bluuebunny/crossref_metadata_2025_split huggingface dataset:
Decay and preservation of polychaetes: taphonomic thresholds in soft-bodied organisms
Authors: Briggs Derek E. G. , Kear Amanda J. 
Published: July 2016

A series of experiments was carried out to investigate the nature and controls (oxygen, microbial populations, agitation) on the degradation of soft tissues. Decay was monitored in terms of morphological change, weight loss, and change in chemical composition in the polychaete Nereis virens. Polychaetes include a range of tissue types of differing chemical composition and preservation potential: muscle, cuticle, setae, and jaws. Regardless of conditions, all the muscle had broken down and fluid loss through the ruptured cuticle had reduced the carcass to two dimensions within 8 days at 20°C. In most cases some cuticle, in addition to the jaws and setae, remained after 30 days. Where oxygen was completely eliminated, the rate of decay of the more volatile issues was significantly reduced. The degree of both osmotic uptake of water by the carcass and changes in water pH differed depending on whether the system was open or closed to oxygen diffusion. Autolytic and chemical processes are not sufficient to fully degrade the carcass in the absence of bacteria. Where internal bacteria are present, the presence or absence of water column bacteria made little difference to decay rate. Initial degradation (in the first 3 days) affects mainly the lipid fraction and the collagen of the cuticle. Later decay reduces the nonsoluble protein and increases the relative proportion of refractory structural components (tanned chitin and collagen) to more than 95% by day 30. Thus, only the sclerotized tissues are likely to survive beyond 30 days in the absence of early diagenetic mineralization. The sequence of degradation predicted from the relative decay resistance of macromolecules in the sedimentary record (protein → carbohydrate → lipid) is not, therefore, a consistent indicator of the preservation potential of structural tissues which incorporate them.The experiments reveal five stages in the decay of polychaete carcasses; whole/shriveled, flaccid, unsupported gut, cuticle sac, jaws and setae. All are represented in the fossil record. This allows an estimation of how far decay proceeded before it was halted by the fossilization process. The most complete preservations occur in the Cambrian where the Burgess Shale preserves evidence of muscle tissues. Traces of the gut and cuticle are more widely preserved, as at Mazon Creek, Grès à Voltzia, Solnhofen, and Hakel. Preservation varies within Konservat-Lagerstätten. The most common whole body preservation includes only the more recalcitrant tissues, jaws (where present) and setae, with an impression of the body outline. The stage of decay can be used as a taphonomic threshold, to provide an indication of how significantly the diversity of an exceptionally preserved biota is likely to have been reduced by taphonomic loss.
Is a new and general theory of evolution emerging?
Authors: Gould Stephen Jay 
Published: July 2016

The modern synthesis, as an exclusive proposition, has broken down on both of its fundamental claims: extrapolationism (gradual allelic substitution as a model for all evolutionary change) and nearly exclusive reliance on selection leading to adaptation. Evolution is a hierarchical process with complementary, but different, modes of change at its three major levels: variation within populations, speciation, and patterns of macroevolution. Speciation is not always an extension of gradual, adaptive allelic substitution to greater effect, but may represent, as Goldschmidt argued, a different style of genetic change—rapid reorganization of the genome, perhaps non-adaptive. Macroevolutionary trends do not arise from the gradual, adaptive transformation of populations, but usually from a higher-order selection operating upon groups of species, while the individual species themselves generally do not change following their geologically instantaneous origin. I refer to these two discontinuities in the evolutionary hierarchy as the Goldschmidt break (between change in populations and speciation) and the Wright break (between speciation and trends as differential success among species).A new and general evolutionary theory will embody this notion of hierarchy and stress a variety of themes either ignored or explicitly rejected by the modern synthesis: punctuational change at all levels, important non-adaptive change at all levels, control of evolution not only by selection, but equally by constraints of history, development and architecture—thus restoring to evolutionary theory a concept of organism.
Recognizing morphospecies in colonial reef corals: I. Landmark-based methods
Authors: Budd Ann F. , Johnson Kenneth G. , Potts Donald C. 
Published: July 2016

