15 Works

Data from: Population structure of riverine and coastal dolphins Sotalia fluviatilis and Sotalia guianensis: PATTERNS of nuclear and mitochondrial diversity AND implications for conservation

Susana Caballero, Claudia Hollatz, Sebastian Rodríguez, Fernando Trujillo & C. Scott Baker
Coastal and freshwater cetaceans are particularly vulnerable due to their proximity to human activity, localized distributions and small home ranges. These species include Sotalia guianensis, found in the Atlantic and Caribbean coastal areas of central and South America, and Sotalia fluviatilis, distributed in the Amazon River and tributaries. We investigated the population structure and genetic diversity of these two species by analyses of mtDNA control region and 8-10 microsatellite loci. MtDNA analyses revealed strong regional...

Stable leaders pave the way for cooperation under time-dependent exploration rates

Flávio L. Pinheiro, Jorge M. Pacheco & Francisco C. Santos
The exploration of different behaviors is part of the adaptation repertoire of individuals to new environments. Here, we explore how the evolution of cooperative behavior is affected by the interplay between exploration dynamics and social learning, in particular when individuals engage on the Prisoner's Dilemma along the edges of a social network. We show that when the population undergoes a transition from strong to weak exploration rates a decline in the overall levels of cooperation...

Gaps in DNA sequence libraries for Macaronesian marine macroinvertebrates imply decades till completion and robust monitoring

Pedro Vieira, Ana Sofia Lavrador, Manuela Parente, Paola Parretti, Ana Costa, Filipe Costa & Sofia Duarte
Aim: DNA metabarcoding has great potential to improve biomonitoring in island’s marine ecosystems, which are highly vulnerable to global change and non-indigenous species (NIS) introductions. However, the depth and accuracy of the taxonomic identifications are largely dependent on reference libraries containing representative and reliable sequences for the targeted species. In this study, we evaluated the gaps in the availability of DNA sequences and their accuracy, for macroinvertebrates inhabiting Macaronesia’s shallow marine habitats. Location: Macaronesia (Azores,...

Data from: SNPs selected by information content outperform randomly selected microsatellite loci for delineating genetic identification and introgression in the endangered dark European honeybee (Apis mellifera mellifera)

Irene Muñoz, Dora Henriques, Laura Jara, J. Spencer Johnston, Julio Chávez-Galarza, Pilar De La Rúa & M. Alice Pinto
The honeybee (Apis mellifera) has been threatened by multiple factors, including pests and pathogens, pesticides, and loss of locally adapted gene complexes due to replacement and introgression. In western Europe, the genetic integrity of the native A.m. mellifera (M-lineage) is endangered due to trading and intensive queen breeding with commercial subspecies of eastern European ancestry (C-lineage). Effective conservation actions require reliable molecular tools to identify purebred A.m. mellifera colonies. Microsatellites have been preferred for identification...

Data from: Interplay between fungicides and parasites: tebuconazole, but not copper, suppresses infection in a Daphnia-Metschnikowia experimental model

Ana Patrícia Cuco, Nelson Abrantes, Fernando Gonçalves, Justyna Wolinska & Bruno B. Castro
Natural populations are commonly exposed to complex stress scenarios, including anthropogenic contamination and their biological enemies (e.g., parasites). The study of the pollutant-parasite interplay is especially important, given the need for adequate regulations to promote improved ecosystem protection. In this study, a host-parasite model system (Daphnia spp. and the microparasitic yeast Metschnikowia bicuspidata) was used to explore the reciprocal effects of contamination by common agrochemical fungicides (copper sulphate and tebuconazole) and parasite challenge. We conducted...

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...

Data from: Starting a DNA barcode reference library for shallow water polychaetes from the southern European Atlantic coast

Jorge Lobo, Marcos A. L. Teixeira, Luisa M. S. Borges, Maria S. G. Ferreira, Claudia Hollatz, Pedro T. Gomes, Ronaldo Sousa, Ascensão Ravara, Maria H. Costa & Filipe O. Costa
Annelid polychaetes have been seldom the focus of dedicated DNA barcoding studies, despite their ecological relevance and often dominance, particularly in soft-bottom estuarine and coastal marine ecosystems. Here, we report the first assessment of the performance of DNA barcodes in the discrimination of shallow water polychaete species from the southern European Atlantic coast, focusing on specimens collected in estuaries and coastal ecosystems of Portugal. We analysed cytochrome oxidase I DNA barcodes (COI-5P) from 164 specimens,...

Data from: Revisiting the Iberian honey bee (Apis mellifera iberiensis) contact zone: maternal and genome-wide nuclear variation provide support for secondary contact from historical refugia

M. Alice Pinto, Julio C. Chávez-Galarza, Dora Henriques, J. Spencer Johnston, Miguel Carneiro, José Rufino & John C. Patton
Dissecting diversity patterns of organisms endemic to Iberia has been truly challenging for a variety of taxa, and the Iberian honey bee is no exception. Surveys of genetic variation in the Iberian honey bee are among the most extensive for any honey bee subspecies. From these, differential and complex patterns of diversity have emerged, which have yet to be fully resolved. Here, we used a genome-wide data set of 309 neutrally tested single nucleotide polymorphisms...

