bluuebunny/crossref_metadata_2025_split huggingface dataset:
Likelihood tests of hypothesized durations: determining and accommodating biasing factors
Authors: Wagner Peter J. 
Published: July 2006

Paleobiologists frequently hypothesize that a taxon's duration (i.e., the true span from origination to extinction) exceeds its stratigraphic range (i.e., the span from first appearance to last appearance in the fossil record). One can test hypothesized duration by assessing the plausibility of the implicitly hypothesized gaps between origination and first appearance and / or between last appearance and extinction. Several tests assess the probability of not finding a taxon over some stratigraphic gap. Because the likelihood of a hypothesis given data reflects the probability of the data given that hypothesis, these probabilities also give the likelihood of a hypothesized duration. However, many probability / likelihood tests require simplifying assumptions about unknown sampling parameters such as the consistency of sampling over time, sampling intensities for unknown ancestors, and actual sampling intensities themselves.This paper examines the effects of sampling parameters on probability / likelihood tests and presents methods for testing hypotheses about these unknowns while testing hypotheses about true durations. Two data sets are used here as examples. One analysis tests the origination times among Paleozoic gastropods implied by phylogenetic inferences. The other analysis tests the extinction times among Maastrichtian ammonites implied by different numbers of extinction events. In both cases, hypotheses positing many gaps in the fossil record become more likely after accommodating uncertainty about sampling. However, the increased likelihoods are insufficient to prevent these hypotheses from being rejected in favor of hypotheses positing fewer gaps. In both cases, the conclusions are identical to those derived by simple methods using simple models for unknown sampling parameters. Although numerous factors can exaggerate the implausibility of gaps, making these factors parts of testable hypotheses is possible. Thus, excessive assumptions about sampling parameters need not hinder empirical testing of hypothesized durations.
Homoplasy and the evolution of dinosaur locomotion
Authors: Carrano Matthew T. 
Published: July 2006

In this paper, I survey hindlimb and pelvic anatomy across non-avian dinosaurs and analyze these within a cladistic framework to quantify patterns of change within the locomotor apparatus. Specifically, I attempt to identify where homoplasy constitutes parallelism and may thereby be used to infer similar selective pressures on hindlimb function. Traditional methods of discrete character optimization are used along with two methods for evaluating changes in continuous characters in a phylogenetic context (squared-change parsimony and clade rank correlation). Resultant patterns are evaluated in light of the biomechanics of locomotion and the relationship between form and function in extant terrestrial vertebrates.Although non-avian dinosaurian locomotor morphology is strikingly uniform, these analyses reveal the repeated derivations of several morphological features that have potential relevance for hindlimb locomotor function. Anterior and posterior iliac expansion, a medially oriented femoral head, and an elevated femoral lesser trochanter each evolved independently multiple times within Dinosauria. These changes probably reflect enlargement of several hindlimb muscles as well as a general switch in their predominant function from abduction-adduction (characteristic of “sprawling” limb postures) to protraction-retraction (characteristic of parasagittal, or “erect,” limb postures). Several “avian” characteristics are shared with more basal theropods, and many were acquired convergently in other dinosaurian lineages. The evolution of the avian hindlimb therefore represents a cumulative acquisition of characters, many of which were quite far removed in time and function from the origin of flight.
A theoretical morphologic analysis of convergently evolved erect helical colony form in the Bryozoa
Authors: McGhee George R. , McKinney Frank K. 
Published: July 2006

Exploration of the theoretical morphospace of erect helical colony form in Bryozoa, created by McKinney and Raup (1982), reveals that only a small volume of the three-dimensional space of hypothetical form is occupied by actual colonies of the Paleozoic fenestrates (Class Stenolaemata) Archimedes and Helicopora, helical species of the cheilostome (Class Gymnolaemata) Bugula, and the cyclostome (Class Stenolaemata) Crisidmonea archimediformis. Actual helical-colony bryozoans are not found in regions of the morphospace characterized by colony geometries that possess the largest surface areas of filtration sheet. Examination of computer-simulated colonies in the theoretical morphospace reveals that, although possessing high surface areas, colonies in the empty region of high-surface-area morphospace possess other aspects of geometry that are unrealistic as filter-feeding geometries: the filtration-sheet whorls are held at small acute angles to the central colony axis and are deeply nested within one another, both of which are disadvantageous conditions for the system of filter feeding used by the extant cheilostome Bugula, and presumably by extinct helical-colony bryozoans as well.Even though actual bryozoans are found only in the low to intermediate surface-area regions of the theoretical morphospace, surface area of filtration sheet is a major determinant of form in these helical colonies, as is evidenced by a negative correlation in values of the parameters BWANG and ELEV exhibited by the colony data. Minimum values of BWANG are even further constrained by the apparent need of the Archimedes colonies to maintain filtration-sheet branching densities within the range of 20 to 50.
Evolution of hindlimb posture in nonmammalian therapsids: biomechanical tests of paleontological hypotheses
Authors: Blob Richard W. 
Published: July 2006

