The mechanisms for nitration and nitrotyrosine formation in vitro and in vivo: Impact of diet

The detection of 3-nitro-L-tyrosine residues associated with many disease states, including gastric cancer, has implicated a role for peroxynitrite in vivo, and thus endogenously produced nitric oxide and superoxide. Additionally, dietary nitrate has been suggested to be involved in the pathogenesis of gastric cancer through a mechanism involving reduction to nitrite and subsequent formation of potentially mutagenic nitrosocompounds. Studies have now demonstrated that a multitude of reactive nitrogen species other than peroxynitrite are capable of producing nitrotyrosine. Thus, we have reviewed the evidence that dietary nitrate, amongst other reactive nitrogen species, may contribute to the body burden of nitrotyrosine.     

The mechanisms for nitration and nitrotyrosine formation in vitro and in vivo: Impact of diet

The detection of 3-nitro-L-tyrosine residues associated with many disease states, including gastric cancer, has implicated a role for peroxynitrite in vivo, and thus endogenously produced nitric oxide and superoxide. Additionally, dietary nitrate has been suggested to be involved in the pathogenesis of gastric cancer through a mechanism involving reduction to nitrite and subsequent formation of potentially mutagenic nitrosocompounds. Studies have now demonstrated that a multitude of reactive nitrogen species other than peroxynitrite are capable of producing nitrotyrosine. Thus, we have reviewed the evidence that dietary nitrate, amongst other reactive nitrogen species, may contribute to the body burden of nitrotyrosine.     

A pragmatic approach to the species problem from a paleontological perspective

The ideal scenario for paleontologists would be for the species they designate to be equivalent to the species recognized for modern animals, in the sense that they were formed as a result of the same evolutionary processes. This would mean, for example, that we could be confident that in combining extant and extinct taxa in phylogenetic analyses we would be dealing with equivalent operational taxonomic units. Notwithstanding the many thousands of pages that have been spent arguing over species concepts, the only concept that has won widespread acceptance for the designation of modern species is Mayr's Biological Species Concept (BSC).¹ In fact, whenever we complete a cladistic analysis, we assume reproductive isolation of our terminal taxa because otherwise their similarities could be the product of interbreeding rather than common ancestry. Fundamentally, we all behave as though the BSC is true.     

Feather eating in Great Crested Grebes Podiceps cristatus: a unique solution to the problems of debris and gastric parasites in fish-eating birds

The occurrence of feathers in stomachs of 407 Great Crested Grebes Podiceps cristatus from Lake IJsselmeer, The Netherlands, is described. Only four of the 8718 identified stomach feathers originated from a species other than Great Crested Grebes. In all, 68% were breast and belly feathers and 19% were flank feathers. Flank feathers were positively selected from those becoming available during moult, and also occurred more in the ejected feather pellets than expected from the intake. This suggests that flank feathers, which are long and curved and have a black tip, may be especially suited for the formation of pellets. Feather ingestion was more than balanced by feather production. Feathers were most abundant in stomachs in autumn and were least numerous in winter. Most of this variation can be explained by seasonal differences in the intensity of body moult. In addition, the type of prey was related to the number of ingested feathers. When the diet consisted of smelt, which leave little indigestible matter, more feathers were eaten than with a diet of perch and pikeperch, which leave more fish debris. We suggest the hypothesis that ingested feathers, in the absence of other indigestible matter, contribute substance to the stomach content, enabling the formation of pellets that can be ejected. The habit of regularly ejecting the stomach contents minimizes the chance that any serious population of gastric parasites will build up in the upper part of the alimentary tract.     

襀翅目化石稚虫口器及其食性分析

本文概述了现生襀翅目稚虫的食性,其通常分为腐食-植食性、肉食性和杂食性;食性不同,其口器结构差异明显.古生物学家根据化石保存的口器结构,利用将今论古、形态功能分析等手段推测襀翅目化石稚虫的食性有腐食-植食性、刮食性、肉食性,以及因化石保存等因素导致的食性不确定.此外,选取热河昆虫群中襀翅目昆虫的优势种类Perlidae的一代表化石稚虫,对其保存的口器形态及其食性的关系进行了分析,推断其食性为捕食性.     

