Molecular Clocks without Rocks: New Solutions for Old Problems.

Molecular data have been used to date species divergences ever since they were described as documents of evolutionary history in the 1960s. Yet, an inadequate fossil record and discordance between gene trees and species trees are persistently problematic. We examine how, by accommodating gene tree discordance and by scaling branch lengths to absolute time using mutation rate and generation time, multispecies coalescent (MSC) methods can potentially overcome these challenges. We find that time estimates can differ - in some cases, substantially - depending on whether MSC methods or traditional phylogenetic methods that apply concatenation are used, and whether the tree is calibrated with pedigree-based mutation rates or with fossils. We discuss the advantages and shortcomings of both approaches and provide practical guidance for data analysis when using these methods

Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case.

Primates have long been a test case for the development of phylogenetic methods for divergence time estimation. Despite a large number of studies, however, the timing of origination of crown Primates relative to the Cretaceous-Paleogene (K-Pg) boundary and the timing of diversification of the main crown groups remain controversial. Here, we analysed a data set of 372 taxa (367 Primates and 5 outgroups, 3.4 million aligned base pairs) that includes nine primate genomes. We systematically explore the effect of different interpretations of fossil calibrations and molecular clock models on primate divergence time estimates. We find that even small differences in the construction of fossil calibrations can have a noticeable impact on estimated divergence times, especially for the oldest nodes in the tree. Notably, choice of molecular rate model (autocorrelated or independently distributed rates) has an especially strong effect on estimated times, with the independent rates model producing considerably more ancient age estimates for the deeper nodes in the phylogeny. We implement thermodynamic integration, combined with Gaussian quadrature, in the program MCMCTree, and use it to calculate Bayes factors for clock models. Bayesian model selection indicates that the autocorrelated rates model fits the primate data substantially better, and we conclude that time estimates under this model should be preferred. We show that for eight core nodes in the phylogeny, uncertainty in time estimates is close to the theoretical limit imposed by fossil uncertainties. Thus, these estimates are unlikely to be improved by collecting additional molecular sequence data. All analyses place the origin of Primates close to the K-Pg boundary, either in the Cretaceous or straddling the boundary into the Palaeogene

Ant Fauna on Cecropia pachystachya Trécul (Urticaceae) Trees in an Atlantic Forest Area, Southeastern Brazil

Cecropia are pioneer successional trees frequently associated with ants. Generally a single dominant colony of Azteca ant inhabits each mature Cecropia tree, but other ant species may be found living or foraging on the same tree. In this study, we assessed the diversity of ant species on Cecropia pachystachya trees in two sites in the Brazilian Atlantic Forest: a dust-free roadside and a dusty roadside. We also investigated the influence of tree architecture on ant species richness. We found a total of 24 ant species distributed in 11 genera and five subfamilies on C. pachystachya trees; 18 in the dust-free roadside and 14 in the dusty roadside. We found up to five ant species on a single tree, but only Azteca alfari was frequently encountered. Ant species richness per tree did not differ significantly between sites and was related to tree architectural traits. On the other hand, ant species composition on trees differed significantly between sites. Our study indicates that heavy dust deposition on Cecropia trees may affect associated ant communities, not by changing ant species richness, but by causing different species to live and forage on trees under different dust exposure

Molecular Evolutionary Characterization of a V1R Subfamily Unique to Strepsirrhine Primates

