What Was George Forrest's Plant Collection Journey like in China?

Since the 16th century, Western countries have conducted extensive plant collections in Asia, particularly in China, driven by the need to collect botanical resources and foster academic development. These activities have not only significantly enriched the Western botanical specimen collections but have also had a profound impact on the development of related disciplines such as botany, ecology, and horticulture. During this process, a large number of renowned plant hunters emerged, whose discoveries and contributions are still remembered today. George Forrest (1873-1932) was one of these distinguished plant hunters. From 1904 to 1932, he visited China seven times to collect plants and became famous for the regional distinctiveness of the species he collected. However, due to the lack of systematic collection, organization, and analysis of specimens collected by Forrest, only a few species, such as the species Rhododendron, are well-known among the many species he introduced to the West. Furthermore, the personal collecting characteristics and the characteristic species collected by Forrest are also not clear. This limits a comprehensive understanding of the specimen collection history and impact of Forrest in China. Therefore, systematic organization and analysis of Forrest's plant specimens collected in China are crucial to understanding his impact on botanical classification, Rhododendrons introduction, global horticulture, and plant propagation. This study aims to systematically organize and analyze the plant specimens collected by George Forrest in China to investigate the family, genus, and species composition of the collected specimens and the seven collection expeditions of Forrest in China, as well as the time and altitude of these collections. Furthermore, it seeks to discuss Forrest's scientific contributions to the global spread of plants, the widespread application of the Rhododendron, and his impact on the development of modern gardens, providing a theoretical basis and data reference for related research and professional development. To this end, we extensively consulted important historical literature related to Forrest and systematically collected data from online specimen databases. The conclusions drawn from the available data include 38,603 specimens, with 26,079 collection numbers, belonging to 233 families, 1395 genera, and 5426 species, which account for 48.24%, 32.63%, and 14.17% of the plant families, genera, and species in China, respectively. Rhododendron specimens made up 17.20% of the specimens collected in this study. The collection locations cover three provinces or autonomous regions, 11 prefecture-level cities, and 25 counties. Furthermore, we found that Forrest's collections were concentrated in spring and summer, mainly in high-altitude areas, with 135 species found below 1500 m and 3754 species at 1500 m and above. Rhododendron specimens were mostly found above 3000 m.

Interactive three-dimensional atlas of the mineralized skeleton of the sand tiger shark Carcharias taurus

Non-invasive computed tomography (CT) of an adult sand tiger shark Carcharias taurus Rafinesque, 1810 is used to provide an interactive three-dimensional 'general' shark (Selachimorpha) anatomy atlas. Given its post-cranial body morphology, the sand tiger shark appeared to be a well-chosen candidate and through comparison of the sand tiger shark with several other representatives of all eight established orders of sharks, we confirm that the relatively large degree of mineralization of the endoskeleton, along with the overall size, makes the sand tiger shark an ideal candidate for skeletal segmentation and construction of a skeletal atlas using conventional CT. This atlas both increases accessibility to the internal morphological features of the sand tiger shark and provides a more generalized overview of the skeletal anatomy of sharks and can aid as a supplement to destructive fresh dissection of specimens in the future and the construction of future skeletal atlases of other less mineralized sharks.

Lions & sea lions & bears, oh my: utilizing museum specimens to study the ossification sequence of carnivoran taxa

BACKGROUND

Mammalian skeletons are largely formed before birth. Heterochronic changes in skeletal formation can be investigated by comparing the order of ossification for different elements of the skeleton. Due to the challenge of collecting prenatal specimens in viviparous taxa, opportunistically collected museum specimens provide the best material for studying prenatal skeletal development across many mammalian species. Previous studies have investigated ossification sequence in a range of mammalian species, but little is known about the pattern of bone formation in Carnivora. Carnivorans have diverse ecologies, diets, and biomechanical specializations and are well-suited for investigating questions in evolutionary biology. Currently, developmental data on carnivorans is largely limited to domesticated species. To expand available data on carnivoran skeletal development, we used micro-computed tomography (micro-CT) to non-invasively evaluate the degree of ossification in all prenatal carnivoran specimens housed in the Harvard Museum of Comparative Zoology. By coding the presence or absence of bones in each specimen, we constructed ossification sequences for each species. Parsimov-based genetic inference (PGi) was then used to identify heterochronic shifts between carnivoran lineages and reconstruct the ancestral ossification sequence of Carnivora.

RESULTS

We used micro-CT to study prenatal ossification sequence in six carnivora species: Eumetopias jubatus (Steller sea lion, n = 6), Herpestes javanicus (small Indian mongoose, n = 1), Panthera leo (lion, n = 1), Urocyon cinereoargenteus (gray fox, n = 1), Ursus arctos arctos (Eurasian brown bear, n = 1), and Viverricula indica (small Indian civet, n = 5). Due to the relatively later stage of collection for the available specimens, few heterochronic shifts were identified. Ossification sequences of feliform species showed complete agreement with the domestic cat. In caniforms, the bear and fox ossification sequences largely matched the dog, but numerous heterochronic shifts were identified in the sea lion.

CONCLUSIONS

We use museum specimens to generate cranial and postcranial micro-CT data on six species split between the two major carnivoran clades: Caniformia and Feliformia. Our data suggest that the ossification sequence of domestic dogs and cats are likely good models for terrestrial caniforms and feliforms, respectively, but not pinnipeds.

AI-based discovery of habitats from museum collections

Museum collection records are a source of historic data for species occurrence, but little attention is paid to the associated descriptions of habitat at the sample locations. We propose that artificial intelligence methods have potential to use these descriptions for reconstructing past habitat, to address ecological and evolutionary questions.

Lack of country-wide systematic herpetology collections in Portugal jeopardizes future research and conservation

Natural History Collections (NHCs) represent the world's largest repositories of long-term biodiversity datasets. Specimen collection and voucher deposition has been the backbone of NHCs since their inception, but recent decades have seen a drastic decline in rates of growth via active collecting. Amphibians and reptiles are amongst the most threatened zoological groups on the planet and are historically underrepresented in most worldwide NHCs. As part of an ongoing project to review the Portuguese zoological collections in the country's NHCs, herpetological data from its three major museums and smaller collections was gathered and used to examine the coverage and representation of the different taxa extant in Portugal. These collections are not taxonomically, geographically, or temporally complete. Approximately 90% of the Portuguese herpetological taxa are represented in the country's NHCs, and around half of the taxa are represented by less than 50 specimens. Geographically, the collections cover less than 30% of the country's territory and almost all of the occurring taxa have less than 10% of their known distribution represented in the collections. A discussion on the implications for science of such incomplete collections and a review of the current status of Portuguese NHCs is presented.

