Middle Pliocene vegetation: reconstructions, paleoclimatic inferences, and boundary conditions for climate modeling

The general characteristics of global vegetation during the middle Pliocene warm period can be reconstructed from fossil pollen and plant megafossil data. The largest differences between Pliocene vegetation and that of today occurred at high latitudes in both hemispheres, where warming was pronounced relative to today. In the Northern Hemisphere coniferous forests lived in the modern tundra and polar desert regions, whereas in the Southern Hemisphere southern beech apparently grew in coastal areas of Antarctica.Pliocene middle latitude vegetation differed less, although moister-than-modern conditions supported forest and woodland growth in some regions now covered by steppe or grassland. Pliocene tropical vegetation reflects essentially modem conditions in some regions and slightly cooler-than-or warmer-than- modern climates in other areas. Changes in topography induced by tectonics may be responsible for many of the climatic changes since the Pliocene in both middle and lower latitudes. However, the overall latitudinal progression of climatic conditions on land parallels that seen in the reconstruction of middle Pliocene sea-surface temperatures.Pliocene paleovegetational data was employed to construct a 2 ° × 2 ° global grid of estimated mid-Pliocene vegetational cover for use as boundary conditions for numerical General Circulation Model simulations of middle Pliocene climates. Continental outlines and topography were first modified to represent the Pliocene landscape on the 2 ° × 2 ° grid. A modern 1 ° × 1 ° vegetation grid was simplified and mapped on this Pliocene grid, and then modified following general geographic trends evident in the Pliocene paleovegetation data set.     

The spatial structure of potamophytoplankton in extreme environmental conditions of northeastern Siberia

The basic patterns of the spatial structure of phytoplankton in large oligotrophic rivers of northeastern Siberia were determined using principle component analysis (PCA), factor analysis, and cluster analysis. It was found that in extreme conditions of oligotrophic subarctic rivers the formation of the spatial structure of the phytoplankton generally occurs under the influence of climate, rather than physicochemical water properties. Among the developmental parameters of the phytoplankton, the floristic structure of phytoplankton is the most dependent on the abiotic factor.     

The Quaternary eolian sequence of Madeira: stratigraphy, chronology, and paleoenvironmental interpretation

A thick (ca. 40 m) sequence of coastal eolian sediments occurs on a narrow peninsula on the eastern end of the island of Madeira, located in the Eastern Atlantic at 33°N latitude. The sediments consist of black volcanic sands (with or without bioclasts) as well as clay units up to 2 m thick. A series of inceptisols (Eutrochrepts) and one alfisol (a Hapludalf) are developed in these sediments. Land snail shells and secondary carbonates, in the form of well-developed rhizoliths, calcretes, fissure-fills, and soil nodules, are present in abundance. The chronology of the sequence was determined by ¹⁴C and U---Th analyses of land snail shells and secondary carbonates and amino acid epimerization analysis of land snail shells. All sediments, including the clay units, are originally of eolian origin, derived from the beach to the south of the deposit, but some have been redeposited by colluviation. Temporal variation in the lithology of the sediments relates to variations in sea-level, with black sands being deposited during lower sea level stands and clays at the lowest. It is suggested that fine marine sediments, exposed during low sea-level stands, may also be the dominant source of silty or clayey units in other coastal eolian deposits in the subtropical Atlantic and Mediterranean.

The sequence spans from 200,000–300,000 years ago up to the 20th century. Sedimentation was discontinuous and often rapid; erosional hiatuses are present. During the Holocene, eolian sands started accumulating at 8200 yr B.P. during a transgressive phase and stopped at 4500 yr B.P. as sea level approached its present height. Colluviation increased dramatically following the first human settlement of the island in the 15th century and continued up to the 20th century, as dated by amino acid epimerization analysis of land snails. Earlier periods of colluviation were identified from the age distribution of land snail shells redeposited in younger colluvium.

