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

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

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

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

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

Taphonomy and Palaeoenvironments a new early Permian Tetrapod fauna from Brazil

The Early Permian Pedra de Fogo Formation of Brazil accumulated in a large intracontinentalsag-basin (Parnaíba Basin) located in sub-tropical Gondwana around 20oS(palaeolatitude). With progressive climatic drying, palaeoenvironments changed from a large,shallow lake to expansive exposed mudflats surrounding a shrinking lacustrine wetland,culminating in isolated playas fed by ephemeral streams which finally became an aeoliandune field.Our team has collected over 500 fossils from this formation in northeastern Brazil. Theyinclude actinopterygians, dipnoans and chondrichthyans, together with two fully-articulatedcoelacanths, at least four temnospondyl taxa (the archegosaurid Prionosuchus, thetrimerorhachid Procuhy, the dvinosaur Timonya, and a rhinesuchid), small-to-mid-sizedcaptorhinid reptiles (cf. Captorhinus/Captorhinikos), and a small parareptile, as well asabundant fish-scale bearing spiral coprolites.Three gradationally superimposed sedimentary facies associations are recognized in the Pedrade Fogo Formation: offshore lacustrine, shoreline/carbonate mudflats and finally anephemeral stream/dune complex. The taphonomic style of vertebrate fossils varies withdepositional facies reflecting different modes of post mortem burial.Offshore facies comprise thick beds of massive siltstone and finely-laminatedsiltstone/mudstone couplets showing algal crenulations but no infaunal burrowing, indicativeof an anoxic lake bed. Scattered actinopterygian fish skeletons with scales are rare, but somefine sandstone turbidite/inundate interbeds contain more fully-articulated aquatic tetrapods,some with soft tissue preservation, indicative of death and burial caused by storm induceddensity underflows.The carbonate mudflats facies association contains silicified algal-laminated limestonesdisplaying stromatolite mounds, tepee and desiccation structures typical of alkaline lakeshorelines. Clusters of coprolites and fish-hash lenses comprising masses of isolated teeth andscales are suggestive of heavy predation within drying ponds and channels.The ephemeral stream/dunite facies contains most of the plant material, mainly tree trunksand in places at the top of the formation rare 3-D petrifications of leaves and fructifications.We are revealing a previously unknown diversity of early Permian (+/-280 Mya) tetrapods inGondwana. While some aspects of the fauna (e.g., caporhinids, trimerorhcachids) are similarto those known from the classic Permian redbeds of the southwestern United States, thepresence of taxa such as rhinesuchids suggest that the Gondwanan tropics were an importantcradle of later Permo-Triassic biodiversity. Dvinosaurian temnospondyls were a majorcomponent of these Gondwanan tetrapod communities that originated, and diversified in andaround tropical saline to brackish water lakes and wetlands.Fil: Smith, Roger. University of the Witwatersrand; SudáfricaFil: Cisneros, Juan. Universidade Federal do Piaui; BrasilFil: Angielczyk, Ken. Field Museum of National History; Estados UnidosFil: 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: Kammerer, Christian. North Carolina Museum of Natural Sciences; Estados UnidosFil: Frobisch, Jorg. Humboldt-Universität zu Berlin; Alemania20th Palaeontological Society of Southern Africa Biennial MeetingBloemfonteinSudáfricaThe National Museum, Bloemfontei

New Specimen of CF. Asiatosuchus (Crocodyloidea) from the Middle Eocene Drazinda Formation of the Sulaiman Range, Punjab (Pakistan)

163-189http://deepblue.lib.umich.edu/bitstream/2027.42/48655/2/ID522.pd

Deep-scaled fish (Osteichthyes: Actinopterygii) from the lower Permian (Cisuralian) lacustrine deposits of the Parnaíba Basin, NE Brazil

The richly fossiliferous deposits of the Brazilian Pedra de Fogo Formation originated in an extensive aquatic system in tropical Pangaea, and grade from marginal lacustrine into marine deposits at the depocenter in the western part of the Parnaíba Basin. In addition to the well-known tetrapod and macrofloral records from these deposits, the Pedra de Fogo Formation yields extensive fish fossils indicating a diverse and abundant ichthyofauna. Among the actinopterygians, deep-bodied morphotypes are represented by whole fish as well as disarticulated dermal scales found at various localities in the states of Maranhão and Piauí. The gross morphology, ornamentation, and histology of some of these scales is highly distinctive, indicating the presence of a novel taxon (Piratata rogersmithii gen. et sp. nov.). The external surface of a Piratata scale is covered in multiple round-to-slightly elongated tubercles. The scale lacks a ganoin cover and is made up of cellular bone and odontocomplexes of orthodentine composing the tuberculated scale surface. The scale morphology and ornamentation most closely resemble that of Cleithrolepis granulatus from the Triassic of Australia and Cleithrolepis extoni from the Triassic Stormberg Beds of South Africa, but the new taxon differs from previously described species in several diagnostic morphological features. The use of scale characters in the taxonomy of ray-finned fishes and the palaeogeographic, palaeoenvironmental, and geochronological implications of the new taxon are discussed.Fil: Richter, Martha. British Museum (Natural History); Reino UnidoFil: Cisneros, Juan C.. Universidade Federal do Piaui; BrasilFil: Kammerer, Christian. North Carolina Museum Of Natural Sciences; Estados UnidosFil: Pardo, Jason. Field Museum of National History; Estados UnidosFil: 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: Frobisch, Jorg. Staatliches Museum fur Naturkunde Stuttgart; AlemaniaFil: Angielczyk, Ken. Field Museum of National History; Estados Unido