A Phylogenetic Appraisal of Pachycormus Bollensis

Självständigt arbete Nr 31 A Phylogenetic Appraisal of Pachycormus bollensis: Implications for Pachycormiform Evolution A Phylogenetic Appraisal of Maria Lindkvist Pachycormus bollensis: Implications for The Pachycormiformes were a successful group of stem-teleosts. Although they persisted for more than 100 million years in the Pachycormiform Evolution Mesozoic seas and occupied a significant space of the ecosystem, little is known about this most diverse group. One of the earliest pachycormiformes is the lower Jurassic Pachycormus bollensis. A reconstruction of the phylogeny with the early P. bollensis together with more derived and earlier studied species has yielded important information about the relationships within the group. Both a parsimony analysis and a Bayesian analysis were performed. Three Maria Lindkvist exceptionally complete specimens of P. bollensis from the Holzmaden-locality were used for the study. The resulting trees strongly supported pachycormiform monophyly. Three major ecomorphological clades were returned from the analyses: the filter- feeders, hyper carnivores and a more generalist predator radiation that included P. bollensis. Despite, node support within the pachycormiformes are generally weak. The tooth-structure and the phylogenetic position of P. bollensis might indicate an intermediate grade between the filter-feeders and the hyper carnivores.

Uppsala universitet, Institutionen för geovetenskaper Kandidatexamen i Geovetenskap, 180 hp Självständigt arbete i geovetenskap, 15 hp Tryckt hos Institutionen för geovetenskaper Geotryckeriet, Uppsala universitet, Uppsala, 2012. Självständigt arbete Nr 31

A Phylogenetic Appraisal of Pachycormus bollensis: Implications for Pachycormiform Evolution

Maria Lindkvist

Supervisor: Benjamin Kear Abstract

The Pachycormiformes were a successful group of stem-teleosts. Although they persisted for more than 100 million years in the Mesozoic seas and occupied a significant space of the ecosystem, little is known about this most diverse group. One of the earliest pachycormiformes is the lower Jurassic Pachycormus bollensis.

A reconstruction of the phylogeny with the early P. bollensis together with more derived and earlier studied species has yielded important information about the relationships within the group. Both a parsimony analysis and a Bayesian analysis were performed. Three exceptionally complete specimens of P. bollensis from the Holzmaden-locality were used for the study. The resulting trees strongly supported pachycormiform monophyly. Three major ecomorphological clades were returned from the analyses: the filter-feeders, hyper carnivores and a more generalist predator radiation that included P. bollensis. Despite, node support within the pachycormiformes are generally weak. The tooth-structure and the phylogenetic position of P. bollensis might indicate an intermediate grade between the filter-feeders and the hyper carnivores.

Sammanfattning

Pachycormiformer var en mycket framgångsrik ordning utav stam-teleoster. Trots att de överlevde i mer än 100 miljoner år i de Mesosoiska haven och erövrat ett flertal olika platser i ekosystemet, är denna mågfacetterade grupp som helhet tämligen okänd. Pachycormus bollensis från yngre jura är en av de tidigste arterna i denna grupp.

En fylogenetiskt rekonstruktion av den tidiga P. bollensis tillsammans med yngre, mer utvecklade arter kan ge viktig information om släktskapen inom gruppen. En parsimonisk analys och en Bayesian analys utfördes. Tre exceptionellt bevarade exemplar av Pachycormus bollensis från Holzmaden användes i studien. Resultatet visar på ett stark monofyletiskt sammanband inom pachycormiformerna. Båda analyserna visade robusta resultat för tre övergripande grupper; filtrerare, karnivorer och en mer generell predator linje som inkluderar P. bollensis. Dock hade de interna släktskapen inom varje större grupp svagt stöd. Tand-stukturen tillsammans med den fylogenetiska placeringen av P. bollensis kan tyda på en intermediär grupp mellan filterarna och karnivorerna.

Table of Contents 1. Introduction ...... 5 1.1 The Pachycormiformes ...... 5 1.2 Geology of Holzmaden – the Posidonia Shale ...... 6 2. Materials and methods ...... 7 2.1 Phylogenetic methods ...... 7 2.2 The parsimony analysis ...... 7 2.3 The Bayesian analysis ...... 8 2.4 Source specimens ...... 9 3. Results and discussion ...... 10 3.1 Parsimony analysis ...... 10 3.1.1 Nodal support ...... 10 3.1.2 Character evolution ...... 11 3.2 Bayesian analysis ...... 14 3.3 Discussion of Matt Friedman et al. (2010) ...... 15 4. Conclusions ...... 17 5. Acknowledgement ...... 17 6. References ...... 18 6.1 Printed sources ...... 18 6.2 Internet sources ...... 19 Appendix I ...... 20 Appendix II ...... 29 Appendix III ...... 34 Appendix IV ...... 39 Appendix V ...... 41

1. Introduction

1.1 The Pachycormiformes Despite being a versatile, long-lived and successful clade of stem-teleosts, the pachycormiformes are an extremely poorly known group of bony fishes. Friedman et al. (2010) published a review and comprehensive phylogenetic data set, hypothesising a 100 million year range for the lineage and an important eco-system adaptation.

Within in the pachycormiformes a wide range of different life habits are represented; hyper carnivores with enlarged fangs (e.g. Australopachycormus; Kear, 2007) and toothless filter-feeders (e.g. Bonnerichthys; Friedman, et al, 2010). Filter-feeders had and still have the ability to sometimes reach significant sizes, like the modern whale shark but the (at least) 9 meter long Leedsichthys, a filter-feeding pachycormid was possibly the largest bony fish of all time (Friedman, et al. 2010).

A well-documented fossil-record supports the existence of the pachycormiformes from the lower Jurassic (the Toarcian, 183-167 Myr) to the end of the Cretaceous (65 Myr) (Friedman, et al. 2010). The group is considered to be monophyletic and can be diagnosed by some very distinctive characters: large scythe-formed pectoral fin (figure 1); a rostrodermethmoid (figure 2), which is an anterodorsal tooth-bearing bone; the absence of supraorbitals with the dermosphenotic in the dorsal part of the orbital margin; two plate-like supraorbital bones and the absence of extrascapulars (bones carrying a sensory canal) (Arratia, 2004, Kear, 2007 and Stiassny et. al. 1996).

Figure 1: The scythe-formed pectoral fin of a Figure 2: The arrow is pointing at the Pachycormus bollensis rostrodermethmoid

1.2 Geology of Holzmaden – the Posidonia Shale Three specimens of Pachycormus bollensis, all with the same origin, have been studied for this project. They come from the famous locality of Holzmaden in the Württemberg-Baden-region, near Stuttgart, in southern Germany. The Posidonia shale (or Lower Toarcian black shale, ε) has been of considerable scientific interest for over a century (Röhl et al., 2001). The extremely high preservation-rate has made this locality extremely famous for assessing the palaeoecology and palaeobiology marine-faunas from the Toarcian age (183-176 Myr).

It is the exceptional preservation of vertebrate fossils, which has made this Lagerstätte so important. Thousands of marine reptiles and fishes have been found, sometimes with their soft tissues preserved (Etter & Tang, 2002). Ichthyosaurs in particular, have even been found with traces of skin and gut-contents (Etter & Tang, 2002). The rich marine fossil fauna also contains fishes, both Osteichthyes (bony fishes) and cartilaginous-fishes, crinoids, bivalves, other marine reptiles, like crocodiles and plesiosaurus and cephalopods such as ammonites and belemnites (Hauff, 1953).

The lithology, in general, consists of four components; carbonates (derived mostly from phytoplankton), siliciclastics, pyrite, and organic matter (Röhl et al., 2000). The lower Toarcian has three facies represented. A lower-most mudstone sequence with light-coloured marl covers nearly the whole Tenuicostatum zone (lower part of lower Toarcian) (Röhl, et al., 2001). The Total Organic Carbon (TOC) from this unit is low (below 1%) (Röhl et al., 2001). Intense bioturbation also indicates a substantial benthic-fauna. The next successional facies is a bituminous mudstone with some unclear lamination (Röhl, et al., 2001). This is overlain by microlaminated oil shale, deposited during the lower and middle Falciferum zone (Schmid-Röhl et al., 2002). The TOC is between 10% and 16 % and the benthic fauna is almost absent (Schmid-Röhl et al., 2002).