Paleoenvironmental reconstruction was based mainly on soil and sediment features (including rhizolith morphology) and land snail faunas but also on stable isotope variations (¹³C, ¹⁸O) in land snails and secondary carbonates, pollen (generally not well preserved), and phytoliths. Most of the portion of the Middle Pleistocene represented in the sequence was characterized by moderately dry conditions, in comparison to the late Pleistocene and Holocene. During the last interglacial, relatively wet conditions occurred, wetter than during the Holocene interglacial. Moderately moist conditions were present during the accumulation of the thick unit dating to ca. 80,000 yr B.P. As sea level fell subsequent to this period, conditions appear to have become drier. Starting ca. 50,000–55,000 yr B.P., conditions were especially wet, but prior to the last glacial maximum, markedly arid conditions ensued. Toward the end of the last glacial, wet conditions returned and produced the best-developed soil preserved in the sequence. Moderately moist conditions occurred during the early to middle Holocene but apparently become slightly drier after 4500 yr B.P. The impact of human settlement can be seen in the loss of woody vegetation and enhanced gullying and colluviation during the last ca. 500 years.     

Holocene radiocarbon-dated sites in northeastern Siberia: issues of temporal frequency, reservoir age, and human-nature interaction

The existing corpus of data on radiocarbon dates for Holocene sites in Northeastern Siberia was used as proxy to reconstruct the chronology of human occupation of the region. The problem of reservoir age correction in the Bering Sea region complicated this task and this issue needs to be solved in order to obtain more reliable age determinations for coastal archaeological sites. Using a chronology built after excluding the questionable dates from the database, the major patterns of human population dynamics and their possible correlation with climatic fluctuations were examined. No direct relationship appears to exist between these two processes. Additional archaeological and paleo environmental work needs to be carried out in this region of the North.     

Patagonian ostracods as indicators of climate-related hydrological variables: implications for paleoenvironmental reconstructions in Southern South America

Different precipitation regimes across Patagonia generate an environmental gradient that is expected to reflect upon the solute composition and concentration of lake water through the ensuing differences in water balance. In turn, this hydrochemical gradient could influence the occurrence and distribution of ostracods in the area. A cluster analysis on hydrochemical data of 36 Southern Patagonian waterbodies shows that low salinity, bicarbonate-dominated waters characterize Andean and ecotonal lakes, located in the wetter part of the precipitation gradient, while their steppe counterparts, which receive a much lower precipitation input, are more saline, enriched in all major anions and sodium-dominated. Kruskal–Wallis tests followed by Mann–Whitney pairwise comparisons show statistically significant differences in the ostracod species each water type hosts, with L. patagonica, E. cecryphalium, P. smaragdina and P. incae being found in the more dilute waters characteristic of Andean and ecotonal lakes and Limnocythere rionegroensis in the mesohaline, evaporatively evolved waters typical of steppe lakes. Other species studied do not appear to have such distinct distributions, having been found throughout the range of conditions studied. These findings promote the use of the aforementioned ostracods as semi-quantitative paleohydrological indicators, which could improve paleoclimatic reconstructions in Patagonia.     

Sedimentary facies and paleoenvironmental interpretation of the Oligocene larger-benthic-foraminifera-dominated Qom Formation in the northeastern margin of the Tethyan Seaway

The well-exposed outcrops of the Bujan, northern Abadeh, and Varkan stratigraphic sections of the Qom Formation in the Iranian part of the “northeastern margin” of the Tethyan Seaway were characterized by abundant biogenic components dominated by foraminifers, coralline red algae, and corals. The Qom Formation is Rupelian–Chattian in age in the study areas. Based on the field investigations, depositional textures, and dominant biogenic components, fifteen (carbonate and terrigenous) facies were identified. These facies can be grouped into four depositional environments: open marine, open lagoon, restricted lagoon, and continental braided streams. The marine facies were deposited on a ramp-type platform. The euphotic inner ramp was characterized mainly by imperforate foraminifera, with co-occurrence of some perforate taxa. These facies passed basinward into a mesophotic (middle) ramp with Neorotalia packstone (F5), coral, coralline algae, perforate foraminiferal packstone (F4), and coral patch reefs (F7). The deeper, oligophotic ramp facies were marly packstones with planktonic and hyaline benthic foraminifera, including large lepidocyclinids and nummulitids. The abundance of perforate foraminifera and the absence of facies indicating restricted lagoonal or intertidal settings suggest that the Varkan section was deposited mainly in open marine settings with normal salinity. The prevalence of larger benthic foraminiferal and red algal assemblages, together with the coral facies, indicates that carbonate production took place in tropical–subtropical waters.     

