Tracing the Enterococci from Paleozoic Origins to the Hospital.

We examined the evolutionary history of leading multidrug resistant hospital pathogens, the enterococci, to their origin hundreds of millions of years ago. Our goal was to understand why, among the vast diversity of gut flora, enterococci are so well adapted to the modern hospital environment. Molecular clock estimation, together with analysis of their environmental distribution, phenotypic diversity, and concordance with host fossil records, place the origins of the enterococci around the time of animal terrestrialization, 425-500 mya. Speciation appears to parallel the diversification of hosts, including the rapid emergence of new enterococcal species following the End Permian Extinction. Major drivers of speciation include changing carbohydrate availability in the host gut. Life on land would have selected for the precise traits that now allow pathogenic enterococci to survive desiccation, starvation, and disinfection in the modern hospital, foreordaining their emergence as leading hospital pathogens.

Marine anoxia linked to abrupt global warming during Earth's penultimate icehouse.

Piecing together the history of carbon (C) perturbation events throughout Earth's history has provided key insights into how the Earth system responds to abrupt warming. Previous studies, however, focused on short-term warming events that were superimposed on longer-term greenhouse climate states. Here, we present an integrated proxy (C and uranium [U] isotopes and paleo CO2) and multicomponent modeling approach to investigate an abrupt C perturbation and global warming event (∼304 Ma) that occurred during a paleo-glacial state. We report pronounced negative C and U isotopic excursions coincident with a doubling of atmospheric CO2 partial pressure and a biodiversity nadir. The isotopic excursions can be linked to an injection of ∼9,000 Gt of organic matter­derived C over ∼300 kyr and to near 20% of areal extent of seafloor anoxia. Earth system modeling indicates that widespread anoxic conditions can be linked to enhanced thermocline stratification and increased nutrient fluxes during this global warming within an icehouse.

Reconstruction of an enigmatic Pennsylvanian cone reveals a relationship to Sphenophyllales.

PREMISE: We studied the 3D morphology of a small, well-preserved cone from the Pennsylvanian Mazon Creek Lagerstätte to characterize its structure and determine its systematic affinity. Previously tentatively assigned to the enigmatic Tetraphyllostrobus, we show that it differs in key respects from that genus as described. METHODS: We systematically compared the new fossil with relevant Paleozoic cone genera and employed advanced imaging techniques, including scanning electron microscopy, Airyscan confocal super-resolution microscopy, optical microscopy, and X-ray microcomputed tomography to visualize and reconstruct the fossil cone in 3D. RESULTS: The analyses demonstrate unequivocally that the sporophylls of the new Mazon Creek cone are arranged in whorls of six and have characters typical of Sphenophyllales, including epidermal cells with undulatory margins and in situ spores assignable to Columinisporites. The combination of characters, including sporophyll arrangement, anatomy, and spore type, supports the establishment of Hexaphyllostrobus kostorhysii gen. et sp. nov. within Sphenophyllales. Furthermore, we show that Tetraphyllostrobus, although originally described as possessing smooth monolete spores, actually possesses Columinisporites-type spores, indicating that it, too, was most likely a sphenophyll. CONCLUSIONS: The recognition of Hexaphyllostrobus contributes to our knowledge of Pennsylvanian sphenophyll diversity, and in particular increases the number of species with in situ Columinisporites-type spores. Attribution of Hexaphyllostrobus to Sphenophyllales calls into question current interpretations of Tetraphyllostrobus suggesting that future research on better-preserved macrofossil material may demonstrate a sphenophyllalean relationship.

Intensity of the Earth's magnetic field: Evidence for a Mid-Paleozoic dipole low.

