1 Phylogenetic dataset

Analysis was performed on a new matrix of 48 lophotrochozoan taxa, coded for 354 morphological characters (220 neomorphic, 134 transformational). The matrix can be viewed interactively at Morphobank project 3262; a static version can be downloaded directly in Nexus or TNT format.

Taxa include sipunculans and molluscs, which have previously been interpreted as having affinities with hyoliths. Other lophotrochozoan groups help to constrain the outgroup topology, and a diversity of brachiozoans helps to resolve the position of hyoliths within this group.

Characters are coded following the recommendations of Brazeau et al. (2019):

  • We have employed reductive coding (Wilkinson, 1995), using a distinct state to mark character inapplicability. Character specifications follow the structural syntax of Sereno (2007) in order to highlight ontological dependence between characters and emphasize the structure of the dataset.

  • We have distinguished between neomorphic and transformational characters (sensu Sereno, 2007) by reserving the token 0 to refer to the absence of a neomorphic (i.e. presence/absence) character. The states of transformational characters (i.e. characters that describe a property of a feature) are represented by the tokens 1, 2, 3, …

  • We code the absence of neomorphic ontologically dependent characters (sensu Vogt, 2018) as absence, rather than inapplicability.

The complete dataset comprises 6774 character codings, plus 2240 inapplicable codings. (The amount and quality of data that is coded is more instructive than the number of cells that are ambiguous (Wiens, 1998, 2003), which, for completeness, is 7978). Of the 354 characters, the number that were coded with an applicable token for each taxon is:

Acaenoplax hayae 106 Heliomedusa orienta 82 Paterimitra 88
Calvapilosa kroegeri 94 Kulindroplax perissokomos 107 Pedunculotheca diania 72
Canadia spinosa 111 Leptochiton 228 Pelagiella 87
Capitella 223 Lingula 263 Pelagodiscus atlanticus 210
Chaetoderma 219 Loxosomella 217 Phoronis 250
Conocardium elongatum 85 Mickwitzia muralensis 78 Phthipodochiton thraivensis 79
Cotyledion tylodes 79 Micrina 76 Pojetaia runnegari 88
Dailyatia 71 Micromitra 86 Polysacos vickersianum 76
Dentalium 234 Mopalia 226 Serpula 227
Eccentrotheca 61 Mytilus 210 Siphogonuchites multa 46
Flustra 217 Namacalathus 76 Sipunculus 259
Gasconsia 76 Neopilina 192 Terebratulina 238
Glaphurochiton carbonarius 77 Novocrania 247 Tonicella 265
Haliotis 256 Odontogriphus omalus 95 Wirenia 193
Halkieria evangelista 80 Orthis 76 Wiwaxia corrugata 109
Haplophrentis carinatus 102 Orthrozanclus 81 Yilingia spiciformis 56

References

Brazeau, M. D., Guillerme, T., & Smith, M. R. (2019). An algorithm for morphological phylogenetic analysis with inapplicable data. Systematic Biology, online ahead of print. doi: 10.1093/sysbio/syy083

Sereno, P. C. (2007). Logical basis for morphological characters in phylogenetics. Cladistics, 23(6), 565–587. doi: 10.1111/j.1096-0031.2007.00161.x

Vogt, L. (2018). The logical basis for coding ontologically dependent characters. Cladistics, 34(4), 438–458. doi: 10.1111/cla.12209

Wiens, J. J. (1998). Does adding characters with missing data increase or decrease phylogenetic accuracy? Systematic Biology, 47(4), 625–640. doi: 10.1080/106351598260635

Wiens, J. J. (2003). Missing data, incomplete taxa, and phylogenetic accuracy. Systematic Biology, 52(4), 528–538. doi: 10.1080/10635150390218330

Wilkinson, M. (1995). Coping with abundant missing entries in phylogenetic inference using parsimony. Systematic Biology, 44(4), 501–514. doi: 10.1093/sysbio/44.4.501