mosbrugger, V., Spicer, R.A., 2014. The Coexistence Approach—theoretical background and practical considerations of using plant fossils for climate quantification. Palaeogeogr. Palaeoclimat. Palaeoecol. 410, 58–73.

Downloadable data

Find below a (alphabetically ordered) list of archives including primary data, analyses and results files used in our evolutionary and other studies. For details refer to the original literature and text files included in each archive. Anyone is invited to use this data for whatever purpose, even if you want to show that we were wrong, but in any case, you use it at your own risk: Archives have been tested and should be free of viruses, trojans, worms, cladistics, etc., but in today's dangerous world, you never know.

• Banag et al. BMC Evol. Biol., 17: 131. (2017) This ZIP archive (99MB) includes the matrices (NEXUS-formatted) and BI, MJ and ML analysis files as well as support consensus (bipartition) networks depicting alternative/competing BS supports and PP.
  
  
• Bomfleur et al. BMC Evol. Biol., 15: 126. (2015) This ZIP archive (21MB) includes supplementary files, morphological and molecular character matrices, and analysis files.
  
  
• Bomfleur et al., PeerJ, 5: e3433 (2017). This is a mirror of the Supplementary Data Archive (82 MB) published via Dryad. It includes all data and analysis files (including nonparametric bootstrapping of several taxon-sets under maximum likelihood using both substitution models implemented in RAxML for categorical data), hence the size. Most analyses were done to rebut a wish of one of the anonymous reviewers, who wanted parsimony trees (which we didn't want to provide, given the complex data structure of the underlying matrix). Contact me if you need a smaller version.
  
  
• Denk & Grimm, Rev. Palaeobot. Palynol., 158: 83–100 (2009). This ZIP archive (33kB) includes the morphological character matrices, tree files, and distance matrices in NEXUS-format.
  
  
• Denk & Grimm, Taxon, 59:351–366 (2010). This ZIP archive (1.7MB) includes the molecular character matrices (ITS, 5S-IGS), untransformed and transformed distance matrices in extented PHYLIP-format (the basis for the phylogenetic networks), RAxML log files, and inferred ML trees based on untransformed (clones) and transformed (individual- or species-consensus) data (nucleotide sequences).
  
  
• Denk et al., Biogeosciences, 10:7927–7942 (2013). Supplement (2.4MB) to the paper including ClimGrim database v 0.2 [Archive mirrored on the journal homepage]
  
  
• Friis et al., Grana, 54: 184–212 (2015). This ZIP archive includes supplement files S1–S3 (used morphological and genetic matrices; and trait mapping) and the result files of the ML tree inference and bootstrapping.
  
  
• Grimm, Genealogical World of Networks (ed. D. Morrison), blogpost (17/10/2017). This ZIP archive (1.5 MB) includes the matrix (a morphological matrix of mosasaurs by Madzia & Cau) and analysis files (tree inference and bootstrapping analyses under different optimality criteria) relating to the post.
  
  
• Grimm & Denk, Taxon, 59:134–147 (2010). This ZIP archive (121kB) includes the molecular character matrices (ITS, 5S-IGS, LFYi2), untransformed and transformed distance matrices in extented PHYLIP-format(the basis for the phylogenetic networks), and inferred ML trees.
  
  
• Grimm & Denk, Rev. Palaeobot. Palynol., 172:33–47 (2012). This ZIP archive (8MB) includes the electronic supplementary files, a GoogleEarth location file, and GIS files relevant to the study. Click here for a smaller version (3MB) of the archive not including the folder with GIS files.
  
  
• Grimm & Denk, Turk. J. Bot., 38:1050–1066 (2014). This ZIP archive (3.3MB) includes the supplementary files and figures, ITS data matrix, and analysis files.
  
  
• Grimm & Renner, Bot. J. Linn. Soc., 172: 465–477 (2013). This ZIP archive (1.9MB) includes basic sequence alignments and transformed matrices with strict species consensus data (NEXUS/extended PHYLIP-formatted) and the result files of ML tree inferences and bootstrap analyses performed with RAxML.
  
