DOI: 10.5061/dryad.gb5mkkx03
title: Data from: Practical guide and review of fossil tip-dating in phylogenetics

description: Phylogenetic tip-dating has been and still is revolutionizing evolutionary
 biology in several ways. Tip-dating, where fossils are placed into a
 phylogeny as tips based on molecular and/or morphological character
 information, provides a more principled approach to infer time-calibrated
 phylogenies compared with node-dating. Additionally, phylogenetic trees
 with fossils as tips become more and more important to elucidate
 evolutionary processes in macroevolutionary studies, e.g., deciphering
 diversification patterns and directional phenotypic evolution. Tip-dating
 is slowly gathering popularity in empirical applications and has
 progressed substantially since its first demonstration in 2011, with
 respect to improved statistical models, software, and datasets.
 Nevertheless, executing a phylogenetic tip-dating analysis is complicated
 and comes with many challenges. Here, we provide an extensive review and
 overview of methods and models for phylogenetic tip-dating analyses. We
 focus both on data collection and preparation as well as on modeling
 choices. We start with a survey of all published phylogenetic tip-dating
 studies to date, showing common data and modeling choices as well as
 trends towards new approaches. Then, we walk readers through sections of
 molecular evolution, morphological evolution (both for discrete and
 continuous data), and lineage evolution (the fossilized-birth-death
 process). In each section, we describe the data and standard models with
 their underlying assumptions, and provide an outlook and practical
 recommendations.
description: We conducted a literature survey in order to gather information
 about tip-dating analyses on empirical datasets. We used Google Scholar to
 look at all publications citing a selection of foundational tip-dating
 studies, and among those, we identified publications performing tip-dating
 analyses on empirical datasets. We compiled relevant
 information---including software of choice, dataset size, types of data
 used, and clock and tree models employed. When it was possible, this
 information was extracted directly from data and script files provided as
 supplementary material of each publication; otherwise, we used the
 information written in the methodological sections of the main and
 supplementary texts. <br> While we originally
 included tip-dating studies without morphological data in which either the
 whole topology was fixed or topological constraints were applied to
 extinct taxa, we pruned those studies from our survey before downstream
 analyses for summary figures and statistics. This is because we wanted to
 focus on studies that use tip-dating as an analytical approach to
 co-estimate the topological position of extinct taxa with divergence
 times, rather than just estimating divergence times on an a priori fixed
 topology, or pruning extinct tips afterwards to obtain a dated
 phylogenetic tree of only extant species.
description: # Data from: Practical guide and review of fossil tip-dating in
 phylogenetics
 [https://doi.org/10.5061/dryad.gb5mkkx03](https://doi.org/10.5061/dryad.gb5mkkx03) # Description of the data and file structure ## `Supplementary_Table_S1.xlsx` This file contains a literature survey of all the tip-dating studies to date. Additional information about scoring for missing (`?`) and not applicable (`NA`) entries are explained below. The spreadsheet contains 35 columns which are as follows: 1. Publication Name [author*s (year)]" - The title of the publication. 2. Publication Link - Online link to the publication in the publisher's website. 3. Journal - The journal where the paper is published. 4. Year - Published year 5. Software - Software used for the tip-dating study. 6. Kingdom - Kingdom of taxa under study. 7. Category - Category of organisms under study. E.g., Amphibians, Mammals, Reptiles etc. 8. Focal taxon - Specific taxon under study. 9. NTaxa (total) - Total number of taxa in the study. 10. NTaxa (morpho) - Number of taxa with morphological character data. 11. NTaxa (mol) - Number of taxa with molecular sequence data. 12. NTaxa (mol+morph overlap) - Number of taxa with both molecular sequence data and morphological character data. 13. NTaxa (fossil) - Number of fossils included in the study. 14. N. morphological characters - Number of morphological characters in the morphological data matrix. 15. Percent missing morpho - Percentage of missing or not applicable morphological characters in taxa with morphological data. 16. Max N. of morphological character states - Number of maximal value for morphological character state 17. Continuous characters? - Usage of continuous characters in the study 18. Morpho substitution model - Use of morphological substitution model in the study 19. Ordered morpho characters? - Use of ordered characters in modeling morphological evolution. 20. Morpho state frequencies - Whether the state frequencies were estimated or set as equal. 21. Morpho partition - Partitioning approach for the morphological data 22. Morpho branch lengths across partitions - Linked vs unlinked partitions; applicable only to partitioned datasets. 23. N. molecular characters - Length of molecular sequence used in the study. 24. N. molecular partitions - Number of subsets of molecular data used. 25. Molecular data type - Type of molecular data used (DNA or Amino Acid) 26. Molecular branch lengths across partitions - Linked vs unlinked; applicable only to partitioned datasets 27. Tree prior - Type of tree prior distribution was used in the study. 28. Molecular clock model - Clock model applied to molecular data 29. Morphological clock model - Clock model applied to morphological data 30. Clock partitions - Is every data subset modeled with its own clock? 31. Sampled ancestors? - Allowance of sampled ancestors. 32. Fossil tip age prior - What prior is specified for the fossil tip. 33. Topological constraints - Use of topological constrains in the analyses. 34. Root age prior - What prior is specified for the root age. 35. Additional age constraints - Use of additional node calibrations ### Not Applicable (NA) Columns related to molecular data (e.g., N. molecular characters, Molecular clock model) will be empty for studies that used only morphological data. Columns related to data partitioning (e.g., Morpho branch lengths across partitions) will be empty if the study did not partition its data. The Morphological clock model column will be empty if the study did not include morphological data in the clock model analysis. ### Not Available ? In general, '?' in a cell means that the information could not be retrieved from the study. For example, a cell in the `Percent missing morpho` column might be empty because, although the study used a morphological matrix, the authors did not report the percentage of missing data. Similarly, a cell in the `Root age prior` column might be empty if the authors did not explicitly state the prior used for the root age. In all cases, a blank cell means the information could not be coded from the source publication, and users of this dataset should treat it as a missing value (NA) in their analyses. A value of zero (0) is used only when it is an explicitly reported quantity (e.g., zero fossil taxa). ## Software/Code N/A