DIVERSIFICATION TRENDS INFERRED FROM THE FOSSIL RECORD

Macroevolution focuses on patterns and processes occurring above the level of species and over geological timescales (Raia, 2016). Investigating diversification processes, both morphological and taxonomical, gives a chance to answer important questions in evolutionary biology. Why do some clades have more species than others? Why do some groups undergo striking adaptive radiations, but others persist for millions of years as living fossils? Why do some groups have much more ecological or morphological diversity than others? Does anything limit the number of species on earth and what? These complex questions share a common underlying feature: all, to some degree, concern rates of macroevolutionary change that occur across geological timescales (Rabosky & Slater, 2014). The aim of my project was to produce a coherent array of new methods to investigate phenotypic and taxonomic diversification by using phylogenies including extinct species. I started by developing RRphylo, a new phylogenetic comparative method based on phylogenetic ridge regression, which works with a phylogenetic tree and phenotypic data (univariate or multivariate either) to estimate branch-wise rates of phenotypic evolution and ancestral characters simultaneously. The main innovations, which translate in advantages of RRphylo over existing methods, lies in the absence of any a priori hypothesis about the mode of phenotypic evolution and in its ability to deal with fossil phylogenies. Both these factors make RRphylo very suitable to study phenotypic evolution in its different facets. I further implemented RRphylo to locate clade- or state-related shifts in absolute rates of phenotypic evolution, to integrate the effect of additional (to the phylogeny) predictors on rates estimation, to identify temporal trends in phenotypic mean and evolutionary rates occurring on the entire tree or pertaining individual clades, to identify instances of morphological convergence, to include ancestral character information derived from the fossil record, and to work with discrete variables. All these tools are collected into the RRphylo R package, online from April 2018, and counting > 14000 downloads on CRAN to date. I have been handling the maintenance and updates of the RRphylo package for both the release (https://cran.r-project.org/web/packages/RRphylo/index.html) and development (https://github.com/pasraia/RRphylo) versions, and creating/updating explanatory vignettes to facilitate its usage

New criteria for selecting elderly patients for breast cancer adjuvant treatment studies.

Learning Objectives After completing this course, the reader will be able to: List the factors that should be considered when choosing the appropriate adjuvant treatment for an elderly women with operable breast cancer.Discuss the possible explanations that account for the underrepresentation of elderly patients in breast cancer clinical trials.Describe the clinical trials that are being specifically conducted in elderly patients with early breast cancer to evaluate different forms of adjuvant treatments. CME Access and take the CME test online and receive 1 AMA PRA Category 1 Credit™ at CME.TheOncologist.co

THE ARGOMARINE PROJECT: A LOW COST PLATFORM TO INTEGRATE DATA AND THE EXPLORATORY USE OF NEW TOOLS IN MONITORING OIL SPILL

One of the key aim of ARGOMARINE focuses on the development of a platform to integrate different maritime data (such as metoceanographic data, transport data, pollution data, etc). Major national organizations such as Navies and Coast Guards are aiming to integrate different types of information to define a maritime picture on a wide scale. This entails developing complex, expensive and classified "hubs" to collect, store, analyze and disseminate the maritime data. ARGOMARINE plans to develop a Marine Information System (MIS), a connected group of ICT subsystems performing data storage, mining and analysis, decision-support, as well as a web-GIS portal for the access and usage of the products and services released to System Managers and end-users. MIS will integrate remote sensing data, field experiment results, forecast models with tools for data storage and retrieval, data manipulation, analysis and presentation; all these features will be accessible through a common interface. Operationally, the following sub-systems have been confirmed for the MIS platform: SAR (Synthetic Aperture Radar) image processing, hyperspectral-thermal image analysis, mathematical simulation for forecast models, dynamic risk maps management, Autonomous Underwater Vehicle (AUV) management and data analysis, marine traffic monitoring through Automatic Identification System (AIS), Environmental Decision Support (EDS), and data mining/warehousing through operational and historical databases. Data integration of all data from these different systems is an innovative approach to maritime surveillance.JRC.G.4-Maritime affair

Arothron: An R package for geometric morphometric methods and virtual anthropology applications

