1 Phylogenetic dataset

Analysis was performed on a new matrix of 54 lophotrochozoan taxa, coded for 225 morphological characters (129 neomorphic, 96 transformational). The matrix can be viewed interactively at Morphobank project 2800; 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. (2018):

  • 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 4975 character codings, plus 1133 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 6042). Of the 225 characters, the number that were coded with an applicable token for each taxon is:

Acanthotretella spinosa 70 Gasconsia 70 Novocrania 186
Alisina 84 Glyptoria 73 Orthis 70
Amathia 157 Halkieria evangelista 65 Paramicrocornus 57
Antigonambonites planus 85 Haplophrentis carinatus 82 Paterimitra 67
Askepasma toddense 78 Heliomedusa orienta 67 Pauxillites 56
Bactrotheca 53 Kutorgina chengjiangensis 84 Pedunculotheca diania 63
Botsfordia 75 Lingula 205 Pelagodiscus atlanticus 166
Clupeafumosus socialis 76 Lingulellotreta malongensis 87 Phoronis 169
Conotheca 60 Lingulosacculus 60 Salanygolina 79
Coolinia pecten 80 Longtancunella chengjiangensis 61 Serpula 170
Cotyledion tylodes 65 Loxosomella 164 Siphonobolus priscus 74
Craniops 66 Maxilites 61 Sipunculus 168
Cupitheca holocyclata 63 Mickwitzia muralensis 72 Terebratulina 184
Dailyatia 55 Micrina 71 Tomteluva perturbata 58
Dentalium 169 Micromitra 81 Tonicella 188
Eccentrotheca 54 Mummpikia nuda 55 Ussunia 53
Eoobolus 81 Namacalathus 59 Wiwaxia corrugata 75
Flustra 168 Nisusia sulcata 80 Yuganotheca elegans 56

References

Brazeau, M. D., Guillerme, T., & Smith, M. R. (2018). An algorithm for morphological phylogenetic analysis with inapplicable data. Systematic Biology. doi:10.1101/209775

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

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