38 Works

Data from: Unexpected but welcome. Artificially selected traits may increase fitness in wild boar

Domenico Fulgione, Daniela Rippa, Maria Buglione, Martina Trapanese, Simona Petrelli & Valeria Maselli
Artificial selection affects phenotypes differently by natural selection. Domestic traits, which pass into the wild, are usually negatively selected. Yet, exceptionally, this axiom may fail to apply if genes, from the domestic animals, increase fertility in the wild. We studied a rare case of a wild boar population under the framework of Wright's interdemic selection model, which could explain gene flow between wild boar and pig, both considered as demes. We analysed the MC1R gene...

Data from: Human face-off: a new method for mapping evolutionary rates on three-dimensional digital models

Silvia Castiglione, Marina Melchionna, Antonio Profico, Gabriele Sansalone, Maria Modafferi, Alessandro Mondanaro, Stephen Wroe, Paolo Piras & Pasquale Raia
Modern phylogenetic comparative methods allow estimating evolutionary rates of phenotypic change, how these rates differ across clades, and assessing whether the rate remained constant over time. Unfortunately, currently available phylogenetic comparative tools express the rate in terms of a scalar dimension, hence they do not allow us to determine rate variations among different parts of a single, complex phenotype, or charting of realized rate variation directly onto the phenotype. Herein, we present a new method...

Variation in the strength of allometry drives rates of evolution in primate brain shape - Supplementary Material

Gabriele Sansalone, Kari Allen, Justin Ledogar, Sarah Heinz Ledogar, D. Rex Mitchell, Antonio Profico, Silvia Castiglione, Marina Melchionna, Carmela Serio, Alessandro Mondanaro, Pasquale Raia & Stephen Wroe
Large brains are a defining feature of primates, as is a clear allometric trend between body mass and brain size. However, important questions on the macroevolution of brain shape in primates remain unanswered. Here we address two: (i), does the relationship between the brain size and its shape follow allometric trends and (ii), is this relationship consistent over evolutionary time? We employ three-dimensional geometric morphometrics and phylogenetic comparative methods to answer these questions, based on...

Broad-scale patterns of geographic avoidance between species emerge in the absence of fine-scale mechanisms of coexistence

Roberto Novella-Fernandez, Javier Juste, Carlos Ibanez, Hugo Rebelo, Danilo Russo, Antton Alberdi, Andreas Kiefer, Laura Graham, Patrick Doncaster, Hynek Paul & Orly Razgour
Aim: The need to forecast range shifts under future climate change has motivated an increasing interest in better understanding the role of biotic interactions in driving diversity patterns. The contribution of biotic interactions to shaping broad-scale species distributions is however, still debated, partly due to the difficulty of detecting their effects. We aim to test whether spatial exclusion between potentially competing species can be detected at the species range scale, and whether this pattern relates...

Data from: Genic rather than genome-wide differences between sexually deceptive Ophrys orchids with different pollinators

Khalid E. M. Sedeek, Giovanni Scopece, Yannick M. Staedler, Jürg Schönenberger, Salvatore Cozzolino, Florian P. Schiestl & Philipp M. Schlüter
High pollinator specificity and the potential for simple genetic changes to affect pollinator attraction make sexually deceptive orchids an ideal system for the study of ecological speciation, in which change of flower odour is likely important. This study surveys reproductive barriers and differences in floral phenotypes in a group of four closely related, co-flowering sympatric Ophrys species, and uses a genotyping by sequencing (GBS) approach to obtain information on the proportion of the genome that...

Data from: Is floral divergence sufficient to maintain species boundaries upon secondary contact in Mediterranean food-deceptive orchids?

Giovanni Scopece, Anis Zitari, Ahmed N. Helal, Alex Widmer & Salvatore Cozzolino
Analysing the processes that determine whether species boundaries are maintained upon secondary contact may shed light on the early phase of speciation. In Anacamptis morio and A. longicornu, two Mediterranean orchid sister-species, we used molecular and morphological analyses, together with estimates of pollination success and experimental crosses, to assess whether floral isolation can shelter the species' genomes from genetic admixture upon secondary contact. We found substantial genetic and morphological homogenization in sympatric populations in combination...

Data from: Pollinator shifts between Ophrys sphegodes populations: might adaptation to different pollinators drive population divergence?

Hendrik Breitkopf, Philipp M. Schlüter, Shuqing Xu, Florian P. Schiestl, Salvatore Cozzolino & Giovanni Scopece
Local adaptation to different pollinators is considered one of the possible initial stages of ecological speciation as reproductive isolation is a by-product of the divergence in pollination systems. However, pollinator-mediated divergent selection will not necessarily result in complete reproductive isolation, because incipient speciation is often overcome by gene flow. We investigated the potential of pollinator shift in the sexually deceptive orchids Ophrys sphegodes and Ophrys exaltata and compared the levels of floral isolation vs. genetic...