The exceptional fossil preservation had been linked to specific palaeoevironmental-conditions. The traditional model was introduced by Pompeckj in 1901 and is called “the stagnant basin model”. Several scientists have embraced this hypothesis and developed it through time. The premise suggests a stagnant water column with anoxic bottom water which restricted the range of bottom living organisms (Röhl et al., 2001). This is evidenced by clear lamina-preservation, lack of bioturbation, predominantly pelagic fauna and the high TOC amount (Etter & Tang, 2002). However, the presence of benthic faunal elements (including crustaceans, bivalves, gastropods and echinoderms) suggest that the bottom waters were not uniformly anoxic (Etter & Tang, 2002). Thus Kauffman’s “benthic island model” has subsequently been proposed which suggests normal oxygenation above the sediment-water interface, with subsurface anoxia below this boundary (Etter & Tang, 2002). Anoxic water was trapped under a mat of algae and fungi. The well oxygenated conditions above this redox-boundary favoured colonization by benthic organisms upon any raised surface (such as sunken ammonite shells) to create the so called “benthic islands” (Röhl et al., 2001). Storm-generated currents occasionally destroyed the algal mat and released the trapped anoxic bottom water to create periods of anoxia for the colonies (Röhl et al., 2001 and Etter & Tang, 2002).

Schmid-Röhl et al. (2002) conducted a multidisciplinary investigation (including sedimentology, palaeoecology and geochemistry) of the Posidonia Shale. Their study revealed that sea level changes and palaeoclimate where the main controlling factors for deposition.

Fluctuations of sea level made it possible for the water to oxygenate during high stand and created stagnant-basin conditions during low stands; this would have conversely favoured or disadvantaged the benthic fauna respectively (Schmid-Röhl et al., 2002).

2. Materials and methods

2.1 Phylogenetic methods Friedman et al. (2010) used a parsimony-based phylogenetic analysis to obtain their trees. Their data set and parameters were also utilised for this study, but an alternative Bayesian assessment of tree structure was also employed.

The parsimony method of tree construction selects for hypotheses with the least number of steps required to explain a certain character-distribution. Different character optimizations can be used to evaluate alternative character reconstructions within cladograms of the same value (Agnarsson & Miller, 2008). The most common used optimization algorithms are accelerated transformation (ACCTRAN) and delayed transformation (DELTRAN). The ACCTRAN-criteria forces the transformations toward the root of the tree while DELTRAN forces the transformations towards the branches (Agnarsson & Miller, 2008) ACCTRAN is the default setting of most software used in phylogenetic studies. Nonetheless, both ACCTRAN and DELTRAN were applied for the optimization in this study.

Different methods are available to estimate statistical support for character changes at individual nodes. Bremer decay and bootstrap analysis are two of the most common methods. The Bremer decay (or Decay Index) assesses node stability indicating how many additional steps are necessary before a particular node collapses?” (Forey, 2008). A high Decay Index or high number of steps indicates strong support for that individual node.

Bootstrapping is a statistical method where the data matrix for the remaining characters is duplicated to its original size, and both the original analysis and the groupings are iterated a certain number of times (Forey, 2008). The result is a majority-rule consensus tree with bootstrap-values at the nodes. A bootstrap-value of 100 indicates a very well supported node, a node with 70 is acceptable supported and nodes with 50 or below rejected, as not reliable (Hills & James, 1993).

The concept of a Bayesian analysis is based on a quantity called the posterior probability distribution of trees (Walsh, 2002). In a Bayesian analysis, a Markov Chain Monte Carlo (MCMC) method is used. One tree is generated as a starting tree, and then a new, altered tree is produced. The likelihood of the two trees is compared. If the InL (InLikelihood) is higher for the altered tree than for the starting tree, the altered tree will be kept and used as the starting tree in the next run. If the InL is lower for the altered tree, a random number between 0 and 1 is picked and if the difference between the InL’s for the starting tree and the altered tree is higher than the random picked number, the altered tree will be set as the new starting tree. If the difference is lower than the random number, the initial starting tree will be kept (Budd, 2012). This described loop will be repeated between 5 and 10 million times.

2.2 The parsimony analysis Parsimony analyses were conducted using PAUP* 4.0b10. The Friedman et al. (2010) data matrix, comprising 93 characters (Appendix I) and 26 taxa, (Appendix II) was treated as the phylogenetic

7 framework for scoring. 39 characters from the Pachycormus bollensis specimens were able to score. A branch-and-bound search option was chosen for the bootstrap-analysis. Pteronisculus (a stem- neopterygian living during the Triassic) (Friedman, et al., 2010) was set as outgroup. Both Delayed transformation (DELTRAN) and Accelerated transformation (ACCTRAN) were applied as alternative character optimizations.

2.3 The Bayesian analysis Bayesian estimation was undertaken with MrBayes 3.1. To test for the effects of missing data from incomplete fossils, three sets analyses were run: all taxa included; deletion of taxa missing more than 50% of their data; and deletion of taxa missing more than 60% of their data.

The parameters for the Bayesian analyses were as follows.

 Seed=1001 The random number of seed is generated in the beginning of every new MrBayes session. If the “seed”-parameter is set to a specific number, an exact repetition of the analysis is possible.

 Ngen=10 000 000 Ngen gives the number of generated MCMC algorithm cycles.

 Nruns=2 2 independent analyses were started simultaneously.

 Nchains=4 4 is default for number of chains run for the MCMCMC variant, this means 1 cold chain and 3 heated chains.

 Diagnfreq=1000 1000 generations between the calculations of the MCMC diagnostic will be printed to file. MCMC diagnostics include acceptance ratio of moves and swaps and convergence diagnostics for the tree topology.

 Samplefreq=1000 The Markov chain was sampled with a frequency of 1000.

 prset ratepr=variable The site specific rates model is specified to vary across the partitions. But the average rate of the substitutions across the partitions is 1.

All information about the specific parameters (except “prset ratepr”) was taken from Bates, (http://mrbayes.sourceforge.net/Help/mcmc.html, 2012-06-06).

Information about parameter “prset ratepr” was taken from Bates, (http://mrbayes.sourceforge.net/Help/prset.html, 2012-06-06).

2.4 Source specimens Three specimens of Pachycormus bollensis (PMU 24796, PMU 24797 and PMU 24798) from the Holzmaden-locality were studied at the Museum of Evolution at Uppsala University. These skeletons were all exposed in a lateral view with some dorsal and ventral structures also visible. Sizes of the individuals ranged between 400 millimetres to 850 millimetres (figures 3-5). The smallest individual (PMU 24798) might represent a juvenile.

Figure 3: The largest specimen is 85 centimeters and exposed in a right-lateral view (PMU 24796 ). Figure 4: The middle-size specimen is exposed in a left-lateral view (PMU 24797 ). Figure 5: The smallest specimen is 40 centimeters and exposed in a right-lateralventral view (PMU 24798 ).

3. Results and discussion

3.1 Parsimony analysis The strict consensus tree from the parsimony analysis is shown in figure 6. All other generated trees are presented in Appendix III, figures A1-A4. The general distribution of the taxa was consistent in all generated trees. The division of three subgroups within the pachycormiformes were distinct. The subgroups are marked in blue, green and yellow in the strict consensus tree (figure 6). The blue group represents the Pachycormus-species, the green group includes the hyper carnivores and the yellow group contains the filer-feeders. The three subgroups represent the pachycormiformes. The interesting nodes are encircled and will be discussed further (see below).

Figure 6: The generated strict consensus tree from the parsimony analysis. The distinct subgroups are marked with colours; blue (pachycormus-species), green (filter-feeders) and yellow (hyper carnivores). Marked nodes are discussed in the text.

3.1.1 Nodal support The bootstrap analysis was performed on a 50% majority-rule consensus tree (see figure A2 in Appendix III for the complete tree). The nodal support analysis gave a high robustness for the node that represents the pachycormiformes (figure 6, node 1). Node 1 (figure 6) is supported to 95%, this strongly supports the pachycormiformes to be a monophyletic group. Node 2 (figure 6) is strong supported to 88%; this node represents two of the most derived hyper carnivores, the sword-fish like Protosphyraena spp and Australopachycormus hurleyi. The other nodes within the hyper carnivores (green group, figure 6) have bootstrap values between 55-61%, these are acceptable values but not considered high supported. The interrelationships should be interpreted with carefulness. The node representing the filter-feeder (node 3, figure 6) shows a robustness of 76%. The value of 76% is acceptable to sate the node as supported enough to enable further interpretation. The group of filter-feeders show no resolution (see figure 6 and figure A2 in Appendix III) and no interpretation

10 can be done. The conclusion of the bootstrap analysis is that the interrelationships of the pachycormiformes are weak supported except in special cases.

