A longirostrine Temnodontosaurus (Ichthyosauria) with comments on Early Jurassic ichthyosaur niche partitioning and disparity

Abstract: We describe an almost complete ichthyosaur skeleton from the middle Toarcian (Lower Jurassic) of the Beaujolais foothills near Lyon, France, and assign it to Temnodontosaurus azerguensis sp. nov. This new species exhibits cranial peculiarities such as a thin, elongated and possibly edentulous rostrum, as well as a reduced quadrate. These characters indicate dietary preferences that markedly differ from other species referred to Temnodontosaurus, a genus previously considered as the top predator of the Early Jurassic seas. Despite a conservative postcranial skeleton, we propose that Temnodontosaurus is one of the most ecologically disparate genera of ichthyosaurs, including apex predators and now a soft prey longirostrine hunter. Ammonites collected from the same stratigraphic level as the described specimen indicate that the new species is somewhat younger (bifrons ammonite zone) than the most known Toarcian ichthyosaurs and therefore slightly postdates the interval of severe environmental changes and marine invertebrate extinctions known as the Toarcian Oceanic Anoxic Event. The present study therefore raises the question of whether postcrisis recovery of vertebrate faunas, including the radiation of Temnodontosaurus into a new ecological niche, may have been a consequence of marine ecosystem reorganization across this event.     

Multivariate extensions of McNemar's test

This article considers global tests of differences between paired vectors of binomial probabilities, based on data from two dependent multivariate binary samples. Difference is defined as either an inhomogeneity in the marginal distributions or asymmetry in the joint distribution. For detecting the first type of difference, we propose a multivariate extension of McNemar's test and show that it is a generalized score test under a generalized estimating equations (GEE) approach. Univariate features such as the relationship between the Wald and score tests and the dropout of pairs with the same response carry over to the multivariate case and the test does not depend on the working correlation assumption among the components of the multivariate response. For sparse or imbalanced data, such as occurs when the number of variables is large or the proportions are close to zero, the test is best implemented using a bootstrap, and if this is computationally too complex, a permutation distribution. We apply the test to safety data for a drug, in which two doses are evaluated by comparing multiple responses by the same subjects to each one of them.     

Rare arctic-alpine plants of the European Alps have different immigration histories: the snow bed species Minuartia biflora and Ranunculus pygmaeus

Minuartia biflora and Ranunculus pygmaeus are circumarctic plants with a few isolated occurrences in the European Alps. We analysed amplified fragment length polymorphism (AFLP) and chloroplast DNA sequence data to unravel the history of their immigration into the Alps and to provide data on their circumpolar phylogeography. In spite of the similar ecological requirements of the two species, they exhibit strikingly different immigration histories into the Alps. In M. biflora, the Alpine populations are most probably derived from source populations located between the Alpine and Scandinavian ice sheets, in accordance with the traditional biogeographic hypothesis. In contrast, the Alpine populations of R. pygmaeus cluster with those from the Tatra Mountains and the Taymyr region in northern Siberia, indicating that the distant Taymyr area served as source for the Alpine populations. Both species showed different levels of genetic diversity in formerly glaciated areas. In contrast to the considerable AFLP diversity observed in M. biflora, R. pygmaeus was virtually nonvariable over vast areas, with a single phenotype dominating all over the Alps and another, distantly related one dominating the North Atlantic area from Greenland over Svalbard to Scandinavia. The same pattern was observed in chloroplast DNA sequence data. Thus, postglacial colonization of R. pygmaeus was accompanied by extreme founder events.     

Perturbation at the sea floor during the Paleocene–Eocene Thermal Maximum: Evidence from benthic foraminifera at Contessa Road, Italy

Detailed analyses of the benthic foraminiferal assemblages extracted with the cold acetolyse method together with high resolution geochemical and mineralogical investigations across the Paleocene/Eocene (P/E) boundary of the classical succession at Contessa Road (western Tethys), allowed to recognize and document the Paleocene–Eocene Thermal Maximum (PETM) interval, the position of the Benthic Extinction Event (BEE) and the early recovery of benthic faunas in the aftermath of benthic foraminiferal extinction. The stratigraphical interval spanning the P/E boundary consists of dominantly pelagic limestones and two prominent marly beds. Benthic foraminifera indicate that these sediments were deposited at lower bathyal depth, not deeper than 1000–1500 m. The Carbon Isotope Excursion (CIE) interval is characterized by high barite abundance with a peak at the base of the same stratigraphic interval, indicating a complete, although condensed record of the early CIE. A succession of events and changes in the taxonomic structure of benthic foraminifera has been recognized that may be of use for supra-regional stratigraphic correlation across the P/E boundary interval. The composition of the benthic foraminiferal assemblages, dominated by infaunal taxa, indicates mesotrophic and changing conditions on the sea floor during the last  45 kyr of the Paleocene. The BEE occurs at the base of the CIE within the lower marly bed and it is recorded by the extinction of several deep-water cosmopolitan taxa. Then, the lysocline/CCD rose and severe carbonate dissolution occurred. Preservation deteriorated, the faunal density and simple diversity dropped to minimum values and a peak of Glomospira spp. has been observed. Stress-tolerant and opportunistic groups, represented mainly by bi-and triserial taxa, dominate the low-diversity post-extinction assemblages, indicating a benthic foraminiferal recovery under environmental unstable conditions, probably within a context of sustained food transfer to the bottom. A three-phase pattern of faunal recovery is recognizable. At first the lysocline/CCD started to descend and then recovered. Small-sized “Bulimina”, Oridorsalis umbonatus, and Tappanina selmensis rapidly repopulated the severely stressed environment. Later on, Siphogenerinoides brevispinosa massively returns, dominating the assemblage together with other buliminids, Nuttallides truempyi, and Anomalinoides sp.1. Finally, a marked drop in abundance of S. brevispinosa is followed by a bloom of the opportunistic and recolonizer agglutinated Pseudobolivina that, for the first time, is recorded within the main CIE. A second interval of dissolution, but less severe than the previous one, has been recognized within the upper marly bed (uppermost part of the main CIE interval) and it is interpreted as a renewed, less pronounced shoaling of the lysocline/CCD that interrupted the recovery of benthic faunas. This further rise likely represents a response to persistent instability of ocean geochemistry in this sector of the Tethys before the end of the CIE. In the CIE recovery and post CIE intervals, the composition of the benthic foraminiferal assemblages suggests mesotrophic and unstable conditions at the sea floor. According to the geochemical proxy for redox conditions, the deposition of the PETM sediments at Contessa Road occurred in well-oxygenated waters, leading out a widespread oxygen depletion as major cause of the BEE. Changing oceanic productivity, carbonate corrosivity and global warming appear to have played a much more important role in the major benthic foraminiferal extinction at the P/E boundary.     

