The palaeogenetics of cat dispersal in the ancient world

Ottoni, C. et al. (2017) The palaeogenetics of cat dispersal in the ancient world. Nat. Ecol. Evol. 1, 0139.

The cat has long been important to human societies as a pest-control agent, object of symbolic value and companion animal, but little is known about its domestication process and early anthropogenic dispersal. Here we show, using ancient DNA analysis of geographically and temporally widespread archaeological cat remains, that both the Near Eastern and Egyptian populations of Felis silvestris lybica contributed to the gene pool of the domestic cat at different historical times. While the cat’s worldwide conquest began during the Neolithic period in the Near East, its dispersal gained momentum during the Classical period, when the Egyptian cat successfully spread throughout the Old World. The expansion patterns and ranges suggest dispersal along human maritime and terrestrial routes of trade and connectivity. A coat-colour variant was found at high frequency only after the Middle Ages, suggesting that directed breeding of cats occurred later than with most other domesticated animals.

Integrating social ecology in explanations of wolf–dog behavioral differences

Marshall-Pescini, S., Cafazzo, S., Virányi, Z., & Range, F. (2017). Integrating social ecology in explanations of wolf–dog behavioral differences. Current Opinion in Behavioral Sciences, 16, 80-86.

Highlights
• Wolf–dog differences have been explained as a result of human selection for desirable behaviours.
• But wolves and dogs also have different feeding ecologies and social organizations.
• Wolves rely on pack members for group hunting and pup-rearing.
• Dogs mostly forage alone on human refuse and show little allomaternal care.
• Social ecology helps explain observed wolf–dog differences in comparative studies.

Whereas studies in comparative cognition normally invoke ecology and social organization to account for differences in social behaviour and cognition across species, dog–wolf differences have so far been explained mostly as a result of direct human selection for desirable traits (e.g., tameness, attention to humans, sociability). Yet, as will be reviewed in this paper, dogs and wolves also differ considerably in both their feeding niche and social organization (which together we refer to as ‘social ecology’). We suggest that observed wolf–dog differences especially in their interaction with the environment (e.g., neophobia, persistence, risk taking) and conspecifics (e.g., tolerance, cooperation, communication) need to be considered also in regard to their social ecology. We propose that social ecology alongside human selection should be recognized as a potentially important factor affecting dogs’ behaviour, and suggest a number of potential avenues for future research, which can more directly test the relative importance of these selection forces.

Changes in the feeding ecology and social organization from wolves to dogs and how these may affect their behaviour towards conspecifics and the environment.

Ancient wolf genome reveals an early divergence of domestic dog ancestors and admixture into high-latitude breeds

Skoglund, P., Ersmark, E., Palkopoulou, E., & Dalén, L. (2015). Ancient wolf genome reveals an early divergence of domestic dog ancestors and admixture into high-latitude breeds. Current Biology, 25(11), 1515-1519.

The origin of domestic dogs is poorly understood, with suggested evidence of dog-like features in fossils that predate the Last Glacial Maximum  conflicting with genetic estimates of a more recent divergence between dogs and worldwide wolf populations. Here, we present a draft genome sequence from a 35,000-year-old wolf from the Taimyr Peninsula in northern Siberia. We find that this individual belonged to a population that diverged from the common ancestor of present-day wolves and dogs very close in time to the appearance of the domestic dog lineage. We use the directly dated ancient wolf genome to recalibrate the molecular timescale of wolves and dogs and find that the mutation rate is substantially slower than assumed by most previous studies, suggesting that the ancestors of dogs were separated from present-day wolves before the Last Glacial Maximum. We also find evidence of introgression from the archaic Taimyr wolf lineage into present-day dog breeds from northeast Siberia and Greenland, contributing between 1.4% and 27.3% of their ancestry. This demonstrates that the ancestry of present-day dogs is derived from multiple regional wolf populations.

A model of population history (admixture graph) fitted to the data

3D morphometric analysis of fossil canid skulls contradicts the suggested domestication of dogs during the late Paleolithic

Drake, A. G., Coquerelle, M., & Colombeau, G. (2015). 3D morphometric analysis of fossil canid skulls contradicts the suggested domestication of dogs during the late Paleolithic. Scientific reports, 5.

