58 Works

Photosynthesis from stolen chloroplasts can support sea slug reproductive fitness

Paulo Cartaxana, Felisa Rey, Charlotte LeKieffre, Diana Lopes, Cedric Hubas, Jorge E. Spangenberg, Stéphane Escrig, Bruno Jesus, Gonçalo Calado, Rosário Domingues, Michael Kühl, Ricardo Calado, Anders Meibom & Sónia Cruz
Some sea slugs are able to steal functional chloroplasts (kleptoplasts) from their algal food sources, but the role and relevance of photosynthesis to the animal host remain controversial. While some researchers claim that kleptoplasts are slowly digestible ‘snacks’, others advocate that they enhance the overall fitness of sea slugs much more profoundly. Our analysis show light-dependent incorporation of 13C and 15N in the albumen gland and gonadal follicles of the sea slug Elysia timida, representing...

Pollination and plant reproductive success of two ploidy levels in red clover (Trifolium pratense L.)

Shuxuan Jing, Per Kryger, Bo Markussen & Birte Boelt
This dataset includes hand pollination, honey bee pollination and pollen germination experiments described in the article "Pollination and plant reproductive success of two ploidy levels in red clover (Trifolium pratense L.)", published in Frontiers in Plant Science (DOI: 10.3389/fpls.2021.720069). In a series of hand pollination experiments, the influence of visitation rate (10, 20, 40, 80 pollinated florets per flower head) on the seed number per pollinated floret and seed number per flower head were investigated,...

An approach for estimating haplotype diversity from sequences with unequal lengths

Ping Fan, Jon Fjeldså, Xuan Liu, Yafei Dong, Yongbin Chang, Yanhua Qu, Gang Song & Fumin Lei
1. Genetic diversity is an essential component of biodiversity. Developing robust quantification methods is critically important in depicting the genetic diversity underlying the geographical distributions of species, especially for the sequence data with unequal lengths. 2. Traditional calculation of genetic diversity depends on sequences of equal length. However, many homologous sequences downloaded from online repositories vary in length, posing a significant challenge to quantify the genetic diversity, especially haplotype diversity. We developed a new approach...

Speciation in the abyss - genomics and morphology reveal a new species of beaked whale

Emma L. Carroll, Michael R. McGowen, Morgan L. McCarthy, Felix G. Marx, Natacha Aguilar De Soto, Merel L. Dalebout, Sascha Dreyer, Oscar E. Gaggiotti, Sabine S. Hansen, Anton Van Helden, Aubrie B. Onoufriou, Robin W. Baird, C. Scott Baker, Simon Berrow, Danielle Cholewiak, Diane Claridge, Rochelle Constantine, Nicholas J. Davison, Catarina Eira, R. Ewan Fordyce, John Gatesy, G. J. Greg Hofmeyr, Vidal Martin, James G. Mead, Antonio A. Mignucci-Giannoni … & Morten T. Olsen
Earth’s deep oceans remains less well understood than the surface of Mars. Beaked whales (ziphiids) are among the most visible inhabitants of the abyss, due to their large size and worldwide distribution, yet their diversity and ecology remain obscure. We combine genomic and morphometric analyses to reveal a new Southern Hemisphere ziphiid species, Ramari’s beaked whale, Mesoplodon eueu, whose name is linked to the Indigenous people of the lands from which the species holotype and...

Analysis of independent cohorts of outbred CFW mice reveals novel loci for behavioral and physiological traits and identifies factors determining reproducibility

Jennifer Zou, Shyam Gopalakrishnan, Clarissa Parker, Jerome Nicod, Richard Mott, Na Cai, Arimantas Lionikas, Robert Davies, Abraham Palmer & Jonathan Flint
Combining samples for genetic association is standard practice in human genetic analysis of complex traits, but is rarely undertaken in rodent genetics. Here, using 23 phenotypes and genotypes from two independent laboratories, we obtained a sample size of 3,076 commercially available outbred mice and identified 70 loci, more than double the number of loci identified in the component studies. Fine-mapping in the combined sample reduced the number of likely causal variants, with a median reduction...

