The Role of Canids in Ritual and Domestic Contexts: New Ancient DNA Insights from Complex Hunter-Gatherer Sites in Prehistoric Central California

This study explores the interrelationship between the genus Canis and hunter–gatherers through a case study of prehistoric Native Americans in the San Francisco Bay-Sacramento Delta area. A distinctive aspect of the region\u27s prehistoric record is the interment of canids, variously classified as coyotes, dogs, and wolves. Since these species are difficult to distinguish based solely on morphology, ancient DNA analysis was employed to distinguish species. The DNA study results, the first on canids from archaeological sites in California, are entirely represented by domesticated dogs (including both interments and disarticulated samples from midden deposits). These results, buttressed by stable isotope analyses, provide new insight into the complex interrelationship between humans and canids in both ritual and prosaic contexts, and reveal a more prominent role for dogs than previously envisioned

Three-Dimensional Geometric Morphometric Analysis of Fossil Canid Mandibles and Skulls

Acknowledgements We thank C.P. Klingenberg for critical discussion of methodology. A. Drake and R. Losey were supported by a grant from the Social Sciences and Humanities Research Council of Canada grant (#SSHRC IG 435-2014-0075) and a European Research Council Grant to D. Anderson (#295458). M. Sablin acknowledges participation of ZIN RAS (state assignment № АААА-А17-117022810195-3) to this research. Supplementary information accompanies this paper at doi:10.1038/s41598-017-10232-1Peer reviewedPublisher PD

Bayesian phylogenetic estimation of fossil ages

Recent advances have allowed for both morphological fossil evidence and molecular sequences to be integrated into a single combined inference of divergence dates under the rule of Bayesian probability. In particular the fossilized birth-death tree prior and the Lewis-Mk model of discrete morphological evolution allow for the estimation of both divergence times and phylogenetic relationships between fossil and extant taxa. We exploit this statistical framework to investigate the internal consistency of these models by producing phylogenetic estimates of the age of each fossil in turn, within two rich and well-characterized data sets of fossil and extant species (penguins and canids). We find that the estimation accuracy of fossil ages is generally high with credible intervals seldom excluding the true age and median relative error in the two data sets of 5.7% and 13.2% respectively. The median relative standard error (RSD) was 9.2% and 7.2% respectively, suggesting good precision, although with some outliers. In fact in the two data sets we analyze the phylogenetic estimates of fossil age is on average < 2 My from the midpoint age of the geological strata from which it was excavated. The high level of internal consistency found in our analyses suggests that the Bayesian statistical model employed is an adequate fit for both the geological and morphological data, and provides evidence from real data that the framework used can accurately model the evolution of discrete morphological traits coded from fossil and extant taxa. We anticipate that this approach will have diverse applications beyond divergence time dating, including dating fossils that are temporally unconstrained, testing of the "morphological clock", and for uncovering potential model misspecification and/or data errors when controversial phylogenetic hypotheses are obtained based on combined divergence dating analyses.Comment: 28 pages, 8 figure

Nyctereutes terblanchei: The raccoon dog that never was

Fossils of the raccoon dog (genus Nyctereutes) are particularly rare in the African PlioPleistocene record, whilst the sole living representative, Nyctereutes procyonoides, is found in eastern Asia and parts of Europe. In southern Africa, only one fossil species of raccoon dog has been identiied – Nyctereutes terblanchei. N. terblanchei is recognised from a handful of Plio-Pleistocene sites in South Africa: Kromdraai, Kromdraai–Coopers and Sterkfontein in Gauteng, as well as Elandsfontein in the Western Cape Province. The validity of this species identiication was questioned on the basis of the rarity of southern African fossils assigned to Nyctereutes, that is, fewer than 10 specimens have been identified as Nyctereutes. This study examined this fossil sample of the raccoon dog from the Gauteng sites and compared dental and cranial metrics of the fossil with samples of modern canids and published data. Morphological traits used to distinguish Nyctereutes, such as the pronounced subangular lobe on the mandible and the relatively large size of the lower molars, were observed to be variable in all samples. Analysis showed that the size of the dentition of the southern African fossil samples was larger than that of living raccoon dogs, but fell well within the range of that of African jackals. These results suggest that fossil Nyctereutes cannot be distinguished from other canid species based on metric data alone, and may only be diagnosable using combinations of non-metric traits of the dentition and skull. However, based on the degree of morphological variability of the traits used to diagnose Nyctereutes, as well as the rarity of this genus in the African fossil record, these fossils are more likely to belong to a species of jackal or fox

Whole-genome sequence analysis shows that two endemic species of North American wolf are admixtures of the coyote and gray wolf.

Protection of populations comprising admixed genomes is a challenge under the Endangered Species Act (ESA), which is regarded as the most powerful species protection legislation ever passed in the United States but lacks specific provisions for hybrids. The eastern wolf is a newly recognized wolf-like species that is highly admixed and inhabits the Great Lakes and eastern United States, a region previously thought to be included in the geographic range of only the gray wolf. The U.S. Fish and Wildlife Service has argued that the presence of the eastern wolf, rather than the gray wolf, in this area is grounds for removing ESA protection (delisting) from the gray wolf across its geographic range. In contrast, the red wolf from the southeastern United States was one of the first species protected under the ESA and was protected despite admixture with coyotes. We use whole-genome sequence data to demonstrate a lack of unique ancestry in eastern and red wolves that would not be expected if they represented long divergent North American lineages. These results suggest that arguments for delisting the gray wolf are not valid. Our findings demonstrate how a strict designation of a species under the ESA that does not consider admixture can threaten the protection of endangered entities. We argue for a more balanced approach that focuses on the ecological context of admixture and allows for evolutionary processes to potentially restore historical patterns of genetic variation