Whether dogs were domesticated during the Pleistocene, when humans were hunter-gatherers, or during the Neolithic, when humans began to form permanent settlements and engage in agriculture, remains controversial. Recently discovered Paleolithic fossil skulls, Goyet dated 31,680 +/− 250 YBP and Eliseevichi MAE 447/5298 dated 13,905 +/− 55 YBP, were previously identified as dogs. However, new genetic studies contradict the identification of these specimens as dogs, questioning the validity of traditional measurements used to morphologically identify canid fossil skulls. We employ 3D geometric morphometric analyses to compare the cranial morphology of Goyet and Eliseevichi MAE to that of ancient and modern dogs and wolves. We demonstrate that these Paleolithic canids are definitively wolves and not dogs. Compared to mesaticephalic (wolf-like breeds) dog skulls, Goyet and Eliseevichi MAE, do not have cranial flexion and the dorsal surface of their muzzles has no concavity near the orbits. Morphologically, these early fossil canids resemble wolves, and thus no longer support the establishment of dog domestication in the Paleolithic.

(a) 3D plot of PC1, PC2 and PC3, (b) 3D morphs of extremes along PC 1, PC 2 and PC 3. 95% Confidence interval ellipsoids of modern dogs, Alaskan wolves, and European wolves are outlined. Unclassified specimens are labelled separately in this and other figures. A 3D version of this figure is available as Supplementary Figure S1.

Genetic traces of historical human‐mediated dispersal of feral cats

Koch, K., Algar, D., & Schwenk, K. (2016). Feral Cat Globetrotters: genetic traces of historical human‐mediated dispersal. Ecology and Evolution.

Endemic species on islands are highly susceptible to local extinction, in particular if they are exposed to invasive species. Invasive predators, such as feral cats, have been introduced to islands around the world, causing major losses in local biodiversity. In order to control and manage invasive species successfully, information about source populations and level of gene flow is essential. Here, we investigate the origin of feral cats of Hawaiian and Australian islands to verify their European ancestry and a potential pattern of isolation by distance. We analyzed the genetic structure and diversity of feral cats from eleven islands as well as samples from Malaysia and Europe using mitochondrial DNA (ND5 and ND6 regions) and microsatellite DNA data. Our results suggest an overall European origin of Hawaiian cats with no pattern of isolation by distance between Australian, Malaysian, and Hawaiian populations. Instead, we found low levels of genetic differentiation between samples from Tasman Island, Lana'i, Kaho'olawe, Cocos (Keeling) Island, and Asia. As these populations are separated by up to 10,000 kilometers, we assume an extensive passive dispersal event along global maritime trade routes in the beginning of the 19th century, connecting Australian, Asian, and Hawaiian islands. Thus, islands populations, which are characterized by low levels of current gene flow, represent valuable sources of information on historical, human-mediated global dispersal patterns of feral cats.

Map of the world representing the main route (Golden Round) used by maritime fur trade (black lines). Boxes show sampling locations in Australia, Hawaii, and South-East Asia with bars indicating graphical output from STRUCTURE analysis for K = 5. Each individual cat is represented by a single vertical line in population's subset plots, which were assigned to their place of origin.

Archeozoology of dogs in fort-village complex at Vindolanda in northern England

Bennett, D., Campbell, G., & Timm, R. M. (2016). The dogs of Roman Vindolanda: Morphometric techniques in differentiating domestic and wild canids. Archaeofauna 25: 79-106

 The Roman-era fort-village complex at Vindolanda in northern England, occupied from about A.D. 50 to A.D. 415, has yielded extensive well-preserved remains of the domestic dog, Canis familiaris. Herein, utilizing a novel combination of biostatistical techniques to identify parameters that best differentiate canids, we test the hypothesis that the inhabitants of Vindolanda selectively bred dogs. We also differentiate dog remains from wolves and foxes, similarly-sized canids that occur throughout Eurasia. The Vindolanda dogs are less morphologically diverse than modern dogs but much more diverse than dogs of the British Neolithic and Iron Age. They are as morphologically diverse as dogs excavated from other Romano–British sites, and only slightly less diverse than the whole known population of Roman-era dogs sampled from across Europe and North Africa. Vindolanda dogs thus underwent greater directional selection than expected from natural environmental forces, suggesting that selective breeding rather than random panmixis maintained diversity. The Vindolanda dog sample will make an ideal subject for DNA analysis, since it contains dogs undergoing incipient diversification from dingo-like ancestors.

