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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., We thank the wet laboratory teams at MPI-SHH, the PalaeoBARN at the University of Oxford and the University of York. We thank David K. James and Lucia Hui of the Alameda County Vector Control Services District for procuring the rat used for the de novo genome. We are grateful to Sarah Nagel at Max Planck Institute for the Evolutionary Anthropology for the single-stranded library preparation, and Dovetail Genomics for the de novo genome assembly service. We thank Maria Spyrou for her suggestions and comments. We acknowledge Ewan Chipping and Helena England (University of York), Carl Phillips, Veronica Lindholm (Ålands Museum), Christine McDonnell and Nienke van Doorn (York Archaeological Trust), Emile Mittendorf (Gemeente Deventer), Inge Riemersma (Archaeological depot, Provincie Zuid-Holland), the Turkish Ministry of Culture & Tourism, Jan Frolík and Iva Herichová (Institute of Archaeology of the Czech Academy of Sciences, Prague), Franz Humer and Eduard Pollhammer (Archaeological Park Carnuntum), Dorottya B. Nyékhelyi and László Daróczi-Szabó (Budapest History Museum), Institut National du Patrimoine (Tunisia), University of Barcelona, Spanish Ministry of Science and Innovation (Project HUM2006-03432/HIST), Spanish Ministry of Culture (program of archaeological excavations abroad 2009); Spanish Agency of International Cooperation for the Development (2009), Catalan Institute of Classical Archaeology (ICAC), Vujadin Ivanisević, Nemanja Marković and Ivan Bugarski (Archaeological Institute 809 Belgrade), the Field Museum Chicago, the British National History Museum and the American Museum of Natural History for providing materials and support. G.L. and A.J. were supported by the ERC (grant ERC-2013-StG-337574-UNDEAD) and A.J. was supported by the Natural Environment Research Council Doctoral Training Program. D.O. was supported by Wellcome (Small Grant in Humanities and Social Science 209817/Z) and the British Academy / Leverhulme Trust (Small Research Grant SG170938). E.R. was supported by Estonian Research Council grant No PRG29. R.K. was supported by the Czech Academy of Sciences institutional support (RVO:67985912). S.V.-L. was supported by the ERC (grant ERC-StG- 716298 ZooMWest). H.E. was funded by an ERC grant (206148) through the Sealinks Project. A.H.B was funded by the Leverhulme Trust (ECF-2017-315). The de novo genome assembly, population genomics study, and radiocarbon dating were funded by the Max Planck Society.

Understanding the historical emergence and growth of long-range fisheries can provide fundamental insights into the timing of ecological impacts and the development of coastal communities during the last millennium. Whole-genome sequencing approaches can improve such understanding by determining the origin of archaeological fish specimens that may have been obtained from historic trade or distant water. Here, we used genome-wide data to individually infer the biological source of 37 ancient Atlantic cod specimens (ca 1050–1950 CE) from England and Spain. Our findings provide novel genetic evidence that eleventh- to twelfth-century specimens from London were predominantly obtained from nearby populations, while thirteenth- to fourteenth-century specimens were derived from distant sources. Our results further suggest that Icelandic cod was indeed exported to London earlier than previously reported. Our observations confirm the chronology and geography of the trans-Atlantic cod trade from Newfoundland to Spain starting by the early sixteenth century. Our findings demonstrate the utility of whole-genome sequencing and ancient DNA approaches to describe the globalization of marine fisheries and increase our understanding regarding the extent of the North Atlantic fish trade and long-range fisheries in medieval and early modern times. This work was supported by the Research Council of Norway project ‘Catching the Past’ (grant no. 262777), the Leverhulme Trust (grant nos. F/00 181/R and MRF-2013-065), the European Union's Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie grant agreement No. 813383 (SeaChanges), the 4-OCEANS Synergy grant agreement no. 951649, the FISHARC-IF 658022 Marie-Curie-Sklodowska-IF fellowship for Career development and the European Molecular Biology Organization (ASTF 354-2016). The European Research Agency is not responsible for any use that may be made of the information this work contains. This research is also under the framework of the PID-118662GB-100 (FISHCIIS - Fishing Isotopes) project from the Spanish Ministry of Science and Innovation.