3.1.2 Character evolution Both ACCTRAN and DELTRAN were used as character optimization. The two trees generated are presented in Appendix III (figures A3 and A4) together with the specific character changes (Appendix IV and V). The specific character changes are explained by Appendix I. Simplified versions of the two generated trees are found below (figure 7). The character evolution-discussion will be based on these trees.

Figure 7: The simplified trees generated from the two character evolution analyses. 7a shows the tree from the analysis with ACCTRAN set as character optimization and 7b shows the DELTRAN equivalent. Notice the difference in sister-group relationships. The numbers indicate nodes that are explained in the text.

The specific character changes for both ACCTRAN and DELTRAN are listed below:

 Node 1 -> 2 (Figure 7a and 7b):  The ossified vertebrae disappear (ACCTARN, DELTRAN)  The lateral keels of caudal peduncle occur (ACCTRAN, DELTRAN)  The pelvic fin disappear (ACCTRAN)  The vagal foramen moves from the anterior of the exoccipital to be a lateral outgrowth of the from the intercalar (DELTRAN)  The anterior myodome disappear (DELTRAN)

 The infraorbitals behind the orbit increased in number to more than six (DELTRAN)  The midline contact of the premaxilla changes from present to absent (DELTRAN)  The pectoral-fin changes in radial morphology from cylindrical to paddle-shape (DELTRAN)

 Node 2 -> 3 (Figure 7a):  The posterior boss on the skull roof appears (ACCTRAN)

 Node 3 -> 4 (Figure 7a):  The supramaxilla changes the position from posterodorsal to dorsal to maxilla (ACCTRAN)  The relative position of the dorsal and anal fins has changes from an overlap in the fin bases to an anterior placement of the dorsal-fin base relative to the anal-fin base (ACCTRAN)

 Node 2 -> 3 (Figure 7b):  The pelvic fin disappear (DELTRAN)

 Node 3 -> 4 (Figure 7b):  The relative position of the dorsal and anal fins has changes from an overlap in the fin bases to an anterior placement of the dorsal-fin base relative to the anal-fin base (DELTRAN)

 Node 4 -> Pachycormus spp (Figure 7a and 7b):  The segmentation of the pectoral-fin rays disappear (ACCTRAN, DELTRAN)  The posterior boss on the skull roof appears (DELTRAN)

 Node 4 -> Pachycormus bollensis (Figure 7a and 7b):  The uppermost hypaxial-caudal rays changes from a dorsal-ventral fin-ray base symmetry to be successively shorter from bottom to top (ACCTRAN, DELTRAN)

Some character changes occur at the same (or comparable) position in the trees for both ACCTRAN and DELTRAN (for example the disappearance of the ossified vertebrae in node 1 -> 2 and the disappearance of the pectoral-fin segmentation in node 4 -> Pachycormus spp). Some character changes appear in both ACCTRAN and DELTRAN but have different positions on the trees. For example the pelvic fin. In DELTRAN, the pelvic fin disappears when the hyper carnivores form an own branch and the filter-feeders and Pachycormus species one other. In ACCTRAN the disappearance of the pelvic fin is positioned in the branching of the Euthynotus spp and the pachycormiformes. Because the hyper carnivores in general have a pelvic fin, it reappears in the branching of the hyper carnivores (Appendix III, figure A3 and Appendix IV). The overall distribution of characters is similar between ACCTRAN and DELTRAN, but the local positions in the trees differs, this is probably due to the different tree-structures yielded.

The three subgroups are enough supported for further interpretations. One possibly correlation is with tooth-structure. The hyper carnivores have big fangs, the filter-feeders have baleen and

12 therefor lack teeth and Pachycormus bollensis have small (centimetre-scale) teeth (figure 8). The appearance of the trees yielded in the parsimony analysis together with the tooth-size might suggest that the Pachycormus-group is an intermediate form (see figure 9). Even if the same tuna-shape caudal-fin is found in all pachycormiformes, the tooth-structures are different and this indicates that different hunting- and eating-behaviours are represented within the pachycormiformes.

Figure 8: The head of a Pachycormus bollensis with the teeth visible.

Figure 9: The correlation between tooth-size and the three subgroups.

3.2 Bayesian analysis The tree generated from the Bayesian analysis with all taxa included is presented in figure 10. High supported nodes are encircled. The trees with a 50% and 60% majority rule consensus are found in Appendix III, figures A5 and A6.

The Bayesian trees correspond very well with the trees yielded from the parsimony analysis. The three subgroups are visible in the Bayesian trees as well, but it is overall a weak support for specific nodes. The strongest supported nodes are marked on the tree (figure 10). Node 1 (figure 10) is supported to 99%, i.e. very well supported, this node corresponds with node 1 (figure 6). The Bayesian further support the pachycormiformes to be a monophyletic group.

The interrelationships of the hyper carnivores show in general a higher resolution that the filter- feeders and the Pachycormus. With support values of 71-97%, the hyper carnivores show rather high node support (node 3 and blue encircled nodes, figure 10). Node 3 has in particular a high support and corresponds to node 2 in figure 6 and represents the interrelationship of Protosphyraena spp and Australopachycormus hurleyi. Node 2 (figure 10) represents a node within the filter-feeders and shows a high support (95%). With an exception of the just mentioned nodes, the interrelationships are weak supported (see figure 10).

The two trees with a majority rule consensus upon show a very high support for the pachycormiformes to be a monophyletic group (see figures A5 and A6 in Appendix III). The subgroups (hyper carnivores, filter-feeder and Pachycormus) are consistent in the trees but the interrelationships of the groups are weak supported and remain unclear.

Figure 10: Tree generated from the Bayesian analysis with all taxa included. Encircled nodes are discussed in the text. 3.3 Discussion of Matt Friedman et al. (2010) The data matrix from Friedman et al. (2010) was used in this study, except one additional taxon, Pachycormus bollensis. The trees generated in this study are there for very similar to the trees generated by Friedman.

A bootstrap value of 100 supports very well the monophyletism of the pachycormiformes (node 1, figure 11). Both Friedman et al. (2010) and this study show a high support for the pachycormiformes to be a monophyletic group. The three subgroups have high to acceptable support in Friedman’s study. The node representing the filter-feeders (node 3, figure 11) shows 95% support, which is notably higher than the 76% maintained in this study. The interrelationships of the filter-feeders are very poor supported in both studies. The hyper carnivores have a higher resolution of their interrelationships, Friedman et al. even states their (the hyper carnivores and the Pachycormus) interrelationships to be stable. The bootstrap values of 55-87% (node 4 and nodes marked with blue dots, figure 11) are more or less acceptable but the conclusion that the interrelationships are stable

15 should be drawn with carefulness. Only the node of Protosphyraena spp and Australopachycormus hurleyi (node 4, figure 11) are strong (87%) supported. This is consistent with the result in this study.

The addition of one more taxa (Pachycormus bollensis) in this study did not change the tree structure from Friedman et al. (2010). The bootstrap analyses in the two studies gave a consistent result. The small notable differences were the higher support for the filter-feeder group (node 3, figure 11) in Friedman et al. and a slither higher support for the pachycormiformes (node 1, figure 11). The correlation between the phylogenetic analyses and the mysticeti replacement of the filter-feeders that is concluded in the article (Friedman et al., 2010) should have been done with greater caution, since the interrelationships of the pachycormiformes (and especially the filter-feeders) are vastly un- stable and the phylogenetic analyses that they performed gave only a weak support for the group.

Figure 11: Strict consensus cladogram modified from Friedman et al. (2010). Bootstrap values are visible as the middle of the three numbers indicating each node. Nodes discussed in the text are marked with numbers and green circles or blue dots.

4. Conclusions 1. Pachycormus belongs to the pachycormiformes and Pachycormus bollensis is a pachycormus. 2. The pachycormiformes are a monophyletic group. 3. Three major groups are strongly supported but no interrelationships within each group can be seen, except for the most derived hyper carnivores. 4. Pachycormus is probably an intermediate group. 5. The interpretations in the article of Friedman at al. (2010) are a bit un-supported.

5. Acknowledgement I want to thank my supervisor Benjamin Kear for always being available and answering my questions. I also want to thank the curator at the Museum of Evolution at Uppsala University, Jan-Ove Ebbestad, for help with the fossils and access to the museum. Thanks to Erik Rubensson for all support and good advices in time of need. And big thanks to all people at Geocentrum for fika-moments and good company.

