106 Works

Data from: Phylogeography and demographic history of two widespread Indo-Pacific mudskippers (Gobiidae: Periophthalmus)

Gianluca Polgar, Lorenzo Zane, Massimiliano Babbucci, Federica Barbisan, Tomaso Patarnello, Lukas Rüber & Chiara Papetti
This study provides a first description of the phylogeographic patterns and evolutionary history of two species of the mudskipper genus Periophthalmus. These amphibious gobies are distributed throughout the whole Indo-Pacific region and Atlantic coast of Africa, in peritidal habitats of soft-bottom coastal ecosystems. Three sequence datasets of two widely distributed species, Periophthalmus argentilineatus and P. kalolo, were obtained by amplifying and sequencing two mtDNA markers (D-loop and 16S rDNA) and the nDNA rag1 region. The...

Data from: High cover of hedgerows in the landscape supports multiple ecosystem services in Mediterranean cereal fields

Matteo Dainese, Silvia Montecchiari, Tommaso Sitzia, Maurizia Sigura & Lorenzo Marini
Field-margin diversification through conservation and restoration of hedgerows is becoming a prominent intervention for promoting biodiversity and associated ecosystem services in intensive agricultural landscapes. However, how increasing cover of hedgerows in the landscape can affect ecosystem services has rarely been considered. Here, we assessed the effect of increased field-margin complexity at the local scale and increasing cover of hedgerows in the landscape on the provision of pest control, weed control and potential pollination. Locally, three...

Data from: \"Transcriptome sequences for Campanula gentilis\" in Genomic Resources Notes accepted 1 April 2015 – 31 May 2015

Töre Demet, Federico Luebert, Guilhem Mansion, Ludo A. H. Muller, M. Vidotto, E. Boscari, L. Congiu, A. Grapputo, L. Zane, Vera Maria Fonseca Almeida-Val, Maria Manuela Coelho, Tiago Filipe Jesus & Demet Töre
In this report, we present the transcriptome of a single accession of Campanula gentilis Kovanda, obtained through the sequencing of both a normalized and a non-normalized cDNA library generated from stem and leaf tissue. The resources we provide include the raw sequence reads, the assembled contigs, the putative open reading frames, the contig/ORF annotations and the normalized as well as non-normalized expression levels.

Data from: The replication of Frataxin gene is assured by activation of dormant origins in the presence of a GAA-repeat expansion

Martina Stevanoni, Elisa Palumbo & Antonella Russo
It is well known that DNA replication affects the stability of several trinucleotide repeats, but whether replication profiles of human loci carrying an expanded repeat differ from those of normal alleles is poorly understood in the endogenous context. We investigated this issue using cell lines from Friedreich’s ataxia patients, homozygous for a GAA-repeat expansion in intron 1 of the Frataxin gene. By interphase, FISH we found that in comparison to the normal Frataxin sequence the...

Data from: Quick-change artists: male guppies pay no cost to repeatedly adjust their sexual strategies

Martina Magris, Gianluca Chimetto, Sofia Rizzi & Andrea Pilastro
Sexually selected traits involved in mate acquisition and fertilization success are usually costly and males often plastically adjust their reproductive investment in response to social conditions. Phenotypic plasticity in male sexual traits is generally assumed to be adaptive, yet its costs are rarely investigated. Male guppies (Poecilia reticulata) adjust their ejaculate production and sexual behavior in response to perceived mating opportunities. In natural populations mating opportunities can fluctuate continuously, and the iterated activation of plastic...

Data from: The interplay of landscape composition and configuration: new pathways to manage functional biodiversity and agro-ecosystem services across Europe

Emily A. Martin, Matteo Dainese, Yann Clough, András Báldi, Riccardo Bommarco, Vesna Gagic, Michael Garratt, Andrea Holzschuh, David Kleijn, Anikó Kovács-Hostyánszki, Lorenzo Marini, Simon G. Potts, Henrik G. Smith, Diab Al Hassan, Matthias Albrecht, Georg K. S. Andersson, Josep Asis, Stephanie Aviron, Mario Balzan, Laura Baños-Picón, Ignasi Bartomeus, Peter Batary, Françoise Burel, Berta Caballero-López, Elena D. Concepcion … & Ingolf Steffan-Dewenter
Managing agricultural landscapes to support biodiversity and ecosystem services is a key aim of a sustainable agriculture. However, how the spatial arrangement of crop fields and other habitats in landscapes impacts arthropods and their functions is poorly known. Synthesising data from 49 studies (1515 landscapes) across Europe, we examined effects of landscape composition (% habitats) and configuration (edge density) on arthropods in fields and their margins, pest control, pollination and yields. Configuration effects interacted with...

