Scientometric Study of The Research Performance on Biodiversity: The Global Perspective

This paper examines on scientometric study of the research performance on biodiversity with the data that have been collected from Web of Science database. The study period was chosen from 2011 to 2020 and retrieved 11902 records for the study. This study was planned to find out year-wise publications on biodiversity research from 2011 to 2020, to examine authorship patterns, to find out the top twenty authors contributions, to find out top twenty institutions that contributed to biodiversity research, to find top twenty sources contributions and to identify top twenty countries contributed on biodiversity research. It was found that the year-wise biodiversity research publications show an increase trend. Among the 17 different document types, in the form of research articles have 9102 papers. Out of the 40843 authors, Schmidt B has occupied the first position with 56 contributed papers. 97.46% papers were contributed by collaborative authors, and very least number of papers published by single authors’. Totally 178 countries were contributed on biodiversity research publications, amongst India is the fifteenth place with 407 publications.

Sharing taxonomic expertise between natural history collections using image recognition

Natural history collections play a vital role in biodiversity research and conservation by providing a window to the past. The usefulness of the vast amount of historical data depends on their quality, with correct taxonomic identifications being the most critical. The identification of many of the objects of natural history collections, however, is wanting, doubtful or outdated. Providing correct identifications is difficult given the sheer number of objects and the scarcity of expertise. Here we outline the construction of an ecosystem for the collaborative development and exchange of image recognition algorithms designed to support the identification of objects. Such an ecosystem will facilitate sharing taxonomic expertise among institutions by offering image datasets that are correctly identified by their in-house taxonomic experts. Together with openly accessible machine learning algorithms and easy to use workbenches, this will allow other institutes to train image recognition algorithms and thereby compensate for the lacking expertise.

Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR

Threats to global biodiversity are increasingly recognised by scientists and the public as a critical challenge. Molecular sequencing technologies offer means to catalogue, explore, and monitor the richness and biogeography of life on Earth. However, exploiting their full potential requires tools that connect biodiversity infrastructures and resources. As a research infrastructure developing services and technical solutions that help integrate and coordinate life science resources across Europe, ELIXIR is a key player. To identify opportunities, highlight priorities, and aid strategic thinking, here we survey approaches by which molecular technologies help inform understanding of biodiversity. We detail example use cases to highlight how DNA sequencing is: resolving taxonomic issues; Increasing knowledge of marine biodiversity; helping understand how agriculture and biodiversity are critically linked; and playing an essential role in ecological studies. Together with examples of national biodiversity programmes, the use cases show where progress is being made but also highlight common challenges and opportunities for future enhancement of underlying technologies and services that connect molecular and wider biodiversity domains. Based on emerging themes, we propose key recommendations to guide future funding for biodiversity research: biodiversity and bioinformatic infrastructures need to collaborate closely and strategically; taxonomic efforts need to be aligned and harmonised across domains; metadata needs to be standardised and common data management approaches widely adopted; current approaches need to be scaled up dramatically to address the anticipated explosion of molecular data; bioinformatics support for biodiversity research needs to be enabled and sustained; training for end users of biodiversity research infrastructures needs to be prioritised; and community initiatives need to be proactive and focused on enabling solutions. For sequencing data to deliver their full potential they must be connected to knowledge: together, molecular sequence data collection initiatives and biodiversity research infrastructures can advance global efforts to prevent further decline of Earth’s biodiversity.

PhyloHerb: A phylogenomic pipeline for processing genome skimming data for plants

Premise of the study: The application of high throughput sequencing, especially to herbarium specimens, is greatly accelerating biodiversity research. Among various techniques, low coverage Illumina sequencing of total genomic DNA (genome skimming) can simultaneously recover the plastid, mitochondrial, and nuclear ribosomal regions across hundreds of species. Here, we introduce PhyloHerb -- a bioinformatic pipeline to efficiently and effectively assemble phylogenomic datasets derived from genome skimming. Methods and Results: PhyloHerb uses either a built-in database or user-specified references to extract orthologous sequences using BLAST search. It outputs FASTA files and offers a suite of utility functions to assist with alignment, data partitioning, concatenation, and phylogeny inference. The program is freely available at https://github.com/lmcai/PhyloHerb/. Conclusions: Using published data from Clusiaceae, we demonstrated that PhyloHerb can accurately identify genes using highly fragmented assemblies derived from sequencing older herbarium specimens. Our approach is effective at all taxonomic depths and is scalable to thousands of species.

ADDITIONS TO THE FLORA OF THE REPUBLIC OF MORDOVIA, RUSSIA

The biodiversity conservation is based on our knowledge of the complete composition of plants and animals within a certain area. In this paper, we present data of biodiversity research in the Republic of Mordovia (European Russia). The obtained results are reflected in six vascular plant found for the first time in the studied region. Of them, four alien taxa (Philadelphus coronarius, Rosa x majorugosa, Spiraea japonica, Syringa josikaea) are known only in the Mordovia State Nature Reserve now. This underlines the need paying our attention to alien plants that escape into the wild (naturalize) in the least disturbed ecosystems of this Protected Area. The Urtica galeopsiifolia distribution needs to be clarified in more details because of its similarity to the widely known Urtica dioica. Thus, a majority of the species under discussion are alien plants considered as cultivated plants escaping in the wild. Taking into account the newly revealed species, the vascular plant flora of the Republic of Mordovia currently includes 1,472 species. In this study, we propose the continuing the study of man-made habitats in terms of accidentally or intentionally introduced alien species, as well as the searching of hidden taxa, such as Urtica galeopsiifolia found in this study.

BioBlitz is More than a Bit of Fun

Emerging in the 1990s, bioblitzes have become flagship events for biodiversity assessments. Although the format varies, a bioblitz is generally an intensive, short-term survey in a specific area. Bioblitzes collect biodiversity data and can therefore play a role in research, discovery of new species at a site and monitoring. They may also promote public engagement, community building, and education and outreach. However, the question remains, how effective are bioblitzes at achieving these goals? To evaluate the value of bioblitzes for these multiple goals, we conducted two meta-analyses, one on sixty published bioblitzes and the other on 1860 bioblitzes conducted using iNaturalist. Furthermore, we made an in-depth analysis of the data collected during a bioblitz we organized ourselves. From these analyses we found bioblitzes are effective at gathering data—collecting on average more than 300 species records—despite limitations of bias, which many types of biodiversity surveys suffer from, such as preferences for charismatic taxa, and uneven sampling effort in time and space. However, because the survey intensity, duration and extent are more controlled, a bioblitz is more repeatable than some other forms of survey. We also found that bioblitzes were highly effective at engaging people in sustained activity after they participated in a bioblitz. A bioblitz may therefore act as a trigger for participation in biological recording, which is supported by the use of technology, particularly smartphone apps. Another important aspect is the involvement of both citizen scientists and professional biologists, creating learning opportunities in both directions. Indeed, it was clear that many bioblitzes acted as brokerage events between individuals and organizations, and between professionals who work in biodiversity research and conservation. Such community building is important for communication and building trust between organizations and citizens to the benefit of biodiversity research and conservation. From the impartial perspective of hypothesis-driven science, bioblitzes may seem like a lot of work with limited scientific gain. However, this largely overlooks how important people, communities and their organizations are in gathering data, and in conserving biodiversity.