6. References

6.1 Printed sources Agnarsson, I., Miller, J.A., 2008: Is ACCTRAN better than DELTRAN?. Wiley-Blackwell. Cladistic 24: 1-7.

Anderson, P.S.L., Westneat, M.W., 2009: A biomechanical model of feeding kinematics for Dunkleosteus terrelli (Arthrodira, Placodermi). Paleobiology, 35 (2): 251-269

Arratia, G. 2004: Mesozoic halecostomes and the early radiation of teleosts. p 279-315. In Arratia, G., Tintori, A. (eds), Mesozoic Fishes 3 – Systematics, Paleoenvironments and Biodiversity. Verlag Dr Freidrich Pfeil, München

Benton, M.J., 2005: Vertebrate Palaeontology. 3rd ed. Blackwell Publishing. Malden. p. 158-186

Budd, G., 2012: Lecture 4 – A refresher rush through phylogenetic reconstruction. Lecture notes for Evolutionary Organismal Biology. Uppsala University. p. 67.

De Iuliis, G., Pulerà, D. 2006: The Dissection of Vertebrates – A Laboratory Manual. Academic Press. Burlington p. 77-87

Etter, W. and Tang C.M. 2002: Posidonia Shale: Germany’s Jurassic Marine Park. p. 265-287. In Bottjer, D.J., Etter, W., Hagadorn, J.W. and Tang, C.M. (eds), Exceptional Fossil Preservation – A Unique View on the Evolution of Marine Life. Columbia University Press. New York.

Forey, P. 2008: Course notes: GEOL 331 Principles of Paleontology, Lecture: Cladistics 5. University of Maryland. Newsletter, 64: 28-34.

Friedman, M., Shimada, K., Martin, L.D., Everhart, M.J., Liston, J., Maltese, A., Triebold. 2010: 100-Million- Year Dynasty of Giant Planktivorous Bony Fishes in the Mesozoic Seas. Science, 327: 990-993 and supporting on-line material

Hillis, D.M. and James, J. 1993: An Empirical Test of Bootstrapping as a Method for Assessing Confidence in Phylogenetic Analysis. Systematic Biology 42(2): 182-192

Kear, P. 2007: First record of a pachycormid fish (Actinopterygii: pachycormiformes) from the lower Cretaceous of Australia. Journal of Vertebrate Paleontology 27(4): 1033-1033

Lindström, M. 1964: Conodonts. Elsevier Publishing Company. Amsterdam. p. 7

Long, J.A. 1995. The Rise of Fishes. The John Hopkins University Press. Baltimore/London. p. 30-63, 100- 159, 180-197

Röhl, H-J., Schmid-Röhl, A., Oschmann, W., Frimmel, A. and Schwark, L. 2001: The Posidonia Shale (Lower Toarcian) of SW-Germany: an oxygen-depleted ecosystem controlled by sea level and palaeoclimate. Palaeogeography, Palaeoclimatology, Palaeoecology 165: 27–52

Schmid-Röhl, A., Röhl, H-J., Oschmann, W., Frimmel, A. and Schwark, L. 2002: Palaeoenvironmental reconstruction of Lower Toarcian epicontinental black shale (Posidonia Shale, SW Germany): global versus regional control. Geobios 35: 13-20

Shu, D-G., Luo, H-L., Conway Morris, S., Zhang, X-L., Hu, S-X., Chen, L., Han, J., Zhu, M., Li, Y. and Chen L-Z. 1999: Lower Cambrian vertebrates from south China. Nature 402: 42-46

Stiassny, M.L., Parenti, L.R., Johnson, G.D. 1996: Interrelationships of Fishes. Academic Press. San Diego. p. 296

Whals, B., 2002: Introduction to Bayesian Analysis. Lecture Notes for EEB 596z. p. 1-21

The geological time scale: 2009 Geologic Time Scale. The Geological Society of America®

6.2 Internet sources

Bates, J., MrBayes -> Help -> MCMC. http://mrbayes.sourceforge.net/Help/mcmc.html. Date of access: 2012-06-06

Bates, J., MrBayes -> Help -> Prset. http://mrbayes.sourceforge.net/Help/prset.html. Date of access: 2012-06-06

All photographs in the report were taken by Maria Lindkvist

Appendix I Appendix I contains the characters used in the phylogenetic analyses. The numbers correspond to the taxonomic matrix (Appendix II) and the ACCTRAN and DELTRAN character-change list (Appendix IV and V).

Neurocranium and associated dermal bones 1. Opisthotic: 0. Present. 1. Absent.

2. Pterotic: 0. Present. 1. Absent.

3. Pterotic fused with dermopterotic: 0. Absent. 1. Present.

4. Epioccipital: 0. Epioccipital bordered anteriorly by cranial fissure. 1. Epioccipital contacts otic region.

5. Intercalar: 0. Present. 1. Absent.

6. Membranous outgrowths of intercalar: 0. Minor. 1. Extensive and medial to jugular. 2. Extensive and lateral to jugular.'

7. Vagal foramen: 0. Anterior to exoccipital. 1. Lateral outgrowths from intercalar form posterior margin. 2. Ventral outgrowths from intercalar lateral margin enclose dorsal margin. 3. Enclosed by exoccipital.

8. Lateral cranial canal: 0. Present. 1. Absent.

9. Subtemporal fossa: 0. Absent. 1. Present.

10. Anterior myodome: 0. Present. 1. Absent.

11. Posterior myodome: 0. Intramural, lined by endoskeletal floor. 1. With incompletely ossified (fenestrate) floor. 2. Absent.

12. Cranial fissures: 0. Ventral otic and otico-occipital fissure confluent via vestibular fontanelle. 1. Fissures non-persistent (closed), or pattern obscured by incomplete ossification.

13. Relationship of dorsal aorta to basicranial region: 0. Enclosed in an endoskeletal canal. 1. Accommodated in pronounced aortic groove. 2. Accommodated in shallow depression in ventral midline of basioccipital. 3. Enclosed in parabasal canal between parasphenoid and basioccipital.

14. Lateral commissure breadth: 0. Anteroposteriorly broad. 1. Slender.

15. Posttemporal fossa and fossa Bridgei: 0. Posttemporal fossa absent, fossa Bridgei rudimentary. 1. Posttemporal fossa small, fossa Bridgei discrete. 2. Posttemporal fossa large, fossa Bridgei discrete. 3. Posttemporal fossa communicates with fossa Bridgei.

16. Spiracular canal: 0. Present. 1. Absent.

17. Vomer(s): 0. Paired. 1. Unpaired (median).

18. Parashenoid corpus in sphenethmoid region: 0. Narrow. 1. Broad.

19. Parasphenoid dentitio: 0. Present. 1. Absent.

20. Basipterygoid process: 0. Well-developed dermal process with endoskeletal component. 1. Basipterygoid process absent.

21. Internal carotid foramen through parasphenoid: 0. Absent. 1. Present.

22. Efferent pseudobranchial foramina through parasphenoid: 0. Absent. 1. Present.

Dermal skull roof and cheek

23. Rostral bone: 0. Cap on snout apex partially or wholly separating the nasals. 1. Of moderate to narrow size. 2. Reduced to a narrow tube with lateral process. 3. Composite ossification (rostrodermethmoid).

24. Rostrodermethmoid: 0. Terminates at anterior tip of mandibular symphysis. 1. Forms a produced rostrum, extending anterior to mandibular symphysis.

25. Marginal teeth on rostrodermethmoid: 0. Present. 1. Absent.

26. Paramedial fangs on rostrodermethmoid: 0. Absent. 1. Present.

27. Parietals: 0. Paired. 1. Single midline ossification.

28. Posterior boss on skull roof: 0. Absent. 1. Present.

29. Posterior margin of skull roof: 0. Straight or concave. 1. 'W'-shaped.

30. Slender posterior processes of dermopterotics: 0. Absent. 1. Present.

31. Dermosphenotic: 0. Hinged to skull roof. 1. Bound or fused to anterior margin of sphenotic.

32. Demosphenotic forms dorsal margin of orbi: 0. No. 1. Yes.

33. Supraorbitals: 0. Absent. 1. Present.

34. Contact between anterior supraorbitals and infraorbitals: 0. Absent. 1. Present.

35. Suborbitals: 0. Present. 1. Absent.

36. Suborbital size: 0. Equal in size or smaller than adjacent infraorbital(s). 1. Much larger than adjacent infraorbital(s).

