20 Works

Biogeography of telomere dynamics in a vertebrate - Datasets S1

Daniele Canestrelli, Roberta Bisconti, Anita Liparoto, Frederic Angelier, Cécile Ribout, Claudio Carere & David Costantini
Telomere length variation has been implicated in processes of ecological and evolutionary importance in a wide range of organisms. However, while the temporal component of this variation has been the subject of much research, we do not know yet whether a spatial component exists within species in telomere dynamics. Here, we investigated for the first time whether the biogeographic history of populations, a key driver of eco-evolutionary processes, can influence telomere dynamics. Based on a...

The dry grasslands of Abruzzo National Park, the oldest protected area in the Apennines (Central Italy): overview of vegetation composition, syntaxonomy, ecology and diversity

Laura Cancellieri, Leonardo Rosati, Michele Brunetti, Leone Davide Mancini, Riccardo Primi, Bruno Ronchi, anna scoppola & Goffredo FILIBECK
The Abruzzo, Lazio and Molise National Park was established in 1923 and is considered a flagship conservation area in Italy. It includes large extensions of semi-natural grasslands, maintained by tradi-tional transhumant grazing for centuries. The patterns and drivers of grassland composition within the Park are still poorly investigated, and the scattered phytosociological data available were often based on relevés with varied and not precisely defined sizes.In order to provide for the first time a general...

Analysis of RNA-seq, DNA target enrichment, and Sanger nucleotide sequence data resolves deep splits in the phylogeny of cuckoo wasps (Hymenoptera: Chrysididae)

Thomas Pauli, Karen Meusemann, Sandra Kukowka, Manuela Sann, Alexander Donath, Christoph Mayer, Jan Philip Oeyen, Yolanda Ballesteros, Alexander Berg, Eric Van Den Berghe, Hermes Escalona, Adalgisa Guglielmino, Manfred Niehuis, Massimo Olmi, Lars Podsiadlowski, Carlo Polidori, Jeroen De Rond, Paolo Rosa, Thomas Schmitt, Franco Strumia, Mareike Wurdack, Shanlin Liu, Xin Zhou, Bernhard Misof, Ralph Peters … & Oliver Niehuis
The wasp family Chrysididae (cuckoo wasps, gold wasps) comprises exclusively parasitoid and kleptoparasitic species, many of which feature a stunning iridescent coloration and phenotypic adaptations to their parasitic life style. Previous attempts to infer phylogenetic relationships among the family’s major lineages (subfamilies, tribes, genera) based on Sanger sequence data were insufficient to statistically resolve the monophyly and the phylogenetic position of the subfamily Amiseginae and the phylogenetic relationships among the tribes Allocoeliini, Chrysidini, Elampini, and...

Data from: Molecular and morphological diversity of on-farm hazelnut (Corylus avellana L.) landraces from southern Europe and their role in the origin and diffusion of cultivated germplasm

P. Boccacci, M. Aramini, N. Valentini, L. Bacchetta, M. Rovira, P. Drogoudi, A. P. Silva, A. Solar, F. Calizzano, V. Erdoğan, V. Cristofori, L. F. Ciarmiello, C. Contessa, J. J. Ferreira, F. P. Marra & R. Botta
Hazelnut (Corylus avellana L.) is a traditional nut crop in southern Europe. Germplasm exploration conducted on-farm in five countries (Portugal, Spain, Italy, Slovenia, and Greece) identified 77 landraces. The present work describes phenotypic variation in nut and husk traits and investigates genetic relationships using 10 simple sequence repeat (SSR) markers among these landraces, 57 well-known references cultivars, and 19 wild accessions. Among the 77 landraces, 42 had unique fingerprints while 35 showed a SSR profile...

Data from: New insights on water buffalo genomic diversity and post-domestication migration routes from medium density SNP chip data

Licia Colli, Marco Milanesi, Elia Vajana, Daniela Iamartino, Lorenzo Bomba, Francesco Puglisi, Marcello Del Corvo, Ezequiel Luis Nicolazzi, Sahar Saad El-Din Ahmed, Jesus Rommel V. Herrera, Libertado Cruz, Shuju Zhang, Aixin Liang, Gouhua Hua, Ligou Yang, Xingjie Hao, Fuyuan Zuo, Song-Jia Lai, Shuilian Wang, Ruyu Liu, Yundeng Gong, Mahdi Mokhber, Yongjiang Mao, Feng Guan, Augustin Vlaic … & Liguo Yang
The domestic water buffalo is native to the Asian continent but through historical migrations and recent importations, nowadays has a worldwide distribution. The two types of water buffalo, i.e., river and swamp, display distinct morphological and behavioral traits, different karyotypes and also have different purposes and geographical distributions. River buffaloes from Pakistan, Iran, Turkey, Egypt, Romania, Bulgaria, Italy, Mozambique, Brazil and Colombia, and swamp buffaloes from China, Thailand, Philippines, Indonesia and Brazil were genotyped with...