Bennett, D., & Timm, R. M. (2016). The dogs of Roman Vindolanda, Part II: Time-stratigraphic occurrence, ethnographic comparisons, and biotype reconstruction. Archaeofauna 25:  107-126

The Roman fort-village complex at Vindolanda in northern England has yielded extensive well-preserved remains of domestic dogs, Canis familiaris. Herein, we pose the questions—did the Romans breed for distinctive dog morphotypes, or were dogs breeding panmictically; and if dogs were bred, was it for functionality.

Biotype reconstructions of the eight dog morphotypes known from Roman Vindolanda

We address these questions utilizing remains that are correlated to age and context; morphometric analysis; dental wear stage; bone pathology; pawprints impressed in tiles, and contemporary written records and artwork. All age classes of dogs are represented. There is no evidence that dogs were butchered for food; survivorship curves suggest the typical U-shaped distribution found in populations at equilibrium. Small, medium-sized, and large dogs are represented with frequency changing over time and corresponding to change in the region of origin of the resident military cohort. Husbandry is confirmed on an individual with healed wounds and with the discovery of a beehive-shaped wattle doghouse. Dogs were used extensively in hunting wild game and bred for that activity. By integrating many diverse kinds of data we are able reconstruct biotypes of Roman dogs, greatly facilitating the interpretation of their functionality.

Genetic signatures underlying feline biology and domestication

Montague, M. J., Li, G., Gandolfi, B., Khan, R., Aken, B. L., Searle, S. M., ... & Driscoll, C. A. (2014). Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication. Proceedings of the National Academy of Sciences, 111(48), 17230-17235.

Little is known about the genetic changes that distinguish domestic cat populations from their wild progenitors. Here we describe a high-quality domestic cat reference genome assembly and comparative inferences made with other cat breeds, wildcats, and other mammals. Based upon these comparisons, we identified positively selected genes enriched for genes involved in lipid metabolism that underpin adaptations to a hypercarnivorous diet. 

We also found positive selection signals within genes underlying sensory processes, especially those affecting vision and hearing in the carnivore lineage. We observed an evolutionary tradeoff between functional olfactory and vomeronasal receptor gene repertoires in the cat and dog genomes, with an expansion of the feline chemosensory system for detecting pheromones at the expense of odorant detection. Genomic regions harboring signatures of natural selection that distinguish domestic cats from their wild congeners are enriched in neural crest-related genes associated with behavior and reward in mouse models, as predicted by the domestication syndrome hypothesis. Our description of a previously unidentified allele for the gloving pigmentation pattern found in the Birman breed supports the hypothesis that cat breeds experienced strong selection on specific mutations drawn from random bred populations. Collectively, these findings provide insight into how the process of domestication altered the ancestral wildcat genome and build a resource for future disease mapping and phylogenomic studies across all members of the Felidae.

Dual origin for domestic dog

Frantz, L.A. F., V. E. Mullin, M. Pionnier-Capitan, O. Lebrasseur, M. Ollivier, A. Perri, A. Linderholm, V. Mattiangeli, M. D. Teasdale, E. A. Dimopoulos, A. Tresset, M. Duffraisse, F. McCormick, L. Bartosiewicz, E. Gál, E. A. Nyerges, M. V. Sablin, S. Bréhard, M. Mashkour, A. Bălăşescu,B. Gillet, S. Hughes, O. Chassaing, C. Hitte, J.-D. Vigne, K. Dobney, C. Hänni, D. G. Bradley, & G. Larson. 2016. Genomic and archaeological evidence suggest a dual origin of domestic dogs. Science, 352 (6290) 1228-1231

The geographic and temporal origins of dogs remain controversial. We generated genetic sequences from 59 ancient dogs and a complete (28x) genome of a late Neolithic dog (dated to ~4800 calendar years before the present) from Ireland. Our analyses revealed a deep split separating modern East Asian and Western Eurasian dogs. Surprisingly, the date of this . divergence (~14,000 to 6400 years ago) occurs commensurate with, or several millennia after, the first appearance of dogs in Europe and East Asia. Additional analyses of ancient and modern mitochondrial DNA revealed a sharp discontinuity in haplotype frequencies in Europe. Combined, these results suggest that dogs may have been domesticated independently in Eastern and Western Eurasia from distinct wolf populations. East Eurasian dogs were then possibly transported to Europe with people, where they partially replaced European Paleolithic dogs.

Ancient DNA supports lineage replacement in European dog gene pool

Deguilloux, M. F., Moquel, J., Pemonge, M. H., & Colombeau, G. (2009). Ancient DNA supports lineage replacement in European dog gene pool: insight into Neolithic southeast France. Journal of Archaeological Science, 36(2), 513-519.

