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 tokens1
,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