Dental Shape Variation and Phylogenetic Signal in the Rattini Tribe Species of Mainland Southeast Asia

We would like to thank Pierre-Henri Fabre for providing the phylogeny for this study. The collection of specimens used was funded by the French ANR Biodiversity, grant ANR 07 BDIV 012 CERoPath project (www.ceropath.org), and by the French ANR CP&ES, grant ANR 11 CPEL 002 BiodivHealthSEA project (www.biodivhealthsea.org). We also thank Madoudou Garba and Gauthier Dobigny (CBGP-IRD) for providing additional specimens. We greatly thank all local communities and their leaders for permission and invaluable help during field trapping. Special thanks to the CERoPath and BiodivHealthSEA teams and the drivers for their invaluable help during fieldwork. We would also like to thank Maeve McMahon for help with manuscript editing and preparation.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

Digital Zooarchaeology: State of the art, challenges, prospects and synergies

This is the final version. Available on open access from Elsevier via the DOI in this recordDigital technologies are an increasingly pervasive medium for zooarchaeological scholarship, providing a means to document and preserve fragile zooarchaeological specimens, share primary data, address methodological questions, and spread the information to the wider public. During the last decade, a broad array of digital technologies has been widely applied for the creation of three-dimensional images of animal bones, with a number of freely accessible collections being developed and published online. To be beneficial for academic and non-academic audiences, the creation of these collections requires careful planning, and more attention is needed in order to ensure their longevity in the web as well as their future usability. Drawing on an online workshop, organised by the Science and Technology in Archaeology and Culture Research Center of The Cyprus Institute, titled “Zooarchaeology in the Digital Era”, this article aims to provide a snapshot of the current state of art, and the methods and digital tools being employed in the digitisation of animal remains. The article also raises some of the challenges that the international zooarchaeological community is facing in the era of Linked Open Data, including management, archiving, curation, storage, dissemination and communication of digital data to the scientific world and the wider public. In addition, the paper highlights the need for a stronger collaboration between archaeologists and researchers from the Digital Humanities’ sector in order to stimulate an innovative discourse and create fertile ground for the production of new scientific knowledge.European Union Horizon 202

What's the catch? Archaeological application of rapid collagen-based species identification for Pacific Salmon

YesPacific salmon (Oncorhynchus spp.) are ecological and cultural keystone species along the Northwest Coast of North America and are ubiquitous in archaeological sites of the region. The inability to morphologically identify salmonid post-cranial remains to species, however, can limit our understanding of the ecological and cultural role different taxa played in the seasonal subsistence practices of Indigenous groups in the past. Here, we present a rapid, cost-effective ZooMS method to distinguish salmonid species based on collagen peptide mass-fingerprinting. Using modern reference material and an assemblage of 28 DNA-identified salmonid bones from the pre-contact Yup'ik site of Nunalleq, Western Alaska, we apply high-resolution mass spectrometry (LC-MS/MS) to identify a series of potential collagen peptide markers to distinguish Pacific salmon. We then confirm these peptide markers with a blind ZooMS analysis (MALDI-TOF-MS) of the archaeological remains. We successfully distinguish five species of anadromous salmon with this ZooMS approach, including one specimen that could not be identified through ancient DNA analysis. Our biomolecular identification of chum (43%), sockeye (21%), chinook (18%), coho (11%) and pink (7%), confirm the exploitation of all five available species of salmonid at Nunalleq

Boundaries of Semantic Distraction: Dominance and Lexicality Act at Retrieval

Three experiments investigated memory for semantic information with the goal of determining boundary conditions for the manifestation of semantic auditory distraction. Irrelevant speech disrupted the free recall of semantic category-exemplars to an equal degree regardless of whether the speech coincided with presentation or test phases of the task (Experiment 1) and occurred regardless of whether it comprised random words or coherent sentences (Experiment 2). The effects of background speech were greater when the irrelevant speech was semantically related to the to-be-remembered material, but only when the irrelevant words were high in output dominance (Experiment 3). The implications of these findings in relation to the processing of task material and the processing of background speech is discussed

Synchronous diversification of Sulawesi’s iconic artiodactyls driven by recent geological events

The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back 40 Myr ago. Recent studies, however, suggest that much of Sulawesi’s fauna assembled over the last 15 Myr. Here, we test the hypothesis that more recent uplift of previously submerged portions of land on Sulawesi promoted diversification, and that much of its faunal assemblage is much younger than the island itself. To do so, we combined palaeogeographical reconstructions with genetic and morphometric data sets derived from Sulawesi’s three largest mammals: the Babirusa, Anoa, and Sulawesi warty pig. Our results indicate that although these species most likely colonized the area that is now Sulawesi at different times (14 Myr ago to 2-3 Myr ago), they experienced an almost synchronous expansion from the central part of the island. Geological reconstructions indicate that this area was above sea level for most of the last 4 Myr, unlike most parts of the island. We conclude that emergence of land on Sulawesi (~1–2 Myr) may have allowed species to expand synchronously. Altogether, our results indicate that the establishment of the highly endemic faunal assemblage on Sulawesi was driven by geological events over the last few million years

Synchronous diversification of Sulawesi's iconic artiodactyls driven by recent geological events

The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back to 40 Ma. Recent studies, however, suggest that much of Sulawesi's fauna assembled over the last 15 Myr. Here, we test the hypothesis that more recent uplift of previously submerged portions of land on Sulawesi promoted diversification and that much of its faunal assemblage is much younger than the island itself. To do so, we combined palaeogeographical reconstructions with genetic and morphometric datasets derived from Sulawesi's three largest mammals: the babirusa, anoa and Sulawesi warty pig. Our results indicate that although these species most likely colonized the area that is now Sulawesi at different times (14 Ma to 2-3 Ma), they experienced an almost synchronous expansion from the central part of the island. Geological reconstructions indicate that this area was above sea level for most of the last 4 Myr, unlike most parts of the island. We conclude that emergence of land on Sulawesi (approx. 1-2 Myr) may have allowed species to expand synchronously. Altogether, our results indicate that the establishment of the highly endemic faunal assemblage on Sulawesi was driven by geological events over the last few million years

Synchronous diversification of Sulawesi's iconic artiodactyls driven by recent geological events

The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back to 40 Ma. Recent studies, however, suggest that much of Sulawesi’s fauna assembled over the last 15 Myr. Here, we test the hypothesis that more recent uplift of previously submerged portions of land on Sulawesi promoted diversification and that much of its faunal assemblage is much younger than the island itself. To do so, we combined palaeogeographical reconstructionswithgenetic andmorphometric datasets derived from Sulawesi’s three largest mammals: the babirusa, anoa and Sulawesi warty pig. Our results indicate that although these species most likely colonized the area that is now Sulawesi at different times (14 Ma to 2-3 Ma), they experienced an almost synchronous expansion from the central part of the island. Geological reconstructions indicate that this area was above sea level for most of the last 4 Myr, unlike most parts of the island. We conclude that emergence of land on Sulawesi (approx. 1-2 Myr) may have allowed species to expand synchronously. Altogether, our results indicate that the establishment of the highly endemic faunal assemblage on Sulawesiwas driven by geological events over the last few million years

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 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.Competing Interest StatementThe authors have declared no competing interest.- Results and Discussion -- The demographic history of Rattus rattus and its closely related species -- A global phylogeography of the black rat based on mitochondrial DNA -- Ancient genomes reveal the relationships of European black rats over space and time - Discussion - Method