A new Tertiary Ginkgo (Ginkgoaceae) from the Wuyun Formation of Jiayin, Heilongjiang, northeastern China and its paleoenvironmental implications

The living fossil Ginkgo, a relict of a once dominant gymnosperm, existed and flourished early in the Mesozoic, but only a vague outline of its evolutionary history in the Tertiary has been unveiled. Here we describe a new species, Ginkgo jiayinensis sp. nov., from the Wuyun Formation of Jiayin, China, which is another well-established Tertiary species based on leaf fossils besides G. adiantoides. The most remarkable feature of the new species is the amphistomatic leaves, likely representing a distinct evolutionary line of the genus in this time interval. Ginkgo jiayinensis is similar to the co-occurring G. adiantoides and extant G. biloba in the lower cuticle, but the two latter species clearly differ in having hypostomatic leaves. Ginkgo biloba is used as the nearest living equivalent (NLE) species for both G. adiantoides and G. jiayinensis in reconstructing paleo-CO(2), as it has been used for other fossil species with either hypostomatic or amphistomatic leaves. The two Tertiary species are almost identical in stomatal index in abaxial cuticles (8.4 and 8.5, respectively), showing no strong differences in response to atmospheric CO(2). Amphistomatic G. jiayinensis would therefore have used a different ecological strategy from that of G. adiantoides of the same bed.     

Foraminifera diversity changes and paleoenvironmental analysis: the Lower Cretaceous shallow-water carbonates of San Lorenzello, Campanian Apennines, southern Italy

A high-resolution stratigraphic study, carried out on the carbonate platform strata of the San Lorenzello section (Matese Mountains, southern Italy), Valanginian–Hauterivian in age, has allowed to: recognise lithofacies and their associations; assign the lithofacies associations to specific environments and individuate early meteoric diagenetic modifications, recurring at specific horizons. In this frame the vertical variation of benthic foram diversity has been analysed. On the whole, foraminiferal genera diversity decreases from open to restricted marine environments. Moreover, a climatic control on carbonate sedimentation is suggested by a Milankovitch cyclicity organised in elementary cycles, bundles and superbundles as well as by diagenetic characteristics testifying that humid and arid conditions alternated during the Early Cretaceous times. The orbital cyclicity is also documented by foraminiferal diversity changes, even if some discrepancies between the lithofacies and the diversity locally occur. Therefore, the above diversity changes do not appear to provide sufficient information for the sequence-stratigraphic interpretation of shallow-water carbonates.     

The Miocene vertebrate-bearing deposits of Scontrone (Abruzzo,Central Italy): Stratigraphic and paleoenvironmental analysis

The Miocene carbonate deposits of Scontrone (Abruzzo, Central Italy) are well known among palaeontologists because of their fossil vertebrate content that exhibits striking similarities to those of the remarkable “Terre Rosse” faunal complex of the Gargano region, defining the existence of the Miocene Central Mediterranean Apulia paleobioprovince. The main goal of this paper is to establish the age and environment of the Scontrone vertebrate bonebeds. The vertebrate remains are embedded in the basal portion of the Lithothamnion Limestone, a widespread carbonate-ramp lithosome representative of the Tortonian-early Messinian transgression over the entire Apulia Platform. The bonebeds belong to marginal-marine deposits (here called “Scontrone calcarenites”) preserved in a small area below transgressive ravinement surfaces. The rapid vertical and lateral facies variations displayed by the “Scontrone calcarenites”, together with paleoenvironmental considerations deriving from the vertebrate association, document a complex wave-dominated river-mouth depositional setting developed over a large, flat and semi-arid carbonate ramp. The “Scontrone calcarenites” have been split herein into five facies associations representing the stratigraphic response to a discontinuous or punctuated transgression within an overall rise of the relative sea level. Because of the absence of age-diagnostic fossils, the age of the “Scontrone calcarenites” cannot be directly defined through their paleontological content. However, a regional stratigraphic correlation between the Lithothamnion Limestone of Scontrone and the Lithothamnion Limestone of northern Majella, which is biostratigraphically well constrained, allows the attribution of the “Scontrone calcarenites” to the Tortonian.     

Participation of Indo-European tribes in ethnogeny of the mongoloid population of Siberia: analysis of the HLA antigen distribution in mongoloids of Siberia.