37. Suborbital number: 0. Two. 1. Single. 2. More than two.

38. Antorbital shape: 0. Platelike, with minimal (if any) distinct anterior process. 1. Tapering towards slender anterior process; tri-radiate canal with broader, posterior portion. 2. Tubular.

39. Infraorbitals behind orbit: 0. Six or fewer. 1. More than six.

40. Infraorbitals anterior to circumorbital ring: 0. Absent. 1. Present.

41. Posteriorly extensive infraorbital: 0. Present. 1. Absent.

42. Preopercle: 0. With broad dorsal margin. 1. With narrow ascending limb.

Suspensorium, bones of the upper and lower jaws, and marginal dentition

43. Marginal dentition: 0. Present. 1. Absent.

44. Carinae extending length of teeth: 0. Absent. 1. Present.

45. Midline contact of premaxillae 0. Present. 1. Absent.

46. Form of premaxillary dentition: 0. Similar to maxillary teeth. 1. Enlarged relative to maxillary teeth.

47. Mobile premaxilla: 0. Absent. 1. Present.

48. Grooved, notched or perforated premaxillary ascending process: 0. Absent. 1. Present.

49. Maxilla: 0. Fixed to cheek. 1. Free.

50. Maxilla length: 0. Long, extends beneath mid-orbit. 1. Short.

51. Posterior margin of maxilla: 0. Straight or convex. 1. Indented.

52. Thickened ridge on external surface of maxilla: 0. Absent. 1. Present.

53. Supramaxilla: 0. Absent. 1. Present.

54. Supramaxilla position: 0. Dorsal to maxilla. 1. Posterodorsal to maxilla.

55. Quadratojugal: 0. Platelike, lateral to quadrate. 1. Splintlike, free along posterior border of quadrate. 2. Fused to quadrate. 3. Absent.

56. Symplectic articulation: 0. On inner, medial surface of quadrate. 1. Behind quadrate, in loose contact with preopercle. 2. Behind quadrate, with articular connection to lower jaw, may be bound to preopercle with membrane bone.

57. Position of jaw joint: 0. Well behind orbit. 1. Below or anterior to orbit.

58. Quadrate with elongate posteroventral process: 0. Absent. 1. Present.

59. Dentary tooth row(s): 0. Labial row plus lingual row. 1. Single row.

60. Form of anterior dentary dentition: 0. Similar to posterior teeth. 1. Enlarged, procumbent fangs.

61. Surangular in lower jaw: 0. Present. 1. Absent.

62. Anterior coronoid plate: 0. Not inflated. 1. Inflated.

63. Prearticular: 0. Present. 1. Absent.

64. Prearticular dentition: 0. Present. 1. Absent.

Operculogular series, hyoid arch, and branchial arches

65. Exposed dorsal projection of subopercle between preopercle and opercle: 0. Absent. 1. Present.

66. Hypohyal: 0. Single ossification. 1. Separate dorsal and ventral ossifications.

67. Anterior ceratohyal: 0. Long, relatively straight, same depth as posterior element. 1. Long, gently curved with very small posterior element. 2. Short and deep posteriorly. 3. With constricted shaft; hourglass-shaped in lateral view.

68. Gular(s): 0. Present. 1. Absent.

69. Epibranchials: 0. Slender. 1. With uncinate processes.

Median fins and axial skeleton

70. Relative position of dorsal and anal fins: 0. Overlap between dorsal- and anal-fin bases. 1. Dorsal-fin base lies anterior to anal-fin base.

71. Caudal fin segmentation: 0. Segmented. 1. Unsegmented.

72. Ossified vertebrae: 0. Absent. 1. Present.

73. Lateral keels of caudal peduncle (greatly expanded urodermals): 0. Absent. 1. Present.

74. Uroneurals: 0. Absent. 1. Present.

75. Hypural plate: 0. Absent. 1. Present.

76. Shape of hypural plate: 0. Rhomboidal. 1. Oval.

77. .Main hypural plate notched posterodorsally (incomplete fusion with accessory hypurals): 0. Present. 1. Absent.

78. Uppermost hypaxial-caudal rays: 0. Fin-rays successively shorter from bottom to top. 1. Bundle of enlongate fin-ray bases extending over several hypurals. 2. Dorsal and ventral fin-ray bases symmetrical. 3. Fin-rays one-to-one on hypurals.

Appendicular skeleton

79. Clavicle: 0. Present. 1. Absent.

80. Clavicle morphology: 0. Large, caps anterior end of cleithrum. 1. Toothed plates on postbranchial lamina of cleithrum. 2. Clavicle reduced, often with a single row of denticles. 3. Serrated organ (with 12 or more ridges of denticles lateral to cleithrum).

81. One or more accessory postcleithra: 0. Absent. 1. Present.

82. Endoskeletal shoulder girdle ossification reduced to mesocoracoid arch: 0. Absent. 1. Present.

83. Pectoral propterygium: 0. Free. 1. Fused to first pectoral-fin ray.

84. Pectoral-fin radial morphology: 0. Cylindrical. 1. Broad distal area and narrow proximal stalk (paddle-shaped).

85. Scythe-like pectoral fins with lepidotrichia only segmented distally (if segments present): 0. Absent. 1. Present.

86. Complete fusion of fin rays along length of leading edge of pectoral fin: 0. Absent. 1. Present.

87. Bifurcations in pectoral-fin rays: 0. Present. 1. Absent.

88. Asymmetrical 'Y'-type bifurcations in pectoral-fin lepidotrichia: 0. Absent. 1. Present.

89. Segmentation of pectoral-fin rays: 0. Present. 1. Absent.

90. Pelvic fins: 0. Present. 1. Absent.

91. Pelvic fin position: 0. At or posterior to midpoint between anal and pectoral fins. 1. Anterior to midpoint between anal and pectoral fins.

Squamation

92. Ridge scales: 0. Absent. 1. Present.

93. Scale morphology: 0. Rhombic. 1. Round

Appendix II Appendix II shows the taxon-by-taxon matrix

Character number: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22

†Pteronisculus spp 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Amiacalva 1 1 - 1 0 1 2 1 0 0 1 1 2 0 2 0 0 0 0 1 0 0 †Asthenocormust itanius ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? †Australopachycormus hurleyi 0 0 ? ? 0 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? †Bonnerichthys gladius 0 0 0 ? 0 ? ? ? ? ? ? ? 1 1 ? ? 0 1 1 1 1 0 †Caturus spp 1 1 - 1 0 1 2 0 1 0 1 1 2 1 2 ? 0 0 0 1 0 0 †Discoserra pectinodon 0 0 ? 1 0 0 0+2 ? ? ? 0 1 ? 1 2+3 0 ? ? ? 1 0 ? Elops hawaiensis 1 0 1 1 0 2 3 1 1 1 1 1 2 1 3 1 ? ? ? 1 1 0 †Euthynotus spp ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 ? ? ? ? Hiodon alosoides 1 0 1 1 0 2 3 1 1 0 1 1 1 1 3 1 1 0 0 1 1 1 †Hypsocormus insignis ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 ? ? ? ? ? †'Hypsocormus' tenuirostris ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 0 0 1 ? ? †Leedsichthys problematicus ? ? ? ? ? ? ? ? ? ? ? ? 2 ? ? ? ? 1 1 ? ? ? †Lepidotes spp 1 1 - 1 1 ? 3 0 1 ? 1 1 1 1 2+3 ? 0 0 1 0 0 0 Lepisosteus platostomus 1 1 - 1 1 ? 3 0 0 1 2 1 2 0 0 0 0 0 0 0 0 0 †Macrepistius rostratus 0 0 1 1 0 1 2 ? 1 0 1 1 ? 1 2 ? ? 0 1 1 0 0 †Macrosemius rostratus 1 0 0 1 ? ? 3 0 ? ? 1 1 2 ? ? ? 0 0 1 0 0 1 †Martillichthys renwickae ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 1 ? ? ? †Orthocormus spp 0 ? ? ? 0 ? 1 ? ? 1 ? 0 ? 1 ? ? 0 0 ? ? ? ? †Pachycormus spp 0 0 0 0 0 ? 1 0 1 1 1 0 1 1 3 0 0 0 0 1 1 0 †Pholidophorous bechei 0 0 1 0 0 0 0 0 1 0 1 0 1 1 1 0 1 0 0 0 1 1 †Protosphyraena spp 0 0 0 0 0 ? 1 ? 1 ? ? 0 1 1 3 ? 0 0 0 1 1 0 †Rhinconichthyst aylori ? 0 0 ? ? ? ? ? 1 ? 1 ? 2 1 3 ? 0 1 ? 1 ? ? †Semionotus elegans 1 1 - 1 1 ? 3 ? ? ? 1 ? 2 ? ? ? 0 0 0 0 0 0 †Watsonulus eugnathoides 0 0 ? 0 0 0 0 0 ? 0 1 0 2 1 1 0 0 0 0 0 0 0 Oolite †pachycormid ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? †Pachycormus bollensis ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 29 ?