The first full body diffusible iodine-based contrast-enhanced computed tomography dataset and teaching materials for a member of the Testudines

Diffusible iodine-based contrast-enhanced Computed Tomography (diceCT) is now a widely used technique for imaging metazoan soft anatomy. Turtles present a particular challenge for anatomists; gross dissection is inherently destructive and irreversible, whereas their near complete shell of bony plates, covered with keratinous scutes, presents a barrier for iodine diffusion and significantly increases contrast-enhanced CT preparation time. Consequently, a complete dataset visualizing the internal soft anatomy of turtles at high resolution and in three dimensions has not yet been successfully achieved. Here we outline a novel method that augments traditional diceCT preparation with an iodine injection technique to acquire the first full body contrast-enhanced dataset for the Testudines. We show this approach to be an effective method of staining the soft tissues inside the shell. The resulting datasets were processed to produce anatomical 3D models that can be used in teaching and research. As diceCT becomes a widely employed method for nondestructively documenting the internal soft anatomy of alcohol preserved museum specimens, we hope that methods applicable to the more challenging of these, such as turtles, will contribute toward the growing stock of digital anatomy in online repositories.

Increasing the impact of vertebrate scientific collections through 3D imaging: The openVertebrate (oVert) Thematic Collections Network

The impact of preserved museum specimens is transforming and increasing by three-dimensional (3D) imaging that creates high-fidelity online digital specimens. Through examples from the openVertebrate (oVert) Thematic Collections Network, we describe how we created a digitization community dedicated to the shared vision of making 3D data of specimens available and the impact of these data on a broad audience of scientists, students, teachers, artists, and more. High-fidelity digital 3D models allow people from multiple communities to simultaneously access and use scientific specimens. Based on our multiyear, multi-institution project, we identify significant technological and social hurdles that remain for fully realizing the potential impact of digital 3D specimens.

Medicinal plants meet modern biodiversity science

Plants have been an essential source of human medicine for millennia. In this review, we argue that a holistic, interdisciplinary approach to the study of medicinal plants that combines methods and insights from three key disciplines - evolutionary ecology, molecular biology/biochemistry, and ethnopharmacology - is poised to facilitate new breakthroughs in science, including pharmacological discoveries and rapid advancements in human health and well-being. Such interdisciplinary research leverages data and methods spanning space, time, and species associated with medicinal plant species evolution, ecology, genomics, and metabolomic trait diversity, all of which build heavily on traditional Indigenous knowledge. Such an interdisciplinary approach contrasts sharply with most well-funded and successful medicinal plant research during the last half-century, which, despite notable advancements, has greatly oversimplified the dynamic relationships between plants and humans, kept hidden the larger human narratives about these relationships, and overlooked potentially important research and discoveries into life-saving medicines. We suggest that medicinal plants and people should be viewed as partners whose relationship involves a complicated and poorly explored set of (socio-)ecological interactions including not only domestication but also commensalisms and mutualisms. In short, medicinal plant species are not just chemical factories for extraction and exploitation. Rather, they may be symbiotic partners that have shaped modern societies, improved human health, and extended human lifespans.

Readjusting observational grids in dragonfly field guides

Wildlife field guide books present salient features of species, from colour and form to behaviour, and give their readers a vocabulary to express what these features look like. Such structures for observation, or observational grids, allow users to identify wildlife species through what Law and Lynch have called 'the difference that makes the difference'. In this article, we show how these grids, and the characteristics that distinguish species, change over time in response to wider concerns in the community that use and make the field guides. We use the development of Dutch field guides for dragonflies to show how the ethics of observing wildlife, the recreational value of dragonfly observation, the affordances of observational tools, and biodiversity monitoring and conservation goals all have repercussions for how dragonflies are to be identified. Ultimately, this affects not only how dragonflies are to be observed and identified, but also what is taken to be 'out there'. The article is based on a transdisciplinary cooperation between a dragonfly enthusiast with emic knowledge and access, and an STS researcher. We hope the articulation of our approach might inspire analyses of other observational practices and communities.

Sample Size and Geometric Morphometrics Methodology Impact the Evaluation of Morphological Variation

Geometric morphometrics has had a profound impact on our understanding of morphological evolution. However, factors such as sample size and the views and elements selected for two-dimensional geometric morphometric (2DGM) analyses, which are often dictated by specimen availability and time rather than study design, may affect the outcomes of those analyses. Leveraging large intraspecific sample sizes (n > 70) for two bat species, Lasiurus borealis and Nycticeius humeralis, we evaluate the impact of sample size on calculations of mean shape, shape variance, and centroid size. Additionally, we assessed the concordance of multiple skull 2D views with one another and characterized morphological variation in skull shape in L. borealis and N. humeralis, as well as a closely related species, Lasiurus seminolus. Given that L. seminolus is a morphologically cryptic species with L. borealis, we assessed whether differences in skull shape and in 2DGM approach would allow species discrimination. We found that reducing sample size impacted mean shape and increased shape variance, that shape differences were not consistent across views or skull elements, and that trends shown by the views and elements were not all strongly associated with one another. Further, we found that L. borealis and L. seminolus were statistically different in shape using 2DGM in all views and elements. These results underscore the importance of selecting appropriate sample sizes, 2D views, and elements based on the hypothesis being tested. While there is likely not a generalizable sample size or 2D view that can be employed given the wide variety of research questions and systems evaluated using 2DGM, a generalizable solution to issues with 2DGM presented here is to run preliminary analyses using multiple views, elements, and sample sizes, thus ensuring robust conclusions.

Humans in the loop: Community science and machine learning synergies for overcoming herbarium digitization bottlenecks

Premise

Among the slowest steps in the digitization of natural history collections is converting imaged labels into digital text. We present here a working solution to overcome this long-recognized efficiency bottleneck that leverages synergies between community science efforts and machine learning approaches.

Methods

We present two new semi-automated services. The first detects and classifies typewritten, handwritten, or mixed labels from herbarium sheets. The second uses a workflow tuned for specimen labels to label text using optical character recognition (OCR). The label finder and classifier was built via humans-in-the-loop processes that utilize the community science Notes from Nature platform to develop training and validation data sets to feed into a machine learning pipeline.

Results

Our results showcase a >93% success rate for finding and classifying main labels. The OCR pipeline optimizes pre-processing, multiple OCR engines, and post-processing steps, including an alignment approach borrowed from molecular systematics. This pipeline yields >4-fold reductions in errors compared to off-the-shelf open-source solutions. The OCR workflow also allows human validation using a custom Notes from Nature tool.

Discussion

Our work showcases a usable set of tools for herbarium digitization including a custom-built web application that is freely accessible. Further work to better integrate these services into existing toolkits can support broad community use.

