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Ancient DNA (aDNA) approaches have been successfully used to infer the long-term impacts of climate change, domestication, and human exploitation in a range of terrestrial species. Nonetheless, studies investigating such impacts using aDNA in marine species are rare. Atlantic cod (Gadus morhua), is an economically important species that has experienced dramatic census population declines during the last century. Here, we investigated 48 ancient mitogenomes from historical specimens obtained from a range of archeological excavations in northern Europe dated up to 6,500 BCE. We compare these mitogenomes to those of 496 modern conspecifics sampled across the North Atlantic Ocean and adjacent seas. Our results confirm earlier observations of high levels of mitogenomic variation and a lack of mutation-drift equilibrium—suggestive of population expansion. Furthermore, our temporal comparison yields no evidence of measurable mitogenomic changes through time. Instead, our results indicate that mitogenomic variation in Atlantic cod reflects past demographic processes driven by major historical events (such as oscillations in sea level) and subsequent gene flow rather than contemporary fluctuations in stock abundance. Our results indicate that historical and contemporaneous anthropogenic pressures such as commercial fisheries have had little impact on mitogenomic diversity in a wide-spread marine species with high gene flow such as Atlantic cod. These observations do not contradict evidence that overfishing has had negative consequences for the abundance of Atlantic cod and the importance of genetic variation in implementing conservation strategies. Instead, these observations imply that any measures toward the demographic recovery of Atlantic cod in the eastern Atlantic, will not be constrained by recent loss of historical mitogenomic variation.

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.

More than fifty years ago, Anneke T. Clason published the first English-language archaeozoological study on Dutch faunal assemblages. Inspired by the anniversary of this landmark publication, this paper presents a status overview of Dutch archaeozoology organized in twelve themes (e.g. rituals, Mesolithic-Neolithic transition, medieval period). The paper also discusses the common methods applied in Dutch archaeozoology, and includes extensive supplementary material that summarizes data from gray literature in Dutch. Our aim is to provide a guide to archaeozoological questions pertaining to the Netherlands and open a window for researchers working outside the Netherlands to the highly active world of Dutch archaeozoology.

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40The field of ancient DNA is taxonomically dominated by studies focusing on mammals. This 41 taxonomic bias limits our understanding of endogenous DNA preservation for vertebrate taxa 42 with different bone physiology, such as teleost fish. In contrast to most mammalian bone, teleost 43 bone is typically brittle, porous, lightweight and is characterized by a lack of bone remodeling 44 during growth. Using high-throughput shotgun sequencing, we here investigate the preservation 45 of DNA in a range of different bone elements from over 200 archaeological Atlantic cod (Gadus 46 morhua) specimens from 38 sites in northern Europe, dating up to 8000 years before present. We 47 observe that the majority of archaeological sites (79%) yield endogenous DNA, with 40% of sites 48 providing samples that contain high levels (> 20%). Library preparation success and levels of 49 endogenous DNA depend mainly on excavation site and pre-extraction laboratory treatment. The 50 use of pre-extraction treatments lowers the rate of library success, although -if successful -the 51 fraction of endogenous DNA can be improved by several orders of magnitude. This trade-off 52 between library preparation success and levels of endogenous DNA allows for alternative 53 extraction strategies depending on the requirements of down-stream analyses and research 54 questions. Finally, we find that -in contrast to mammalian bones -different fish bone elements 55 yield similar levels of endogenous DNA. Our results highlight the overall suitability of 56 archaeological fish bone as a source for ancient DNA and provide novel evidence for a possible 57 role of bone remodeling in the preservation of endogenous DNA across different classes of 58 vertebrates. 59 60 Dabney et al., 2013), with the inclusion of a pre-digestion step (DD, Damgaard et al., 2015), or with 129

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 generated a de novo genome assembly of the black rat, 67 ancient black rat mitogenomes and 36 ancient nuclear genomes from sites spanning the 1st-17th centuries CE in Europe and North Africa. Analyses of mitochondrial DNA 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.