Phylogeny of Paleozoic limbed vertebrates reassessed through revision and expansion of the largest published relevant data matrix

Abstract

The largest published phylogenetic analysis of early limbed vertebrates (Ruta M, Coates MI. 2007. Journal of Systematic Palaeontology 5:69–122) recovered, for example, Seymouriamorpha, Diadectomorpha and (in some trees) Caudata as paraphyletic and found the “temnospondyl hypothesis” on the origin of Lissamphibia (TH) to be more parsimonious than the “lepospondyl hypothesis” (LH)—though only, as we show, by one step. We report 4,200 misscored cells, over half of them due to typographic and similar accidental errors. Further, some characters were duplicated; some had only one described state; for one, most taxa were scored after presumed relatives. Even potentially continuous characters were unordered, the effects of ontogeny were not sufficiently taken into account, and data published after 2001 were mostly excluded. After these issues are improved—we document and justify all changes to the matrix—but no characters are added, we find (Analysis R1) much longer trees with, for example, monophyletic Caudata, Diadectomorpha and (in some trees) Seymouriamorpha; Ichthyostega either crownward or rootward of Acanthostega; and Anthracosauria either crownward or rootward of Temnospondyli. The LH is nine steps shorter than the TH (R2; constrained) and 12 steps shorter than the “polyphyly hypothesis” (PH—R3; constrained). Brachydectes (Lysorophia) is not found next to Lissamphibia; instead, a large clade that includes the adelogyrinids, urocordylid “nectrideans” and aïstopods occupies that position. As expected from the taxon/character ratio, most bootstrap values are low. Adding 56 terminal taxa to the original 102 increases the resolution (and decreases most bootstrap values). The added taxa range in completeness from complete articulated skeletons to an incomplete lower jaw. Even though the lissamphibian-like temnospondyls Gerobatrachus, Micropholis and Tungussogyrinus and the extremely peramorphic salamander Chelotriton are added, the difference between LH (R4; unconstrained) and TH (R5) rises to 10 steps, that between LH and PH (R6) to 15; the TH also requires several more regains of lost bones than the LH. Casineria, in which we tentatively identify a postbranchial lamina, emerges rather far from amniote origins in a gephyrostegid-chroniosuchian grade. Bayesian inference (Analysis EB, settings as in R4) mostly agrees with R4. High posterior probabilities are found for Lissamphibia (1.00) and the LH (0.92); however, many branches remain weakly supported, and most are short, as expected from the small character sample. We discuss phylogeny, approaches to coding, methods of phylogenetics (Bayesian inference vs. equally weighted vs. reweighted parsimony), some character complexes (e.g. preaxial/postaxial polarity in limb development), and prospects for further improvement of this matrix. Even in its revised state, the matrix cannot provide a robust assessment of the phylogeny of early limbed vertebrates. Sufficient improvement will be laborious—but not difficult.

Histological skeletochronology indicates developmental plasticity in the early Permian stem lissamphibian Doleserpeton annectens

“…Doleserpeton annectens Bolt, is an early Permian amphibamiform, a clade of small‐bodied dissorophoid temnospondyls that has been frequently hypothesized to be closely related to some (e.g., Anderson, Reisz, Scott, Fröbisch, & Sumida, ; Pardo, Small, & Huttenlocker, ) or all (e.g., Bolt, ; Schoch, ; Sigurdsen & Bolt, ) of the lissamphibian crown groups (but see Marjanović & Laurin, , for an advocacy of a monophyletic origin within the lepospondyls). Doleserpeton annectens is known only from the karst deposits near Richards Spur, Oklahoma, where it occurs as part of the diverse tetrapod assemblage interpreted to represent an upland ecosystem (MacDougall, Tabor, Woodhead, Daoust, & Reisz, ).…”

Parsimony‐based test for identifying changes in evolutionary trends for quantitative characters: implications for the origin of the amniotic egg

“…Exact counts vary between hypotheses because there is controversy about the origin of lissamphibians and amniotes (e.g. Ruta and Coates, ; Marjanović and Laurin, ), but under all hypotheses, stem‐amphibians and amniotes are well‐represented.…”

“…Recent work has resulted in a slight shift in the established soft consensus on stegocephalian phylogeny, but to facilitate comparisons with the results of Laurin (), we reanalysed the data using our new methods on the same set of phylogenies, to better highlight the differences in results reflecting the methodological innovations introduced by Didier () and here (see below). In addition, we produced two new trees that reflect more recent analyses that place Solenodonsaurus either at the base of lepospondyls (Danto et al., ) or stemward of seymouriamorphs (Marjanović and Laurin, ). Other than that, only minor changes would need to be made to reflect the current consensus; recent research has confirmed that the trees used here still adequately represent the current views on early stegocephalian phylogeny (Marjanović and Laurin, ).…”

Predicting Evolutionary Transitions in Tooth Complexity With a Morphogenetic Model

“…At the same time there has been a trend toward ever larger morphological character matrices (e.g. 18, 19) whose underlying properties such as substitution rates and independence remain largely unknown. These concerns have contributed to a widespread scepticism about the reliability of morphological data for building and dating phylogenies (14, 20–22).…”