Ancestry informative markers in wolves and dogs demonstrate hybridization events

Figure 1 from Godinho et al. (2014) (a) Wolf–dog hybrid from 

Barbanza. Photo courtesy of A. Perez. (b) Location of wolf 

reference samples. Approximate wolf distribution area is 

showen in dark grey (Alvares et al. 2005). The red arrow 
shows the location of Barbanza. (c) Distribution of wolf packs 

(100-km2 circles) in Barbanza (red circle) and the surrounding 

area (black circles) between 1999 and 2003. Dots denote the

location of NIS.

Across the globe, millions of free-ranging dogs coexist with a few tens of thousands of wolves. Wolf-dog hybridization provide a classic example of the ecological and conservation implications of hybridization events between wild and domesticated forms. However the ability to understanding the implications of hybridization has been hampered by high genetic similarity and the difficulties in obtaining tissue samples. Consequently, there are many opportunities for wolves and dogs to hybridize, and cumulative data suggest that hybridization may be more frequent than previously suspected. Previous hybridization studies have required the slow and expensive use of tissue samples collected from dead or trapped animals, thus limiting population-level assessments. Furthermore, difficulties have been reported in correctly identifying wolf–dog backcrosses using simulated individuals and sets of 16–18 microsatellites, typically resulting in a large threshold implemented in clustering analyses.

In a forthcoming article Godinho et al. (2014) assess the occurrence and extension of hybridization in a pack of wolf–dog hybrids in northwestern Iberia, Godinho et al. compare the power of 52 nuclear markers implemented on tissue samples with a subset of 13 ancestry informative markers (AIMs) typed in noninvasive samples (NIS).

Godinho et al. (2014) find the 13 AIMs are as accurate as the 52 markers that were chosen without regard to the power to differentiate between wolves and dogs. The AIMs also having the advantage of being rapidly screened on noninvasive samples. The efficiency of AIMs significantly outperformed ten random sets of similar size and an additional commercial set of 18 markers.

Bayesian clustering analysis implemented on AIMs and NIS identified nine hybrids, two wolves and two dogs. Four hybrids were unambiguously assigned to F¹ x Wolf backcrosses. The new approach (AIMs + NIS) overcomes previous difficulties related to sample availability and informative power of markers, allowing a quick identification of wolf–dog hybrids in the first phases of hybridization episodes. This provides managers with a reliable tool to evaluate hybridization and estimate the success of their actions. This approach may be easily adapted for other pairs of wild/domesticated species, thus improving our understanding of the introgression of domestication genes into natural populations.

The hybridization event at Barbanza started with a cross between a female wolf and a male dog, as inferred by the presence of an Iberian wolf mtDNA haplotype in all hybrids, corresponding to the typical direction of wolf–dog hybridization. Despite the uncertainty of the impact of these crosses in the genetic composition of wolf populations (for example, due to difficulties of hybrid integration in packs), the results do suggest that the Barbanza pack has quickly evolved towards a hybrid swarm, with a minimum of two generations of backcrossing to wolves. These findings are alarming because wolf packs in nonexpanding populations generally consist of related individuals, and thus, other unobserved individuals in the area may also exhibit admixed ancestries.

Identifying wolf–dog hybrids is crucial for conservation and management strategies, particularly in the first phases of an episode of hybridization, as well as to evaluate the success of the strategies that have been implemented. Assuming a minimum territory size of 100 km² centered in the rendezvous site of the Barbanza pack, the area sampled covered a substantial portion of that territory (40%).

Moreover, the authors identified 11 wolf-like canids, 80% of the estimated population, which is fully compatible with the values reported in Iberia for pack size after reproduction, plus some floater animals, suggesting that the AIM’s method allows a comprehensive evaluation of hybridization in a given area. The goal to obtain a quick method to identify hybridization events was successful. Once there is the suspicion of a hybridization event, an estimate of about two months would be required to know the extent of the problem in an area equivalent to a pack territory.

Finally, the authors note that the logistic and economic investment to evaluate hybridization in this area was feasible (ca. 1500€ for the fieldwork – one person working 8 days – plus ca. 5000€ for laboratory work – one person working 3 weeks). Current management guidelines state that every practical measure should be implemented to remove obvious hybrids from the wild once an event of hybridization has been detected. This implies mainly lethal control, although keeping hybrids in captivity and sterilization have also been suggested. Nevertheless, the efficiency of removing hybrids from the wild remains very uncertain. Therefore, the methods shown here constitute a step forward towards the effective management of wolf–dog hybridization. The combination of NIS and AIMs may offer an opportunity to better understand the extension and persistence of hybridization between wolves and dogs at a global scale and its ecological, evolutionary and conservation consequences.