Data from: Like a pig out of water: seaborne spread of domestic pigs in Southern Italy and Sardinia during the Bronze and Iron Ages

Clelia Lega, Domenico Fulgione, Angelo Genovese, Lorenzo Rook, Marco Masseti, Meirav Meiri, Antonella Cinzia Marra, Francesco Carotenuto & Pasquale Raia
Southern Italy has a long history of human occupation and passage of different cultures since the Early Holocene. Repeated, ancient introductions of pigs in several geographic areas in Europe make it difficult to understand pig translocation and domestication in Italy. The archeozoological record may provide fundamental information on this, hence shedding light on peopling and on trading among different ancient cultures in the Mediterranean. Yet, because of the scanty nature of the fossil record, ancient...

Data from: Cushion plant morphology controls biogenic capability and facilitation effects of Silene acaulis along an elevation gradient

Giuliano Bonanomi, Adriano Stinca, Giovanni Battista Chirico, Giampiero Ciaschetti, Antonio Saracino & Guido Incerti
The stress-gradient hypothesis (SGH) predicts that the balance of plant–plant interactions shifts along abiotic environmental gradients, with facilitation becoming more frequent under stressful conditions. However, recent studies have challenged this perspective, reporting that positive interactions are, in some cases, more common at the intermediate level of environmental severity gradients. Here, we test whether and how neighbour effects by Silene acaulis cushions vary along a 700 m wide altitudinal transect, in relation to cushion morphological traits...

Data from: The Solanum commersonii genome sequence provides insights into adaptation to stress conditions and genome evolution of wild potato relatives

Riccardo Aversano, Felice Contaldi, Maria Raffaella Ercolano, Valentina Grosso, Massimo Iorizzo, Filippo Tatino, Luciano Xumerle, Alessandra Dal Molin, Carla Avanzato, Alberto Ferrarini, Massimo Delledonne, Walter Sanseverino, Riccardo Aiese Cigliano, Salvador Capella-Gutierrez, Toni Gabaldón, Luigi Frusciante, James M. Bradeen & Domenico Carputo
Here, we report the draft genome sequence of Solanum commersonii, which consists of ∼830 megabases with an N50 of 44,303 bp anchored to 12 chromosomes, using the potato (Solanum tuberosum) genome sequence as a reference. Compared with potato, S. commersonii shows a striking reduction in heterozygosity (1.5% versus 53 to 59%), and differences in genome sizes were mainly due to variations in intergenic sequence length. Gene annotation by ab initio prediction supported by RNA-seq data...

Data from: Climate change increases ecogeographic isolation between closely related plants

Karl J. Duffy & Hans Jacquemyn
1. Ecogeographic isolation is a fundamental prezygotic barrier to reproduction and a step toward diversification in flowering plants. However, whether ecogeographic isolation acts as a reproductive barrier between species and thus as a mechanism for species divergence is unclear and is expected to change as species distributions shift under climate change. 2. Using a Maxent framework, we quantified the extent of ecogeographic isolation of nine closely related species of the European plant genus Pulmonaria, which...

Deciphering voids in Dasycladales, the case of Dragastanella transylvanica, a new Lower Cretaceous triploporellacean genus from Romania

Filippo Barattolo, Ioan Bucur & Alexandru Marian
Dragastanella transylvanica n.gen. n.sp. is described. Its calcified skeleton contains numerous voids, partly related to the moulds of soft parts of the alga, but also to lack of calcification. Interpretation of these voids, especially their attribution to original structures (e.g., primary lateral vs. reproductive organ), has important implications for the taxonomic position of the alga, even at family level. Examination of key sections that include the boundary between sterile and fertile parts of the alga...

Data from: Global patterns of functional trait variation along aridity gradients in bats

Irene Conenna, Luca Santini, Ricardo Rocha, Ara Monadjem, Mar Cabeza & Danilo Russo
Aim: Our understanding of the biological strategies employed by species to cope with challenges posed by aridity is still limited. Despite being sensitive to water loss, bats successfully inhabit a wide range of arid lands. We here investigated how functional traits of bat assemblages vary along the global aridity gradient to identify traits that favour their persistence in arid environments. Methods: We mapped the assemblage-level averages of four key bat traits describing wing morphology, echolocation...