Objectives The statistical analysis of fossil remains is essential to understand the evolution of the genus Homo. Unfortunately, the human fossil record is straight away scarce and plagued with severe loss of information caused by taphonomic processes. The recently developed field of Virtual Anthropology helps to ameliorate this situation by using digital techniques to restore damaged and incomplete fossils. Materials and methods We present the package Arothron, an R software suite meant to process and analyze digital models of skeletal elements. Arothron includes tools to digitally extract virtual cavities such as cranial endocasts, to statistically align disarticulated or broken bony elements, and to visualize local variations between surface meshes and landmark configurations. Results We describe the main functionalities of Arothron and illustrate their usage through reproducible case studies. We describe a tool for segmentation of skeletal cavities by showing its application on a malleus bone, a Neanderthal tooth, and a modern human cranium, reproducing their shape and calculating their volume. We illustrate how to digitally align a disarticulated model of a modern human cranium, and how to combine piecemeal shape information on individual specimens into one. In addition, we present useful visualization tools by comparing the morphological differences between the right hemisphere of the Neanderthal and the modern human brain. Conclusions The Arothron R package is designed to study digital models of fossil specimens. By using Arothron, scientists can handle digital models with ease, investigate the inner morphology of 3D skeletal models, gain a full representation of the original shapes of damaged specimens, and compare shapes across specimens

Current Options for Visualization of Local Deformation in Modern Shape Analysis Applied to Paleobiological Case Studies

In modern shape analysis, deformation is quantified in different ways depending on the algorithms used and on the scale at which it is evaluated. While global affine and non-affine deformation components can be decoupled and computed using a variety of methods, the very local deformation can be considered, infinitesimally, as an affine deformation. The deformation gradient tensor F can be computed locally using a direct calculation by exploiting triangulation or tetrahedralization structures or by locally evaluating the first derivative of an appropriate interpolation function mapping the global deformation from the undeformed to the deformed state. A suitable function is represented by the thin plate spline (TPS) that separates affine from non-affine deformation components. F, also known as Jacobian matrix, encodes both the locally affine deformation and local rotation. This implies that it should be used for visualizing primary strain directions (PSDs) and deformation ellipses and ellipsoids on the target configuration. Using C = FTF allows, instead, one to compute PSD and to visualize them on the source configuration. Moreover, C allows the computation of the strain energy that can be evaluated and mapped locally at any point of a body using an interpolation function. In addition, it is possible, by exploiting the second-order Jacobian, to calculate the amount of the non-affine deformation in the neighborhood of the evaluation point by computing the body bending energy density encoded in the deformation. In this contribution, we present (i) the main computational methods for evaluating local deformation metrics, (ii) a number of different strategies to visualize them on both undeformed and deformed configurations, and (iii) the potential pitfalls in ignoring the actual three-dimensional nature of F when it is evaluated along a surface identified by a triangulation in three dimensions

Testing for changes in rate of evolution and position of the climatic niche of clades

1. There is solid recognition that phylogenetic effects must be acknowledged to appreciate climatic niche variability among species clades properly. Yet, most currently available methods either work at the intra- specific level (hence they ignore phylogeny) or rely on the Brownian motion model of evolution to estimate phylogenetic effects on climatic niche variation. The Brownian mo-tion model may be inappropriate to describe niche evolution in several cases, and even a significant phylogenetic signal in climatic variables does not in-dicate that the effect of shared ancestry was relevant to niche evolution.2. We introduce a new phylogenetic comparative method which describes sig-nificant changes in the width and position of the climatic niche at the inter-specific (clade) level, while making no a priori assumption about how niche evolution took place.3. We devised the R function phylo.niche.shift to estimate whether the climatic niches of individual clades in the tree are either wider or narrower than expected, and whether the niche occupies unexpected climates. We tested phylo.niche.shift on realistic virtual species’ distribution patterns applied to a phylogeny of 365 extant primate species.4. We demonstrate via simulations that the new method is fast and accurate under widely different climatic niche evolution scenarios. phylo.niche.shift showed that the capuchin monkeys and langurs occupy much wider, and prosimian much narrower, climatic niche space than expected by their phylogenetic positions.5. phylo.niche.shift may help to improve research on niche evolution by allow-ing researchers to test specific hypotheses on the factors affecting clades’ realised niche width and position, and the potential effects of climate change on species’ distribution

Decoupling Functional and Morphological Convergence, the Study Case of Fossorial Mammalia