Phylogenetic analysis of HIV-1 shows frequent cross-country transmission and local population expansions

Marc Bennedbæk, Anna Zhukova, Man-Hung Eric Tang, Jaclyn Bennet, Paula Munderi, Kiat Ruxrungtham, Magnus Gisslen, Michael Worobey, Jens D Lundgren & Rasmus L Marvig
Understanding of pandemics depends on characterization of pathogen collections from well-defined and demographically diverse cohorts. Since its emergence in Congo almost a century ago, HIV-1 has geographically spread and genetically diversified into distinct viral subtypes. Phylogenetic analysis can be used to reconstruct the ancestry of the virus to inform on the origin and distribution of subtypes. We sequenced two 3.6 kb amplicons of HIV-1 genomes from 3,197 participants in a clinical trial with consistent and...

Raw data for predicting sample success for large-scale ancient DNA studies on marine mammals

Xénia Keighley & Morten Tange Olsen
In recent years, non-human ancient DNA studies have begun to focus on larger sample sizes and whole genomes, offering the potential to reveal exciting and hitherto unknown answers to ongoing biological and archaeological questions. However, one major limitation to the feasibility of such studies is the substantial financial and time investments still required during sample screening, due to uncertainty regarding successful sample selection. This study investigates the effect of a wide range of sample properties...

Drieschia sp. MicroCT-Scans for 3D reconstruction

Marc Christian Allentoft-Larsen, Brett C. Gonzalez, Joost Daniels, Kakani Katija, Karen Osborn & Katrine Worsaae
Annelids are predominantly found along the seafloor, but over time have colonised a vast diversity of habitats, such as the water column, where different modes of locomotion are necessary. Yet, little is known about their potential muscular adaptation to the continuously swimming required in the water column. The musculature and motility were examined for five scale worm species of Polynoidae (Aphroditiformia, Annelida) found in shallow waters, deep sea and caves that exhibit crawling, occasional swimming...

Gesiella jameensis MicroCT-scans for 3D reconstruction

Marc Christian Allentoft-Larsen, Brett C. Gonzalez, Joost Daniels, Kakani Katija, Karen Osborn & Katrine Worsaae
Annelids are predominantly found along the seafloor, but over time have colonised a vast diversity of habitats, such as the water column, where different modes of locomotion are necessary. Yet, little is known about their potential muscular adaptation to the continuously swimming required in the water column. The musculature and motility were examined for five scale worm species of Polynoidae (Aphroditiformia, Annelida) found in shallow waters, deep sea and caves that exhibit crawling, occasional swimming...

Genotyping by sequencing data of five legume tree species widespread in the rainforests of West and Central Africa

Rosalía Piñeiro, Olivier J Hardy, Carolina Tovar, Shyam Gopalakrishnan, Filipe Garrett Vieira & M. Thomas P. Gilbert
Although today the forest cover is continuous in Central Africa this may have not always been the case, as the scarce fossil record in this region suggests that arid conditions might have significantly reduced tree density during the Ice Ages. Our aim was to investigate whether the dry ice-age periods left a genetic signature on tree species that can be used to infer the date of the past fragmentation of the rainforest. We sequenced reduced...

Immune challenges increase network centrality in a queenless ant

Giacomo Alciatore, Line V. Ugelvig, Erik Frank, Jérémie Bidaux, Asaf Gal, Thomas Schmitt, Daniel J.C. Kronauer & Yuko Ulrich
Social animals display a wide range of behavioural defences against infectious diseases, some of which inherently increase social contacts with infectious individuals (e.g., mutual grooming), while others decrease them (e.g., social exclusion). These defences often rely on the detection of infectious individuals, but this can be achieved in several ways that are difficult to differentiate. Here, we combine non-pathogenic immune challenges with automated tracking in colonies of the clonal raider ant to ask whether ants...

Movement data of barnacle Chelonibia testudinaria

Benny Chan, Yue Him Wong, Nathan Robinson, , Sing-Pei Yu, Niklas Dreyer, I-Jiung Cheng, Jens T. Høeg & John D. Zardus
Movement is a fundamental characteristic of life, yet some taxa, such as barnacles, lose their capacity for locomotion as swimming larvae to become permanently affixed to a substratum as adults. Barnacles adopted this type of sessile life-stage at least 500 million years ago; however, we unequivocally confirm a prior report that the epizoic sea-turtle barnacle, Chelonibia testudinaria, has the capacity for self-directedlocomotion in the adult stage. We used time-series field and laboratory photographs to document...

