DOI: 10.5061/dryad.3r2280gpn
title: Data from: Far away from home? Ancient DNA shows presence of bicoloured shrew (Crocidura leucodon) in Bronze Age Denmark

description: 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.
description: 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
 (<em>Crocidura</em>) 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).
description: # Far away from home? Ancient DNA shows presence of bicoloured shrew
 (Crocidura leucodon) in Bronze Age Denmark
 ## 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.