Data from: Microsatellite genotyping of medieval cattle from central Italy suggests an old origin of Chianina and Romagnola cattle

Maria Gargani, Lorraine Pariset, Johannes A. Lenstra, Elisabetta De Minicis & Alessio Valentini
Analysis of DNA from archaeological remains is a valuable tool to interpret the history of ancient animal populations. So far most studies of ancient DNA target mitochondrial DNA (mtDNA), which reveals maternal lineages, but only partially the relationships of current breeds and ancient populations. In this study we explore the feasibility of nuclear DNA analysis. DNA was extracted from 1000-years old cattle bone collected from Ferento, an archaeological site in central Italy. Amplification of 15...

Innovafrica project data on agricultural food value chains

Chiara Perelli, Giacomo Branca, Luca Cacchiarelli, Donald Njarui, Esther Lupafya, Feyisa Hundessa, Joseph Hella, Mercy Mburu, Mokhele Moeletsi, Mufunanji Magalasi, Mupenzi Mutimura & Alessandro Sorrentino
A dataset was generated using the baseline survey data of the project entitled "Innovations in Technology, Institutional and Extension Approaches towards Sustainable Agriculture and enhanced Food and Nutrition Security in Africa (Acronym - Innovafrica)", which involved 16 istitutions from Europe and Africa and was implemented in six countries namely Ethiopia, Kenya, Malawi, Rwanda, South Africa and Tanzania. It includes the following information: smallholders' socio-demographic and economic characteristics; improved agriculture practices and seed systems adopted; climate...

Data from: Evolution of pre-mating reproductive isolation among conspecific populations of the sea rock-pool beetle Ochthebius urbanelliae driven by reinforcing natural selection

Daniele Porretta & Sandra Urbanelli
How natural selection might be involved in speciation remains a fundamental question in evolutionary biology. When two or more species co-occur in the same areas, natural selection may favour divergence in mating traits. By acting in sympatric but not allopatric populations, natural selection can also affect mate choice within species and ultimately initiate speciation among conspecific populations. Here we address this potential effect in the sea rock-pool beetles Ochthebius quadricollis and O.urbanelliae. The two species,...

Data from: Isotopic methods for non-destructive assessment of carbon dynamics in shrublands under long-term climate change manipulation

Louise C. Andresen, Maria T. Dominguez, Sabine Reinsch, Andy R. Smith, Inger Kappel Schmidt, Per Ambus, Claus Beier, Pascal Boeckx, Roland Bol, Giovanbattista De Dato, Bridget A. Emmett, Marc Estiarte, Mark H. Garnett, György Kröel-Dulay, Sharon L. Mason, Cecilie S. Nielsen, Josep Penuelas, Albert Tietema & Andrew R. Smith
1.Long-term climate change experiments are extremely valuable for studying ecosystem responses to environmental change. Examination of the vegetation and the soil should be non-destructive to guarantee long-term research. In this paper, we review field methods using isotope techniques for assessing carbon dynamics in the plant-soil-air continuum, based on recent field experience and examples from a European climate change manipulation network. 2.Eight European semi-natural shrubland ecosystems were exposed to warming and drought manipulations. One field site...

Shock or jump: deimatic behaviour is repeatable and polymorphic in a yellow-bellied toad

Andrea Chiocchio, Giuseppe Martino, Roberta Bisconti, Claudio Carere & Daniele Canestrelli
Inter-individual variation in antipredatory strategies has long attracted curiosity among scientists. Deimatisms is a complex and time-structured antipredatory strategy consisting in prey suddenly unleashing unexpected defences to frighten predators and stop their attack. Being deimatism traditionally considered as a stereotyped antipredatory response, the inter-individual variation in phenotypic traits related to deimatic displays is almost unexplored. In this study, we employed common garden experiments on 71 yellow-bellied toad Bombina pachypus to investigate the extent and pattern...

Lacistorhynchidae family 28S alignment

Mario Santoro, Bruno Bellisario, Fabio Crocetta, Barbara Degli Uberti & Marialetizia Palomba
Aim: Trypanorhyncha cestodes comprise a wide range of heteroxenous parasites infecting elasmobranchs as definitive hosts, with crustaceans, squids, and fishes acting as intermediate/paratenic hosts. Limited data exist on the larval infection of these cestodes and the role of intermediate and paratenic hosts in the life cycle of these parasites. In this study, we investigated the factors that determine the occurrence and the level of infection of Grillotia plerocerci in the skeletal muscles of various deep...

Genetic divergence across glacial refugia despite interglacial gene flow in a crested newt

Ben Wielstra, Daniele Salvi & Daniele Canestrelli
MtDNA-based phylogeography has illuminated the impact of the Pleistocene Ice Age on species distribution dynamics and the build-up of genetic divergence. The well-known shortcomings of mtDNA in biogeographical inference can be compensated by integrating multilocus data and species distribution modelling into phylogeography. We re-visit the phylogeography of the Italian crested newt (Triturus carnifex), a species distributed in two of Europe’s main glacial refugia, the Balkan and Italian Peninsulas. While a new 51 nuclear DNA marker...

