scholarly journals Applying computer vision to digitised natural history collections for climate change research: temperature-size responses in British butterflies

2021 ◽  
Author(s):  
Rebecca J Wilson ◽  
Alexandre F de Siqueira ◽  
Stephen J Brooks ◽  
Benjamin W Price ◽  
Lea M Simon ◽  
...  
Keyword(s):  
Climate Change ◽  
Computer Vision ◽  
Natural History ◽  
Global Change ◽  
Adult Size ◽  
Phenotypic Data ◽  
Climate Change Research ◽  
Biotic Response ◽  
Natural History Collections ◽  
Global Change Research

Natural history collections (NHCs) are invaluable resources for understanding biotic response to global change. Museums around the world are currently imaging specimens, capturing specimen data, and making them freely available online. In parallel to the digitisation effort, there have been great advancements in computer vision (CV): the computer trained automated recognition/detection, and measurement of features in digital images. Applying CV to digitised NHCs has the potential to greatly accelerate the use of NHCs for biotic response to global change research. In this paper, we apply CV to a very large, digitised collection to test hypotheses in an established area of biotic response to climate change research: temperature-size responses. We develop a CV pipeline (Mothra) and apply it to the NHM iCollections of British butterflies (>180,000 specimens). Mothra automatically detects the specimen in the image, sets the scale, measures wing features (e.g., forewing length), determines the orientation of the specimen (pinned ventrally or dorsally), and identifies the sex. We pair these measurements and meta-data with temperature records to test how adult size varies with temperature during the immature stages of species and to assess patterns of sexual-size dimorphism across species and families. Mothra accurately measures the forewing lengths of butterfly specimens and compared to manual baseline measurements, Mothra accurately determines sex and forewing lengths of butterfly specimens. Females are the larger sex in most species and an increase in adult body size with warm monthly temperatures during the late larval stages is the most common temperature size response. These results confirm suspected patterns and support hypotheses based on recent studies using a smaller dataset of manually measured specimens. We show that CV can be a powerful tool to efficiently and accurately extract phenotypic data from a very large collection of digital NHCs. In the future, CV will become widely applied to digital NHC collections to advance ecological and evolutionary research and to accelerate the use of NHCs for biotic response to global change research.

scholarly journals Using insect natural history collections to study global change impacts: challenges and opportunities

2018 ◽  
Vol 374 (1763) ◽  
pp. 20170405 ◽  
Author(s):  
Heather M. Kharouba ◽  
Jayme M. M. Lewthwaite ◽  
Rob Guralnick ◽  
Jeremy T. Kerr ◽  
Mark Vellend
Keyword(s):  
Natural History ◽  
Global Change ◽  
Global Changes ◽  
Genomic Information ◽  
Theme Issue ◽  
The Past ◽  
Natural History Collections ◽  
Global Change Research ◽  
Challenges And Opportunities

Over the past two decades, natural history collections (NHCs) have played an increasingly prominent role in global change research, but they have still greater potential, especially for the most diverse group of animals on Earth: insects. Here, we review the role of NHCs in advancing our understanding of the ecological and evolutionary responses of insects to recent global changes. Insect NHCs have helped document changes in insects' geographical distributions, phenology, phenotypic and genotypic traits over time periods up to a century. Recent work demonstrates the enormous potential of NHCs data for examining insect responses at multiple temporal, spatial and phylogenetic scales. Moving forward, insect NHCs offer unique opportunities to examine the morphological, chemical and genomic information in each specimen, thus advancing our understanding of the processes underlying species’ ecological and evolutionary responses to rapid, widespread global changes. This article is part of the theme issue ‘Biological collections for understanding biodiversity in the anthropocene’.

scholarly journals Closing Gaps But Increasing Bias In North American Butterfly Inventory Completeness

2020 ◽  
Author(s):  
Vaughn Shirey ◽  
Michael W. Belitz ◽  
Vijay Barve ◽  
Robert Guralnick
Keyword(s):  
Climate Change ◽  
Natural History ◽  
Data Sources ◽  
Museum Specimens ◽  
Biodiversity Data ◽  
Human Footprint ◽  
Natural History Collections ◽  
Global Change Research ◽  
Under Sampling ◽  
Community Science

AbstractAggregate biodiversity data from museum specimens and community observations have promise for macroscale ecological analyses. Despite this, many groups are under-sampled, and sampling is not homogeneous across space. Here we used butterflies, the best documented group of insects, to examine inventory completeness across North America. We separated digitally accessible butterfly records into those from natural history collections and burgeoning community science observations to determine if these data sources have differential spatio-taxonomic biases. When we combined all data, we found startling under-sampling in regions with the most dramatic trajectories of climate change and across biomes. We also found support for the hypothesis that community science observations are filling more gaps in sampling but are more biased towards areas with the highest human footprint. Finally, we found that both types of occurrences have familial-level taxonomic completeness biases, in contrast to the hypothesis of less taxonomic bias in natural history collections data. These results suggest that higher inventory completeness, driven by rapid growth of community science observations, is partially offset by higher spatio-taxonomic biases. We use the findings here to provide recommendations on how to alleviate some of these gaps in the context of prioritizing global change research.

scholarly journals Integrating natural history collections and comparative genomics to study the genetic architecture of convergent evolution

2019 ◽  
Vol 374 (1777) ◽  
pp. 20180248 ◽  
Author(s):  
Sangeet Lamichhaney ◽  
Daren C. Card ◽  
Phil Grayson ◽  
João F. R. Tonini ◽  
Gustavo A. Bravo ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Natural History ◽  
Convergent Evolution ◽  
Phenotypic Diversity ◽  
Taxonomic Diversity ◽  
Gold Rush ◽  
Phenotypic Data ◽  
Natural History Collections ◽  
Natural History Collection ◽  
Genomic Studies

