34 Works

Data from: Phylogenetic analysis of 47 chloroplast genomes clarifies the contribution of wild species to the domesticated apple maternal line

Svetlana V. Nikiforova, Duccio Cavalieri, Riccardo Velasco & Vadim Goremykin
Both the origin of domesticated apple and the overall phylogeny of the genus Malus are still not completely resolved. Having this as a target, we built a 134,553 position long alignment including two previously published cpDNAs and 45 de novo sequenced, fully co-linear chloroplast genomes from cultivated apple varieties and wild apple species. The data produced are free from compositional heterogeneity and from substitutional saturation, which can adversely affect phylogeny reconstruction. Phylogenetic analyses based on...

Data from: Genetic and ecological data reveal species boundaries between viviparous and oviparous lizard lineages

Luca Cornetti, G. Francesco Ficetola, Sean Hoban & Cristiano Vernesi
Identification of cryptic species is an essential aim for conservation biologists to avoid premature extinctions of ‘unrecognized’ species. Integrating different types of data can undoubtedly aid in resolving the issue of species delimitation. We studied here two lineages of the common lizard Zootoca vivipara that display different reproductive mode (the viviparous Z. v. vivipara and the oviparous Z. v. carniolica) and that overlap their distributional ranges in the European Alps. With the purpose of delimiting...

Data from: Genetic variation and population structure in the endangered Hermann’s tortoise: the roles of geography and human-mediated processes

Melanie Perez, Barbara Livoreil, Sara Mantovani, Marie-Catherine Boisselier, Barbara Crestanello, Jawad Abdelkrim, Céline Bonillo, Vassilis Goutner, Josie Lambourdière, Massimo Pierpaoli, Bogoljub Sterijovski, Ljiljana Tomovic, Sibelle Vilaca, Stefano Mazzotti & Giorgio Bertorelle
The Hermanni’s tortoise (Testudo hermanni) is an endangered land tortoise distributed in disjoint populations across Mediterranean Europe. We investigated its genetic variation by typing one mitochondrial locus and nine nuclear microsatellites in approximately 300 individuals from 22 localities. Our goal was to understand the relative impact of natural and human-mediated processes in shaping the genetic structure, and to identify the genetic priorities for the conservation of this species. We found that i) all geographic areas...

Large carnivore expansion in Europe is associated with human population density and land cover changes

Marta Cimatti, Nathan Ranc, Ana Ana Benítez-López, Luigi Maiorano, Luigi Boitani, Francesca Cagnacci, Mirza Čengić, Paolo Ciucci, Mark Huijbregts, Miha Krofel, José López Bao, Nuria Selva, Henrik Andren, Carlos Bautista, Duško Cirovic, Heather Hemmingmoore, Ilka Reinhardt, Miha Marenče, Yorgos Mertzanis, Luca Pedrotti, Igor Trbojević, Andreas Zetterberg, Tomasz Zwijacz-Kozica & Luca Santini
Aim: The recent recovery of large carnivores in Europe has been explained as resulting from a decrease in human persecution driven by widespread rural land abandonment, paralleled by forest cover increase and the consequent increase in availability of shelter and prey. We investigated whether land cover and human population density changes are related to the relative probability of occurrence of three European large carnivores: the grey wolf (Canis lupus), the Eurasian lynx (Lynx lynx) and...

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: Extracting spatio-temporal patterns in animal trajectories: an ecological application of sequence analysis methods

Johannes De Groeve, Nico Van De Weghe, Nathan Ranc, Tijs Neutens, Lino Ometto, Omar Rota-Stabelli & Francesca Cagnacci
Digital tracking technologies have considerably increased the amount and quality of animal trajectories, enabling the study of habitat use and habitat selection at a fine spatial and temporal scale. However, current approaches do not yet explicitly account for a key aspect of habitat use, namely the sequential variation in the use of different habitat features. To overcome this limitation, we propose a tree-based approach that makes use of sequence analysis methods, derived from molecular biology,...

Data from: How many routes lead to migration? Comparison of methods to assess and characterise migratory movements

Francesca Cagnacci, Stefano Focardi, Anne Ghisla, Bram Van Moorter, Eliezer Gurarie, Marco Heurich, Atle Mysterud, John Linnell, Manuela Panzacchi, Evelyn Merrill, Roel May, Torgeir Nygård, Christer Rolandsen, Mark Hebblewhite & Evelyn H. Merrill
1. Decreasing rate of migration in several species as a consequence of climate change and anthropic pressure, together with increasing evidence of space-use strategies intermediate between residency and complete migration, are very strong motivations to evaluate migration occurrence and features in animal populations. 2. The main goal of this paper was to perform a relative comparison between methods for identifying and characterising migration at the individual and population level on the basis of animal location...

