Celebrating 30 years of scholarly publishing at Pensoft! | Blog

“Openly accessible and digital-first since the very start, the ZooKeys journal was born on a sunny morning in California during the Entomological Society of America meeting in 2007, when Prof Lyubomir Penev and his renowned colleague Dr Terry Erwin from the Smithsonian Institution agreed over breakfast that zoologists from around the world could indeed use a new-age taxonomic journal. What the community at the time was missing was a scholarly outlet that would not only present a smooth fast track for their research papers, while abiding by the highest and most novel standards in the field, but do so freely and openly to any reader at any time and in any place. Fast forward to 2021, ZooKeys remains the most prolific open-access journal in zoology….”

 

CamoEvo: An open access toolbox for artificial camouflage evolution experiments – Hancock – – Evolution – Wiley Online Library

Abstract:  Camouflage research has long shaped our understanding of evolution by natural selection, and elucidating the mechanisms by which camouflage operates remains a key question in visual ecology. However, the vast diversity of colour patterns found in animals and their backgrounds, combined with the scope for complex interactions with receiver vision presents a fundamental challenge for investigating optimal camouflage strategies. Genetic algorithms have provided a potential method for accounting for these interactions, but with limited accessibility. Here, we present CamoEvo, an open-access toolbox for investigating camouflage pattern optimisation by using tailored genetic algorithms, animal and egg maculation theory and artificial predation experiments. This system allows for camouflage evolution within the span of just 10–30 generations (?1-2 min per generation), producing patterns that are both significantly harder to detect and that are optimised to their background. CamoEvo was built in ImageJ to allow for integration with an array of existing open access camouflage analysis tools. We provide guides for editing and adjusting the predation experiment and genetic algorithm as well as an example experiment. The speed and flexibility of this toolbox makes it adaptable for a wide range of computer based phenotype optimisation experiments.

 

First-of-its-kind global catalog of bird shapes yields ecological ‘gold mine’ | Science | AAAS

“Now, a team of 115 researchers from 30 countries, led by Sheard’s Ph.D. adviser, Imperial College London ecologist Joseph Tobias, has published anatomical measurements of all 11,009 living bird species—not just passerines such as robins, but everything from ducks and penguins to vultures and ostriches. “It’s a gold mine,” says geneticist Nancy Chen of the University of Rochester, who was not involved in the project.

The open-source data set, called AVONET, debuts this month in a special issue of Ecology Letters along with papers describing its value for studying bird evolution and ecology, as well as the impact of changes in climate and habitat on vulnerable species. “For the first time, we are gaining a global, quantitative perspective on bird biodiversity, which is really amazing,” says ecologist Brian Enquist of the University of Arizona….”

Assessing Open Science Practices in Phytolith Research

Abstract:  Open science is an integral part of all scientific research, but the extent of open science practices in phytolith research is unknown. Phytolith analysis examines silica bodies that are initially formed within and between plant cells during the life of the plant but become deposited in sediments once the plant dies. The use of phytoliths in archaeobotanical and palaeoecological studies has been increasing in recent years resulting in an upsurge in publications. The aims of this article are to assess open science practices in phytolith research by reviewing data and metadata sharing, and open access, in a sample of journal articles containing primary phytolith data from 16 prominent archaeological and palaeoecological journals (341 articles). This study builds on similar studies conducted for zooarchaeology (Kansa et al. 2020) and macro-botanical remains (Lodwick 2019). This study shows that 53% of papers shared data in any format but only 4% of papers contained reusable data, 74% included some pictures of phytolith morphotypes for identification purposes, 69% had a fully described method, 47% used the International code for phytolith nomenclature (ICPN 1.0) and only 13% of articles were open access. Steps forward are then proposed, including planning for open projects, making more articles openly accessible and implementing the FAIR data principles, to use as a starting point for discussions in the wider phytolith and archaeological communities to develop guidelines for greater integration of open science practices.