We report palaeogenetic analysis of domesticated dog (Canis familiaris) remains excavated from three archaeological sites from southeast France and dating from Middle Neolithic. Ancient DNA analysis was attempted on teeth and bone samples taken from 11 dogs. Three 266-base-pair fragments of the mitochondrial genome Hypervariable Region I (HVR-I) could be retrieved and revealed two haplotypes belonging to HVR-I lineage C. These three sequences were compared to the sequences of Swedish and Italian Neolithic dogs and permitted to confirm that clade C was largely represented all over Western Europe during this period. One haplotype defined in Neolithic French dog was observed for the first time in Canis mtDNA, underlining the loss of mitochondrial diversity in Europe since the Neolithic. Finally, these results point out mitochondrial lineage replacement in Europe, since lineage C represents only 5% of extant European dogs. Altogether, these results support the proposition that palaeogenetic studies are essential for the reconstruction of the past demographic history and the domestication process of dogs. 

East Asian possible origin of domestic dog

Wang, G. D., Zhai, W., Yang, H. C., Wang, L., Zhong, L., Liu, Y. H., Fan, R-X., Yin T.-T., Zhu C-L., Poyarkov, A.D., Irwin, D. M., Hytönen, M.K., Lohi, H., Wu, C.-I., Savolainen, P. & Zhang, Y.-P. (2016). Out of southern East Asia: the natural history of domestic dogs across the world. Cell research, 26(1), 21-33.

The origin and evolution of the domestic dog remains a controversial question for the scientific community, with basic aspects such as the place and date of origin, and the number of times dogs were domesticated, open to dispute. Using whole genome sequences from a total of 58 canids (12 gray wolves, 27 primitive dogs from Asia and Africa, and a collection of 19 diverse breeds from across the world), we find that dogs from southern East Asia have significantly higher genetic diversity compared to other populations, and are the most basal group relating to gray wolves, indicating an ancient origin of domestic dogs in southern East Asia 33 000 years ago.

Around 15 000 years ago, a subset of ancestral dogs started migrating to the Middle East, Africa and Europe, arriving in Europe at about 10 000 years ago. One of the out of Asia lineages also migrated back to the east, creating a series of admixed populations with the endemic Asian lineages in northern China before migrating to the New World. For the first time, our study unravels an extraordinary journey that the domestic dog has traveled on earth.

Selfish mothers

Paul, M., Majumder, S. S., Nandi, A. K., & Bhadra, A. (2015). Selfish mothers indeed! Resource-dependent conflict over extended parental care in free-ranging dogs. Royal Society Open Science, 2(12), 150580.
Parent–offspring conflict (POC) theory provides an interesting premise for understanding social dynamics in facultatively social species. In free-ranging dogs, mothers increase conflict over extended parental care with their pups beyond the weaning stage. In this study, we investigated whether resource quality affects POC in the dogs that typically live in a highly competitive environment as scavengers. We built a theoretical model to predict the alternative options available to the mother in the context of food sharing with her pups when protein-rich food (meat) is provided, as compared to carbohydrate-rich food (biscuits). We fit the mothers’ response from experimental data to the model and show that the mothers choose a selfish strategy, which can in turn ensure higher lifetime reproductive success, while depriving the current litter access to better resources. These results have interesting implications for understanding the social dynamics of the dogs, and the emergence of facultative sociality in a species that evolved from strongly social ancestors. We speculate that the tendency of increased conflict in resource-rich conditions might have driven the process of domestication in the ancestors of dogs which defected from their groups in favour of richer resources around human settlements.

Graphical representations of the models for mother’s strategy where y representing the conflict and x representing the conflict period vary between 0 and 1. (a) The selfish strategy: mother reserves a fixed amount of food for her offspring and takes any extra food for herself. Line 1 is conflict for food F, and line 2 is conflict for food F′, where F′>F (F represents the total food available to the mother, whereas F′ represents the more nutritious food than the food F, available to the mother). (b) The altruistic strategy: mother reserves a fixed amount of food for herself and allows the pups to have the rest. Line 1 is conflict for food F, and line 2 is conflict for food F′, where F′ > F

Baboons kidnap and raise feral dogs as pets

The Canine Cooperation Hypothesis

 Range, F. & Virányi, Z. (2014) Tracking the evolutionary origins of dog-human cooperation: The ‘Canine Cooperation Hypothesis’. Front. Psychol. 5:1582. doi:10.3389/fpsyg.2014.01582

