Naturalis Research Articles

Assessment of targeted enrichment locus capture across time and museums using odonate specimens

Abstract The use of gDNAs isolated from museum specimens for high throughput sequencing, especially targeted sequencing in the context of phylogenetics, is a common practice. Yet, little understanding has been focused on comparing the quality of DNA and results of sequencing museum DNAs. Dragonflies and damselflies are ubiquitous in freshwater ecosystems and are commonly collected and preserved insects in museum collections hence their use in this study. However, the history of odonate preservation across time and museums has resulted in wide variability in the success of viable DNA extraction, necessitating an assessment of their usefulness in genetic studies. Using Anchored Hybrid Enrichment probes, we sequenced DNA from samples at 2 museums, 48 from the American Museum of Natural History (AMNH) in NYC, USA and 46 from the Naturalis Biodiversity Center (RMNH) in Leiden, Netherlands ranging from global collection localities and across a 120-year time span. We recovered at least 4 loci out of an >1,000 locus probe set for all samples, with the average capture being ~385 loci (539 loci on average when a clade of ambiguous taxa omitted). Neither specimen age nor size was a good predictor of locus capture, but recapture rates differed significantly between museums. Samples from the AMNH had lower overall locus capture than the RMNH, perhaps due to differences in specimen storage over time.

Type specimens of non-passerines in Naturalis Biodiversity Center (Animalia, Aves).

The non-passerine type specimens in Naturalis Biodiversity Center, Leiden are listed as an update to Van den Hoek Ostende et al. (1997) 'Type-specimens of birds in the National Museum of Natural History, Leiden, Part 1. Non-Passerines' and Roselaar and Prins (2000) 'List of type specimens of birds in the Zoological Museum of the University of Amsterdam (ZMA), including taxa described by ZMA staff but without types in the ZMA'. All new names published by Temminck and Schlegel are listed, even when types are not in Naturalis but in other collections. We have added 380 new names and deleted 13 names originally listed in Van den Hoek Ostende et al. (1997).

Salvinia plants in trade: what species are we actually talking about?

AbstractIncorrect labelling of plants in trade and misidentification are widespread. Likewise, in trade numerous names are being used for the ornamental aquatic plant known as ‘Kariba weed’, but rarely the correct scientific name Salvinia molesta Mitch. For inspection services of EPPO member countries, correct identification of S. molesta has become important since the species was added to the EPPO A2 List and the List of Union concern in accordance with EU regulation 1143/2014 based on an EPPO Pest Risk Analysis (PRA) for the species. Inspections and a targetted survey of Salvinia plants in trade in the Netherlands were performed and additional material was obtained from wild sources in South Africa, Hungary and the United States. Specimen identification was verified by comparison with the herbarium collection at Naturalis Biodiversity Center in Leiden and with the sequences available in NCBI GenBank database. This paper provides the tools to correctly identity the relevant Salvinia species.

The book herbaria of Jacob Breyne (1637–1697) in the collection of Naturalis Biodiversity Center (Leiden, the Netherlands)

Historic herbaria can provide a wealth of information on a diversity of topics, including the past occurrence of plants, their abundance, names and uses. However,16th and 17th century herbaria are rare and very fragile, and can best be studied after digitization. The collection of Naturalis Biodiversity Center in Leiden, the Netherlands, contains two book herbaria by Jacob Breyne (1637–1697) of Danzig (presently Gdańsk, Poland). These herbaria, dated 1659 and 1673, contain a total of 105 specimens in various states of intactness, and with or without original labels. The identity of the specimens in the Leiden Breyne herbaria was not completely assessed previously. Here we discuss the taxa represented within these two historic herbaria as well as the information contained in the handwritten texts with in them. The two Breyne herbaria combined were found to contain 62 species, representing 24 plant families. Both herbaria contain several species now rare around Gdańsk, including two species currently considered regionally extinct (Swertia perennis (Gentianaceae) and Dactylorhiza viridis (Orchidaceae)). Labels with the specimens give a range of information on the collecting locations, ecology, abundance and/or use of the species. The Leiden Breyne herbaria reveal changes in the flora of northern Poland over the course of three centuries, as well as pre-Linnaean nomenclature, historic uses of plants and international correspondence between scientists.

