bluuebunny/crossref_metadata_2025 huggingface dataset:
Testate amoebae in the Neoproterozoic Era: evidence from vase-shaped microfossils in the Chuar Group, Grand Canyon
Authors: Porter Susannah M. , Knoll Andrew H.
Published: July 2006

Vase-shaped microfossils (VSMs) occur globally in Neoproterozoic rocks, but until now their biological relationships have remained problematic. Exceptionally preserved new populations from the uppermost Chuar Group, Grand Canyon, Arizona, display details of morphology and taphonomy that collectively point to affinities with the testate amoebae. The fossils are tear-shaped tests, ∼20–300 μm long and ∼10–200 μm wide, that are circular in transverse section, expand aborally toward a rounded or slightly pointed pole, and taper orally toward a “neck” that ends in a single aperture. Apertures may be circular, hexagonal, triangular, or crenulate, and may be rimmed by a distinct collar. Approximately 25% of the Chuar VSMs are curved, such that the oral and aboral poles do not lie opposite each other. Tests are preserved as mineralized casts and molds, commonly coated with organic debris or iron minerals, but they were originally composed of nonresistant organic matter. Approximately 1% have a “honeycomb-patterned” wall attributable to the original presence of mineralized scales whose bases were arranged regularly in the test wall. Scale-bearing testate amoebae, such as members of the Euglyphidae, are essentially identical to the honeycomb VSMs, and a close relationship between other Grand Canyon VSMs and additional testate amoebae, both lobose and filose, is likely. The VSM population therefore most likely represents a multispecies assemblage whose spatial association reflects a common habitat and/or taphonomic circumstances that favor test preservation. The assignment of these fossils to the testate amoebae strengthens the case for a major diversification of eukaryotic organisms by mid-Neoproterozoic times and, more significantly, provides the earliest morphological evidence for heterotrophic eukaryotes in marine ecosystems.
Longbone histology of the Tendaguru sauropods: implications for growth and biology
Authors: Sander P. Martin
Published: July 2006

A new sampling technique for fossil bone (coring with a 5/8″ bit) was used to sample longbones of all four sauropod genera from the Upper Jurassic Tendaguru beds of Tanzania for paleohistological study. Brachiosaurus and Barosaurus are represented by growth series of humeri and femora, while Dicraeosaurus could be sampled in fewer specimens and only one bone of Janenschia was available. Although all samples are dominated by fibrolamellar bone tissue, taxa can be distinguished by the degree and nature of bone remodeling and the presence and spacing of a peculiar kind of growth line (here termed “polish lines”). In addition, Barosaurus bone revealed two types of histology, tentatively interpreted as sexual morphs. The Tendaguru sauropods show a common growth pattern in which growth is determinate but sexual maturity is achieved well before maximum size is reached. For Brachiosaurus and Barosaurus, size at sexual maturity can be estimated and was reached at about 40% and 70% maximum size, respectively. Quantification of growth is possible in Janenschia using polish lines: the specimen studied reached sexual maturity at ≥11 years, attained maximum size at ≥26 years, and died at ≥38 years.
Theoretical morphology of hinge and shell form in Bivalvia: geometric constraints derived from space conflict between umbones
Authors: Ubukata Takao
Published: July 2006

Geometric properties of the shells of 123 species of extant Bivalvia were analyzed from the viewpoint of theoretical morphology. The effects of shell form and the structure of ligament on the interumbonal space and the maximum shell opening received particular attention. The results of computer simulation and morphospace analysis indicate that possessing both prosogyrous shell form and an extended hinge without the parivincular ligament tends to cause space conflict between umbones or dorsal shell margins of right and left valves. To a large degree, a prosogyrous shell form with a long parivincular ligament helps shell opening without umbonal conflict, if the shell is flat enough to avoid the mutual interference between dorsal shell margins of closed valves. Extension of the ligament and plunging of the anterior part of the coiling axis into the ventral side provide enough space along the dorsal shell margins in which a parivincular ligament and its substrata are developed.
Silurian trilobite alpha diversity and the end-Ordovician mass extinction
Authors: Adrain Jonathan M. , Westrop Stephen R. , Chatterton Brian D. E. , Ramsköld Lars
Published: July 2006

Following the end-Ordovician extinction, global clade diversity of Silurian trilobites dropped to about half of Ordovician levels. Although clade diversity failed to recover, this extinction had surprisingly little long-term impact on the number of trilobite species that occupied local habitats (alpha diversity). A new compilation of data from Laurentia and other continents indicates that Silurian trilobite alpha diversities in all major environments were comparable to those of the Late Cambrian and Ordovician; shallow subtidal diversity reached an all-time high during the Late Ordovician. The profound differences in patterns at local and global levels demonstrate the necessity for a hierarchical approach to analyses of diversity. Factors governing global clade diversity are lodged at hierarchical levels beyond those controlling local species richness and must be sought in studies of between-habitat (beta) or geographic (gamma) diversity.
Diversity of coralline red algae: origination and extinction patterns from the Early Cretaceous to the Pleistocene
Authors: Aguirre Julio , Riding Robert , Braga Juan C.
Published: July 2006

Data from a comprehensive literature survey for the first time provide stage-level resolution of Early Cretaceous through Pleistocene species diversity for nongeniculate coralline algae. Distributions of a total of 655 species in 23 genera were compiled from 222 publications. These represent three family-subfamily groupings each with distinctive present-day distributions: (1) Sporolithaceae, low latitude, mainly deep water; (2) Melobesioid corallinaceans, high latitude, shallow water, to low latitude, deep water; (3) Lithophylloid/mastophoroid corallinaceans, mid- to low latitude, shallow water.