At present, beyond the fact that dogs can be easier socialized with humans than wolves, we know little about the motivational and cognitive effects of domestication. Despite this, it has been suggested that during domestication dogs have become socially more tolerant and attentive than wolves. These two characteristics are crucial for cooperation, and it has been argued that these changes allowed dogs to successfully live and work with humans. However, these domestication hypotheses have been put forward mainly based on dog-wolf differences reported in regard to their interactions with humans. Thus, it is possible that these differences reflect only an improved capability of dogs to accept humans as social partners instead of an increase of their general tolerance, attentiveness and cooperativeness. At the Wolf Science Center, in order to detangle these two explanations, we raise and keep dogs and wolves similarly socializing them with conspecifics and humans and then test them in interactions not just with humans but also conspecifics. When investigating attentiveness towards human and conspecific partners using different paradigms, we found that the wolves were at least as attentive as the dogs to their social partners and their actions. Based on these findings and the social ecology of wolves, we propose the Canine Cooperation Hypothesis suggesting that wolves are characterized with high social attentiveness and tolerance and are highly cooperative. This is in contrast with the implications of most domestication hypotheses about wolves. We argue, however, that these characteristics of wolves likely provided a good basis for the evolution of dog-human cooperation.

A review of dog domestication from the Paleolithic to the Iron Age

Horard-Herbin, M-P., A. Tresset & J-D.Vigne. 2014. Domestication and uses of the dog in western Europe from the Paleolithic to the Iron Age. Animal Frontiers, 4 (3) 23-31 doi: 10.2527/af.2014-0018 

This paper reviews the knowledge of the history of the dog in western Europe acquired through archaeozoology.

The first part examines the question of domestication of the wolf during the Upper Paleolithic, by highlighting the sometimes contradictory archeological and genetic findings. It also briefly lays out the different controversies regarding the site or sites of domestication of the dog in the world and the presumed dates of this major phenomenon in human history.

The second part deals with the evolution of canine morphology from the Paleolithic to the Iron Age, integrating, for example, the latest discoveries regarding domestic coat colors in the Mesolithic.

Finally, the presumed and attested uses of dogs throughout European pre- and protohistory are presented, including certain practices that lasted over time.

Two studies on Paleolithic dogs and a controversy

Germonpré, M., Sablin, M. V., Stevens, R. E., Hedges, R. E., Hofreiter, M., Stiller, M., & Després, V. R. (2009). Fossil dogs and wolves from Palaeolithic sites in Belgium, the Ukraine and Russia: osteometry, ancient DNA and stable isotopes. Journal of Archaeological Science, 36(2), 473-490.

Using multivariate techniques, several skulls of fossil large canids from sites in Belgium, Ukraine and Russia were examined to look for possible evidence of the presence of Palaeolithic dogs. Reference groups constituted of prehistoric dogs, and recent wolves and dogs. The fossil large canid from Goyet (Belgium), dated at c. 31,700 BP is clearly different from the recent wolves, resembling most closely the prehistoric dogs. Thus it is identified as a Palaeolithic dog, suggesting that dog domestication had already started during the Aurignacian. The Epigravettian Mezin 5490 (Ukraine) and Mezhirich (Ukraine) skulls are also identified as being Palaeolithic dogs. Selected Belgian specimens were analyzed for mtDNA and stable isotopes. All fossil samples yielded unique DNA sequences, indicating that the ancient Belgian large canids carried a substantial amount of genetic diversity. Furthermore, there is little evidence for phylogeographic structure in the Pleistocene large canids, as they do not form a homogenous genetic group. Although considerable variation occurs in the fossil canid isotope signatures between sites, the Belgian fossil large canids preyed in general on horse and large bovids.

Dorsal view of the skulls from (a) Goyet (dog); (b) Trou Balleux (wolf); (c) Trou des Nutons (wolf),
showing the relative wide braincase of the Goyet dog 

Germonpré, M., Lázničková-Galetová, M., & Sablin, M. V. (2012). Palaeolithic dog skulls at the Gravettian Předmostí site, the Czech Republic. Journal of Archaeological Science, 39(1), 184-202.