Data from: \"Transcriptome resources for two highly divergent Silene latifolia populations\" in Genomic Resources Notes accepted 1 February 2015 – 31 March 2015

Peter Fields, Laura Weingartner & Lynda Delph
Here we have used next-generation Illumina sequencing to generate transcriptomes of four S. latifolia individuals from two morphologically divergent populations from disparate habitats, including including two females from Xativa, Spain and two males from Zagreb, Croatia. Spanish plants experience a much hotter, drier climate than Croatian plants, and the populations have ecologically relevant differences in floral and leaf characteristics (e.g., Spain has thicker leaves and produces fewer, larger flowers in comparison) (data not shown). This...

Reconstructing hotspots of genetic diversity from glacial refugia and subsequent dispersal in Italian common toads (Bufo bufo)

Andrea Chiocchio, Jan Arntzen, Iñigo Martínez-Solano, Wouter De Vries, Roberta Bisconti, Alice Pezzarossa, Luigi Maiorano & Daniele Canestrelli
Genetic diversity feeds the evolutionary process and allows populations to adapt to environmental changes. However, we still lack a thorough understanding of why hotspots of genetic diversity are so 'hot'. Here, we analysed the relative contribution of bioclimatic stability and genetic admixture between divergent lineages in shaping spatial patterns of genetic diversity in the common toad Bufo bufo along the Italian peninsula. We combined population genetic, phylogeographic and species distribution modelling (SDM) approaches to map...

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: \"Development of the draft genome sequence of the marbled flounder Pseudopleuronectes yokohamae as a reference of population genomic analysis\" in Genomic Resources Notes accepted 1 February 2015 – 31 March 2015

Yuki Minegishi, Minoru Ikeda, Lynda F. Delph, Laura A. Weingartner, Peter D. Fields, Laura Bertini, Carla Caruso, Silvia Proietti, Wolfgang Arthofer, Francesco Cicconardi, Heike Ritthammer, Birgit C. Schlick-Steiner, Florian M. Steiner, Gregor A. Wachter & Herbert C. Wagner
This article documents the public availability of the draft genome sequence data (raw reads, assembled contigs and unassembled reads) and RAD-tag read data of the marbled flounder Pseudopleuronectes yokohamae (Pleuronectiformes; Pleuronectidae).

Data from: \"A reduced representation libraries approach for nuclear marker development via 454 sequencing applied on Tetramorium (Hymenoptera: Formicidae)\" in Genomic Resources Notes Accepted 1 February 2015 to 31 March 2015

Herbert C. Wagner, Francesco Cicconardi, Gregor A. Wachter, Heike Ritthammer, Florian M. Steiner, Birgit C. Schlick-Steiner & Wolfgang Arthofer
To clarify species boundaries in the cryptic Tetramorium caespitum/impurum ant species complex, a multi-disciplinary approach is necessary. Nuclear DNA markers constitute one important step in species delimitation. We established a reduced representation library (RRL) based on amplified fragment-length polymorphism (AFLP) PCR products of four species. Amplicons were size-selected by gel-electrophoresis, DNA-fragments recovered from the agarose gels, and 454 libraries constructed by a commercial provider. Pyrosequencing yielded 490,155 reads, from which we designed cross-species amplifying primer...

Data from: Hybridization, natural selection and evolution of reproductive isolation: a 25-years survey of an artificial sympatric area between two mosquito sibling species of the Aedes mariae complex

Sandra Urbanelli, Daniele Porretta, Valentina Mastrantonio, Romeo Bellini, Giuseppe Pieraccini, Riccardo Romoli, Graziano Crasta & Giuseppe Nascetti
Natural selection can act against maladaptive hybridization between co-occurring divergent populations leading to evolution of reproductive isolation among them. A critical unanswered question about this process that provides a basis for the theory of speciation by reinforcement, is whether natural selection can cause hybridization rates to evolve to zero. Here we investigated this issue in two sibling mosquitoes species, Aedes mariae and Ae. zammitii, that show post-mating reproductive isolation (F1 males sterile) and partial pre-mating...

Data from: Evolution of pre-mating reproductive isolation among conspecific populations of the sea rock-pool beetle Ochthebius urbanelliae driven by reinforcing natural selection

Daniele Porretta & Sandra Urbanelli
How natural selection might be involved in speciation remains a fundamental question in evolutionary biology. When two or more species co-occur in the same areas, natural selection may favour divergence in mating traits. By acting in sympatric but not allopatric populations, natural selection can also affect mate choice within species and ultimately initiate speciation among conspecific populations. Here we address this potential effect in the sea rock-pool beetles Ochthebius quadricollis and O.urbanelliae. The two species,...

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