10 Works

Image-based taxonomic classification of bulk biodiversity samples using deep learning and domain adaptation

Tomochika Fujisawa, Víctor Noguerales, Emmanouil Meramveliotakis, Anna Papadopoulou & Alfried Vogler
Complex bulk samples of invertebrates from biodiversity surveys present a great challenge for taxonomic identification, especially if obtained from unexplored ecosystems. High-throughput imaging combined with machine learning for rapid classification could overcome this bottleneck. Developing such procedures requires that taxonomic labels from an existing source data set are used for model training and prediction of an unknown target sample. Yet the feasibility of transfer learning for the classification of unknown samples remains to be tested....

Chemical and Mineralogical analysis, SEM images and elemental diffusion timescales

Chiara M Petrone
Major and trace elements data for whole rock and clinopyroxene; major elements data for glassy groundmasses; BSE (back-scattered electron) images of clinopyroxene; Fe-Mg elemental diffusion timescales of clinopyroxene; LA-ICP-MS chemical maps of clinopyroxene.

Data from: Community assembly and metaphylogeography of soil biodiversity: insights from haplotype-level community DNA metabarcoding within an oceanic island

Carmelo Andújar Fernández, Paula Arribas, Heriberto López, Yurena Arjona, Antonio José Pérez-Delgado, Pedro Oromí, Alfried P. Vogler & Brent C. Emerson
Most of our understanding of island diversity comes from the study of aboveground systems, while the patterns and processes of diversification and community assembly for belowground biotas remain poorly understood. Here we take advantage of a relatively young and dynamic oceanic island to advance our understanding of eco-evolutionary processes driving community assembly within soil mesofauna. Using whole organism community DNA (wocDNA) metabarcoding and the recently developed metaMATE pipeline, we have generated spatially explicit and reliable...

The life and times of Pteridinium simplex

Simon Darroch, Brandt Gibson, Maggie Syversen, Imran Rahman, Rachel Racicot, Frances Dunn, Susana Gutarra-Diaz, Eberhard Schindler, Achim Wehrmann & Marc Laflamme
Pteridinium simplex is an iconic erniettomorph taxon best known from late Ediacaran successions in South Australia, Russia, and Namibia. Despite nearly 100 years of study, there remain fundamental questions surrounding the paleobiology and -ecology of this organism, including it’s life position relative the sediment-water interface, and how it fed and functioned within benthic communities. Here, we combine a re-description of specimens housed at the Senckenberg Forschungsinstitut und Naturmuseum Frankfurt with field observations of fossiliferous surfaces...

SYNTHESYS3 Deliverable report D4.1 \"Developing edge detection technology for natural history images\"

Lawrence Hudson, Laurence Livermore & Vladimir Blagoderov

Individual repeatability of avian migration phenology: a systematic review and meta-analysis

Kirsty Franklin, Malcolm Nicoll, Simon Butler, Ken Norris, Norman Ratcliffe, Shinichi Nakagawa & Jennifer Gill
Changes in phenology and distribution are being widely reported for many migratory species in response to shifting environmental conditions. Understanding these changes and the situations in which they occur can be aided by understanding consistent individual differences in phenology and distribution and the situations in which consistency varies in strength or detectability. Studies tracking the same individuals over consecutive years are increasingly reporting migratory timings to be a repeatable trait, suggesting that flexible individual responses...

Bemisia tabaci cryptic species: supplementary materials

Norman MacLeod, Roy Canty & Andrew Polaszek
This archive contains supplementary materials relating to the investigation of morphological differences in Bemisia tabcai puparia as rescribed in MacLeod, N., Canty, R.J., and Polazek, A., 2022, Morphology-based identification of Bemisia tabaci cryptic species puparia via embedded group-contrast convolution neural network analysis: Systematic Biology. The materials archived include (1) and inventory of all puparial images, (2) full sets of results files for the image-based t-SNE and embedded, group-contrasts CNN analyses, (3) Wolfram Mathematical™ scripting code...

First large-scale quantification study of DNA preservation in insects from natural history collections using genome-wide sequencing

Victoria Elizabeth Mullin, William Stephen, Andres Arce, Will Nash, Calum Raine, David Notton, Ashleigh Whiffin, Vladimir Blagoderov, Karim Gharbi, James Hogan, Tony Hunter, Naomi Irish, Simon Jackson, Steve Judd, Chris Watkins, Wilfried Haerty, Jeff Ollerton, Selina Brace, Richard Gill & Ian Barnes
Insect declines are a global issue with significant ecological and economic ramifications. Yet we have a poor understanding of the genomic impact these losses can have. Genome-wide data from historical specimens has the potential to provide baselines of population genetic measures to study population change, with natural history collections representing large repositories of such specimens. However, an initial challenge in conducting historical DNA data analyses, is to understand how molecular preservation varies between specimens. Here,...

DiSSCo Prepare Deliverable report D5.1 \"DiSSCo Knowledgebase for technical development\"

Sabine von Mering, Julia Pim Reis & Mareike Petersen

Scan files, 3D reconstructions, data spreadsheet and supplementary files for Heterochrony and parallel evolution of echinoderm, hemichordate and cephalochordate internal bars

Nidia Álvarez Armada, Christopher Cameron, Jennifer Bauer & Imran Rahman
Deuterostomes comprise three phyla with radically different body plans. Phylogenetic bracketing of the living deuterostome clades suggests the latest common ancestor of echinoderms, hemichordates and chordates was a bilaterally symmetrical worm with pharyngeal openings, with these characters lost in echinoderms. Early fossil echinoderms with pharyngeal openings have been described, but their interpretation is highly controversial. Here, we critically evaluate the evidence for pharyngeal structures (gill bars) in the extinct stylophoran echinoderms Lagynocystis pyramidalis and Jaekelocarpus...

Registration Year

  • 2022
    10

Resource Types

  • Dataset
    8
  • Text
    2

Affiliations

  • Natural History Museum
    10
  • Instituto de Productos Naturales y Agrobiología
    2
  • University of Oxford
    2
  • Tullie House Museum and Art Gallery
    1
  • Botanic Garden and Botanical Museum Berlin
    1
  • University of Michigan–Ann Arbor
    1
  • University of Montreal
    1
  • Earlham Institute
    1
  • University of Suffolk
    1
  • University of La Laguna
    1