Disappearance or overlooked or untouched? - A brief history of aquatic gastropods of Malaysian Borneo

The aquatic gastropods (marine and freshwater) in Malaysian Borneo (MYB) have an ancient history of 255 years, while the first record was observed in 1767 by the pioneer Carl Linnaeus. Over time, many European, native taxonomists and conservationists have worked on the diverse group of gastropods in the Malaysian part of Borneo (states of Sabah and Sarawak). No previous work has been conducted to assess the historical status of this particular class of Mollusca. The study objective was to reveal the types of aquatic gastropods and the number of published research and expeditions conducted in MYB. The bibliometric analysis found 145 research publications mentioning the names of the region and reporting at least one gastropod species from this geographic region. Over the history of 255 years, a total of 559 gastropod species were reported by different research groups. Between 1767 and 1900, a total of 150 gastropod species were reported, followed by 79 species from 1900 to 2000 and 330 species from 2001 to 2022. The Grubbs test (p<0.05) identified outlier years for the reporting of gastropod species from MYB with 54 new species each in 2011 and 2020 and 39 species in 2001. Over the history of aquatic gastropod research in MYB, the taxonomists making the greatest contribution were Han Raven and his colleagues from Naturalis Biodiversity Center, The Netherlands, The Netherlands, who reported 111 new species from the region, followed by Nur Leena Wong from Universiti Putra Malaysia (54 new species). The results suggested that reporting of new species from MYB is increasing, which may reflect the many unexplored sites and suggests the existence of as yet unrecorded species in this ecoregion. In this regard further expeditions and research should improve estimates of the true number of aquatic gastropod species in this area. These results can help the regional governments in making a regional biodiversity database as well as in taking decisions regarding aquatic gastropod research and management.

Optimisation of the measurement and evaluation process through an information system

This paper deals with the digitalisation of production documentation and optimisation of measurement and evaluation processes through the DRM information system, its functionality and use The business environment is constantly changing, shaping and adapting to market requirements. Due to these changes, it is becoming increasingly difficult to think predictively and strategically and identify future opportunities or threats. Among these changes' most recent and significant triggers, we can consider the global pandemic caused by the covid-19 disease, which highlights the essence and nature of IS and digitalisation more than anything else. The importance of information systems is thus to process data from a company's inputs to generate helpful information for managing business operations and processes.

Ammonia in the interstellar medium of a starbursting disc at z = 2.6

ABSTRACT We report the detection of the ground state rotational emission of ammonia, ortho-NH3 (JK = 10 → 00) in a gravitationally lensed intrinsically hyperluminous star-bursting galaxy at z = 2.6. The integrated line profile is consistent with other molecular and atomic emission lines which have resolved kinematics well modelled by a 5 kpc-diameter rotating disc. This implies that the gas responsible for NH3 emission is broadly tracing the global molecular reservoir, but likely distributed in pockets of high density (n ≳ 5 × 104 cm−3). With a luminosity of 2.8 × 106 L⊙, the NH3 emission represents 2.5 × 10−7 of the total infrared luminosity of the galaxy, comparable to the ratio observed in the Kleinmann–Low nebula in Orion and consistent with sites of massive star formation in the Milky Way. If $L_{\rm NH_3}/L_{\rm IR}$ serves as a proxy for the ‘mode’ of star formation, this hints that the nature of star formation in extreme starbursts in the early Universe is similar to that of Galactic star-forming regions, with a large fraction of the cold interstellar medium in this state, plausibly driven by a storm of violent disc instabilities in the gas-dominated disc. This supports the ‘full of Orions’ picture of star formation in the most extreme galaxies seen close to the peak epoch of stellar mass assembly.