Whether or not the wolf was domesticated during the early Upper Palaeolithic remains a controversial issue. We carried out detailed analyses of the skull material from the Gravettian Předmostí site, Czech Republic, to investigate the issue. Three complete skulls from Předmostí were identified as Palaeolithic dogs, characterized by short skull lengths, short snouts, and wide palates and braincases relative to wolves. One complete skull could be assigned to the group of Pleistocene wolves. Three other skulls could not be assigned to a reference group; these might be remains from hybrids or captive wolves. Modifications by humans of the skull and canine remains from the large canids of Předmostí indicate a specific relationship between humans and large canids.

Highlights

► Accepting an Aurignacian beginning of the domestication of the wolf is controversial. ►The Gravettian canid skulls from Předmostí were studied to check for the presence of dogs. ►Ancient dogs are characterized by short skulls and snouts, and wide palates and braincases. ►Using these criteria three Předmostí skulls were singled out as Gravettian dogs. ►Human modifications of the skulls hint at a specific human/large canid relationship.

Susan J. Crockford, S.J. & Y.V. KuzminComments on Germonpré et al., Journal of Archaeological Science 36, 2009 “Fossil dogs and wolves from Palaeolithic sites in Belgium, the Ukraine and Russia: osteometry, ancient DNA and stable isotopes”, and Germonpré, Lázkičková-Galetová, and Sablin, Journal of Archaeological Science 39, 2012 “Palaeolithic dog skulls at the Gravettian Předmostí site, the Czech Republic” Journal of Archaeological Science, 39(8):2797–2801. DOI: 10.1016/j.jas.2012.04.033

Issues related to the identification of Late Pleistocene dogs from different sites in Eurasia, triggered by recent publications (see Germonpré et al., 2009, 2012; Ovodov et al., 2011), are discussed. The main focus is the problem of how to distinguish wolves from early dogs on the basis of skull and teeth morphology. The studies by 18 and 19, reporting so-called ‘Palaeolithic dogs’ from Předmostí, Goyet, and other sites in Eastern and Central Europe, have some serious deficiencies. In our opinion, more work needs to be done to understand the biological mechanisms involved in wolf domestication and until then, it is premature to classify these Palaeolithic canids as fully domesticated dogs or even incipient dogs.

Highlights


► We discuss issues related to so-called ‘Palaeolithic dogs’ from sites in Eurasia. ► Our comments pertain to studies described in 18 and 19. ► We suggest it is premature to classify these Palaeolithic canids as fully domesticated dogs.

Germonpré, M., Sablin, M. V., Després, V., Hofreiter, M., Lázničková-Galetová, M., Stevens, R. E., & Stiller, M. (2013). Palaeolithic dogs and the early domestication of the wolf: a reply to the comments of Crockford and Kuzmin (2012). Journal of Archaeological Science, 40(1), 786-792.

This is a response to the comments of Crockford and Kuzmin (2012) on our identification of Palaeolithic dogs from different European Palaeolithic sites. In their comments Crockford and Kuzmin (2012) present some errors, misunderstandings and misrepresentations that we remedy here. In our opinion, the early wolf domestication must be regarded as an intimate relationship between humans and canids including the breeding of the latter by prehistoric people, resulting in the European Palaeolithic dogs.

Highlights

► Accepting an Aurignacian beginning of the domestication of the wolf is controversial. ► Crockford and Kuzmin (2012) conjecture such an early domestication. ► This is a response to the comments of Crockford and Kuzmin (2012) on our identification of European Palaeolithic dogs. ► Two large canid types occur in certain European Palaeolithic sites. ► This is explained by the presence of Palaeolithic dogs and Pleistocene wolves.

see also 

Mitochondrial genomes suggest European origin of dogs

Thalmann, O., B. Shapiro, P. Cui, V. J. Schuenemann, S. K. Sawyer, D. L. Greenfield, M. B. Germonpré, M. V. Sablin, F. López-Giráldez, X. Domingo-Roura, H. Napierala, H-P. Uerpmann, D. M. Loponte, A. A. Acosta, L. Giemsch, R. W. Schmitz, B. Worthington, J. E. Buikstra, A. Druzhkova, A. S. Graphodatsky, N. D. Ovodov, N. Wahlberg, A. H. Freedman, R. M. Schweizer, K.-P. Koepfli, J. A. Leonard, M. Meyer, J. Krause, S. Pääbo, R. E. Green &R. K. Wayne. 2013. Complete Mitochondrial Genomes of Ancient Canids Suggest a European Origin of Domestic Dogs. Science 342 (6160): 871-874 DOI: 10.1126/science.1243650

The geographic and temporal origins of the domestic dog remain controversial, as genetic data suggest a domestication process in East Asia beginning 15,000 years ago, whereas the oldest doglike fossils are found in Europe and Siberia and date to >30,000 years ago. We analyzed the mitochondrial genomes of 18 prehistoric canids from Eurasia and the New World, along with a comprehensive panel of modern dogs and wolves. The mitochondrial genomes of all modern dogs are phylogenetically most closely related to either ancient or modern canids of Europe. Molecular dating suggests an onset of domestication there 18,800 to 32,100 years ago. These findings imply that domestic dogs are the culmination of a process that initiated with European hunter-gatherers and the canids with whom they interacted.

