Character state transformations and the fit of phylogenies to the fossil record

There is only one true history of life, and the biostratigraphic record and the phylogenetic relationships of organisms provide the most important information regarding this history. Ideally, the historical signal preserved in each of the data sets should be the same, and several methods have been proposed to compare the fit of phylogenies to the fossil record. All of these techniques use stratigraphic data associated with taxa, but our ability to recognize taxa and reconstruct their phylogenetic relationships ultimately is based on patterns of character state distributions that we observe. This raises the question of whether character states can be used to measure the fit of a phylogeny to the fossil record. Here I argue that we can, if the order of appearance of character states is considered. Optimization of character states on a phylogeny results in a predicted order of appearance of character states; derived states must arise after basal states. This order can be compared to that predicted by the fossil record. Although a number of factors can affect the frequency at which derived character states are sampled before basal states in the fossil record, conflicts between the two data sets should be relatively rare. Phylogenies that imply a large number of character state transformations that are inconsistent with the fossil record may need to be reconsidered before the fossil record is criticized.Palaeo-Anthropology Scientific Trust; French Embassy in South Africa; Co-operation and Cultural Servic

On the stratigraphic range of the dicynodont taxon Emydops (Therapsida: Anomodontia) in the Karoo Basin, South Africa

The dicynodont specimen SAM-PK-708 has been referred to the genera Pristerodon and Emydops by various authors, and was used to argue that the first appearance of Emydops was in the Tapinocephalus Assemblage Zone in the Karoo Basin of South Africa. However, the specimen never has been described in detail, and most discussions of its taxonomic affinities were based on limited data. Here we redescribe the specimen and compare it to several small dicynodont taxa from the Tapinocephalus and Pristerognathus assemblage zones. Although the specimen is poorly preserved, it possesses a unique combination of features that allows it to be assigned confidently to Emydops. The locality data associated with SAM-PK-708 are vague, but they allow the provenance of the specimen to be narrowed down to a relatively limited area southwest of the town of Beaufort West. Strata from the upper Tapinocephalus Assemblage Zone and the Pristerognathus Assemblage Zone crop out in this area, but we cannot state with certainty from which of these biostratigraphic divisions the specimen was collected. Nevertheless, SAM-PK-708 is an important datum because it demonstrates that the stratigraphic range of Emydops must be extended below its widely-accepted first appearance in the Tropidostoma Assemblage Zone. This range extension is significant because it implies that the divergence between the emydopid and dicynodontid lineages must have occurred no later than Pristerognathus Assemblage Zone times, and that most of the major lineages of Permian dicynodonts had emerged by a relatively early point in the history of the group.K.D.A. is supported by NSF DBI-0306158 and a Royal Society USA/Canada Research Fellowship. J.F. is supported by a full scholarship from the Government of Canada Awards

Phylogenetic stability, tree shape, and character compatibility: a case study using early tetrapods

Phylogenetic tree shape varies as the evolutionary processes affecting a clade change over time. In this study, we examined an empirical phylogeny of fossil tetrapods during several time intervals, and studied how temporal constraints manifested in patterns of tree imbalance and character change. The results indicate that the impact of temporal constraints on tree shape is minimal and highlights the stability through time of the reference tetrapod phylogeny. Unexpected values of imbalance for Mississippian and Pennsylvanian time slices strongly support the hypothesis that the Carboniferous was a period of explosive tetrapod radiation. Several significant diversification shifts take place in the Mississippian and underpin increased terrestrialization among the earliest limbed vertebrates. Character incompatibility is relatively high at the beginning of tetrapod history, but quickly decreases to a relatively stable lower level, relative to a null distribution based on constant rates of character change. This implies that basal tetrapods had high, but declining, rates of homoplasy early in their evolutionary history, although the origin of Lissamphibia is an exception to this trend. The time slice approach is a powerful method of phylogenetic analysis and a useful tool for assessing the impact of combining extinct and extant taxa in phylogenetic analyses of large and speciose clades

Do cladistic and morphometric data capture common patterns of morphological disparity?

