Resolution of the type material of the Asian elephant, Elephas maximus Linnaeus, 1758 (Proboscidea, Elephantidae)

Cappellini, Enrico; Gentry, A. W.; Palkopoulou, Eleftheria; Ishida, Yasuko; Cram, David; Roos, Anna-Marie; Watson, Mick; Johansson, Ulf S.; Fernholm, Bo; Agnelli, Paolo; Barbagli, Fausto; Littlewood, D. Tim J.; Kelstrup, Christian D.; Olsen, Jesper V.; Lister, Adrian M.; Roca, Alfred L.; Dalén, Love; Gilbert, Martin

doi:10.1111/zoj12084

Cited by 22 publications

(27 citation statements)

References 23 publications

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“…Dental calculus was removed from archaeological specimens using a sterile dental scaler and stored in sterile 2.0-mL tubes. Peptides were extracted from decalcified dental calculus using a filter-aided sample preparation (FASP) protocol modified for degraded samples (Cappellini et al 2014) according to previously published protocols (Warinner et al 2014a, b). The extracted peptides were then analysed using shotgun protein tandem mass spectrometry (MS/MS) at the Central Proteomics Facility, Target Discovery Institute, Oxford on a Q-Exactive tandem mass spectrometer (see Supplementary Information).…”

Section: Methodsmentioning

confidence: 99%

New insights into Neolithic milk consumption through proteomic analysis of dental calculus

Charlton

Ramsøe

Collins

et al. 2019

Archaeol Anthropol Sci

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There has long been debate over the origins of dairy consumption within European populations. Whilst it was previously assumed that lactase persistence (LP) was under positive selection following the advent of agriculture, recent genetic studies of prehistoric human remains have revealed LP may have only emerged in Europe in the last 4000 years. These findings stand in contrast to organic residue analysis of Neolithic pottery indicating the utilisation of dairy products, and zooarchaeological mortality profiles consistent with dairying herds at Neolithic sites. The recent discovery of the milk protein β-lactoglobulin (BLG) within human dental calculus presents a new method via which to explore dairy product consumption in the archaeological past. Here, we apply shotgun proteomic analysis to dental calculus samples from three British Neolithic sites, revealing the earliest identification of BLG in human dental calculus to date. The presence of BLG peptides in individuals who are unlikely to possess LP provides new insight into dairying in the British Neolithic, suggesting the potential processing of milk by Neolithic populations to reduce the lactose content of dairy products.

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Section: Methodsmentioning

confidence: 99%

New insights into Neolithic milk consumption through proteomic analysis of dental calculus

Charlton

Ramsøe

Collins

et al. 2019

Archaeol Anthropol Sci

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“…While the example is contrived, in practice such type reinterpretations are not infrequent (e.g. Ribot et al., ; Woodley et al., ; Cappellini et al., ; Laloy et al., ; Witteveen, ). Reassessments of the taxonomic identity of type specimens are very frequently involved in determining heterotypic synonymy.…”

Section: Methodsmentioning

confidence: 99%

A logic approach to modelling nomenclatural change

2017

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We utilize an Answer Set Programming (ASP) approach to show that the principles of nomenclature are tractable in computational logic. To this end we design a hypothetical, 20 nomenclatural taxon use case, with starting conditions that embody several overarching principles of the International Code of Zoological Nomenclature, including Binomial Nomenclature, Priority, Coordination, Homonymy, Typification and the structural requirement of Gender Agreement. The use case ending conditions are triggered by the reinterpretation of the diagnostic features of one of 12 type specimens anchoring the corresponding species-level epithets. Permutations of this child-to-parent reassignment action lead to 36 alternative scenarios, where each scenario requires a set of 1-14 logically contingent nomenclatural emendations. We show that an ASP transition system approach can correctly infer the Code-mandated changes for each scenario, and visually output the ending conditions. The results provide a foundation for further developing logic-based nomenclatural change optimization and validation services, which could be applied in global nomenclatural registries. More generally, logic explorations of nomenclatural and taxonomic change scenarios provide a novel means of assessing design biases inherent in the principles of nomenclature, and can therefore inform the design of future, big data-compatible identifier systems that recognize and mitigate these constraints.

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“…The conservation and management of biological diversity rely heavily on clear definitions of appropriate target units, such as populations, subspecies and species (Waples & Gaggiotti, ; ICZN, ; IUCN, ), as well as appropriate methods and data repositories to identify, describe and refer to such units (e.g. Cappellini et al ., ; Olsen et al ., ; Scheel et al ., ; Crampton‐Platt et al ., ; GBIF, ). The present‐day binary scientific nomenclature was implemented in 1758 based on the 10th edition of Carl Linnaeus’ Systema Naturae (Linné, ).…”

Section: Introductionmentioning

confidence: 99%

The forgotten type specimen of the grey seal [Halichoerus grypus(Fabricius, 1791)] from the island of Amager, Denmark

et al. 2016

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The conservation and management of biological diversity rely heavily on clear definitions of appropriate target units, such as populations, subspecies and species. However, the nomenclature of the grey seal [Halichoerus grypus (Fabricius 1791)] has for many years been misled by two persistent assumptions; that there was no type specimen for the species and that the type locality lay in Greenland. Here, we describe a grey seal skull held in the collections of the Natural History Museum of Denmark, and present written and morphological evidence to demonstrate that this skull is identical to Fabricius' original specimen collected in 1788 near Copenhagen on the island of Amager, Denmark. In addition, we perform genetic analyses to clearly affiliate this specimen with the Baltic grey seal subspecies. Accordingly, we appoint this specimen (ZMUC M11-1525) the holotype of the grey seal and the island of Amager, Denmark, the type locality of the species. Hereby, the Baltic subspecies of the grey seal by definition becomes the nominate race of the species to henceforth be classified as Halichoerus grypus grypus, putting the hitherto used subspecies name macrorhynchus in reference to Hornschuch & Schilling (1850) in junior synonymy. As a further consequence, we resurrect Halichoerus grypus atlantica in reference to Nehring (1886) as the earliest available name for the Atlantic subspecies. The type specimen's digital, morphological and genetic data are made publicly available for future reference and as an inspiration for baseline data to include in descriptions of other type specimens.

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Resolution of the type material of the Asian elephant, Elephas maximus Linnaeus, 1758 (Proboscidea, Elephantidae)

Cited by 22 publications

References 23 publications

New insights into Neolithic milk consumption through proteomic analysis of dental calculus

New insights into Neolithic milk consumption through proteomic analysis of dental calculus

A logic approach to modelling nomenclatural change

The forgotten type specimen of the grey seal [Halichoerus grypus(Fabricius, 1791)] from the island of Amager, Denmark

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