An Ecological and Evolutionary Framework for Commensalism in Anthropogenic Environments

Acknowledgements We would like to thank Jean-Denis Vigne, members of the Searle lab, and SNEEB at Cornell University for a stimulating environment and many early discussions and comments. We would also like to thank Maeve McMahon for comments on the manuscript.Peer reviewedPublisher PD

Sperm competition as an under-appreciated factor in domestication

Humans created an environment that increased selective pressures on subgroups of those species that became domestic. We propose that the domestication process may in some cases have been facilitated by changes in mating behaviour and resultant sperm competition. By adapting to sperm competition, proto-domestic animals could potentially have outcompeted their wild counterparts in human-constructed niches. This could have contributed to the restriction of gene flow between the proto-domesticates and their wild counterparts, thereby promoting the fixation of other domestication characteristics. Further to this novel perspective for domestication, we emphasise the general potential of postcopulatory sexual selection in the restriction of gene flow between populations, and urge more studies

A landmark-based approach for assessing the reliability of mandibular tooth crowding as a marker of dog domestication

Acknowledgements We are grateful to the curators and staff of many museums and institutions for kindly providing access to collections under their care, especially Marc Nussbaumer & Andre Rehazek of Naturhistorisches Museum Bern, Jack Tseng of the American Museum of Natural History, and Richard Meadow of Peabody Museum, Harvard University. Additionally, we are thankful to Richard Allen, Anna Linderholm and Angela Perri for their help with sourcing and collecting data for this study. This work was supported by NERC (NE/K003259/1), and the European Research Council (ERC-2013-StG 337574-UNDEAD).Peer reviewedPublisher PD

The use of close-range photogrammetry in zooarchaeology : Creating accurate 3D models of wolf crania to study dog domestication

Acknowledgements We thank the Muséum National d'Histoire Naturelle, Paris, that provided access to the specimens, and access to the morphometric platform where the surface scans were performed. We also thank Raphael Cornette and Julien Claude for the fruitful discussions we had when writing the manuscript. This work was supported by NERC (grant number NE/K003259/1) and the European Research Council (ERC-2013-StG 337574-UNDEAD). This is publication ISEM 2016-127. We thank the two anonymous reviewers who greatly helped to improve the manuscript.Peer reviewedPublisher PD

GeoOrigins: A new method and R package for trait mapping and geographic provenancing of specimens without categorical constraints

Biologists often seek to geographically provenance organisms using their traits. This is typically achieved by defining spatial groups using distinct patterns of trait variation. Here, we present a new spatial provenancing and trait boundary identification methodology, based on correlations between geographic and trait distances that require no a priori group assumptions. We apply this to three datasets where spatial provenance is sought: morphological rat and vole dentition data (human commensal translocation datasets); and birdsong data (cultural transmission dataset). We also present the results of cross‐validation testing. Spatial provenancing is possible with differing degrees of accuracy for each dataset, with birdsong providing the most accurate geographic origin (identifying an average spatial region of 0.22 km2 as the area of origin with 99.9% confidence). Our method has a wide range of potential applications to diverse data types—including phenotypic, genetic and cultural—to identify trait boundaries and spatially provenance the origin of unknown or translocated specimens where trait differences are geographically structured and correlated with spatial separation

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

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.Peer reviewe

Reconstructing Asian faunal introductions to eastern Africa from multi-proxy biomolecular and archaeological datasets

Human-mediated biological exchange has had global social and ecological impacts. In subS-aharan Africa, several domestic and commensal animals were introduced from Asia in the pre-modern period; however, the timing and nature of these introductions remain contentious. One model supports introduction to the eastern African coast after the mid-first millennium CE, while another posits introduction dating back to 3000 BCE. These distinct scenarios have implications for understanding the emergence of long-distance maritime connectivity, and the ecological and economic impacts of introduced species. Resolution of this longstanding debate requires new efforts, given the lack of well-dated fauna from high-precision excavations, and ambiguous osteomorphological identifications. We analysed faunal remains from 22 eastern African sites spanning a wide geographic and chronological range, and applied biomolecular techniques to confirm identifications of two Asian taxa: domestic chicken (Gallus gallus) and black rat (Rattus rattus). Our approach included ancient DNA (aDNA) analysis aided by BLAST-based bioinformatics, Zooarchaeology by Mass Spectrometry (ZooMS) collagen fingerprinting, and direct AMS (accelerator mass spectrometry) radiocarbon dating. Our results support a late, mid-first millennium CE introduction of these species. We discuss the implications of our findings for models of biological exchange, and emphasize the applicability of our approach to tropical areas with poor bone preservation

Dire wolves were the last of an ancient New World canid lineage

Dire wolves are considered to be one of the most common and widespread large carnivores in Pleistocene America1, yet relatively little is known about their evolution or extinction. Here, to reconstruct the evolutionary history of dire wolves, we sequenced five genomes from sub-fossil remains dating from 13,000 to more than 50,000 years ago. Our results indicate that although they were similar morphologically to the extant grey wolf, dire wolves were a highly divergent lineage that split from living canids around 5.7 million years ago. In contrast to numerous examples of hybridization across Canidae2,3, there is no evidence for gene flow between dire wolves and either North American grey wolves or coyotes. This suggests that dire wolves evolved in isolation from the Pleistocene ancestors of these species. Our results also support an early New World origin of dire wolves, while the ancestors of grey wolves, coyotes and dholes evolved in Eurasia and colonized North America only relatively recently