The Megachilidae (Hymenoptera, Apoidea, Apiformes) of the Democratic Republic of Congo curated at the Royal Museum for Central Africa (RMCA, Belgium)

Natural history collections are a cornerstone of entomology, and the conservation of specimens is the essential prerequisite for the development of research into systematics, biogeography, ecology, evolution and other disciplines. Yet, specimens collected during decades of entomological research conducted in less developed countries across Sub-Saharan Africa on pests, beneficial insects and insect biodiversity in general have largely been exported to be permanently preserved in developed countries, mainly in Europe and the United States of America. This is particularly true for the Democratic Republic of the Congos (DRC) diverse wild bee fauna, which has been investigated throughout the colonial period by visiting or resident entomologists and missionaries who have then transferred their collected material primarily to Belgium as part of a wider legacy of scientific exploration and colonialism. Digitizing NHC is one way to mitigate this current bias, by making samples accessible to researchers from the target post-colonial countries as well as to the wider international scientific community. In this study, we compiled and digitized 6,490 specimens records relevant to 195 wild bee species grouped in 18 genera within the biodiverse family Megachilidae, essentially from the colonial era (i.e., mostly between 19051960, with additional records up to 1978), and curated at the Royal Museum for Central Africa in Belgium. We provide a detailed catalogue of all records with updated locality and province names, including 29 species only available as type specimens. We also explore the historical patterns of diversity and distribution across DRC, and we provide a list of the research entomologists involved. This study is an important first step that uses digital technologies to democratize and repatriate important aspects of DRCs natural heritage of insect biodiversity, to stimulate more contemporary field surveys and modern taxonomic revisions, as well as to identify and characterize research gaps and biodiversity shortfalls in some of the less-explored regions of Sub-Saharan Africa.

From Dormant Collections to Repositories for the Study of Habitat Changes: The Importance of Herbaria in Modern Life Sciences

In recent decades, the advent of new technologies for massive and automatized digitization, together with the availability of new methods for DNA sequencing, strongly increased the interest and relevance of herbarium collections for the study of plant biodiversity and evolution. These new approaches prompted new projects aimed at the creation of a large dataset of molecular and phenological data. This review discusses new challenges and opportunities for herbaria in the context of the numerous national projects that are currently ongoing, prompting the study of herbarium specimens for the understanding of biodiversity loss and habitat shifts as a consequence of climate changes and habitat destruction due to human activities. With regard to this, the National Biodiversity Future Center (active in Italy since 2022) started a large-scale digitization project of the Herbarium Centrale Italicum in Florence (Italy), which is the most important Italian botanical collection, consisting of more than 4 million samples at present.

Temporal collections to study invasion biology

Biological invasions represent an extraordinary opportunity to study evolution. This is because accidental or deliberate species introductions have taken place for centuries across large geographical scales, frequently prompting rapid evolutionary transitions in invasive populations. Until recently, however, the utility of invasions as evolutionary experiments has been hampered by limited information on the makeup of populations that were part of earlier invasion stages. Now, developments in ancient and historical DNA technologies, as well as the quickening pace of digitization for millions of specimens that are housed in herbaria and museums globally, promise to help overcome this obstacle. In this review, we first introduce the types of temporal data that can be used to study invasions, highlighting the timescale captured by each approach and their respective limitations. We then discuss how ancient and historical specimens as well as data available from prior invasion studies can be used to answer questions on mechanisms of (mal)adaptation, rates of evolution, or community-level changes during invasions. By bridging the gap between contemporary and historical invasive populations, temporal data can help us connect pattern to process in invasion science. These data will become increasingly important if invasions are to achieve their full potential as experiments of evolution in nature.

Digitization of the historical Herbarium of Michele Guadagno at Pisa (PI-GUAD)

The herbarium digitization process is an essential first step in transforming the vast amount of data associated with a physical specimen into flexible digital data formats. In this framework, the Herbarium of the University of Pisa (international code PI), at the end of 2018 started a process of digitization focusing on one of its most relevant collections: the Herbarium of Michele Guadagno (1878-1930). This scholar studied flora and vegetation of different areas of southern Italy, building a large herbarium including specimens collected by himself, plus many specimens obtained through exchanges with Italian and foreign botanists. The Herbarium is composed by 547 packages of vascular plants. Metadata were entered into the online database Virtual Herbaria JACQ and mirrored into a personalized virtual Herbarium of the Botanic Museum. After the completion of the digitization process, the number of sheets preserved in the Herbarium amounts to 44,345. Besides Guadagno, who collected 42% of his specimens, a further 1,102 collectors are represented. Most specimens were collected in Europe (91%), but all the continents are represented. As expected, Italy is the most represented country (59%), followed by France, Spain, Germany, and Greece. The specimens cover a time span of 99 years, from 1830 to 1929, whereas the specimens collected by Guadagno range between 1889 and 1928. Furthermore, we traced 134 herbarium sheets associated with documents, among which 75 drawings handmade by Guadagno, 34 letters from various corresponding authors, 16 copies of publications, and 14 copies of published iconographies.

Botanical Collection Patterns and Conservation Categories of the Most Traded Timber Species from the Ecuadorian Amazon: The Role of Protected Areas

The Ecuadorian Amazon is home to a rich biodiversity of woody plant species. Nonetheless, their conservation remains difficult, as some areas remain poorly explored and lack georeferenced records. Therefore, the current study aims predominantly to analyze the collection patterns of timber species in the Amazon lowlands of Ecuador and to evaluate the conservation coverage of these species in protected areas. Furthermore, we try to determine the conservation category of the species according to the criteria of the IUCN Red List. We identified that one third of the timber species in the study area was concentrated in three provinces due to historical botanical expeditions. However, a worrying 22.0% of the species had less than five records of presence, and 29.9% had less than ten records, indicating a possible underestimation of their presence. In addition, almost half of the species evaluated were unprotected, exposing them to deforestation risks and threats. To improve knowledge and conservation of forest biodiversity in the Ecuadorian Amazon, it is recommended to perform new botanical samplings in little-explored areas and digitize data in national herbaria. It is critical to implement automated assessments of the conservation status of species with insufficient data. In addition, it is suggested to use species distribution models to identify optimal areas for forest restoration initiatives. Effective communication of results and collaboration between scientists, governments, and local communities are key to the protection and sustainable management of forest biodiversity in the Amazon region.

Complex climate-mediated effects of urbanization on plant reproductive phenology and frost risk

Urbanization can affect the timing of plant reproduction (i.e. flowering and fruiting) and associated ecosystem processes. However, our knowledge of how plant phenology responds to urbanization and its associated environmental changes is limited. Herbaria represent an important, but underutilized source of data for investigating this question. We harnessed phenological data from herbarium specimens representing 200 plant species collected across 120 yr from the eastern US to investigate the spatiotemporal effects of urbanization on flowering and fruiting phenology and frost risk (i.e. time between the last frost date and flowering). Effects of urbanization on plant reproductive phenology varied significantly in direction and magnitude across species ranges. Increased urbanization led to earlier flowering in colder and wetter regions and delayed fruiting in regions with wetter spring conditions. Frost risk was elevated with increased urbanization in regions with colder and wetter spring conditions. Our study demonstrates that predictions of phenological change and its associated impacts must account for both climatic and human effects, which are context dependent and do not necessarily coincide. We must move beyond phenological models that only incorporate temperature variables and consider multiple environmental factors and their interactions when estimating plant phenology, especially at larger spatial and taxonomic scales.

