Integrating genomics with the fossil record to explore the evolutionary history of Echinoidea

Echinoidea constitutes one of five major clades of living echinoderms, marine animals uniquely characterized by a pentaradial symmetry. Approximately 1,000 living and 10,000 extinct species have been described, including many commonly known as sea urchins, heart urchins and sand dollars. Today, echinoids are ubiquitous in benthic marine environments, where they strongly affect the functioning of biodiverse communities such as coral reefs and kelp forests. Given the quality of their fossil record, their remarkable morphological complexity and our thorough understanding of their development, echinoids provide unparalleled opportunities to explore evolutionary questions in deep-time, providing access to the developmental and morphological underpinnings of evolutionary innovation. These questions cannot be addressed without first resolving the phylogenetic relationships among living and extinct lineages. The goal of this dissertation is to advance our understanding of echinoid relationships and evolutionary history, as well as to explore more broadly the integration of phylogenomic, morphological and paleontological data in phylogenetic reconstruction and macroevolutionary inference.In Chapter 1, I report the results of the first phylogenomic analysis of echinoids based on the sequencing of 17 novel echinoid transcriptomes. Phylogenetic analyses of this data resolve the position of several clades—including the sand dollars—in disagreement with traditional morphological hypotheses. I demonstrate the presence of a strong phylogenetic signal for these novel resolutions, and explore scenarios to reconcile these findings with morphological evidence. In Chapter 7, I extend this approach with a more thorough taxon sampling, resulting in a robust topology with a near-complete sampling of major echinoid lineages. This effort reveals that apatopygids, a clade of three species with previously unclear affinities, represent the only living descendants of a once diverse Mesozoic clade. I also perform a thorough time calibration analysis, quantifying the relative effects of choosing among alternative models of molecular evolution, gene samples and clock priors. I introduce the concept of a chronospace and use it to reveal that only the last among the aforementioned choices affects significantly our understanding of echinoid diversification. Molecular clocks unambiguously support late Permian and late Cretaceous origins for crown group echinoids and sand dollars, respectively, implying long ghost ranges for both. Fossils have been shown to improve the accuracy of phylogenetic comparative methods, warranting their inclusion alongside extant terminals when exploring evolutionary processes across deep timescales. However, their impact on topological inference remains controversial. I explore this topic in Chapter 3 with the use of simulations, which show that morphological phylogenies are more accurate when fossil taxa are incorporated. I also show that tip-dated Bayesian inference, which takes stratigraphic information from fossils into account, outperforms uncalibrated methods. This approach is complemented in Chapter 2 with the analysis of empirical datasets, confirming that incorporating fossils reshapes phylogenies in a manner that is entirely distinct from increased sampling of extant taxa, a result largely attributable to the occurrence of distinctive character combinations among fossils. Even though phylogenomic and paleontological data are complementary resources for unraveling the relationships and divergence times of lineages, few studies have attempted to fully integrate them. Chapter 4 revisits the phylogeny of crown group Echinoidea using a total-evidence dating approach combining phylogenomic, morphological and stratigraphic information. To this end, I develop a method (genesortR) for subsampling molecular datasets that selects loci with high phylogenetic signal and low systematic biases. The results demonstrate that combining different data sources increases topological accuracy and helps resolve phylogenetic conflicts. Notably, I present a new hypothesis for the origin and early morphological evolution of the sand dollars and close allies. In Chapter 6, I compare the behavior of genesortR against alternative subsampling strategies across a sample of phylogenomic matrices. I find this method to systematically outperform random loci selection, unlike commonly-used approaches that target specific evolutionary rates or minimize sources of systematic error. I conclude that these methods should not be used indiscriminately, and that multivariate methods of phylogenomic subsampling should be favored. Finally, in Chapter 5, I explore the macroevolutionary dynamics of echinoid body size across 270 million years using data for more than 5,000 specimens in a phylogenetically explicit context. I also develop a method (extendedSurface) for parameterizing adaptive landscapes that overcomes issues with existing approaches and finds better fitting models. While echinoid body size has been largely constrained to evolve within a single adaptive peak, the disparity of the clade was generated by regime shifts driving the repeated evolution of miniaturized and gigantic forms. Most innovations occurred during the latter half of the Mesozoic, and were followed by a drastic slowdown in the aftermath of the Cretaceous-Paleogene mass extinction

Preliminary Design of Bilio-digestive Anastomosis by Magnetic Compression.

International audienceSome experiments have been realized to determine the characteristics of magnets allowing for bilio-digestive anastomosis by magnetic compression using a ferromagnetic gel and a magnet. The attraction distance between the ferromagnetic gel and the magnet was determined experimentally, under several configurations: magnet shape, strength, number and arrangements. Two magnets with a strength of 14 000 Gauss and a diameter of 12,7mm were necessary to attract 0,353mL of ferrofluid contained in a plastic sheath placed at 1cm of the magnet. So the magnet is able to attract the ferrofluid. However, this procedure needs a large powerful magnet which is not compatible for an immediate use in the human body. Nevertheless, this preliminary result opens promising investigation paths

Activity of metazoa governs biofilm structure formation and enhances permeate flux during Gravity-Driven Membrane (GDM) filtration