Vomeronasal receptor genes have frequently been invoked as integral to the establishment and maintenance of species boundaries among mammals due to the elaborate one-to-one correspondence between semiochemical signals and neuronal sensory inputs. Here, we report the most extensive sample of vomeronasal receptor class 1 (V1R) sequences ever generated for a diverse yet phylogenetically coherent group of mammals, the tooth-combed primates (suborder Strepsirrhini). Phylogenetic analysis confirms our intensive sampling from a single V1R subfamily, apparently unique to the strepsirrhine primates. We designate this subfamily as V1Rstrep. The subfamily retains extensive repertoires of gene copies that descend from an ancestral gene duplication that appears to have occurred prior to the diversification of all lemuriform primates excluding the basal genusDaubentonia (the aye-aye). We refer to the descendent clades as V1Rstrep-a and V1Rstrep-b. Comparison of the two clades reveals different amino acid compositions corresponding to the predicted ligand-binding site and thus potentially to altered functional profiles between the two. In agreement with previous studies of the mouse lemur (genus, Microcebus), the majority of V1Rstrep gene copies appear to be intact and under strong positive selection, particularly within transmembrane regions. Finally, despite the surprisingly high number of gene copies identified in this study, it is nonetheless probable that V1R diversity remains underestimated in these nonmodel primates and that complete characterization will be limited until high-coverage assembled genomes are available

Sectoral specialisation in the EU a macroeconomic perspective

This paper analyses trends in sectoral specialisation in the EU and concludes the following: 1) The European production structure appears more homogenous than that of the US. 2) While sectoral specialisation has shown a slight increase in some smaller euro area countries towards the end-1990s, it is too early to detect any potential impact of EMU. 3) Despite some changes in sectoral composition, the business cycles of euro area countries became more synchronised over the 1990s, which may be seen as reassuring from the point of view of the single monetary policy. 4) Sectoral re-allocation accounts for as much as 50% of the increase in labour productivity growth in business sector services in the euro area. 5) The slowdown of European labour productivity growth relative to the US since the mid-1990s is explained by a stronger performance in the US wholesale and retail trade, financial intermediation and high-tech manufacturing sectors.

Geogenetic patterns in mouse lemurs (genus Microcebus) reveal the ghosts of Madagascar's forests past.

Phylogeographic analysis can be described as the study of the geological and climatological processes that have produced contemporary geographic distributions of populations and species. Here, we attempt to understand how the dynamic process of landscape change on Madagascar has shaped the distribution of a targeted clade of mouse lemurs (genus Microcebus) and, conversely, how phylogenetic and population genetic patterns in these small primates can reciprocally advance our understanding of Madagascar's prehuman environment. The degree to which human activity has impacted the natural plant communities of Madagascar is of critical and enduring interest. Today, the eastern rainforests are separated from the dry deciduous forests of the west by a large expanse of presumed anthropogenic grassland savanna, dominated by the Family Poaceae, that blankets most of the Central Highlands. Although there is firm consensus that anthropogenic activities have transformed the original vegetation through agricultural and pastoral practices, the degree to which closed-canopy forest extended from the east to the west remains debated. Phylogenetic and population genetic patterns in a five-species clade of mouse lemurs suggest that longitudinal dispersal across the island was readily achieved throughout the Pleistocene, apparently ending at ∼55 ka. By examining patterns of both inter- and intraspecific genetic diversity in mouse lemur species found in the eastern, western, and Central Highland zones, we conclude that the natural environment of the Central Highlands would have been mosaic, consisting of a matrix of wooded savanna that formed a transitional zone between the extremes of humid eastern and dry western forest types

The effect of open lung ventilation on right ventricular and left ventricular function in lung-lavaged pigs

INTRODUCTION: Ventilation according to the open lung concept (OLC) consists of recruitment maneuvers, followed by low tidal volume and high positive end-expiratory pressure, aiming at minimizing atelectasis. The minimization of atelectasis reduces the right ventricular (RV) afterload, but the increased intrathoracic pressures used by OLC ventilation could increase the RV afterload. We hypothesize that when atelectasis is minimized by OLC ventilation, cardiac function is not affected despite the higher mean airway pressure. METHODS: After repeated lung lavage, each pig (n = 10) was conventionally ventilated and was ventilated according to OLC in a randomized cross-over setting. Conventional mechanical ventilation (CMV) consisted of volume-controlled ventilation with 5 cmH2O positive end-expiratory pressure and a tidal volume of 8-10 ml/kg. No recruitment maneuvers were performed. During OLC ventilation, recruitment maneuvers were applied until PaO2/FiO2 > 60 kPa. The peak inspiratory pressure was set to obtain a tidal volume of 6-8 ml/kg. The cardiac output (CO), th