Citation

Godinho, R., López‐Bao, J. V., Castro, D., Llaneza, L., Lopes, S., Silva, P., & Ferrand, N. (2014). Real‐time assessment of hybridization between wolves and dogs: combining noninvasive samples with ancestry informative markers. Molecular Ecology Resources. Early On-line.

Abstract: Is black coat color in wolves of Iran an evidence of admixed ancestry with dogs?

A European black wolf, by Charles Hamilton Smith

Abstract: Melanism is not considered a typical characteristic in wolves of Iran and dark wolves are believed to have originated from crossbreeding with dogs. Such hybrid individuals can be identified with the combined use of genetic and morphological markers. We analyzed two black wolves using a 544 base pairs (bp) fragment of the mtDNA control region and 15 microsatellite loci in comparison with 28 dogs, 28 wolves, and four known hybrids. The artificial neural networks (ANNs) method was applied to microsatellite data to separate genetically differentiated samples of wolves, dogs, and hybrids, and to determine the correct class for the black specimens. Individual assignments based on ANNs showed that black samples were genetically closer to wolves. Also, in the neighbor-joining network of mtDNA haplotypes, wolves and dogs were separated, with the dark specimens located in the wolf branch as two separate haplotypes. Furthermore, we compared 20 craniometrical characters of the two black individuals with 14 other wolves. The results showed that craniometrical measures of the two black wolves fall within the range of wolf skulls. We found no trace of recent hybridization with free-ranging dogs in the two black wolves. Dark coat color might be the result of a natural combination of alleles in the coat-color-determining gene, mutation in the K locus due to past hybridization with free-ranging dogs, or the effect of ecological factors and adaption to habitat conditions.

Citation

Khosravi, R., Aghbolaghi, M. A., Rezaei, H. R., Nourani, E., & Kaboli, M. 2014. Is black coat color in wolves of Iran an evidence of admixed ancestry with dogs?  Journal of Applied Genetics, 1-9.

The Donggyeong, a poorly known dog from Korea

Native dogs of Korea

The Cultural Heritage Administration (Korea) registered the Donggyeong breed on its list of natural monuments in 2012. This is a state-designated heritage classification for animals, plants and biological and geological features carrying exceptional historical, cultural, scientific, aesthetic or academic value. The Jindo and the Sapsal dogs had been previously given this designation (see photos to the left).

The oldest reference to the Donggyeong is in The Chronicles of the Three Kingdoms, a book about Korea’s Three Kingdoms era, a period between the fourth and seventh centuries, and written during the Goryeo period (918-1392). One of the chapters of the book, “Assorted Information on the Donggyeong,” is dedicated to the dog. The Donggyeong was also a model for dogs appearing on earthenware made by during the Silla Dynasty (B.C. 57-935). 

At first glance, the Donggyeong looks very similar to the Jindo. However, the key distinction is in the tail: While the Jindo’s tail is long and curved, the Donggyeong has  a bobtail or completely lacks a tail.

In 2007 locals initiated a project to preserve the breed, forming an organization called the Korea Preservation Association for Gyeongju Dog Donggyeong and started breeding the dog in Gyeongju. Today, there are some 306 Donggyeong dogs which are officially recognized by the CHA.

In a forthcoming paper in the Journal of Veterinary Medical Science (Japan) Gil-jae Cho and colleagues analyze 10 microsatellite markers in the Donggyeong dog and compare it to 12 other dog breeds (369 individual dogs). The number of alleles per locus varied from 5 to 10 with a mean value of 7.6 in the Donggyeong dog. This study found specific alleles in the Donggyeong dog when compared with other dog breeds. Also, the results showed two Korean native dogs cluster together while other dog breeds form a distinctly different cluster. The closest distance (0.1184) was observed between the Donggyeong and Jindo suggesting a common ancestor.

Citations

Lee, E. W., Choi, S. K., & Cho, G. J. (in press, 2014). Molecular Genetic Diversity of the Gyeongju Donggyeong Dog in Korea. The Journal of veterinary medical science/the Japanese Society of Veterinary Science.