Raw data show overall Early Cretaceous-early Miocene increase to 245 species in the Aquitanian, followed by collapse to only 43 species in the late Pliocene. Rarefaction analysis confirms the pattern of increase but suggests that scarcity of publications exaggerates Neogene decline, which was actually relatively slight.

Throughout the history of coralline species, species richness broadly correlates with published global paleotemperatures based on benthic foraminifer δ18O values. The warm-water Sporolithaceae were most species-abundant during the Cretaceous, but they declined and were rapidly overtaken by the Corallinaceae as Cenozoic temperatures declined.

Trends within the Corallinaceae during the Cenozoic appear to reflect environmental change and disturbance. Cool- and deep-water melobesioids rapidly expanded during the latest Cretaceous and Paleocene. Warmer-water lithophylloid/mastophoroid species increased slowly during the same period but more quickly in the early Oligocene, possibly reflecting habitat partitioning as climatic belts differentiated and scleractinian reef development expanded near the Eocene/Oligocene boundary. Melobesioids abruptly declined in the late Pliocene-Pleistocene, while lithophylloid/mastophoroids increased again. Possibly, onset of glaciation in the Northern Hemisphere (~2.4 Ma) sustained or accentuated latitudinal differentiation and global climatic deterioration, disrupting high-latitude melobesioid habitats. Simultaneously, this could have caused moderate environmental disturbance in mid- to low-latitude ecosystems, promoting diversification of lithophylloids/mastophoroids through the “fission effect.”

Extinction events that eliminated >20% of coralline species were most severe (58–67% of species) during the Late Cretaceous and late Miocene-Pliocene. Each extinction was followed by substantial episodes of origination, particularly in the Danian and Pleistocene.
Heart urchins at the Cretaceous/Tertiary boundary: a tale of two clades
Authors: Jeffery Charlotte H.
Published: July 2006

Previous estimates of the global generic diversity loss for echinoids at the Cretaceous/Tertiary boundary have been as high as 65%. However, these estimates are based on compilations of occurrence data from the existing literature and are plagued by problems of inconsistent taxonomic usage. Analysis of a taxonomically standardized, phylogenetically framed data set demonstrates that the generic extinction rate for heart urchins was 33%, and that the two constituent orders suffered markedly different fates. Whereas holasteroids lost 56% of their generic diversity at the end of the Cretaceous, only 17% of spatangoid genera became extinct. Correlation of extinction with a range of geographical, environmental, and biological factors has been explored. Survivorship is significantly correlated only with feeding strategy, implying that the extinctions of atelostomate echinoids at the Cretaceous/Tertiary boundary were nutrient driven. In addition, feeding strategy is correlated with atelostomate clade affinity, explaining the differential fates of holasteroids and spatangoids at the end of the Cretaceous.
Taphonomic decoding of the paleobiological information locked in a lower Pleistocene assemblage of large mammals
Authors: Palmqvist Paul , Arribas Alfonso
Published: July 2006

The processes of fossilization have usually been perceived by paleontologists as destructive ones, leading to consecutive (and in most cases irretrievable) losses of paleobiological information. However, recent developments of conceptual issues and methodological approaches have revealed that the decrease in paleobiological information runs parallel to the gain of taphonomic information. This taphonomic imprinting often makes it possible to decode the fraction of paleobiological information that was lost during fossilization, and may also contribute new data for deciphering paleobiological information that was not originally preserved in the assemblage, such as paleoethology. A good example is the study of the macrovertebrate assemblage from the lower Pleistocene site at Venta Micena (Orce, southeastern Spain). Taphonomic analysis showed that the giant, short-faced hyenas (Pachycrocuta brevirostris) selectively transported ungulate carcasses and body parts to their maternity dens as a function of the mass of the ungulates scavenged. The fracturing of major limb bones in the dens was also highly selective, correlating with marrow content and mineral density. Important differences in bone-cracking intensity were related to which species the bones came from, which in turn biased the composition of the bone assemblage. The analysis of mortality patterns deduced for ungulate species from juvenile/adult proportions revealed that most skeletal remains were scavenged by the hyenas from carcasses of animals hunted by hypercarnivores, such as saber-tooths and wild dogs. Analytical study of the Venta Micena assemblage has unlocked paleobiological information that was lost during its taphonomic history, and has even provided paleobiological information that was not preserved in the original bone assemblage, such as the paleoethology ofP. brevirostris, which differed substantially from modern hyenas in being a strict scavenger of the prey hunted by other carnivores.
Are Mesozoic wood growth rings climate-induced?
Authors: Brison Anne-Lise , Philippe Marc , Thevenard Frédéric
Published: July 2006