Macroevolution is more than repeated rounds of microevolution

SUMMARY Arguments over macroevolution versus microevolution have waxed and waned through most of the twentieth century. Initially, paleontologists and other evolutionary biologists advanced a variety of non-Darwinian evolutionary processes as explanations for patterns found in the fossil record, emphasizing macroevolution as a source of morphologic novelty. Later, paleontologists, from Simpson to Gould, Stanley, and others, accepted the primacy of natural selection but argued that rapid speciation produced a discontinuity between micro- and macroevolution. This second phase emphasizes the sorting of innovations between species. Other discontinuities appear in the persistence of trends (differential success of species within clades), including species sorting, in the differential success between clades and in the origination and establishment of evolutionary novelties. These discontinuities impose a hierarchical structure to evolution and discredit any smooth extrapolation from allelic substitution to large-scale evolutionary patterns. Recent developments in comparative developmental biology suggest a need to reconsider the possibility that some macroevolutionary discontinuites may be associated with the origination of evolutionary innovation. The attractiveness of macroevolution reflects the exhaustive documentation of large-scale patterns which reveal a richness to evolution unexplained by microevolution. If the goal of evolutionary biology is to understand the history of life, rather than simply document experimental analysis of evolution, studies from paleontology, phylogenetics, developmental biology, and other fields demand the deeper view provided by macroevolution.     

Biodiversity among haptophyte algae

The division Haptophyta is represented only by about 300 extant species showing wide diversity in morphology, biochemistry and ecology. They have a world-wide distribution and are numerically important in phytoplankton populations in nearly all marine environments. Evidence from the geological record shows that they have been the major constituent of calcareous deposits since the Late Triassic and, as they have evolved quickly through time, their coccoliths have always shown wide morphological diversity. In today's oceans they occasionally produce extensive blooms, visible by satellite imagery, which have ecological impact. As a consequence of these blooms the haptophyte algae are now receiving greater attention, as their role in the global sulphur and carbon cycles may influence the world's climate, and their potential as nuisance bloom algae have implications for commercial fishing and the marine ecosystem. As it is likely that these organisms have always produced such blooms, these effects may have been in operation for the last 200 million years.     

Body Size Overlap,Habitat Partitioning and Living Space Requirements of Terrestrial Vertebrate Predators: Implications for the Paleoecology of Large Theropod Dinosaurs

Ecological studies of extant tetrapod predators indicate that morphologically similar species which coexist in the same habitats routinely reduce interspecific competition for food by regular spacing of body size. The biggest predator species in the assemblage often differ more from one another in size than the smallest species. When coexisting carnivore species do not differ greatly in size, they commonly show morphological differences related to prey handling that may reduce dietary overlap. If carnivore species are very similar in both size and morphology, competition is avoided by habitat partitioning. Two tyrannosaurid species from the late Campanian Dinosaur Park Formation of western Canada are similar in both size and morphology, suggesting that they were segregated on the basis of habitat and/or biogeographic province. However; consideration of the living-space requirements of predator species of such large body size suggests that this kind of spatial separation would only have been possible had tyrannosaurids been more like ectotherms than endotherms in their metabolic rates. Distribution of different large theropod species across different, and surprisingly small (for the size of the animals) portions of Mesozoic landscapes may also account for the remarkably high diversity of morphologically similar large theropods in other dinosaur faunas.     

Epistemic values in the Burgess Shale debate

Focusing primarily on papers and books discussing the evolutionary and systematic interpretation of the Cambrian animal fossils from the Burgess Shale fauna, this paper explores the role of epistemic values in the context of a discipline (paleontology) striving to establish scientific authority within a larger domain of epistemic problems and issues (evolutionary biology). The focal point of this analysis is the repeated claims by paleontologists that the study of fossils gives their discipline a unique ‘historical dimension’ that makes it possible for them to unravel important aspects of evolution invisible to scientists who study the extant biosphere. The first part of the paper explores the shifting of emphasis in the writings of paleontologists between two strategies that employ opposing views on the classical positivist and physicalist ideal of science. The second part analyzes paleontologists’ claims of privileged access to life’s historical dimension in a situation where a theoretical upheaval occurring independent of the epistemical problem at hand completely shifts the standards for evaluating the legitimacy of various knowledge claims. Though the various strategies employed in defending the privileged historical perspective of paleontology have been disparate and, to an extent contradictory, each impinges on the acceptance of a specific epistemic ideal or set of values and success or failure of each depends on the compatibility of this ideal with the surrounding community of scientists.     