The Mesozoic Dipole Low (MDL) is a period, covering at least ∼80 My, of low dipole moment that ended at the start of the Cretaceous Normal Superchron. Recent studies of Devonian age Siberian localities identified similarly low field values a few tens of million years prior to the Permo-Carboniferous Reverse Superchron (PCRS). To constrain the length and timing of this potential dipole low, this study presents paleointensity estimates from Strathmore (∼411 to 416 Ma) and Kinghorn (∼332 Ma) lava flows, United Kingdom. Both localities have been studied for paleomagnetic poles (Q values of 6 to 7), and the sites were assessed for their suitability for paleointensity from paleodirections, rock magnetic analysis, and microscopy. Thermal and microwave experiments were used to determine site mean paleointensity estimates of ∼3 to 51 µT (6 to 98 ZAm2) and 4 to 11 µT (9 to 27 ZAm2) from the Strathmore and Kinghorn localities, respectively. These, and all the sites from 200 to 500 Ma from the (updated) Paleointensity database (PINT15), were assessed using the Qualitative Paleointensity criteria (QPI). The procurement of reliable (QPI ≥ 5) weak paleointensity estimates from this and other studies indicates a period of low dipole moment (median field strength of 17 ZAm2) from 332 to 416 Ma. This "Mid-Paleozoic Dipole Low (MPDL)" bears a number of similarities to the MDL, including the substantial increase in field strength near the onset of the PCRS. The MPDL also adds support to the inverse relationship between reversal frequency and field strength and a possible ∼200-My cycle in paleomagnetic behavior relating to mantle convection.

Fitting fangs in a finite face: A novel fang accommodation strategy in a 280-million-year-old ray-finned fish.

Though Paleozoic ray-finned fishes are considered to be morphologically conservative, we report a novel mode of fang accommodation (i.e., the fitting of fangs inside the jaw) in the Permian actinopterygian †Brazilichthys macrognathus, whereby the teeth of the lower jaw insert into fenestrae of the upper jaw. To better understand how fishes have accommodated lower jaw fangs through geologic time, we synthesize the multitude of ways living and extinct osteichthyans have housed large mandibular dentition. While the precise structure of fang accommodation seen in †Brazilichthys has not been reported in any other osteichthyans, alternate strategies of upper jaw fenestration to fit mandibular fangs are present in some extant ray-finned fishes-the needlejaws Acestrorhynchus and the gars of the genus Lepisosteus. Notably, out of our survey, only the two aforementioned neopterygians bear upper jaw fenestration for the accommodation of mandibular fangs. We implicate the kinetic jaws of neopterygians in this trend, whereby large mandibular fangs are more easily fit between the multitude of upper jaw and palatal bones. The restricted space available in early osteichthyan jaws may have led to a proliferation of novel ways to accommodate large dentition. We recommend a greater survey of Paleozoic actinopterygian jaw morphology, in light of these results and other recent reevaluations of jaw structure in early fossil ray-fins.

Teratological trilobites from the Silurian (Wenlock and Ludlow) of Australia.

Documentation of malformed trilobites has presented invaluable insight into the palaeobiology of a wholly extinct euarthropod group. Although the northern hemisphere record is relatively well documented, examples of abnormal trilobites from Australia are limited. Furthermore, most recorded specimens are from Cambrian-aged rocks. To extend this limited record, we document five new examples of malformed Australian trilobites from the Middle and Late Silurian (Wenlock and Ludlow) deposits of the Yarralumla Formation of the Australian Capital Territory and Yarwood Siltstone Member, Black Bog Shale in New South Wales. We record the first examples of abnormal pygidial and thoracic nodes and present new evidence for bifurcating pygidial ribs. These abnormal features are considered teratological morphologies. The aberrant nodes likely arose through developmental malfunctions, while the bifurcating ribs represent either similar defects, or an injury that developed into a teratological feature. Explanations for the limited record of malformed Australian trilobites and for the decrease in injured trilobites after the end-Ordovician are presented. Further documentation of malformed Australian trilobites from the middle-to-late Paleozoic will undoubtedly paint a more complete picture of how Gondwanan taxa recovered from injuries or unfortunate developmental complications.

Pacing of Paleozoic macroevolutionary rates by Milankovitch grand cycles.