Morphological similarity between biological structures in phylogenetically distant species is usually regarded as evidence of convergent evolution. Yet, phenotypic similarity is not always a sign of natural selection acting on a particular trait, therefore adaptation to similar conditions may fail to generate convergent lineages. Herein we tested whether convergent evolution occurred in the humerus of fossorial mammals, one of the most derived biological structures among mammals. Clades adapting to digging kinematics possess unusual, by mammalian standards, humeral shapes. The application of a new, computationally fast morphological test revealed a single significant instance of convergence pertaining to the Japanese fossorial moles (Mogera) and the North-American fossorial moles (Scalopini). Yet, the pattern only manifests when trade-off performance data (derived from finite element analysis) are added to shape data. This result indicates that fossorial mammals have found multiple solutions to the same adaptive challenge, independently moving around multiple adaptive peaks. This study suggests the importance of accounting for functional trade-off measures when studying morpho-functional convergence. We revealed that fossorial mammals, a classic example of convergent evolution, evolved multiple strategies to exploit the subterranean ecotope, characterized by different functional trade-offs rather than converging toward a single adaptive optimum

A new, fast method to search for morphological convergence with shape data

Morphological convergence is an intensely studied macroevolutionary phenomenon. It refers to the morphological resemblance between phylogenetically distant taxa. Currently available methods to explore evolutionary convergence either: rely on the analysis of the phenotypic resemblance between sister clades as compared to their ancestor, fit different evolutionary regimes to different parts of the tree to see whether the same regime explains phenotypic evolution in phylogenetically distant clades, or assess deviations from the congruence between phylogenetic and phenotypic distances. We introduce a new test for morphological convergence working directly with non-ultrametric (i.e. paleontological) as well as ultrametric phylogenies and multivariate data. The method (developed as the function search.conv within the R package RRphylo) tests whether unrelated clades are morphologically more similar to each other than expected by their phylogenetic distance. It additionally permits using known phenotypes as the most recent common ancestors of clades, taking full advantage of fossil information. We assessed the power of search.conv and the incidence of false positives by means of simulations, and then applied it to three well-known and long-discussed cases of (purported) morphological convergence: the evolution of grazing adaptation in the mandible of ungulates with high-crowned molars, the evolution of mandibular shape in sabertooth cats, and the evolution of discrete ecomorphs among anoles of Caribbean islands. The search.conv method was found to be powerful, correctly identifying simulated cases of convergent morphological evolution in 95% of the cases. Type I error rate is as low as 4-6%. We found search.conv is some three orders of magnitude faster than a competing method for testing convergence

Trapped in the morphospace: The relationship between morphological integration and functional performance

The evolution of complex morphological structures can be characterized by the interplay between different anatomical regions evolving under functional integration in response to shared selective pressures. Using the highly derived humeral morphology of talpid moles as a model, here we test whether functional performance is linked to increased levels of evolutionary integration between humerus subunits and, if so, what the strength is of the relationship. Combining two-dimensional geometric morphometrics, phylogenetic comparative methods, and functional landscape modeling, we demonstrate that the high biomechanical performance of subterranean moles' humeri is coupled with elevated levels of integration, whereas taxa with low-performance values show intermediate or low integration. Theoretical morphs occurring in high-performance areas of the functional landscape are not occupied by any species, and show a marked drop in covariation levels, suggesting the existence of a strong relationship between integration and performance in the evolution of talpid moles' humeri. We argue that the relative temporal invariance of the subterranean environment may have contributed to stabilize humeral morphology, trapping subterranean moles in a narrow region of the landscape and impeding any attempt to reposition on a new ascending slope

Impact of obesity on diagnosis and treatment of breast cancer

In this population-based study, we evaluated the impact of obesity on presentation, diagnosis and treatment of breast cancer. Among all women diagnosed with invasive breast cancer in the canton Geneva (Switzerland) between 2003 and 2005, we identified those with information on body mass index (BMI) and categorized them into normal/underweight (BMI <25kg/m2), overweight (BMI ≥-<30kg/m2) and obese (BMI ≥30kg/m2) women. Using multivariate logistic regression, we compared tumour, diagnosis and treatment characteristics between groups. Obese women presented significantly more often with stage III-IV disease (adjusted odds ratio [ORadj]: 1.8, 95% CI: 1.0-3.3). Tumours ≥1cm and pN2-N3 lymph nodes were significantly more often impalpable in obese than in normal/underweight patients (ORadj 2.4, [1.1-5.3] and ORadj 5.1, [1.0-25.4], respectively). Obese women were less likely to have undergone ultrasound (ORadj 0.5, [0.3-0.9]) and MRI (ORadj 0.3, [0.1-0.6]) and were at increased risk of prolonged hospital stay (ORadj 4.7, [2.0-10.9]). This study finds important diagnostic and therapeutic differences between obese and lean women, which may impair survival of obese women with breast cancer. Specific strategies are needed to optimize the care of obese women with or at risk of breast cance