Domestication of horses fundamentally transformed long-range mobility and warfare. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling at Botai, Central Asia around 3500 bc3. Other longstanding candidate regions for horse domestication, such as Iberia and Anatolia, have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 bc, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 bc driving the spread of Indo-European languages. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium bc Sintashta culture., The work by G. Boeskorov is done on state assignment of DPMGI SB RAS. This project was supported by the University Paul Sabatier IDEX Chaire d’Excellence (OURASI); Villum Funden miGENEPI research programme; the CNRS ‘Programme de Recherche Conjoint’ (PRC); the CNRS International Research Project (IRP AMADEUS); the France Génomique Appel à Grand Projet (ANR-10-INBS-09-08, BUCEPHALE project); IB10131 and IB18060, both funded by Junta de Extremadura (Spain) and European Regional Development Fund; Czech Academy of Sciences (RVO:67985912); the Zoological Institute ZIN RAS (АААА-А19-119032590102-7); and King Saud University Researchers Supporting Project (NSRSP–2020/2). The research was carried out with the financial support of the Russian Foundation for Basic Research (19-59-15001 and 20-04-00213), the Russian Science Foundation (16-18-10265, 20-78-10151, and 21-18-00457), the Government of the Russian Federation (FENU-2020-0021), the Estonian Research Council (PRG29), the Estonian Ministry of Education and Research (PRG1209), the Hungarian Scientific Research Fund (Project NF 104792), the Hungarian Academy of Sciences (Momentum Mobility Research Project of the Institute of Archaeology, Research Centre for the Humanities); and the Polish National Science Centre (2013/11/B/HS3/03822). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie (grant agreement 797449). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreements 681605, 716732 and 834616).

Horses have been valued for their diversity of coat colour since prehistoric times; this is especially the case since their domestication in the Caspian steppe in ~3,500 BC. Although we can assume that human preferences were not constant, we have only anecdotal information about how domestic horses were influenced by humans. Our results from genotype analyses show a significant increase in spotted coats in early domestic horses (Copper Age to Iron Age). In contrast, medieval horses carried significantly fewer alleles for these phenotypes, whereas solid phenotypes (i.e., chestnut) became dominant. This shift may have been supported because of (i) pleiotropic disadvantages, (ii) a reduced need to separate domestic horses from their wild counterparts, (iii) a lower religious prestige, or (iv) novel developments in weaponry. These scenarios may have acted alone or in combination. However, the dominance of chestnut is a remarkable feature of the medieval horse population.

Today there are ~56 million horses worldwide, but nearly all of them are descendants of one stallion., Present-day domestic horses are immensely diverse in their maternally inherited mitochondrial DNA, yet they show very little variation on their paternally inherited Y chromosome. Although it has recently been shown that Y chromosomal diversity in domestic horses was higher at least until the Iron Age, when and why this diversity disappeared remain controversial questions. We genotyped 16 recently discovered Y chromosomal single-nucleotide polymorphisms in 96 ancient Eurasian stallions spanning the early domestication stages (Copper and Bronze Age) to the Middle Ages. Using this Y chromosomal time series, which covers nearly the entire history of horse domestication, we reveal how Y chromosomal diversity changed over time. Our results also show that the lack of multiple stallion lineages in the extant domestic population is caused by neither a founder effect nor random demographic effects but instead is the result of artificial selection—initially during the Iron Age by nomadic people from the Eurasian steppes and later during the Roman period. Moreover, the modern domestic haplotype probably derived from another, already advantageous, haplotype, most likely after the beginning of the domestication. In line with recent findings indicating that the Przewalski and domestic horse lineages remained connected by gene flow after they diverged about 45,000 years ago, we present evidence for Y chromosomal introgression of Przewalski horses into the gene pool of European domestic horses at least until medieval times.