Achieving zero extinction for land plants

Despite the importance of plants for humans and the threats to their future, plant conservation receives far less support compared with vertebrate conservation. Plants are much cheaper and easier to conserve than are animals, but, although there are no technical reasons why any plant species should become extinct, inadequate funding and the shortage of skilled people has created barriers to their conservation. These barriers include the incomplete inventory, the low proportion of species with conservation status assessments, partial online data accessibility, varied data quality, and insufficient investment in both in and ex situ conservation. Machine learning, citizen science (CS), and new technologies could mitigate these problems, but we need to set national and global targets of zero plant extinction to attract greater support.

Challenges and directions in analytical paleobiology

Over the last 50 years, access to new data and analytical tools has expanded the study of analytical paleobiology, contributing to innovative analyses of biodiversity dynamics over Earth's history. Despite-or even spurred by-this growing availability of resources, analytical paleobiology faces deep-rooted obstacles that stem from the need for more equitable access to data and best practices to guide analyses of the fossil record. Recent progress has been accelerated by a collective push toward more collaborative, interdisciplinary, and open science, especially by early-career researchers. Here, we survey four challenges facing analytical paleobiology from an early-career perspective: (1) accounting for biases when interpreting the fossil record; (2) integrating fossil and modern biodiversity data; (3) building data science skills; and (4) increasing data accessibility and equity. We discuss recent efforts to address each challenge, highlight persisting barriers, and identify tools that have advanced analytical work. Given the inherent linkages between these challenges, we encourage discourse across disciplines to find common solutions. We also affirm the need for systemic changes that reevaluate how we conduct and share paleobiological research.

When the absence of evidence is not the evidence of absence: Nasa (Loasaceae) rediscoveries from Peru and Ecuador, and the contribution of community science networks

Documentation of plant taxa has long been subject to the temporal and spatial selectivity of professional research expeditions, especially in tropical regions. Therefore, rare and/or narrowly endemic species are sometimes known only from very few and very old herbarium specimens. However, these taxa are very important from a conservation perspective. The lack of observations of living plants and confirmation of the actual occurrence of taxa hinders the planning and implementation of effective conservation measures. Community science networks have recently made tremendous contributions to documenting biodiversity in many regions across the globe. The rediscovery of six species of Nasa (Loasaceae) from Peru and Ecuador primarily via the platform iNaturalist, is reported.

Insect collecting bias in Arizona with a preliminary checklist of the beetles from the Sand Tank Mountains

Background

The State of Arizona in the south-western United States supports a high diversity of insects. Digitised occurrence records, especially from preserved specimens in natural history collections, are an important and growing resource to understand biodiversity and biogeography. Underlying bias in how insects are collected and what that means for interpreting patterns of insect diversity is largely untested. To explore the effects of insect collecting bias in Arizona, the State was regionalised into specific areas. First, the entire State was divided into broad biogeographic areas by ecoregion. Second, the 81 tallest mountain ranges were mapped on to the State. The distribution of digitised records across these areas were then examined.A case study of surveying the beetles (Insecta, Coleoptera) of the Sand Tank Mountains is presented. The Sand Tanks are a low-elevation range in the Lower Colorado River Basin subregion of the Sonoran Desert from which a single beetle record was published before this study.

New information

The number of occurrence records and collecting events are very unevenly distributed throughout Arizona and do not strongly correlate with the geographic size of areas. Species richness is estimated for regions in Arizona using rarefaction and extrapolation. Digitised records from the disproportionately highly collected areas in Arizona represent at best 70% the total insect diversity within them. We report a total of 141 species of Coleoptera from the Sand Tank Mountains, based on 914 digitised voucher specimens. These specimens add important new records for taxa that were previously unavailable in digitised data and highlight important biogeographic ranges.Possible underlying mechanisms causing bias are discussed and recommendations are made for future targeted collecting of under-sampled regions. Insect species diversity is apparently at best 70% documented for the State of Arizona with many thousands of species not yet recorded. The Chiricahua Mountains are the most densely sampled region of Arizona and likely contain at least 2,000 species not yet vouchered in online data. Preliminary estimates for species richness of Arizona are at least 21,000 and likely much higher. Limitations to analyses are discussed which highlight the strong need for more insect occurrence data.

The colonial legacy of herbaria

Herbarium collections shape our understanding of Earth's flora and are crucial for addressing global change issues. Their formation, however, is 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 and magnitude of this disparity have not been quantified. Here we examine the colonial legacy of botanical collections, analysing 85,621,930 specimen records and assessing survey responses from 92 herbarium collections across 39 countries. We find an inverse relationship between where plant diversity exists in nature and where it is housed in herbaria. Such disparities persist across physical and digital realms despite overt colonialism ending over half a century ago. We emphasize the need for acknowledging the colonial history of herbarium collections and implementing a more equitable global paradigm for their collection, curation and use.

Review and guide to the isopods (Crustacea, Isopoda) of littoral and sublittoral marine habitats in the Southern California Bight

The isopod crustaceans reported from or expected to occur in littoral and sublittoral marine habitats of the Southern California Bight (SCB) in the northeastern Pacific Ocean are reviewed. A total of 190 species, representing 105 genera in 42 families and six suborders are covered. Approximately 84% of these isopods represent described species with the remaining 16% comprising well-documented "provisional" but undescribed species. Cymothoida and Asellota are the most diverse of the six suborders, accounting for ca. 36% and 29% of the species, respectively. Valvifera and Sphaeromatidea are the next most speciose suborders with between 13-15% of the species each, while the suborder Limnorioidea represents fewer than 2% of the SCB isopod fauna. Finally, the mostly terrestrial suborder Oniscidea accounts for ca. 5% of the species treated herein, each which occurs at or above the high tide mark in intertidal habitats. A key to the suborders and superfamilies is presented followed by nine keys to the SCB species within each of the resultant groups. Figures are provided for most species. Bathymetric range, geographic distribution, type locality, habitat, body size, and a comprehensive list of references are included for most species.

Reimagining the future of natural history museums with compassionate collection

Compassionate collection involves minimizing harm while collecting museum data in the field. By adopting this practice, natural history museums could better maintain existing collections, accommodate more nonlethal specimens and data, and foster an inclusive community.