Data from: Behavioural patterns of vocal greeting production in four primate species

Pawel Fedurek, Christof Neumann, Yaelle Bouquet, Stephanie Mercier, Martina Magris, Fredy Quintero & Klaus Zuberbühler
Social animals have evolved a range of signals to avoid aggressive and facilitate affiliative interactions. Vocal behaviour is especially important in this respect with many species, including various primates, producing acoustically distinct ‘greeting calls’ when two individuals approach each other. While the ultimate function of greeting calls has been explored in several species, little effort has been made to understand the mechanisms of this behaviour across species. The aim of this study was to explore...

Data from: Familiarity mediates equitable social associations in guppies

Silvia Cattelan, Tyrone Lucon-Xiccato, Andrea Pilastro & Matteo Griggio
Several fish species are characterized by social systems in which individuals prefer to interact with specific group mates. However, there is no clear evidence that such associations are equitable, i.e. they are mutual between individuals. We addressed this issue in the guppy (Poecilia reticulata), a species in which social network analyses have evidenced non-random social associations between individuals. We measured the mutual preference in pairs of guppies that previously familiarized in groups of either two...

Along-shelf connectivity and circumpolar gene flow in Antarctic silverfish (Pleuragramma antarctica)

Jilda Alicia Caccavo, Chiara Papetti, , Rainer Knust, Julian R. Ashford & Lorenzo Zane
The Antarctic silverfish (Pleuragramma antarctica) is a critically important forage species with a circumpolar distribution and is unique among other notothenioid species for its wholly pelagic life cycle. Previous studies have provided mixed evidence of population structure over regional and circumpolar scales. The aim of the present study was to test the recent population hypothesis for Antarctic silverfish, which emphasizes the interplay between life history and hydrography in shaping connectivity. A total of 1067 individuals...

Data from: Extra food provisioning reduces extra-pair paternity in the lesser kestrel (Falco naumanni)

Alessandra Costanzo, Nicola Tommasi, Andrea Galimberti, Giorgia Scesa, Roberto Ambrosini, Matteo Griggio, Jacopo G. Cecere & Diego Rubolini
Female promiscuity can function to acquire both direct and indirect benefits from their social mate and extra-pair males. In many raptor species, intense mate-feeding significantly contributes to female energy requirements before and during egg laying. Moreover, females may use mate-feeding effort to assess male quality. In this study of the lesser kestrel (Falco naumanni), we aimed at experimentally manipulating the female’s perception of mate quality by providing females with extra food during egg laying, and...

Simultaneous two-photon voltage or calcium imaging and multi-channel LFP recordings in barrel cortex of awake and anesthetized mice

Claudia Cecchetto, Stefano Vassanelli & Bernd Kuhn
Neuronal population activity, both spontaneous and sensory-evoked, generates propagating waves in cortex. However, high spatiotemporal-resolution mapping of these waves is difficult as calcium imaging, the work horse of current imaging, does not reveal subthreshold activity. Here, we present a platform combining voltage or calcium two-photon imaging with multi-channel local field potential (LFP) recordings in different layers of the barrel cortex from anesthetized and awake head-restrained mice. A chronic cranial window with access port allows injecting...

Additional file 7 of Unlocking the molecular basis of wheat straw composition and morphological traits through multi-locus GWAS

Salvatore Esposito, Francesca Taranto, Paolo Vitale, Donatella Bianca Maria Ficco, Salvatore Antonio Colecchia, Piergiorgio Stevanato & Pasquale De Vita
Additional file 7: Supplementary Table 1. BLUPs values for the traits under study.