Divergence Times and the Evolutionary Radiation of New World Monkeys (Platyrrhini,Primates): An Analysis of Fossil and Molecular Data

The estimation of phylogenetic relationships and divergence times among a group of organisms is a fundamental first step toward understanding its biological diversification. The time of the most recent or last common ancestor (LCA) of extant platyrrhines is one of the most controversial among scholars of primate evolution. Here we use two molecular based approaches to date the initial divergence of the platyrrhine clade, Bayesian estimations under a relaxed-clock model and substitution rate plus generation time and body size, employing the fossil record and genome datasets. We also explore the robustness of our estimations with respect to changes in topology, fossil constraints and substitution rate, and discuss the implications of our findings for understanding the platyrrhine radiation. Our results suggest that fossil constraints, topology and substitution rate have an important influence on our divergence time estimates. Bayesian estimates using conservative but realistic fossil constraints suggest that the LCA of extant platyrrhines existed at ca. 29 Ma, with the 95% confidence limit for the node ranging from 27–31 Ma. The LCA of extant platyrrhine monkeys based on substitution rate corrected by generation time and body size was established between 21–29 Ma. The estimates based on the two approaches used in this study recalibrate the ages of the major platyrrhine clades and corroborate the hypothesis that they constitute very old lineages. These results can help reconcile several controversial points concerning the affinities of key early Miocene fossils that have arisen among paleontologists and molecular systematists. However, they cannot resolve the controversy of whether these fossil species truly belong to the extant lineages or to a stem platyrrhine clade. That question can only be resolved by morphology. Finally, we show that the use of different approaches and well supported fossil information gives a more robust divergence time estimate of a clade.     

Limits to randomness in paleobiologic models: the case of Phanerozoic species diversity

The question of how random, or unconstrained, paleobiologic models should be is examined with a case study: Signor's (1982, 1985) inverse calculation of levels of marine species diversity through the Phanerozoic. His calculation involved an ingenious model that estimated species numbers and species abundances in the world oceans of the past by correcting known numbers of fossil species for variations in sedimentary rocks available for sampling and in effort paleontologists might devote to sampling. The model proves robust to changes in possible shapes of species-abundance distributions, but it is sensitive to alterations in the assumption that paleontologists collect fossils at random. If it is assumed that ease of collecting varies with age of sediment (with the Cenozoic offering easy sampling) or that paleontologists tend to seek out rarer fossils, results of the inverse calculation change. In particular, the magnitude of the calculated Cenozoic diversity increase always declines from the factor of about seven as originally reported to something considerably smaller. This leaves open the problem of the magnitude of Cenozoic increase in marine species diversity, awaiting better empirical data and, perhaps, more exacting models, random or otherwise.     

A morphometric analysis of extant and early miocene fossil hominoid maxillo-dental specimens

It is demonstrated in this paper that before we can hope to formulate phylogenetic relationships between and amongst fossil hominoid material it is first necessary to sex the material accurately. In order to determine whether the morphological and morphometrical variability seen in fossil specimens is due to sexual or inter species dimorphism, it is necessary to calibrate fossil specimens against extant hominoid species' morphologies. Only after fossil specimens have been sexed is it possible to differentiate between morphologies that are related to sex and those that are species specific. This will help reduce fossil misallocation. A morphometric analysis of extant and fossilProconsul hominoid material is presented. Each fossil specimen has been sexed according to symplesiomorphic sex morphologies as defined in this paper. After the fossil specimens have been sexed they are analyzed using multivariate statistics. The identification of differing sex patterns within the specimens examined here suggests that a new species ofProconsul may have to be considered.     

Acquisition of the paired fins: a view from the sequential evolution of the lateral plate mesoderm

The origin of paired fins has long been a focus of both paleontologists and developmental biologists. Fossil records indicate that the first pair of fin‐like structures emerged in the body wall of early vertebrates. However, extant agnathan lampreys and hagfishes lack paired fins, and thus it has been difficult to determine the developmental processes underlying the ancestral acquisition of paired fins in vertebrates. Fortunately, recent advances in our knowledge of the developmental mechanisms of the lateral plate mesoderm among different taxa have provided clues for understanding the evolutionary origin of vertebrate paired appendages.     