Occurrence of photosynthetic microbial mats in a Lower Cretaceous black shale (central Italy): a shallow-water deposit

Cretaceous oceanic anoxic events (OAEs) were periods of high organic carbon burial corresponding to intervals with excellent organic matter (OM) preservation. This work focuses on the Urbino level, i.e., OAE1b, which is thought to be of regional extent. A detailed microscopical study of OM shows a dominance of microbial activity, characterized by a typical arrangement of exopolymeric substances (EPS) related to microbial mats, bacterial bodies, and some photosynthetic microorganisms, as shown by thylakoids. The latter lived where they have been found, i.e., at the sea bottom, which indicates that OM results from the diagenesis of benthic photosynthetic microbial mats, an interpretation supported through the comparison with a recent analogue. The exceptional preservation of such organic structures in OM points to the joint role of the selective and sorptive preservation pathways. These data and interpretation strongly differ from previous observations in OAE1b equivalents. They suggest that the Urbino level might be an atypical OAE of regional/local extent which was formed within the photic zone.     

Partly functional temporal process regression with semiparametric profile estimating functions

Summary .  Marginal mean models of temporal processes in event time data analysis are gaining more attention for their milder assumptions than the traditional intensity models. Recent work on fully functional temporal process regression (TPR) offers great flexibility by allowing all the regression coefficients to be nonparametrically time varying. The existing estimation procedure, however, prevents successive goodness-of-fit test for covariate coefficients in comparing a sequence of nested models. This article proposes a partly functional TPR model in the line of marginal mean models. Some covariate effects are time independent while others are completely unspecified in time. This class of models is very rich, including the fully functional model and the semiparametric model as special cases. To estimate the parameters, we propose semiparametric profile estimating equations, which are solved via an iterative algorithm, starting at a consistent estimate from a fully functional model in the existing work. No smoothing is needed, in contrast to other varying-coefficient methods. The weak convergence of the resultant estimators are developed using the empirical process theory. Successive tests of time-varying effects and backward model selection procedure can then be carried out. The practical usefulness of the methodology is demonstrated through a simulation study and a real example of recurrent exacerbation among cystic fibrosis patients.     

Specialization on Guadua Bamboo Seeds by Three Bird Species in the Atlantic Forest of Argentina

Most bamboos are semelparous. Their synchronous masting events occur on a cycle of 3–120 yr and represent an extremely pulsed resource for granivorous birds. Although many bird species feed occasionally on bamboo seeds, there are constraints to specializing on such a fluctuating resource and few bird species are known to specialize on bamboo seeds. Three of these bird species are endemic to the Atlantic forest of South America: the purple-winged ground-dove Claravis godefrida , buff-fronted seedeater Sporophila frontalis , and Temminck's seedeater Sporophila falcirostris . All three species are irregularly recorded in the province of Misiones, Argentina. We compared the temporal and spatial patterns of records of these birds in Misiones to masting events of the five common bamboos: yatevó Guadua trinii , takuaruzú Guadua chacoensis , takuapí Merostachys claussenii , pitinga Chusquea tenella , and takuarembó Chusquea ramosissima . All bird records coincided with times and places where Guadua bamboos ( G. trinii and G. chacoensis ) were known or estimated to have seeds. None of the bird species occurred during masting events of Merostachys or Chusquea , unless Guadua was also masting. We discuss relevant ecological and morphological features of the birds that might bear on their association with Guadua bamboos and that might be key to their conservation.     

Association Tests for a Censored Quantitative Trait and Candidate Genes in Structured Populations with Multilevel Genetic Relatedness

Summary Several statistical methods for detecting associations between quantitative traits and candidate genes in structured populations have been developed for fully observed phenotypes. However, many experiments are concerned with failure‐time phenotypes, which are usually subject to censoring. In this article, we propose statistical methods for detecting associations between a censored quantitative trait and candidate genes in structured populations with complex multiple levels of genetic relatedness among sampled individuals. The proposed methods correct for continuous population stratification using both population structure variables as covariates and the frailty terms attributable to kinship. The relationship between the time‐at‐onset data and genotypic scores at a candidate marker is modeled via a parametric Weibull frailty accelerated failure time (AFT) model as well as a semiparametric frailty AFT model, where the baseline survival function is flexibly modeled as a mixture of Polya trees centered around a family of Weibull distributions. For both parametric and semiparametric models, the frailties are modeled via an intrinsic Gaussian conditional autoregressive prior distribution with the kinship matrix being the adjacency matrix connecting subjects. Simulation studies and applications to the Arabidopsis thaliana line flowering time data sets demonstrated the advantage of the new proposals over existing approaches.     

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