Multi-tissue RNA-Seq analysis and long-read-based genome assembly reveal complex sex-specific gene regulation and molecular evolution in the Manila clam

Ran Xu, Jacopo Martelossi, Morgan Smits, Mariangela Iannello, Luca Peruzza, Massimiliano Babbucci, Massimo Milan, Joseph P. Dunham, Sophie Breton, Liliana Milani, Sergey V Nuzhdin, Luca Bargelloni, Marco Passamonti & Fabrizio Ghiselli
The genome anntation.

Data from: Tactic-specific differences in seminal fluid influence sperm performance

Lisa Locatello, Federica Poli & Maria B. Rasotto
Seminal fluid often makes up a large part of an ejaculate, yet most empirical and theoretical studies on sperm competition have focused on how sperm characteristics (number and quality) affect fertilization success. However, seminal fluid influences own sperm performance and may potentially influence the outcome of sperm competition, by affecting also that of rivals. As a consequence males may be expected to allocate their investment in both sperm and seminal fluid in relation to the...

Data from: Cross–generational effects of sexual harassment on female fitness in the guppy

Clelia Gasparini, Alessandro Devigili & Andrea Pilastro
A large number of studies have identified several direct costs of sexual harassment, including energy expenditure and reduced foraging ability. However, the fitness consequences of sexual harassment over a longer time-scale have never been investigated. Here, we estimated the effects of male sexual harassment on female fitness in the guppy, Poecilia reticulata, a small tropical fish in which sexual conflict over mating rates is particularly pronounced. We compared the lifetime fecundity and survival of two...

Data from: MHC-similarity and sexual selection: different doesn't always mean attractive

Clelia Gasparini, Leonardo Congiu & Andrea Pilastro
Females that mate multiply have the possibility to exert postcopulatory choice and select more compatible sperm to fertilize eggs. Prior work suggests that dissimilarity in major histocompatibility complex (MHC) plays an important role in determining genetic compatibility between partners. Favouring a partner with dissimilar MHC alleles would result in offspring with high MHC diversity and therefore with enhanced survival thanks to increased resistance to pathogens and parasites. The high variability of MHC genes may further...

Data from: Organic farming enhances parasitoid diversity at the local and landscape scale

Diego J. Inclán, Pierfilippo Cerretti, Doreen Gabriel, Tim G. Benton, Steven M. Sait, William E. Kunin, Mark A. K. Gillespie & Lorenzo Marini
1. The magnitude of the benefits derived from organic farming within contrasting managed landscapes remains unclear and, in particular, the potential scale-dependent response of insect parasitoids is relatively unexplored. Identifying the scale at which parasitoids are affected by organic farming will be an important step to enhance their conservation. 2. We sampled tachinid parasitoids at the centre and margin of arable and grassland fields on paired organic and conventional farms located in landscapes with different...

Data from: Extending RAD tag analysis to microbial ecology: a comparison between multi locus sequence typing (MLST) and 2b-RAD to investigate Listeria monocytogenes genetic structure

Marianna Pauletto, Lisa Carraro, Massimiliano Babbucci, Rosaria Lucchini, Luca Bargelloni & Barbara Cardazzo
The advent of next-generation sequencing (NGS) has dramatically changed bacterial typing technologies, increasing our ability to differentiate bacterial isolates. Despite it is now possible to sequence a bacterial genome in a few days and at reasonable costs, most genetic analyses do not require whole-genome sequencing, which also remains impractical for large population samples due to the cost of individual library preparation and bioinformatics. More traditional sequencing approaches, however, such as MultiLocus Sequence Typing (mlst) are...

Data from: Axial growth gradients across the postprotaspid ontogeny of the Silurian trilobite Aulacopleura koninckii

Giuseppe Fusco, Paul S. Hong & Nigel C. Hughes
Recent morphometric analysis revealed a juvenile (meraspid) axial growth gradient in the trunk of the ~429 Myr old trilobite Aulacopleura koninckii that resulted from growth control based on positional specification, as is common among extant organisms. Here we explore axial growth gradients in the more anterior body region, the cephalon, and in the cephalon and trunk during subsequent development in the holaspid period. We detected an axial growth gradient in the cephalon in the meraspid...