Growth rings of Mesozoic fossil woods have often been used for paleoclimatological inferences. Most of the studies, however, rest upon uniformitarian deductions based on the observation of conifers from the present boreal temperate realm, whereas warm climates dominated during the Mesozoic. We propose a new approach, based on the study of the distribution of growth ring types among 643 samples from the Jurassic-Cretaceous interval. A clear picture emerges from analysis, consistent with what is known of Mesozoic climates from other sources. Woods with no rings are encountered in a wide latitudinal zone, extending up to 75°N and 65°S during the Late Cretaceous. Woods with well-developed latewood do not occur at low latitude and disappeared from the Northern Hemisphere during the Late Cretaceous. Our data set also shows that the taxonomic distribution of growth ring types is not regular. Among the genera encountered, 40% can build only one type of ring. The genus Agathoxylon never displays thick latewood, although it ranges from 75°S to 70°N. This demonstrates that growth ring studies must include a taxonomic analysis.
Co-ossified vertebrae of mosasaurs and cetaceans: implications for the mode of locomotion of extinct marine reptiles
Authors: Mulder Eric W. A.
Published: July 2006

Co-ossified pygal and caudal vertebrae in Late Cretaceous mosasaurs from the southeast Netherlands, northeast Belgium, and North America are compared with lumbar and caudal vertebrae from fossil and extant whales. Both infectious spondylitis and idiopathic vertebral hyperostosis afflicted these marine tetrapods. The causes of the infectious disease and of the idiopathic disease are similar in the compared life forms. The location of idiopathic hyperostosis along the vertebral column implicates axial locomotion in mosasaurs, as in whales.
Leanchoilia guts and the interpretation of three-dimensional structures in Burgess Shale-type fossils
Authors: Butterfield Nicholas J.
Published: July 2006

The Burgess Shale arthropod Leanchoilia superlata Walcott 1912, commonly preserves a three-dimensional axial structure generally interpreted as gut contents. Thin-section examination shows this instead to be phosphatized biserially repeated midgut glands, including exceptional preservation of subcellular features. The preferential mineralization of these structures is related to their unusually high chemical reactivity and probably to an internal source of phosphate. Sub-millimetric lineations previously interpreted as annular musculature are in fact planar, sometimes radially arranged, subdivisions of these glands. Ventral rows of isolated phosphate patches appear to represent the same tissue.

In extant arthropods, extensively developed midgut glands are related to a rich but infrequent diet with a primary function in storage. Their conspicuous occurrence in unambiguous fossil predators such as Sidneyia and Laggania (Anomalocaris) suggests they served a similar role in the Cambrian; by extension, their conspicuous occurrence in Leanchoilia suggests it was a predator or scavenger.

Phosphatized midguts with a structure essentially indistinguishable from that of Leanchoilia are also found in Burgess Shale Odaraia, Canadaspis, Perspicaris, Sidneyia, Anomalocaris, and Opabinia. All are characterized by a distinctive sub-millimetric arrangement of planar elements that is not found in extant arthropods or trilobites, suggesting they diverged before the last common ancestor of extant forms; i.e., they represent stem-group arthropods.

Three-dimensionally preserved guts are widely preserved in the Lower Cambrian Chengjiang biota but, unlike those in the Burgess Shale, appear to be filled with sediment. Although generally interpreted as evidence of deposit feeding, the form of these structures points to early permineralization of (sediment-free) midgut glands that were subsequently altered to clay minerals. There is no evidence of deposit feeding in the Chengjiang; indeed, there is a case to be made for deposit feeding not being generally exploited generally until after the Cambrian.

Fossils with three-dimensionally preserved axes from the Lower Cambrian Sirius Passet biota have been interpreted as lobopodians; however, most of the putative lobopodian features find alternative interpretations as aspects of Leanchoilia-type midgut glands. Although Kerygmachela is reliably identified as a stem-group arthropod, its phylogenetic position remains unresolved owing to the non-preservation of critical external features and to the plesiomorphic nature of its Leanchoilia-type midgut.
Mitotic topologies and mechanics of Neoproterozoic algae and animal embryos
Authors: Xiao Shuhai
Published: July 2006

Cell division is a key biological process in growth, morphogenesis, and reproduction. Despite our improved understanding of the genetics and dynamics of cell division in all major groups of living organisms, paleontological evidence for cell division is largely restricted to silicified (and some carbonaceous) algae and vascular plants where three-dimensional observation is possible. Animal cell division has been documented in the fossil record to a lesser extent; however, such knowledge is highly desirable in the recently revitalized field of evolutionary developmental biology. Two fundamentally different mitotic cell division topologies are preserved in late Neoproterozoic Doushantuo phosphorites (ca. 550–600 million years old) in South China. Doushantuo algal cells (∼20 μm in diameter) are successively cleaved by mitotic division planes that are offset but not deformed by subsequent cytokinesis. Mitotic division planes in successively cleaving Doushantuo animal embryos (several hundred microns in diameter) are also offset. However, in sharp contrast to Doushantuo algae, Doushantuo animal blastomeres repeatedly shift to mechanically stable configurations by disturbing preexisting division planes. This divergence reflects the underlying cytological and developmental differences between algae and animals. Specifically, the presence/absence of rigid cell walls and different cytokinetic mechanisms, coupled with mechanics at mitotic offsets, contribute to the diverging mitotic topologies in Doushantuo algae and animal embryos. These findings not only confirm previous interpretation of Doushantuo fossils but also provide direct paleontological evidence of cell movement in the development of these early animal fossils.
A Renaissance victory for the dual Alessandro
Authors: Gould Stephen Jay
Published: July 2006