Hyperostotic tympanic bone spicules in domestic and wild animal species

Hyperostotic tympanic bone spicules (HTBS), or "mucoperiosteal exostoses" (ME, syn.) are small, globular (>= 1 mm in diameter), mostly stalked and drumstick-like, bony structures, which arise from the inner wall of the tympanic bulla and project into the middle ear cavity. HTBS present as mineral densities inside the tympanic bulla on radiographs or computed tomographic (CT) images. They have previously been referred to as "otoliths" and were thought to represent mineral concretions secondary to otitis media. Recently, it was shown that HTBS actually consist of regularly composed bone tissue, covered by normal middle ear mucosa. So far, HTBS have only extensively been described in dogs, where they occur with a prevalence of up to >45%. A recent study detected ME, most likely representing HTBS, in the tympanic cavities of skeletonised skull bones of African lions. To estimate the occurrence of HTBS in other mammal species, the middle ears of adult animals of 78 different domestic, wild, and zoo species undergoing routine necropsy at the Institute of Veterinary Pathology of the LMU Munich, Germany were examined in the present study. HTBS were found in the tympanic bullae of carnivorous species, such as canids (wolf, fox), and in several large felid species (lion, tiger, leopard, cheetah). In contrast, HTBS were not present in domestic cats (more than to 200 cases), small carnivorous species such as mustelids, nor in any primate, ungulate, ruminant, pig, insectivore, or rodent species. The detectability of HTBS by CT of the tympanic bullae of large felids was demonstrated in an African lion. Histologically, HTBS consisted of mature lamellar bone, covered by periosteum and a partially ciliated, flat epithelium, regularly without any apparent inflammatory alterations. The present study demonstrates that HTBS may frequently occur in large felids and in different canid species. These findings should be taken into account when examining the middle ear, or interpreting bulla radiographs/CT-images of the respective species. However, the factors triggering the development of HTBS remain to be identified

Grotta Romanelli (Southern Italy, Apulia). Legacies and issues in excavating a key site for the Pleistocene of the Mediterranean

Grotta Romanelli, located on the Adriatic coast of southern Apulia (Italy), is considered a key site for the Mediterranean Pleistocene for its archaeological and palaeontological contents. The site, discovered in 1874, was re-evaluated only in 1900, when P. E. Stasi realised that it contained the first evidence of the Palaeolithic in Italy. Starting in 1914, G. A. Blanc led a pioneering excavation campaign, for the first-time using scientific methods applied to systematic palaeontological and stratigraphical studies. Blanc proposed a stratigraphic framework for the cave. Different dating methods (C-14 and U/Th) were used to temporally constrain the deposits. The extensive studies of the cave and its contents were mostly published in journals with limited distribution and access, until the end of the 1970s, when the site became forgotten. In 2015, with the permission of the authorities, a new excavation campaign began, led by a team from Sapienza University of Rome in collaboration with IGAG CNR and other research institutions. The research team had to deal with the consequences of more than 40 years of inactivity in the field and the combined effect of erosion and legal, as well as illegal, excavations. In this paper, we provide a database of all the information published during the first 70 years of excavations and highlight the outstanding problems and contradictions between the chronological and geomorphological evidence, the features of the faunal assemblages and the limestone artefacts

Wild dogs at stake: deforestation threatens the only Amazon endemic canid, the short-eared dog (Atelocynus microtis)

The persistent high deforestation rate and fragmentation of the Amazon forests are the main threats to their biodiversity. To anticipate and mitigate these threats, it is important to understand and predict how species respond to the rapidly changing landscape. The short-eared dog Atelocynus microtis is the only Amazon-endemic canid and one of the most understudied wild dogs worldwide. We investigated short-eared dog habitat associations on two spatial scales. First, we used the largest record database ever compiled for short-eared dogs in combination with species distribution models to map species habitat suitability, estimate its distribution range and predict shifts in species distribution in response to predicted deforestation across the entire Amazon (regional scale). Second, we used systematic camera trap surveys and occupancy models to investigate how forest cover and forest fragmentation affect the space use of this species in the Southern Brazilian Amazon (local scale). Species distribution models suggested that the short-eared dog potentially occurs over an extensive and continuous area, through most of the Amazon region south of the Amazon River. However, approximately 30% of the short-eared dog's current distribution is expected to be lost or suffer sharp declines in habitat suitability by 2027 (within three generations) due to forest loss. This proportion might reach 40% of the species distribution in unprotected areas and exceed 60% in some interfluves (i.e. portions of land separated by large rivers) of the Amazon basin. Our local-scale analysis indicated that the presence of forest positively affected short-eared dog space use, while the density of forest edges had a negative effect. Beyond shedding light on the ecology of the short-eared dog and refining its distribution range, our results stress that forest loss poses a serious threat to the conservation of the species in a short time frame. Hence, we propose a re-assessment of the short-eared dog's current IUCN Red List status (Near Threatened) based on findings presented here. Our study exemplifies how data can be integrated across sources and modelling procedures to improve our knowledge of relatively understudied species

Split, Send, Reassemble: A Formal Specification of a CAN Bus Protocol Stack

We present a formal model for a fragmentation and a reassembly protocol running on top of the standardised CAN bus, which is widely used in automotive and aerospace applications. Although the CAN bus comes with an in-built mechanism for prioritisation, we argue that this is not sufficient and provide another protocol to overcome this shortcoming.Comment: In Proceedings MARS 2017, arXiv:1703.0581