The multidimensional nutritional niche of fungus-cultivar provisioning in free-ranging colonies of a neotropical leafcutter ant

Antonin Crumière, Aidan James, Pol Lannes, Sophie Mallett, Anders Michelsen, Riikka Rinnan & Jonathan Shik
Foraging trails of leafcutter colonies are iconic scenes in the Neotropics, with ants collecting freshly-cut plant fragments to provision a fungal food crop. We hypothesized that the fungus-cultivar’s requirements for macronutrients and minerals govern the foraging niche breadth of Atta colombica leafcutter ants. Analyses of plant fragments carried by foragers showed how nutrients from fruits, flowers, and leaves combine to maximize cultivar performance. While the most commonly foraged leaves delivered excess protein relative to the...

A tipping-point in carbon storage when forest expands into tundra is related to mycorrhizal recycling of nitrogen

Karina E Clemmensen, Mikael B Durling, Anders Michelsen, Sara Hallin, Roger D Finlay & Björn D Lindahl
Tundra ecosystems are global belowground sinks for atmospheric CO2. Ongoing warming-induced encroachment by shrubs and trees risks turning this sink into a CO2 source, resulting in a positive feedback on climate warming. To advance mechanistic understanding of how shifts in mycorrhizal types affect long-term carbon (C) and nitrogen (N) stocks, we studied small-scale soil depth profiles of fungal communities and C-N dynamics across a subarctic-alpine forest-heath vegetation gradient. Belowground organic stocks decreased abruptly at the...

IUCN Red List protects avian genetic diversity

Elisabetta Canteri, Damien Fordham, Sen Li, Peter Hosner, Carsten Rahbek & David Nogues-Bravo
Despite well-established links between low genetic diversity and extinction processes, intra-specific genetic diversity is rarely considered in global conservation assessments, potentially leading to biased estimates of species’ extinction risk. We show that birds ranked as “threatened” by the IUCN Red List have lower intra-specific genetic diversity than “non-threatened” species, confirming that threat criteria, used by the IUCN, effectively protect genetically depleted species. However, some “non-threatened” species harbour low levels of genetic diversity, indicating an undetected...

The biomolecular characterisation of a finger ring contextually dated to the emergence of the Early Neolithic from Syltholm, Denmark

Theis Jensen, Meaghan Mackie, Alberto Taurozzi, Liam Lannigan, Carsten Gundelach, Jesper Olsen, Søren Sørensen, Matthew Collins, Mikkel Sørensen & Hannes Schroeder
We present the analysis of an osseous finger ring from a predominantly early Neolithic context in Denmark. To characterise the artefact and identify the raw material used for its manufacture, we performed micro-computed tomography (Micro CT) scanning, zooarchaeology by mass spectrometry (ZooMS) peptide mass fingerprinting, as well as protein sequencing by liquid chromatography tandem mass spectrometry (LC-MS/MS). We conclude that the ring was made from long bone or antler due to the presence of osteons...

Green fluorescent protein-like pigments optimize the internal light environment in symbiotic reef building corals

Elena Bollati
Pigments homologous to the Green Fluorescent Protein (GFP) have been proposed to fine-tune the internal light microclimate of corals, facilitating photoacclimation of photosynthetic coral symbionts (Symbiodiniaceae) to life in different reef habitats and environmental conditions. However, direct measurements of the in vivo light conditions inside the coral tissue supporting this conclusion are lacking. Here, we quantified the intra-tissue spectral light environment of corals expressing GFP-like proteins from widely different light regimes. We focus on (1)...

Spatial reconstruction parameters for the atom probe analysis of common minerals

Denis Fougerouse, David Saxey, William Rickard, Steven Reddy & Rick Verberne

Antibody features towards VAR2CSA and CSA binding infected erythrocytes in a cohort of pregnant women from PNG

Elizabeth Aitken, Amaya Ortega-Pajares, Agersew Alemu, Wina Hasang, Saber Dini, Holger Unger, Maria Ome-Kaius, Morten Nielsen, Ali Salanti, Joe Smith, Stephen Kent, P Mark Hogarth, Bruce Wines, Julie Simpson, Timon Damelang, Amy Chung & Stephen Rogerson
Plasmodium falciparum causes placental malaria, which results in adverse outcomes for mother and child. P. falciparum infected erythrocytes that express the parasite protein VAR2CSA on their surface can bind to placental chondroitin sulfate-A. It has been hypothesized that naturally acquired antibodies towards VAR2CSA protect against placental infection, but it has proven difficult to use measures of antibody to identify individuals protected from disease. We used a systems serology approach to identify naturally acquired antibody features...