Wind-pattern circulation as a palaeogeographic indicator: case study of the 1.5-1.6 Ga Mangabeira Formation, São Francisco Craton, Northeast Brazil

The preserved deposits of dune-scale aeolian bedforms provide valuable palaeoenvironmental indicators of atmospheric circulation patterns and the latitudinal position and distribution of land masses. However, no attempts to use palaeowind directions and palaeogeographic reconstructions of ancient land mass distribution have been published to model Precambrian atmospheric circulation. The Mangabeira Formation is a large Mesoproterozoic aeolian erg succession (1.6 to 1.5 Ga) composed of two aeolian units that accumulated in the São Francisco Craton, Brazil. The Lower Unit records multiple drying-upward depositional cycles, each of which represents an episode of erg expansion and contraction driven by climate changes. The Upper Unit is composed dominantly of stacked aeolian dune strata that lack intervening interdune deposits and which record extreme aridity. Palaeowind directions recorded from cross-strata of transverse, crescentic aeolian dunes of the Lower and Upper Units record dune migration under the influence of two dominant winds that blew to the southeast and northwest. Analysis of these palaeowind data in relation to assessment of regional palaeogeographic reconstructions for the period 1.6 to 1.5 Ga reveals a correlation between atmospheric circulation and land mass distribution. At this time the São Francisco Craton was located between the mid-latitudes and the equatorial zone. The wind regime determined from analysis of dip azimuths of cross-strata of the Lower Unit (1.6 to 1.54 Ga) are consistent with a palaeogeographic position between 25° to 35° S. Analysis of cross-strata dip azimuths of the Upper Unit indicate northwest-directed palaeowinds and a dominant monsoonal wind pattern from 1.54 to 1.5 Ga. During this time the large land mass of the São-Francisco-Congo and Siberian cratons drifted northwards through the equatorial zone from palaeolatitude 30° S to 30°N

The diagnosis and management of pre-invasive breast disease: editor's reply

Introduction: The letter from Badve [1] relating to the series on pre-invasive breast disease, published in the September and November issues of Breast Cancer Research [2-10], is timely and very welcome. It rightly points out that one should be careful in changing classification systems based on limited knowledge and that perhaps discarding the term atypical ductal hyperplasia at the present time may be premature. I completely agree with him; however, there are a few issues I feel obliged to clarify

Does the acidity of self-etching primers affect bond strength and surface morphology of enamel?

Purpose: This study examined the ultrastructure and microtensile bond strengths (TBS) of self-etching (with different acidity) and conventional adhesive systems bonded to unground enamel. Materials and Methods: Resin composite (Filtek Z250) buildups were bonded to unground enamel surfaces of third molars after adhesive application with the following materials: Clearfil SE Bond (CSE); Optibond Solo Plus Self-Etch (OP); Tyrian Self Priming Etching (TY), and the controls Scotchbond Multi-Purpose Plus (SBMP) and Single Bond (SB). Six teeth were assigned to each material. After storage in water for 24 h at 37 degrees C, the bonded specimens were sectioned into beams of approximately 0.8 mm(2) and subsequently subjected to mu TBS testing at a crosshead speed of 0.5 mm/min. The average values were subjected to one-way ANOVA (alpha = 0.05). The effect of surface conditioning of each material was observed under scanning electron microscopy (SEM). Results: The highest resin-enamel bond strength was observed for SBMP (22.7 +/- 5.2) and SB (26.7 +/- 5.2 MPa). The lowest mean bond strengths were 10.9 +/- 3.2 and 7.8 +/- 1.5 MPa for TY and OP, respectively. CSE showed an intermediate performance (18.7 +/- 4.6 MPa). An overall increase in porosity was evident along the entire enamel surface treated with the self-etching primers; however, no selective demineralization similar to that with 35% phosphoric acid was observed. Conclusion: The highest bond strength means and the more retentive etching pattern were observed for the two-step etch-and-rinse adhesives. Among the self-etching systems studied, Clearfil SE Bond should be preferred.82758