Taxonomic over-splitting of extinct or endangered taxa, due to an incomplete knowledge of both skeletal morphological variability and the geographical ranges of past populations, continues to confuse the link between isolated extant populations and their ancestors. This is particularly problematic with the genusEquus.To more reliably determine the evolution and phylogeographic history of the endangered Asiatic wild ass, we studied the genetic diversity and inter-relationships of both extinct and extant populations over the last 100,000 years, including samples throughout its previous range from Western Europe to Southwest and East Asia. Using 229 bp of the mitochondrial hypervariable region, an approach which allowed the inclusion of information from extremely poorly preserved ancient samples, we classify all non-African wild asses into nine clades that show a clear phylogeographic structure revealing their phylogenetic history. This study places the extinct European wild ass,E. hydruntinus, the phylogeny of which has been debated since the end of the 19thcentury, into its phylogenetic context within the Asiatic wild asses and reveals recent gene flow events between populations currently regarded as separate species. The phylogeographic organization of clades resulting from these efforts can be used not only to improve future taxonomic determination of a poorly characterized group of equids, but also to identify historic ranges, interbreeding events between various populations, and the impact of ancient climatic changes. In addition, appropriately placing extant relict populations into a broader phylogeographic and genetic context can better inform ongoing conservation strategies for this highly endangered species.

Leopard complex spotting is inherited by the incompletely dominant locus,LP, which also causes congenital stationary night blindness in homozygous horses. We investigated an associated single nucleotide polymorphism in theTRPM1gene in 96 archaeological bones from 31 localities from Late Pleistocene (approx. 17 000 YBP) to medieval times. The first genetic evidence ofLPspotting in Europe dates back to the Pleistocene. We tested for temporal changes in theLPassociated allele frequency and estimated coefficients of selection by means of approximate Bayesian computation analyses. Our results show that at least some of the observed frequency changes are congruent with shifts in artificial selection pressure for the leopard complex spotting phenotype. In early domestic horses from Kirklareli–Kanligecit (Turkey) dating to 2700–2200 BC, a remarkably high number of leopard spotted horses (six of 10 individuals) was detected including one adult homozygote. However,LPseems to have largely disappeared during the late Bronze Age, suggesting selection against this phenotype in early domestic horses. During the Iron Age,LPreappeared, probably by reintroduction into the domestic gene pool from wild animals. This picture of alternating selective regimes might explain how genetic diversity was maintained in domestic animals despite selection for specific traits at different times.

Cortés-Sánchez, Miguel et al., Numerous studies along the northern Mediterranean borderland have documented the use of shellfish by Neanderthals but none of these finds are prior to Marine Isotopic Stage 3 (MIS 3). In this paper we present evidence that gathering and consumption of mollusks can now be traced back to the lowest level of the archaeological sequence at Bajondillo Cave (Málaga, Spain), dated during the MIS 6. The paper describes the taxonomical and taphonomical features of the mollusk assemblages from this level Bj19 and briefly touches upon those retrieved in levels Bj18 (MIS 5) and Bj17 (MIS 4), evidencing a continuity of the shellfishing activity that reaches to MIS 3. This evidence is substantiated on 29 datings through radiocarbon, thermoluminescence and U series methods. Obtained dates and paleoenvironmental records from the cave include isotopic, pollen, lithostratigraphic and sedimentological analyses and they are fully coherent with paleoclimate conditions expected for the different stages. We conclude that described use of shellfish resources by Neanderthals (H. neanderthalensis) in Southern Spain started ~150 ka and were almost contemporaneous to Pinnacle Point (South Africa), when shellfishing is first documented in archaic modern humans., The works at Bajondillo Cave and the shellfish harvesting in the Natural Park of Maro-Cerro Gordo were approved by the Junta de Andalucía (Spain). The manuscript was greatly improved by the instructive comments and suggestions of two anonymous reviewers.