Ecological history and latent conservation potential: large and giant tortoises as a model for taxon substitutions

Starting in the late 1970s, ecologists began unraveling the role of recently extinct large vertebrates in evolutionary ecology and ecosystem dynamics. Three decades later, practitioners are now considering the role of ecological history in conservation practice, and some have called for restoring missing ecological functions and evolutionary potential using taxon substitutes – extant, functionally similar taxa – to replace extinct species. This pro‐active approach to biodiversity conservation has proved controversial. Yet, rewilding with taxon substitutes, or ecological analogues, is now being integrated into conservation and restoration programmes around the world. Empirical evidence is emerging that illustrates how taxon substitutions can restore missing ecological functions and evolutionary potential. However, a major roadblock to a broader evaluation and application of taxon substitution is the lack of practical guidelines within which they should be conducted. While the International Union for Conservation of Nature's reintroduction guidelines are an obvious choice, they are unsuitable in their current form. We recommend necessary amendments to these guidelines to explicitly address taxon substitutions. A second impediment to empirical evaluations of rewilding with taxon substitutions is the sheer scale of some proposed projects; the majority involves large mammals over large areas. We present and discuss evidence that large and giant tortoises (family Testudinidae) are a useful model to rapidly provide empirical assessments of the use of taxon substitutes on a comparatively smaller scale. Worldwide, at least 36 species of large and giant tortoises went extinct since the late Pleistocene, leaving 32 extant species. We examine the latent conservation potential, benefits, and risks of using tortoise taxon substitutes as a strategy for restoring dysfunctional ecosystems. We highlight how, especially on islands, conservation practitioners are starting to employ extant large tortoises in ecosystems to replace extinct tortoises that once played keystone roles.     

Eusociality and the success of the termites: insights from a supertree of dictyopteran families

Sociality in insects may negatively impact on species richness. We tested whether termites have experienced shifts in diversification rates through time. Supertree methods were used to synthesize family‐level relationships within termites, cockroaches and mantids. A deep positive shift in diversification rate is found within termites, but not in the cockroaches from which they evolved. The shift is responsible for most of their extant species richness suggesting that eusociality is not necessarily detrimental to species richness, and may sometimes have a positive effect. Mechanistic studies of speciation and extinction in eusocial insects are advocated.     

Origins and introgression of polyploid species in Mentzelia section Trachyphytum (Loasaceae)

? Premise of the study: Polyploid speciation has been important in plant evolution. However, the conditions that favor the origination and persistence of polyploids are still not well understood. Here, we examine origins of 16 polyploid species in Mentzelia section Trachyphytum. ? Methods: We used phylogeny reconstructions based on DNA sequences from plastid regions and the nuclear gene isocitrate dehydrogenase (idh) to construct hypotheses of introgression and polyploidization. ? Key results: Molecular data suggest that homoploid hybridization has been surprisingly common in Trachyphytum. Diploid species had unequal involvement in polyploid origins, but most polyploid taxa had allopolyploid origins from extant progenitors. A few polyploids with extreme phenotypes did not appear to have extant progenitors. We infer that the progenitors of these species were derived from extinct diploid lineages or ancestral lineages of multiple extant diploids. In agreement with other recent studies, we recovered molecular evidence of multiple phylogenetically distinct origins for several polyploid taxa, including the widespread octoploid M. albicaulis. ? Conclusions: Evidence of high levels of introgression and allopolyploidy suggests that hybridization has played an important role in the evolution of Trachyphytum. Although idh sequences exhibited complicated evolution, including gene duplication, deletion, and recombination, they provided a higher percentage of informative characters for phylogeny reconstruction than the most variable plastid regions, allowing tests of hypotheses regarding polyploid origins. Given the necessity for rapidly evolving low-copy nuclear genes, researchers studying hybridization and polyploidy may increasingly turn to complex sequence data.     

