bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rates of evolution and fossils in phylogenetic analysis: a computer simulation approach
Authors: Huelsenbeck John P. , Hillis David M. 
Published: January 2018

Whereas many studies have examined the performance of various character-data sets in phylogenetic analysis, little work has been done on the effect that various classes of taxa have on phylogenetic reconstruction. In particular, the “fossil versus living taxa” debate has concentrated mainly on the effects of fossils in reconstructing vertebrate and plant relationships. While this work has contributed to the understanding of the role that fossils play in systematics, a computer model clarifies the relationship among the main determinants of the fossil-taxa problem. In addition, simulations of phylogenies over a wide spectrum of evolutionary rates clarify the relative efficiencies of various tree-estimation procedures.In this study, computer generated phylogenies were used to examine the relationship between the temporal position and completeness of additional taxa in a phylogenetic analysis and the rate of evolution or, equivalently, the temporal scope of the phylogenetic problem. In the simulations, four fossil taxa of varying temporal position and completeness were added to an analysis that included four living taxa. Additional taxa varied in completeness (25%, 50%, 75%, and 100% completeness) and in temporal position (0%, 33%, 66%, and 100% of the distance from the ancestor to the living time plane). Fifty trees were generated each for low, low intermediate, high intermediate, and high rates of evolution or temporal scope. Because additional taxa that are 100% complete and 100% of the distance to the living time plane are equivalent to the addition of living taxa, this study directly compares the effects of addition of living versus fossil taxa in phylogenetic analysis.The importance of fossil taxa varied depending on their completeness and temporal position and on the rate of evolution under which the phylogeny was generated. In general, high completeness and temporal position near the ancestor of a clade improved phylogenetic resolution as measured by the percentage of the tree-length distribution that contains the real tree. Furthermore, the conditions of completeness and temporal position under which fossil taxa improved phylogenetic resolution over living taxa became less restrictive as the rate of evolution or the temporal scope of the tree increased.
Molluscan diversification and extinction on opposite sides of the Isthmus of Panama
Authors: Jackson Jeremy B. C. , Jung Peter 
Published: January 2018

Molluscs are the most diverse and abundant tropical American macrofossils, but their distributions and evolution are not well understood. Classic studies by Olsson and Woodring documented a rich Late Miocene to Early Pliocene “Gatunian” fauna throughout the Caribbean and tropical Eastern Pacific, with many species in common between the oceans. This fauna was divided by formation of the Isthmus of Panama, and diverged into distinct Pacific and Caribbean faunas sometime thereafter. Diversity also decreased by about half in the Caribbean. However, the timing, rates and correlation of these major biological changes with changes in environmental conditions have not been resolved because of imprecise dating and taxonomy and failure to consider problems of sampling and biofacies in biological comparisons. We used the newly revised late Neogene stratigraphy for Panama and Costa Rica to date for the first time the radiation and extinction of molluscs on opposite sides of the Isthmus. Data include occurrences throughout tropical America for nearly 100 species of the Strombina-group (Gastropoda, Columbellidae) and for more than 500 gastropod and bivalve genera from 240 Late Miocene to Pleistocene isthmian collections.All evidence suggests that final closure of the Isthmus of Panama occurred between 3.5 and 2.5 My. Subgeneric divergence between the oceans was well developed, and trans-isthmian species were rare by the Early Pliocene, at least 2 Ma before final closure. Caribbean diversity remained high until 1.8 to 1.5 Ma when massive but selective extinction occurred. This was at least 1 Ma after final closure of the Isthmus, and may be correlated with onset of slightly cooler Caribbean sea surface temperatures in the Pleistocene. In contrast, Eastern Pacific diversity did not decline, and even increased during the Pleistocene.
Color in ostracode shells: taphonomy and paleotemperature interpretation
Authors: Kontrovitz Mervin , Slack Jerry Marie , Ainsworth Nigel R. , Burnett Richard D. 
Published: January 2018