A droplet reactor on a super-hydrophobic surface allows control and characterization of amyloid fibril growth

Peng Zhang, Enzo Di Fabrizio, Manola Moretti, Marco Allione, Yuansi Tian, Javier Ordonez-Loza, Davide Altamura, Cinzia Giannini, Bruno Torre, Gobind Das, Erqiang Li, Sigurdur T. Thoroddsen, Mani Sarathy, Ida Autiero, Andrea Giugni, Francesco Gentile, Natalia Malara & Monica Marini
Methods to produce protein amyloid fibrils, in vitro, and in situ structure characterization, are of primary importance in biology, medicine, and pharmacology. We first demonstrated the droplet on a super-hydrophobic substrate as the reactor to produce protein amyloid fibrils with real-time monitoring of the growth process by using combined light-sheet microscopy and thermal imaging. The molecular structures were characterized by Raman spectroscopy, X-ray diffraction and X-ray scattering. We demonstrated that the convective flow induced by...

NEXMIF encephalopathy: DeNovogear output of WES data of the family

Maria Cristina Cioclu, Antonietta Coppola, Manuela Tondelli, Anna Elisabetta Vaudano, Giada Giovannini, S. Krithika, Michele Iacomino, Federico Zara, Sanjay Sisodiya & Stefano Meletti
The developmental and epileptic encephalopathies (DEE) are the most severe group of epilepsies. Recently, NEXMIF mutations have been shown to cause a DEE in females, characterized by myoclonic–atonic epilepsy and recurrent nonconvulsive status. Here we used advanced neuroimaging techniques in a patient with a novel NEXMIF de novo mutation presenting with recurrent absence status with eyelid myoclonia, to reveal brain structural and functional changes that can bring the clinical phenotype to alteration within specific brain...

A comprehensive suite of earthquake catalogues for the 2016-2017 Central Italy seismic sequence

Lauro Chiaraluce, Maddalena Michele, Felix Waldhauser, Yen Joe Tan, Marcus Herrmann, Daniele Spallarossa, Gregory Beroza, Claudio Chiarabba, Pasquale De Gori, Raffaele Di Stefano, William Ellsworth, Ian Main, Simone Mancini, Lucia Margheriti, Warner Marzocchi, Men-Andrin Meyer, Davide Scafidi, David Schaff & Margarita Segou
A set of six large catalogues documenting the seismic sequence that occurred in central Italy between 2016 and 2017, characterized by a cascade of four MW5.5–6.5 events. The earthquake catalogues possess different levels of resolution and completeness that result from progressive enhancements in both detection sensitivity and hypocentral location determination. These quality differences reflect the subsequent application of advanced methods.

Data from: Temperature and storage time strongly affect the germination success of perennial Euphorbia species in Mediterranean regions

Antonia Cristaudo, Stefania Catara, Antonio Mingo, Alessia Restuccia & Andrea Onofri
This study aims to explore the effect of environmental factors (temperature,light, storage time) on germination response and dormancy patterns in eight Mediterranean native wildplants, belonging to the Euphorbia L. genus. In detail, we considered E. amygdaloides subsp. arbuscula, E. bivonae subsp. bivonae, E. ceratocarpa, E. characias, E. dendroides, E. melapetala, E. myrsinites, E. rigida. We collected seeds from natural plant populations and performed germination assays in climatic chambers at seven constant temperatures (from 5 to...

DNA barcoding of native Caucasus herbal plants: potentials and limitations in complex groups and implications for phylogeographic patterns

Donata Cafasso
DNA barcoding rapidly became a useful complementary tool in floristic investigations particularly for identifying specimens that lack diagnostic characters. Here we assess the capability of three DNA barcode markers (chloroplast rpoB, accD and nuclear ITS) in correctly species assignment in a floristic survey on Caucasus. We focused on two herbal groups with potential for ornamental applications, namely orchids and asterids. On these two plant groups we tested whether our selection of barcode markers allows identification...

Data from: Testing the occurrence of convergence in the cranio-mandibular shape evolution of living carnivorans

Davide Tamagnini, Carlo Meloro, Pasquale Raia & Luigi Maiorano
Convergence consists in the independent evolution of similar traits in distantly related species. The mammalian cranio-mandibular complex constitutes an ideal biological structure to investigate ecomorphological dynamics and the carnivorans, due to their phenotypic variability and ecological flexibility, offer an interesting case-study to explore the occurrence of convergent evolution. Here, we applied multiple pattern-based metrics to test the occurrence of convergence in the cranio-mandibular shape of extant carnivorans. To this aim, we tested for convergence in...

