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.

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.

Introduction of dogs in Australia and the Pacific

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.

Oskarsson, M. C., Klütsch, C. F., Boonyaprakob, U., Wilton, A., Tanabe, Y., & Savolainen, P. (2012). 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, 279(1730), 967-974.

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.

Identifying seabirds' predators with DNA and cams

Steffens, K. E., Sanders, M. D., Gleeson, D. M., Pullen, K. M., & Stowe, C. J. (2012). Identification of predators at black-fronted tern Chlidonias albostriatus nests, using mtDNA analysis and digital video recorders. New Zealand Journal of Ecology, 36(1), 48. 

Predators at black-fronted tern (Chlidonias albostriatus) nests on the Wairau braided riverbed in Marlborough, New Zealand, were identified using (1) mtDNA analysis of 438 swabs from shell remains, nest contents, and carcass remains, and (2) digital video surveillance of 85 nests. DNA analysis suggested harriers (Circus approximans) were the main predator of tern eggs (171 of 192 shell samples containing predator DNA). Cats (Felis catus) and stoats (Mustela erminea) were the probable predators of the majority of adult terns killed (9 and 8 respectively, of swabs from 19 carcasses). Video results were broadly, though not entirely, consistent with the DNA results, and showed that harriers were the main predator of eggs (9 of 19 videoed predation events), followed by Southern black-backed gulls (Larus dominicanus dominicanus; 3/19); hedgehogs (Erinaceus europaeus occidentalis; 2/19), ship rats (Rattus rattus; 2/19), pied oystercatchers (Haematopus finschi; 2/19) and stoats (1/19). DNA was analysed from nine of the 19 videoed nests but the only predator DNA obtained was from harriers (four nests). Sixty-four percent of depredated nests (683/1063) contained no eggshell remains at the next monitoring visit after predation. DNA analysis of nest material from 71 of these empty nests yielded only one predator result; video footage was therefore essential to identify the cause of 12 empty nests at 19 videoed nest predations. Terns removed the depredated egg remains from eight nests; blackbacked gulls consumed eggs at three nests; and a stoat carried the eggs away from one nest. Hedgehog DNA was not found on shell remains from nests with videoed hedgehog predations. Analysing DNA from eggshell and carcass remains is a valuable new tool in wildlife research and management because it can identify predator species and indicate their relative importance. However, our results show that predator species are not equally detectable using this technique, leading to biases in the DNA results. This ‘detectability bias’ needs to be further quantified, and recognised when interpreting DNA results.

DNA to prove cat predation on native carnivores

Glen, A. S., Berry, O., Sutherland, D. R., Garretson, S., Robinson, T., & De Tores, P. J. (2010). Forensic DNA confirms intraguild killing of a chuditch (Dasyurus geoffroii) by a feral cat (Felis catus). Conservation Genetics, 11(3), 1099-1101.

Because animals killed by predators are often found partially consumed or decomposed, identification of the predator is often unachievable by post mortem examination. Forensic DNA offers an alternative in such situations. Using a novel method to analyse DNA from bite wounds on a freshly-killed chuditch Dasyurus geoffroii, we describe the first confirmed instance in this species of intraguild killing by a feral cat. Unlike post mortem examination, our method of DNA melt curve analysis is highly accurate and requires less time and expense than DNA sequencing.

Dog attacks to livestock in Spain

Echegaray, J. & Vilà, C. (2010). Noninvasive monitoring of wolves at the edge of their distribution and the cost of their conservation. Animal Conservation, 13(2), 157-161.

