*Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, P. O. Box 643, Beijing 100044, China
†Department of Evolutionary Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18A, SE-752 36 Uppsala, Sweden
Supplementary Methods I, Phylogenetic analysis. We performed the analysis using the software package PAUP3.1 with the data matrix of ref. 11 which scored 29 taxa for 99 morphological
characters. Based on additional materials or new examination, Kenichthys was complemented with 31 additional morphological characters coded (in bold below). Character 39 is re-coded for 9 genera. We used the same algorithms as in ref. 11, i.e. most parsimonious trees were identified using the heuristic search algorithm, stepwise addition, with 500 random iterations. All characters were weighted equally. Characters 15, 20, 25, 32 and 80 were ordered, and all other characters were unordered. Note that Characters 23 and 70 (ordered in ref. 11, of two-state in the data matrix) were unordered. The analysis yielded 18 most parsimonious trees showing the same major groupings (except the resolution of three megalichthyids) as ref. 11. For the purpose of the comparison, we also performed the analysis with all characters unordered, that yielded 12 most parsimonious trees. Two consensus trees only differed in the resolution of Youngolepis as the sister group of Diabolepis + Dipterus. Kenichthys always appeared as the most basal tetrapodomorph.
II, Character list of ref.11with new codings for Kenichthys in bold. Characters 7 and 98 are redefined (in italics).
1 Parasymphysial plate: 0 - long, sutured to coronoid, denticulated or with tooth row; 1 - short, not sutured to coronid, denticulated; 2 - carrying tooth whorl (unordered).
2 Splenial: 0 - not sutured to prearticular; 1 - sutured to prearticular.
3 Anterior end of prearticular: 0 - not forked; 1 - forked.
4 Prearticular and angular: 0 - separated by ventral exposure of Meckelian bone; 1 - in contact.
5 Prearticular: 0 - rear part with conspicuous horizontal ledge; 1 - rear part flat.
Glyptolepis 01010 0010
IV, Consensus of 18 most parsimonious trees based on the data matrix of ref.11 with complementary codings for Kenichthys and the redefinition of Characters 7 and 98. Character 39 is re-coded for 9 genera. Bremer support values are shown at nodes. Tree length, 194 steps; Consistency index (CI), 0.572; Homoplasy index (HI), 0.428; CI excluding uninformative characters, 0.556; HI excluding uninformative characters, 0.444; Retention index (RI), 0.778; Rescaled consistency index (RC), 0.445.