ARISE: Building an infrastructure for species recognition and biodiversity monitoring in the Netherlands

ARISE (Authoritative and Rapid Identification System for Essential biodiversity information) is a digital infrastructure with the mission to provide semi-automated identification of all multicellular species in the Netherlands and innovate on biodiversity monitoring solutions. By applying DNA barcoding, artificial intelligence for species recognition based on images, sound and radar, and emerging technology for biodiversity monitoring, we can radically speed up the inventory of life on earth. The infrastructure relies on a species reference database, which brings together new and existing biodiversity information on all multicellular species in the Netherlands. ARISE will be open-access and organize data according to FAIR principles (findable, accessible, interoperable and reusable). We will develop the infrastructure for the Dutch research community with financial support from the Dutch Research Council. ARISE is a partnership between the Naturalis Biodiversity Center, the University of Amsterdam, Westerdijk Institute and the University of Twente. With an Agile development approach, we will build iteratively guided by use cases and real-life challenges. Facilities and services include streamlined and accesible species sampling and (meta)barcoding, machine learning services to analyse digital input and a digital platform where all data and services come together powered by a state of the art data management system based on digital objects. We will be driven by continuous feedback from external scientists and representatives of species monitoring organizations. With ARISE, we will provide the scientific community with the foundation for automated recognition and monitoring of the entire Dutch biodiversity. Furthermore, ARISE will provide a basis for better biodiversity monitoring to provide policy makers with more reliable information on biodiversity and ecosystem change. This presentation will give an overview of work in progress, demonstrating several pilot versions of facilities and services, and what we envision to build in the future.

Results of a small terrestrial mammal survey in the remote Boé region of Guinea‐Bissau, with discovery of two new shrew records for the country

AbstractThe Boé region in the south‐east of Guinea‐Bissau has remained untouched by large‐scale human influence and development due to its isolated location. The region consists mainly of savannah interspersed with gallery forests and hosts a unique and valuable biodiversity though very little is known of small terrestrial mammal diversity. In 2013, a terrestrial small mammal live trapping survey was conducted around Béli, a small village in the South of the Boé region. Five survey locations of three ecotypes were selected, and a combination of pitfall traps and live traps was used to capture and release small mammals. A selection of mammals that could not be identified as well as accidental mortalities in the traps were collected as voucher specimens and sent to Naturalis Biodiversity Center in the Netherlands. Over 96 survey days, a total of 331 small terrestrial mammals were trapped from 21 unique species, which include two new species records for the country: shrew species Crocidura lamottei and Crocidura crossei. Extrapolation from species accumulation curves suggested an overall species richness of 22 species for the region, with substantial differences in community composition among sampled habitats. The results of this study are an important part of the scientific record for small terrestrial mammals in the Boé region and set a baseline reference for future conservation efforts.

Mediterranean specimens of the Prussian Botanist Jacob Breyne (1637–1697) in the Van Royen Herbarium, Leiden, The Netherlands

ABSTRACT Directors of the Leiden botanic garden Adriaan van Royen (1704–1779) and his nephew David van Royen (1727–1799) accumulated a large number of plant specimens in their herbarium collection. The “Van Royen herbarium” at Naturalis Biodiversity Center (Leiden, the Netherlands) holds 89 specimens currently attributed to the Prussian botanist Jacob Breyne (1637–1697). The identity, provenance and history of these Breyne specimens were never studied, although this collection may contain specimens missing from two book herbaria by Breyne (dated 1659 and 1673). Here, we reveal the species represented by the Breyne specimens in the Van Royen collection, as well as their origin and the information contained on their labels. A total of 75 species were identified in Breyne’s specimens, mostly collected in the surroundings of Montpellier (south-eastern France). Of the 89 specimens attributed to Breyne, 54 contain labels in his own handwriting, confirming they were collected (or at least owned) by him. The specimens are not derived from Breyne’s book herbaria also kept in the Leiden collection, as these contain mostly Polish plants. Breyne most likely did not collect these specimens himself, but received them from one or several of his correspondents with ties to Montpellier. It is not known how Breyne’s specimens ended up in the Van Royen herbarium (possibly through his son Johann Philipp), but they provide an insight in the flora of Mediterranean France in the 17th century, and reflect changes in nomenclature and the state of botanical science at that time.