Dog of Silla royalty gets heritage designation. Korea JoogAng Daily. April 9, 2012.

Detection dogs and big cats

Greg Davidson and detection dog Chevy searching for cougar scat.

Detection dogs can be trained to locate explosives, illegal drugs, wildlife scat, or human remains. They have even been trained to locate illicit mobile phones in prisons. But, they have become extremely valuable for wildlife biologists and have been used to collect data on invasive species as well as endangered species.

In a forthcoming study in the Journal of Wildlife Management, Greg Davidson and colleagues from Find it Detection Dogs, used detection dogs to estimate the population size of cougars in northeast Oregon. Cougars are solitary, elusive, and have large home ranges. The researchers surveyed a 220 km² area using conservation detection dogs trained to locate cougar scat. Two hundred and seventy-two scat samples were collected, and 249 were analyzed for individual identification using DNA.  From 73 samples, 21 cougars (9 males and 12 females) could be recognized. The authors evaluated four models to estimate cougar densities: Huggins closed population capture–recapture (Huggins), CAPWIRE, multiple detections with Poisson (MDP), and spatially explicit capture–recapture (SECR). Their population estimates for the study area were 26 (9 males and 17 females) from Huggins models, 24 (9 males and 15 females) from CAPWIRE, and 27 (9 males and 18 females) from the MDP model.

This study demonstrates the efficacy of using detection dogs to collect cougar scat. The results suggest the probability of a dog finding a cougar’s scat on the landscape (given scat was available) in any of the 4 surveys was 0.99 for males and 0.68 for females. As a result, the authors were able to collected scat from all 4 GPS-collared cougars known to occupy a portion of the study area. The reported capture probabilities of this study were the largest observed for any previous study conducted with wild felids, which highlight the benefits of using scat detecting dogs to estimate cougar densities. Determining the age of the cougars captured was not possible because of the use of scat; so, their estimates included adults, subadults, and juveniles old enough to leave den sites.

Citation

Davidson, G. A., Clark, D. A., Johnson, B. K., Waits, L. P., & Adams, J. R. (in press, 2014). Estimating cougar densities in northeast Oregon using conservation detection dogs. The Journal of Wildlife Management. DOI: 10.1002/jwmg.758

How long ago did the dog and wolf separate from their ancestor?

Dates for the most recent common ancestor (MRCA) for dogs and wolves are remarkable recent. When Stan Olsen (1983) wrote his classic work on domestic dog fossils (1983) he noted the oldest known remains were from Palegawra Cave in northeastern Iraq with an estimated age of 12 thousand years before present (YBP).

But subsequent evidence suggests that dogs split from wolves much latter than those fossils would imply. Deep in Chauvet cave, in France, Garcia (2005) found a track of footprints from a large canid associated with one of a child. Torch wipes made by this child were dated at about 26,000 YBP. Based on the short length of medial fingers in the footprints the canid track was interpreted as being made by a large dog.

Genetic data also suggests that the dogs originated prior to the often cited 15,000 YBP. Ostrander and Wayne (2005) report that mitochondrial DNA (mtDNA) sequence analysis shed some light on the location of dog domestication as well as the number of founding matralines. They found dog sequences in at least four distinct clades, suggesting a single origin event and at least three other origination or interbreeding events. They also found nucleotide diversity high, implying an origin date of 135 to 40 thousand YBP. And Ostrander and Wayne (2005) suggests dogs may have had a long prehistory when they were not phenotypically distinct from wolf progenitors. Therefore early dogs may not have been recognized as domesticated in the archaeological record prior to 15,000 YBP because of their physical similarity to gray wolves.

However, a group of morphologically distinct canids hypothesized to be early domesticated dogs have been identified by Germonpré et al., (2009, 2012). Seven complete large canid skulls and 26 skull fragments from the Gravettian Předmostí site in the Czech Republic were examined, three skulls were identified as European Palaeolithic dogs, characterized by short skulls, short snouts, wide palates and braincases, and even-sized carnassials. The presence of dogs at Předmostí supports the hypothesis that domestication of dogs began long before the Late Glacial. One of the skulls was identified as a Pleistocene wolf, three other skulls could not be assigned to a group. Furthermore, at Předmostí, several human modifications of the skulls and canines hint at a specific relationship between humans and large canids.