The impact of different feed waters in terms of eukaryotic populations and organic carbon content on the biofilm structure formation and permeate flux during Gravity-Driven Membrane (GDM) filtration was investigated in this study. GDM filtration was performed at ultra-low pressure (65 mbar) in dead-end mode without control of the biofilm formation. Different feed waters were tested (River water, pre-treated river water, lake water, and tap water) and varied with regard to their organic substrate content and their predator community. River water was manipulated either by chemically inhibiting all eukaryotes or by filtering out macrozoobenthos (metazoan organisms). The structure of the biofilm was characterized at the meso- and micro-scale using Optical Coherence Tomography (OCT) and Confocal Laser Scanning Microscopy (CLSM), respectively. Based on Total Organic Carbon (TOC) measurements, the river waters provided the highest potential for bacterial growth whereas tap water had the lowest. An increasing content in soluble and particulate organic substrate resulted in increasing biofilm accumulation on membrane surface. However, enhanced biofilm accumulation did not result in lower flux values and permeate flux was mainly influenced by the structure of the biofilm. Metazoan organisms (in particular nematodes and oligochaetes) built-up protective habitats, which resulted in the formation of open and spatially heterogeneous biofilms composed of biomass patches. In the absence of predation by metazoan organisms, a flat and compact biofilm developed. It is concluded that the activity of metazoan organisms in natural river water and its impact on biofilm structure balances the detrimental effect of a high biofilm accumulation, thus allowing for a broader application of GDM filtration. Finally, our results suggest that for surface waters with high particulate organic carbon (POC) content, the use of worms is suitable to enhance POC removal before ultrafiltration units

Measurement of the air-to-fuel ratio inside a passive pre-chamber of a fired spark-ignition engine

This paper investigates the local air-to-fuel ratio measurement within the pre-chamber of a spark-ignition engine by determining the absorption of light from hydrocarbons using an infrared sensor. The measurement was performed during fired and motored engine operation points and compared to the more common exhaust lambda measurements. The experiment provided data to compare the mixture preparation in a hot and cold environment of pre-chamber and main combustion chamber. The experiment also gives an indication regarding the possible use of a pre-chamber sensor in a motored engine at higher boost pressures and fuel mass flows, operation points that would overheat the sensor in a fired engine. The work also includes the analysis of the fuel delivery into the pre-chamber of a direct and indirect injection engine. Furthermore, pressure and temperature measurement within the pre-chamber provides information about the critical sensor environment and helps to understand the gas exchange between the two volumes

Development and Validation of the Open Matrices Item Bank

Figural matrices tasks are one of the most prominent item formats used in intelligence tests, and their relevance for the assessment of cognitive abilities is unquestionable. However, despite endeavors of the open science movement to make scientific research accessible on all levels, there is a lack of royalty-free figural matrices tests. The Open Matrices Item Bank (OMIB) closes this gap by providing free and unlimited access (GPLv3 license) to a large set of empirically validated figural matrices items. We developed a set of 220 figural matrices based on well-established construction principles commonly used in matrices tests and administered them to a sample of N = 2572 applicants to medical schools. The results of item response models and reliability analyses demonstrate the excellent psychometric properties of the items. In the discussion, we elucidate how researchers can already use the OMIB to gain access to high-quality matrices tests for their studies. Furthermore, we provide perspectives for features that could additionally improve the utility of the OMIB

Provisional COVID-19 infrastructure induces large, rapid increases in cycling

The bicycle is a low-cost means of transport linked to low risk of transmission of infectious disease. During the COVID-19 crisis, governments have therefore incentivized cycling by provisionally redistributing street space. We evaluate the impact of this new bicycle infrastructure on cycling traffic using a generalized difference in differences design. We scrape daily bicycle counts from 736 bicycle counters in 106 European cities. We combine these with data on announced and completed pop-up bike lane road work projects. Within 4 mo, an average of 11.5 km of provisional pop-up bike lanes have been built per city and the policy has increased cycling between 11 and 48% on average. We calculate that the new infrastructure will generate between $1 and$7 billion in health benefits per year if cycling habits are sticky

Secondary task engagement, risk-taking, and safety-related equipment use in Gerrnan bicycle and e-scooter riders - an observation

lt has been shown that engagement in secondary tasks may contribute to cyclists crash risk [1 ], meditated by cycling errors or risky behaviors. For influences on secondary task: engagement, it is generally found that phone use is negatively correlated with age. In most studies, males are more found engaged in phone tasks than females. lt was also found that users of a bicycle-sharing program more often to wear headphones and engage in more unsafe behavior. The use of safety gear (e.g., wearing a helmet, using reflectors) is often negatively correlated with distracted cycling. Also, cyclists engaged in a secondary task exhibit other risky behaviors more often [2]. The present study's first aim was to get (an updated) estimate of the observable frequency of different secondary tasks, use of additional safety equipment, and rule violations while riding bicycles and e-scooters in Germany. The second aim was to examine possible differences in secondary task: engagement, use of additional safety equipment, and rule violations between different types of users of the cycling infrastructure, i.e., riders of conventional bikes, e-bikes, scooters, and e-scooters. A third aim was to explore whether riders' secondary task engagement is related to active safety precautions (e.g., wearing a helmet), traffic rule violations, and at-fault conflicts and if there are rider profiles regarding safety-related behaviors. As the study is explorative, no hypotheses were formulated. [From: Introduction