A historical specimen of the Fishing Cat, Prionailurus viverrinus (Bennett, 1833) (Carnivora, Felidae) from Singapore in the zoological collection of the Naturalis Biodiversity Center, Leiden

The Fishing Cat is not a species known to inhabit Singapore. However, a historical specimen stated to have come from Singapore in 1819 and attributed to Pierre-Médard Diard (RMNH.MAM.59688) is now housed at Naturalis Biodiversity Center, Leiden, the Netherlands. Two hundred years after it was obtained, the mounted skin and skull of this specimen, including specimen labels, were photographed and digitally catalogued. Four sets of annotations from labels and a document detailing records and a receipt of specimens sent by Diard to Leiden are presented to ascertain the specimen’s identity, followed by a historical account of Diard based on a reconstruction of the timeline of key events of Singapore’s natural history. Subsequently, the specimen is examined to confirm its taxonomic identity using comparative morphometrics with other museum specimens, and data associated with the specimen are analysed to determine the origins of this specimen. We conclude that the current evidence does not allow confirmation of the specimen’s status as having been collected in Singapore or being obtained from the pet trade. If the specimen was an imported specimen, it would point towards a trade in rare and large animals in Singapore and the region from as early as 1819. Presently, the specimen remains one of the few extant zoological specimens obtained in Singapore in 1819 and the only one currently known outside of England.

The four W's of two 18th century Dutch herbaria: the 'Zierikzee Herbarium' and the herbarium of Simon D'Oignies

One of the objects of the Municipal Museum Zierikzee (Province of Zealand, The Netherlands) is a historical herbarium referred to by the name the 'Zierikzee Herbarium'. The characteristics of the specimens in the Zierikzee Herbarium are so similar to those in a herbarium at Naturalis Biodiversity Center, Leiden(L), that both must originate from the same place and time. About the latter herbarium little is known, except that it was once owned by the army-surgeon Simon(e) d'Oignies (1740–1782). The Zierikzee Herbarium was recently described and analysed in detail by Offerhaus et al. (2021). It is hypothesised that the Zierikzee Herbarium is part of a herbarium made by Professor Martinus Wilhelmus Schwencke (1707–1785) and was used during his lectures for future pharmacists in his botanical garden in The Hague in the 1750s, and auctioned in Leiden in 1785. The presence in the Zierikzee Herbarium of a virtually complete set of medicinal plants mentioned in the 'Pharmacopoea Hagana' (Anonymous 1738) eventually led to the conclusion that these could not have been assembled before 1730. Based on the printed ornaments that are used to mount the plants in these, and the major Dutch herbaria of the 18th century, I argue that the plants in the Zierikzee Herbarium and the herbarium of D'Oignies were remounted at a later date. The hypothesis by Offerhaus et al. (2021: 12) that the Zierikzee Herbarium was started between 1710 and 1720 is rejected. Arguments are given why it is unlikely that the Zierikzee Herbarium, as is suggested by Offerhaus et al. (2021: 12), is the herbarium of the head gardener of the Leiden botanic garden, Jacob Ligtvoet (1684–1752) and was auctioned in 1752.

A list of water mite types transferred from the Museum of the Natural History in Podgorica and deposited in other museums

A list of the water mites (Acari, Hydrachnidia) types originally stated to be deposited in the Museum of Natural History in Montenegro, Podgorica, Montenegro and later on transferred to Museum of Natural History in Basel (Switzerland) and Naturalis Biodiversity Center in Leiden (the Netherlands) is given.

