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

Preliminary phylogenetic analysis and stratigraphc congruence of the dicynodont anomodonts (Synapsida: Therapsida)

A preliminary phylogenetic analysis of 20 well-known dicynodont taxa was conducted using modern cladistic methods. Many past phylogenetic hypotheses were corroborated, but others conflict with the results of this analysis. Most notably, Diictodon, Robertia, and Pristerodon are reconstructed in more basal positions than previously suggested, whereas Endothiodon and Chelydontops occupy a more crown ward position. These findings are consistent with novel evolutionary scenarios for characters such as the presence of postcanine teeth and anterior palatal ridges. The Relative Completeness Index and Gap Excess Ratio were used to examine the degree of fit between the most parsimonious cladograms of this study and the stratigraphic record of the dicynodonts. Although the results of this analysis suggest that the preferred cladogram is relatively consistent with stratigraphy, the presence of some ghost ranges and ghost lineages imply that the fossil record of dicynodonts is not as complete as is sometimes stated. These findings are important because there is a long tradition of intensive collecting in regions where dicynodont fossils are common; sections of several dicynodont lineages may not be preserved in these areas.The Council's Research Committee, University of the Witwatersrand; National Research Foundation (NRF); Palaeo-Anthropology Scientific Trust (PAST); Collections Usage Grant (AMNH); Grant-in-Aid-of Research (Berkeley Chapter of Sigma Xi);Samuel P. Welles Fund of the UCM

Diversification of the ruminant skull along an evolutionary line of least resistance.

Clarifying how microevolutionary processes scale to macroevolutionary patterns is a fundamental goal in evolutionary biology, but these analyses, requiring comparative datasets of population-level variation, are limited. By analyzing a previously published dataset of 2859 ruminant crania, we find that variation within and between ruminant species is biased by a highly conserved mammalian-wide allometric pattern, CREA (craniofacial evolutionary allometry), where larger species have proportionally longer faces. Species with higher morphological integration and species more biased toward CREA have diverged farther from their ancestors, and Ruminantia as a clade diversified farther than expected in the direction of CREA. Our analyses indicate that CREA acts as an evolutionary line of least resistance and facilitates morphological diversification due to its alignment with the browser-grazer continuum. Together, our results demonstrate that constraints at the population level can produce highly directional patterns of phenotypic evolution at the macroevolutionary scale. Further research is needed to explore how CREA has been exploited in other mammalian clades

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

A new record of \u3ci\u3eProcynosuchus delaharpeae\u3c/i\u3e (Therapsida: Cynodontia) from the Upper Permian Usili Formation, Tanzania

Procynosuchus, the best-known Permian cynodont, has a remarkably broad geographic range, with records stretching from southern Africa to Europe. Fossils\u27 of Procynosuchus are most common in the Upper Permian Dicynodon Assemblage Zone of South Africa, but also occur in coeval East African rocks. Currently, there is one documented occurrence from the Madumabisa Mudstone Formation of Zambia, and two specimens from the Usili (=Kawinga) Formation of Tanzania. The Tanzanian specimens include a poorly preserved, incomplete skull and a partial cranium originally attributed to Parathrinaxodon proops. The latter is now considered a subjective junior synonym of Procynosuchus delaharpeae. Here we report on a new specimen collected in 2007 near the base of Kingori Mountain in Tanzania. It preserves the postorbital region of the skull and the posterior portions of both lower jaws, each containing several intact teeth. A well-preserved postcanine tooth exhibits the dental hallmarks of Procynosuchus and permits unambiguous referral to this taxon. Recent fieldwork corroborates previous suggestions that the Usili tetrapod fauna includes representatives of the Tropidostoma, Cistecephalus and Dicynodon assemblage zones of South Africa. Moreover, the presence of several endemic Usili taxa (e.g. Katumbia, Kawingasaurus, Peitobatrachus), suggests that a straightforward correlation between the Usili tetrapod fauna and a particular assemblage zone from the Beaufort Group may not be possible