Mass production of unvouchered records fails to represent global biodiversity patterns

The ever-increasing human footprint even in very remote places on Earth has inspired efforts to document biodiversity vigorously in case organisms go extinct. However, the data commonly gathered come from either primary voucher specimens in a natural history collection or from direct field observations that are not traceable to tangible material in a museum or herbarium. Although both datasets are crucial for assessing how anthropogenic drivers affect biodiversity, they have widespread coverage gaps and biases that may render them inefficient in representing patterns of biodiversity. Using a large global dataset of around 1.9 billion occurrence records of terrestrial plants, butterflies, amphibians, birds, reptiles and mammals, we quantify coverage and biases of expected biodiversity patterns by voucher and observation records. We show that the mass production of observation records does not lead to higher coverage of expected biodiversity patterns but is disproportionately biased toward certain regions, clades, functional traits and time periods. Such coverage patterns are driven by the ease of accessibility to air and ground transportation, level of security and extent of human modification at each sampling site. Conversely, voucher records are vastly infrequent in occurrence data but in the few places where they are sampled, showed relative congruence with expected biodiversity patterns for all dimensions. The differences in coverage and bias by voucher and observation records have important implications on the utility of these records for research in ecology, evolution and conservation research.

Dots on a screen: The past, present, and future of morphometrics in the study of nonavian dinosaurs

Using morphometrics to study nonavian dinosaur fossils is a practice that predates the origin of the word "dinosaur." By the 1970s, linear morphometrics had become established as a valuable tool for analyzing intra- and interspecific variation in nonavian dinosaurs. With the advent of more recent techniques such as geometric morphometrics and more advanced statistical approaches, morphometric analyses of nonavian dinosaurs have proliferated, granting unprecedented insight into many aspects of their biology and evolution. I outline the past, present, and future of morphometrics as applied to the study of nonavian dinosaurs zeroing in on five aspects of nonavian dinosaur paleobiology where morphometrics has been widely utilized to advance our knowledge: systematics, sexual dimorphism, locomotion, macroevolution, and trackways. Morphometric methods are especially susceptible to taphonomic distortion. As such, the impact of taphonomic distortion on original fossil shape is discussed as are current and future methods for quantifying and accounting for distortion with the goal of reducing the taphonomic noise to biological signal ratio. Finally, the future of morphometrics in nonavian dinosaur paleobiology is discussed as paleobiologists move into a "virtual paleobiology" framework, whereby digital renditions of fossils are captured via methods such as photogrammetry and computed tomography. These primary data form the basis for three-dimensional (3D) geometric morphometric analyses along with a slew of other forms of analyses. These 3D specimen data form part of the extended specimen and help to democratize paleobiology, unlocking the specimen from the physical museum and making the specimen available to researchers across the world.

Temporal stability of the hybrid zone between Calocitta magpie-jays revealed through comparison of museum specimens and iNaturalist photos

Hybrid zones are natural experiments for the study of avian evolution. Hybrid zones can be dynamic, moving as species adjust to new climates and habitats, with unknown implications for species and speciation. There are relatively few studies that have comparable modern and historic sampling to assess change in hybrid zone location and width over time, and those studies have generally found mixed results, with many hybrid zones showing change over time, but others showing stability. The white-throated magpie-jay (Calocitta formosa) and black-throated magpie-jay (Calocitta colliei) occur along the western coast of Mexico and Central America. The two species differ markedly in throat color and tail length, and prior observation suggests a narrow hybrid zone in southern Jalisco where individuals have mixed throat color. This study aims to assess the existence and temporal stability of this putative hybrid zone by comparing throat color between georeferenced historical museum specimens and modern photos from iNaturalist with precise locality information. Our results confirm the existence of a narrow hybrid zone in Jalisco, with modern throat scores gradually increasing from the parental ends of the cline toward the cline center in a sigmoidal curve characteristic of hybrid zones. Our temporal comparison suggests that the hybrid zone has not shifted its position between historical (pre-1973) and modern (post-2005) time periods-a surprising result given the grand scale of habitat change to the western Mexican lowlands during this time. An anomalous pocket of white-throated individuals in the northern range of the black-throated magpie-jay hints at the possibility of prehistorical long-distance introduction. Future genomic data will help disentangle the evolutionary history of these lineages and better characterize how secondary contact is affecting both the DNA and the phenotype of these species.

Is the world wormier than it used to be? We'll never know without natural history collections

Many disease ecologists and conservation biologists believe that the world is wormier than it used to be-that is, that parasites are increasing in abundance through time. This argument is intuitively appealing. Ecologists typically see parasitic infections, through their association with disease, as a negative endpoint, and are accustomed to attributing negative outcomes to human interference in the environment, so it slots neatly into our worldview that habitat destruction, biodiversity loss and climate change should have the collateral consequence of causing outbreaks of parasites. But surprisingly, the hypothesis that parasites are increasing in abundance through time remains entirely untested for the vast majority of wildlife parasite species. Historical data on parasites are nearly impossible to find, which leaves no baseline against which to compare contemporary parasite burdens. If we want to know whether the world is wormier than it used to be, there is only one major research avenue that will lead to an answer: parasitological examination of specimens preserved in natural history collections. Recent advances demonstrate that, for many specimen types, it is possible to extract reliable data on parasite presence and abundance. There are millions of suitable specimens that exist in collections around the world. When paired with contemporaneous environmental data, these parasitological data could even point to potential drivers of change in parasite abundance, including climate, pollution or host density change. We explain how to use preserved specimens to address pressing questions in parasite ecology, give a few key examples of how collections-based parasite ecology can resolve these questions, identify some pitfalls and workarounds, and suggest promising areas for research. Natural history specimens are 'parasite time capsules' that give ecologists the opportunity to test whether infectious disease is on the rise and to identify what forces might be driving these changes over time. This approach will facilitate major advances in a new sub-discipline: the historical ecology of parasitism.

Integrating habitat-masked range maps with quantifications of prevalence to estimate area of occupancy in IUCN assessments

Estimates of species geographic ranges constitute critical input for biodiversity assessments, including those for the International Union for the Conservation of Nature (IUCN) Red List of Threatened Species. Area of occupancy (AOO) is one metric that IUCN uses to quantify a species' range, but data limitations typically lead to either under- or overestimates (and unnecessarily wide bounds of uncertainty). Fortunately, existing methods in which range maps and land-cover data are used to estimate the area currently holding habitat for a species can be extended to yield an unbiased range of plausible estimates for AOO. Doing so requires estimating the proportion of sites (currently containing habitat) that a species occupies within its range (i.e., prevalence). Multiplying a quantification of habitat area by prevalence yields an estimate of what the species inhabits (i.e., AOO). For species with intense sampling at many sites, presence-absence data sets or occupancy modeling allow calculation of prevalence. For other species, primary biodiversity data (records of a species' presence at a point in space and time) from citizen-science initiatives and research collections of natural history museums and herbaria could be used. In such cases, estimates of sample prevalence should be corrected by dividing by the species' detectability. To estimate detectability from these data sources, extensions of inventory-completeness analyses merit development. With investments to increase the quality and availability of online biodiversity data, consideration of prevalence should lead to tighter and more realistic bounds of AOO for many taxonomic groups and geographic regions. By leading to more realistic and representative characterizations of biodiversity, integrating maps of current habitat with estimates of prevalence should empower conservation practitioners and decision makers and thus guide actions and policy worldwide.

