31 Works

Data from: The number of markers and samples needed for detecting bottlenecks under realistic scenarios, with and without recovery: a simulation-based study

Sean M. Hoban, Oscar E. Gaggiotti & Giorgio Bertorelle
Detecting bottlenecks is a common task in molecular ecology. While several bottleneck detection methods exist, evaluations of their power have focused only on severe bottlenecks (e.g. to Ne ~10). As a component of a recent review, Peery et al. () analysed the power of two approaches, the M-ratio and heterozygote excess tests, to detect moderate bottlenecks (e.g. to Ne ~100), which is realistic for many conservation situations. In this Comment, we address three important points...

Mira varietas lectionum

Raffaella Cantore, Chiara Telesca & Fjodor Montemurro
[Italiano]: Con l’espressione mira varietas lectionum si suole indicare, già a partire dalla filologia del Settecento, la straordinaria ricchezza di varianti nella tradizione di un testo antico; se da un lato l’aggettivo mirus tradisce un certo stupore e quasi un fastidio per l’eccessivo proliferare delle lezioni, dall’altro esso acquisisce il senso positivo dello straordinario guadagno di conoscenze che ne ricaviamo per la storia della tradizione e della trasmissione del testo. Lo studio della mira varietas...

Risoluzione della nuvola di punti SfM per rilievi a breve distanza: limiti e considerazioni

Alessandra Rossetti, Arianna Pesci, Fabiana Loddo & Giordano Teza
A reasonable estimate of the resolution of a point cloud obtained by Structure-from-Motion (SfM) photogrammetry is mandatory in order to perform a correct analysis of the detected object. The knowledge of the expected resolution and of its limits allows one to establish, right from the measurement design stage, realistic hypothesis on the achievable degree of detail. This paper shows a case study designed for applications in the architectural field, where the distances involved generally range...

Data from: Demographic history and adaptation account for clock gene diversity in humans

Irene Dall'Ara, Silvia Ghirotto, Selene Ingusci, Giulia Ilaria Bagarolo, Cristiano Bertolucci & Guido Barbujani
Circadian clocks give rise to daily oscillations in behavior and physiological functions that often anticipate upcoming environmental changes generated by the Earth rotation. In model organisms a relationship exists between several genes affecting the circadian rhythms and latitude. We investigated the allele distributions at 116 000 single-nucleotide polymorphisms (SNPs) of 25 human clock and clock-related genes from the 1000Genomes Project, and at a reference data set of putatively neutral polymorphisms. The global genetic structure at...

Data from: Rhythmic motor behavior influences perception of visual time

Alice Tomassini, Tiziana Vercillo, Francesco Torricelli & Maria Concetta Morrone
Temporal processing is fundamental for an accurate synchronization between motor behavior and sensory processing. Here we investigate how motor timing during rhythmic tapping influences perception of visual time. Participants listen to a sequence of four auditory tones played at 1 Hz and continue the sequence (without auditory stimulation) by tapping four times with their finger. During finger tapping, they are presented with an empty visual interval and are asked to judge its length compared to...

Data from: From pristine forests to high-altitude pastures: an ecological approach to prehistoric human impact on vegetation and landscapes in the western Italian Alps

Roberta Pini, Cesare Ravazzi, Luca Raiteri, Antonio Guerreschi, Lorenzo Castellano & Roberto Comolli
1. This paper addresses the origin and development of the oldest prehistoric pasture in the timberline ecotone known so far in the Alps and its relation to anthropogenic pressure and natural climate change. 2. Paleoecological and geochemical techniques were applied on the Crotte Basse mire stratigraphy (2365 m asl, western Italy) to describe changes in vegetation composition, forest biomass, land use and fertilization between ca. 6400 - 1800 yrs cal BP. 3. Subalpine forests dominated...

Data from: Ancient DNA reveals differences in behaviour and sociality between brown bears and extinct cave bears

Gloria Gonzalez-Fortes, Aurora Grandal-D'Anglade, Ben Kolbe, Daniel Fernandes, Ioana N. Meleg, Ana Garcia-Vazquez, Ana C. Pinto-Llona, Silviu Constantin, Trino J. De Torres, Jose E. Ortiz, Christine Frischauf, Gernot Rabeder, Michael Hofreiter, Axel Barlow & Gloria G. Fortes
Ancient DNA studies have revolutionized the study of extinct species and populations, providing insights on phylogeny, phylogeography, admixture and demographic history. However, inferences on behaviour and sociality have been far less frequent. Here, we investigate the complete mitochondrial genomes of extinct Late Pleistocene cave bears and middle Holocene brown bears that each inhabited multiple geographically proximate caves in northern Spain. In cave bears, we find that, although most caves were occupied simultaneously, each cave almost...

