Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history

Abstract

The distribution of the black rat (Rattus rattus) has been heavily influenced by its association with humans. The dispersal history of this non-native commensal rodent across Europe, however, remains poorly understood, and different introductions may have occurred during the Roman and medieval periods. Here, in order to reconstruct the population history of European black rats, we first generate a de novo genome assembly of the black rat. We then sequence 67 ancient and three modern black rat mitogenomes, and 36 ancient and three modern nuclear genomes from archaeological sites spanning the 1st-17th centuries CE in Europe and North Africa. Analyses of our newly reported sequences, together with published mitochondrial DNA sequences, confirm that black rats were introduced into the Mediterranean and Europe from Southwest Asia. Genomic analyses of the ancient rats reveal a population turnover in temperate Europe between the 6th and 10th centuries CE, coincident with an archaeologically attested decline in the black rat population. The near disappearance and re-emergence of black rats in Europe may have been the result of the breakdown of the Roman Empire, the First Plague Pandemic, and/or post-Roman climatic cooling.

Can demographic histories explain long‐term isolation and recent pulses of asymmetric gene flow between highly divergent grey fox lineages?

“…We additionally filtered SNPs to include those with a minor allele frequency ≥5% (‐minMaf 0.05), and we applied more stringent quality filters including base and mapping quality scores ≥30 (‐minQ 30, ‐minMapQ 30). Based on distributions of read depths, we retained sites with a combined global read depth between 110× (0.5× the sample mean) and 450× (2× the sample mean; Calfee et al, 2020; Yu et al, 2022), and those with genotypes present in ≥80% of individuals (‐minInd 34).…”

Ancient DNA sequence quality is independent of fish bone weight

“…Prior to 2017, the majority of micromammal ancient DNA studies focused on sequencing segments of the mitogenome, such as the cytB sequence (Woods and Melissa, 2017). However, recent studies have shown that micromammal remains can also yield whole-genome sequences (Cucchi et al, 2020;Yu et al, 2022). Thus, smaller quantities of bone powder and small-boned specimens should be considered viable options for ancient DNA sequence analysis rather than discarded or immediately pooled into bulk-bone sequencing.…”

Commensal black rats Rattus rattus select wild vegetation over urbanised habitats

“…Ultimately, our findings suggest that multiple millennia of coexistence with human environments, and associated selection, do not necessarily translate into a preference for urban habitats. This tight association is often assumed not only in ecological studies but also in other disciplines, for example archaeological studies using evidence of commensals including black rats to understand patterns of human settlement (Yu et al 2022). Black rats have been described as 'archetypal commensals' (Banks and Smith 2015), highly dependent on humans to survive (Hulme-Beaman et al 2016), but their abundance outside urban areas indicates otherwise.…”