Character number: 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44

†Pteronisculus spp 0 - - - 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 0 0 Amiacalva 1 - - - 0 0 0 0 1 0 0 - 1 - - 1 0 0 0 1 0 0 †Asthenocormust itanius 3 0 - - 0 0 1 0 ? ? 0 - ? ? ? ? ? ? ? ? 1 - †Australopachycormus hurleyi 3 1 1 1 1 0 0 ? ? ? ? ? ? ? ? ? ? ? ? ? 0 1 †Bonnerichthys gladius 3 0 - - ? ? ? 1 0 1 0 - ? ? ? 0 ? ? ? ? 1 - †Caturus spp 2 - - - 0 0 0 1 1 0 0 - 0 1 0 1 0 0 1 1 0 0 †Discoserra pectinodon 0 - - - 0 0 ? 0 0 0 1 0 0 0 2 ? 0 0 1 1 0 0 Elops hawaiensis 0 - - - 0 0 0 0 0 0 1 0 1 - - 2 0 0 0 1 0 0 †Euthynotus spp 3 0 0 0 ? 0 0 ? 0 1 0 - 0 1 0 0 ? 0 1 1 0 0 Hiodon alosoides 0 - - - 0 0 0 0 0 0 0 - 1 - - - 0 0 0 1 0 0 †Hypsocormus insignis 3 0 0 1 ? 1 ? 0 ? ? 0 - 0 1 0 ? 1 ? 1 1 0 0 †'Hypsocormus' tenuirostris 3 1 0 1 ? 1 0 0 ? ? ? ? 0 ? ? ? ? ? ? 1 0 0 †Leedsichthys problematicus ? ? - - ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 - †Lepidotes spp 2 - - - 0 0 0 0 0 0 1 1 0 1 2 1 0 1 1 1 0 0 Lepisosteus platostomus 1 - - - 0 0 0 0 0 0 1 1 0 0 2 1 0 1 1 1 0 0 †Macrepistius rostratus 2 - - - 0 0 0 0 1 0 1 0 0 0 2 ? 0 0 1 1 0 0 †Macrosemius rostratus ? - - - 0 0 0 0 0 0 0 - 1 - - 2 0 1 1 1 0 0 †Martillichthys renwickae 3 0 - - 0 0 1 0 0 1 0 - ? ? ? ? ? ? ? 1 1 - †Orthocormus spp 3 1 1 1 1 1 ? ? 0 1 0 - 0 1 0 0 ? 0 1 1 0 0 †Pachycormus spp 3 0 0 0 0 1 0 0 0 1 0 - 0 1 0 0 1 0 1 1 0 0 †Pholidophorous bechei 0 - - - 0 - 0 0 0 0 1 0 0 1 1 0 0 0 0 1 0 0 †Protosphyraena spp 3 1 1 1 1 1 0 1 0 1 0 - 0 1 ? 0 ? 0 ? ? 0 1 †Rhinconichthyst aylori ? ? - - 0 0 1 1 ? ? ? ? ? ? ? ? ? ? ? ? 1 - †Semionotus elegans ? - - - 0 0 0 0 0 0 1 1 0 1 1 1 0 1 1 1 0 0 †Watsonulus eugnathoides 2 - - - 0 0 0 0 1 0 1 1 1 - - 1 0 0 1 0 0 0 Oolite †pachycormid 3 0 - - ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 - †Pachycormus bollensis 3 0 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 0

Character number: 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66

†Pteronisculus spp 0 0 0 0 0 0 0 0 0 - 0 - 0 0 0 0 0 0 0 0 0 0 Amiacalva 0 0 0 1 1 0 1 0 1 0 3 2 0 0 1 0 0 0 0 0 1 0 †Asthenocormust itanius ? - ? ? 1 0 0 ? 0 - ? ? 1 ? - - ? ? ? ? 0 ? †Australopachycormus hurleyi 1 1 0 0 ? ? 0 ? ? ? ? ? ? ? 1 1 ? 1 ? ? ? ? †Bonnerichthys gladius - - 0 - 1 0 0 1 0 - 3 ? 0 0 - - ? ? 0 1 0 ? †Caturus spp 0 0 0 1 1 0 1 0 1 0 3 2 0 0 1 0 0 0 0 0 1 0 †Discoserra pectinodon 0 0 0 0 0 1 0 0 0 - 3 1 - 0 1 0 ? ? ? ? - ? Elops hawaiensis 0 0 1 0 1 0 0 0 1 0 3 0 1 1 ? 0 1 - 1 - 0 1 †Euthynotus spp - 0 - - 1 0 0 0 1 1 3 0 0 ? 1 0 ? ? ? ? 0 ? Hiodon alosoides 0 0 1 0 1 0 0 0 0 - 3 0 1 1 1 0 1 - 1 - 0 1 †Hypsocormus insignis 1 0 0 ? 1 0 0 ? 1 1 ? ? 0 ? 0 0 ? ? ? ? 0 ? †'Hypsocormus' tenuirostris 1 1 0 0 1 0 0 0 1 1 ? ? 0 ? 0 1 0 0 0 0 ? ? †Leedsichthys problematicus ? - ? ? 1 ? ? ? ? ? ? ? ? ? - - ? ? ? ? ? 0 †Lepidotes spp 0 0 0 1 1 1 0 0 1 0 1 1 - 0 1 0 ? 0 0 0 1 ? Lepisosteus platostomus 0 0 0 1 0 1 0 0 0 - 1 1 - 0 0 0 0 0 0 0 1 0 †Macrepistius rostratus 0 0 0 ? 1 0 1 0 1 0 ? ? 1 ? ? 0 ? ? 0 0 1 ? †Macrosemius rostratus 0 0 0 1 1 1 0 0 0 - 2 ? - 0 1 0 0 0 0 0 1 0 †Martillichthys renwickae ? - ? ? 1 0 0 1 0 - 3 0 1 0 - - 0 0 0 1 ? 0 †Orthocormus spp 1 1 0 0 1 0 0 0 1 1 ? ? 0 ? 0 1 ? ? ? ? ? ? †Pachycormus spp 1 0 0 0 1 0 0 0 1 ? 3 0 0 0 1 0 0 0 0 0 0 0 †Pholidophorous bechei 0 0 1 0 1 0 0 0 1 0 3 0 1 1 1 0 0 ? 0 ? 0 0 †Protosphyraena spp 1 1 0 0 1 0 0 ? 0 - 3 0 0 0 0 1 0 1 0 0 ? 0 †Rhinconichthyst aylori ? - ? ? 1 0 0 1 0 - ? ? 0 ? - - ? ? 0 ? ? 0 †Semionotus elegans 0 0 0 1 1 1 0 0 1 0 1 1 - 0 1 0 0 0 0 0 1 0 †Watsonulus eugnathoides 0 0 0 1 1 0 1 0 1 0 3 2 0 0 1 0 0 0 0 0 1 0 Oolite †pachycormid ? ? ? ? ? 0 ? ? ? ? ? ? ? ? ? ? ? ? 0 ? ? ? †Pachycormus bollensis 1 0 ? ? 1 0 0 0 1 0 3 ? 0 0 1 0 0 0 ? ? 0 ?