Periodic fluctuations in past biodiversity, speciation, and extinction have been proposed, with extremely long periods ranging from 26 to 62 million years, although forcing mechanisms remain speculative. In contrast, well-understood periodic Milankovitch climate forcing represents a viable driver for macroevolutionary fluctuations, although little evidence for such fluctuation exists except during the Late Cenozoic. The reality, magnitude, and drivers of periodic fluctuations in macroevolutionary rates are of interest given long-standing debate surrounding the relative roles of intrinsic biotic interactions vs. extrinsic environmental factors as drivers of biodiversity change. Here, we show that, over a time span of 60 million years, between 9 and 16% of the variance in biological turnover (i.e., speciation probability plus species extinction probability) in a major Early Paleozoic zooplankton group, the graptoloids, can be explained by long-period astronomical cycles (Milankovitch "grand cycles") associated with Earth's orbital eccentricity (2.6 million years) and obliquity (1.3 million years). These grand cycles modulate climate variability, alternating times of relative stability in the environment with times of maximum volatility. We infer that these cycles influenced graptolite speciation and extinction through climate-driven changes to oceanic circulation and structure. Our results confirm the existence of Milankovitch grand cycles in the Early Paleozoic Era and show that known processes related to the mechanics of the Solar System were shaping marine macroevolutionary rates comparatively early in the history of complex life. We present an application of hidden Markov models to macroevolutionary time series and protocols for the evaluation of statistical significance in spectral analysis.

Early fossil record of Euarthropoda and the Cambrian Explosion.

Euarthropoda is one of the best-preserved fossil animal groups and has been the most diverse animal phylum for over 500 million years. Fossil Konservat-Lagerstätten, such as Burgess Shale-type deposits (BSTs), show the evolution of the euarthropod stem lineage during the Cambrian from 518 million years ago (Ma). The stem lineage includes nonbiomineralized groups, such as Radiodonta (e.g., Anomalocaris) that provide insight into the step-by-step construction of euarthropod morphology, including the exoskeleton, biramous limbs, segmentation, and cephalic structures. Trilobites are crown group euarthropods that appear in the fossil record at 521 Ma, before the stem lineage fossils, implying a ghost lineage that needs to be constrained. These constraints come from the trace fossil record, which show the first evidence for total group Euarthropoda (e.g., Cruziana, Rusophycus) at around 537 Ma. A deep Precambrian root to the euarthropod evolutionary lineage is disproven by a comparison of Ediacaran and Cambrian lagerstätten. BSTs from the latest Ediacaran Period (e.g., Miaohe biota, 550 Ma) are abundantly fossiliferous with algae but completely lack animals, which are also missing from other Ediacaran windows, such as phosphate deposits (e.g., Doushantuo, 560 Ma). This constrains the appearance of the euarthropod stem lineage to no older than 550 Ma. While each of the major types of fossil evidence (BSTs, trace fossils, and biomineralized preservation) have their limitations and are incomplete in different ways, when taken together they allow a coherent picture to emerge of the origin and subsequent radiation of total group Euarthropoda during the Cambrian.

On the Planar Geometric Patterns of the Exoskeletal Relief Formation in Early Vertebrates (Osteostraci, Agnatha).

A study of the diversity of sculpture and histological structure of the exoskeleton in various osteostracan taxa (Osteostraci, Agnatha) enabled the first characterization of the main elements (geometric modules) of the planar organization of the complex relief on their armor surface. The armor relief was analyzed using a circular model of the formation of exoskeletal hard structures. The model was applied to unique material, fragments of a shield of the osteostracan Oeselaspis pustulata (Patten, 1931) from the Silurian of the Severnaya Zemlya Archipelago (Russia).

Dimetrodon (Synapsida: Sphenacodontidae) from the cave system at Richards Spur, OK, USA, and a comparison of Early Permian-aged vertebrate paleoassemblages.