 

AVONET: morphological, ecological and geographical data for all birds – Tobias – 2022 – Ecology Letters – Wiley Online Library

Abstract:  Functional traits offer a rich quantitative framework for developing and testing theories in evolutionary biology, ecology and ecosystem science. However, the potential of functional traits to drive theoretical advances and refine models of global change can only be fully realised when species-level information is complete. Here we present the AVONET dataset containing comprehensive functional trait data for all birds, including six ecological variables, 11 continuous morphological traits, and information on range size and location. Raw morphological measurements are presented from 90,020 individuals of 11,009 extant bird species sampled from 181 countries. These data are also summarised as species averages in three taxonomic formats, allowing integration with a global phylogeny, geographical range maps, IUCN Red List data and the eBird citizen science database. The AVONET dataset provides the most detailed picture of continuous trait variation for any major radiation of organisms, offering a global template for testing hypotheses and exploring the evolutionary origins, structure and functioning of biodiversity.

 

Frontiers | Sounding the Call for a Global Library of Underwater Biological Sounds | Ecology and Evolution

Abstract:  Aquatic environments encompass the world’s most extensive habitats, rich with sounds produced by a diversity of animals. Passive acoustic monitoring (PAM) is an increasingly accessible remote sensing technology that uses hydrophones to listen to the underwater world and represents an unprecedented, non-invasive method to monitor underwater environments. This information can assist in the delineation of biologically important areas via detection of sound-producing species or characterization of ecosystem type and condition, inferred from the acoustic properties of the local soundscape. At a time when worldwide biodiversity is in significant decline and underwater soundscapes are being altered as a result of anthropogenic impacts, there is a need to document, quantify, and understand biotic sound sources–potentially before they disappear. A significant step toward these goals is the development of a web-based, open-access platform that provides: (1) a reference library of known and unknown biological sound sources (by integrating and expanding existing libraries around the world); (2) a data repository portal for annotated and unannotated audio recordings of single sources and of soundscapes; (3) a training platform for artificial intelligence algorithms for signal detection and classification; and (4) a citizen science-based application for public users. Although individually, these resources are often met on regional and taxa-specific scales, many are not sustained and, collectively, an enduring global database with an integrated platform has not been realized. We discuss the benefits such a program can provide, previous calls for global data-sharing and reference libraries, and the challenges that need to be overcome to bring together bio- and ecoacousticians, bioinformaticians, propagation experts, web engineers, and signal processing specialists (e.g., artificial intelligence) with the necessary support and funding to build a sustainable and scalable platform that could address the needs of all contributors and stakeholders into the future.

Dynamic visualisation of million?tip trees: The OneZoom project – Wong – – Methods in Ecology and Evolution – Wiley Online Library

Abstract:  

 

The complete tree of life is now available, but methods to visualise it are still needed to meet needs in research, teaching and science communication. Dynamic visualisation of million-tip trees requires many challenges in data synthesis, data handling and computer graphics to be overcome.
Our approach is to automate data processing, synthesise data from a wide range of available sources, then to feed these data to a client-side visualisation engine in parts. We develop a way to store the whole tree topology locally in a highly compressed form, then dynamically populate metadata such as text and images as the user explores.
The result is a seamless and smooth way to explore the complete tree of life, including images and metadata, even on relatively old mobile devices.
The underlying methods developed have applications that transcend tree of life visualisation. For the whole complete tree, we describe automated ID mappings between well known resources without resorting to taxonomic name resolution, automated methods to collate sets of public domain representative images for higher taxa, and an index to measure public interest of individual species.
The visualisation layout and the client user interface are both abstracted components of the codebase enabling other zoomable tree layouts to be swapped in, and supporting multiple applications including exhibition kiosks and digital art.
After 10 years of work, our tree of life explorer is now broadly complete, it has attracted nearly 1.5 million online users, and is backed by a novel long-term sustainability plan. We conclude our description of the OneZoom project by suggesting the next challenges that need to be solved in this field: extinct species and guided tours around the tree.”

“The Google Earth of Biology” – Visually Stunning Tree of All Known Life Unveiled Online

 

“The OneZoom explorer – available at onezoom.org – maps the connections between 2.2 million living species, the closest thing yet to a single view of all species known to science. The interactive tree of life allows users to zoom in to any species and explore its relationships with others, in a seamless visualisation on a single web page. The explorer also includes images of over 85,000 species, plus, where known, their vulnerability to extinction.