Analyses of limb joint morphology in nonmammalian therapsid “mammal-like reptiles” have suggested that among many lineages, individual animals were capable of shifting between sprawling and upright hindlimb postures, much like modern crocodilians. The ability to use multiple limb postures thus might have been ancestral to the generally more upright posture that evolved during the transition from “mammal-like reptiles” to mammals. Here I derive a biomechanical model to test this hypothesis through calculations of expected posture-related changes in femoral stress for therapsid taxa using different limb postures. The model incorporates morphological data from fossil specimens and experimental data from force platform experiments on iguanas and alligators.Experimental data suggest that the evolutionary transition from sprawling to nonsprawling posture was accompanied by a change in the predominant loading regime of the limb bones, from torsion to bending. Changes in the cross-sectional morphology of the hindlimb bones between sphenacodontid “pelycosaurs” and gorgonopsid therapsids are consistent with the hypothesis that bending loads increased in importance early in therapsid evolution; thus, bending stresses are an appropriate model for the maximal loads experienced by the limb bones of theriodont therapsids. Results from the model used to estimate stresses in these taxa do not refute the use of both sprawling and more upright stance among basal theriodont therapsids. Thus, the hypothesis that the use of multiple postures was ancestral to the more upright posture typical of most mammals is biomechanically plausible. Model calculations also indicate that the axial rotation of the femur typical in sprawling locomotion can reduce peak bending stresses. Therefore, as experimental data from alligators and iguanas suggest, the evolution of nonsprawling limb posture and kinematics in therapsids might have been accompanied by increased limb bone bending stress.
Comparative osteohistology of some embryonic and perinatal archosaurs: developmental and behavioral implications for dinosaurs
Authors: Horner John R. , Padian Kevin , de Ricqlès Armand 
Published: July 2006

Histologic studies of embryonic and perinatal longbones of living birds, non-avian dinosaurs, and other reptiles show a strong phylogenetic signal in the distribution of tissues and patterns of vascularization in both the shafts and the bone ends. The embryonic bones of basal archosaurs and other reptiles have thin-walled cortices and large marrow cavities that are sometimes subdivided by erosion rooms in early stages of growth. The cortices of basal reptiles are poorly vascularized, and osteocyte lacunae are common but randomly organized. Additionally, there is no evidence of fibrolamellar tissue organization around the vascular spaces. Compared with turtles, basal archosaurs show an increase in vascularization, better organized osteocytes, and some fibrolamellar tissue organization. In dinosaurs, including birds, vascularization is greater than in basal archosaurs, as is cortical thickness, and the osteocyte lacunae are more abundant and less randomly organized. Fibrolamellar tissues are evident around vascular canals and form organized primary osteons in older perinates and juveniles.Metaphyseal (“epiphyseal”) morphology varies with the acquisition of new features in derived groups. The cartilage cone, persistent through the Reptilia (crown-group reptiles, including birds), is completely calcified in ornithischian dinosaurs before it is eroded by marrow processes; cartilage canals, absent in basal archosaurs, are present in Dinosauria; a thickened calcified hypertrophy zone in Dinosauria indicates an acceleration of longitudinal bone growth.Variations in this set of histological synapomorphies overlap between birds and non-avian dinosaurs. In birds, these variations are strongly correlated with life-history strategies. This overlap, plus independent evidence from nesting sites, reinforces the hypothesis that variations in bone growth strategies in Mesozoic dinosaurs reflect different life-history strategies, including nesting behavior of neonates and parental care.
A multiplicative multifractal model for originations and extinctions
Authors: Plotnick Roy E. , Sepkoski J. John 
Published: July 2006

Recent works have suggested that the fossil record exhibits a fractal structure; i.e., that processes, such as extinction, follow a power-law size distribution and their time series show a 1/f power spectrum. This structure has been used as evidence that evolutionary dynamics are an example of a self-organized critical (SOC) process. We have reexamined this claim by analyzing a detailed record of marine genus-level extinctions and originations. Our results indicate that neither extinctions nor origination metrics show the power-law size distribution or a 1/f power spectrum characteristic of SOC and related models. We also believe that the underlying assumptions of SOC are incompatible with our understanding of the processes controlling macroevolutionary patterns.Statistical analyses of the data sets are compatible, however, with the presence of multifractal self-similarity in both records, consistent with a hierarchical and multiplicative generating process. This model assumes that multiple causal mechanisms, acting over many spatial and temporal scales, interact to promote or inhibit originations and extinctions. In this view, the same event can have quite different impacts depending on the state of the biotic or physical system at the time that it occurs. This may at least partially explain such phenomena as the imperfect correlation between eustatic sea-level changes and macroevolutionary processes and the apparent nonlinear response of biotic systems to bolide impacts.
Digital reconstruction of calcified early metazoans, terminal Proterozoic Nama Group, Namibia
Authors: Watters Wesley A. , Grotzinger John P. 
Published: July 2006