Data from: \"Characterization of two Iberian freshwater fish transcriptomes, Squalius carolitertii and Squalius torgalensis, living in distinct environmental conditions\" in Genomic Resources Notes Accepted 1 April 2015 to 31 May 2015

Tiago Filipe Jesus, Ana Rita Grosso, Vera Maria Fonseca Almeida-Val & Maria Manuela Coelho
The advance of NGS technologies opened exciting research avenues, as for example expanding the study of the mechanisms underlying adaptation from model organisms to natural systems. We used NGS technologies to sequence 12 RNA-seq libraries, and provide the first transcriptomes of two endemic Iberian Cyprinids. The species Squalius carolitertii and S. torgalensis inhabit different regions of Portugal with distinct climate types, Atlantic in the North and Mediterranean in the South, respectively. While northern regions present...

Data from: Conservation tillage mitigates the negative effect of landscape simplification on biological control

Giovanni Tamburini, Serena De Simone, Maurizia Sigura, Francesco Boscutti & Lorenzo Marini
Biological pest control is a key ecosystem service, and it depends on multiple factors acting from the local to the landscape scale. However, the effects of soil management on biological control and its potential interaction with landscape are still poorly understood. In a field exclusion experiment, we explored the relative effect of tillage system (conservation vs. conventional tillage) on aphid biological control in 15 pairs of winter cereal fields (barley and wheat) selected along a...

Data from: How much would it cost to monitor farmland biodiversity in Europe?

Ilse R. Geijzendorffer, Stefano Targetti, Manuel K. Schneider, Dick J. Brus, Philippe Jeanneret, Robert H. G. Jongman, Martin Knotters, Davide Viaggi, Siyka Angelova, Michaela Arndorfer, Debra Bailey, Katalin Balzacs, András Báldim, Marion M. B. Bogers, Robert G.H. Bunce, Jean-Philippe Choisis, Peter Dennis, Sebastian Eiter, Wendy Fjellstad, Jürgen F. Friedel, Tiziano Gomiero, Arjan Griffioen, Max Kainz, Anikó Kovács-Hostyánszki, Gisela Lüscher … & András Báldi
To evaluate progress on political biodiversity objectives, biodiversity monitoring provides information on whether intended results are being achieved. Despite scientific proof that monitoring and evaluation increase the (cost) efficiency of policy measures, cost estimates for monitoring schemes are seldom available, hampering their inclusion in policy programme budgets. Empirical data collected from 12 case studies across Europe were used in a power analysis to estimate the number of farms that would need to be sampled per...

Data from: Demographic stochasticity and resource autocorrelation control biological invasions in heterogeneous landscapes

Andrea Giometto, Florian Altermatt & Andrea Rinaldo
Mounting theoretical evidence suggests that demographic stochasticity, environmental heterogeneity and biased movement of organisms individually affect the dynamics of biological invasions and range expansions. Studies of species spread in heterogeneous landscapes have traditionally characterized invasion velocities as functions of the mean resource density throughout the landscape, thus neglecting higher-order moments of the spatial resource distribution. Here, we show theoretically that different spatial arrangements of resources lead to different spread velocities even if the mean resource...

Data from: TMS reveals flexible use of form and motion cues in biological motion perception

George Mather, Luca Battaglini & Gianluca Campana
The perception of human movement is a key component of daily social interactions. Although extrastriate area MT+/V5 is closely associated with motion processing, its role in the processing of sparse 'biological motion' displays is still unclear. We developed two closed matched psychophysical tasks to assess simple coherent motion perception and biological motion perception, and measured changes in performance caused by application of TMS over MT+/V5. Performance of the simple motion discrimination task was significantly depressed...

Data from: Stabilizing selection on sperm number revealed by artificial selection and experimental evolution

Silvia Cattelan, Andrea Di Nisio & Andrea Pilastro
Sperm competition is taxonomically widespread in animals and is usually associated with large sperm production, being the number of sperm in the competing pool the prime predictor of fertilization success. Despite the strong postcopulatory selection acting directionally on sperm production, its genetic variance is often very high. This can be explained by trade-offs between sperm production and traits associated with mate acquisition or survival, that may contribute to generate an overall stabilizing selection. To investigate...

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