Large predators are recolonizing areas in industrialized countries, where they have been absent for decades or centuries. As they reach these areas, the predators often encounter unwary livestock and unprepared keepers, which translates into large economic costs. The cost per individual may have important repercussions on the conservation and management of large predators. During the years 2003–2004, we collected 136 feces preliminarily identified as belonging to gray wolves Canis lupus along the north-eastern limit of the wolf range in the Iberia peninsula (Basque Country, Spain). Genetic analyses allowed us to identify the species of origin in 86 cases: 31 corresponded to wolves, two to red foxes Vulpes vulpes and 53 to dogs Canis familiaris. Among the wolves, we identified 16 different individuals. We estimated the cost of conserving wolves to be >€3000 per wolf per year, based on the cost of damage compensation and prevention during the 2003–2004 period. However, most of the wolf feces contained wild prey whereas dog feces contained mostly remains of domestic animals. This finding suggests that uncontrolled dogs could be responsible for some of the attacks on livestock, contributing to negative public attitudes toward wolf conservation and increasing its cost.

Forensics to identify livestock predators

Caniglia, R., Fabbri, E., Mastrogiuseppe, L., & Randi, E. (2012). Who is who? Identification of livestock predators using forensic genetic approaches. Forensic Science International: Genetics, 7(3): 397-404.

Molecular identifications of salivary DNA are increasingly applied in wildlife forensic investigations, and are successfully used to identify unknown livestock predators, or elucidate cases of large carnivore attacks to humans. In Europe most of livestock predations are attributed to wolves (Canis lupus), thought free-ranging dogs are sometime the responsible, and false predations are declared by breeders to obtain compensations.
 In this study we analyzed 33 salivary DNA samples collected from the carcasses of 13 sheep and a horse presumably predated by wolves in seven farms in central Italy. Reliable individual genotypes were determined in 18 samples (corresponding to samples from nine sheep and the horse) using 12 unlinked autosomal microsatellites, mtDNA control-region sequences, a male-specific ZFX/ZFY restriction-site and four Y-linked microsatellites. Results indicate that eight animals were killed by five wolves (a male and four different females), the ninth by a female dog while the horse was post-mortem consumed by a male dog. The genotype of one female wolf matched with the genetic profile of a female wolf that was non-invasively sampled 4 years before in the same area near livestock predation remains. Genetic identifications always supported the results of veterinary reports. These findings show that salivary DNA genotyping, together with detailed veterinary field and necropsy reports, provides evidence which helps to correctly identify species, gender and individual genetic profiles of livestock predators, thus contributing to clarify attack dynamics and to evaluate the impact of wolf predations on husbandry.

DNA to identify canid predation on livestock

Sundqvist, A. K., Ellegren, H., & Vilà, C. (2008). Wolf or dog? Genetic identification of predators from saliva collected around bite wounds on prey.Conservation Genetics, 9(5), 1275-1279.
Wolf predation on livestock is a management problem in many areas and is often used to justify control measures against the wolves. However, wolves coexist with dogs across their range, and dogs could be responsible for attacks blamed on wolves. In this study we evaluate the possibility of obtaining sufficient DNA for species identification of the predator from saliva remaining close to bite wounds following a canid attack. Predator DNA of reasonably high quality was successfully extracted from bite wounds on two sheep that had been attacked on a farm and were genotyped using six informative microsatellite markers. A single consensus genotype could be constructed from the bite wounds of both sheep which we compared to genotypes obtained from Scandinavian wolves and dogs. The results clearly showed that the saliva sampled originated from a single dog. This report thus demonstrates the feasibility of predator species identification from bite wounds and also illustrates that it can not be taken for granted that wolves are responsible for canid livestock kills.

DNA to prove dog attacks

Clarke, M., & Vandenberg, N. (2010). Dog attack: the application of canine DNA profiling in forensic casework. Forensic science, medicine, and pathology,6(3), 151-157.

More than 100,000 dog attacks occur each year in Australia and many go unsolved. Dog attacks are not only a cause of human injury but may also involve injury and death to family pets, prized livestock and wildlife. Canine biological evidence can often be left behind on a victim or at the scene of an attack. Our laboratory provides canine DNA profiling for forensic investigations, utilising an in-house panel of 11 canine-specific autosomal short tandem repeat markers previously validated for use in casework. Case studies will be presented that outline methods for sampling of suspected canine biological evidence, profiling of canine DNA, statistical analysis, case outcomes and challenges for investigators.