Evolutionary convergence has been long considered primary evidence of adaptation driven by natural selection and provides opportunities to explore evolutionary repeatability and predictability. In recent years, there has been increased interest in exploring the genetic mechanisms underlying convergent evolution, in part, owing to the advent of genomic techniques. However, the current ‘genomics gold rush’ in studies of convergence has overshadowed the reality that most trait classifications are quite broadly defined, resulting in incomplete or potentially biased interpretations of results. Genomic studies of convergence would be greatly improved by integrating deep ‘vertical’, natural history knowledge with ‘horizontal’ knowledge focusing on the breadth of taxonomic diversity. Natural history collections have and continue to be best positioned for increasing our comprehensive understanding of phenotypic diversity, with modern practices of digitization and databasing of morphological traits providing exciting improvements in our ability to evaluate the degree of morphological convergence. Combining more detailed phenotypic data with the well-established field of genomics will enable scientists to make progress on an important goal in biology: to understand the degree to which genetic or molecular convergence is associated with phenotypic convergence. Although the fields of comparative biology or comparative genomics alone can separately reveal important insights into convergent evolution, here we suggest that the synergistic and complementary roles of natural history collection-derived phenomic data and comparative genomics methods can be particularly powerful in together elucidating the genomic basis of convergent evolution among higher taxa. This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions’.

scholarly journals The colonial legacy of herbaria

2021 ◽  
Author(s):  
DA S Park ◽  
Xiao Feng ◽  
Shinobu Akiyama ◽  
Marlina Ardiyani ◽  
Neida Avendano ◽  
...  
Keyword(s):  
Natural History ◽  
Global Change ◽  
Inverse Relationship ◽  
Plant Biodiversity ◽  
Colonial Era ◽  
Colonial Legacy ◽  
Natural History Collections ◽  
History Of ◽  
Global North ◽  
Herbarium Collections

Herbarium collections shape our understanding of the world's flora and are crucial for addressing global change and biodiversity conservation. The formation of such natural history collections, however, are not free from sociopolitical issues of immediate relevance. Despite increasing efforts addressing issues of representation and colonialism in natural history collections, herbaria have received comparatively less attention. While it has been noted that the majority of plant specimens are housed in the global North, the extent of this disparity has not been rigorously quantified to date. Here, by analyzing over 85 million specimen records and surveying herbaria across the globe, we assess the colonial legacy of botanical collections and how we may move towards a more inclusive future. We demonstrate that colonial exploitation has contributed to an inverse relationship between where plant biodiversity exists in nature and where it is housed in herbaria. Such disparities persist in herbaria across physical and digital realms despite overt colonialism having ended over half a century ago, suggesting ongoing digitization and decolonization efforts have yet to alleviate colonial-era discrepancies. We emphasize the need for acknowledging the inconvenient history of herbarium collections and the implementation of a more equitable, global paradigm for their collection, curation, and use.

scholarly journals Collectively, we need to accelerate Arctic specimen sampling

2017 ◽  
Vol 3 (3) ◽  
pp. 515-524
Author(s):  
Kevin Winker ◽  
Jack Withrow
Keyword(s):  
Climate Change ◽  
Natural History ◽  
Biological Systems ◽  
The Arctic ◽  
Future Research ◽  
Individual Species ◽  
Time And Space ◽  
Natural History Collections ◽  
Specimen Resource ◽  
Specimen Sampling

Natural history collections are not often thought of as observatories, but they are increasingly being used as such to observe biological systems and changes within them. Objects and the data associated with them are archived for present and future research. These specimen collections provide many diverse scientific benefits, helping us understand not only individual species or populations but also the environments in which they live(d). Despite these benefits, the specimen resource is inadequate to the tasks being asked of it — there are many gaps, taxonomically and in time and space. We examine and highlight some of these gaps using bird collections as an example. Given the speed of climate change in the Arctic, we need to collectively work to fill these gaps so we can develop and wield the science that will make us better stewards of Arctic environments.

scholarly journals Digitization and the Future of Natural History Collections

BioScience ◽  
2020 ◽  
Vol 70 (3) ◽  
pp. 243-251 ◽  
Author(s):  
Brandon P Hedrick ◽  
J Mason Heberling ◽  
Emily K Meineke ◽  
Kathryn G Turner ◽  
Christopher J Grassa ◽  
...  
Keyword(s):  
Natural History ◽  
Global Change ◽  
Large Scale ◽  
Anthropogenic Impacts ◽  
Digital Content ◽  
Global Community ◽  
New Approaches ◽  
Natural History Collections ◽  
Data Links ◽  
Critical Issues

Abstract Natural history collections (NHCs) are the foundation of historical baselines for assessing anthropogenic impacts on biodiversity. Along these lines, the online mobilization of specimens via digitization—the conversion of specimen data into accessible digital content—has greatly expanded the use of NHC collections across a diversity of disciplines. We broaden the current vision of digitization (Digitization 1.0)—whereby specimens are digitized within NHCs—to include new approaches that rely on digitized products rather than the physical specimen (Digitization 2.0). Digitization 2.0 builds on the data, workflows, and infrastructure produced by Digitization 1.0 to create digital-only workflows that facilitate digitization, curation, and data links, thus returning value to physical specimens by creating new layers of annotation, empowering a global community, and developing automated approaches to advance biodiversity discovery and conservation. These efforts will transform large-scale biodiversity assessments to address fundamental questions including those pertaining to critical issues of global change.

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