33,000 years old incipient dog from Siberia

Ovodov, N. D., Crockford, S. J., Kuzmin, Y. V., Higham, T. F., Hodgins, G. W., & van der Plicht, J. (2011). A 33,000-year-old incipient dog from the Altai Mountains of Siberia: Evidence of the earliest domestication disrupted by the Last Glacial Maximum. PLoS One, 6(7), e22821.

Background

Virtually all well-documented remains of early domestic dog (Canis familiaris) come from the late Glacial and early Holocene periods (ca. 14,000–9000 calendar years ago, cal BP), with few putative dogs found prior to the Last Glacial Maximum (LGM, ca. 26,500–19,000 cal BP). The dearth of pre-LGM dog-like canids and incomplete state of their preservation has until now prevented an understanding of the morphological features of transitional forms between wild wolves and domesticated dogs in temporal perspective.

Methodology/Principal Finding

We describe the well-preserved remains of a dog-like canid from the Razboinichya Cave (Altai Mountains of southern Siberia). Because of the extraordinary preservation of the material, including skull, mandibles (both sides) and teeth, it was possible to conduct a complete morphological description and comparison with representative examples of pre-LGM wild wolves, modern wolves, prehistoric domesticated dogs, and early dog-like canids, using morphological criteria to distinguish between wolves and dogs. It was found that the Razboinichya Cave individual is most similar to fully domesticated dogs from Greenland (about 1000 years old), and unlike ancient and modern wolves, and putative dogs from Eliseevichi I site in central Russia. Direct AMS radiocarbon dating of the skull and mandible of the Razboinichya canid conducted in three independent laboratories resulted in highly compatible ages, with average value of ca. 33,000 cal BP.

Conclusions/Significance

The Razboinichya Cave specimen appears to be an incipient dog that did not give rise to late Glacial – early Holocene lineages and probably represents wolf domestication disrupted by the climatic and cultural changes associated with the LGM. The two earliest incipient dogs from Western Europe (Goyet, Belguim) and Siberia (Razboinichya), separated by thousands of kilometers, show that dog domestication was multiregional, and thus had no single place of origin (as some DNA data have suggested) and subsequent spread.

Origin of dingoes and Polynesian dogs

Oskarsson, M. C., Klütsch, C. F., Boonyaprakob, U., Wilton, A., Tanabe, Y., & Savolainen, P. (2011). Mitochondrial DNA data indicate an introduction through Mainland Southeast Asia for Australian dingoes and Polynesian domestic dogs. Proceedings of the Royal Society B: Biological Sciences, rspb20111395.

In the late stages of the global dispersal of dogs, dingoes appear in the Australian archaeological record 3500 years BP, and dogs were one of three domesticates brought with the colonization of Polynesia, but the introduction routes to this region remain unknown. This also relates to questions about human history, such as to what extent the Polynesian culture was introduced with the Austronesian expansion from Taiwan or adopted en route, and whether pre-Neolithic Australia was culturally influenced by the surrounding Neolithic world. We investigate these questions by mapping the distribution of the mtDNA founder haplotypes for dingoes (A29) and ancient Polynesian dogs (Arc1 and Arc2) in samples across Southern East Asia (n = 424) and Island Southeast Asia (n = 219). All three haplotypes were found in South China, Mainland Southeast Asia and Indonesia but absent in Taiwan and the Philippines, and the mtDNA diversity among dingoes indicates an introduction to Australia 4600–18 300 years BP. These results suggest that Australian dingoes and Polynesian dogs originate from dogs introduced to Indonesia via Mainland Southeast Asia before the Neolithic, and not from Taiwan together with the Austronesian expansion. This underscores the complex origins of Polynesian culture and the isolation from Neolithic influence of the pre-Neolithic Australian culture.

