PoMo : an allele frequency-based approach for species tree estimation

This work was supported by a grant from the Austrian Science Fund (FWF, P24551-B25 to C.K.). N.D.M. and D.S. were members of the Vienna Graduate School of Population Genetics which is supported by a grant of the Austrian Science Fund (FWF, W1225-B20). N.D.M. was partially supported by the Institute for Emerging Infections, funded by the Oxford Martin School.Incomplete lineage sorting can cause incongruencies of the overall species-level phylogenetic tree with the phylogenetic trees for individual genes or genomic segments. If these incongruencies are not accounted for, it is possible to incur several biases in species tree estimation. Here, we present a simple maximum likelihood approach that accounts for ancestral variation and incomplete lineage sorting. We use a POlymorphisms-aware phylogenetic MOdel (PoMo) that we have recently shown to efficiently estimate mutation rates and fixation biases from within and between-species variation data. We extend this model to perform efficient estimation of species trees. We test the performance of PoMo in several different scenarios of incomplete lineage sorting using simulations and compare it with existing methods both in accuracy and computational speed. In contrast to other approaches, our model does not use coalescent theory but is allele frequency based. We show that PoMo is well suited for genome-wide species tree estimation and that on such data it is more accurate than previous approaches.Publisher PDFPeer reviewe

Linking great apes genome evolution across time scales using polymorphism-aware phylogenetic models

The genomes of related species contain valuable information on the history of the considered taxa. Great apes in particular exhibit variation of evolutionary patterns along their genomes. However, the great ape data also bring new challenges, such as the presence of incomplete lineage sorting and ancestral shared polymorphisms. Previous methods for genome-scale analysis are restricted to very few individuals or cannot disentangle the contribution of mutation rates and fixation biases. This represents a limitation both for the understanding of these forces as well as for the detection of regions affected by selection. Here, we present a new model designed to estimate mutation rates and fixation biases from genetic variation within and between species. We relax the assumption of instantaneous substitutions, modeling substitutions as mutational events followed by a gradual fixation. Hence, we straightforwardly account for shared ancestral polymorphisms and incomplete lineage sorting. We analyze genome-wide synonymous site alignments of human, chimpanzee, and two orangutan species. From each taxon, we include data from several individuals. We estimate mutation rates and GC-biased gene conversion intensity. We find that both mutation rates and biased gene conversion vary with GC content. We also find lineage-specific differences, with weaker fixation biases in orangutan species, suggesting a reduced historical effective population size. Finally, our results are consistent with directional selection acting on coding sequences in relation to exonic splicing enhancers.Publisher PDFPeer reviewe

Disease and Disorders of Freshwater Unionid Mussels: A Brief Overview of Recent Studies

The use of aquatic invertebrates in biomedical research and as environmental sentinels has dramatically grown in recent decades, with an increased need in understanding of comparative pathology. The Unionids freshwater mussels are a group of worldwide distributed bivalves residing small ditches and ponds, lakes, canals and rivers, often used as animal test in eco-toxicological studies. Once one of the most abundant bivalve molluscs in ancient rivers around the world, now many of them are declining in many countries and consequently are nearly extinct in many areas. The causes of this decline are not fully understood but alteration and degradation of the freshwater habitat seemed to play a central role. To date, link causality to the observed losses during episode of mussel die-offs has been more difficult to establish, and disease and pathogen presence have been scarcely considered. In this article we provide a brief overview of unionids freshwater mussel conservation status, also describing reported diseases and pathogens and illustrating a few relatively well-documented studies

Estimating empirical codon hidden Markov models

Empirical codon models (ECMs) estimated from a large number of globular protein families outperformed mechanistic codon models in their description of the general process of protein evolution. Among other factors, ECMs implicitly model the influence of amino acid properties and multiple nucleotide substitutions (MNS). However, the estimation of ECMs requires large quantities of data, and until recently, only few suitable data sets were available. Here, we take advantage of several new Drosophila species genomes to estimate codon models from genome-wide data. The availability of large numbers of genomes over varying phylogenetic depths in the Drosophila genus allows us to explore various divergence levels. In consequence, we can use these data to determine the appropriate level of divergence for the estimation of ECMs, avoiding overestimation of MNS rates caused by saturation. To account for variation in evolutionary rates along the genome, we develop new empirical codon hidden Markov models (ecHMMs). These models significantly outperform previous ones with respect to maximum likelihood values, suggesting that they provide a better fit to the evolutionary process. Using ECMs and ecHMMs derived from genome-wide data sets, we devise new likelihood ratio tests (LRTs) of positive selection. We found classical LRTs very sensitive to the presence of MNSs, showing high false-positive rates, especially with small phylogenies. The new LRTs are more conservative than the classical ones, having acceptable false-positive rates and reduced power.Publisher PDFPeer reviewe

Invariant methods for an ensemble-based sensitivity analysis of a passive containment cooling system of an AP1000 nuclear power plant

open4noSensitivity Analysis (SA) is performed to gain fundamental insights on a system behavior that is usually reproduced by a model and to identify the most relevant input variables whose variations affect the system model functional response. For the reliability analysis of passive safety systems of Nuclear Power Plants (NPPs), models are Best Estimate (BE) Thermal Hydraulic (TH) codes, that predict the system functional response in normal and accidental conditions and, in this paper, an ensemble of three alternative invariant SA methods is innovatively set up for a SA on the TH code input variables. The ensemble aggregates the input variables raking orders provided by Pearson correlation ratio, Delta method and Beta method. The capability of the ensemble is shown on a BE-TH code of the Passive Containment Cooling System (PCCS) of an Advanced Pressurized water reactor AP1000, during a Loss Of Coolant Accident (LOCA), whose output probability density function (pdf) is approximated by a Finite Mixture Model (FMM), on the basis of a limited number of simulations.Di Maio, Francesco; Nicola, Giancarlo; Borgonovo, Emanuele; Zio, EnricoDI MAIO, Francesco; Nicola, Giancarlo; Borgonovo, Emanuele; Zio, Enric

