Insular evolution from an archaeological perspective:A case study of Orkney house mouse

Archaeological material adds a temporal dimension to evolutionary studies, valuable for elucidating long-term population stability and evolutionary shifts for species closely associated with humans. Here a 2D geometric morphometrics approach on first upper molars was applied to modern and archaeological samples to assess the evolution of house mice in Orkney, an archipelago north of Scotland. Modern populations included localities in Orkney, north Scotland and France. Two archaeological sites in Orkney represented the Norse period: Birsay Beachview (Mainland) and Tuquoy (Westray) (10th – 14th/15th centuries AD). The archaeological specimens were larger than modern specimens from similar settings, suggesting processes leading to a recent size decline of Orkney house mice. Molar morphology and associated non-metric traits distinct to the Orkney lineage were already established in the Norse period, as indicated by morphological similarity of the Birsay samples to modern Orkney and north Scotland populations. Human settlement stability likely influences morphological evolution in house mice. The Birsay site, located in Birsay village which has been inhabited since Norse times, may represent the ancestral house mice population in Orkney; while Tuquoy, a settlement abandoned by the end of the medieval period, provided samples different from modern house mice populations in Westray and neighbouring isles

Glacial cycles drive rapid divergence of cryptic field vole species

Understanding the factors that contribute to the generation of reproductively isolated forms is a fundamental goal of evolutionary biology. Cryptic species are an especially interesting challenge to study in this context since they lack obvious morphological differentiation that provides clues to adaptive divergence that may drive reproductive isolation. Geographical isolation in refugial areas during glacial cycling is known to be important for generating genetically divergent populations, but its role in the origination of new species is still not fully understood and likely to be situation dependent. We combine analysis of 35,434 single‐nucleotide polymorphisms (SNPs) with environmental niche modeling (ENM) to investigate genomic and ecological divergence in three cryptic species formerly classified as the field vole (Microtus agrestis). The SNPs demonstrate high genomic divergence (pairwise FST values of 0.45–0.72) and little evidence of gene flow among the three field vole cryptic species, and we argue that genetic drift may have been a particularly important mechanism for divergence in the group. The ENM reveals three areas as potential glacial refugia for the cryptic species and differing climatic niches, although with spatial overlap between species pairs. This evidence underscores the role that glacial cycling has in promoting genetic differentiation and reproductive isolation by subdivision into disjunct distributions at glacial maxima in areas relatively close to ice sheets. Future investigation of the intrinsic barriers to gene flow between the field vole cryptic species is required to fully assess the mechanisms that contribute to reproductive isolation. In addition, the Portuguese field vole (M. rozianus) shows a high inbreeding coefficient and a restricted climatic niche, and warrants investigation into its conservation status

Pests or prey? Micromammal species within an ancient anthropic environment at the Norse settlement site of Tuquoy (Westray, Orkney)

Excel file with five tables containing Tuquoy micromammal data (four tables) and references from Andrews 1990 (one table)

Corrigendum to “Species identification of archaeological marine mammals using collagen fingerprinting” [YJASC 41 (2014) 631–641]

Throughout human history, coastal and marine resources have been a vital part of human subsistence. As a result archaeological faunal assemblages from coastal sites often contain large quantities of skeletal remains indicative of human interaction with marine mammals. However, these are often hard to identify due to a unique combination of factors regarding the procurement, utilisation, morphological and physical characteristics of marine mammal bones. These factors often result in a large number of archaeological cetacean and pinniped specimens fragmented beyond visual recognition, being labelled ‘whale’ or ‘marine mammal’. In this paper we report the development of a Zooarchaeology by Mass Spectrometry (ZooMS) method of collagen fingerprinting, for efficient and low cost discrimination of a wide range of marine mammal species including cetaceans and pinnipeds. We apply the technique to more than fifty archaeological specimens from seven different North Atlantic sites ranging from the Mesolithic until the Early Modern period

Entanglement Evolution in the Presence of Decoherence

The entanglement of two qubits, each defined as an effective two-level, spin 1/2 system, is investigated for the case that the qubits interact via a Heisenberg XY interaction and are subject to decoherence due to population relaxation and thermal effects. For zero temperature, the time dependent concurrence is studied analytically and numerically for some typical initial states, including a separable (unentangled) initial state. An analytical formula for non-zero steady state concurrence is found for any initial state, and optimal parameter values for maximizing steady state concurrence are given. The steady state concurrence is found analytically to remain non-zero for low, finite temperatures. We also identify the contributions of global and local coherence to the steady state entanglement.Comment: 12 pages, 4 figures. The second version of this paper has been significantly expanded in response to referee comments. The revised manuscript has been accepted for publication in Journal of Physics

Skimming genomes for systematics and DNA barcodes of corals

Numerous genomic methods developed over the past two decades have enabled the discovery and extraction of orthologous loci to help resolve phylogenetic relationships across various taxa and scales. Genome skimming (or low-coverage genome sequencing) is a promising method to not only extract high-copy loci but also 100s to 1000s of phylogenetically informative nuclear loci (e.g., ultraconserved elements [UCEs] and exons) from contemporary and museum samples. The subphylum Anthozoa, including important ecosystem engineers (e.g., stony corals, black corals, anemones, and octocorals) in the marine environment, is in critical need of phylogenetic resolution and thus might benefit from a genome-skimming approach. We conducted genome skimming on 242 anthozoan corals collected from 1886 to 2022. Using existing target-capture baitsets, we bioinformatically obtained UCEs and exons from the genome-skimming data and incorporated them with data from previously published target-capture studies. The mean number of UCE and exon loci extracted from the genome skimming data was 1837 ± 662 SD for octocorals and 1379 ± 476 SD loci for hexacorals. Phylogenetic relationships were well resolved within each class. A mean of 1422 ± 720 loci was obtained from the historical specimens, with 1253 loci recovered from the oldest specimen collected in 1886. We also obtained partial to whole mitogenomes and nuclear rRNA genes from \u3e95% of samples. Bioinformatically pulling UCEs, exons, mitochondrial genomes, and nuclear rRNA genes from genome skimming data is a viable and low-cost option for phylogenetic studies. This approach can be used to review and support taxonomic revisions and reconstruct evolutionary histories, including historical museum and type specimens

Combined visual and biochemical analyses confirm depositor and diet for Neolithic coprolites from Skara Brae

Coprolites (fossilized faeces) can provide valuable insights into species’ diet and related habits. In archaeozoological contexts, they are a potential source of information on human-animal interactions as well as human and animal subsistence. However, despite a broad discussion on coprolites in archaeology, such finds are rarely subject to detailed examination by researchers, perhaps due to the destructive nature of traditional analytical methods. Here, we have examined coprolitic remains from the Neolithic (third millennium BCE) settlement at Skara Brae, Orkney, using a range of modern methods: X-ray computed tomography, scanning electron microscopy, lipid and protein analysis (shotgun proteomics of the coprolite matrix as well as collagen peptide mass fingerprinting of isolated bone fragments). This combined approach minimised destructiveness of sampling, leaving sufficient material for subsequent study, while providing more information than traditional morphological examination alone. Based on gross visual examination, coprolites were predominantly attributed to domestic dogs (Canis familiaris), with morphologically identified bone inclusions derived from domestic sheep (Ovis aries) and common voles (Microtus arvalis). Partial dissection of a coprolite provided bone samples containing protein markers akin to those of domestic sheep. Considering the predominance of vertebral and distal limb bone fragments, Skara Brae dogs were probably consuming human butchery or meal refuse, either routinely fed to them or scavenged. The presumably opportunistic consumption of rodents may also have played a role in pest control