Background: The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20 × data from 1987 individuals, including 1611 dogs (321 breeds), 309 village dogs, 63 wolves, and four coyotes, we identify genomic variation across the canid family, setting the stage for detailed studies of domestication, behavior, morphology, disease susceptibility, and genome architecture and function. Results: We report the analysis of > 48 M single-nucleotide, indel, and structural variants spanning the autosomes, X chromosome, and mitochondria. We discover more than 75% of variation for 239 sampled breeds. Allele sharing analysis indicates that 94.9% of breeds form monophyletic clusters and 25 major clades. German Shepherd Dogs and related breeds show the highest allele sharing with independent breeds from multiple clades. On average, each breed dog differs from the UU_Cfam_GSD_1.0 reference at 26,960 deletions and 14,034 insertions greater than 50 bp, with wolves having 14% more variants. Discovered variants include retrogene insertions from 926 parent genes. To aid functional prioritization, single-nucleotide variants were annotated with SnpEff and Zoonomia phyloP constraint scores. Constrained positions were negatively correlated with allele frequency. Finally, the utility of the Dog10K data as an imputation reference panel is assessed, generating high-confidence calls across varied genotyping platform densities including for breeds not included in the Dog10K collection. Conclusions: We have developed a dense dataset of 1987 sequenced canids that reveals patterns of allele sharing, identifies likely functional variants, informs breed structure, and enables accurate imputation. Dog10K data are publicly available.

Dogs exhibit an exceptional range of morphological diversity as a result of their long-term association with humans. Attempts to identify when dog morphological variation began to expand have been constrained by the limited number of Pleistocene specimens, the fragmentary nature of remains, and difficulties in distinguishing early dogs from wolves on the basis of skeletal morphology. In this study, we used three-dimensional geometric morphometrics to analyze the size and shape of 643 canid crania spanning the past 50,000 years. Our analyses show that a distinctive dog morphology first appeared at about 11,000 calibrated years before present, and substantial phenotypic diversity already existed in early Holocene dogs. Thus, this variation emerged many millennia before the intense human-mediated selection shaping modern dog breeds beginning in the 19th century.

A new early Miocene large castorid, Minocastor godai gen. et sp. nov., from the Dota locality, Gifu Prefecture in central Japan, is described on the basis of dentaries and teeth. The material comes from the Kani basin, where limnofluviatile clay and sandstones of the Nakamura Formation (Mizunami Group) are exposed on the southern (left) bank of the Kiso River. It represents the richest sample of a Miocene small mammal in the Japanese fossil record thus far known. Based on jaw and tooth morphology, this new castorid most likely represents a primitive anchitheriomyine. However, it lacks the marked striations on the incisors that are characteristic of the advanced large, middle Miocene anchitheriomyines like Anchitheriomys and Amblycastor. The new castorid shares this dental feature with other primitive anchitheriomyines from Asia and North America, like Propalaeocastor, Oligotheriomys, and Miotheriomys. For these genera, a new tribe, Minocastorini, is proposed as sister group to the Anchitheriomyini. The incisor enamel microstructure of the new castorid largely exhibits plesiomorphic characters but also apomorphic features such as pseudo-pauciserial Hunter-Schreger bands. Additionally, the outer portion of the enamel band is rather thick in comparison to that of other beavers. Based on the rodent taxa associated with Minocastor godai gen. et sp. nov., Dota can be correlated with European Neogene mammal units MN 3/4. Magnetostratigraphic studies and radiometric dates obtained from the Mizunami Group indicate that Dota is more likely correlated with MN 3, with an absolute age of around 18.5 Ma. http://zoobank.org/urn:lsid:zoobank:org:pub:B1886424-1759-4BDA-A5CC-D122436E1A76 Citation for this article: Mörs, T., Y. Tomida, and D. C. Kalthoff. 2016. A new large beaver (Mammalia, Castoridae) from the early Miocene of Japan. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2016.1080720.

The black rhinoceros (Diceros bicornis L.) is a critically endangered species historically distributed across sub-Saharan Africa. Hunting and habitat disturbance have diminished both its numbers and distribution since the 19th century, but a poaching crisis in the late 20th century drove them to the brink of extinction. Genetic and genomic assessments can greatly increase our knowledge of the species and inform management strategies. However, when a species has been severely reduced, with the extirpation and artificial admixture of several populations, it is extremely challenging to obtain an accurate understanding of historic population structure and evolutionary history from extant samples. Therefore, we generated and analyzed whole genomes from 63 black rhinoceros museum specimens collected between 1775 and 1981. Results showed that the black rhinoceros could be genetically structured into six major historic populations (Central Africa, East Africa, Northwestern Africa, Northeastern Africa, Ruvuma, and Southern Africa) within which were nested four further subpopulations (Maasailand, southwestern, eastern rift, and northern rift), largely mirroring geography, with a punctuated north–south cline. However, we detected varying degrees of admixture among groups and found that several geographical barriers, most prominently the Zambezi River, drove population discontinuities. Genomic diversity was high in the middle of the range and decayed toward the periphery. This comprehensive historic portrait also allowed us to ascertain the ancestry of 20 resequenced genomes from extant populations. Lastly, using insights gained from this unique temporal data set, we suggest management strategies, some of which require urgent implementation, for the conservation of the remaining black rhinoceros diversity.

The blue antelope (Hippotragus leucophaeus) is the only large African mammal species to have become extinct in historical times, yet no nuclear genomic information is available for this species. A recent study showed that many alleged blue antelope museum specimens are either roan (Hippotragus equinus) or sable (Hippotragus niger) antelopes, further reducing the possibilities for obtaining genomic information for this extinct species. While the blue antelope has a rich fossil record from South Africa, climatic conditions in the region are generally unfavorable to the preservation of ancient DNA. Nevertheless, we recovered two blue antelope draft genomes, one at 3.4× mean coverage from a historical specimen (∼200 years old) and one at 2.1× mean coverage from a fossil specimen dating to 9,800–9,300 cal years BP, making it currently the oldest paleogenome from Africa. Phylogenomic analyses show that blue and sable antelope are sister species, confirming previous mitogenomic results, and demonstrate ancient gene flow from roan into blue antelope. We show that blue antelope genomic diversity was much lower than in roan and sable antelope, indicative of a low population size since at least the early Holocene. This supports observations from the fossil record documenting major decreases in the abundance of blue antelope after the Pleistocene–Holocene transition. Finally, the persistence of this species throughout the Holocene despite low population size suggests that colonial-era human impact was likely the decisive factor in the blue antelope's extinction.