Morphologic discrimination of species of scleractinian reef corals has long been plagued by a shortage of independent characters and by high ecophenotypic plasticity. Because of these two factors, many species appear to intergrade morphologically. We outline a newly developed protocol for the morphometric recognition of species, which uses size and shape coordinates derived from landmark data. The landmarks consist of spatially homologous points digitized in three dimensions on upper calical surfaces. The approach is more powerful than linear measurements at detecting subtle distinctions among species; and the distinctions are easy to visualize and interpret biologically, which increases the accuracy and resolution of subsequent phylogenetic and large-scale faunal analyses.As an example, we distinguish morphospecies in collections of Porites made at three Caribbean locations. Size and shape coordinates are analyzed using principal component analysis, average linkage cluster analysis, and a series of iterative discriminant analyses. Positions of different corallites from the same colonies are examined on cluster dendrograms to determine cutoffs for group recognition, and discriminant classifications for different corallites from the same colonies are compared to maximize group assignments. The results yield seven morphospecies, which are generally in 90% agreement with classification of the same animals using allozyme electrophoresis. Measures of corallite size and the relative heights and locations of the pali and septal denticles all reveal unique patterns of variation among morphospecies.
A study of stasis and change in two species lineages from the Middle Devonian of New York state
Authors: Lieberman Bruce S. , Brett Carlton E. , Eldredge Niles 
Published: July 2016

More than 5000 measurements were taken on over 1000 specimens of two species of brachiopods,Mediospirifer audaculusandAthyris spiriferoides,from the Middle Devonian Hamilton Group of New York state. Statistical analyses were performed on these data, with specimens partitioned by their occurrence in one of many paleoenvironments and stratigraphic horizons. Neither species showed substantial morphological departures between first appearance and extinction (the range of the Hamilton Group, roughly 5 m.y.). However, oscillations in morphology were discovered in both taxa.For the two species we studied, groups of organisms occurring in a single paleoenvironment undergo moderate morphological change through time; however, the net sum of changes through time in all paleoenvironments in which these species occur is essentially zero. Therefore, stasis may be partly a property of the organization of species into different environmental populations. Different “environmental populations” may evolve, but they will typically do so in several different “directions,” generally producing no net change. The difference between the morphology of species in different environments over the whole interval of the Hamilton Group is also nil, thereby ruling out any major role that ecophenotypic effects could play in the patterns recognized herein.
Observed phenotypic variation in a Paleozoic bryozoan
Authors: Hageman Steven J. 
Published: July 2016

Documentation of morphologic variation within and among fossil species (and larger clades) provides fundamental data needed for studies of evolution, paleoecology, and the systematic foundation required for most fields of paleobiology. In paleontological (and, frequently, biological) studies, morphologic variation is used as a general proxy for genetic variation. Although the occurrence of ecophenotypic variation is well appreciated in these studies, it is only with the use of colonial (clonal) organisms that the scope and significance of phenotypic variation can be evaluated directly. Systematic evaluation of intracolonial morphologic variation (transects through growth series) can yield insights about ecophenotypic variation in bryozoans and suggest the most appropriate methods for data collection in paleobiologic and taxonomic studies.In this study, morphological conservatism is documented within local segments of bryozoan colonies; each zooid is generally more similar to adjacent zooids than to distant zooids within the same colony. One region of a colony, therefore, can be more similar to a region of a different colony than to a distant region of its own colony. Variation within one colony does not, however, represent the total variation among a group of specimens, indicating a colonial level of morphologic control (genetic or macroenvironmental) over morphogenesis. Directional morphogenetic gradients (associated with successive ontogenetic histories) are not recognized in these specimens, but fluctuating trends within colonies (some cyclic), were observed and are indicative of changing microenvironmental influence during skeletal formation. In order to best document morphologic variation within a population, for any type of paleobiological study, individual measurements should be widely distributed over large colony fragments and (or) a minimal number of measurements collected from each of a large number of smaller fragments.Direct extrapolation of these results to non-colonial organisms is not appropriate at this time. However, additional, related studies with bryozoans and other colonial organisms (e.g., corals, graptolites), should provide a greater, general appreciation of relationships between morphology and genetics.
The Feeding Habits of the Shovel-Tusked Gomphotheres: Evidence From Tusk Wear Patterns
Authors: Lambert W. David 
Published: July 2016