The distinctly non-random diversity of organismal form manifests itself in discrete clusters of taxa that share a common body plan. As a result, analyses of disparity require a scalable comparative framework. The difficulties of applying geometric morphometrics to disparity analyses of groups with vastly divergent body plans are overcome partly by the use of cladistic characters. Character-based disparity analyses have become increasingly popular, but it is not clear how they are affected by character coding strategies or revisions of primary homology statements. Indeed, whether cladistic and morphometric data capture similar patterns of morphological variation remains a moot point. To address this issue, we employ both cladistic and geometric morphometric data in an exploratory study of disparity focussing on caecilian amphibians. Our results show no impact on relative intertaxon distances when different coding strategies for cladistic characters were used or when revised concepts of homology were considered. In all instances, we found no statistically significant difference between pairwise Euclidean and Procrustes distances, although the strength of the correlation among distance matrices varied. This suggests that cladistic and geometric morphometric data appear to summarize morphological variation in comparable ways. Our results support the use of cladistic data for characterizing organismal disparity

Combining geometric morphometrics and finite element analysis with evolutionary modeling:towards a synthesis

<p>Geometric morphometrics (GM) and finite element analysis (FEA) are increasingly common techniques for the study of form and function. We show how principles of quantitative evolution in continuous phenotypic traits can link the two techniques, allowing hypotheses about the relative importance of different functions to be tested in a phylogenetic and evolutionary framework. Finite element analysis is used to derive quantitative surfaces that describe the comparative performance of different morphologies in a morphospace derived from GM. The combination of two or more performance surfaces describes a quantitative adaptive landscape that can be used to predict the direction morphological evolution would take if a combination of functions was selected for. Predicted paths of evolution also can be derived for hypotheses about the relative importance of multiple functions, which can be tested against evolutionary pathways that are documented by phylogenies or fossil sequences. Magnitudes of evolutionary trade-offs between functions can be estimated using maximum likelihood. We apply these methods to an earlier study of carapace strength and hydrodynamic efficiency in emydid turtles. We find that strength and hydrodynamic efficiency explain about 45% of the variance in shell shape; drift and other unidentified functional factors are necessary to explain the remaining variance. Measurement of the proportional trade-off between shell strength and hydrodynamic efficiency shows that throughout the Cenozoic aquatic turtles generally sacrificed strength for streamlining and terrestrial species favored stronger shells; this suggests that the selective regime operating on small to mid-sized emydids has remained relatively static.</p> <p>SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at <a href="http://www.tandfonline.com/UJVP" target="_blank">www.tandfonline.com/UJVP</a></p> <p>Citation for this article: Polly, P. D., C. T. Stayton, E. R. Dumont, S. E. Pierce, E. J. Rayfield, and K. D. Angielczyk. 2016. Combining geometric morphometrics and finite element analysis with evolutionary modeling: towards a synthesis. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2016.1111225.</p

Bringing Dicynodonts Back to Life: Paleobiology and Anatomy of a New Emydopoid Genus from the Upper Permian of Mozambique

Dicynodontia represent the most diverse tetrapod group during the Late Permian. They survived the Permo-Triassic extinction and are central to understanding Permo-Triassic terrestrial ecosystems. Although extensively studied, several aspects of dicynodont paleobiology such as, neuroanatomy, inner ear morphology and internal cranial anatomy remain obscure. Here we describe a new dicynodont (Therapsida, Anomodontia) from northern Mozambique: Niassodon mfumukasi gen. et sp. nov. The holotype ML1620 was collected from the Late Permian K5 formation, Metangula Graben, Niassa Province northern Mozambique, an almost completely unexplored basin and country for vertebrate paleontology. Synchrotron radiation based micro-computed tomography (SRµCT), combined with a phylogenetic analysis, demonstrates a set of characters shared with Emydopoidea. All individual bones were digitally segmented allowing a 3D visualization of each element. In addition, we reconstructed the osseous labyrinth, endocast, cranial nerves and vasculature. The brain is narrow and the cerebellum is broader than the forebrain, resembling the conservative, "reptilian-grade" morphology of other non-mammalian therapsids, but the enlarged paraflocculi occupy the same relative volume as in birds. The orientation of the horizontal semicircular canals indicates a slightly more dorsally tilted head posture than previously assumed in other dicynodonts. In addition, synchrotron data shows a secondary center of ossification in the femur. Thus ML1620 represents, to our knowledge, the oldest fossil evidence of a secondary center of ossification, pushing back the evolutionary origins of this feature. The fact that the specimen represents a new species indicates that the Late Permian tetrapod fauna of east Africa is still incompletely known.Mozambique (Ministério dos Recursos Minerais), National Geographic Society, TAP airlines and other anonymous patrons, financial support from DESY through the I-20110184 EC project

