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Sensitivity tests of plant data and their results (Table S1), and captions for Suppementary Figures (Files NBetal_Supplementary_Fig_S1 and NBetal_Supplementary_Fig_S2)

The tetrapod herbivore dataset in the form used for analysis; number of occurences in each formation, number of localities and the lower and upper age boundaries on each formation

The amniote clade Parareptilia is notable in that members of the clade exhibited a wide array of morphologies, were successful in a variety of ecological niches and survived the end-Permian mass extinction. In order to better understand how mass extinction events can affect clades that survive them, we investigate both the species richness and morphological diversity (disparity) of parareptiles over the course of their history. Furthermore, we examine our observations in the context of other metazoan clades, in order to identify post-extinction survivorship patterns that are present in the clade. The results of our study indicate that there was an early increase in parareptilian disparity, which then fluctuated over the course of the Permian, before it eventually declined sharply towards the end of the Permian and into the Triassic, corresponding with the end-Permian mass extinction event. Interestingly, this is a different trend to what is observed regarding parareptile richness, that shows an almost continuous increase until its overall peak at the end of the Late Permian. Moreover, richness did not experience the same sharp drop at the end of the Permian, reaching a plateau until the Anisian, before dropping sharply and remaining low, with the clade going extinct at the end of the Triassic. This observed pattern is likely to be due to the fact that, despite the extinction of several morphologically distinct parareptile clades, the procolophonoids, one of the largest parareptilian clades, were diversifying across the Permian–Triassic boundary. With the clade's low levels of disparity and eventually declining species richness, this pattern most resembles a ‘dead clade walking’ pattern.

Supplementary Methods, Results, Figures1-6 and Table 1

Studies of diversity, whether of species richness within regions (alpha diversity) or faunal turnover between regions (beta diversity), will depend heavily on the “bioregions” into which a study area is divided. However, such studies in the palaeontological literature have often been extremely arbitrary in their definition of bioregions and have employed a wide variety of spatial scales, from individual localities to formations/basins to entire continents. Such bioregions will not necessarily be separated by biologically meaningful boundaries, and results obtained at different spatial scales will not be directly comparable. In many neontological studies, however, bioregions are defined more rigorously, usually as areas of endemicity. Here a procedure is proposed whereby this principal may be applied to palaeontological datasets. In each time bin/assemblage localities are subjected to two hierarchical cluster analyses, the first grouping the localities by geographic distance, the second by taxonomic distance. Clusters shared between the two will represent geographically continuous areas of endemicity and so may be used as bioregions. When calculating alpha or beta diversity through time, the spatial scale at which the bioregions are defined needs to be standardized between each time bin. This is done by grouping clusters of localities below a predefined geographic cluster node height. This approach is used to assess changes in beta diversity of Palaeozoic tetrapods and resolve disagreements regarding changes in faunal provinciality across the Carboniferous/Permian boundary. When the bioregions are defined at a smaller spatial scale, splitting the globe into many small regions, beta diversity decreases substantially during the earliest Permian. However, when the bioregions are defined at larger spatial scales, representing areas roughly the size of continents, beta diversity remains high. This result indicates that local environmental barriers to dispersal were decreasing in importance, rejecting previous suggestions that the rainforest collapse caused an “island biogeography” effect. Instead, dispersal at this time is restricted by continental-scale barriers, with the increased orogenic uplift as a possible control.

Studies of diversity, whether of species richness within regions (alpha diversity) or faunal turnover between regions (beta diversity), will depend heavily on the “bioregions” into which a study area is divided. However, such studies in the palaeontological literature have often been extremely arbitrary in their definition of bioregions and have employed a wide variety of spatial scales, from individual localities to formations/basins to entire continents. Such bioregions will not necessarily be separated by biologically meaningful boundaries, and results obtained at different spatial scales will not be directly comparable. In many neontological studies, however, bioregions are defined more rigorously, usually as areas of endemicity. Here a procedure is proposed whereby this principal may be applied to palaeontological datasets. In each time bin/assemblage localities are subjected to two hierarchical cluster analyses, the first grouping the localities by geographic distance, the second by taxonomic distance. Clusters shared between the two will represent geographically continuous areas of endemicity and so may be used as bioregions. When calculating alpha or beta diversity through time, the spatial scale at which the bioregions are defined needs to be standardized between each time bin. This is done by grouping clusters of localities below a predefined geographic cluster node height. This approach is used to assess changes in beta diversity of Palaeozoic tetrapods and resolve disagreements regarding changes in faunal provinciality across the Carboniferous/Permian boundary. When the bioregions are defined at a smaller spatial scale, splitting the globe into many small regions, beta diversity decreases substantially during the earliest Permian. However, when the bioregions are defined at larger spatial scales, representing areas roughly the size of continents, beta diversity remains high. This result indicates that local environmental barriers to dispersal were decreasing in importance, rejecting previous suggestions that the rainforest collapse caused an “island biogeography” effect. Instead, dispersal at this time is restricted by continental-scale barriers, with the increased orogenic uplift as a possible control.

Phreatophasma aenigmaticum is a mysterious tetrapod from the earliest middle Permian of Russia, represented by a single femur. At various times since its original description it has been considered a therapsid synapsid, a pelycosaurian-grade synapsid from the family Caseidae, and most recently a seymouriamorph amphibian. Using up-to-date knowledge of the postcranial morphology and evolution of early synapsids, the specimen is re-evaluated and subjected to cladistic analysis. Seymouriamorph and therapsid affinities are rejected, and a caseid affinity is supported based on the deep intertrochanteric fossa; the widely spaced distal condyles; the short, robust femoral shaft; and the lack of a longitudinal ridge enclosing the posterior margin of the intertrochanteric fossa. When included in two cladistic matrices, the first a global analysis of basal synapsids and the second devoted to caseids, Phreatophasma is found to occupy a basal position within caseids, retaining plesiomorphic characters such as the lack of compression of the anterior condyle of the femur and the almost identical distal extent of the two condyles. The recognition of Phreatophasma as a basal caseid has great implications for the evolution and biogeography of this family. This is only the second example of a caseid from the palaeo-temperate region of Russia, and it is not closely related to the first (Ennatosaurus tecton), implying at least two distinct dispersal events from the palaeoequatorial to temperate latitudes. It also implies that a number of plesiomorphic characteristics of caseids, including small body size and a relatively long femur, were retained as late as the middle Permian, a time when caseids were otherwise represented by large herbivorous taxa.

Formations included and justifications, R code, and discussion of faunal composition.