The shovel-tusked gomphotheres are normally portrayed scooping up water plants with their shovellike mandibular tusks. This portrayal is based on speculation about the possible functions of the lower tusks and misinterpretation of mandibular-tusk wear patterns that goes back to the 1920s and 1930s. In addition, most literature concerning shovel-tusker feeding behavior ignores the possibility that the upper tusks may have had a role in feeding, as they do in modern African elephants. Because wear patterns on tusks provide direct evidence as to how tusks were used during feeding, I examined and interpreted patterns on the lower and upper tusks of shovel-tusked gomphotheres on the basis of theoretical models of tusk wear to determine how the tusks were used in feeding.This examination led to the following conclusions. (1) The genus Amebelodon was characterized by feeding opportunism, gathering food with both its lower and upper tusks in a variety of ways. (2) There is evidence for similar flexibility within the genus Serbelodon. (3) Wear patterns on mandibular tusks of Platybelodon grangeri and Torynobelodon barnumbrowni indicate that these taxa did not practice mandibular shoveling but used these tusks to cut tough vegetation in a specialized fashion. (4) The flaplike trunks (probosces) generally attributed to shovel-tusked gomphotheres in restorations are shown almost certainly to be erroneous; morphological and functional evidence suggests that these animals had trunks similar to those of modern elephants. (5) Strong tusk sexual dimorphism is unknown in the shovel-tusked gomphotheres except for Platybelodon and should not be found in any taxa that relied on their tusks for procuring food. New restorations of both Amebelodon and Platybelodon are provided that are more consistent with the actual evidence bearing on their feeding behavior.
Trilobite biogeography in the Middle Devonian: geological processes and analytical methods
Authors: Lieberman Bruce S. , Eldredge Niles 
Published: July 2016

Phylogenetic patterns of trilobite clades were used to deduce biogeographic patterns during the Middle Devonian, a time of active plate collision between North America (Laurentia) and other plates, coincident with several major episodes of sea-level rise and fall. The mapping of biogeographic states onto phylogenies for asteropyginid and proetid trilobites indicated that during their history these trilobite clades often shifted the areas they occupied, and also underwent vicariant differentiation, followed by range expansion, followed by subsequent vicariance. Biogeographic patterns in these individual phylogenies were evaluated and synthesized using a modified version of Brooks Parsimony Analysis, which is discussed. This method makes it possible using cladistic methods to distinguish between episodes of vicariance and episodes of dispersal. Two types of dispersal are recognized herein: (1) the individualistic responses of certain taxa in a single clade that cannot be generalized, i.e., traditional ad hoc dispersal, and (2) those patterns of congruent range expansion that are replicated across several clades. The latter are not treated as true dispersal, expansion of a taxon's range over a barrier accompanied by diversification, but rather as a result of the temporary removal of barriers to marine taxa, due either to relative sea-level rise or to the collision of formerly disjunct plates. These are interpreted as changes in the structure of areas, and this type of dispersal is referred to as geo-dispersal. Geo-dispersal was found to have occurred in the Middle Devonian trilobite fauna of Eastern North America.Biogeographic analysis indicated that Eastern North America is a strongly supported area, with the Appalachian and Michigan Basins as sister areas. Armorica and the Canadian Arctic are also sister areas. Congruence was found between area cladograms produced by vicariance and dispersal analyses for Middle Devonian trilobites, suggesting that in some cases the geological processes governing vicariance, such as sea-level changes, were the same as those that caused dispersal.
Comparative taphonomy of bivalves and foraminifera from Holocene tidal flat sediments, Bahia la Choya, Sonora, Mexico (Northern Gulf of California): taphonomic grades and temporal resolution
Authors: Martin Ronald E. , Wehmiller John F. , Harris M. Scott , Liddell W. David 
Published: July 2016