While this has been controversial (see Crockford and Kuzmin, 2012), the evidence continues to mount supporting a much older origin of dogs. Druzhkova et al. (2013) provide molecular evidence that the 33,000-year old Pleistocene dog from Altai has a unique haplotype and the Altai dog is more closely related to modern dogs and prehistoric New World canids than it is to extant wolves.

In a forthcoming article in Quaternary International Pat Shipman of Pennsylvania State University asks the question, how do you kill 86 mammoths. The author examines a series of Eurasian archaeological sites formed between about 40 and 15 thousand years ago that feature unusually large numbers of mammoth remains with abundant artifacts and, often, mammoth bone dwellings. 

Since the late 19th century, archaeological sites dominated by mammoth remains have been a focus for research. How the bones of large numbers of mammoths, ranging from a minimum number of five individuals to hundreds of individuals, were deposited in one place remains an un-answered question. And, despite previous investigation, the cause of death of mammoths in these sites has remained controversial.

Two predominate hypotheses have been used to explain these megasites (a reference to the large number of mammoth remains): (1) the mammoths died natural deaths which were subsequently scavenged by humans; (2) or that specialized human hunting resulted in the deaths of the mammoths. Questions about collection and excavation techniques pose challenges for synthesizing the information, but the wealth of material has produced numerous published zooarchaeological analyses of the sites, including number of non-mammoth species represented, minimum numbers of mammoths at each site, mammoth age at death, and mammoth age profiles from individual sites.

All of these mammoth megasites are dated after the appearance of modern humans in Eurasia. These unusual sites are of interest given the obvious successes of the humans that made them. But, also because of the large number of individual mammoths and the scarcity of carnivore tooth marks and gnawing.  The evidence suggest the mammoth hunters had invented a new ability to retain and control the mammoth carcasses – protecting all of that valuable protein from scavengers.

Age profiles of mammoths at the megasites differ statistically at the p < 0.01 level from age profiles of African elephant populations that died of either attritional or catastrophic causes. However, age profiles from some mammoth sites exhibit a chain of linked resemblances with each other through time and space, again suggesting hunter behavioral and technological innovation.

The megasites Shipman analyzed are spread across most of the Eurasian continent and over a substantial time span. The introduction and spread of complex projectile weaponry by modern humans was probably important in producing the abrupt changes in assemblages associated with hominins that started about 45,000 YBP. Previous authors observed that reduced weight projectile weapons are a “niche-broadening technology” because they are easily carried, retain energy longer in flight, and they reduce the risk of injury when hunting dangerous animals or in combat when fighting other people. Thus early modern humans may have broaden their ecological niche. The reduced weight projectile weapons transforms the hunters from ambush predators (as Neanderthals were) to being long-distance hunters. Shipman also suggests a second advance which occurred during MIS 3 (marine isotope stage 3, which started 57,000 YBP) may have enhanced the advantages of reduced weight projectile weapon technology - a quasi-domesticated large canids willing to work cooperatively with humans.

Shipman (2014) hypothesize that this innovation may have been facilitated by an early attempt to domesticate dogs, as indicated by a group of genetically and morphologically distinct large canids which first appear in archaeological sites at about 32,000 YBP.

Thus at the moment it would appear that the MRCA of dogs and wolves is indeed much older than 15,000 YBP. It also appears that dogs, were co-operating with humans at least 32,000 YPB. But did humans domesticate the dog, or did dogs evolve from wolves all on their own?

Citations

Crockford, S. J., & Kuzmin, Y. V. (2012). Comments 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.

Druzhkova AS, Thalmann O, Trifonov VA, Leonard JA, Vorobieva NV, et al. (2013) Ancient DNA Analysis Affirms the Canid from Altai as a Primitive Dog. PLoS ONE 8(3): e57754. doi:10.1371/journal.pone.0057754.

Garcia, M.A., 2005. Ichnologie ge’ne’ rale de la grotte Chauvet. Bulletin de la Socie’ te’ pre’ historique francaise 102, 103–108.

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: 473-490.

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.

Kolosov, P. N. (2014). Primitive Mammoth Hunters and the Earliest Breed of Dog. Natural Resources, 2014.

Olsen, S. J. (1985). Origins of the domestic dog: the fossil record. University of Arizona Press, Tucson. 117 pp.

Ostrander, E. A., & Wayne, R. K. (2005). The canine genome. Genome research, 15(12), 1706-1716.

Shipman, P. (in press, 2014). How do you kill 86 mammoths? Taphonomic investigations of mammoth megasites. Quaternary International.