How to use natural history collections to resurrect information on historical parasite abundances

Many of the most contentious questions that concern the ecology of helminths could be resolved with data on helminth abundance over the past few decades or centuries, but unfortunately these data are rare. A new sub-discipline - the historical ecology of parasitism - is resurrecting long-term data on the abundance of parasites, an advancement facilitated by the use of biological natural history collections. Because the world's museums hold billions of suitable specimens collected over more than a century, these potential parasitological datasets are broad in scope and finely resolved in taxonomic, temporal and spatial dimensions. Here, we set out best practices for the extraction of parasitological information from natural history collections, including how to conceive of a project, how to select specimens, how to engage curators and receive permission for proposed projects, standard operating protocols for dissections and how to manage data. Our hope is that other helminthologists will use this paper as a reference to expand their own research programmes along the dimension of time.

The herbarium of the future

The ~400 million specimens deposited across ~3000 herbaria are essential for: (i) understanding where plants have lived in the past, (ii) forecasting where they may live in the future, and (iii) delineating their conservation status. An open access 'global metaherbarium' is emerging as these specimens are digitized, mobilized, and interlinked online. This virtual biodiversity resource is attracting new users who are accelerating traditional applications of herbaria and generating basic and applied scientific innovations, including e-monographs and floras produced by diverse, interdisciplinary, and inclusive teams; robust machine-learning algorithms for species identification and phenotyping; collection and synthesis of ecological trait data at large spatiotemporal and phylogenetic scales; and exhibitions and installations that convey the beauty of plants and the value of herbaria in addressing broader societal issues.

Sampling and curation of rove beetles (Insecta, Coleoptera, Staphylinidae) for comprehensive and DNA-grade collections to enhance biodiversity exploration in Northern Eurasia

Staphylinidae beetles form a major portion of terrestrial biodiversity globally and, in particular, in Northern Eurasia, a large area with a historically better known north temperate, subarctic and arctic biota. However, even here, rove beetles remain amongst the so-called "dark taxa" with a high fraction of taxonomically unknown lineage diversity. The propagation of DNA-based technologies in systematic entomology in recent decades has brought new opportunities for biodiversity exploration, true also for Staphylinidae. Simultaneously, new methods have revealed limitations of specimens sampled and curated by traditional practices, as existing legacy collections, whether institutional or private, unfortunately do not always qualify as a source of DNA-grade material. In addition, both legacy and newly-collected DNA-grade material of Staphylinidae remain highly biased towards Central Europe, a region with a traditionally well-developed scientific infrastructure and long-established culture for the maintenance of entomological collections. To increase the degree of biodiversity knowledge for our target organismal group across the globe, efficient sampling of DNA-grade material and, in particular, the development of comprehensive local collections in under-studied regions is highly desirable. To facilitate that, here we provide a practical guide for collecting and curation of Staphylinidae with a focus on capacity building for DNA-grade collections in Siberia and elsewhere in Northern Eurasia.

Endemic vascular plants in the Ukrainian Carpathians

Background

This dynamic dataset aims to gather all available data, extracted mostly from the preserved material deposited at the leading Ukrainian herbaria on the distribution of the endemic vascular plants in the Ukrainian Carpathians and adjacent territories. This dataset is created in the framework of mapping the distribution of the endemic plants and is aimed to unveil the patterns of their spatial distribution, ecological preferences and temporal trends in the flora of the Ukrainian Carpathians. A total of 76 species and subspecies of vascular plants belonging to 49 genera and 27 families are reported herein to occur in the Ukrainian Carpathians and close regions. Amongst the total number of reported 6,427 occurrence records, 1,961 records are georeferenced and supported with a translation of Cyrillic information into English. The remaining occurrence records will be georeferenced and translated into English in the near future, as well as the dataset being completed with new records obtained from the new sources.

New information

In total, 6,427 occurrence records of the endemic vascular plants distributed in the Ukrainian Carpathians were published.

Phototank setup and focus stack imaging method for reptile and amphibian specimens (Amphibia, Reptilia)

Fluid-preserved reptile and amphibian specimens are challenging to photograph with traditional methods due to their complex three-dimensional forms and reflective surfaces when removed from solution. An effective approach to counteract these issues involves combining focus stack photography with the use of a photo immersion tank. Imaging specimens beneath a layer of preservative fluid eliminates glare and risk of specimen desiccation, while focus stacking produces sharp detail through merging multiple photographs taken at successive focal steps to create a composite image with an extended depth of field. This paper describes the wet imaging components and focus stack photography workflow developed while conducting a large-scale digitization project for targeted reptile and amphibian specimens housed in the University of Colorado Museum of Natural History Herpetology Collection. This methodology can be implemented in other collections settings and adapted for use with fluid-preserved specimen types across the Tree of Life to generate high-quality, taxonomically informative images for use in documenting biodiversity, remote examination of fine traits, inclusion in publications, and educational applications.

Role of digitalization in environment, social and governance, and sustainability: Review-based study for implications

Digitalization gives people access to a vast network of untapped data, which has the potential to help society and the environment. Smart systems connected to the internet can systematically provide a unique opportunity to solve difficulties related to long-term sustainability. The goals are to create an egalitarian, ecologically sustainable, and healthy society. Technological resources are envisioned as game-changing instruments. Three key concerns integration benefits are highlighted here: (i) sustainable development goals, (ii) socio-economic development, and (iii) the role of digital technology in environmental sustainability. This viewpoint describes the potential that digitization can create a future sustainable society. The technological network would unite the urban and rural worlds under a shared banner of sustainable development, keeping all social elements in the loop. Nations that take a comprehensive strategy will be able to provide equitable growth and an efficient, sustainable, and digital existence for their citizens. As a result, digitization provides better living conditions, active public involvement, clean governance, and transparency in public welfare programs and processes. People who are well-informed, self-aware, and digitally equipped will be better learners, thinkers, reformers, participators, and change and growth agents, marching forward on sustainable progress. The advantages of digitization in hastening the transition to sustainable industrial processes and improving people's health and happiness are explored. Finally, the perspective encapsulates the advantages of digitization by offering a holistic vision of how technology could aid in addressing major challenges such as endangered world biodiversity and climate change.

The ecological implications of intra- and inter-species variation in phenological sensitivity

Plant-pollinator mutualisms rely upon the synchrony of interacting taxa. Climate change can disrupt this synchrony as phenological responses to climate vary within and across species. However, intra- and interspecific variation in phenological responses is seldom considered simultaneously, limiting our understanding of climate change impacts on interactions among taxa across their ranges. We investigated how variation in phenological sensitivity to climate can alter ecological interactions simultaneously within and among species using natural history collections and citizen science data. We focus on a unique system, comprising a wide-ranged spring ephemeral with varying color morphs (Claytonia virginica) and its specialist bee pollinator (Andrena erigeniae). We found strongly opposing trends in the phenological sensitivities of plants vs their pollinators. Flowering phenology was more sensitive to temperature in warmer regions, whereas bee phenology was more responsive in colder regions. Phenological sensitivity varied across flower color morphs. Temporal synchrony between flowering and pollinator activity was predicted to change heterogeneously across the species' ranges in the future. Our work demonstrates the complexity and fragility of ecological interactions in time and the necessity of incorporating variation in phenological responses across multiple axes to understand how such interactions will change in the future.