Synoptic revision of Kolobopetalum and Rhigiocarya (Menispermaceae) with the description of a new Kolobopetalum species from Gabon, and a new specific combination in Rhigiocarya from West Africa

Background and aims – In the framework of the Menispermaceae treatment for the Flore du Gabon, the closely related genera Kolobopetalum and Rhigiocarya are synoptically revised.Material and methods – Standard practices of herbarium taxonomy have been applied to study the relevant herbarium material from B, BM, BR, BRLU, HBG, K, L, P, U, and WAG. The relevant collecting data are stored in the Botany Section of the Naturalis Biodiversity Center, Leiden, The Netherlands.Key results – The distinction between the genera Kolobopetalum and Rhigiocarya is further investigated and improved. As a result, Kolobopetalum leonense is transferred to Rhigiocarya. The Gabonese collections of Kolobopetalum contained a new species named K. synsepalum, which is described and illustrated. Rhigiocarya nervosa is resurrected as a distinct species. The distribution of all species is mapped. Illustrations are provided to facilitate the use of the key for the two genera and their species.

Addition to a checklist of the water mites of Turkey (Acari: Hydrachnidia) with description of two new species

In the publication of Erman et al. (2010), the depository for the holotypes of Atractides (Atractides) anatolicus Pešić, Erman &amp; Esen sp. nov. and Atractides (Atractides) martini Pešić, Erman &amp; Esen sp. nov., respectively, was not given. Therefore, the names of both species are invalid (International Code of Zoological Nomenclature 1999, Art. 16.4.2). We declare here that the holotype male of Atractides anatolicus and the holotype male of Atractides martini are deposited in the Naturalis Biodiversity Center in Leiden (RMNH). The purpose of this note is to validate the name of both new species (International Code of Zoological Nomenclature 1999, Art. 13.1.2).

A checklist of Scoliidae (Insecta: Hymenoptera) from China

A checklist of all confirmed species of the family Scoliidae (Hymenoptera) from China is made based on the Chinese specimens in the Naturalis Biodiversity Center (RMNH, Leiden) and on additional specimens from the Chinese Academy of Insect Science (IOZ, Beijing), the Zhejiang University (ZJUH, Hangzhou), and the Sun Yat-sen University (SYSUBM, Guangzhou). The Scoliid species from China belong to one subfamily, two tribes, 11 genera and 52 species. Two species are deleted from the fauna of China: Campsomeriella ilanensis (Tsuneki, 1972) and Scolia (Discolia) quadripustulata Fabricius, 1782. One subspecies, i.e., Carinoscolia vittifrons nipponensis Uchida, 1933, status nov., is elevated to species rank. Scolia (Discolia) formosicola Betrem, 1928, status nov. and S. (D.) inouyei Okamoto, 1924 are re-instated valid species.

Illustrated keys to Scoliidae (Insecta, Hymenoptera, Scolioidea) from China.

The Scoliidae occur predominantly in tropical and subtropical regions and are ectoparasitoids of Scarabaeoidea larvae (especially of Melolonthinae) which are immobilised, parasitised by the female wasp in their terrestrial larval gallery and buried deeper in a special cell by the female wasp. Herein, we provided, for the first time, illustrated keys to 11 genera and 52 species of Scoliidae from China, based on specimens in the Naturalis Biodiversity Center (RMNH, Leiden) and additional specimens from the Chinese Academy of Insect Science (Beijing), Zhejiang University (ZJUH, Hangzhou) and Sun Yat-sen University (SYSU, Guangzhou) and it is a first attempt to make keys available for all the Scoliidae species in China.

Redescription of Paraclimenes gorgonicola (Bruce, 1969) (Crustacea: Decapoda: Palaemonidae) and establishing P. franklini (Bruce, 1990) as its junior synonym.

The octocoral associated species Paraclimenes gorgonicola is a deep-sea palaemonid shrimp briefly described in Bruce (1969) without illustrations. Paraclimenes franklini, the type species of the genus Paraclimenes, has been considered as a valid species and distinguished from P. gorgonicola by the presence of articulated postrostral teeth on the carapace. Paraclimenes gorgonicola is herein fully redescribed and illustrated on the basis of the type series which is deposited in Naturalis Biodiversity Center, Leiden, The Netherlands and recently collected specimens from shallow waters around Jejudo Island, Korea, and compared with P. franklini. It is demonstrated that both taxa are conspecific and thus P. franklini is considered to be a junior synonym of P. gorgonicola.