  
• Grimm et al., bioRxiv, doi:10.1101/016378 (2015) / Rev. Palaeobot. Palynol., 233, 216–235 (2016). This ZIP archive includes supplement tables S1&S4 and various background data files (Files S1–S6).
  
  
• Grimm et al., Syst. Biol., doi:10.1093/sysbio/syu108 (2014). This ZIP archive includes supplement figures S1&S2, tables S1–S4 and a data folder (geno-morphological matrix; raw chronograms), deposited with the Dryad Digital Repository, which should be referenced in addition to the paper if you use these data.
  
  
• Grímsson et al., Rev. Palaeobot. Palynol., 200: 161–187 (2014). This ZIP archive (1.9MB) including supplementary information, genetic and morphological character matrices and result files of phylogenetic inferences.
  
  
• Grímsson et al., Grana, 55: 101–163 (2016). This XLSX spread sheet file (100kB) includes Köppen signatures of species that are potential modern analogues for Fagales and Rosales present at the Lavanttal locality as included in the ClimGrim v. 0.2.1 database
  
  
• Grímsson et al., Grana, TBA: 000–000 (2018). This ZIP archive (9.3MB) includes supplement files S1 to S7, and all files for molecular-phylogenetic analyses done for the paper (see ReadMe.txt) and in response (File S6, folder Su_et_al) to uninformed/data-naive comments of two (anonymous) of the three reviewers, which disallowed the editors to make a quicker decision on publishing this pollen(!)-focussed (not mol-phyl) study.
  
  
• Grímsson et al., J. Biogeogr., doi: 000–000 (2017). ZIP archive (8MB) including appendices (mirrored), supplement files, ML analyses-related files, and R-scripts/R-output for establishing semi-quantitative Köppen signatures (based on GBIF data; see main-text) and mapping quantitative and qualitative characters in a probabilistic framework (Potts &amb; Grimm, 2017). Please give the appropriate credit when using the R scripts.
  
  
• Khanum et al., Taxon, 65: 467–486 (2016). This ZIP archive (40MB) includes supplement files S1 and S2, supplementary figures (S1–S3), and all data (genetic matrices) and analysis (ML using RAxML, BI using MrBayes) files.
  Disclaimer: This is a mirror of the archive submitted with the (1st) revised version of the paper, check the finally accepted version of the paper for the reference to the actual final OSA.
  
  
  
• Mendes et al., Grana, 53: 283–301 (2014). This ZIP archive (1.5MB) includes supplement files S1–S3, as well as utilised morphological and genetic matrices and the result files of the ML tree inference and bootstrapping.
  
  
• Schliep et al., Meth. Ecol. Evol., TBA000–000 (2017). This ZIP archive (10MB) includes the primary analysis files (RAxML in- and output files) for the bear data set by Kutschera et al. (2014) used as example in the study (Y-chromosome data, mitochondrial data, comprehensive and species-consensus autosomal intron data, the latter analysed using the ML-A and ML-I, see Potts et al. 2014).
  
  
• Simeone et al., PeerJ, 4:e1897 (2016). This ZIP archive (32MB) includes the supplement files S1–S3, the genetic matrix used in the study, the RAxML and GARLI analysis files, and raw pairwise distance spread sheets illustrating general levels of divergence in the used plastid regions in Fagales in comparison to the oaks.
  
  
• Surveswaran et al., Bot. J. Linn. Soc., 174:601–619 (2014). This ZIP archive (19MB) includes the genetic matrices used in the study, and all RAxML, GARLI, MrBayes input and output files.
  
  
• Stamatakis et al., Evol. Bioinform., 6:73–90 (2010). This ZIP archive (1.6MB) includes all files for analysis.
  
  
• Wanntorp et al., Taxon, 63: 89–102 (2014). This ZIP archive (1.6MB) includes several files with supplementary information (mirrored from the journal's homepage) and the result files of the ML analyses performed with RAxML (tree-inference and nonparametric bootstrapping).