The impact of fossil stratigraphic ranges on tip-calibration,and the accuracy and precision of divergence time estimates

The molecular clock provides the only viable means of establishing realistic evolutionary timescales but it remains unclear how best to calibrate divergence time analyses. Calibrations can be applied to the tips and/or to the nodes of a phylogeny. Tip-calibration is an attractive approach since it allows fossil species to be included alongside extant relatives in molecular clock analyses. However, most fossil species are known from multiple stratigraphical horizons and it remains unclear how such age ranges should be interpreted to codify tip-calibrations. We use simulations and empirical data to explore the impact on precision and accuracy of different approaches to informing tip-calibrations. In particular, we focus on the effect of using tip-calibrations defined using the oldest vs youngest stratigraphic occurrences, the full stratigraphical range, as well as confidence intervals on these data points. The results of our simulations show that using different calibration approaches leads to different divergence-time estimates and demonstrate that concentrating tip-calibrations near the root of the dated phylogeny improves both precision and accuracy of estimated divergence times. Finally, our results indicate that the highest levels of accuracy and precision are achieved when fossil tips are calibrated based on the fossil occurrence from which the morphological data were derived. These trends were corroborated by analysis of an empirical dataset for Ursidae. Overall, we conclude that tip-dating analyses should, in particular, employ tip calibrations close to the root of the tree and they should be calibrated based on the age of the fossil used to inform the morphological data used in Total Evidence Dating.     

Chemical preservation of tail feathers from Anchiornis huxleyi,a theropod dinosaur from the Tiaojishan Formation (Upper Jurassic,China)

A panel of geochemical techniques is used here to investigate the taphonomy of fossil feathers preserved in association with the skeleton of the Jurassic theropod Anchiornis huxleyi. Extant feathers were analysed in parallel to test whether the soft tissues morphologically preserved in the fossil also exhibit a high degree of chemical preservation. Scanning electron microscopy (SEM) and energy dispersive spectroscopy (EDS) indicate that clays and iron oxide pseudomorphs occur in the surrounding sediment and also reveal the preservation of melanosome-like microbodies in the fossil. Carbon gradient along a depth profile and co-occurrence of carbon and sulphur are shown in the fossil by elastic backscattering (EBS) and particle-induced x-ray emission (PIXE), which are promising techniques for the elemental analysis of fossil soft tissues. The molecular composition of modern and fossil soft tissues was assessed from micro-attenuated total reflectance fourier transform infrared spectroscopy (micro-ATR FTIR), solid-state ¹³C nuclear magnetic resonance (CP-MAS ¹³C NMR) and pyrolysis gas chromatography mass spectrometry in the presence of TMAH (TMAH-Py-GC-MS). Results indicate that the proteinaceous material that comprises the modern feathers is not present in the fossil feathers. The fossil feathers and the embedding sediment exhibit a highly aliphatic character. However, substantial differences exist between these samples, revealing that the organic matter of the fossil feathers is, at least partially, derived from original constituents of the feathers. Our results suggest that, despite the morphological preservation of Anchiornis feathers, original proteins, that is keratin, were probably not preserved in the 160-myr-old feathers.     

Functional morphology and light-gathering ability of podocopid ostracod eyes and the palaeontological implications

The optical features of lateral ocelli of the eye were examined in 29 Recent species of the major ostracod group Podocopida using a theoretical morphological model. A cuticular lens–tapetum model was used for this purpose. Ray tracing was simulated on each model in order to assess the light-gathering abilities of the various forms of eyes. The results of computer simulations and morphospace analyses indicated that the light-gathering ability of the eye is dominantly affected by the thickness and curvature of the outer surface of the lens. On the basis of a combination of form and light-gathering ability, four eye types (LG1, LG2, MG, and HG) were recognized. The results of the phototactic experiment and the light intensity from each microhabitat were concordant with estimated scores on the light-gathering abilities using the theoretical models. Phylogenetic analyses and the fossil record indicate that the MG type is the most plesiomorphic, and that the other types derive from this. The present study also suggests that the optical structure that determines the light-gathering ability is closely related to the development of surface ornamentation on the valve.  © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society , 2006, 147 , 97–108.     

The Late Triassic Schilderia Adamanica and Woodworthia Arizonica Trees of the Petrified Forest National Park, Arizona, Usa

Two fossil tree species, both with unusual characteristics, occur in the Upper Triassic of the Petrified Forest National Park, Arizona, USA and adjacent areas. The first, Schilderia adamanica , has a highly idiosyncratic secondary xylem structure which contains normal uniseriate and broad complex multiseriate 'herring-bone' rays. The trunk cross-section of the secondary xylem may be either of a normal pycnoxylic type with a central pith and rays radiating from that or it may consist of appressed 'xylem masses' with rays curving towards one another at their extremities. The second, Woodworthia arizonica , has narrow, horizontal vascular traces traversing the entire radial width of the secondary xylem. By analogy with extant tree species, these traces would have terminated on preventitious buds deeply embedded in the bark which, in the case of these fossil trunks, have failed to be silicified. Such buds have the capacity to develop into epicormic shoots when the crown foliage of the tree is damaged. A further specimen of W. arizonica is recorded for the first time from the Permian of southern Brazil. Reconstruction drawings of both trees are produced.     