We compare the preservation (taphonomic grade) and age ofChione(bivalve) and foraminifera from modern siliciclastic tidal flat sediments of Bahia la Choya, Sonora, Mexico (northern Gulf of California). Disarticulated shells ofChionecollected from the sediment-water interface of Choya Bay exhibit a substantial range in taphonomic grade and age, several hundred years to ∼80–125 ka based on Accelerator Mass Spectrometer14C dates and D-Alloisoleucine/L-Isoleucine values. There is not, however, a one-to-one correspondence between age and taphonomic alteration ofChione:old (or young) valves may be highly altered or they may be relatively pristine. In contrast toChione, most foraminiferal tests at Choya Bay are quite pristine, which suggests a quite young age, but tests are surprisingly old (up to ∼2,000 calendar years based on Accelerator Mass Spectrometer14C dates).We suggest that following seasonal pulses in reproduction, some foraminiferal tests are rapidly incorporated into a subsurface shell layer by “Conveyor Belt” deposit feeders and preserved there, while the rest of the reproductive pulse rapidly dissolves. Ultimately, some of these buried tests, along withChione, are transported back to the surface by biological activity and storms. The much greater range of taphonomic grades and ages amongChioneshells suggests that they, unlike foraminifera, are sufficiently large and preservable (low surface/volume ratio and chemical reactivity) to undergo many cycles of degradation, burial, and exhumation before complete destruction. The age of foraminiferal tests indicates that time-averaging of microfossil assemblages at Choya Bay is much more insidious than would be expected considering the relatively pristine state of the tests alone.Based on our studies, the lower limit of temporal resolution of shallow shelf microfossil assemblages appears to be ∼1000 years. We caution, however, that each depositional setting (taphofacies) should be evaluated on a case-by-case basis before gross generalizations are made. Indeed, the discrepancy between age and taphonomic grade of fossil assemblages at Choya Bay suggests that neither hardpart size or taphonomic grade are infallible indicators of test preservability or likely temporal resolution of the host assemblage, and that the dynamics of hardpart input and loss must also be evaluated.
Fossil preservation and the stratigraphic ranges of taxa
Authors: Foote Mike , Raup David M. 
Published: July 2016

The incompleteness of the fossil record hinders the inference of evolutionary rates and patterns. Here, we derive relationships among true taxonomic durations, preservation probability, and observed taxonomic ranges. We use these relationships to estimate original distributions of taxonomic durations, preservation probability, and completeness (proportion of taxa preserved), given only the observed ranges. No data on occurrences within the ranges of taxa are required. When preservation is random and the original distribution of durations is exponential, the inference of durations, preservability, and completeness is exact. However, reasonable approximations are possible given non-exponential duration distributions and temporal and taxonomic variation in preservability. Thus, the approaches we describe have great potential in studies of taphonomy, evolutionary rates and patterns, and genealogy.Analyses of Upper Cambrian-Lower Ordovician trilobite species, Paleozoic crinoid genera, Jurassic bivalve species, and Cenozoic mammal species yield the following results: (1) The preservation probability inferred from stratigraphic ranges alone agrees with that inferred from the analysis of stratigraphic gaps when data on the latter are available. (2) Whereas median durations based on simple tabulations of observed ranges are biased by stratigraphic resolution, our estimates of median duration, extinction rate, and completeness are not biased. (3) The shorter geologic ranges of mammalian species relative to those of bivalves cannot be attributed to a difference in preservation potential. However, we cannot rule out the contribution of taxonomic practice to this difference. (4) In the groups studied, completeness (proportion of species [trilobites, bivalves, mammals] or genera [crinoids] preserved) ranges from 60% to 90%. The higher estimates of completeness at smaller geographic scales support previous suggestions that the incompleteness of the fossil record reflects loss of fossiliferous rock more than failure of species to enter the fossil record in the first place.
Fourier analysis applied toStephanomys(Rodentia, Muridae) molars: nonprogressive evolutionary pattern in a gradual lineage
Authors: Renaud Sabrina , Michaux Jacques , Jaeger Jean-Jacques , Auffray Jean-Christophe 
Published: July 2016