From data pipelines to FAIR data infrastructures: A vision for the new horizons of bio- and geodiversity data for scientific research

Natural science collections are vast repositories of bio- and geodiversity specimens. These collections, originating from natural history cabinets or expeditions, are increasingly becoming unparalleled sources of data facilitating multidisciplinary research (Meineke et al. 2018, Heberling et al. 2019, Cook et al. 2020, Thompson et al. 2021). Due to various global data mobilization and digitisation efforts (Blagoderov et al. 2012,Nelson and Ellis 2018), this digitised information about specimens includes database records along with two/three-dimensional images, sonograms, sound or video recordings, computerised tomography scans, machine-readable texts from labels on the specimens as well as media items and notes related to the discovery sites and acquisition (Hedrick et al. 2020,Phillipson 2022).

The scope and practice of specimen gathering are also evolving. The term extended specimen was coined to refer to the specimen and associated data extending beyond the singular physical object to other physical or digital entities such as chemical composition, genetic sequence data or species data. Thus the specimen becomes an interconnected network of data resources that have incredible potential to enhance integrative and data-driven research (Webster 2017,Lendemer et al. 2019,Hardisty et al. 2022). These practices also reflect the role of data and the curatorial data life-cycle starting from the initial material sampling process to the downstream analysis. We are also seeing growing acknowledgement that disparate and domain specific data elements prevent interdisciplinarity which is crucial for a holistic understanding of biodiversity and climate crisis (Hicks et al. 2010, Craven et al. 2019, Folk and Siniscalchi 2021).

Thus the data elements are not just records or rows in a database or data pipelines going from one repository to another. They have the potential to become self-describing digital artefacts that can revolutionise how machines interpret and work with specimen data. Within this context, the Distributed System of Scientific Collections (DiSSCo), a new European Research Infrastructure for natural science collections, envisions an infrastructure based on FAIR Digital Objects (FDO) that can unify more than 170 European natural science collections under common and FAIR-compliant (Findable, Accessible, Interoperable, Reusable) (Wilkinson et al. 2016) access and curation policies and practices. DiSSCo’s key element in achieving FAIR is the implementation of Digital Specimen (a domain specific FDO) that closely aligns with the extended specimen practices. The idea behind Digital Specimen – an FDO that acts as a digital surrogate for a specific physical specimen in a natural science collection – was influenced by global conversations around the implementation of the Digital Object Architecture for biodiversity data (De Smedt et al. 2020, Islam et al. 2020,Hardisty et al. 2020).

The main purpose of this talk is to explain the vision of how FAIR and FDO can create a data infrastructure that can not only take advantage of existing databases and repositories but at the same time provide support for innovative services such as AI and digital twinning. With scientific use cases in mind, the talk will highlight a few key FAIR and FDO components (persistent identifiers, metadata, ontologies) within the collaborative modelling activity of Digital Specimen specification. These components provide the template for specifying how a Digital Specimen should look so DiSSCo can build a FAIR service ecosystem based on FDOs (Addink et al. 2021). We will also give examples of envisioned services that can help with image feature extraction, and model training (Grieb et al. 2021,Hardisty et al. 2022) and digital twinning (Schultes et al. 2022). We believe this is an exciting new paradigm powered by FAIR and FDO that can help both humans and machines to accelerate the use of specimen data. From physical objects curated over hundred years, we have developed data pipelines, aggregators and repositories (Barberousse 2021). Now is the time to look for solutions where these data records can become FAIR Digital Objects to enable wider access and multidisciplinary research.

Improving species-based area protection in Antarctica

Area protection is a major mechanism deployed for environmental conservation in Antarctica. Yet, the Antarctic protected areas network is widely acknowledged as inadequate, in part because the criteria for area protection south of 60°S are not fully applied. The most poorly explored of these criteria is the type locality of species, which provides the primary legal means for Antarctic species-based area protection and a method for conserving species even if little is known about their habitat or distribution. The type locality criterion has not been systematically assessed since its incorporation into the Protocol on Environmental Protection to the Antarctic Treaty in 1991, so the extent to which the criterion is being met or might be useful for area protection is largely unknown. To address the matter, we created and analyzed a comprehensive database of Antarctic type localities of terrestrial and lacustrine lichens, plants, and animals. We compiled the database via a literature search of key taxonomic and geographic terms and then analyzed the distance between type localities identifiable to a ≤ 25km² resolution and current Antarctic Specially Protected Areas (ASPAs) and human infrastructure. We used a distance-clustering approach for localities outside current ASPAs to determine candidate protected areas that could contain these unprotected localities. Of the 386 type localities analyzed, 108 were within or overlapped current ASPAs. Inclusion of the remaining 278 type localities in the ASPA network would require the designation of a further 105 protected areas. Twenty-four of these areas included human infrastructure disturbance. Given the slow rate of ASPA designation, growing pace of human impacts on the continent, and the management burden associated with ASPAs, we propose ways in which the type locality criterion might best be deployed. These include a comprehensive, systematic conservation planning approach and an alternative emphasis on the habitat of species, rather than on a single locality.

New directions in tropical phenology

Earth's most speciose biomes are in the tropics, yet tropical plant phenology remains poorly understood. Tropical phenological data are comparatively scarce and viewed through the lens of a 'temperate phenological paradigm' expecting phenological traits to respond to strong, predictably annual shifts in climate (e.g., between subfreezing and frost-free periods). Digitized herbarium data greatly expand existing phenological data for tropical plants; and circular data, statistics, and models are more appropriate for analyzing tropical (and temperate) phenological datasets. Phylogenetic information, which remains seldom applied in phenological investigations, provides new insights into phenological responses of large groups of related species to climate. Consistent combined use of herbarium data, circular statistical distributions, and robust phylogenies will rapidly advance our understanding of tropical - and temperate - phenology.

Past and future uses of text mining in ecology and evolution

Ecology and evolutionary biology, like other scientific fields, are experiencing an exponential growth of academic manuscripts. As domain knowledge accumulates, scientists will need new computational approaches for identifying relevant literature to read and include in formal literature reviews and meta-analyses. Importantly, these approaches can also facilitate automated, large-scale data synthesis tasks and build structured databases from the information in the texts of primary journal articles, books, grey literature, and websites. The increasing availability of digital text, computational resources, and machine-learning based language models have led to a revolution in text analysis and natural language processing (NLP) in recent years. NLP has been widely adopted across the biomedical sciences but is rarely used in ecology and evolutionary biology. Applying computational tools from text mining and NLP will increase the efficiency of data synthesis, improve the reproducibility of literature reviews, formalize analyses of research biases and knowledge gaps, and promote data-driven discovery of patterns across ecology and evolutionary biology. Here we present recent use cases from ecology and evolution, and discuss future applications, limitations and ethical issues.