Kepler famously remarked of his great Florentine friend that he could never keep sufficiently straight a man whose first name so resembled his last: Galileo Galilei. Others have labored under (or benefited from) this duality, and this third essay of my series tells a tale of the most obscure, yet highly significant, character that I have ever encountered from the early history of our science: the Neapolitan scholar (1461–1523) who called himself Alessandro ab Alessandro, or Alexander de Alexander, or Alessandro degli Alessandro—all meaning (roughly) Alexander from the family of Alexander.
Quantifying paleogeography using biogeography: a test case for the Ordovician and Silurian of Avalonia based on brachiopods and trilobites
Authors: Lees David C. , Fortey Richard A. , Cocks L. Robin M.
Published: July 2006

Despite substantial advances in plate tectonic modeling in the last three decades, the postulated position of terranes in the Paleozoic has seldom been validated by faunal data. Fewer studies still have attempted a quantitative approach to distance based on explicit data sets. As a test case, we examine the position of Avalonia in the Ordovician (Arenig, Llanvirn, early Caradoc, and Ashgill) to mid-Silurian (Wenlock) with respect to Laurentia, Baltica, and West Gondwana. Using synoptic lists of 623 trilobite genera and 622 brachiopod genera for these four plates, summarized as Venn diagrams, we have devised proportional indices of mean endemism (ME, normalized by individual plate faunas to eliminate area biogeographic effects) and complementarity (C) for objective paleobiogeographic comparisons. These can discriminate the relative position of Avalonia by assessing the optimal arrangement of inter-centroid distances (measured as great circles) between relevant pairs of continental masses. The proportional indices are used to estimate the “goodness-of-fit” of the faunal data to two widely used dynamic plate tectonic models for these time slices, those of Smith and Rush (1998) and Ross and Scotese (1997). Our faunal data are more consistent with the latter model, which we use to suggest relationships between faunal indices for the five time slices and new rescaled inter-centroid distances between all six plate pairs. We have examined linear and exponential models in relation to continental separation for these indices. For our generic data, the linear model fits distinctly better overall. The fits of indices generated by using independent trilobite and brachiopod lists are mostly similar to each other at each time slice and for a given plate, reflecting a common biogeographic signal; however, the indices vary across the time slices. Combining groups into the same matrix in a “total evidence” analysis performs better still as a measure of distance for mean endemism in the “Scotese” plate model. Four-plate mean endemism performs much better than complementarity as an indicator of pairwise distance for either plate model in the test case.
Ontogenetic and evolutionary patterns of shape differentiation during the initial diversification of Paleocene acarininids (planktonic foraminifera)
Authors: Quillévéré Frédéric , Debat Vincent , Auffray Jean-Christophe
Published: July 2006

Previous studies have established a close relationship between the evolutionary origin of new clades of planktonic foraminifera and heterochrony. Studies of the Paleogene radiation of the genusMorozovellarevealed, for example, a temporal pattern of variation consistent with paedomorphosis. Our study focused on the late Paleocene species ofAcarinina, sister group ofMorozovella.Shape variations related to evolution and ontogeny are appraised through a morphometric method based on outline analysis using the elliptic Fourier transform. Patterns of developmental and evolutionary changes are studied and compared within each species (Acarinina nitida, A. subsphaerica, andA. mckannai). As no congruence is found, we suggest that the evolutionary change observed within these species is not related to a heterochronic process. We also test for similarity of both evolutionary and ontogenetic changes among species. Although we observe no significant correlation between temporal patterns of shape change among species, the tight congruence of ontogenetic trajectories suggests that the developmental constraints affecting these trajectories have been preserved in spite of the evolutionary diversification of acarininids. Heterochrony is not clearly involved in the early Paleogene diversification of acarininids and therefore may not be as common as previously claimed. The role of developmental constraints in monitoring morphological evolution therefore needs to be reassessed.
Paleobiogeographical extinction patterns of Permian brachiopods in the Asian–western Pacific region
Authors: Shu-Zhong Shen , Shi G. R.
Published: July 2006

Spatial and temporal variations in biological diversity are critical in understanding the role of biogeographical regulation (if any) on mass extinctions. An analysis based on a latest database of the stratigraphic ranges of 89 Permian brachiopod families, 422 genera, and 2059 species within the Boreal, Paleoequatorial, and Gondwanan Realms in the Asian–western Pacific region suggests two discrete mass extinctions, each possibly with different causes. Using species/family rarefaction analysis, we constructed diversity curves for late Artinskian–Kungurian, Roadian–Wordian, Capitanian, and Wuchiapingian intervals for filtering out uneven sampling intensities. The end-Changhsingian (latest Permian) extinction eliminated 87–90% of genera and 94–96% of species of Brachiopoda. The timing of the end-Changhsingian extinction of brachiopods in the carbonate settings of South China and southern Tibet indicates that brachiopods suffered a rapid extinction within a short interval just below the Permian/Triassic boundary.