CENTRAL MOMENTS AND PROBABILITY DISTRIBUTION OF COLLESS'S COEFFICIENT OF TREE IMBALANCE

The great increase in the number of phylogenetic studies of a wide variety of organisms in recent decades has focused considerable attention on the balance of phylogenetic trees—the degree to which sister clades within a tree tend to be of equal size—for at least two reasons: (1) the degree of balance of a tree may affect the accuracy of estimates of it; (2) the degree of balance, or imbalance, of a tree may reveal something about the macroevolutionary processes that produced it. In particular, variation among lineages in rates of speciation or extinction is expected to produce trees that are less balanced than those that result from phylogenetic evolution in which each extant species of a group has the same probability of speciation or extinction. Several coefficients for measuring the balance or imbalance of phylogenetic trees have been proposed. I focused on Colless's coefficient of imbalance (7) for its mathematical tractability and ease of interpretation. Earlier work on this statistic produced exact methods only for calculating the expected value. In those studies, the variance and confidence limits, which are necessary for testing the departure of observed values of I from the expected, were estimated by Monte Carlo simulation. I developed recursion equations that allow exact calculation of the mean, variance, skewness, and complete probability distribution of I for two different probability-generating models for bifurcating tree shapes. The Equal-Rates Markov (ERM) model assumes that trees grow by the random speciation and extinction of extant species, with all species that are extant at a given time having the same probability of speciation or extinction. The Equal Probability (EP) model assumes that all possible labeled trees for a given number of terminal taxa have the same probability of occurring. Examples illustrate how these theoretically derived probabilities and parameters may be used to test whether the evolution of a monophyletic group or set of monophyletic groups has proceeded according to a Markov model with equal rates of speciation and extinction among species, that is, whether there has been significant variation among lineages in expected rates of speciation or extinction.     

Morphology and ecology of the Antarcticycas plant

The Antarcticycas plant is reconstructed from the co-occurring vegetative organ taxa Antarcticycas schopfii and Yelchophyllum omegapetiolaris and the pollen cone taxon Delemaya spinulosa from permineralized peat of the Fremouw Formation, early Middle Triassic of Antarctica. The association of the organs in the same deposit, assignment of each taxon to Cycadales, and histological features shared among the taxa suggest they were all produced by the same plant. The Antarcticycas plant is reconstructed as a small plant, possibly with a subterranean stem; it was probably similar in habit to small-stemmed species of extant Zamia. Antarcticycas stems are inferred to exhibit apical rather than axillary branching based on reinterpretation of type material that shows a branching axis accompanied by anatomy indicative of the presence of cone domes when observed in extant cycads. The presence of a bulbil on one specimen indicates that branching also took place through adventitious budding. The Antarcticycas plant is similar in its anatomy to extant cycads, although contractile tissue and coralloid roots have yet to be identified and may not have been present in the fossil plant. The plant inhabited a warm temperate polar habitat with protracted periods of winter darkness for which there is no modern equivalent. Evidence for deciduousness in this taxon, previously suggested as a possible adaptation to its warm, light-limited environment, is equivocal. The possibilities that fire played a role in the Fremouw peat ecosystem and that the Antarcticycas plant may have been insect pollinated are explored.     

Mammalian tooth marks on the bones of dinosaurs and other Late Cretaceous vertebrates

Abstract: We describe bones from the Late Cretaceous of Alberta – including bones of large dinosaurs, a femur from the aquatic reptile Champsosaurus, and a dentary from the marsupial Eodelphis– that bear tooth marks made by animals with opposing pairs of teeth. Of the animals known from the Late Cretaceous of North America, only mammals are capable of making such tooth marks. In particular, multituberculates, which have paired upper and lower incisors, are the most likely candidates for the makers of these traces. The traces described here represent the oldest known mammalian tooth marks. Although it is possible that some of these tooth marks represent feeding traces, the tooth marks often penetrate deep into the dense cortices of the bone. This raises the possibility that, much as extant mammals gnaw bone and antler, some Cretaceous mammals may have consumed the bones of dinosaurs and other vertebrates as a source of minerals. However, none of the tooth marks described here resemble the extensive gnaw traces produced by Cenozoic multituberculates or rodents. This suggests that specialized gnawing forms may have been rare or absent in the Late Cretaceous of North America.