OneZoom was developed by Imperial College London biodiversity researcher Dr. James Rosindell and University of Oxford evolutionary biologist Dr. Yan Wong. In a paper published today in Methods in Ecology and Evolution, Drs Wong and Rosindell present the result of over ten years of work, gradually creating what they regard as “the Google Earth of biology.” …”

Dr. Wong added: “It’s extraordinary how much research there is still to be done. Building the OneZoom tree of life was only possible through sophisticated methods to gather and combine existing data – it would have been impossible to curate all this by hand.”

VectorBase.org Updates: Bioinformatic Resources for Invertebrate Vectors of Human Pathogens and Related Organisms – ScienceDirect

Abstract:  VectorBase (VectorBase.org) is part of the VEuPathDB Bioinformatics Resource Center, providing free online access to multi-omics and population biology data, focusing on arthropod vectors and invertebrates of importance to human health. VectorBase includes genomics and functional genomics data from bed bugs, biting midges, body lice, kissing bugs, mites, mosquitoes, sand flies, ticks, tsetse flies, stable flies, house flies, fruit flies, and a snail intermediate host. Tools include the Search Strategy system and MapVEu, enabling users to interrogate and visualize diverse ‘omics and population-level data using a graphical interface (no programming experience required). Users can also analyze their own private data, such as transcriptomic sequences, exploring their results in the context of other publicly-available information in the database. Help Desk: help@vectorbase.org.

 

 

Frontiers | The FAANG Data Portal: Global, Open-Access, “FAIR”, and Richly Validated Genotype to Phenotype Data for High-Quality Functional Annotation of Animal Genomes | Genetics

Abstract:  The Functional Annotation of ANimal Genomes (FAANG) project is a worldwide coordinated action creating high-quality functional annotation of farmed and companion animal genomes. The generation of a rich genome-to-phenome resource and supporting informatic infrastructure advances the scope of comparative genomics and furthers the understanding of functional elements. The project also provides terrestrial and aquatic animal agriculture community powerful resources for supporting improvements to farmed animal production, disease resistance, and genetic diversity. The FAANG Data Portal (https://data.faang.org) ensures Findable, Accessible, Interoperable and Reusable (FAIR) open access to the wealth of sample, sequencing, and analysis data produced by an ever-growing number of FAANG consortia. It is developed and maintained by the FAANG Data Coordination Centre (DCC) at the European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI). FAANG projects produce a standardised set of multi-omic assays with resulting data placed into a range of specialised open data archives. To ensure this data is easily findable and accessible by the community, the portal automatically identifies and collates all submitted FAANG data into a single easily searchable resource. The Data Portal supports direct download from the multiple underlying archives to enable seamless access to all FAANG data from within the portal itself. The portal provides a range of predefined filters, powerful predictive search, and a catalogue of sampling and analysis protocols and automatically identifies publications associated with any dataset. To ensure all FAANG data submissions are high-quality, the portal includes powerful contextual metadata validation and data submissions brokering to the underlying EMBL-EBI archives. The portal will incorporate extensive new technical infrastructure to effectively deliver and standardise FAANG’s shift to single-cellomics, cell atlases, pangenomes, and novel phenotypic prediction models. The Data Portal plays a key role for FAANG by supporting high-quality functional annotation of animal genomes, through open FAIR sharing of data, complete with standardised rich metadata. Future Data Portal features developed by the DCC will support new technological developments for continued improvement for FAANG projects.

 

Inside An Effort To Put Millions Of Biological Specimens Online : Shots – Health News : NPR

“For scientists to pull out detailed information like that, however, they first have to know that a particular specimen even exists. In 2011, the National Science Foundation started handing out grants as part of a ten-year push to bring old-fashioned collections into the Internet age. One of the goals was to put specimen records online and into a searchable portal called iDigBio….

Now, as that program winds down, he and other experts are pondering what needs to happen over the next decade so that biological collections can continue to become more accessible. That’s why the NSF recently asked for some advice from an expert panel convened by the National Academies of Sciences, Engineering, and Medicine.