The Early Permian Richards Spur locality is unique in preserving a highly diverse faunal assemblage in a cave system, composed of synapsids, reptiles, and anamniotes. However, the presence of Dimetrodon, the most common synapsid of Early Permian localities of the southwestern USA, has never been recorded from the site. Here, we describe for the first time the morphology and histology of a small neural spine with the distinctive figure-8 shape attributable to Dimetrodon. Additionally, histological analysis of previously described sphenacodontid teeth suggests the presence of a derived species of Dimetrodon at the Richards Spur locality. The presence of this derived synapsid, typical of the later occurring Kungurian localities of Texas and Oklahoma, is unexpected at the stratigraphically older Richards Spur locality. The cave system at Richards Spur preserves mainly basal synapsid taxa, including small caseid, varanopid, and sphenacodontid skeletal remains. The presence of a derived species of Dimetrodon suggests not only that this animal was more widespread than previously thought, but that there are different patterns of Early Permian synapsid evolution in different ecological settings.

Earliest land plants created modern levels of atmospheric oxygen.

The progressive oxygenation of the Earth's atmosphere was pivotal to the evolution of life, but the puzzle of when and how atmospheric oxygen (O2) first approached modern levels (∼21%) remains unresolved. Redox proxy data indicate the deep oceans were oxygenated during 435-392 Ma, and the appearance of fossil charcoal indicates O2 >15-17% by 420-400 Ma. However, existing models have failed to predict oxygenation at this time. Here we show that the earliest plants, which colonized the land surface from ∼470 Ma onward, were responsible for this mid-Paleozoic oxygenation event, through greatly increasing global organic carbon burial-the net long-term source of O2 We use a trait-based ecophysiological model to predict that cryptogamic vegetation cover could have achieved ∼30% of today's global terrestrial net primary productivity by ∼445 Ma. Data from modern bryophytes suggests this plentiful early plant material had a much higher molar C:P ratio (∼2,000) than marine biomass (∼100), such that a given weathering flux of phosphorus could support more organic carbon burial. Furthermore, recent experiments suggest that early plants selectively increased the flux of phosphorus (relative to alkalinity) weathered from rocks. Combining these effects in a model of long-term biogeochemical cycling, we reproduce a sustained +2‰ increase in the carbonate carbon isotope (δ(13)C) record by ∼445 Ma, and predict a corresponding rise in O2 to present levels by 420-400 Ma, consistent with geochemical data. This oxygen rise represents a permanent shift in regulatory regime to one where fire-mediated negative feedbacks stabilize high O2 levels.

Did trees grow up to the light, up to the wind, or down to the water? How modern high productivity colors perception of early plant evolution.

Contents I. II. III. IV. V. Acknowledgements References SUMMARY: Flowering plants can be far more productive than other living land plants. Evidence is reviewed that productivity would have been uniformly lower and less CO2 -responsive before angiosperm evolution, particularly during the early evolution of vascular plants and forests in the Devonian and Carboniferous. This introduces important challenges because paleoecological interpretations have been rooted in understanding of modern angiosperm-dominated ecosystems. One key example is tree evolution: although often thought to reflect competition for light, light limitation is unlikely for plants with such low photosynthetic potential. Instead, during this early evolution, the capacities of trees for enhanced propagule dispersal, greater leaf area, and deep-rooting access to nutrients and the water table are all deemed more fundamental potential drivers than light.

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.

Tectonic evolution and paleokarstification of carbonate rocks in the Paleozoic Tarim Basin.

Thick carbonate rocks were developed in the depression of the Tarim craton during the Cambrian-Middle Ordovician periods. The compressional tectonic movement during the Middle Caledonian-Hercynian created the paleouplifts, which became the base for the paleokarst in the Ordovician carbonate rocks. Based on the large quantity of seismic, drilling, and geological outcrop data, this study analyzed the paleokarst development in relation to the multi-stage tectonic movements in the Paleozoic Era and different stages of karstification and hypothesized paleogeomorphology and paleokarst water system of those stages. Fractures from the tectonic movements in the carbonate and non-carbonate rocks were essential for water cycle, and therefore, the karst development in deep carbonate rocks. Paleokarsts in the Tarim Basin can be classified into four major types based on the paleogeomorphology, degree of karstification, and the layering, i.e., Tahe type, gentle hill type, high steep hill type, and covered-semi-open type. Relatively, the Tahe type was mostly on hill slopes and had the strongest karstification, the gentle hill type often located in the plain areas or basin bottoms and had least karstification, the high steep hill type was controlled by faults and had medium karstification, the semi-open type was controlled by precipitation and hydraulic gradient, and fracture passages and karst caves were mostly developed along major fractures. Overall, the paleokarsts of the Ordovician carbonate rocks in the Tarim Basin can be characterized by long geologic history, multiple development stages, deep burial depth, and various karst types.