Data from: Migration in geographic and ecological space by a large herbivore

Wibke Peters, Mark Hebblewhite, Atle Mysterud, Derek Spitz, Stefano Focardi, Ferdinando Urbano, Nicolas Morellet, Marco Heurich, Petter Kjellander, John D.C. Linnell, Francesca Cagnacci & John D. C. Linnell
Partial migration, when only part of the population migrates seasonally while the other part remains resident on the shared range, is the most common form of migration in ungulates. Migration is often defined by spatial separation of seasonal ranges and consequently, classification of individuals as migrants or residents is usually only based on geographic criteria. However, the underlying mechanism for migration is hypothesized to be movement in response to spatiotemporal resource variability and thus, migrants...

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...

The effect of high-polyphenol Mediterranean diet on visceral adiposity: the DIRECT PLUS randomized controlled trial

Hila Zelicha, Nora Kloting, Alon Kaplan, Anat Yaskolka Meir, Ehud Rinott, Gal Tsaban, Yoash Chassidim, Matthias Bluher, Uta Ceglarek, Berend Isermann, Michael Stumvoll, Rita Nana Quayson, Martin von Bergen, Beatrice Engelmann, Ulrike E. Rolle-Kampczyk, Sven-Bastiaan Haange, Kieran M. Tuohy, Camilla Diotallevi, Ilan Shelef, Frank B. Hu, Meir J. Stampfer & Iris Shai
Abstract Background Mediterranean (MED) diet is a rich source of polyphenols, which benefit adiposity by several mechanisms. We explored the effect of the green-MED diet, twice fortified in dietary polyphenols and lower in red/processed meat, on visceral adipose tissue (VAT). Methods In the 18-month Dietary Intervention Randomized Controlled Trial PoLyphenols UnproceSsed (DIRECT-PLUS) weight-loss trial, 294 participants were randomized to (A) healthy dietary guidelines (HDG), (B) MED, or (C) green-MED diets, all combined with physical activity....

Data from: The geographical and environmental determinants of genetic diversity for four alpine conifers of the European Alps

Elena Mosca, Andrew J. Eckert, Erica A. Di Pierro, Duccio Rocchini, Nicola La Porta, Piero Belletti & David B. Neale
Climate is one of the most important drivers of local adaptation in forest tree species. Standing levels of genetic diversity and structure within and among natural populations of forest trees are determined by the interplay between climatic heterogeneity and the balance between selection and gene flow. To investigate this interplay single nucleotide polymorphisms (SNPs) were genotyped in 24 to 37 populations from four subalpine conifers, Abies alba Mill., Larix decidua L., Pinus cembra L. and...

Data from: Different diversification rates between sexual and asexual organisms

Diego Fontaneto, Cuong Q. Tang, Ulrike Obertegger, Francesca Leasi & Timothy G. Barraclough
Patterns of diversity reflect the balance between speciation and extinction over time. Here we estimate net diversification rates for samples of sexual and asexual rotifers using phylogenetic reconstructions from sequence data of one mtDNA locus, cytochrome oxidase c subunit I. All four clades of bdelloid rotifers, obligate asexuals, had higher number of species per clade and significantly higher accumulation of diversification events towards the root of the trees than the four clades of their sexual...

Data from: The evolutionary root of flowering plants

Vadim V. Goremykin, Svetlana V. Nikiforova, Patrick J. Biggs, Bojian Zhong, Peter DeLange, William Martin, Stefan Woetzel, Robin A. Atherton, Patricia McLenachan, Peter James Lockhart & Patricia A. Mclenachan
Correct rooting of the angiosperm radiation is both challenging and necessary for understanding the origins and evolution of physiological and phenotypic traits in flowering plants. The problem is known to be difficult due to the large genetic distance separating flowering plants from other seed plants and the sparse taxon sampling among basal angiosperms. Here we provide further evidence for concern over substitution model misspecification in analyses of chloroplast DNA sequences. We show that support for...

Data from: Interactions among morphotype, nutrition, and temperature impact fitness of an invasive fly.

