A total-evidence approach to dating with fossils, applied to the early radiation of the Hymenoptera

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A hymenopterists' guide to the hymenoptera anatomy ontology: utility, clarification, and future directions

Hymenoptera exhibit an incredible diversity of phenotypes, the result of ~240 million years of evolution and the primary subject of more than 250 years of research. Here we describe the history, development, and utility of the Hymenoptera Anatomy Ontology (HAO) and its associated applications. These resourc¬es are designed to facilitate accessible and extensible research on hymenopteran phenotypes. Outreach with the hymenopterist community is of utmost importance to the HAO project, and this paper is a direct response to questions that arose from project workshops. In a concerted attempt to surmount barriers of understanding, especially regarding the format, utility, and development of the HAO, we discuss the roles of homology, “preferred terms”, and “structural equivalency”. We also outline the use of Universal Resource Identifiers (URIs) and posit that they are a key element necessary for increasing the objectivity and repeatability of science that references hymenopteran anatomy. Pragmatically, we detail a mechanism (the “URI table”) by which authors can use URIs to link their published text to the HAO, and we describe an associated tool (the “Analyzer”) to derive these tables. These tools, and others, are available through the HAO Portal website (http://portal.hymao.org). We conclude by discussing the future of the HAO with respect to digital publication, cross-taxon ontology alignment, the advent of semantic phenotypes, and community-based curation.Katja C. Seltmann... Andrew D. Austin... John T. Jennings... et al

Supplementary Figure 1. Morphological versus molecular branch lengths

Figure showing the molecules-only and morphology-only trees, as well as the correlation between morphological and molecular branch lengths

Data from: A total-evidence approach to dating with fossils, applied to the early radiation of the Hymenoptera

Phylogenies are usually dated by calibrating interior nodes against the fossil record. This relies on indirect methods that, in the worst case, misrepresent the fossil information. Here, we contrast such node dating with an approach that includes fossils along with the extant taxa in a Bayesian total-evidence analysis. As a test case, we focus on the early radiation of the Hymenoptera, mostly documented by poorly preserved impression fossils that are difficult to place phylogenetically. Specifically, we compare node dating using nine calibration points derived from the fossil record with total-evidence dating based on 343 morphological characters scored for 45 fossil (4–20% complete) and 68 extant taxa. In both cases we use molecular data from seven markers (about 5 kb) for the extant taxa. Because it is difficult to model speciation, extinction, sampling, and fossil preservation realistically, we develop a simple uniform prior for clock trees with fossils, and we use relaxed clock models to accommodate rate variation across the tree. Despite considerable uncertainty in the placement of most fossils, we find that they contribute significantly to the estimation of divergence times in the total-evidence analysis. In particular, the posterior distributions on divergence times are less sensitive to prior assumptions and tend to be more precise than in node dating. The total-evidence analysis also shows that four of the seven Hymenoptera calibration points used in node dating are likely to be based on erroneous or doubtful assumptions about the fossil placement. With respect to the early radiation of Hymenoptera, our results suggest that the crown group dates back to the Carboniferous, approximately 309 Ma (95% interval: 291–347 Ma), and diversified into major extant lineages much earlier than previously thought, well before the Triassic

MrBayes_Commands_New

MrBayes commands needed to run the analyses described in the paper

Supplementary Figure 2. Effect of removing the least complete fossils

Supplementary Figure 2. Divergence time estimates from total-evidence analyses based on all data (45 fossils; tree and 95% highest posterior density (HPD) interval bars in red) or only the fossils with more than 10% of the 343 morphological characters scored (31 fossils; green bars). While the topology is the same and the median age estimates are similar, the HPD intervals are in general wider when the most poorly preserved fossils are excluded

R-Scripts_PriorFitting-RelaxedClockModels_New

R scripts used to find appropriate relaxed-clock prior parameters

Appendix-1_MorphoCharacterDescriptions

Appendix 1. Morphological character descriptions