Modeling Variable Phanerozoic Oxygen Effects on Physiology and Evolution.

Geochemical approximation of Earth's atmospheric O2 level over geologic time prompts hypotheses linking hyper- and hypoxic atmospheres to transformative events in the evolutionary history of the biosphere. Such correlations, however, remain problematic due to the relative imprecision of the timing and scope of oxygen change and the looseness of its overlay on the chronology of key biotic events such as radiations, evolutionary innovation, and extinctions. There are nevertheless general attributions of atmospheric oxygen concentration to key evolutionary changes among groups having a primary dependence upon oxygen diffusion for respiration. These include the occurrence of Devonian hypoxia and the accentuation of air-breathing dependence leading to the origin of vertebrate terrestriality, the occurrence of Carboniferous-Permian hyperoxia and the major radiation of early tetrapods and the origins of insect flight and gigantism, and the Mid-Late Permian oxygen decline accompanying the Permian extinction. However, because of variability between and error within different atmospheric models, there is little basis for postulating correlations outside the Late Paleozoic. Other problems arising in the correlation of paleo-oxygen with significant biological events include tendencies to ignore the role of blood pigment affinity modulation in maintaining homeostasis, the slow rates of O2 change that would have allowed for adaptation, and significant respiratory and circulatory modifications that can and do occur without changes in atmospheric oxygen. The purpose of this paper is thus to refocus thinking about basic questions central to the biological and physiological implications of O2 change over geological time.

Cranial anatomy and phylogenetic affinities of Bolosaurus major, with new information on the unique bolosaurid feeding apparatus and evolution of the impedance-matching ear.

Resolving the phylogenetic relationships of early amniotes, in particular stem reptiles, remains a difficult problem. Three-dimensional morphological analysis of well-preserved stem-reptile specimens can reveal important anatomical data and clarify regions of phylogeny. Here, we present the first thorough description of the unusual early Permian stem reptile Bolosaurus major, including the first comprehensive description of a bolosaurid braincase. We describe previously obscured details of the palate, allowing for insight into bolosaurid feeding mechanics. Aspects of the rostrum, palate, mandible, and neurocranium suggest that B. major had a particularly strong bite. We additionally found B. major has a surprisingly slender stapes, similar to that of the middle Permian stem reptile Macroleter poezicus, which may suggest enhanced hearing abilities compared to other Paleozoic amniotes (e.g., captorhinids). We incorporated our new anatomical information into a large phylogenetic matrix (150 OTUs, 590 characters) to explore the relationship of Bolosauridae among stem reptiles. Our analyses generally recovered a paraphyletic "Parareptilia," and found Bolosauridae to diverge after Captorhinidae + Araeoscelidia. We also included B. major within a smaller matrix (10 OTUs, 27 characters) designed to explore the interrelationships of Bolosauridae and found all species of Bolosaurus to be monophyletic. While reptile relationships still require further investigation, our phylogeny suggests repeated evolution of impedance-matching ears in Paleozoic stem reptiles.

Soft-tissue fossilization illuminates the stepwise evolution of the ray-finned fish brain.