A REVISION OF SCOMBRID FISHES (SCOMBROIDEI, PERCIFORMES) FROM THE MIDDLE EOCENE OF MONTE BOLCA, ITALY

Abstract:  A taxonomic revision of mackerel-like fishes (Scombridae, Scombroidei, Perciformes) from the Monte Bolca localities in Italy is presented as part of continuing research into phylogenetic relationships of fossil and Recent scombroids. Three new genera are proposed: † Godsilia , † Pseudauxides and † Thunnoscomberoides . In addition, species generally known as † Thynnus bolcensis , † Thynnus lanceolatus , † Scombrosarda propterygia , † Scomberomorus speciosus and † Scomberomorus tenuis are renamed † Thunnoscomberoides bolcensis comb. nov., † Godsilia lanceolata comb. nov., † Auxides propterygius comb. nov. and † Pseudauxides speciosus comb. nov., respectively. † S. tenuis , a nomen nudum , is a junior synonym of † P. speciosus . Provisional phylogenetic hypotheses of these Monte Bolca scombrids are as follows. † Auxides and † Pseudauxides are most likely primitive sister taxa of the mackerels Scomber and Rastrelliger with † Pseudauxides as the most primitive. † Godsilia may be placed between Scombrinae and Scomberomorinae. † Thunnoscomberoides seems to fit between Scombrinae and Thunnini.     

Palaeobotanical applications of incident-light darkfield microscopy

Incident-light darkfield microscopy permits the direct observation of cellular structure of some plant fossils without the need for maceration. It allows the study of leaf epidermis and sporangial structure where it was previously impossible.     

A new Bennettitalean trunk with unilacunar five-trace nodal structure from the Upper Cretaceous of Hokkaido, Japan

A new species of Bucklandia is described based on a permineralized fossil trunk that was obtained from sediments of Upper Cretaceous age from Hokkaido, Japan. The quality of preservation is exquisite, and anatomical and morphological features are preserved at the cellular level. The specimen is clearly bennettitalean because of the cycadeoidean-type arrangement of vascular bundles in the petiole. However, this specimen is unique among previously described progymnosperms and gymnosperms in possessing a unilacunar five-trace type of nodal structure. The fossil thus contributes to a more complete understanding of the variation of nodal structure in bennettitalean trunks.     

Molecular phylogeography of Dryas integrifolia: glacial refugia and postglacial recolonization

Chloroplast DNA variation in the Arctic plant species Dryas integrifolia (Rosaceae) was analysed in relation to both the present-day geographical distribution of populations and to Pleistocene fossil records of this species. The phylogeographical structure was weak but the analysis of haplotype diversity revealed several groups of haplotypes having present-day geographical ranges that overlap locations postulated from geographical and fossil evidence to have been glacial refugia. Based on this information we infer that two important refugial sources of Arctic recolonization by this species were Beringia and the High Arctic. Two other putative refugia, located southeast of the ice sheet and along coastal regions of the eastern Arctic may have served as sources for recolonization of smaller portions of the Arctic. The genetic substructure in the species is mostly due to variation among populations regardless of the ecogeographical region in which they are found. Spatial autocorrelation at the regional scale was also detected. High levels of diversity both within populations and ecogeographical regions are probably indicative of population establishment from several sources possibly combined with recent gene flow.     

新疆托木尔峰黄土地层中蜗牛化石组合及其意义(腹足纲:肺螺亚纲:柄眼目)

本文记述了采自新疆托木尔峰黄土地层中的蜗牛化石,经鉴定有１２种和１待定种,隶属于６科７属。依据现生蜗牛的生活习性,栖息环境及地理分布相比较,划分蜗牛化石２个组合,即琥珀螺Ｓｕｃｉｎｅａ属组合和华蜗牛Ｃａｔｈａｉｃａ属组合及其所反映的生态环境,讨论了新疆托木尔峰黄土地层形成时期的生物气候环境。     

中国北方化石昆虫群的建立及其演化序列(英文)

作者几十年来已积累了众多的中国北方古生代晚期、中生代和第三纪的昆虫化石标本,对其长期的系统研究结果表明：中国北方昆虫化石演化序列可以划分为三个大的演化阶段,即古生代晚期、中生代和第三纪演化阶段,其中包含14个昆虫群虫和29个昆虫组合。这些昆虫群及其组会既反映了北方昆虫在地质历史上兴衰的发展规律,也为地层划分、对比与地质时代的鉴定提供了依据。