Frequency of the Polynesian haplotypes Arc1 and Arc2, and the dingo founder haplotype A29 in geographical regions. The number of individuals carrying each haplotype, total number of samples for the region and frequency (per cent) are shown. Arrows indicate suggested introduction routes. For Australia, A29 denotes both haplotypes A29 and A29′

Savolainen, P., Leitner, T., Wilton, A. N., Matisoo-Smith, E., & Lundeberg, J. (2004). A detailed picture of the origin of the Australian dingo, obtained from the study of mitochondrial DNA. Proceedings of the National Academy of Sciences of the United States of America, 101(33), 12387-12390.

To determine the origin and time of arrival to Australia of the dingo, 582 bp of the mtDNA control region were analyzed in 211 Australian dingoes sampled in all states of Australia, 676 dogs from all continents, and 38 Eurasian wolves, and 263 bp were analyzed in 19 pre-European archaeological dog samples from Polynesia. We found that all mtDNA sequences among dingoes were either identical to or differing by a single substitution from a single mtDNA type, A29. This mtDNA type, which was present in >50% of the dingoes, was found also among domestic dogs, but only in dogs from East Asia and Arctic America, whereas 18 of the 19 other types were unique to dingoes. The mean genetic distance to A29 among the dingo mtDNA sequences indicates an origin ≈5,000 years ago. From these results a detailed scenario of the origin and history of the dingo can be derived: dingoes have an origin from domesticated dogs coming from East Asia, possibly in connection with the Austronesian expansion into Island Southeast Asia. They were introduced from a small population of dogs, possibly at a single occasion, and have since lived isolated from other dog populations.

Variation of cats under domestication

Kurushima, J. D., Lipinski, M. J., Gandolfi, B., Froenicke, L., Grahn, J. C., Grahn, R. A., & Lyons, L. A. (2013). Variation of cats under domestication: genetic assignment of domestic cats to breeds and worldwide random‐bred populations. Animal genetics, 44(3), 311-324.

Both cat breeders and the lay public have interests in the origins of their pets, not only in the genetic identity of the purebred individuals, but also the historical origins of common household cats. 

The cat fancy is a relatively new institution with over 85% of its 40–50 breeds arising only in the past 75 years, primarily through selection on single-gene aesthetic traits. The short, yet intense cat breed history poses a significant challenge to the development of a genetic marker-based breed identification strategy. Using different breed assignment strategies and methods, 477 cats representing 29 fancy breeds were analysed with 38 short tandem repeats, 148 intergenic and five phenotypic single nucleotide polymorphisms. Results suggest the frequentist method of Paetkau (accuracy single nucleotide polymorphisms = 0.78, short tandem repeats = 0.88) surpasses the Bayesian method of Rannala and Mountain (single nucleotide polymorphisms = 0.56, short tandem repeats = 0.83) for accurate assignment of individuals to the correct breed. Additionally, a post-assignment verification step with the five phenotypic single nucleotide polymorphisms accurately identified between 0.31 and 0.58 of the mis-assigned individuals raising the sensitivity of assignment with the frequentist method to 0.89 and 0.92 single nucleotide polymorphisms and short tandem repeats respectively. This study provides a novel multi-step assignment strategy and suggests that, despite their short breed history and breed family groupings, a majority of cats can be assigned to their proper breed or population of origin, i.e. race.

The ascent of cats

Lipinski, M. J., Froenicke, L., Baysac, K. C., Billings, N. C., Leutenegger, C. M., Levy, A. M., Longerid, M., Niinie, T., Ozpinarf, H., Slaterg, M.R., Pedersen, N.C. & Lyons, L. A. (2008). The ascent of cat breeds: genetic evaluations of breeds and worldwide random-bred populations. Genomics, 91(1), 12-21.

The diaspora of the modern cat was traced with microsatellite markers from the presumed site of domestication to distant regions of the world. Genetic data were derived from over 1100 individuals, representing 17 random-bred populations from five continents and 22 breeds.

The Mediterranean was reconfirmed to be the probable site of domestication. Genetic diversity has remained broad throughout the world, with distinct genetic clustering in the Mediterranean basin, Europe/America, Asia and Africa. However, Asian cats appeared to have separated early and expanded in relative isolation. Most breeds were derived from indigenous cats of their purported regions of origin. However, the Persian and Japanese bobtail were more aligned with European/American than with Mediterranean basin or Asian clusters. Three recently derived breeds were not distinct from their parental breeds of origin. Pure breeding was associated with a loss of genetic diversity; however, this loss did not correlate with breed popularity or age.