One of its recommendations was simple: create a national registry of all collections, so experts know who’s got plants, microbes, or animals of interest.

The U.S. is thought to possess about 1,800 natural history collections, which is about a third of those that exist worldwide. In addition, the country has at least 2,800 “living stock” collections, such as microbe collections, which continually maintain living organisms for research….”

An open access dataset for developing automated detectors of Antarctic baleen whale sounds and performance evaluation of two commonly used detectors | Scientific Reports

Abstract:  Since 2001, hundreds of thousands of hours of underwater acoustic recordings have been made throughout the Southern Ocean south of 60° S. Detailed analysis of the occurrence of marine mammal sounds in these circumpolar recordings could provide novel insights into their ecology, but manual inspection of the entirety of all recordings would be prohibitively time consuming and expensive. Automated signal processing methods have now developed to the point that they can be applied to these data in a cost-effective manner. However training and evaluating the efficacy of these automated signal processing methods still requires a representative annotated library of sounds to identify the true presence and absence of different sound types. This work presents such a library of annotated recordings for the purpose of training and evaluating automated detectors of Antarctic blue and fin whale calls. Creation of the library has focused on the annotation of a representative sample of recordings to ensure that automated algorithms can be developed and tested across a broad range of instruments, locations, environmental conditions, and years. To demonstrate the utility of the library, we characterise the performance of two automated detection algorithms that have been commonly used to detect stereotyped calls of blue and fin whales. The availability of this library will facilitate development of improved detectors for the acoustic presence of Southern Ocean blue and fin whales. It can also be expanded upon to facilitate standardization of subsequent analysis of spatiotemporal trends in call-density of these circumpolar species.

 

 

A database of zooplankton biomass in Australian marine waters – PubMed

Abstract:  Zooplankton biomass data have been collected in Australian waters since the 1930s, yet most datasets have been unavailable to the research community. We have searched archives, scanned the primary and grey literature, and contacted researchers, to collate 49187 records of marine zooplankton biomass from waters around Australia (0-60°S, 110-160°E). Many of these datasets are relatively small, but when combined, they provide >85 years of zooplankton biomass data for Australian waters from 1932 to the present. Data have been standardised and all available metadata included. We have lodged this dataset with the Australian Ocean Data Network, allowing full public access. The Australian Zooplankton Biomass Database will be valuable for global change studies, research assessing trophic linkages, and for initialising and assessing biogeochemical and ecosystem models of lower trophic levels.

 

ZooArchNet: Connecting zooarchaeological specimens to the biodiversity and archaeology data networks

Abstract:  Interdisciplinary collaborations and data sharing are essential to addressing the long history of human-environmental interactions underlying the modern biodiversity crisis. Such collaborations are increasingly facilitated by, and dependent upon, sharing open access data from a variety of disciplinary communities and data sources, including those within biology, paleontology, and archaeology. Significant advances in biodiversity open data sharing have focused on neontological and paleontological specimen records, making available over a billion records through the Global Biodiversity Information Facility. But to date, less effort has been placed on the integration of important archaeological sources of biodiversity, such as zooarchaeological specimens. Zooarchaeological specimens are rich with both biological and cultural heritage data documenting nearly all phases of human interaction with animals and the surrounding environment through time, filling a critical gap between paleontological and neontological sources of data within biodiversity networks. Here we describe technical advances for mobilizing zooarchaeological specimen-specific biological and cultural data. In particular, we demonstrate adaptations in the workflow used by biodiversity publisher VertNet to mobilize Darwin Core formatted zooarchaeological data to the GBIF network. We also show how a linked open data approach can be used to connect existing biodiversity publishing mechanisms with archaeoinformatics publishing mechanisms through collaboration with the Open Context platform. Examples of ZooArchNet published datasets are used to show the efficacy of creating this critically needed bridge between biological and archaeological sources of open access data. These technical advances and efforts to support data publication are placed in the larger context of ZooarchNet, a new project meant to build community around new approaches to interconnect zoorchaeological data and knowledge across disciplines.