Evidence for continent-wide convergent evolution and stasis throughout 150 y of a biological invasion

Adaptive evolution can help species to persist and spread in new environments, but it is unclear how the rate and duration of adaptive evolution vary throughout species ranges and on the decadal timescales most relevant to managing biodiversity for the 21st century. Using herbarium records, we reconstruct 150 y of evolution in an invasive plant as it spread across North America. Flowering phenology evolves to adapt to local growing seasons throughout the range but stalls after about a century. This punctuated, convergent evolution recapitulates long-term dynamics in the fossil record, implicating limits to evolutionary rates that are not evident for the first century of spread.

The extent to which evolution can rescue a species from extinction, or facilitate range expansion, depends critically on the rate, duration, and geographical extent of the evolutionary response to natural selection. Adaptive evolution can occur quickly, but the duration and geographical extent of contemporary evolution in natural systems remain poorly studied. This is particularly true for species with large geographical ranges and for timescales that lie between “long-term” field experiments and the fossil record. Here, we introduce the Virtual Common Garden (VCG) to investigate phenotypic evolution in natural history collections while controlling for phenotypic plasticity in response to local growing conditions. Reconstructing 150 y of evolution in Lythrum salicaria (purple loosestrife) as it invaded North America, we analyze phenology measurements of 3,429 herbarium records, reconstruct growing conditions from more than 12 million local temperature records, and validate predictions across three common gardens spanning 10° of latitude. We find that phenological clines have evolved repeatedly throughout the range, during the first century of evolution. Thereafter, the rate of microevolution stalls, recapitulating macroevolutionary stasis observed in the fossil record. Our study demonstrates that preserved specimens are a critical resource for investigating limits to evolution in natural populations. Our results show how natural selection and trade-offs measured in field studies predict adaptive divergence observable in herbarium specimens over 15 decades at a continental scale.

Decoding family-level features for modern and fossil leaves from computer-vision heat maps

PREMISE

Angiosperm leaves present a classic identification problem due to their morphological complexity. Computer-vision algorithms can identify diagnostic regions in images, and heat map outputs illustrate those regions for identification, providing novel insights through visual feedback. We investigate the potential of analyzing leaf heat maps to reveal novel, human-friendly botanical information with applications for extant- and fossil-leaf identification.

METHODS

We developed a manual scoring system for hotspot locations on published computer-vision heat maps of cleared leaves that showed diagnostic regions for family identification. Heat maps of 3114 cleared leaves of 930 genera in 14 angiosperm families were analyzed. The top-5 and top-1 hotspot regions of highest diagnostic value were scored for 21 leaf locations. The resulting data were viewed using box plots and analyzed using cluster and principal component analyses. We manually identified similar features in fossil leaves to informally demonstrate potential fossil applications.

RESULTS

The method successfully mapped machine strategy using standard botanical language, and distinctive patterns emerged for each family. Hotspots were concentrated on secondary veins (Salicaceae, Myrtaceae, Anacardiaceae), tooth apices (Betulaceae, Rosaceae), and on the little-studied margins of untoothed leaves (Rubiaceae, Annonaceae, Ericaceae). Similar features drove the results from multivariate analyses. The results echo many traditional observations, while also showing that most diagnostic leaf features remain undescribed.

CONCLUSIONS

Machine-derived heat maps that initially appear to be dominated by noise can be translated into human-interpretable knowledge, highlighting paths forward for botanists and paleobotanists to discover new diagnostic botanical characters.

DNA barcoding of the National Museum of Natural History reptile tissue holdings raises concerns about the use of natural history collections and the responsibilities of scientists in the molecular age

Natural history collections are essential to a wide variety of studies in biology because they maintain large collections of specimens and associated data, including genetic material (e.g., tissues) for DNA sequence data, yet they are currently under-funded and collection staff have high workloads. With the advent of aggregate databases and advances in sequencing technologies, there is an increased demand on collection staff for access to tissue samples and associated data. Scientists are rapidly developing large DNA barcode libraries, DNA sequences of specific genes for species across the tree of life, in order to document and conserve biodiversity. In doing so, mistakes are made. For instance, inconsistent taxonomic information is commonly taken from different lending institutions and deposited in data repositories, such as the Barcode of Life Database (BOLD) and GenBank, despite explicit disclaimers regarding the need for taxonomic verification by the lending institutions. Such errors can have profound effects on subsequent research based on these mis-labelled sequences in data repositories. Here, we present the production of a large DNA barcode library of reptiles from the National Museum of Natural History tissue holdings. The library contains 2,758 sequences (2,205 COI and 553 16S) from 2260 specimens (four crocodilians, 37 turtles, and 2,219 lizards, including snakes), representing 583 named species, from 52 countries. In generating this library, we noticed several common mistakes made by scientists depositing DNA barcode data in public repositories (e.g., BOLD and GenBank). Our goal is to raise awareness of these concerns and offer advice to avoid such mistakes in the future to maintain accurate DNA barcode libraries to properly document Earth’s biodiversity.

Ali-Bey - an open collaborative georeferencing web application

Background

Georeferencing preserved specimens represents a major effort at the Museu de Ciències Naturals de Barcelona (MCNB), given the available resources and limited staff that can be allocated to the task. Georeferencing is a labour-intensive and hard-to-automate task that requires software tools that can help in making it as efficient as possible. The tool we present, Ali-Bey, has been slowly developed over 15 years and its functionalities have been gradually built in a process of development, testing, use in production and refinement, rather than as a single development cycle out of a comprehensive specifications requirement document. At the start, the MCNB could not find a tool that fully satisfied the requirements listed as essential and made the decision to develop a custom tool. At the end, the initiative has proved successful since it has delivered a new georeferencing tool that meets the MCNB's needs, all in a context of yearly scarce availability of funds. The tool has been gradually matured and developed over the years, in line with the scarce financing. Only recently, after reaching a notable set of novel features, we considered to release it as an open-source project. The MCNB has supported its development up until this date and decided to open it in order to give the NHC community the opportunity to contribute to its development.

New information

We present the software tool Ali-Bey that provides new functionality for the georeferencing of specimens in Natural History Collections, namely the possibility of cooperation between different institutions, the traceability of georeferences and the capability of managing different versions of a same site name, namely for historical reasons. The tool is an open-source web application implemented in Python and the Django framework that leverages other commonly-used specialised geodatabase and map server tools. An API provides access to the geodatabase to externally-developed tools. In addition, for an easy installation, the tool is provided as a multi-container Docker application.