Data from: Computer assisted detection of axonal bouton structural plasticity in in vivo time-lapse imagesRohan Gala, Daniel Lebrecht, Daniela A. Sahlender, Anne Jorstad, Graham Knott, Anthony Holtmaat & Armen Stepanyants
The ability to measure minute structural changes in neural circuits is essential for long-term in vivo imaging studies. Here, we propose a methodology for detection and measurement of structural changes in axonal boutons imaged with time-lapse two-photon laser scanning microscopy (2PLSM). Correlative 2PLSM and 3D electron microscopy (EM) analysis, performed in mouse barrel cortex, showed that the proposed method has low fractions of false positive/negative bouton detections (2/0 out of 18), and that 2PLSM-based bouton...
Data from: The effect of bioturbation by polychaetes (Opheliidae) on benthic foraminiferal assemblages and test preservationJosé N. Pérez-Asensio, Julio Aguirre & Francisco J. Rodríguez-Tovar
Biological activity such as burrowing can alter benthic foraminiferal shell preservation and may also modify benthic foraminiferal assemblages by vertical mixing, inducing sediment homogenization. Here, we analyse benthic foraminiferal assemblages and taphonomy of upper Miocene marine deposits from Conil de la Frontera (Cádiz, south-western Spain). The deposits consist of marls displaying a pervasive alternation of intensively bioturbated beds dominated by Macaronichnus segregatis traces (ichnofabric index 4–5) and non-bioturbated beds. Benthic foraminiferal assemblages are dominated by...
Current biodiversity assessment and biomonitoring are largely based on the morphological identification of selected bioindicator taxa. Recently, several attempts have been made to use eDNA metabarcoding as an alternative tool. However, until now, most applied metabarcoding studies have been based on the taxonomic assignment of sequences that provides reference to morphospecies ecology. Usually, only a small portion of metabarcoding data can be used due to a limited reference database and a lack of phylogenetic resolution....
Data from: Trunk dental tissue evolved independently from underlying dermal bony plates but is associated to surface bones in living odontode-bearing catfishCarlos J. Rivera-Rivera & Juan I. Montoya-Burgos
Although oral dental tissue is a vertebrate attribute, trunk dental tissue evolved in several extinct vertebrate lineages but is rare among living species. The question of which processes trigger dental-tissue formation in the trunk remains open, and would shed light on odontogenesis evolution. Extra-oral dental structures (odontodes) in the trunk are associated with underlying dermal bony plates, leading us to ask whether the formation of trunk bony plates is necessary for trunk odontodes to emerge....
Data from: Testing the applicability of a benthic foraminiferal-based transfer function for the reconstruction of paleowater depth changes in Rhodes (Greece) during the early PleistoceneYvonne Milker, Manuel F.G. Weinkauf, Jürgen Titschack, Andre Freiwald, Stefan Krüger, Frans J. Jorissen, Gerhard Schmiedl & Manuel F. G. Weinkauf
We present paleo-water depth reconstructions for the Pefka E section deposited on the island of Rhodes (Greece) during the early Pleistocene. For these reconstructions, a transfer function (TF) using modern benthic foraminifera surface samples from the Adriatic and Western Mediterranean Seas has been developed. The TF model gives an overall predictive accuracy of ~50 m over a water depth range of ~1200 m. Two separate TF models for shallower and deeper water depth ranges indicate...
Data from: The population genomics of archaeological transition in west Iberia: investigation of ancient substructure using imputation and haplotype-based methodsRui Martiniano, Lara M. Cassidy, Ros Ó'Maoldúin, Russell McLaughlin, Nuno M. Silva, Licinio Manco, Daniel Fidalgo, Tania Pereira, Maria J. Coelho, Miguel Serra, Joachim Burger, Rui Parreira, Elena Moran, Antonio C. Valera, Eduardo Porfirio, Rui Boaventura, Ana M. Silva & Daniel G. Bradley
We analyse new genomic data (0.05–2.95x) from 14 ancient individuals from Portugal distributed from the Middle Neolithic (4200–3500 BC) to the Middle Bronze Age (1740–1430 BC) and impute genomewide diploid genotypes in these together with published ancient Eurasians. While discontinuity is evident in the transition to agriculture across the region, sensitive haplotype-based analyses suggest a significant degree of local hunter-gatherer contribution to later Iberian Neolithic populations. A more subtle genetic influx is also apparent in...
Data from: Hummingbird pollination and the diversification of angiosperms: an old and successful association in GesneriaceaeMartha Liliana Serrano-Serrano, Jonathan Rolland, John Clark, Nicolas Salamin & Mathieu Perret
The effects of specific functional groups of pollinators in the diversification of angiosperms are still to be elucidated. We investigated whether the pollination shifts or the specific association with hummingbirds affected the diversification of a highly diverse angiosperm lineage in the Neotropics. We reconstructed a phylogeny of 583 species from the Gesneriaceae family and detected diversification shifts through time, inferred the timing and amount of transitions among pollinator functional groups, and tested the association between...
Premise of the study: Despite the extensive phenotypic variation that characterizes the Gesneriaceae family, there is a lack of genomic resources to investigate the molecular basis of their diversity. We developed and compared the transcriptomes for two species of the Neotropical lineage of the Gesneriaceae. Methods and Results: Illumina sequencing and de novo assembly of floral and leaf samples were used to generate multigene sequence data for Sinningia eumorpha and S. magnifica, two species endemic...
Data from: Positive selection on sperm ion channels in a brooding brittle star: consequence of life-history traits evolutionAlexandra A. T. Weber, Laurent Abi-Rached, Nicolas Galtier, Aurélien Bernard, Juan I. Montoya-Burgos, Anne Chenuil & A. A.-T. Weber
Closely related species are key models to investigate mechanisms leading to reproductive isolation and early stages of diversification, also at the genomic level. The brittle star cryptic species complex Ophioderma longicauda encompasses the sympatric broadcast spawning species C3 and the internal brooding species C5. Here we used de novo transcriptome sequencing and assembly in two closely related species displaying contrasting reproductive modes to compare their genetic diversity and to investigate the role of natural selection...
Contact zones between ecotypes are windows for understanding how species may react to climate changes. Here, we analysed the fine-scale genetic and morphological variation in harbour porpoises (Phocoena phocoena) around the UK by genotyping 591 stranded animals at nine microsatellite loci. The data were integrated with a prior study to map at high resolution the contact zone between two previously identified ecotypes meeting in the northern Bay of Biscay. Clustering and spatial analyses revealed that...
Data from: A web platform for landuse, climate, demography, hydrology and beach erosion in the Black Sea catchmentAnthony Lehmann, Yaniss Guigoz, Nicolas Ray, Emanuele Mancuso, Karim C. Abbaspour, Elham Rouholahnejad Freund, Karin Allenbach, Andrea De Bono, Marc Fasel, Ana Gago-Silva, Roger Bär, Pierre Lacroix & Grégory Giuliani
The Black Sea catchment (BSC) is facing important demographic, climatic and landuse changes that may increase pollution, vulnerability and scarcity of water resources, as well as beach erosion through sea level rise. Limited access to reliable time-series monitoring data from environmental, statistical, and socio-economical sources is a major barrier to policy development and decision-making. To address these issues, a web-based platform was developed to enable discovery and access to key environmental information for the region....
University of Geneva11
University of Lausanne2
Swiss Institute of Bioinformatics1
University of Hamburg1
Swiss Federal Institute of Aquatic Science and Technology1
Institut de Recherche et Coordination Acoustique Musique1
University of Groningen1
University of Algarve1
University of Lisbon1
Johannes Gutenberg University of Mainz1