Mycale species of the tropical Indo-West Pacific (Porifera, Demospongiae, Poecilosclerida).

The species of the cosmopolitan sponge genus Mycale occurring in the tropical Indo-West Pacific region and adjacent subtropical waters are reviewed taxonomically. Specimens incorporated in the collections of the Naturalis Biodiversity Center form the basis of this comprehensive study, supplemented by (type) specimens borrowed from or examined in other institutions. Specimens available numbered 351, belonging to 44 species, including 14 species new to science, Mycale (Aegogropila) prognatha sp.nov., Mycale (Carmia) amiri sp.nov., Mycale (Carmia) fungiaphila sp.nov., Mycale (Carmia) monomicrosclera sp.nov., Mycale (Carmia) tenuichela sp.nov., Mycale (Carmia) tubiporicola sp.nov., Mycale (Carmia) tydemani sp.nov., Mycale (Mycale) asigmata sp.nov., Mycale (Mycale) grandoides sp.nov., Mycale (Mycale) sundaminorensis sp.nov., Mycale (Naviculina) mascarenensis sp.nov., Mycale (Paresperella) sceptroides sp.nov., Mycale (Paresperella) seychellensis sp.nov., Mycale (Zygomycale) sibogae sp.nov. Three species, indicated by the designation 'aff.', were not definitely assigned to known or new species due to uncertainty of their identity. The genus Kerasemna, previously considered a junior synonym of Mycale, was revived as an additional subgenus Mycale (Kerasemna). One species, previously assigned to the genus Desmacella as D. lampra De Laubenfels is here reassigned to Mycale, subgenus at present undecided. Additionally, species previously reported from the region but not represented in our collections are briefly characterized and discussed. We propose new names Mycale (Mycale) mauricei nom.nov. for Mycale macrochela Burton (junior primary homonym of Mycale fistulata var. macrochela Hentschel) and Mycale (Mycale) bouryesnaultae nom.nov. for Mycale (Mycale) fibrosa Boury-Esnault Van Beveren (junior primary homonym of Mycale (Aegogropila) adhaerens subsp. fibrosa Koltun). Keys to the species of each subgenus occurring in the region are provided. The opportunity of having studied this comprehensive set of species and specimens from the tropical Indo-West Pacific is taken to review and discuss the morphological and biogeographical data gathered so far on the genus Mycale. The genus currently comprises approximately 255 accepted species, with highest diversity focused in tropical Atlantic and Indo-West Pacific regions as well as in warm-temperate Mediterranean-Atlantic regions.

Revision of the genus Coeliccia Kirby in Borneo part III: Two new species from the C. membranipes-group from Sarawak and Brunei (Odonata: Zygoptera: Platycnemididae).

Coeliccia junis sp. nov. (holotype male from Borneo, Sarawak, Bintulu Division, Planted Forest Project, Bukit Mina Wildlife Corridor, "Day 4" stream near Bukit Nyegoh and Bukit Jugam, near small brown water pool, 10 viii 2018, deposited in the Naturalis Biodiversity Center, Leiden, the Netherlands) and Coeliccia roberti sp. nov. (holotype male from Borneo, Sarawak, Miri Division, Lambir Hills National Park, small stream on Oil Well Trail, 22 iv 2011, deposited in the Naturalis Biodiversity Center, Leiden, the Netherlands) are described from Borneo. Both new species belong to the Coeliccia membranipes-group and bring the number of named species known from the group from Borneo to nine and the total number of named species from Borneo currently placed in Coeliccia to 15. Coeliccia junis is only known from a small area in Sarawak, C. roberti is also known from Brunei. Both species are considered likely to be closely allied with C. macrostigma Laidlaw.