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Data from: Far away from home? Ancient DNA shows presence of bicoloured shrew (Crocidura leucodon) in Bronze Age Denmark

Cite this dataset

Mousavi-Derazmahalleh, Mahsa et al. (2024). Data from: Far away from home? Ancient DNA shows presence of bicoloured shrew (Crocidura leucodon) in Bronze Age Denmark [Dataset]. Dryad. https://doi.org/10.5061/dryad.3r2280gpn

Abstract

An excavation of an Early Iron Age village near Aalborg in Denmark uncovered the jaws and skull fragments from a small mammal that were morphologically identified to the genus Crocidura (white-toothed shrews). Three Crocidura species are known from prehistoric continental Europe but none of them are distributed in Scandinavia, which is why this surprising finding warranted further analyses. The bone was radiocarbon-dated to 2840-2750 calibrated years before present (cal. BP), corresponding to the Late Bronze Age and hence earlier than the Iron Age archaeological context in which it was found. Using highly optimized ancient DNA protocols, we extracted DNA from one tooth and shotgun-sequenced the sample to reconstruct a near-complete mitochondrial reference genome (17,317 bp, 32.6X coverage). Phylogenetic analyses determined this specimen as a bicoloured shrew (Crocidura leucodon) but with a phylogenetic position basal to the clade of known sequences from this species. The confirmation of Crocidura presence in Denmark by the Late Bronze Age sheds new light on the prehistoric natural history of Scandinavia. We discuss the implications of this finding from both zoo-archaeological and ecological perspectives. Furthermore, the mitochondrial genome reconstructed in this study offers a valuable resource for future research exploring the genetic makeup and evolutionary history of Eurasian shrew populations.

README: Far away from home? Ancient DNA shows presence of bicoloured shrew (Crocidura leucodon) in Bronze Age Denmark

https://doi.org/10.5061/dryad.3r2280gpn

Description of the data and file structure

The sequencing file, "merged_trimmedS1-2_collapsePairs_QF.fastq.gz", is the trimmed file in which adapter sequences and reads with phred quality scores below 30 were removed, overlapped paired-end reads and pairs that have not been collapsed but passed the filtering were merged, and any reads less than 30 bp were discarded using AdapterRemoval2. This is the file that was used for downstream analyses including mapping and assembly practices.

Sharing/Access information

The final mitogenome assembly resulted from this research is deposited in GenBank under accession number OR951920.

Cytb and COI Gene sequences that were used for creating the phylogeny trees can be obtained using their respective GenBank accession numbers below:

Species GenBank accession number
Neomys fodiens NC_025559 (KM092492)
Neomys fodiens MN122915
Neomys fodiens MN122912
Sorex araneus MN122909
Sorex araneus MN122847
Sorex araneus NC_027963 (KT210896)
Sorex minutus MN122904
Crocidura russula AY769264
Crocidura russula AY769263
Crocidura shantungenesis JX968507
Crocidura sibirica MH349094.1
Crocidura negrina KR537881
Crocidura tanakae MN128390
Crocidura tanakae NC_046831 (MN128390)
Crocidura tanakae MW429380
Crocidura leucodon ON682409
Crocidura leucodon ON682421
Crocidura leucodon ON682424
Crocidura leucodon ON682426
Crocidura suaveolens AB077280.1
Crocidura suaveolens AB077090.1
Crocidura suaveolens ON682401
Crocidura suaveolens ON682432

Code/Software

Parameters used for running codes are as described in the manuscript itself.

Methods

Between 2013 and 2021, a large-scale excavation in the south-eastern outskirts of Aalborg, Denmark, resulted in a fully excavated rural village from the Early Iron Age. One particularly unexpected zoological discovery was the identification of two jawbones and skull fragments from the white-toothed shrew genus (Crocidura) of which there are no confirmed recording from Denmark. DNA was extracted from one tooth that was removed from the jawbone, using protocols described in Allentoft et al., 2015, and Orlando et al., 2013. The DNA concentration of the library was quantified on an Agilent 2200 Tapestation, and pooled equimolarly with other libraries (from different projects) before sequenced on an Illumina NovaSeq6000 platform (150 PE).