In comparison, the end-Guadalupian/late Guadalupian extinction is less profound and varies temporally in different realms. Brachiopods in the western Pacific sector of the Boreal Realm nearly disappeared by the end-Guadalupian but experienced a relatively long-term press extinction spanning the entire Guadalupian in the Gondwanan Realm. The end-Guadalupian brachiopod diversity fall is not well reflected at the timescale used here in the Paleoequatorial Realm because the life-depleted early Wuchiapingian was overlapped by a rapid radiation phase in the late Wuchiapingian. The Guadalupian fall appears to be related to the dramatic reduction of habitat area for the brachiopods, which itself is associated with the withdrawal of seawater from continental Pangea and the closure of the Sino-Mongolian seaway by the end-Guadalupian.
Long survival of “living fossils” with low taxonomic diversities in an evolving food web
Authors: Yoshida Katsuhiko
Published: July 2006

Living fossils are taxonomic groups surviving for a long time without any remarkable morphological change. Most of them retain low taxonomic diversities. Although some of them have survived in refuges to avoid predators and competitors, not all living fossils live in refuges. The survival of these groups, therefore, should be discussed in the context of biological interaction. I carried out computer simulations of a model food web system, in which each species feeds on others according to its feeding preference. The system evolves via evolution of species. In the simulation, some clades, like “living fossils,” survived for a long time with low species diversities. Such clades consisted of species with low evolutionary rates, which result in high predation pressure and intraclade competition for food. Nevertheless, the clades sustainably utilize prey clades and are consequently provided with sufficient food. In addition, because of the low species diversities of the clades, predators of the clades soon become extinct through lack of food. This study strongly suggests that in an evolving food web system, the low evolutionary rates of living fossils allow the long survival of those groups with low taxonomic diversities.
Measures of global biodiversity dynamics (past and present) are meaningless … or are they? Introductory comments
Authors: Sims Hallie J.
Published: July 2006

One can argue that the critical factors in evolution are competitive interaction, dispersal, and survival in that they determine the life and death of individuals and thus govern gene flow and the waxing and waning of populations; the byproduct of this cascade happens to be the origination and extinction of species and phylogenetic lineages. Perhaps evolutionary “truth” can be found only in petri dish experiments of lichens competing for space, through documentation of the wildly successful ecological invasion of purple loosestrife in ditches of northeastern North America, or by molecular phylogeographic analyses of the distribution of fruit fly lineages across the Hawaiian Islands. Nonetheless, there is something fundamentally intriguing in the fact that there are some 300,000 species of angiosperms currently distributed around the planet; an order of magnitude greater than other, far more ancient clades such as cycads, ferns, and horsetails and a discrepancy that has spurred centuries of evolutionary theorizing on the causes of their high relative diversity—Darwin's “abominable mystery.” These sorts of macroevolutionary questions necessitate research agendas that target global distributions of taxa over long intervals of geological time. Did mammals stay low to the ground until the large-bodied herbivore niches were opened up when an asteroid knocked off the last of the non-avian dinosaurids at the end of the Cretaceous? Was the transition from the dazzling variety of trilobites that dominated Cambrian and Ordovician marine ecosystems to the diverse ammonoid fauna of the later Paleozoic associated with differing intrinsic taxonomic turnover rates? Are species in tightly integrated communities such as reefs more vulnerable to extinction during intervals of climate change than species with lower levels of ecological connectivity?
Dinosaur body temperatures: the occurrence of endothermy and ectothermy
Authors: Seebacher Frank
Published: July 2006

Despite numerous studies, the thermal physiology of dinosaurs remains unresolved. Thus, perhaps the commonly asked question whether dinosaurs were ectotherms or endotherms is inappropriate, and it is more constructive to ask which dinosaurs were likely to have been endothermic and which ones ectothermic. Field data from crocodiles over a large size range show that body temperature fluctuations decrease with increasing body mass, and that average daily body temperatures increase with increasing mass. A biophysical model, the biological relevance of which was tested against field data, was used to predict body temperatures of dinosaurs. However, rather than predicting thermal relations of a hypothetical dinosaur, the model considered correct paleogeographical distribution and climate to predict the thermal relations of a large number of dinosaurs known from the fossil record (>700). Many dinosaurs could have had “high” (>30°) and stable (daily amplitude >2°) body temperatures without metabolic heat production even in winter, so it is unlikely that selection pressure would have favored the evolution of elevated resting metabolic rates in those species. Recent evidence of ontogenetic growth rates indicates that even the juveniles of large species (3000–4000 kg) could have had biologically functional body temperature ranges during early development. Smaller dinosaurs (<100 kg) at mid to high latitudes (>45°) could not have had high and stable body temperatures without metabolic heat production. However, elevated metabolic rates were unlikely to have provided selective advantage in the absence of some form of insulation, so probably insulation was present before endothermy evolved, or else it coevolved with elevated metabolic rates. Superimposing these findings onto a phylogeny of the Dinosauria suggests that endothermy most likely evolved among the Coelurosauria and, to a lesser extent, among the Hypsilophodontidae, but not among the Stegosauridae, Nodosauridae, Ankylosauridae, Hadrosauridae, Ceratopsidae, Prosauropoda, and Sauropoda.
Digital karyotyping: a powerful tool for cancer gene discovery
Authors: Yan Hai , Bigner Darell
Published: July 2006

