Biology subjects

Sabin, R.

Publications and source records attributed to Sabin, R..

5 recordsLinked to original sources

bioRxiv2026

Museum specimens reveal evolutionary drivers and functions of oral microbiome in mammals

The microbiomes of wild animals, despite being integral to host survival, remain largely unexplored, particularly beyond the gut. Here, using > 450 museum-preserved dental calculus samples from 34 ecologically and phylogenetically diverse mammalian species, most of them previously unstudied, we determine the main drivers of oral microbiome evolution. We show that, similar to the gut, the oral microbiome is shaped by host ecology, particularly diet, and to a lesser extent host phylogenetic relationships. It may contribute to host adaptation, by synthesising essential micronutrients and degrading potentially harmful compounds. We also find that some oral microorganisms consistently associated with mammals throughout over evolutionary time scales and provide evidence for a likely oral origin of some rumen taxa. Together our findings demonstrate the importance of this mostly overlooked microbial community for mammalian biology.

evolutionary biology↗

bioRxiv2026

Walrus Population-specific Marine Reservoir Offsets (ΔR) for Calibration of Radiocarbon Dates: Implications for Arctic Chronologies and Medieval Trade

Walruses have long played a vital role in Arctic subsistence and commercial economies, yet accurate radiocarbon dating of walrus-derived archaeological materials is complicated by regional variation in marine reservoir effects. This study presents new {Delta}R values derived from 31 new and 15 legacy radiocarbon dates on known-age walrus specimens spanning multiple populations of Odobenus rosmarus rosmarus and O. r. divergens. The results reveal substantial inter-population variability, with {Delta}R values ranging from -140 (Franz Josef Land) to +295 (Pacific), underscoring the importance of population-specific calibration. A pooled {Delta}R of +17{+/-}12 was calculated for western Greenland and the Canadian Arctic--regions central to the medieval Norse ivory trade--and applied to 12 walrus rostra and ivory artefacts excavated in Trondheim, Norway. The resulting calibrated dates are from the 11th to early 14th centuries CE, confirming that seemingly anomalous post-15th-century finds are residual rather than evidence of continued trade. An alternative {Delta}R estimate of -110{+/-}35, derived solely from archaeological context dates, suggests potential time lags between harvest and deposition. These findings demonstrate the value of known-age walrus {Delta}R data for refining chronologies of Arctic exploitation and long-distance trade, while highlighting the need for provenance studies in archaeological dating and both the pertinence and limitations of mollusk-based reservoir corrections.

paleontology↗

bioRxiv2025

Dental calculus formation is linked to diet and phylogeny in mammals

O_LIAs a point of entry, the oral cavity serves as a potential first area of colonization of the host with environmental bacteria. As such, the oral microbial community not only affects a wide range of internal host processes, including health and digestion but may also reflect the external environment and ecology of the host. C_LIO_LIDental calculus, a mineralized form of dental plaque, preserves the DNA of the host microbiome through time, serving as a rich source of historical microbiota. Despite its potential to provide temporal information on the ecological and evolutionary processes of microbiomes, dental calculus has rarely been explored outside of humans and non-human primates. Hence, it remains unclear how ubiquitous it is across mammals. C_LIO_LIUsing natural history museum collections, we surveyed > 1600 specimens belonging to 142 species, representative of every mammalian order, to investigate the taxonomic distribution of dental calculus, and to identify factors that most strongly contribute to its formation. We found dental calculus to be abundant across mammalian taxa, with 104 of the surveyed species showing calculus deposits. C_LIO_LIHigh fiber diets were most strongly associated with calculus presence and abundance, whereas species with high protein and fat diets showed little to no calculus deposits. We also found evidence of phylogenetic signal in calculus formation, pointing to the effects of oral/dental morphology. In addition, captivity strongly affected dental calculus formation in almost all dietary categories. Using this information, we made predictions about the likelihood of finding dental calculus in unsurveyed mammalian species, with the aim of informing future investigations. C_LIO_LIOur study found that dental calculus is readily available in natural history museum collections, making it an easily accessible source of oral microbiota from wild animals. We highlight the taxonomic diversity of species presenting dental calculus and provide information and suggestions to researchers and museum curators interested in utilizing dental calculus for the study of oral microbiota, past and present. C_LI

ecology↗

bioRxiv2025

Host traits impact the outcome of metagenomic library preparation from dental calculus samples across diverse mammals

Dental calculus metagenomics has emerged as a valuable tool for studying the oral microbiomes of humans and a few select mammals. With increasing interest in wild animal microbiomes, it is important to understand how widely this material can be used across the mammalian tree of life, refine the related protocols and understand the expected outcomes and potential challenges of dental calculus sample processing. In this study we significantly expand the breadth of studied host species, analysing laboratory and bioinformatics metadata of dental calculus samples from 32 ecologically and phylogenetically diverse mammals. While we confirm the presence of an oral microbiome signature in the metagenomes of all studied mammals, the fraction recognised as oral varies between host species, possibly due to both biological differences and methodological biases. The overall success rate of dental calculus processing, from extractions to sequencing, was ~74%. Although input sample weight was positively associated with the number of produced library molecules, we identify a negative impact of enzymatic inhibition on the library preparation protocol. The inhibition was most prevalent in herbivores and frugivores and is likely diet-derived. In contrast, hosts with an animalivore diet posed fewer challenges during laboratory processing, and yielded more DNA relative to sample weight. Our results translate into recommendations for future studies of dental calculus metagenomics from a variety of host species, identifying required sample amounts, and emphasising the utility of dental calculus in exploring the oral microbiome in relation to broader ecological and evolutionary questions.

genomics↗

bioRxiv2024

Stable isotope composition of Antarctic marine mammals collected at the turn of the 20th century: assessing the baseline for long-term changes in the marine ecosystem

Great Antarctic expeditions, seal hunting and whaling industries left a legacy in natural history collections. To provide the basis for analysing the impact of whaling on marine ecosystem structuring, we conducted the bulk isotope analysis from the specimens of baleen whales (Balaenoptera musculus and B. physalus), and seals (Arctocephalus australis and Hydrurga leptonyx) collected between 1843 to 1951 from the South Atlantic, Patagonian waters, Southern Ocean and Antarctic coastal seas, and preserved in the collection of Natural History Museum, London. Analysis of this material indicates the pre-industrial whaling state of these environments, and changes in the trophic position of whales and seals during the period of extensive human pressure. Having controlled for the Suess effect, {delta}13C values in B. musculus, B. physalus and H. leptonyx were different before and after the onset of industrial-scale whaling (1904). Bone collagen {delta}15N values and corresponding trophic position indicate possible trophic changes in A. australis, and variability of the foraging areas of B. musculus. This study highlights the use of museum specimens for tracing historical trends associated with changes in the population structure and distribution of species and which indicate long- term variability in their foraging ecology.

ecology↗