Data from morphology, linguistics, history, and archaeology have all been used to trace the dispersal of chickens from Asian domestication centers to their current global distribution. Each provides a unique perspective which can aid in the reconstruction of prehistory. This study expands on previous investigations by adding a temporal component from ancient DNA and, in some cases, direct dating of bones of individual chickens from a variety of sites in Europe, the Pacific, and the Americas. The results from the ancient DNA analyses of forty-eight archaeologically derived chicken bones provide support for archaeological hypotheses about the prehistoric human transport of chickens. Haplogroup E mtDNA signatures have been amplified from directly dated samples originating in Europe at 1000 B.P. and in the Pacific at 3000 B.P. indicating multiple prehistoric dispersals from a single Asian centre. These two dispersal pathways converged in the Americas where chickens were introduced both by Polynesians and later by Europeans. The results of this study also highlight the inappropriate application of the small stretch of D-loop, traditionally amplified for use in phylogenetic studies, to understanding discrete episodes of chicken translocation in the past. The results of this study lead to the proposal of four hypotheses which will require further scrutiny and rigorous future testing, Excavations in Fais by MI were made possible by a Grant-in-Aid for Scientific Research from the Japan Society for the Promotion of Science. DB gratefully acknowledges support from the Marsden Fund, and the Allan Wilson Centre for Molecular Ecology and Evolution. During the course of this research AS was supported by a Postgraduate Scholarship from the University of Auckland and a Fellowship from the Allan Wilson Centre for Molecular Ecology and Evolution

Atlantic bluefin tuna (Thunnus thynnus; BFT) abundance was depleted in the late 20th and early 21st century due to overfishing. Historical catch records further indicate that the abundance of BFT in the Mediterranean has been fluctuating since at least the 16th century. Here we build upon previous work on ancient DNA of BFT in the Mediterranean by comparing contemporary (2009-2012) specimens with archival (1911-1926) and archaeological (2nd century BCE-15th century CE) specimens that represent population states prior to these two major periods of exploitation, respectively. We successfully genotyped and analysed 259 contemporary and 123 historical (91 archival and 32 archaeological) specimens at 92 SNP loci that were selected for their ability to differentiate contemporary populations or their association with core biological functions. We found no evidence of genetic bottlenecks, inbreeding or population restructuring between temporal sample groups that might explain what has driven catch fluctuations since the 16th century. We also detected a putative adaptive response, involving the cytoskeletal protein synemin which may be related to muscle stress. However, these results require further investigation with more extensive genome-wide data to rule out demographic changes due to overfishing, and other natural and anthropogenic factors, in addition to elucidating the adaptive drivers related to these., We thank two anonymous reviewers whose comments improved the quality of the manuscript. This work was carried out under the provision of the FARB Project (University of Bologna), the ICCAT Atlantic Wide Research Programme for Bluefin Tuna (GBYP) Data Recovery Plan, the International Governance Strategy of Fisheries and Oceans Canada (F5211-180183 and F5211-160166), and the MARES Joint Doctorate programme selected under Erasmus Mundus and coordinated by Ghent University (Grant Number: FPA 2011-0016). This work is also a contribution to the MSCA SeaChanges ITN and was part-funded by EU Horizon 2020 (Grant Number: 813383).

[spa] En el presente trabajo se exponen los resultados del estudio faunístico de diferentes yacimientos catalanes correspondientes al Paleolítico Superior final y Epipaleolítico. De estos se deducen los cambios paleoambientales y los cambios paleoculturales que sufrieron las poblaciones prehistóricas en la adaptación a los nuevos conjuntos faunísticos, fuente de gran parte de los recursos alimentarios. Este cambio fue progresivo y no supuso una transformación drástica de las estrategias de subsistencia. La mejora climática se refleja en la potenciación de unos recursos hasta ahora poco aprovechados en esta zona (lagomorfos y moluscos terrestres), aunque ya consumidos habitualmente en otras regiones más meridionales de la Península Ibérica.