A complex brain is central to the success of backboned animals. However, direct evidence bearing on vertebrate brain evolution comes almost exclusively from extant species, leaving substantial knowledge gaps. Although rare, soft-tissue preservation in fossils can yield unique insights on patterns of neuroanatomical evolution. Paleontological evidence from an exceptionally preserved Pennsylvanian (∼318 Ma) actinopterygian, Coccocephalus, calls into question prior interpretations of ancestral actinopterygian brain conditions. However, the ordering and timing of major evolutionary innovations, such as an everted telencephalon, modified meningeal tissues, and hypothalamic inferior lobes, remain unclear. Here, we report two distinct actinopterygian morphotypes from the latest Carboniferous-earliest Permian (∼299 Ma) of Brazil that show extensive soft-tissue preservation of brains, cranial nerves, eyes, and potential cardiovascular tissues. These fossils corroborate inferences drawn from ✝Coccocephalus, while adding new information about neuroanatomical evolution. Skeletal features indicate that one of these Brazilian morphotypes is more closely related to living actinopterygians than the other, which is also reflected in soft-tissue features. Significantly, the more crownward morphotype shows a key neuroanatomical feature of extant actinopterygians-an everted telencephalon-that is absent in the other morphotype and ✝Coccocephalus. All preserved Paleozoic actinopterygian brains show broad similarities, including an invaginated cerebellum, hypothalamus inferior lobes, and a small forebrain. In each case, preserved brains are substantially smaller than the enclosing cranial chamber. The neuroanatomical similarities shared by this grade of Permo-Carboniferous actinopterygians reflect probable primitive conditions for actinopterygians, providing a revised model for interpreting brain evolution in a major branch of the vertebrate tree of life.

Fossil Wood Analyses: Several Examples from Five Case Studies in the Area of Central and NW Bohemia, Czech Republic.

In the area of the Central and NW Bohemia, Czech Republic, the fossil wood is quite abundant, found in different states of preservation and present from Paleozoic (Pennsylvanian), through Mesozoic (Upper Cretaceous), to Cenozoic (upper Eocene to lower Miocene). So, this small area is ideal to demonstrate various aspects of the fossil wood analyses, including anatomy (unifacial vs. bifacial cambium, formation of tyloses and its significance, early vs. late wood, unambiguity of scientific terminology, stem vs. root wood), taphonomy (completeness of fossil record, influence of environment on mode of preservation, influence of preservation on wood anatomy and preservation potential, discrepancy between the record of wood and other organs), systematics (stem vs. crown group, wide concept of fossil wood genera, "mosaic" species, wood of extinct plants), and palaeoclimatic reconstruction (definition of "wood type," subjective vs. objective methods). The majority of the studied woods were thin-sectioned following the standard techniques and observed with a compound light microscope.

Accretion of "young" Phanerozoic subcontinental lithospheric mantle triggered by back-arc extension-the case of the Ivrea-Verbano Zone.

The subcontinental lithospheric mantle (SCLM) beneath Phanerozoic regions is mostly constituted by fertile lherzolites, which sharply contrast with cratonic mantle made of highly-depleted peridotites. The question of whether this chemical difference results from lower degrees of melting associated with the formation of Phanerozoic SCLM or from the refertilization of ancient depleted SCLM remains a subject of debate. Additionally, the timing and geodynamic environment of accretion of the fertile SCLM in many Phanerozoic regions are poorly constrained. We here document new geochemical and Nd-Hf isotopic data for orogenic lherzolite massifs from the Ivrea-Verbano Zone (IVZ), Southern Alps. Even though a few Proterozoic Re depletion ages are locally preserved in these mantle bodies, our data reveal that the IVZ lherzolitic massifs were "recently" accreted to the SCLM in the Upper Devonian (ca. 370 Ma) during Pangea amalgamation, with a petrochemical evolution characterized by low-degree (~ 5-12%) depletion and nearly contemporaneous pervasive to focused melt migration. The lithospheric accretion putatively took place through asthenospheric upwelling triggered by Variscan intra-continental extension in a back-arc setting related to the subduction of the Rheic Ocean. We thus conclude that the fertile sections of Phanerozoic SCLM can be accreted during "recent" events of back-arc continental extension, even where Os isotopes preserve memories of melting events in much older times.