The Early Tetrapod Supertrees of Ruta, Jefferies and Coates 2003

A decade ago, Ruta et al. (2003) produced two distinct phylogenetic supertrees of early tetrapods by combining 50 trees produced by prior workers. That’s 225 taxa in total, an impressive number! The second analysis excluded source trees that had been superceded by more comprehensive studies. Only a very few of the taxa on both trees are found in the large reptile tree (colorized in Figs. 1, 2).

Figure 1. Click to enlarge. Colors added represent taxa listed on the large reptile tree.

Figure 1. Click to enlarge. Colors added represent taxa listed on the large reptile tree.

Since the large reptile tree includes several pre-amniotes listed here (Figs. 1, 2), I thought it would be interesting to compare and contrast these two trees as Ruta et al. (2003) did, “Outstanding areas of disagreement include the branching sequence of lepospondyls and the content of the amniote crown group, in particular the placement of diadectomorphs as stem diapsids.”

Figure 2. The second super tree created by Ruta et al. 2003. Note the several shifts described in the text.

Figure 2. The second super tree created by Ruta et al. 2003. Note the several shifts described in the text.

Figure 1. Microsaurs and other basal non-amniote tetrapods from the large reptile tree.

Figure 1. Microsaurs and other basal non-amniote tetrapods from the large reptile tree.

Ruta et al. (2003) warn in their abstract: “Supertrees are unsurpassed in their ability to summarize relationship patterns from multiple independent topologies. However, we urge caution in using them as a replacement for character-based cladograms and for inferring macroevolutionary patterns.”

They also report, “supertrees can, in certain circumstances, produce spurious groups (i.e. taxon arrangements that are not found in any of the contributory trees.”

[Hone and Benton (2009) know this only too well!!]

In analysis one,
Ruta et al. report, “Authors hypothesize a close relationship between some or all of the lissamphibians and various lepospondyl groups (figure 1). However, analysis I places lissamphibians as a sister group to a clade of lysorophids and microbrachomorph microsaurs. The amniote crown group and total group are coextensive: no amniote stem was found.”

In analysis two, 
Ruta et al. report, “[The] tree shows a deep split within early tetrapods between stem amniotes and stem lissamphibians analysis II includes a stem amniote branch. Anthracosaurs and seymouriamorphs are successive sister groups to a clade of crown amniotes plus diadectomorphs. This larger group is paired with Solenodonsaurus plus lepospondyls. Caerorhachis is placed at the base of the amniote stem (cf. Ruta et al. 2001, 2003). Finally, Casineria and Westlothiana are successive sister taxa to the crown amniotes. Temnospondyls now appear as stem lissamphibians.”

Spurious results,
Ruta et al. report, “Diadectomorphs are polyphyletic in most MPTs, Diadectes and Limnoscelis being nested within the amniote crown, next to stem diapsids. Solenodonsaurus also appears as a crown amniote, as a sister taxon to the diadectomorph, Tseajaia.”

No, that’s good!
The large reptile tree also recovered Solenodonsaurus, TseajaiaDiadectes and Limnoscelis as amniotes. So what’s the problem!

In their summary, Ruta et al. (2003) remind us,
“Supertree methods are the only practical means of generating summaries of primary results.”

Interesting then,
that when Hone and Benton (2009) following Hone and Benton (2007) in their 2-part supertree analysis decided to drop all reference to Peters (2000) and give false credit for the “prolacertiform” hypothesis to Bennett (1996), they must have discovered that inclusion of the primary results from Peters (2000) would give them the same results as Peters (2000). This they were not keen on doing, considering their subsequent deviations. Their mission, as stated in 2007, was to compare the results of Peters (2000) to Bennett (1996). By dropping the former in their 2009 paper (with published analysis), the latter came out victorious, but only by default and not very clearly.

Later Bennett (2013) noted that Hone and Benton (2009) entered typos into their matrix for Peters (2000) then complained they did not get the same results, among many other problems listed here.

Back to Ruta et al. 
Interesting that the Ruta et al. supertree kept Gephyrostegus apart from basal amniotes, perhaps due to the absence of Cephalerpeton, Brouffia and other basal amniotes. Moreover, Gephyrostegus, Silvanerpeton and Proterogyrinus nested in opposite order with the latter nesting as more derived. We found that opposite order also occurring with the Mortimer dinosaur tree here.

Good fodder for good conversation.
Ultimately we’ll all be of one accord.

Bottom line:
You have to appreciate the efforts of Ruta  et al. 2003 because more taxa in large gamut analyses generally aid in understanding relationships… so long as you don’t “drop the ball” by deleting key taxa (as in Hone and Benton (2007, 2009).

References
Ruta M, Jefferey JE and Coates MI 2003. A supertree of early tetrapods. Proceedings of the Royal Society, London B (2003) 270, 2507–2516.
Hone DWE and Benton MJ 2007. An evaluation of the phylogenetic relationships of the pterosaurs to the archosauromorph reptiles. Journal of Systematic Palaeontology 5:465–469.
Hone DWE and Benton MJ 2009. Contrasting supertree and total evidence methods: the origin of the pterosaurs. Zitteliana B28:35–60.

2 thoughts on “The Early Tetrapod Supertrees of Ruta, Jefferies and Coates 2003

  1. Wait…they should give credit to Peters (2000) instead of Bennett (1996)? If Bennett was published first then, yes, Bennett (1996) does get credit.

  2. Bennett 1996 nested pterosaurs with Scleromochlus. Take away the hind limb characters then Bennett 1996 nested pterosaurs with Erythrosuchus/Proterosuchus. In Bennett 1996 pterosaurs never nested with prolaceriformes, which he used as a suprageneric taxon. Bennett didn’t even consider Langobardisaurus, Cosesaurus, Sharovipteryx or Longisquama. Yeah, it’s a crime what Hone and Benton did and referees approved.

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