Interpretations of geologic history would be enhanced if taphonomic processes, including color changes in shells, were better known. This study deals with the origins and alteration of post-mortem colors in podocopid ostracodes. Modern shells were subjected to elevated temperatures and pressures in reactor vessels with sediments, simulating some burial conditions. Fossil shells from outcrops and boreholes were heated and treated with solvents, in an attempt to identify the coloring agent(s).Modern marine shells are white to pale yellow (Munsell 5Y 8/1 – 2.5Y 8/4). Upon heating at atmosphere, up to about 650°, they became slightly redder, slightly darker, and less color saturated, but never dark (Munsell “value” less than 5). From 650-850° they became yellower and lighter, and above 850° chalky and more yellow. Shells at elevated temperatures and pressures (T-P) with organic-poor sediments and/or iron compounds developed higher color values and lower chromas; they did not become dark. Thus, modern ostracode shells subjected to elevated T-P changed colors, but alone never attained the dark colors seen in many fossils. Only those heated in matured organic-rich sediment and/or crude oils became dark (dark grays, browns, and blacks), like some fossils. Fossil ostracodes from boreholes in Mesozoic and Cenozoic sedimentary rocks showed downhole color differences similar to those from experiments. That is, the colors of fossils are different in hue, value and chroma in different thermal zones and ostracode color appears to be broadly indicative of thermal history.Fossils near igneous intrusions are dark, while the lowered values and chromas of those in metamorphics also are correlatable with paleotemperatures. Reheated dark fossils lightened at about 375-450°, eventually becoming pale yellow to white, apparently indicating that organic coloring agents were driven off. This, and the fact that modern ostracodes develop dark colors only when heated in organic-rich substances, support the contention that the dark color originates from extrinsic organic materials. Pyritized shells become weak red (Munsell 10R 4/4) upon heating; thus, they can be distinguised from those colored by organics.Therefore, ostracode colors appear to be diagnostic of T-P and present the potential for use in paleotemperature reconstructions. A wide range of fossils, including conodonts, phosphatic brachiopods, scolecodonts, and palynomorphs are known to show recognizable and useful evidence of thermal maturation and it is proposed that ostracodes be added to the list.
Biothems: sequence stratigraphic units and their implications for regional tectono-stratigraphic interpretations
Authors: Lane H. R. , Frye M. W. , Couples G. D. 
Published: January 2018

Biothems are regional wedge- or lens-shaped bodies of strata that are: bounded shelfward or cratonward by paleontologically recognizable unconformities; generally thicken on marine shelves, where they are typically conformable with underlying and overlying biothems; are commonly thinner or represent “starved” sequences further basinward; and in their most basinward extent, are either bounded by biostratigraphically recognizable unconformities or are conformable with underlying and overlying biothems. Biothems are practical units whose definition and degree of refinement are dependent on the quality and availability of biostratigraphic control. As recognized to date, biothems have a logical distribution of faunal and floral components, as well as facies groupings that represent internally consistent and logical sequences of depositional environments. The use of biothems as primary sequence stratigraphic units places the emphasis on relative time in a stratigraphic framework.A west-to-east transect within the North American Mississippian System, which extends from the Basin and Range Province, across the Transcontinental Arch (TA) and into the Anadarko Basin, was constructed to demonstrate the regional distribution and tectono-stratigraphic significance of biothems relative to the axis of the TA. The relationships portrayed on the transect, tied to an understanding of North American Mississippian paleogeography, imply that biothems deposited during relative highstand events on one flank of the TA are time-equivalent to biothems deposited during relative lowstand events on the opposite flank of the TA. This distribution is interpreted to have been controlled by intraplate tectonic events that formed “piano-key” basins along the flanks of the TA. The spatial patterns of these basins are not consistent with published models of basin evolution. A further conclusion is that the lack of transgressive or regressive coincident Mississippian biothems on either flank of the TA suggests that it is inadvisable to impose the Mississippi Valley-derived eustasy curve on western flank depositional sequences.
Paleoecology of Cyclocrinites darwini (Miller) - a cyclocrinitid alga from the Cincinnatian series (Upper Ordovician)
Authors: Lask Peter B. 
Published: January 2018