A new Mississippian tetrapod from Fife, Scotland, and its environmental context

The Visean stage of the Mississippian was a time of rapid tetrapod diversification which marks the earliest appearance of temnospondyls, microsaurs and the limbless aïstopods. Tetrapod finds from this stage are very rare and only a dozen sites are known worldwide. Here we announce the discovery of a new Visean site in Fife, Scotland, of Asbian age, and from it describe a new species of the baphetoid Spathicephalus. These specimens represent the oldest known baphetoid by three million years, yet belong to the most specialized members of the clade. Unlike typical baphetoids with large marginal teeth and palatal fangs characteristic of early tetrapods, spathicephalids had very broad flattened heads with a dentition consisting of a large number of small, uniform teeth. Spathicephalids were probably one of the earliest tetrapod groups to use suction feeding on small, aquatic prey. Palynological and sedimentological analysis indicates that the new fossil bed was deposited in a large, stratified, freshwater lake that became increasingly saline

Ontogenetic mechanisms of size change: implications for the Lilliput effect and beyond

Body size has a long history of study in paleobiology and underlies many important phenomena in macroevolution. Body-size patterns in the fossil record are often examined by utilizing size data alone, which hinders our ability to describe the biological meaning behind size change on macroevolutionary timescales. Without data reflecting the biological and geologic factors that drive size change, we cannot assess its mechanistic underpinnings. Existing frameworks for studying ontogeny and phylogeny can remedy this problem, particularly the classic age–size–“shape” space originally developed for studies of heterochrony. When evaluated based on metrics for age, size, and phenotype in populations, proposed mechanisms for size change can be outlined theoretically and tested empirically in the record. Using this framework, we can compare ontogenetic trajectories within and between species and determine how changes in size emerge. Here, we outline ontogenetic mechanisms for evolutionary size change, such as heterochrony, as well as how geologic factors can drive apparent, non-biological size change (e.g., taphonomic size sorting). To demonstrate the utility of this framework in actual paleobiological problems, we apply it to the Lilliput effect, a compelling and widely documented pattern of size decrease during extinction events. However, little is known about the mechanisms underlying this pattern. We provide a brief history of the Lilliput effect and refine its definition in a framework that can be mechanistically tested. Processes that likely produce Lilliput effects include allometric and sequence repatterning (including heterochrony) and evolutionary size-selective sorting. We describe these mechanisms and highlight relevant examples of the Lilliput effect for which feasible empirical tests are possible.</p

The evolution of the tetrapod humerus: morphometrics, disparity, and evolutionary rates

The present study explores the macroevolutionary dynamics of shape changes in the humeri of all major grades and clades of early tetrapods and their fish-like forerunners. Coordinate point eigenshape analysis applied to humeral outlines in extensor view reveals that fish humeri are more disparate than those of most early tetrapod groups and significantly separate from the latter. Our findings indicate sustained changes in humeral shape in the deepest portions of the tetrapod stem group and certain portions of the crown. In the first half of sampled tetrapod history, subclades show larger than expected humeral disparity, suggesting rapid diffusion into morphospace. Later in tetrapod evolution, subclades occupy smaller and non-overlapping morphospace regions. This pattern may reflect in part increasing specialisations in later tetrapod lineages. Bayesian shifts in rates of evolutionary change are distributed discontinuously across the phylogeny, and most of them occur within rather than between major groups. Most shifts with the highest Bayesian posterior probabilities are observed in lepospondyls. Similarly, maximum likelihood analyses of shifts support marked rate accelerations in lepospondyls and in various subclades within that group. In other tetrapod groups, rates either tend to slow down or experience only small increases. Somewhat surprisingly, no shifts are concurrent with structural, functional, or ecological innovations in tetrapod evolution, including the origin of digits, the water-land transition and increasing terrestrialisation. Although counterintuitive, these results are consistent with a model of continual phenotypic innovation that, although decoupled from key evolutionary changes, is possibly triggered by niche segregation in divergent clades and grades of early tetrapods.</p