Data from: Citizen science reveals unexpected continental-scale evolutionary change in a model organism

Jonathan Silvertown, Laurence Cook, Robert Cameron, Mike Dodd, Kevin McConway, Jenny Worthington, Peter Skelton, Christian Anton, Oliver Bossdorf, Bruno Baur, Menno Schilthuizen, Benoît Fontaine, Helmut Sattmann, Giorgio Bertorelle, Maria Correia, Cristina Oliveira, Beata Pokryszko, Małgorzata Ożgo, Arturs Stalažs, Eoin Gill, Üllar Rammul, Péter Sólymos, Zoltan Féher & Xavier Juan
Organisms provide some of the most sensitive indicators of climate change and evolutionary responses are becoming apparent in species with short generation times. Large datasets on genetic polymorphism that can provide an historical benchmark against which to test for recent evolutionary responses are very rare, but an exception is found in the brown-lipped banded snail (Cepaea nemoralis). This species is sensitive to its thermal environment and exhibits several polymorphisms of shell colour and banding pattern...

Data from: Lateralisation correlates with individual differences in inhibitory control in zebrafish

Tyrone Lucon-Xiccato, Giulia Montalbano, Marco Dadda & Cristiano Bertolucci
The study investigated the relationship between cerebral lateralisation and inhibitory control in zebrafish. Lateralisation was assessed using a mirror test. Fish were observed in an apparatus with mirror walls and eye preference for observing the mirror image was recorded. This preference was used to calculate the relative and the absolute lateralisation index. Inhibitory control was assessed using a foraging task. Fish were exposed to live prey enclosed inside a transparent tube. The number of attacks...

Storie di libri e palazzi. Alla scoperta del patrimonio culturale dell'Università di Ferrara

Cristina Baldi & Paola Iannucci

Data from: Ancient, but not recent, population declines have had a genetic impact on alpine yellow-bellied toad populations, suggesting potential for complete recovery

Luca Cornetti, Andrea Benazzo, Sean M. Hoban, Cristiano Vernesi, Giorgio Bertorelle & Sean Hoban
Reduction in population size and local extinctions have been reported for the yellow-bellied toad, Bombina variegata, but the genetic impact of this is not yet known. In this study, we genotyped 200 individuals, using mtDNA cytochrome b and 11 nuclear microsatellites. We investigated fine-scale population structure and tested for genetic signatures of historical and recent population decline, using several statistical approaches, including likelihood methods and approximate Bayesian computation. Five major genetically divergent groups were found,...

Data from: A Western route of prehistoric human migration from Africa into the Iberian Peninsula

Gloria Gonzalez-Fortes, Francesca Tassi, Emiliano Trucchi, Kirstin Henneberger, Johanna L.A. Paijmans, Daviz Diez-Del-Molino, Hannes Schroeder, Cecilio Barroso, Francisco J. Bermudez, Cecilio Barroso-Medina, Ana M.S. Bettencourt, Hugo A. Sampaio, Aurora Grandal-D'Anglade, Antonio Salas, Arturo De Lombera-Hermida, Ramon Fabregas, Manuel Vaquero, Susana Alonso, Maria Lozano, Xavier Rodríguez-Alvarez, Carlos Fernández-Rodríguez, Andrea Manica, Michael Hofreiter & Guido Barbujani
Being at the Western fringe of Europe, Iberia had a peculiar prehistory and a complex pattern of Neolithization. A few studies, all based on modern populations, reported the presence of DNA of likely African origin in this region, generally concluding it was the result of recent gene flow, probably during the Islamic period. Here we provide evidence of much older gene flow from Africa to Iberia by sequencing whole genomes from four human remains from...

Past, present and future of chamois science

Luca Corlatti, Laura Iacolina, Toni Safner, Marco Apollonio, Elena Buzan, Francesco Ferretti, Sabine Hammer, Juan Herrero, Luca Rossi, Emmanuel Serrano, Mari Cruz Arnal, Francesca Brivio, Roberta Chirichella, Antonella Cotza, Barbara Crestanello, Johan Espunyes, Daniel Fernández De Luco, Saskia Friedrich, Dragan Gačić, Laura Grassi, Stefano Grignolio, Heidi Hauffe, Kresmir Kavčić, Andreas Kinser, Francesca Lioce … & Nikica Šprem
The chamois Rupicapra spp. is the most abundant mountain ungulate of Europe and the Near East, where it occurs as two species, the Northern chamois R. rupicapra and the Southern chamois R. pyrenaica. Here, we provide a state-of-the-art overview of research trends and the most challenging issues in chamois research and conservation, focusing on taxonomy and systematics, genetics, life history, ecology and behavior, physiology and disease, management, and conservation. Research on Rupicapra has a longstanding...