Cyclocrinitids are considered to be calcareous green algae closely related to, or members of, the dasycladacean algae. Cyclocrinitids are characterized by a globular thallus 1-5 cm in diameter consisting of whorls of calcified meromes borne from a tubular or spherical central axis. The species Cyclocrinites darwini is distinguished from other cyclocrinitids by the presence of lateral branches arranged in a stellate pattern at the distal end of each merome.C. darwini is restricted to strata of the Cincinnatian Series. Specimens are commonly found in shale-filled channels cutting through nodular, irregularly-bedded limestones within the Mt. Auburn Formation and the lower Sunset Member of the Arnheim Formation. Numerous specimens are also known from the Bellevue Member of the Grant Lake Formation at Maysville, Kentucky. Each of these units has been interpreted to be the top of separate shoaling-upward, third-order cycles. These facies are abundantly fossiliferous, often consisting of broken, abraded, and reworked material.The modern dasyclad Neomeris is cited for its structural similarity to the cyclocrinitids and ecological parallels have been postulated as well. Neomeris and a similar dasyclad Batophora, thrive while attached to pieces of coral rubble at depths of less than 3 m in the high-energy conditions associated with a reef crest environment at Key Largo, Florida.It is likely that C. darwini lived under similar conditions, attached to rubble in shoaling areas. Preservation only occurred in instances when thalli were broken off from their holdfasts and swept into ripple troughs or downslope channels cutting across the shoals. It has been suggested that the presence of cyclocrinitids is indicative of relatively quiet environments below wave base. For Cyclocrinites darwini, the opposite would appear to be the case.
Epibionts on Chlamys hastata and Chlamys rubida: taphonomic and paleoecologic implications
Authors: Lescinsky Halard 
Published: January 2018

Although many fossil epibiont assemblages have been described, the taphonomy of these assemblages is poorly understood. In an effort to investigate the percentage of epibiontic organisms that would likely be preserved in the fossil record, and the contemporaneity of epibionts on a particular shell, I investigated the epibionts on live and dead Chlamys hastata and C. rubida from around San Juan Island, Washington. Using a video imaging system, over 300 shell surfaces were examined and the percent covers of epibionts in eight taxonomic categories were calculated.The left (upper) valves of live Chlamys had an average epibiont cover of 75% that was composed primarily of sponge, or a combination of barnacles and sabellid annelids. The preservable portion of this assemblage (18%) was significantly less than that of epibionts on the exteriors (68%) and interiors (87%) of dead valves. On dead shell surfaces, sponge coverage is <1%, and there are higher proportions of cheilostome and cyclostome bryozoans, and serpulid and spirorbid annelids.On upper surfaces (left valves) of living Chlamys, 10% of the epibiont cover was composed of dead organisms. An even greater percentage of dead epibiont cover existed on lower valves of live individuals (25%), and on dead valves (37-47%). During the study, no unambiguous examples of competitive interactions were found except for barnacles overgrowing barnacles and other epibionts. Numerous other overgrowths were observed, but these resulted from growths over dead organisms, or growths over mineralized skeleton, not living tissue.These results suggest that exact contemporaneity between epibionts should not be assumed in paleoecological studies.and that soft bodied and agglutinating organisms may have been important constituents of some paleocommunities. Encrusting epibiontic sponge actually protects shell surface ornamentation and may be evidenced in the fossil record by particularly clean and unfouled shells.
The ecology of xenophyophores, an enigmatic group of agglutinating rhizopods
Authors: Levin Lisa A. 
Published: January 2018