Three hundred forty-three Yakuts (mongoloids of central Asian type living in Siberia) were tested for HLA-A, -B, and -C loci. The HLA antigen distribution corresponds on the whole to a mongoloid population with high frequency of the HLA-A9, -B15, and -B40 antigens (phenotype frequencies .533, .367, and .405, respectively). At the same time a strikingly high frequency for the "Indo-European" HLA-A1 antigen (phenotype frequency .282) was detected, which in Yakuts is found exclusively with HLA-B17 (haplotype frequency x 1,000 = 87.0; linkage disequilibrium value x 1,000 = 63.8). The present paper deals with a new hypothesis of the Yakut ethnogenesis according to which ancient Aryan tribes formed the substratum which was later assimilated by the mongoloid and Turkic populations. Another hypothesis that I have advanced argues that from analysis of the HLA system the ancient Aryans formed, a local group within the Indo-European entity, with high frequency for HLA-A1 and -B17 antigens and for the HLA-A1,B17 haplotype and with a complete absence of or very low frequency for the HLA-B8 antigen and for the HLA-A1,B8 haplotype. Significant linkage disequilibrium, as it is found in Indians and Yakuts, etc., could have resulted from mixing of the Aryans with non-Indo-European tribes. No significant linkage disequilibrium between A1 and B8 characteristic of the European caucasoids was produced in the mixing.     

L-Measure: a web-accessible tool for the analysis, comparison and search of digital reconstructions of neuronal morphologies

L-Measure (LM) is a freely available software tool for the quantitative characterization of neuronal morphology. LM computes a large number of neuroanatomical parameters from 3D digital reconstruction files starting from and combining a set of core metrics. After more than six years of development and use in the neuroscience community, LM enables the execution of commonly adopted analyses as well as of more advanced functions. This report illustrates several LM protocols: (i) extraction of basic morphological parameters, (ii) computation of frequency distributions, (iii) measurements from user-specified subregions of the neuronal arbors, (iv) statistical comparison between two groups of cells and (v) filtered selections and searches from collections of neurons based on any Boolean combination of the available morphometric measures. These functionalities are easily accessed and deployed through a user-friendly graphical interface and typically execute within few minutes on a set of approximately 20 neurons. The tool is available at http://krasnow.gmu.edu/cn3 for either online use on any Java-enabled browser and platform or download for local execution under Windows and Linux.     

Species of coccidia (Apicomplexa: Eimeriidae) in shrews from Alaska, U.S.A., and northeastern Siberia, Russia, with description of two new species

Fecal samples (n = 636) from 10 species of shrews collected in Alaska (n = 540) and northeastern Siberia (n = 96) were examined for the presence of coccidia (Apicomplexa: Eimeriidae). Five distinct oocyst morphotypes were observed. Three types were consistent with oocysts of previously recognized coccidia species from other shrew hosts. These were Eimeria inyoni, E. vagrantis, and Isospora brevicauda, originally described from the inyo shrew (Sorex tenellus), dusky shrew (S. monticolus), and northern short-tailed shrew (Blarina brevicauda), respectively. We found 5 new host records for E. inyoni, 3 for E. vagrantis, and 3 for I. brevicauda. The 2 additional oocyst morphotypes, both from the tundra shrew (Sorex tundrensis), are putative new species. Sporulated oocysts of Eimeria beringiacea n. sp. are subspheroidal, 17.7 x 15.6 microm (14-24 x 13-20 microm) with a length (L)/width (W) ratio of 1.1 (1.0-1.4); these lack a micropyle (M), an oocyst residuum (OR), and a polar granule (PG). Sporocysts are ellipsoidal, 10.3 x 6.1 microm (7-14 x 4-8 microm), with a L/W ratio of 1.7 (1.3-2.3) and have a Stieda body (SB), Substieda body (SSB), and sporocyst residuum (SR). Oocysts of Eimeria tundraensis n. sp. are spheroidal to subspheroidal, 24.8 x 23.5 microm (23-26 x 22-25 microm), with a L/W ratio of 1.1 (1.0-1.2); these lack a M and OR, but a single PG is present. Sporocysts are elongate ellipsoidal, 15.4 x 8.3 microm (13-17 x 7-9 microm), with a L/W ratio of 1.9 (1.4-2.1) and have a SB, SSB, and SR.     

