Informational Interfaces: A case study of the impact of discovery systems on biodiversity research and search at the Natural History Museum, London, UK

The Natural History Museum is one of the world’s leading research institutions for biological diversity research with collections comprising some 8 million specimens representing a vast wealth of data. It also holds one of the foremost collections of biodiversity-related literature in its Library and Archives, with over one million items catalogued, ranging from artworks and historical manuscripts to born-digital material such as journal articles. This study investigates the impact of discovery systems on search and research at the Natural History Museum with the objectives: to determine exact attitudes to searching for biodiversity information resources using the Library and Archives discovery system and the Data Portal; to explore how biodiversity information is discovered and used through the discovery system; to examine the impact of discovery systems on search and research; and to document the transition toward a digital, networked and aggregated discovery system approach to managing biodiversity information. To date, this is the first case study of the implementation of a discovery system in a natural history museum library with a focus on biodiversity research

Local biodiversity is higher inside than outside terrestrial protected areas worldwide

Protected areas are widely considered essential for biodiversity conservation. However, few global studies have demonstrated that protection benefits a broad range of species. Using a new global biodiversity database with unprecedented geographic and taxonomic coverage, we compare four biodiversity measures at sites sampled in multiple land uses inside and outside protected areas. Globally, species richness is 10.7% higher and abundance 14.5% higher in samples taken inside protected areas compared to samples taken outside, but neither rarefaction-based richness nor endemicity differ significantly. Importantly, we show that the positive effects of protection are mostly attributable to differences in land use between protected and unprotected sites. Nonetheless, even within some human-dominated land uses, species richness and abundance are higher in protected sites. Our results reinforce the global importance of protected areas but suggest that protection does not consistently benefit species with small ranges or increase the variety of ecological niches

Land use and soil characteristics affect soil organisms differently from above-ground assemblages

Background: Land-use is a major driver of changes in biodiversity worldwide, but studies have overwhelmingly focused on above-ground taxa: the effects on soil biodiversity are less well known, despite the importance of soil organisms in ecosystem functioning. We modelled data from a global biodiversity database to compare how the abundance of soil-dwelling and above-ground organisms responded to land use and soil properties. Results: We found that land use affects overall abundance differently in soil and above-ground assemblages. The abundance of soil organisms was markedly lower in cropland and plantation habitats than in primary vegetation and pasture. Soil properties influenced the abundance of soil biota in ways that differed among land uses, suggesting they shape both abundance and its response to land use. Conclusions: Our results caution against assuming models or indicators derived from above-ground data can apply to soil assemblages and highlight the potential value of incorporating soil properties into biodiversity models

Nomenclatural Type Identification of Names in North African Tamarix (Tamaricaceae)

Tamarix is native to Eurasia plus the northern and southern territories of Africa, with some species being introduced into America and Oceania. They are usually found in arid, desertic, or subdesertic areas, often on saline or subsaline soils, in Mediterranean, temperate, or subtropical climates. The genus is renowned for its complex taxonomy, which is usually based on rather variable or unstable characters, which leads to contrasting taxonomic treatments. As part of the taxonomic revision of Tamarix undertaken by the authors, ten names (i.e., T. africana, T. bounopoea, T. brachystylis var. fluminensis, T. malenconiana, T. muluyana, T. tenuifolia, T. tingitana, T. trabutii, T. valdesquamigera, and T. weyleri) published from material collected in the southwestern parts of the Mediterranean basin are taxonomically and nomenclaturally discussed after analysing their original material. Eight intended holotypes are corrected here to lectotypes; one epitype is designated for T. africana to warrant current use of the name; and one isotype, 30 isolectotypes, and 11 syntypes are also identified for the studied names. Further, the taxonomic identity of all names and their eventual synonymic placement are accordingly discussed.This work was partly supported by the European Commission through the H2020 Research and Innovation Staff Exchange Programme, project 645636: ‘Insect-plant relationships: insights into biodiversity and new applications’ (FlyHigh); and by the grants UAUSTI19−08, UAUSTI21−04, UAUSTI22−05, UADIF21−29, UADIF22−28, VIGROB21−166, VIGROB22−166, ACIE18−03, ACIE21−01, and ACIE22−01, from diverse programmes of Universidad de Alicante

Mega-evolutionary dynamics of the adaptive radiation of birds

The origin and expansion of biological diversity is regulated by both developmental trajectories and limits on available ecological niches. As lineages diversify, an early and often rapid phase of species and trait proliferation gives way to evolutionary slow- downs as new species pack into ever more densely occupied regions of ecological niche space. Small clades such as Darwin’s finches demonstrate that natural selection is the driving force of adaptive radiations, but how microevolutionary processes scale up to shape the expansion of phenotypic diversity over much longer evolutionary timescales is unclear. Here we address this problem on a global scale by analysing a crowd-sourced dataset of three-dimensional scanned bill morphology from more than 2,000 species. We find that bill diversity expanded early in extant avian evolutionary history, before transitioning to a phase dominated by packing of morphological space. However, this early phenotypic diversification is decoupled from temporal variation in evolutionary rate: rates of bill evolution vary among lineages but are comparatively stable through time. We find that rare, but major, discontinuities in phenotype emerge from rapid increases in rate along single branches, sometimes leading to depauperate clades with unusual bill morphologies. Despite these jumps between groups, the major axes of within-group bill-shape evolution are remarkably consistent across birds. We reveal that macroevolutionary processes underlying global-scale adaptive radiations support Darwinian and Simpsonian ideas of microevolution within adaptive zones and accelerated evolution between distinct adaptive peaks