Xenophyophores are large, agglutinating protozoans whose modern distribution is limited exclusively to the deep sea (> 500 m water depth). Test morphologies vary from simple discoidal forms to elaborately folded or reticulated forms. Often specific particle sizes or minerals are selected for test construction. Tests are typically 1-5 cm in diameter, but some species may be up to 25 cm in longest dimension. Xenophyophores have been reported from a wide variety of soft- and hard-substrate deep-sea settings, including foram sands, calcareous and hemipelagic oozes, manganese nodule beds, fresh basalts, and hydrothermal oxides. They appear to obtain highest densities (often > 1/m2) on sloped substrates such as occur on seamounts, continental slopes, canyons, and trenches. Most xenophyophores live as epifauna on the sea floor and feed by actively or passively capturing suspended particles, but several species live as infauna and are presumed to be deposit feeders. It has been proposed that xenophyophores may garden bacteria within tests to provide an additional food source. Xenophyophores are distinguished from foraminifera by the occurrence of: (1) protoplasm encased within an organic membrane, (2) barite crystals within the protoplasm, and (3) tightly packed strands of fecal pellets (stercomare) within an organic membrane in the test.Xenophyophore tests and surrounding sediments are known to be hotspots of metazoan activity in a variety of settings. Tests provide habitat and presumably refuge for many invertebrate groups, and sediments beneath epifaunal xenophyophore tests often exhibit elevated densities of macrofauna and meiofauna. Radiochemical studies suggest that xenophyophore tests are sites of enhanced particle flux to the seabed. Associated metazoans may be taking advantage of elevated food supplies in the vicinity of tests, or may be passively trapped by xenophyophore tests during dispersal stages.Xenophyophores are not known from the fossil record. A resemblance between the infaunal xenophyophore Occultammina profunda and the trace fossil Paleodictyon has been noted by Swinbanks. Similar structures have been observed on the mid Atlantic ridge, but their identification as xenophyophores has not been confirmed. Maybury and Evans report a strong resemblance in external morphology, fine structure and barite content between modern xenophyophores in the genus Psammina and some Carboniferous phylloid algae, but fall short of suggesting a systematic relationship. Broader knowledge of xenophyophore morphology and ecology among ichnologists may lead to discovery of possible fossil antecedents. In addition, confirmation of xenophyophore presence could provide valuable information concerning paleohabitats.
Molecular taphonomy of plant tissue at the Miocene Clarkia site, northern Idaho
Authors: Logan Graham 
Published: January 2018

The 17–20 million year old Miocene locality at Clarkia, northern Idaho, has become renowned as the first site to yield amplifiable DNA of geological age. This discovery has opened up the possibility of phylogenetic studies on fossil tissue using preserved DNA. However, the conditions required for DNA preservation in the fossil record are not understood. An organic geochemical study of fossil tissue and sediments has been undertaken at the Clarkia site to assess the preservation of other less labile compounds, such as leaf waxes, structural polysaccharides, cutins, lignins and chlorophyll pigments. Previous organic geochemical studies have developed an understanding of the behaviour of these compound classes in different environments. The relative behaviour of the compound classes and the preservation of individual compounds within each class can therefore help in the interpretation of the biogeochemistry of this site which may in turn shed light on the reported preservation of fossil DNA.Leaf waxes are preserved but a selective loss of long chain esters has occurred, and microbial degradation products of triterpenoids have been identified. Structural polysaccharides and cutins have been lost from the leaf tissues. A highly resistant aliphatic polymer is preserved in the mesophyll and epidermal regions of the leaves, with lignin identified in leaf vein tissues. Various degradation products of chlorophyll have also been identified. The organic geochemical results are all consistent with microbial degradation within the leaf tissues and sediment. Excellent morphological preservation is not accompanied by mutual chemical preservation. The survival of DNA in this environment is extremely surprising. However, preservation of plant polyphenols may provide an answer to this anomaly.
Accelerated development in planktonic foraminifera: adaptive response to reduced ocean mixing
Authors: Lohmann G. P. 
Published: January 2018