Data from: Components of reproductive isolation between Orchis mascula and O. pauciflora

Giovanni Scopece, Antonio Croce, Christian Lexer & Salvatore Cozzolino
Studies of the strength and nature of reproductive isolation (RI) between species can greatly contribute to our understanding of speciation. Although the role of RI in speciation is well recognized, there is a dearth of information on the contributions of different barriers between related plant species. Here, we estimated multiple components of RI between two Mediterranean orchid sister species (Orchis mascula and Orchis pauciflora), disentangling the strength and absolute contributions of seven different isolating mechanisms....

Data from: Combined use of molecular markers and high resolution melting (HRM) to assess chromosome dosage in potato hybrids

Clizia Villano, Valeria Miraglia, Massimo Iorizzo, Riccardo Aversano & Domenico Carputo
In plants, the most widely used cytological techniques to assess parental genome contributions are based on in situ hybridization (FISH and GISH), but they are time-consuming and need specific expertise and equipment. Recent advances in genomics and molecular biology have made PCR-based markers a straightforward, affordable technique for chromosome typing. Here, we describe the development of a molecular assay that uses single-copy conserved ortholog set II (COSII)-based single nucleotide polymorphisms (SNPs) and the high-resolution melting...

Data from: Evolution of an insect immune barrier through horizontal gene transfer mediated by a parasitic wasp

Angela Amoresano, Paola Varricchio, Ilaria Di Lelio, Pietro Pucci, Luca Gianfranceschi, Anna Illiano, Silvia Caccia, Federica Astarita, David Horner & Francesco Pennacchio
Genome sequencing data have recently demonstrated that eukaryote evolution has been remarkably influenced by the acquisition of a large number of genes by horizontal gene transfer (HGT) across different kingdoms. However, in depth-studies on the physiological traits conferred by these accidental DNA acquisitions are largely lacking. Here we elucidate the functional role of Sl gasmin, a gene of a symbiotic virus of a parasitic wasp that has been transferred to an ancestor of the moth...

Species‐specific root proliferation of tree seedlings in tropical litter: do nutrients matter?

Tushar C. Sarker, Giulia Maisto, Anna De Marco, Valeria Memoli, Speranza C. Panico, Riccardo Motti, Mohamed Idbella, Guido Incerti, Stefano Mazzoleni & Giuliano Bonanomi
Litter decomposition mobilizes nutrients that sustain ecosystem productivity, but decomposition by-products may also hamper root proliferation by phytotoxicity. The aim of this study was to assess the litter substrate preferences of tropical tree seedlings in relation to litter chemical traits. We characterized 44 litter types (11 species at 4 decomposition ages; 0, 30, 90 and 180 days) for nutrients (N, P, K, Mg, Mn, Na, Fe and Zn) and proximate chemical parameters (cellulose, extractive, lignin...

Data from: Genome-wide association analysis of type 2 diabetes in the EPIC-InterAct study

Lina Cai, Eleanor Wheeler, Nicola D. Kerrison, Jian'an Luan, Panos Deloukas, Paul W. Franks, Pilar Amiano, Eva Ardanaz, Catalina Bonet, Guy Fagherazzi, Leif C. Groop, Rudolf Kaaks, José María Huerta, Giovanna Masala, Peter M. Nilsson, Kim Overvad, Valeria Pala, Salvatore Panico, Miguel Rodriguez-Barranco, Olov Rolandsson, Carlotta Sacerdote, Matthias B. Schulze, Annemieke M.W. Spijkeman, Anne Tjonneland, Rosario Tumino … & Nicholas J. Wareham
Type 2 diabetes (T2D) is a global public health challenge. Whilst the advent of genome-wide association studies has identified >400 genetic variants associated with T2D, our understanding of its biological mechanisms and translational insights is still limited. The EPIC-InterAct project, centred in 8 countries in the European Prospective Investigations into Cancer and Nutrition study, is one of the largest prospective studies of T2D. Established as a nested case-cohort study to investigate the interplay between genetic...

Wide-range viscoelastic compression forces in microfluidics to probe cell-dependent nuclear structural and mechanobiological responses

Maria Isabella Maremonti, Valeria Panzetta, David Dannhauser, Filippo Causa & Paolo Antonio Netti
The cell nucleus plays a critical role in mechanosensing and mechanotransduction processes, by adaptive changes of its envelope composition to external biophysical stimuli such as substrate rigidity and tensile forces. Current measurement approaches lack of precise control in stress application on nuclei, thus significantly impairing a complete mechanobiological study of cells. Here, we present a contactless microfluidic approach capable to exert a wide-range of viscoelastic compression forces (10-103 μN) -as an alternative to adhesion-related techniques-...

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  • University of Naples Federico II
  • Sapienza University of Rome
  • University of Zurich
  • University of New England
  • Liverpool John Moores University
  • Institute of Biotechnology
  • University of Edinburgh
  • University College London
  • University of Exeter
  • University of Porto