Data from: Using ABC and microsatellite data to detect multiple introductions of invasive species from a single source

Sean Hoban, Silvia Ghirotto, Sibelle Vilaca & Andrea Benazzo
The introduction of invasive species to new locations (that is, biological invasions) can have major impact on biodiversity, agriculture and public health. As such, determining the routes and modality of introductions with genetic data has become a fundamental goal in molecular ecology. To assist with this goal, new statistical methods and frameworks have been developed, such as approximate Bayesian computation (ABC) for inferring invasion history. Here, we present a model of invasion accounting for multiple...

Data from: Partial genomic survival of cave bears in living brown bears

Axel Barlow, James A. Cahill, Stefanie Hartmann, Christoph Theunert, Georgios Xenikoudakis, Gloria G. Fortes, Johanna L. A. Paijmans, Gernot Rabeder, Christine Frischauf, Aurora Grandal-D'Anglade, Ana García-Vázquez, Marine Murtskhvaladze, Urmas Saarma, Peeter Anijalg, Tomaž Skrbinšek, Giorgio Bertorelle, Boris Gasparian, Guy Bar-Oz, Ron Pinhasi, Montgomery Slatkin, Love Dalén, Beth Shapiro & Michael Hofreiter
Although many large mammal species went extinct at the end of the Pleistocene epoch, their DNA may persist due to past episodes of interspecies admixture. However, direct empirical evidence of the persistence of ancient alleles remains scarce. Here, we present multifold coverage genomic data from four Late Pleistocene cave bears (Ursus spelaeus complex) and show that cave bears hybridized with brown bears (Ursus arctos) during the Pleistocene. We develop an approach to assess both the...

Dietary stress increases the total opportunity for sexual selection and modifies selection on condition-dependent traits

Silvia Cattelan, Jonathan P. Evans, Francisco Garcia-Gonzalez, Elisa Morbiato & Andrea Pilastro
Although it is often expected that adverse environmental conditions depress the expression of condition-dependent sexually-selected traits, the full consequences of environmental change for the action of sexual selection, in terms of the opportunity for total sexual selection and patterns of phenotypic selection, are unknown. Here we show that dietary stress in guppies, Poecilia reticulata, reduces the expression of several sexually-selected traits and increases the opportunity for total sexual selection (standardized variance in reproductive success) in...

Environmental drivers of Sphagnum growth in peatlands across the Holarctic region

Fia Bengtsson, Håkan Rydin, Jennifer Baltzer, Luca Bragazza, Zhao-Jun Bu, Simon Caporn, Ellen Dorrepaal, Kjell Ivar Flatberg, Olga Galanina, Mariusz Gałka, Anna Ganeva, Irina Goia, Nadezhda Goncharova, Michal Hajek, Akira Haraguchi, Lorna Harris, Elyn Humphreys, Martin Jiroušek, Katarzyna Kajukało, Edgar Karofeld, Natalia Koronatova, Natalia Kosykh, Anna Laine, Mariusz Lamentowicz, Elena Lapshina … & Richard J. Payne
The relative importance of global versus local environmental factors for growth and thus carbon uptake of the bryophyte genus Sphagnum – the main peat-former and ecosystem engineer in northern peatlands – remains unclear. 2) We measured length growth and net primary production (NPP) of two abundant Sphagnum species across 99 Holarctic peatlands. We tested the importance of previously proposed abiotic and biotic drivers for peatland carbon uptake (climate, N deposition, water table depth, and vascular...

Size-selective mortality induces evolutionary changes in group risk-taking behavior and the circadian system in a fish

Valerio Sbragaglia, Valerio Sbragaglia, Jose Fernando López-Olmeda, Elena Frigato, Cristiano Bertolucci & Robert Arlinghaus
1. Intensive and trait-selective mortality of fish and wildlife can cause evolutionary changes in a range of life-history and behavioral traits. These changes might in turn alter the circadian system due to coevolutionary mechanisms or correlated selection responses both at behavioral and molecular levels, with knock-on effects on daily physiological processes and behavioral outputs. 2. We examined the evolutionary impact of size-selective harvesting on group risk-taking behavior and the circadian system in a model fish...

Mapping the geographic origin of captive and confiscated Hermann’s tortoises: a genetic toolkit for conservation and forensic analyses

Roberto Biello, Zampiglia Mauro, Corti Claudia, Deli Gianluca, Biaggini Marta, Crestanello Barbara, Delaugerre Michel, Di Tizio Luciano, Leonetti Francesco Luigi, Stefano Casari, Olivieri Oliviero, Pellegrino Francesco, Romano Antonio, Sperone Emilio, Hauffe Heidi Christine, Trabalza-Marinucci Massimo, Giorgio Bertorelle & Canestrelli Daniele
The illegal trade has been threatening tortoise populations worldwide for decades. Nowadays, however, DNA typing and forensic genetic approaches allow us to investigate the geographic origin of confiscated animals and to relocate them into the wild, providing that suitable molecular tools and reference data are available. Here we assess the suitability of a small panel of microsatellite markers to investigate patterns of illegal translocations and to assist forensic genetic applications in the endangered Mediterranean land...