A method is presented for the digital reconstruction of weakly calcified fossils within the Nama Group, Namibia. These recently described fossils (Grotzinger et al. 2000) are preserved as calcitic void-fill in a calcite matrix, and individual specimens cannot be freed by conventional techniques. The technique presented here has several integrated steps: (1) the analysis of cross-sections of fossil specimens, (2) the construction of a three-dimensional “tomographic” model that is assembled from the cross-sections, (3) the development of an idealized mathematical model based upon geometric parameters measured from the tomographic model, and (4) the visualization of randomly oriented cross-sections through the mathematical model, which can be compared with fossil cross-sections in outcrop.In this procedure, rocks containing the fossils are ground and digitally photographed at thickness intervals of 25 μm. A battery of image-processing techniques is used to obtain the contour outlines of the fossils in serial cross-sections. A Delaunay triangulation method is then used to reconstruct the morphology from tetrahedrons which connect the contours in adjacent layers. We found that most of the fossils represent a single morphology with some well-defined characters that vary slightly among individual specimens. This fossil morphology was described by Grotzinger et al. (2000) as Namacalathus hermanastes. A mathematical description of the morphology is used to obtain a database of randomly oriented synthetic cross-sections. This database reproduces the vast majority of cross-sections observed in outcrop.
The imbalance of paleontological trees
Authors: Harcourt-Brown Katherine G. , Pearson Paul. N. , Wilkinson Mark 
Published: July 2006

One of the most extensively studied aspects of phylogenetic tree shape is balance, which is the extent to which nodes divide a tree into clades of equal size. Several authors have stressed the importance of tree balance for understanding patterns of evolution. It has been remarked that paleontological studies commonly produce very unbalanced trees (also called pectinate cladograms or “Hennigian combs”). This claim is tested here by comparing the balance of 50 paleontological trees and 50 neontological trees, all taken from the recent literature. Each tree was reanalyzed from the published data matrix to ensure its accuracy. The results confirm that paleontological trees tend to be more imbalanced than neontological trees.That paleontological trees are more imbalanced has been represented as a shortcoming of fossil data sets, but here it is argued that this is the expected result. Even under a simple Markovian model in which all speciations and extinctions occur randomly and with equal probability in all parts of the tree, trees based on taxa from a single time period (e.g., the present day) are generally more balanced than trees based on all taxa that ever existed within the clade. Computer simulation is used to calculate the expected balance and standard deviation of trees for up to 40 terminal taxa over the entire history of a model clade. The balance is measured using Colless's index, Ic, and the expected balance conforms well with published paleontological trees. The study underlines the difficulty of applying neontological tree statistics in paleontology.
How phylogenetic inference can shape our view of heterochrony: examples from thecideide brachiopods
Authors: Jaecks Glenn. S. , Carlson Sandra. J. 
Published: July 2006

Heterochrony is considered to be an important and ubiquitous mechanism of evolutionary change. Three components are necessary to describe heterochrony: phylogenetic relationships, size and shape change, and timing of developmental events. Patterns and processes of heterochrony are all too often invoked before all three components have been investigated. Phylogenetic hypotheses affect the interpretation of heterochrony in three ways: rooting of a clade, topology of a clade, and character polarity. To study these effects we examined the distribution of shell microstructure, lophophore support structures, and body size in four different phylogenetic hypotheses of thecideide brachiopods (Triassic to Recent), a group of minute, cryptic, benthic marine invertebrates.Thecideides are consistently monophyletic in experiments using terebratulide, strophomenate, and spire-bearing outgroups together and separately, varying ingroup membership, and experimentally withholding certain character complexes. Thecideide monophyly is also supported by bootstrap analysis. Hypotheses of heterochrony in thecideide origins and evolution are therefore not merely artifacts of classification and can be pursued further. Using either strophomenate or spire-bearing outgroups, TriassicThecospirais the most primitive thecideide. Trees constructed using terebratulide outgroups are rooted instead atEudesella, a taxon derived in every other phylogenetic reconstruction, and the Triassic thecideides occupy derived rather than primitive positions.Our phylogenetic results support the traditional interpretation of the reduction or loss of the secondary fibrous shell layer as a paedomorphic pattern, whereas the evolution of lophophore support structures suggests a peramorphic pattern. Reduction in thecideide adult body size is gradual, phylogenetically, and results in an overall paedomorphic pattern. Heterochrony in these three character suites may play a role in the subsequent evolution of the clade, but apparently not in the origin of the clade, as is commonly thought. Heterotopy, rather than—or in addition to—heterochrony, may account for both the origin and evolution of the lophophore support structures and in the reduction and loss of the secondary shell layer. These phylogenetic hypotheses suggest that heterochrony can result from a complex mosaic of processes and provide specific, testable predictions about the processes responsible for producing the patterns, whether heterochronic or not. Categorizing an entire clade (such as thecideides), rather than individual characters, as globally paedomorphic may allow interesting peramorphic patterns in individual characters to be overlooked.
Rate heterogeneity in shell character evolution among lophospiroid gastropods
Authors: Wagner Peter. J. 
Published: July 2006