Force on a large sphere immersed in an expanded water-fluidized bed over a wide range of voidage values

The presence of large objects immersed in a fluidized bed has been long studied in order to verify to what extent can the analogy with a buoyant body in a liquid represent the object-to-suspension interaction (1). One of the most useful information resulting from such study is the effective drag force exerted on the object and how it is related to the suspension properties, particularly with respect to the expansion degree. Implications are found also in the formulation of drag force expressions for homogeneous polydisperse systems. In the present work an experimental series of tests has been conducted on a 10 cm diameter, 2 m height fluidization column using glass beads in two sizes (300 and 600 m) as solid and water as fluidizing medium. A 2.1 cm diameter sphere held by a balance was immersed and kept fixed at the center of the cross-section but free to move axially. Measurements of the hydrodynamic force were carried out at voidage values as high as 0.94, allowing the full range of bed expansion conditions to be covered. Different vertical positions of the large particle was also considered. Results for the drag force indicate that while at low and intermediate expansions the analogy with buoyancy works quite well, at higher voidage values, starting from about = 0.8, the trend departs and additional force contributions are required to explain, though partially, the observed deviations. REFERENCES R. Di Felice, P.U. Foscolo, L.G. Gibilaro. The experimental determination of the interaction force on spheres submerged in liquid fluidized beds. Chem. Eng. Process. 25: 27-34, 1989

La collezione cetologica di Stefano delle Chiaje presso il Gabinetto di Anatomia Generale e Patologica dell'Università di Napoli

Nel corso di una ricerca sulla vita privata e professionale di Stefano delle Chiaje, lo studio di alcuni documenti ha fatto supporre che la Balenottera Minore esposta nel Museo Zoologico di Napoli fosse quella donata dallo scienziato al Gabinetto di Anatomia Patologica dell'Università (GAGP) nel 1848 e segnalata all'epoca dalla apposizione di una targa – Dono di Stefano delle Chiaje – grazie al permesso ottenuto, in riconoscenza del donativo, direttamente dal Re. In questo lavoro viene riportato il risultato di indagini effettuate sulla collezione cetologica del GAGP raccolta da Stefano delle Chiaje durante la sua direzione. Tale collezione risultava essere composta da almeno 13 reperti appartenenti ad almeno quattro specie di Cetacei: otto reperti di Balaenoptera acutorostrata, 6 dei quali (cranio e parte dello scheletro assile, sterno, osso ioide, rudimenti pelvici, bulle timpaniche e fanoni montati su base) riconducibili ad un individuo e due fanoni appartenenti ad un altro esemplare; un feto di Balaenopteridae gen. sp.; due esemplari di Lagenorhynchus acutus (uno scheletro e un feto); uno scheletro di Stenella coeruleoalba; un cranio di Tursiops truncatus. Almeno nove di questi reperti sono ancora oggi nel Museo Zoologico di Napoli: scheletro, sterno, osso ioide, bulle timpaniche e fanoni di un individuo di B. acutorostrata; un fanone di un altro individuo di B. acutorostrata; gli scheletri di l. acutus e di S. coeruleoalba; il cranio di T. truncatus. L'esemplare più interessante è lo scheletro di Balenottera minore che delle Chiaje nel 1846 acquistò personalmente da W. F. K. Christie, Direttore del Museo Zoologico dell'Università di Bergen in Norvegia, per farne dono all'Università di Napoli

Short-range template switching in great ape genomes explored using pair hidden Markov models.

Many complex genomic rearrangements arise through template switch errors, which occur in DNA replication when there is a transient polymerase switch to an alternate template nearby in three-dimensional space. While typically investigated at kilobase-to-megabase scales, the genomic and evolutionary consequences of this mutational process are not well characterised at smaller scales, where they are often interpreted as clusters of independent substitutions, insertions and deletions. Here we present an improved statistical approach using pair hidden Markov models, and use it to detect and describe short-range template switches underlying clusters of mutations in the multi-way alignment of hominid genomes. Using robust statistics derived from evolutionary genomic simulations, we show that template switch events have been widespread in the evolution of the great apes' genomes and provide a parsimonious explanation for the presence of many complex mutation clusters in their phylogenetic context. Larger-scale mechanisms of genome rearrangement are typically associated with structural features around breakpoints, and accordingly we show that atypical patterns of secondary structure formation and DNA bending are present at the initial template switch loci. Our methods improve on previous non-probabilistic approaches for computational detection of template switch mutations, allowing the statistical significance of events to be assessed. By specifying realistic evolutionary parameters based on the genomes and taxa involved, our methods can be readily adapted to other intra- or inter-species comparisons

CMAPLE: Efficient Phylogenetic Inference in the Pandemic Era

We have recently introduced MAPLE (MAximum Parsimonious Likelihood Estimation), a new pandemic-scale phylogenetic inference method exclusively designed for genomic epidemiology. In response to the need for enhancing MAPLE's performance and scalability, here we present two key components: (i) CMAPLE software, a highly optimized C++ reimplementation of MAPLE with many new features and advancements, and (ii) CMAPLE library, a suite of application programming interfaces to facilitate the integration of the CMAPLE algorithm into existing phylogenetic inference packages. Notably, we have successfully integrated CMAPLE into the widely used IQ-TREE 2 software, enabling its rapid adoption in the scientific community. These advancements serve as a vital step toward better preparedness for future pandemics, offering researchers powerful tools for large-scale pathogen genomic analysis