Digital karyotyping is a genome‐wide approach that is designed to provide a global genomic content profiling of cells at high resolution. In cancer cells, knowledge of gene‐specific genetic content alterations has the power to expedite the process of cancer gene discovery.
Nanocasting: A Versatile Strategy for Creating Nanostructured Porous Materials
Authors: Lu A.‐H. , Schüth F.
Published: July 2006

Nanocasting is a powerful method for creating materials that are more difficult to synthesize by conventional processes. We summarize recent developments in the synthesis of various structured porous solids, covering silica, carbon, and other nonsiliceous solids that are created by a nanocasting pathway. Structure replication on the nanometer length scale allows materials' properties to be manipulated in a controlled manner, such as tunable composition, controllable structure and morphology, and specific functionality. The nanocasting pathway with hard templates opens the door to the design of highly porous solids with multifunctional properties and interesting application perspectives.
Cover Picture: Surfactant‐Mediated Generation of Iso‐Oriented Dense and Mesoporous Crystalline Metal‐Oxide Layers (Adv. Mater. 14/2006)
Authors: Brezesinski T. , Groenewolt M. , Pinna N. , Amenitsch H. , Antonietti M. , Smarsly B.
Published: July 2006

For certain metal oxides (e.g., MoO3) ordered mesoporous films can be obtained with the nanocrystals in the pore walls being uniformly oriented with respect to the substrate by applying evaporation‐induced self‐assembly followed by heating. This surprisingly facile process, described by Smarsly and co‐workers on p. 1827, works on different polar substrates (glass, metals, etc.) for oxides with anisotropic unit cells, based on the interaction with surfactants during nucleation (“soft‐epitaxy”).
Inside Front Cover: Anisotropic Growth of PbSe Nanocrystals on Au–Fe3O4 Hybrid Nanoparticles (Adv. Mater. 14/2006)
Authors: Shi W. , Sahoo Y. , Zeng H. , Ding Y. , Swihart M. T. , Prasad P. N.
Published: July 2006

PbSe nanorods and branched nanorods can be grown using binary Au/Fe3O4 nanoparticles as seeds, as reported by Swihart, Zeng, Prasad, and co‐workers on p. 1889. PbSe nucleates on the Au portion of the seed particle and grows anisotropically as one or more straight or branched nanorods. The background images show PbSe nanorods (top), and ternary Fe3O4–Au–PbSe hybrid nanocrystals (bottom). High‐resolution TEM images show Fe3O4(purple)–Au(gold)–PbSe (green) ternary nanocrystals. A ball‐and‐stick cartoon model illustrates the approximate size of these structures relative to the individual atoms.
Steady‐state and transient analysis of a CH4–catalytic partial oxidation reformer
Authors: Tavazzi Ivan , Maestri Matteo , Beretta Alessandra , Groppi Gianpiero , Tronconi Enrico , Forzatti Pio
Published: July 2006

In this work dynamic and steady‐state CH4 partial oxidation tests, performed in an insulated lab‐scale reactor over a Rh‐based catalyst supported onto Al2O3 spheres, are presented and discussed. To gain insight in the complex observed phenomena a previously developed 1D heterogeneous mathematical model of adiabatic reactor was applied to data analysis. The model implemented an indirect reaction scheme independently derived in previous works. In experiments at low flow rates the heat dispersion significantly affected the steady‐state response of the reactor; the process was governed by thermodynamics. By increasing the flow rate the catalytic bed progressively heated up and the adiabatic behavior was approached as a result of the predominance of the reaction enthalpy release over the heat losses; a kinetic effect of contact time was observed. Under these conditions start‐up dynamics of the process were acquired. The temporal evolution of the product distribution along with the shape of axial temperature profiles at steady state were consistent with the occurrence of an indirect reaction path leading to the formation of synthesis gas. A sensitivity analysis showed that the description of the temperature profiles and conversion/selectivity performances at steady state is greatly influenced by the rate of the reforming reactions; the simulation of the reactor start‐up dynamics is highly sensitive to the initial solid temperature. The comparison between measured temperature profiles and model predictions suggested that the thermocouple measurements were mainly influenced by the temperature of the flowing gas. © 2006 American Institute of Chemical Engineers AIChE J, 2006
Freshwater mussel assemblage structure in a regulated river in the Lower Mississippi River Alluvial Basin, USA
Authors: Haag Wendell R. , Warren Melvin L.
Published: July 2006

This paper documents a diverse, reproducing freshwater mussel community (20 species) in Lower Lake — an impounded, regulated portion of the Little Tallahatchie River below Sardis Dam in Panola Co., Mississippi, USA.