Hypotheses about constraints, selection, and other evolutionary processes often predict different rates of change among different characters. For example, it is thought that gross soft anatomical characters change less frequently than do general shell characters. However, some shell characters on primitive gastropods, such as the sinus and selenizone, are thought to be linked to soft anatomy. If both premises are true, then selenizone/sinus characters should change less frequently than other characters. Workers also have documented active trends among gastropod shell characters. One explanation is a driven trend, where the rate of change in one direction (i.e., gain or loss, increase or decrease) is greater than the rate of change in the opposite direction.Hypotheses about relative rates and biased change are tested here for lophospiroid gastropods. Likelihood analyses test whether hypotheses positing many different rates predict data significantly better than do hypotheses positing few rates. One tree-based approach assumes that a phylogeny is known and thus treats a tree as a model. A second tree-based approach treats phylogeny as an additional hypothesis. This multiparameter approach allows competing rate hypotheses to “assume” a phylogeny that maximizes their likelihoods.Likelihood tests reject hypotheses of low rate heterogeneity among lophospiroid characters. The most likely hypothesis (which treats phylogeny as an unknown) posits seven rates, with biased changes among three characters (preferential reduction of both sinus depth and sinus width and preferential addition of ornament). The distribution of rates among different character classes is consistent with the prediction that characters associated with internal anatomy should show generally lower rates of change than those associated with gross shell morphology. Evaluating significance when contrasting hypotheses posit different phylogenies is problematic, but the difference in support (log-likelihood) is overwhelming. Even if a model phylogeny is used, we still reject all hypotheses using fewer than six rates and not invoking trends in sinus characters. Thus, it is difficult to avoid rejecting the hypothesis that shell characters are uniformly plastic.
Evolutionary trends in coiling of tropical Paleogene planktic foraminifera
Authors: Norris Richard. D. , Nishi Hiroshi 
Published: July 2006

Populations of planktic foraminifera display “proportionate” coiling (approximately 50% sinistral and dextral individuals given the data at hand) or may have “biased“ coiling, in which populations are dominated by either sinistral or dextral individuals. The major radiations of planktic foraminifera in the Late Cretaceous, the Paleocene to early Eocene, the middle Eocene, and the Neogene were each initiated by clades with proportionate coiling but subsequently accumulated sinistral and dextral species over time. Upper Maastrichtian foraminifera were predominantly dextral, but only the small number of species with proportionate coiling actually survived the Cretaceous/Paleogene mass extinction. The first Paleocene species with biased coiling appeared about four million years after the extinction and gradually came to represent as much as 50–60% of the tropical species diversity by the latest Paleocene. Tropical taxa with biased coiling suffered a second extinction in the late early Eocene and renewed a trend toward an increased abundance of species with biased coiling in the middle Eocene.Our results for the Paleogene reflect a recurring theme in foraminifer evolution. In each radiation, once the founding species of a clade developed a biased-coiling mode, the descendants tended to maintain biased coiling until the extinction of the clade. The iterative evolution of biased coiling appears to represent an example in which a fundamental feature of development becomes fixed in a clade and inhibits reversion to an ancestral state. Apparently, coiling patterns are heritable in contrast with previous interpretations that coiling is environmentally controlled. On evolutionary timescales, species with proportionate coiling are less susceptible to extinction than species dominated by sinistral or dextral forms. Differential survivorship ensures that each radiation is initiated from founders with proportionate coiling following mass extinction. Hence, coiling preferences represent a case where the establishment of an evolutionary trend is caused by drift away from a “limiting boundary,” much like the evolution of large body size from ubiquitous small ancestors.