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

Paleozoic Crown Lungfishes from Gondwana foreshadow the Early Triassic Recovery Fauna

Modern lungfishes are renowned for tolerance of extreme environmental variation, which is thought to contribute to their abundance during the recovery from the Permo-Triassic Mass Extinction (PTME). However, the Paleozoic origins of this clade and its biogeographic context remains unclear, with a 60 Ma ghost lineage at the base of the crown lungfish diversification spanning much of the Upper Carboniferous and the entirety of the Permian. This gap is particularly perplexing given the exceptional record of archaic lungfishes within this interval, particularly within paleoequatorial Euramerica, but also within eastern Europe. One possibility is that the assembly of the crown lungfish bauplan from known Carboniferous and Permian archaic lungfish groups occurred rapidly in the recovery from the PTME. However, an alternative explanation is that the crown lungfish bauplan evolved earlier in geographic regions outside the well-sampled Carboniferous and Permian basins of Euramerica, Russia, and South Africa. The sudden appearance of a diverse crown lungfish fauna in the earliest Triassic would then represent a biogeographic release in response to climate or diversity trends associated with the PTME. New lungfish faunas from outside these basins provide an opportunity to test these hypotheses. Here we report a diverse lungfish fauna from the Early Permian Pedra de Fogo Formation (Parnaíba Basin, northeastern Brazil) comprised of abundant lungfish toothplates and rarer associated or articulated skeletal remains. This fauna lacks archaic lungfish taxa (e.g. sagenodontids, ctenodontids, and conchopomatids) characteristic of contemporary localities in equatorial Euramerica. Instead, the Parnaíba fauna preserves a diverse assemblage of derived lungfishes, including a gnathorhizid and several crown lungfishes (ceratodontiforms). The gnathorhizid is represented by abundant toothplates and several partial skulls, and shows similarities to the North American gnathorhizid genera Persephonichthys and Gnathorhiza. The ceratodontiform, which is represented by toothplates as well as several partial skulls and skeletons, shows affinities with Triassic ptychoceratodontids and arganodontids, currently considered early members of the lepidosireniform stem group. Comparison with lungfish toothplate assemblages from the Paraná Basin of southern Brazil shows that the lungfish assemblage from the Parnaíba basin is also present in the Middle Permian of Brazil, likely representing a persistent biogeographic province in western Gondwana. We hypothesize that the lungfish crown group originated early in western Gondwana, but remained biogeographically restricted until the PTME eliminated incumbent competition in better-known biogeographical provinces.Fil: Pardo, Jason. University of Calgary; CanadáFil: Kammerer, Christian. Museum Fur Naturkunde; AlemaniaFil: Marsicano, Claudia Alicia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Estudios Andinos "Don Pablo Groeber". Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Estudios Andinos "Don Pablo Groeber"; ArgentinaFil: Angielczyk, Kenneth D.. Field Museum of National History; Estados UnidosFil: Fröbisch, Jörg. No especifíca;Fil: Smith, Roger M. H.. University of Cape Town; SudáfricaFil: Cisneros, Juan C.. Universidade Federal do Piaui; BrasilAnnual Meeting Society Vertebrate PaleontologyEstados UnidosSociety of Vertebrate Paleontolog

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

Best practices for justifying fossil calibrations.

Our ability to correlate biological evolution with climate change, geological evolution, and other historical patterns is essential to understanding the processes that shape biodiversity. Combining data from the fossil record with molecular phylogenetics represents an exciting synthetic approach to this challenge. The first molecular divergence dating analysis (Zuckerkandl and Pauling 1962) was based on a measure of the amino acid differences in the hemoglobin molecule, with replacement rates established (calibrated) using paleontological age estimates from textbooks (e.g., Dodson 1960). Since that time, the amount of molecular sequence data has increased dramatically, affording ever-greater opportunities to apply molecular divergence approaches to fundamental problems in evolutionary biology