Despite being regulated and impounded, the lake has a heterogeneous array of habitats that differ markedly in mussel community attributes. Four distinct habitat types were identified based on current velocity and substrate characteristics, representing a gradient from habitats having lotic characteristics to lentic habitats. All four habitat types supported mussels, but habitats most resembling unimpounded, lotic situations (relatively higher current velocity and coarser substrate) had the highest mussel abundance and species density (10.1 mussels m−2, 1.8 species m−2, respectively). Lentic habitats (no flow, fine substrate) were characterized by lower abundance and species density (2.0 mussels m−2, 0.8 species m−2, respectively), but supported mussel assemblages distinctive from lotic habitats.

Evidence of strong recent recruitment was observed for most species in the lake and was observed in all four habitat types.

Although impounded and regulated, Lower Lake represents one of the few areas of stable large‐stream habitat in the region. The presence of a diverse, healthy mussel community in this highly modified habitat suggests that a large component of the regional mussel fauna is relatively resilient and adaptable and is limited primarily by the absence of stable river reaches. Management actions that increase stream stability are likely to result in expansion of the mussel fauna and restoration of a valuable component of ecosystem function in this region.

Published in 2006 by John Wiley & Sons, Ltd.
Response of the riverine fish community to the construction and operation of a diversion hydropower plant in central Chile
Authors: Habit Evelyn , Belk Mark C. , Parra Oscar
Published: July 2006

Chilean rivers have a large potential for hydropower development, and they also contain a unique native fish fauna with a high level of endemism. Several diversion hydropower plants have recently been constructed in Chile; however, the response of fish communities to these new hydropower plant designs is not well known.

Responses of native and non‐native fish to the construction and operation of a new hydropower plant that diverts water from two rivers were quantified. The Laja River is highly regulated and manipulated with three older (40 yr) dam‐based hydropower plants and irrigation diversions located upstream from the new facility. In contrast, the Rucúe River has no other hydropower facilities and is comparatively undisturbed.

Prior to construction, the Laja River had a fish community with lower species richness compared with the Rucúe River. The fish community structure in the Laja River was dramatically altered after the new hydropower facility began operation. On the other hand, in the Rucúe River, even though abundance of fish declined, there was less of a change in the total fish community structure. The fish community in the Rucúe River exhibited greater resistance to change compared with the Laja River.

The species most affected were the introduced salmonids and an endangered native speciesPercilia irwini.

Although diversion hydropower designs may have less impact than traditional dam‐based hydropower facilities, results of this study indicate that diversion hydropower structures can cause large changes in the fish community.

Copyright © 2006 John Wiley & Sons, Ltd.
Testing for correspondence between coral reef invertebrate diversity and marine park designation on the Masoala Peninsula of eastern Madagascar
Authors: McClanahan T.R.
Published: July 2006

Justifying the designation of protected areas often depends on the ability to select areas in good ecological conditions, with high taxonomic richness, and unique habitats or species assemblage characteristics.

The ecology of scleractinian coral and prosobranch snails were examined along the Masoala Peninsula of north‐eastern Madagascar using rapid assessment methods to evaluate the correspondence between unique invertebrate faunal characteristics and park designation.

The reefs along this peninsula are in good ecological condition and have a coral and snail fauna similar to most of the western Indian Ocean, with no indications of local endemism in these groups. There was no relationship between the taxonomic richness of snails and corals. Corals were better at distinguishing locations based on taxonomic richness while snails were better based on unique faunal characteristics.

Corals had the highest taxonomic richness on the extreme windward north and south and the lowest richness on the leeward side of the peninsula. The leeward side did, however, have an unusual habitat of corals growing on granite rock with a unique coral and snail fauna. A northern and southern assemblage characterized snail fauna on the windward side of the peninsula.

The composite findings indicate that the currently designated park areas cover two of the three areas that have either high diversity or unique faunas.

Copyright © 2006 John Wiley & Sons, Ltd.
Alien and endemic flora at reference and non‐reference sites in Mediterranean‐type streams in Portugal
Authors: Aguiar Francisca C. , Ferreira M. Teresa , Albuquerque António , Moreira Ilídio
Published: July 2006

A comparison was made between a variety of alien and endemic plant species from 272 aquatic and riparian habitats in Portuguese Mediterranean‐type streams in reference condition — i.e. near‐natural river corridors — and non‐reference condition. The objective was to detect differences in relative proportion and cover between these species groups. The differences in endemic and alien flora from siliceous and calcareous river types were also analysed. Environmental and human disturbance factors were related with the richness and cover of both species groups.

A total of 568 species were found, of which 44 were alien and 28 were endemic. Alien species were present at 91% of the surveyed locations, and were consistently more widespread at non‐reference sites than at reference ones for both river types, with calcareous sites having a higher invasibility. Endemic species occurred at 45% of the sampling sites and displayed a significantly lower richness and cover than their alien counterparts.

Alien richness and cover were positively related to direct human disturbance within the river systems, and with floodplain uses such as urban occupation, intensive agriculture, and nutrient inputs. Endemic species also respond to anthropogenic variables, rather than to climatic and geographical ones, with richness and cover increasing as human impacts on fluvial systems and related floodplains decrease.