Shedding new light on the origin and spread of the brinjal eggplant (Solanum melongena L.; Solanaceae) and its wild relatives

• While brinjal eggplant (Solanum melongena L.) is the second most important solanaceaous vegetable crop, we lack firm knowledge of its evolutionary relationships. This in turn limits efficient use of crop wild relatives in eggplant improvement. Here, we examine the hypothesis of linear step-wise expansion of the eggplant group from Africa to Asia. • We use museum collections to generate nuclear and full-plastome data for all species of the eggplant clade. We combine a phylogenomic approach with distribution data to infer a biogeographic scenario for the clade. • The eggplant clade has Pleistocene origins in northern Africa. Dispersions to tropical Asia gave rise to Solanum insanum, the wild progenitor of the eggplant, and to Africa distinct lineages of widespread and southern-African species. Results suggest that spread of species to southern Africa is recent and was likely facilitated by large mammal herbivores feeding on Solanum fruits (African elephant, impala). • Rather than a linear ‘Out Of Africa’ sequence, our results are more consistent with an initial event into Asia, and subsequent wide dispersion and differentiation across Africa driven by large mammalian herbivores. Our evolutionary results will impact future work on eggplant domestication and use of wild relatives in breeding of this increasingly important solanaceous crop.Peer reviewe

The Finnish Biodiversity Information Facility as a best-practice model for biodiversity data infrastructures

Biodiversity informatics has advanced rapidly with the maturation of major biodiversity data infrastructures (BDDIs), such as the Global Biodiversity Information Facility sharing unprecedented data volumes. Nevertheless, taxonomic, temporal and spatial data coverage remains unsatisfactory. With an increasing data need, the global BDDIs require continuous inflow from local data mobilisation, and national BDDIs are being developed around the world. The global BDDIs are specialised in certain data types or data life cycle stages which, despite possible merits, renders the BDDI landscape fragmented and complex. That this often is repeated at the national level creates counterproductive redundancy, complicates user services, and frustrates funders. Here, we present the Finnish Biodiversity Information Facility (FinBIF) as a model of an all-inclusive BDDI. It integrates relevant data types and phases of the data life cycle, manages them under one IT architecture, and distributes the data through one service portal under one brand. FinBIF has experienced diverse funder engagement and rapid user uptake. Therefore, we suggest the integrated and inclusive approach be adopted in national BDDI development.peerReviewe

Towards the analysis of coral skeletal density-banding using deep learning

Abstract: X-ray micro–computed tomography (µCT) is increasingly used to record the skeletal growth banding of corals. However, the wealth of data generated is time consuming to analyse for growth rates and colony age. Here we test an artificial intelligence (AI) approach to assist the expert identification of annual density boundaries in small colonies of massive Porites spanning decades. A convolutional neural network (CNN) was trained with µCT images combined with manually labelled ground truths to learn banding-related features. The CNN successfully predicted the position of density boundaries in independent images not used in training. Linear extension rates derived from CNN-based outputs and the traditional method were consistent. In the future, well-resolved 2D density boundaries from AI can be used to reconstruct density surfaces and enable studies focused on variations in rugosity and growth gradients across colony 3D space. We recommend the development of a community platform to share annotated images for AI.Copyright © The Author(s) 2021. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The linked document is the published version of the article.NHM Repositor

Crop wild relatives of the brinjal eggplant ( Solanum melongena ): Poorly represented in genebanks and many species at risk of extinction

This is the publisher's Early View pdf without final pagination .© 2016 Botanical Society of America. This is an open access article, available to all readers online, published under a creative commons license. The attached file is the published version of the article

New names and status for Pacific spiny species of Solanum (Solanaceae, subgenus Leptostemonum Bitter; the Leptostemonum Clade)

Five new species of spiny solanums (Solanum subgenus Leptostemonum Bitter; the Leptostemonum Clade) are described from the islands of the Pacific. Two of the new species are from Fiji (S. pseudopedunculatum D.McClelland, sp. nov. and S. ratale D.McClelland, sp. nov.), two from New Caledonia (S. memoayanum D.McClelland, sp. nov. and S. semisucculentum D.McClelland, sp. nov.), one from Papua New Guinea (S. labyrinthinum D.McClelland, sp. nov.) and another from Vanuatu (S. vanuatuense D.McClelland, sp. nov.). A new status and combination is provided for the rare Hawaiian endemic S. caumii (F.Br.) D.McClelland, comb. et stat. nov. and a new type designated for S. peekelii Bitter of Papua New Guinea, for which a description is also provided. All species are illustrated with digitized herbarium specimens, mapped and have been assigned a preliminary conservation status using current IUCN guidelines. Details of all specimens examined are provided in a Suppl. materials 1: file SM1.This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.NHM Repositor