McFarlane, T. | bioRxiv Science

bioRxiv2026

Sedimentary ancient DNA reveals Late Pleistocene faunal connectivity between Ireland and Eurasia

Late Pleistocene sea-level fluctuations and glacial corridors intermittently connected the island of Ireland to Britain and continental Eurasia, shaping patterns of megafaunal dispersal and occupation. However, the scarcity of genetic data from ancient Irish fauna has limited our understanding of their demographic histories and relationships to continental populations. To address this, we generated sedimentary ancient DNA sequences from Castlepook Cave in southwest Ireland, detecting twelve ancient taxa, including two without zooarchaeological records at the site. We recovered the first mitochondrial sequences from Irish cave hyenas and woolly mammoths, providing new insights into their maternal population history: cave hyenas carried mtDNA haplogroup A1, previously identified in Late Pleistocene European populations, while woolly mammoths belonged to clade III/B2, which was replaced in Europe at approximately the same time. We also identify two mitochondrial clades (1b and 2), consistent with pre-Last Glacial Maximum mitochondrial lineage turnover in Ireland. Together, these results indicate that Irish megafauna formed a biogeographical continuum with their conspecifics in Europe, extend the known geographical range of several mtDNA lineages, and support faunal connectivity at the northwestern edge of Europe prior to the Last Glacial Maximum.

evolutionary biology↗

bioRxiv2024

Purified diets containing high levels of soluble fiber and grain-based diets promote similar gastrointestinal morphometry yet distinct microbial communities

Grain-based diets (GBDs) are widely used in rodent studies but their utility is limited due to batch-to-batch variability resulting from inconsistent ingredients. Purified diets (PDs) are composed of only known and refined ingredients and offer a solution to the constraints of GBDs. However, unlike GBDs, PDs commonly used as control diets typically contain little to no soluble fiber. We therefore sought to identify a combination of fibers in PDs that best recapitulates the gastrointestinal morphometry and intestinal microbial composition of mice fed GBDs. Adult male mice (n=30) were randomly assigned to one of six diets--two GBDs and four PDs with varying insoluble and soluble fiber composition--for 28 days. 16S rRNA gene sequencing was used to compare microbial profiles across different gastrointestinal (GI) niches and diets. Gut microbiotas and cecal weights were distinct between mice fed the two GBDs, indicating that GBDs are unreliable controls in diet-based studies. Unexpectedly, intestinal microbial richness decreased as the amount of soluble fiber in the PDs increased and the addition of multiple soluble fibers did not rescue this effect. Mice fed PDs with high soluble fiber content ([≥] 75% of dietary fiber was soluble fiber) best recapitulated GI morphometry of mice fed GBDs, but intestinal microbial communities were distinct between PD- and GBD-fed mice. Although supplementing PDs with soluble fiber improved GI morphometry, further research to determine the optimal mixture of soluble and insoluble fibers is required to more closely mirror the intestinal microbial diversity observed in mice fed GBDs. ImportanceDietary fibers are essential for maintaining gut health. Insoluble fibers aid in fecal bulking and water retention while soluble fiber is a fermentative substrate for intestinal microbial communities. GBDs are commonly used in preclinical research but the variability in ingredients across batches impedes reproducibility. PDs, which are composed of highly refined ingredients, pose a potential solution but the most widely used low-fat control PDs contain no soluble fiber. This study intended to identify a PD with a combination of fibers that promotes murine gut health and microbial diversity. A PD with optimal fiber composition would aid in the standardization and reproducibility of studies investigating intestinal physiology and the gut microbiota.

microbiology↗