Character number: 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88

†Pteronisculus spp 0 0 0 0 0 0 0 0 0 - - 0 0 0 0 0 0 0 0 0 0 0 Amiacalva 1 0 0 0 0 1 0 0 0 - - 3 0 3 0 0 0 0 0 0 0 0 †Asthenocormust itanius 0 0 ? ? 1 0 ? ? 1 1 1 2 ? ? ? ? ? ? 1 0 0 1 †Australopachycormus hurleyi ? ? ? ? 1 0 ? ? ? ? ? 2 ? ? ? ? ? ? 1 ? 1 - †Bonnerichthys gladius 0 0 0 ? ? 0 ? ? 1 1 1 ? 1 - ? 0 ? 1 1 1 0 1 †Caturus spp 1 0 1 0 0 1 0 0 0 - - 1 0 3 1 0 0 0 0 0 0 0 †Discoserra pectinodon 3 0 ? 0 0 0 0 0 0 - - 0 1 - 0 ? ? ? 0 0 ? 0 Elops hawaiensis 0 0 1 1 0 1 0 1 0 ? - 1 1 - 1 0 ? ? 0 0 ? 0 †Euthynotus spp ? ? ? 0 0 1 0 1 1 0 0 2 1 - 1 ? ? ? 1 0 0 1 Hiodon alosoides 3 1 1 0 0 1 0 1 0 - - 1 1 - 0 0 1 0 0 0 0 0 †Hypsocormus insignis ? 0 ? 0 0 0 1 1 1 0 0 2 ? ? ? ? ? ? 1 0 0 1 †'Hypsocormus' tenuirostris ? ? ? ? 0 0 ? ? 1 0 0 2 ? ? ? ? 1 ? 1 0 ? ? †Leedsichthys problematicus ? 0 0 ? 1 0 ? ? ? ? ? 2 ? ? ? ? ? 1 1 0 0 1 †Lepidotes spp 0 1 1 0 0 0 0 0 0 - - ? 0 2 1 ? 0 0 0 0 0 0 Lepisosteus platostomus 0 1 0 0 0 1 0 0 0 - - 1 0 1 1 1 0 ? 0 0 0 0 †Macrepistius rostratus 1 0 ? 0 0 1 0 0 ? ? - ? ? ? 1 ? ? 0 ? ? ? ? †Macrosemius rostratus 2 1 1 0 0 1 0 0 0 - - 0 0 2 1 ? 0 0 0 0 0 0 †Martillichthys renwickae 0 0 0 0 1 0 ? ? ? ? ? 2 ? ? ? ? ? ? 1 0 0 1 †Orthocormus spp 0 ? ? 0 0 0 1 1 ? ? ? 2 1 - 1 0 1 ? 1 0 0 1 †Pachycormus spp 0 0 0 1 0 0+1 1 1 1 0 0 2 1 - 1 0 1 1 1 0 ? 1 †Pholidophorous bechei ? 0 ? 1 0 1 0 1 0 - - 1 1 - 0 ? 1 ? 0 0 0 0 †Protosphyraena spp ? 0 ? ? 1 0 ? 1 1 0 0+1 2 1 - ? 0 1 1 1 1 1 - †Rhinconichthyst aylori 0 0 0 ? ? 0 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? †Semionotus elegans 0 1 1 0 0 0 0 0 0 - - 0 0 2 1 1 ? ? 0 0 0 0 †Watsonulus eugnathoides 0 0 ? 0 0 1 0 0 0 - - 1 0 0 1 0 ? ? 0 0 ? 0 Oolite †pachycormid ? 0 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? †Pachycormus bollensis 0 ? ? 1 0 0 1 1 1 0 0 0 ? ? ? 0 1 1 1 0 0 1

Character number: 89 90 91 92 93

†Pteronisculus spp 0 0 0 0 0 Amiacalva 0 0 0 0 1 †Asthenocormust itanius 1 1 - 0 - †Australopachycormus hurleyi 1 ? ? ? ? †Bonnerichthys gladius 1 ? ? ? ? †Caturus spp 0 0 0 0 0 †Discoserra pectinodon 0 0 0 1 0 Elops hawaiensis ? 0 0 0 1 †Euthynotus spp 1 0 1 0 0 Hiodon alosoides 0 0 0 0 1 †Hypsocormus insignis 1 0 1 0 0 †'Hypsocormus' tenuirostris ? ? ? ? 0 †Leedsichthys problematicus 1 ? ? ? ? †Lepidotes spp 0 0 0 1 0 Lepisosteus platostomus 0 0 0 0 0 †Macrepistius rostratus ? ? ? 0 0 †Macrosemius rostratus 0 0 0 0 0 †Martillichthys renwickae 1 ? ? 0 - †Orthocormus spp 0+1 0 1 0 0 †Pachycormus spp 0 1 - 0 0 †Pholidophorous bechei 0 0 0 0 0 †Protosphyraena spp 1 0 1 0 ? †Rhinconichthyst aylori ? ? ? ? ? †Semionotus elegans 0 0 0 1 0 †Watsonulus eugnathoides 0 0 0 0 0 Oolite †pachycormid ? ? ? ? ? †Pachycormus bollensis 1 1 - 0 0

Appendix III Appendix III contains the remaining cladograms generated from the parsimony and Bayesian analyses.

Figure A1: Tree generated from the parsimony analysis with a 50% majority rule consensus.

Figure A2: Tree generated from the parsimony analysis with Bootstrap as nodal support method applied. The bootstrap- values are visible on the tree.

Figure A3: Tree generated from the parsimony analysis with ACCTRAN as applied character optimization. See Appendix IV for the specific character changes.

Figure A4: Tree generated from the parsimony analysis with DELTRAN as applied character optimization. See Appendix V for the specific character changes.

Figure A5: Tree generated from the Bayesian analysis with a 50% majority rule consensus.

Figure A6: Tree generated from the Bayesian analysis with a 60% majority rule consensus.

Appendix IV Appendix IV shows the specific character changes for each node in the tree for the parsimony analysis with ACCTRAN (figure A3, Appendix III).

Branch Character Change Branch Character Change

Pteronisculus sp --> node 51 9 0 --> 1 78 1 --> 3 13 0 --> 1 81 1 --> 0 14 0 --> 1 93 0 --> 1 15 0 --> 2 node 28 --> Caturus spp 30 0 --> 1 20 0 --> 1 69 0 --> 1 33 0 --> 1 node 32 --> node 31 5 0 --> 1 37 0 --> 2 7 2 --> 3 41 0 --> 1 10 0 --> 1 42 0 --> 1 20 1 --> 0 55 0 --> 3 31 1 --> 0 59 0 --> 1 40 0 --> 1 79 0 --> 1 50 0 --> 1 node 51 --> node 50 11 0 --> 1 51 1 --> 0 36 0 --> 1 53 1 --> 0 49 0 --> 1 55 3 --> 1 53 0 --> 1 56 2 --> 1 72 0 --> 1 67 1 --> 0 78 0 --> 1 68 0 --> 1 81 0 --> 1 82 0 --> 1 node 50 --> node 34 13 1 --> 2 node 31 --> node 30 19 0 --> 1 23 0 --> 2 69 0 --> 1 31 0 --> 1 78 1 --> 0 34 0 --> 1 80 1 --> 2 38 0 --> 1 node 30 --> node 29 53 0 --> 1 48 0 --> 1 72 1 --> 0 51 0 --> 1 92 0 --> 1 56 0 --> 2 node 29 --> Lepidotes spp 13 2 --> 1 65 0 --> 1 node 29 --> Semionotus elega 19 1 --> 0 79 1 --> 0 37 2 --> 1 node 34 --> node 33 4 0 --> 1 node 30 --> Macrosemius rost 2 1 --> 0 6 0 --> 1 22 0 --> 1 7 0 --> 2 33 1 --> 0 12 0 --> 1 35 0 --> 1 67 0 --> 1 38 1 --> 2 80 0 --> 1 55 1 --> 2 node 33 --> node 32 1 0 --> 1 67 0 --> 2 2 0 --> 1 node 31 --> Lepisosteus plat 9 1 --> 0 node 32 --> node 28 33 1 --> 0 11 1 --> 2 37 2 --> 0 14 1 --> 0 80 1 --> 3 15 2 --> 0 node 28 --> Amia calva 8 0 --> 1 23 2 --> 1 9 1 --> 0 36 1 --> 0 14 1 --> 0 49 1 --> 0 23 2 --> 1 59 1 --> 0 35 0 --> 1 node 33 --> Macrepistius ros 3 0 --> 1 41 1 --> 0 19 0 --> 1