Data from: Evidence for past and present hybridization in three Antarctic icefish species provides new perspectives on an evolutionary radiation

Ilaria A. M. Marino, Andrea Benazzo, Cecilia Agostini, Massimo Mezzavilla, Sean M. Hoban, Tomaso Patarnello, Lorenzo Zane & Giorgio Bertorelle
Determining the timing, extent, and underlying causes of inter-specific gene exchange during or following speciation is central to understanding species’ evolution. Antarctic notothenioid fish, thanks to the acquisition of antifreeze glycoproteins during Oligocene transition to polar conditions, experienced a spectacular radiation to >100 species during Late Miocene cooling events. The impact of recent glacial cycles on this group is poorly known, but alternating warming and cooling periods may have affected species’ distributions, promoted ecological divergence...

Data from: Taxonomic and functional turnover are decoupled in European peat bogs

Bjorn J. M. Robroek, Vincent E. J. Jassey, Richard J. Payne, Magalí Martí, Luca Bragazza, Albert Bleeker, Alexandre Buttler, Simon J. M. Caporn, Nancy B. Dise, Jens Kattge, Katarzyna Zając, Bo H. Svensson, Jasper Van Ruijven & Jos T. A. Verhoeven
In peatland ecosystems, plant communities mediate a globally significant carbon store. The effects of global environmental change on plant assemblages are expected to be a factor in determining how ecosystem functions such as carbon uptake will respond. Using vegetation data from 56 Sphagnum-dominated peat bogs across Europe, we show that in these ecosystems plant species aggregate into two major clusters that are each defined by shared response to environmental conditions. Across environmental gradients, we find...

Data from: Diversity patterns of native and exotic fish species suggest homogenization processes, but partly fail to highlight extinction threats

Anna Gavioli, Marco Milardi, Giuseppe Castaldelli, Elisa Anna Fano & Janne Soininen
Exotic species are a major threat to biodiversity and have modified native communities worldwide. Invasion processes have been extensively studied, but studies on species richness and beta diversity patterns of exotic and native species are rare. We investigate such patterns among exotic and native fish communities in upland and lowland rivers to explore their relationship with environmental drivers. Location: Northern Italy. Exotic and native fish beta diversity patterns were investigated separately in lowland and upland...

Data from: Comparative evaluation of potential indicators and temporal sampling protocols for monitoring genetic erosion

Sean Hoban, Jan A. Arntzen, Michael W. Bruford, José A. Godoy, A. Rus Hoelzel, Gernot Segelbacher, Carles Vilà & Giorgio Bertorelle
Genetic biodiversity contributes to individual fitness, species' evolutionary potential, and ecosystem stability. Temporal monitoring of the genetic status and trends of wild populations' genetic diversity can provide vital data to inform policy decisions and management actions. However, there is a lack of knowledge regarding which genetic metrics, temporal sampling protocols, and genetic markers are sufficiently sensitive and robust, on conservation-relevant timescales. Here, we tested six genetic metrics and various sampling protocols (number and arrangement of...

Rilievo fotogrammetrico SfM very close range per applicazioni in ambito archeometrico: test e considerazioni

Alessandra Rossetti & Arianna Pesci
SfM (Structure from Motion) photogrammetry offers great versatility in survey and restitution operations. The most important feature that allows this technique to be applied to a wide range of observation distances is the resolution of the images intended both as the quantity and quality of the pixels that compose them. With the same digital camera, equipped with a good sensor (CMOS) and operating in good light conditions, it is possible to acquire images over large...

European Database of Seismogenic Faults (EDSF)

Roberto Basili, Vanja Kastelic, Mine Betül Demircioglu, David Garcia Moreno, Eliza S. Nemser, Patrizio Petricca, Sotiris P. Sboras, Glenda M. Besana-Ostman, João Cabral, Thierry Camelbeeck, Riccardo Caputo, Laurentiu Danciu, Hilal Domaç, João Filipe de Barros Duarte Fonseca, Julián García-Mayordomo, Domenico Giardini, Branislav Glavatovic, Levent Gulen, Yigit Ince, Spyros Pavlides, Karin Sesetyan, Gabriele Tarabusi, Mara Monica Tiberti, Murat Utkucu, Gianluca Valensise … & Jochen Wössner
The European Database of Seismogenic Faults (EDSF) was compiled in the framework of the EU Project SHARE, Work Package 3, Task 3.2. EDSF includes only faults that are deemed to be capable of generating earthquakes of magnitude equal to or larger than 5.5 and aims at ensuring a homogenous input for use in ground-shaking hazard assessment in the Euro-Mediterranean area. Several research institutions participated in this effort with the contribution of many scientists (see the...

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