Data from: Causal reasoning in rats' behaviour systems

Robert Ian Bowers & William Timberlake
Conceiving of stimuli and responses as causes and effects, and assuming that rats acquire representational models of causal relations from Pavlovian procedures, previous work by Causal Model Theory proponents attempted to train rat subjects to represent Light as a cause of both Tone and food. By these assumptions, with formal help from Bayesian Networks, self-production of the Tone should reduce expectation of alternative causes, including Light, and their effects, including food. Reduced feeder-directed responding to...

Towards a taxonomically unbiased EU Biodiversity Strategy for 2030

Stefano Mammola, Nicoletta Riccardi, Vincent Prié, Ricardo Correia, Pedro Cardoso, Manuel Lopes-Lima & Ronaldo Sousa
Through the Habitats Directive (92/43/EEC) and the LIFE projects financial investments, Europe has been the world’s experimental arena for biological conservation. With an estimated budget of €20 billion/year, the EU Biodiversity Strategy for 2030 has set an ambitious goal of reaching 30% Protected Areas and ensure no deterioration in conservation trends and status of all protected species. We analyzed LIFE projects focused on animals from 1992 to 2018 and we found that investment towards vertebrates...

Data from: DNA metabarcoding for high-throughput monitoring of estuarine macrobenthic communities

Jorge Lobo, Shadi Shokralla, Maria Helena Costa, Mehrdad Hajibabaei & Filipe Costa
Morphology-based profiling of benthic communities has been extensively applied to aquatic ecosystems' health assessment. However, it remains a low-throughput, and sometimes ambiguous, procedure. Despite DNA metabarcoding has been applied to marine benthos, a comprehensive approach providing species-level identifications for estuarine macrobenthos is still lacking. Here we report a combination of experimental and field studies to assess the aptitude of COI metabarcoding to provide robust species-level identifications for high-throughput monitoring of estuarine macrobenthos. To investigate the...

Data from: As time goes by: 20 years of changes in the aquatic macroinvertebrate metacommunity of Mediterranean river networks

Miguel Cañedo-Argüelles, Cayetano Guitiérrez-Cánovas, Raul Acosta, Daniel Castro, Núria Cid, Pau Fortuño, Antoni Munné, Cesc Múrria, Rita Rodrigues, Romain Sarremejane, Maria Soria, Pol Tarrats, Iraima Verkaik, Narcís Prat & Núria Bonada
Aim: to analyse temporal metacommunity dynamics in river networks in relation to hydrological conditions and dispersal. Location: 15 river reaches from the Llobregat, Besòs and Foix catchments in the North-Eastern Iberian Peninsula. Taxon: aquatic macroinvertebrates belonging to 99 different families. Methods: we sampled aquatic macroinvertebrate communities during spring in 20 consecutive years. We built two environmental distances (one related with water chemistry and another one with river flow regime) and two spatial distances (network distance...

Data from: A reliable DNA barcode reference library for the identification of the European shelf fish fauna

Thomas Knebelsberger, Gary R. Carvalho, Silke Laakmann, Michael J. Raupach, Hermann Neumann, Patrick D. Campbell, Monica Landi & Filipe O. Costa
Valid fish species identification is an essential step both for fundamental science and fisheries management. The traditional identification is mainly based on external morphological diagnostic characters, leading to inconsistent results in many cases. Here, we provide a sequence reference library based on mitochondrial cytochrome c oxidase subunit I (COI) for a valid identification of 93 North Atlantic fish species originating from the North Sea and adjacent waters, including many commercially exploited species. Neighbour-joining analysis based...

Data from: Magnetoliposomes containing magnesium ferrite nanoparticles as nanocarriers for the model drug curcumin

Beatriz D. Cardoso, Irina S.R. Rio, Ana Rita O. Rodrigues, Francisca C.T. Fernandes, Bernardo G. Almeida, Ana Pires, André M. Pereira, João P. Araújo, Elisabete M.S. Castanheira & Paulo J.G. Coutinho
Magnesium ferrite nanoparticles, with diameters around 25 nm, were synthesized by coprecipitation method. The magnetic properties indicate a superparamagnetic behavior, with a maximum magnetization of 16.2 emu/g, a coercive field of 22.1 Oe and a blocking temperature of 183.2 K. These MgFe2O4 nanoparticles were used to produce aqueous and solid magnetoliposomes, with sizes below 130 nm. The potential drug curcumin was successfully incorporated in these nanosystems, with high encapsulation efficiencies (above 89%). Interaction by fusion...

Data from: Developing reduced SNP assays from whole-genome sequence data to estimate introgression in an organism with complex genetic patterns, the Iberian honeybee (Apis mellifera iberiensis)

Dora Henriques, Melanie Parejo, Alain Vignal, David Wragg, Andreas Wallberg, Matthew Webster, M. Alice Pinto & Matthew T. Webster
The most important managed pollinator, the honeybee (Apis mellifera L.), has been subject to a growing number of threats. In Western Europe one such threat is large-scale introductions of commercial strains (C-lineage ancestry), which is leading to introgressive hybridization and even the local extinction of native honeybee populations (M-lineage ancestry). Here, we developed reduced assays of highly informative SNPs from 176 whole genomes to estimate C-lineage introgression in the most diverse and evolutionarily complex subspecies...

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