Arctic fox (Alopex lagopus) from the North Sea

The first record of arctic fox Alopex lagopus (Linnaeus, 1758) from the Eurogeul area (North Sea) is reported based on a distal humerus fragment collected by private collectors from dredged sediments on ‘De Zandmotor’. It was radiocarbon dated to 29,900 + 550/- 490 BP (GrA-69520), which is younger than most Late Pleistocene fossils from this area. Besides adding a new species to the faunal list of the Eurogeul area, this specimen also demonstrates the value of beaches nourished with dredged sediments and highlights the importance of close cooperation between all parties interested in palaeontology: from collector to researcher. The discovery prompted re-examination of the other arctic fox specimen from the North Sea, a femur of which the identification is here confirmed and measurements are provided

Multiproxy analysis of permafrost preserved faeces provides an unprecedented insight into the diets and habitats of extinct and extant megafauna

The study of faecal samples to reconstruct the diets and habitats of extinct megafauna has traditionally relied on pollen and macrofossil analysis. DNA metabarcoding has emerged as a valuable tool to complement and refine these proxies. While published studies have compared the results of these three proxies for sediments, this comparison is currently lacking for permafrost preserved mammal faeces. Moreover, most metabarcoding studies have focused on a single plant-specific DNA marker region. In this study, we target both the commonly used chloroplast trnL P6 loop as well as nuclear ribosomal ITS (nrITS). The latter can increase taxonomic resolution of plant identifications but requires DNA to be relatively well preserved because of the target length (∼300–500 bp). We compare DNA results to pollen and macrofossil analyses from permafrost and ice-preserved faeces of Pleistocene and Holocene megafauna. Samples include woolly mammoth, horse, steppe bison as well as Holocene and extant caribou. Most plant identifications were found using DNA, likely because the studied faeces contained many vegetative remains that could not be identified using macrofossils or pollen. Several taxa were, however, identified to lower taxonomic levels uniquely with macrofossil and pollen analysis. The nrITS marker provides species level taxonomic resolution for commonly encountered plant families that are hard to distinguish using the other proxies (e.g. Asteraceae, Cyperaceae and Poaceae). Integrating the results from all proxies, we are able to accurately reconstruct known diets and habitats of the extant caribou. Applying this approach to the extinct mammals, we find that the Holocene horse and steppe bison were not strict grazers but mixed feeders living in a marshy wetland environment. The mammoths showed highly varying diets from different non-analogous habitats. This confirms the presence of a mosaic of habitats in the Pleistocene ‘mammoth steppe’ that mammoths could fully exploit due to their flexibility in food choice

Natural History Museum Rotterdam - Specimens

Specimen database of the Natural History Museum Rotterdam. The total collection is estimated to hold 373.200 specimens, of which around 85% are digitized at the specimen level and contained in this dataset. Arthropods (56%; mostly European) and molluscs (30%; worldwide recent specimens, fossil specimens from North-West Europe) make up the bulk of the collection. Chordates make up 9% of the collection and include a significant amount of fossil terrestrial and marine vertebrates from the Netherlands and the southern North Sea, while recent specimens predominantly originate from the Netherlands. Plants make up 5% of the collection and originate almost exclusively from the Netherlands. The collections of other taxonomic groups, e.g. Fungi and various marine invertebrates, are small, but do contain well documented interesting records

Supplementary aDNA sequences from a Pleistocene ground squirrel midden, Yukon

Data consists of sequence data of plants and fungi from a Pleistocene ground squirrel midden (collected from a small placer goldmine on Little Blanche Creek, Klondike area near Dawson City, Yukon Territory, Canada; coordinates: 63°50'35"N 139°05'41"W). Three subsamples from this midden were sequenced with various primers, which yielded genetic products of various sizes. This resulted in six different tables, explained below. From the midden itself other subsamples were studied for macro- and microfossils of plants and fungi

Palaeoproteomics of fossil bird bones for taxonomic classification

We used proteomic profiling to taxonomically classify extinct, alongside extant bird species using mass spectrometry on ancient bone-derived collagen chains COL1A1 and COL1A2. Proteins of Holocene and Late Pleistocene-aged bones from dodo (Raphus cucullatus) and great auk (Pinguinus impennis), as well as bones from chicken (Gallus gallus), rock dove (Columba livia), zebra finch (Taeniopygia guttata) and peregrine falcon (Falco peregrinus), of various ages ranging from the present to 1455 years old were analysed. HCl and guandine-HCL-based protein extractions from fresh bone materials yielded up to 60% coverage of collagens COL1A1 and COL1A2, and extractions from ancient materials yielded up to 46% coverage of collagens COL1A1 and COL1A2. Data were retrieved from multiple peptide sequences obtained from different specimens and multiple extractions. Upon alignment, and in line with the latest evolutionary insights, protein data obtained from great auk grouped with data from a recently sequenced razorbill (Alca torda) genome. Similarly, protein data obtained from bones of dodo and modern rock dove grouped in a single clade. Lastly, protein data obtained from chicken bones, both from ancient and fresh materials, grouped as a separate, basal clade. Our proteomic analyses enabled taxonomic classification of all ancient bones, thereby complementing phylogenetics based on DNA