Dalila Rendon, Vaughn Walton, Gabriella Tait, Jessica Buser, Ivana Lemos Souza, Anna Wallingford, Greg Loeb & Jana Lee
Invasive animals depend on finding a balanced nutritional intake to colonize, survive, and reproduce in new environments. This can be especially challenging during situations of fluctuating cold temperatures and food scarcity, but phenotypic plasticity may offer an adaptive advantage during these periods. We examined how lifespan, fecundity, pre-oviposition periods, and body nutrient contents were affected by dietary protein and carbohydrate (P:C) ratios at variable low temperatures in two morphs (winter morphs WM and summer morphs...

Additional file 1 of The effect of high-polyphenol Mediterranean diet on visceral adiposity: the DIRECT PLUS randomized controlled trial

Hila Zelicha, Nora Kloting, Alon Kaplan, Anat Yaskolka Meir, Ehud Rinott, Gal Tsaban, Yoash Chassidim, Matthias Bluher, Uta Ceglarek, Berend Isermann, Michael Stumvoll, Rita Nana Quayson, Martin von Bergen, Beatrice Engelmann, Ulrike E. Rolle-Kampczyk, Sven-Bastiaan Haange, Kieran M. Tuohy, Camilla Diotallevi, Ilan Shelef, Frank B. Hu, Meir J. Stampfer & Iris Shai
Additional file 1: S1. Adherence to the intervention. S2. Sensitivity analysis. S3. Inclusion and Exclusion criteria. S4. Physical activity recommendations protocol. S5. Polyphenol-rich foods, provided at no cost to participants. S6. Magnetic resonance imaging. S7. Clinical parameters, laboratory methodology, and blood and urine polyphenols assessments. S8. Sample size and power calculations. Fig. S1. DIRECT PLUS flow chart. Fig. S2. Heatmap of abdominal adipose depots and metabolic and cardiovascular parameters at baseline. Fig. S3. The effect...

Additional file 1 of dynamAedes: a unified modelling framework for invasive Aedes mosquitoes

Daniele Da Re, Wim Van Bortel, Friederike Reuss, Ruth Müller, Sebastien Boyer, Fabrizio Montarsi, Silvia Ciocchetta, Daniele Arnoldi, Giovanni Marini, Annapaola Rizzoli, Gregory L’Ambert, Guillaume Lacour, Constantianus J. M. Koenraadt, Sophie O. Vanwambeke & Matteo Marcantonio
Additional file 1: Figure S1. Overview of the temperature-dependent functions used in the model for the four Aedes species. Figure S2. Overview of the temperature-dependent functions used in the model for Ae. aegypti. Figure S3. Overview of the temperature-dependent functions used in the model for Ae. albopictus. Figure S4. Overview of the temperature-dependent functions used in the model for Ae. japonicus. Figure S5. Overview of the temperature-dependent functions used in the model for Ae. koreicus....

dynamAedes: a unified modelling framework for invasive Aedes mosquitoes

Daniele Da Re, Wim Van Bortel, Friederike Reuss, Ruth Müller, Sebastien Boyer, Fabrizio Montarsi, Silvia Ciocchetta, Daniele Arnoldi, Giovanni Marini, Annapaola Rizzoli, Gregory L’Ambert, Guillaume Lacour, Constantianus J. M. Koenraadt, Sophie O. Vanwambeke & Matteo Marcantonio
Abstract Mosquito species belonging to the genus Aedes have attracted the interest of scientists and public health officers because of their capacity to transmit viruses that affect humans. Some of these species were brought outside their native range by means of trade and tourism and then colonised new regions thanks to a unique combination of eco-physiological traits. Considering mosquito physiological and behavioural traits to understand and predict their population dynamics is thus a crucial step...

dynamAedes: a unified modelling framework for invasive Aedes mosquitoes

Daniele Da Re, Wim Van Bortel, Friederike Reuss, Ruth Müller, Sebastien Boyer, Fabrizio Montarsi, Silvia Ciocchetta, Daniele Arnoldi, Giovanni Marini, Annapaola Rizzoli, Gregory L’Ambert, Guillaume Lacour, Constantianus J. M. Koenraadt, Sophie O. Vanwambeke & Matteo Marcantonio
Abstract Mosquito species belonging to the genus Aedes have attracted the interest of scientists and public health officers because of their capacity to transmit viruses that affect humans. Some of these species were brought outside their native range by means of trade and tourism and then colonised new regions thanks to a unique combination of eco-physiological traits. Considering mosquito physiological and behavioural traits to understand and predict their population dynamics is thus a crucial step...