Branch Character Change Branch Character Change

34 1 --> 0 62 0 --> 1 36 1 --> 0 node 40 --> node 39 44 0 --> 1 57 0 --> 1 53 1 --> 0 node 34 --> Watsonulus eugna 15 2 --> 1 71 0 --> 1 20 1 --> 0 86 0 --> 1 35 0 --> 1 87 0 --> 1 42 1 --> 0 node 39 --> Australopachycor 28 1 --> 0 node 50 --> node 49 15 2 --> 3 59 0 --> 1 21 0 --> 1 node 44 --> node 43 54 1 --> 0 37 2 --> 0 70 0 --> 1 74 0 --> 1 node 43 --> Pachycormus spp 89 1 --> 0 83 0 --> 1 node 43 --> Pachycormus boll 78 2 --> 0 node 49 --> node 46 7 0 --> 1 node 49 --> node 48 3 0 --> 1 10 0 --> 1 17 0 --> 1 23 0 --> 3 22 0 --> 1 32 0 --> 1 37 0 --> 1 33 1 --> 0 41 1 --> 0 39 0 --> 1 47 0 --> 1 45 0 --> 1 57 0 --> 1 54 0 --> 1 58 0 --> 1 75 0 --> 1 69 0 --> 1 78 1 --> 2 70 0 --> 1 84 0 --> 1 81 1 --> 0 85 0 --> 1 node 48 --> node 47 1 0 --> 1 88 0 --> 1 4 0 --> 1 89 0 --> 1 6 0 --> 2 91 0 --> 1 7 0 --> 3 node 46 --> node 45 72 1 --> 0 8 0 --> 1 73 0 --> 1 12 0 --> 1 90 0 --> 1 16 0 --> 1 node 45 --> node 38 18 0 --> 1 35 0 --> 1 19 0 --> 1 38 0 --> 2 29 0 --> 1 61 0 --> 1 43 0 --> 1 63 0 --> 1 52 0 --> 1 66 0 --> 1 53 1 --> 0 93 0 --> 1 64 0 --> 1 node 47 --> Elops hawaiensis 10 0 --> 1 71 0 --> 1 13 1 --> 2 76 0 --> 1 22 1 --> 0 77 0 --> 1 81 0 --> 1 node 38 --> node 35 57 0 --> 1 node 47 --> Hiodon alosoides 33 1 --> 0 node 38 --> node 37 30 0 --> 1 53 1 --> 0 node 37 --> Bonnerichthys gl 86 0 --> 1 67 0 --> 3 node 37 --> node 36 13 1 --> 2 68 0 --> 1 node 45 --> node 44 28 0 --> 1 70 1 --> 0 node 44 --> node 42 26 0 --> 1 node 48 --> Pholidophorous b 15 3 --> 1 27 0 --> 1 20 1 --> 0 59 1 --> 0 node 51 --> Discoserra pecti 4 0 --> 1 90 1 --> 0 12 0 --> 1 node 42 --> node 41 24 0 --> 1 50 0 --> 1 46 0 --> 1 56 0 --> 1 60 0 --> 1 67 0 --> 3 node 41 --> node 40 25 0 --> 1 92 0 --> 1

30 0 --> 1 40

Appendix V Appendix V shows the specific character changes for each node in the tree for the parsimony analysis with DELTRAN (figure A4, Appendix III). Branch Character Change Branch Character Change

Pteronisculus sp --> node 52 14 0 --> 1 20 1 --> 0 15 0 --> 2 31 1 --> 0 20 0 --> 1 34 0 --> 1 33 0 --> 1 37 0 --> 2 41 0 --> 1 40 0 --> 1 42 0 --> 1 50 0 --> 1 55 0 --> 3 51 1 --> 0 59 0 --> 1 55 3 --> 1 node 52 --> node 51 9 0 --> 1 56 2 --> 1 11 0 --> 1 68 0 --> 1 49 0 --> 1 82 0 --> 1 53 0 --> 1 node 31 --> node 30 69 0 --> 1 72 0 --> 1 78 1 --> 0 78 0 --> 1 80 0 --> 2 node 51 --> node 34 13 0 --> 2 node 30 --> node 29 36 0 --> 1 23 0 --> 2 72 1 --> 0 31 0 --> 1 92 0 --> 1 38 0 --> 1 node 29 --> Lepidotes spp 13 2 --> 1 48 0 --> 1 19 0 --> 1 51 0 --> 1 node 29 --> Semionotus elega 37 2 --> 1 56 0 --> 2 node 30 --> Macrosemius rost 2 1 --> 0 65 0 --> 1 19 0 --> 1 81 0 --> 1 22 0 --> 1 node 34 --> node 33 4 0 --> 1 33 1 --> 0 6 0 --> 1 35 0 --> 1 7 0 --> 2 38 1 --> 2 12 0 --> 1 53 1 --> 0 node 33 --> node 32 1 0 --> 1 55 1 --> 2 2 0 --> 1 67 0 --> 2 node 32 --> node 28 33 1 --> 0 node 31 --> Lepisosteus plat 9 1 --> 0 67 0 --> 1 10 0 --> 1 80 0 --> 3 11 1 --> 2 node 28 --> Amia calva 8 0 --> 1 14 1 --> 0 9 1 --> 0 15 2 --> 0 14 1 --> 0 23 2 --> 1 23 2 --> 1 49 1 --> 0 35 0 --> 1 53 1 --> 0 41 1 --> 0 59 1 --> 0 78 1 --> 3 80 0 --> 1 81 1 --> 0 node 33 --> Macrepistius ros 3 0 --> 1 93 0 --> 1 19 0 --> 1 node 28 --> Caturus spp 30 0 --> 1 37 0 --> 2 36 0 --> 1 57 0 --> 1 69 0 --> 1 67 0 --> 1 node 32 --> node 31 5 0 --> 1 node 34 --> Watsonulus eugna 15 2 --> 1 7 2 --> 3 20 1 --> 0

Branch Character Change Branch Character Change

34 0 --> 1 27 0 --> 1 35 0 --> 1 node 43 --> node 42 44 0 --> 1 42 1 --> 0 62 0 --> 1 node 51 --> node 50 13 0 --> 1 71 0 --> 1 15 2 --> 3 87 0 --> 1 21 0 --> 1 node 42 --> Australopachycor 28 1 --> 0 36 0 --> 1 59 0 --> 1 74 0 --> 1 node 42 --> Protosphyraena s 30 0 --> 1 79 0 --> 1 53 1 --> 0 83 0 --> 1 86 0 --> 1 node 50 --> node 47 23 0 --> 3 node 47 --> Euthynotus spp 54 0 --> 1 32 0 --> 1 node 50 --> node 49 3 0 --> 1 33 1 --> 0 17 0 --> 1 75 0 --> 1 41 1 --> 0 78 1 --> 2 47 0 --> 1 81 0 --> 1 57 0 --> 1 85 0 --> 1 58 0 --> 1 88 0 --> 1 node 49 --> node 48 1 0 --> 1 89 0 --> 1 4 0 --> 1 91 0 --> 1 6 0 --> 2 node 47 --> node 46 7 0 --> 1 7 0 --> 3 10 0 --> 1 8 0 --> 1 39 0 --> 1 12 0 --> 1 45 0 --> 1 16 0 --> 1 72 1 --> 0 35 0 --> 1 73 0 --> 1 61 0 --> 1 84 0 --> 1 63 0 --> 1 node 46 --> node 41 90 0 --> 1 66 0 --> 1 node 41 --> node 39 18 0 --> 1 69 0 --> 1 19 0 --> 1 93 0 --> 1 29 0 --> 1 node 48 --> Elops hawaiensis 10 0 --> 1 43 0 --> 1 13 1 --> 2 52 0 --> 1 38 0 --> 2 53 1 --> 0 70 0 --> 1 64 0 --> 1 81 0 --> 1 71 0 --> 1 node 48 --> Hiodon alosoides 22 0 --> 1 76 0 --> 1 33 1 --> 0 77 0 --> 1 53 1 --> 0 node 39 --> node 35 57 0 --> 1 67 0 --> 3 node 39 --> node 38 30 0 --> 1 68 0 --> 1 node 36 --> Bonnerichthys gl 86 0 --> 1 node 49 --> Pholidophorous b 15 3 --> 1 node 38 --> node 37 13 1 --> 2 20 1 --> 0 node 41 --> node 40 70 0 --> 1 22 0 --> 1 node 40 --> Pachycormus spp 28 0 --> 1 37 0 --> 1 89 1 --> 0 70 0 --> 1 node 40 --> Pachycormus boll 78 2 --> 0 node 52 --> Discoserra pecti 4 0 --> 1 node 46 --> node 45 26 0 --> 1 12 0 --> 1 28 0 --> 1 37 0 --> 2 54 0 --> 1 50 0 --> 1 59 1 --> 0 56 0 --> 1 node 45 --> node 44 24 0 --> 1 67 0 --> 3 46 0 --> 1 79 0 --> 1 60 0 --> 1 92 0 --> 1 node 44 --> node 43 25 0 --> 1 42