Environmental metabolomics: a SWOT analysis (strengths, weaknesses, opportunities, and threats)

Metabolomic approaches have the potential to make an exceptional contribution to understanding how chemicals and other environmental stressors can affect both human and environmental health. However, the application of metabolomics to environmental exposures, although getting underway, has not yet been extensively explored. This review will use a SWOT analysis model to discuss some of the strengths, weaknesses, opportunities, and threats that are apparent to an investigator venturing into this relatively new field. SWOT has been used extensively in business settings to uncover new outlooks and identify problems that would impede progress. The field of environmental metabolomics provides great opportunities for discovery, and this is recognized by a high level of interest in potential applications. However, understanding the biological consequence of environmental exposures can be confounded by inter- and intra-individual differences. Metabolomic profiles can yield a plethora of data, the interpretation of which is complex and still being evaluated and researched. The development of the field will depend on the availability of technologies for data handling and that permit ready access metabolomic databases. Understanding the relevance of metabolomic endpoints to organism health vs adaptation vs variation is an important step in understanding what constitutes a substantive environmental threat. Metabolomic applications in reproductive research are discussed. Overall, the development of a comprehensive mechanistic-based interpretation of metabolomic changes offers the possibility of providing information that will significantly contribute to the protection of human health and the environment.     

Mechanics of the brain: perspectives,challenges, and opportunities

The human brain is the continuous subject of extensive investigation aimed at understanding its behavior and function. Despite a clear evidence that mechanical factors play an important role in regulating brain activity, current research efforts focus mainly on the biochemical or electrophysiological activity of the brain. Here, we show that classical mechanical concepts including deformations, stretch, strain, strain rate, pressure, and stress play a crucial role in modulating both brain form and brain function. This opinion piece synthesizes expertise in applied mathematics, solid and fluid mechanics, biomechanics, experimentation, material sciences, neuropathology, and neurosurgery to address today’s open questions at the forefront of neuromechanics. We critically review the current literature and discuss challenges related to neurodevelopment, cerebral edema, lissencephaly, polymicrogyria, hydrocephaly, craniectomy, spinal cord injury, tumor growth, traumatic brain injury, and shaken baby syndrome. The multi-disciplinary analysis of these various phenomena and pathologies presents new opportunities and suggests that mechanical modeling is a central tool to bridge the scales by synthesizing information from the molecular via the cellular and tissue all the way to the organ level.     

Advances in Cambrian stratigraphy and paleontology: Integrating correlation techniques, paleobiology, taphonomy and paleoenvironmental reconstruction

Papers resulting from the Fourth International Symposium on the Cambrian System, held in Nanjing, China, in 2005 cover three major aspects of geology and paleontology: (1) the developing global standard for Cambrian chronostratigraphy or regional correlation schemes; (2) regional lithostratigraphy, sedimentology and paleoenvironments; (3) organismal paleobiology, phylogenetic affinities and taphonomy.A generalized curve of carbon isotopes (δ¹³C) through the Cambrian suggests a relationship between major biotic events, sea level history and the development of deposits of exceptional preservation (Lagerstätten). Recognition of this relationship increases the importance of the δ¹³C profile as a tool for intercontinental and intracontinental correlation. Significant δ¹³C excursions in the Cambrian are: BACE (negative excursion at the base of the Cambrian System); ZHUCE (positive excursion in the lower part of Stage 2); SHICE (negative excursion in the middle part of Stage 2); CARE (positive excursion near the base of Stage 3); MICE (positive excursion in the lower part of Stage 4); AECE (negative excursion in the middle part of Stage 4); ROECE (negative excursion near the base of Stage 5); DICE (negative excursion beginning near the base of the Drumian Stage); SPICE (positive excursion beginning at the base of the Paibian Stage); TOCE (negative excursion near the top of Stage 10). All acronyms other than SPICE are newly proposed.     

Computational sequence analysis revisited: new databases, software tools, and the research opportunities they engender.

The increasing quantity and complexity of sequences and structural data for proteins and nucleic acids create both problems and opportunities for biomedical researchers. Fortunately, a new generation of practical computer tools for data analysis and integrated information retrieval is emerging. Recent developments in fast database searching, multiple sequence alignment, and molecular modeling are discussed and windows-based, mouse-driven software for CD-ROM and network information retrieval are described. Each method is illustrated with a practical example pertinent to lipid research. In particular, the connection among cholesteryl ester transfer protein, bactericidal permeability-increasing protein, and lipopolysaccharide-binding proteins is determined; novel repetitive sequence motifs in mammalian farnesyltransferase subunits and related yeast prenyltransferases are derived; biochemical insights from a three-dimensional model of human apolipoprotein D based on two insect lipocalins are discussed; the relationship between apolipoprotein D and gross cystic disease fluid protein from human breast is reviewed; and prospects for modeling apolipoprotein E-related proteins are described. In addition, information on a number of general and special-purpose sequence, motif, and structural databases is included.