Planktonic foraminifera grow by adding chambers to their shells, increasing shell size and changing shell shape. Shell development can be distinguished from shell size either by counting the chambers or by measuring the allometry associated with developmental shape changes. It is necessary to make this distinction when trying to understand the life history adaptations of planktonic foraminifera to their environment because there is wide variation in shell size among individuals at the same stage of development.While the life cycle of many species of planktonic foraminifera is adapted to the monthly lunar cycle, certain deep-living species such as Globorotalia truncatulinoides and G. hirsuta are adapted to the annual cycle of late winter nutrient upwelling and spring bloom, the mechanism that drives primary productivity in subtropical latitudes. These deep-living species grow while sinking from the surface ocean through the upper 500 to 1000m of the water column and then reproduce at depth. Juveniles must somehow return to surface waters.For such a life cycle, size may affect reproductive success in two opposing ways: while the number of gametes produced is directly proportional to size, the bouyancy of the offspring and so the likelihood that they will reach surface waters are inversely proportional to size. The balance between the reproductive benefits of large size and the difficulty of returning large juveniles to surface waters can be altered by vertically mixing the water column. The deep mixing that brings nutrients to surface waters can also help juvenile foraminifera reach the surface.Today the largest shells of G. truncatulinoides are found in populations growing on the poleward margins of the subtropical gyres, areas where the scale of mixing is greatest. As the vertical scale of this mixing decreases toward the tropics, shells at each stage of development shift toward smaller average sizes. This apparent acceleration in development reflects a loss of large shells, which decreases both the average size and the overall abundance of the species.The relationship of apparent developmental rate to the scale of vertical mixing produces the previously reported “ecophenotypic cline” in which G. truncatulinoides changes from a compressed biconvex form in high latitudes to a highly conical form in the tropics. By design, the study reporting this observation was based on shells from a narrow range of size in an attempt to minimize any developmental sources of morphologic variation. Paradoxically, this strategy focussed observations on the systematic shift in the relationship between shell size and development caused by differences in upper ocean mixing. The apparent cline consists of shells of the same size but at different stages of development. A similar explanation may account for the apparent gradual “evolution” observed in G. truncatulinoides during the Late Pleistocene.
Lyginopterid seed ferns in basal Upper Carboniferous marine black shale deposits of midcontinent North America
Authors: Mapes Gene , Rothwell Gar W. , Cook Jeremy G. 
Published: January 2018

Permineralized plant remains occur individually and in small mats within anoxic and dysoxic marine black shales deposited seaward of the Wedington delta (Fayetteville Formation, Middle Chester) in northwestern Arkansas. Plant debris and associated cephalopods occur within 20 km of offshore bars that developed at the mouths of delta distributary channels. The bars were produced by longshore paleocurrents flowing eastward among the southwestern margin of the Ozark Dome. The flora includes several genera of arborescent lycopods, zygopteridalean ferns, filicalean ferns, calamites, medullosan seed ferns and seed fern remains with features that are characteristic of the Lyginopteridaceae. Among the lyginopteridalean stems are specimens that have been described as Megaloxylon wheelerae, an arborescent form, as well as several undescribed species.Two stems with prominent leaf scars represent one species of a new genus. The stems measure 35 cm and 34 cm long, and are approximately 2.5 cm in diameter. Leaf arrangement is helical, approaching a 3/8 phyllotaxis, with internodal lengths of about 3 cm. Stems are eustelic with a polygonal primary body 3-4 mm in diameter. Each leaf trace diverges from the cauline bundle as a single strand. The strand trifurcates in the cortex to produce a distinctive configuration of two c-shaped lateral bundles separated by a tangentially elongated central strand.Pith cells are large with prominent walls. Some show internal contents suggestive of secretory substances. The primary body is surrounded by a distinctive zone of wood 3-4 cm wide. Large rays 2-5 cells wide and more than 8 mm high separate wedges of tracheids that typically are 2-4 cells wide. Secondary tracheids display multiseriate oval bordered pits on the radial walls. Vascular cambium and secondary phloem are present, but incompletely preserved. The cortex is differentiated into an inner parenchymatous zone with horizontally elongated “sclerotic” nests, and an outer zone of alternating bands of vertically elongated sclerenchyma and parenchyma.This material significantly increases our knowledge of Namurian floras inhabiting non peat-forming environments, and emphasizes the systematic diversity among hydrasperman gymnosperms at the base of the Upper Carboniferous.