MERFISH measurements in the mouse ileum

Jeffrey Moffitt, Rosalind Xu, Peter Kharchenko, Viktor Petukhov, Paolo Cadinu, Ruslan Soldatov & Konstantin Khodosevich
Spatial transcriptomics protocols based on in situ sequencing or multiplexed RNA fluorescent hybridization can reveal detailed tissue organization. However, distinguishing the boundaries of individual cells in such data is challenging, and can hamper downstream analysis. Current methods generally approximate cells positions using nuclei stains. We describe a segmentation method, Baysor, which optimizes 2D or 3D cell boundaries considering joint likelihood of transcriptional composition and cell morphology. While Baysor can take into account segmentation based on...

Harmothoe imbricata MicroCT-scans for 3D reconstruction

Marc Christian Allentoft-Larsen, Brett C. Gonzalez, Joost Daniels, Kakani Katija, Karen Osborn & Katrine Worsaae
Annelids are predominantly found along the seafloor, but over time have colonised a vast diversity of habitats, such as the water column, where different modes of locomotion are necessary. Yet, little is known about their potential muscular adaptation to the continuously swimming required in the water column. The musculature and motility were examined for five scale worm species of Polynoidae (Aphroditiformia, Annelida) found in shallow waters, deep sea and caves that exhibit crawling, occasional swimming...

Microsatellite data from various African buffalo (Syncerus caffer) populations throughout Africa

Pim Van Hooft, Wayne Getz, Ben Greyling, Rasmus Heller, Knut Røed & Armanda Bastos
1280 African buffalo (Syncerus caffer) samples genotyped with up to 19 microsatellites. 1275 samples are from East (12 populations) and southern Africa (4 populations). 5 samples are from central Africa (2 populations).

Emergence and radiation of distemper viruses in terrestrial and marine mammals - Input files, bash and R codes for analysing PDV and CDV sequence data

Iben Stokholm, Wendy Puryear, Kaitlin Sawatzki, Steen Wilhelm Knudsen, Thilde Terkelsen, Paul Becher, Ursula Siebert & Morten Tange Olsen
Canine distemper virus (CDV) and phocine distemper virus (PDV) are major pathogens to terrestrial and marine mammals. Yet little is known about the timing and geographical origin of distemper viruses and to what extent it was influenced by environmental change and human activities. To address this, we i) performed the first comprehensive time-calibrated phylogenetic analysis of the two distemper viruses; ii) mapped distemper antibody and virus detection data from marine mammals collected between 1972-2018; iii)...

Non-invasive surveys of mammalian viruses using environmental DNA

Niccolò Alfano, Anisha Dayaram, Jan Axtner, Kyriakos Tsangaras, Marie-Louise Kampmann, Azlan Mohamed, Seth T. Wong, M. Thomas Gilbert, Andreas Wilting & Alex D. Greenwood
This dataset provides supplemental information to interpret the data published in Alfano & Dayaram et al. 2021. The study investigates how environmental DNA (eDNA) and invertebrate-derived DNA (iDNA) can be used to characterize the yet largely unknown virome present in mammalian wildlife. Environmental DNA and iDNA are used to survey biodiversity non-invasively to mitigate difficulties in obtaining wildlife samples, particularly in remote areas or for rare species. Recently, eDNA/iDNA were used to monitor known wildlife...

Data from: Biosystematics of Platanthera bifolia s.l. (Orchidaceae): Inferences from analysis of Scandinavian population samples

Henrik Æ. Pedersen & Conny Bruun Asmussen Lange
Over the years, various authors have (sub)divided the Eurasian moth pollinated Platanthera bifolia into several taxa. Advanced studies using multivariate morphometric analysis and/or genetic fingerprinting have all included regions where the situation appears particularly complex. With the aim to resolve variation patterns in a region where the situation seems less complex, we analysed morphometric and AFLP data from 13 Scandinavian populations using a range of uni- and multivariate statistical methods. Variation was largely continuous, though...

Registration Year

  • 2021
    58

Resource Types

  • Dataset
    58

Affiliations

  • University of Copenhagen
    58
  • Smithsonian Institution
    8
  • Monterey Bay Aquarium Research Institute
    7
  • Aarhus University
    4
  • The Arctic University of Norway
    3
  • University of Aveiro
    2
  • University of Lausanne
    2
  • University of Tasmania
    2
  • University of La Laguna
    2
  • University of Gothenburg
    2