Comprehensive control of alien invasive species and the protection of endemic plant populations will require attempts at monitoring ecological river integrity, and the achievement of ‘good ecological status’ — one of the goals of the European Union's Water Framework Directive. Portuguese riparian areas must be managed in such a way as to protect the relatively few preserved riparian habitats by lowering the direct and indirect pressures in fluvial corridors and thus preventing future alien plant invasions.

Copyright © 2006 John Wiley & Sons, Ltd.
Priority habitats for the conservation of large river fish in the Ganges river basin
Authors: Sarkar Uttam Kumar , Bain Mark B.
Published: July 2006

Three classes of habitat used by groups of fish species classified as conservation and management priorities were developed for the Gerua River (also known as the Girwa River, Karnali River) in the Ganges river basin. This river is large (mean annual discharge ca 1500 m3 s−1, up to 900 m wide), surrounded by protected lands of India and Nepal, and upstream of major diversions and river alterations.

Fish and habitat sampling was conducted at 45 sites from 2000 to 2003. Data were analysed for 2172 fish of 14 species. Species and life stages found occupying a statistically distinct subset of the river habitats were grouped to identify classes of river habitat for conservation.

Most species and life‐stage groups specialized on specific habitat conditions revealed by multivariate analyses of variance and a principal component analysis. The most numerous and diverse group (six species, 15 life stages) was associated with deep depositional habitats with sandy substrate. Two species covering three life stages were primarily oriented to erosional habitat marked by fast current velocity with pebble and cobble substrate. A third group of three species of adults and juveniles were intermediate in habitat use.

River conservation for fish faunas should maintain both erosional and depositional channel habitats with depths, substrates, and current velocity inclusive of the ranges reported. The erosional and depositional nature of the key habitats requires that rivers be maintained with flows capable of channel‐forming functions.

Copyright © 2006 John Wiley & Sons, Ltd.
Comparative assessment of stream acidity using diatoms and macroinvertebrates: implications for river management and conservation
Authors: Lewis Bethan R. , Jüttner Ingrid , Reynolds Brian , Ormerod S.J.
Published: July 2006

Macroinvertebrates and phytobenthic organisms (e.g. diatoms) are frequently used as bioindicators of water quality, yet few studies compare their effectiveness despite both being emphasized in the EC Water Framework Directive.

Here, as a case study, the efficacy of each group in assessing acid–base status in the catchment of the Welsh River Wye was evaluated from surveys in 2 years.

Ordination showed that both diatom and macroinvertebrate assemblages varied highly significantly with pH, alkalinity and calcium concentrations. Moreover, ordination scores were highly inter‐correlated between these groups in both study years.

There were also contrasts, with diatoms and macroinvertebrates changing in differing ways with catchment land‐use and channel hydromorphology. These differing responses suggest complementary indicator value, while variation in generation times between diatoms and macroinvertebrates suggests potentially contrasting speeds of response to variations over different timescales.

These data reveal that significant water quality problems in the River Wye, a proposed Special Area of Conservation, are generated from the continued acidification of low‐order, headwater streams and this has considerable significance for the objectives of the Water Framework Directive, and the EC Habitats Directive.

Copyright © 2006 John Wiley & Sons, Ltd.
Learning to classify documents according to genre
Authors: Finn Aidan , Kushmerick Nicholas
Published: July 2006

Current document‐retrieval tools succeed in locating large numbers of documents relevant to a given query. While search results may be relevant according to the topic of the documents, it is more difficult to identify which of the relevant documents are most suitable for a particular user. Automatic genre analysis (i.e., the ability to distinguish documents according to style) would be a useful tool for identifying documents that are most suitable for a particular user. We investigate the use of machine learning for automatic genre classification. We introduce the idea of domain transfer—genre classifiers should be reusable across multiple topics—which does not arise in standard text classification. We investigate different features for building genre classifiers and their ability to transfer across multiple‐topic domains. We also show how different feature‐sets can be used in conjunction with each other to improve performance and reduce the number of documents that need to be labeled.
Feature instability as a criterion for selecting potential style markers
Authors: Koppel Moshe , Akiva Navot , Dagan Ido
Published: July 2006

We introduce a new measure on linguistic features, called stability, which captures the extent to which a language element such as a word or a syntactic construct is replaceable by semantically equivalent elements. This measure may be perceived as quantifying the degree of available “synonymy” for a language item. We show that frequent, but unstable, features are especially useful as discriminators of an author's writing style.
A qualitative feature‐based characterization of 2D architectural style
Authors: Jupp Julie R. , Gero John S.
Published: July 2006

Architectural plans are design diagrams that describe building layout where space is planned according to design requirements. Style in architecture is generally characterized as common features appearing in a particular class of building design. This research seeks to address how to recognize architectural design style from a 2D plan diagram. We explore this question in a computational encoder‐analyzer (E‐A) model for 2D plans, where a characterization of 2D style is based on qualitative spatial representation and information theoretic measures. In a preliminary study of a prominent architect's plans, we demonstrate the effectiveness of our approach. We conclude by discussing practical applications of automated plan recognition and classification in design support tools.