Size and shape are analyzed for Pliocene lineages of the rodent genusStephanomysSchaub 1938. Previous phylogenetic studies were based mainly on size variation and descriptive comparisons, without any attempt to quantify shape changes. Hence, on the basis of regular size increase,Stephanomyshas been considered a prime example of phyletic gradualism. In order to quantify morphological variation within the lineage, a method for analyzing complex outlines, the elliptic Fourier transform, was applied to tooth contour (upper and lower first molars). It was then possible to compare evolution in size, estimated by tooth area, as well as evolution of shape, represented by Fourier coefficients.While size seems to change gradually through time, morphology gives a rather discontinuous evolutionary pattern for both the upper and lower molar. Such a discrepancy between the evolution of size and shape of a single structure suggests that different genetic determinisms and mechanical constraints may act on size and shape. Hence it may be misleading to infer generalized evolutionary processes from either size or shape alone.
Isotopic evidence for interspecies habitat differences during evolution of the Neogene planktonic foraminiferal clade Globoconella
Authors: Schneider Cynthia E. , Kennett James P. 
Published: July 2016

Oxygen and carbon isotopic analyses have been conducted on Miocene to Pliocene (6.0 to 2.9 Ma) members of the gradually evolving, deep-dwelling planktonic foraminiferal clade, Globoconella, in temperate waters of the southwest Pacific, Deep Sea Drilling Project (DSDP) Site 593. In the late Miocene the clade began with Globoconella conoidea, and continued through G. conomiozea, G. sphericomiozea, and G. puncticulata to the extant form G. inflata. Isotopic analyses were performed on ancestor-descendant species within the clade to determine if isotopic differences exist between these species which would, in turn, suggest depth and/or seasonal habitat differences and perhaps segregation, as well as ecological changes in the clade. Isotopic analyses were also conducted on the relatively shallow-dwelling planktonic foraminifer Orbulina universa and the benthic form Cibicidoides wuellerstorfi to determine if any relationships exist between the evolution of Globoconella and paleoceanographic/paleoclimatic change.Small (usually 0.1–0.15 ‰ but up to 0.3 ‰) oxygen isotopic differences exist between ancestor and descendant forms that we believe represent small (∼1°) temperature differences. These temperature differences are inferred to indicate depth and/or seasonal habitat differences and possible segregation between the species during the gradual evolution. The largest differences in oxygen isotopic values occur between ancestor and descendant forms during the most conspicuous morphological transition within the clade near the Miocene/Pliocene boundary. During this interval, the clade underwent a transformation from conical to spherical forms and there was a loss of the keel. No consistent differences were observed between ancestor and descendant carbon isotopic values.Both morphological and ecological evolution appear to have been associated with paleoceanographic/paleoclimatic changes. Intervals marked by warming of surface-to-upper intermediate waters are associated with evolution of forms with a spherical test and inferred adaptation to cooler waters relative to ancestral forms. We propose two alternative models for the evolution of the Globoconella clade. In the first model, we assume that depth and/or seasonal segregation between ancestor and descendant forms provided a partial barrier to gene flow and that evolution resulted from genetic drift and/or differential selective pressures acting on each morphotype. In the second model, we assume that coeval members of Globoconella formed a vertical and/or seasonal morphocline in the water column and that segregation did not provide an effective barrier to gene flow. Evolution proceeded as directional selection acted on morphotypes of Globoconella inhabiting selectively advantageous positions in the water column.