Data from: Multiple refugia and barriers explain the phylogeography of the Valais shrew, Sorex antinorii (Mammalia: Soricomorpha)

Glenn Yannic, Loïc Pellissier, Sylvain Dubey, Rodrigo Vega, Patrick Basset, Stefano Mazzotti, Elena Pecchioli, Cristiano Vernesi, Heidi C. Hauffe, Jeremy B. Searle & Jacques Hausser
The aim of the present study was to investigate the genetic structure of the Valais shrew (Sorex antinorii) by a combined phylogeographical and landscape genetic approach, and thereby to infer the locations of glacial refugia and establish the influence of geographical barriers. We sequenced part of the mitochondrial cytochrome b (cyt b) gene of 179 individuals of S. antinorii sampled across the entire species' range. Six specimens attributed to S. arunchi were included in the...

Data from: Fast and cost-effective genetic mapping in apple using next-generation sequencing

Kyle M. Gardner, Thomas F. Cooke, Patrick J. Brown, Scott Cann, Fabrizio Costa, Carlos D. Bustamante, Riccardo Velasco, Michela Troggio, Sean Myles, P. Brown & C. Bustamante
Next-generation DNA sequencing (NGS) produces vast amounts of DNA sequence data, but it is not specifically designed to generate data suitable for genetic mapping. Recently developed DNA library preparation methods for NGS have helped solve this problem, however, by combining the use of reduced representation libraries with DNA sample barcoding to generate genome-wide genotype data from a common set of genetic markers across a large number of samples. Here we use such a method, called...

Data from: Genetic drift linked to heterogeneous landscape and ecological specialization drives diversification in the Alpine endemic columbine Aquilegia thalictrifolia

Margherita Lega, Simone Fior, Mingai Li, Stefano Leonardi & Claudio Varotto
The European Alpine system is an extensive mountain range, whose heterogeneous landscape together with Quaternary climatic oscillations significantly affected organismal diversity and distribution in Europe. The model genus Aquilegia represents a textbook example of a rapid and recent radiation through the Northern hemisphere, with the majority of the European taxa occuring in the Alpine system. However, the processes governing genetic differentiation of the genus in this complex geographic area are still widely unexplored. In this...

Data from: How to map forest structure from aircraft, one tree at a time

Michele Dalponte, Lorenzo Frizzera & Damiano Gianelle
Forest structure is strongly related to forest ecology and it is a key parameter to understand ecosystem processes and services. Airborne laser scanning (ALS) is becoming an important tool in environmental mapping. It is increasingly common to collect ALS data at high enough point density to recognize individual tree crowns (ITCs) allowing analyses to move beyond classical stand level approaches. In this paper an effective and simple method to map ITCs, and their stem diameter...

Data from: Fear of the dark? contrasting impacts of humans vs lynx on diel activity of roe deer across Europe

Nadège C. Bonnot, Ophélie Couriot, Anne Berger, Francesca Cagnacci, Simone Ciuti, Johannes De Groeve, Benedikt Gehr, Marco Heurich, Petter Kjellander, Max Kröschel, Nicolas Morellet, Leif Sönnichsen & A.J. Mark Hewison
Humans, as super predators, can have strong effects on wildlife behaviour, including profound modifications of diel activity patterns. Subsequent to the return of large carnivores to human-modified ecosystems, many prey species have adjusted their spatial behaviour to the contrasting landscapes of fear generated by both their natural predators and anthropogenic pressures. The effects of predation risk on temporal shifts in diel activity of prey, however, remain largely unexplored in human-dominated landscapes. We investigated the influence...

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...

Body size and digestive system shape resource selection by ungulates: a cross-taxa test of the Forage Maturation Hypothesis

Saeideh Esmaeili, Brett Jesmer, Shannon Albeke, Ellen Aikens, Kathryn Schoenecker, Sarah King, Briana Abrahms, Bayarbaatar Buuveibaatar, Jeffrey Beck, Randall Boone, Francesca Cagnacci, Simon Chamaillé-Jammes, Buyanaa Chimeddorj, Paul Cross, Nandintsetseg Dejid, Jagdag Enkhbayar, Ilya Fischhoff, Adam Ford, Kate Jenks, Mahmoud-Reza Hemami, Jacob Hennig, Takehiko Ito, Petra Kaczensky, Matthew Kauffman, John Linnell … & Jacob Goheen
The Forage Maturation Hypothesis (FMH) states that energy intake for ungulates is maximized when forage biomass is at intermediate levels. Nevertheless, metabolic allometry and different digestive systems suggest that resource selection should vary across ungulate species. By combining GPS relocations with remotely-sensed data on forage characteristics and surface water, we quantified the effect of body size and digestive system in determining movements of 30 populations of hindgut fermenters (equids) and ruminants across biomes. Selection for...

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