Palaeoproteomics of bird bones for taxonomic classification

We used proteomic profiling to taxonomically classify extinct, alongside extant bird species using mass spectrometry on ancient bone-derived collagen chains COL1A1 and COL1A2. Proteins of Holocene and Late Pleistocene-aged bones from dodo (Raphus cucullatus) and great auk (Pinguinus impennis), as well as bones from chicken (Gallus gallus), rock dove (Columba livia), zebra finch (Taeniopygia guttata) and peregrine falcon (Falco peregrinus), of various ages ranging from the present to 1455 years old were analysed. HCl and guandine-HCL-based protein extractions from fresh bone materials yielded up to 60% coverage of collagens COL1A1 and COL1A2, and extractions from ancient materials yielded up to 46% coverage of collagens COL1A1 and COL1A2. Data were retrieved from multiple peptide sequences obtained from different specimens and multiple extractions. Upon alignment, and in line with the latest evolutionary insights, protein data obtained from great auk grouped with data from a recently sequenced razorbill (Alca torda) genome. Similarly, protein data obtained from bones of dodo and modern rock dove grouped in a single clade. Lastly, protein data obtained from chicken bones, both from ancient and fresh materials, grouped as a separate, basal clade. Our proteomic analyses enabled taxonomic classification of all ancient bones, thereby complementing phylogenetics based on DNA

Stable Isotope Analysis of Specimens of Opportunity Reveals Ocean-Scale Site Fidelity in an Elusive Whale Species

Elusive wildlife are challenging to study, manage, or conserve, as the difficulty of obtaining specimens or conducting direct observations leads to major data deficiencies. Specimens of opportunity, such as salvaged carcasses or museum specimens, are a valuable source of fundamental biological and ecological information on data-deficient, elusive species, increasing knowledge of biodiversity, habitat and range, and population structure. Stable isotope analysis is a powerful indirect tool that can be used to infer foraging behavior and habitat use retrospectively from archived specimens. Beaked whales are a speciose group of cetaceans that are challenging to study in situ, and although Sowerby's beaked whale (Mesoplodon bidens) was discovered >200 years ago, little is known about its biology. We measured δ13C and δ15N stable isotope composition in bone, muscle, and skin tissue from 102 Sowerby's beaked whale specimens of opportunity collected throughout the North Atlantic Ocean to infer movement ecology and spatial population structure. Median δ13C and δ15N values in Sowerby's beaked whale bone, muscle, and skin tissues significantly differed between whales sampled from the east and west North Atlantic Ocean. Quadratic discriminant analysis that simultaneously considered δ13C and δ15N values correctly assigned >85% of the specimens to their collection region for all tissue types. These findings demonstrate Sowerby's beaked whale exhibits both short- and long-term site fidelity to the region from which the specimens were collected, suggest that this species is composed of two or more populations or exhibits a metapopulation structure, and have implications for conservation and management policy. Stable isotope analysis of specimens of opportunity proved a highly successful means of generating new spatial ecology data for this elusive species and is a method that can be effectively applied to other elusive species

Stable isotope analysis of specimens of opportunity reveals ocean-scale site fidelity in an elusive whale species

Elusive wildlife are challenging to study, manage, or conserve, as the difficulty of obtaining specimens or conducting direct observations leads to major data deficiencies. Specimens of opportunity, such as salvaged carcasses or museum specimens, are a valuable source of fundamental biological and ecological information on data-deficient, elusive species, increasing knowledge of biodiversity, habitat and range, and population structure. Stable isotope analysis is a powerful indirect tool that can be used to infer foraging behavior and habitat use retrospectively from archived specimens. Beaked whales are a speciose group of cetaceans that are challenging to study in situ, and although Sowerby's beaked whale (Mesoplodon bidens) was discovered >200 years ago, little is known about its biology. We measured δ13C and δ15N stable isotope composition in bone, muscle, and skin tissue from 102 Sowerby's beaked whale specimens of opportunity collected throughout the North Atlantic Ocean to infer movement ecology and spatial population structure. Median δ13C and δ15N values in Sowerby's beaked whale bone, muscle, and skin tissues significantly differed between whales sampled from the east and west North Atlantic Ocean. Quadratic discriminant analysis that simultaneously considered δ13C and δ15N values correctly assigned >85% of the specimens to their collection region for all tissue types. These findings demonstrate Sowerby's beaked whale exhibits both short- and long-term site fidelity to the region from which the specimens were collected, suggest that this species is composed of two or more populations or exhibits a metapopulation structure, and have implications for conservation and management policy. Stable isotope analysis of specimens of opportunity proved a highly successful means of generating new spatial ecology data for this elusive species and is a method that can be effectively applied to other elusive species