Basenjis, Dingoes, and Wolves Contribute to a Revised Perspective on

Dog Domestication
by Karla Schreiber and Dr. Jo Thompson
With the advent of three recently developed statistical modeling methods1, Freedman,
et.al. (2014)2, have offered a new interpretation of the origin of domestic dogs. They
used seven high-quality genome sequences from:
three living wolves (Figure 1) whose lines of descent represent the broad regions
where dog domestication hypothetically took place (an Israeli Wolf from the
Middle East, a Chinese Wolf from Southeast Asia, and a Croatian Wolf from
Europe),
two primitive dogs (Basenji and Dingo; Figure 1) whose ancestral lines represent
the earliest examples of domestic dogs to characterize the branch/clade of the
canine phylogenetic tree and who were selected because they "represent
divergent lineages relative to the [domestic dog] Boxer genome and maximize
the opportunity to capture distinct alleles present in the earliest dogs" (Freedman,
et.al., 2014, p.2),
a Boxer as a reference for modern dogs, and
a Golden Jackal as the comparison group to which all of the above are related
through a common earlier ancestor, but who formed a separate ancestral group
from dogs and wolves before any of them branched away from each other.

Figure 1. Map illustrating geographic distribution of sampled lineages for the three wolves, Basenji, and
Dingo. The range of modern wolves is shown in red.
1

Pairwise Sequential Markovian Coalescent or PSMC (Li and Durbin, 2011), the ABBA/BABA test
(Durand et al., 2011) and the Generalized Phylogenetic Coalescent Sampler or G-PhoCS (Gronau, et al.,
2011). PSMC was used to infer ancestral population size trajectories. ABBA/BABA test was used to
detect gene flow between two divergent populations, wolves and dogs. G-PhoCS produces a single
detailed image of demographic parameters such as population divergence times, ancestral population
sizes, and rates of post-divergence gene flow.
2

The full article is available free online through open access (with complete figures, tables, and
supporting materials) at http://tinyurl.com/mdhnsar.

A Basenji and a Dingo were selected to represent ancient dog lineages in the analysis
because their geographic isolation in Africa and Australia respectively places them
south of the natural range for all living wolf lineages (Figure 1), thereby reducing the
likelihood that shared genes would be a result of inbreeding with modern wolves.
The combination of these three new modeling methods allowed the authors to
reinterpret: 1) the size of the ancestral shared population at the time of the wolf/dog
divergence; 2) the geographic origins and timing of dog domestication; 3) postdivergence inbreeding between dogs and wolves; and 4) lineage-specific characteristics
of the recently discovered dog-specific AMY2B expansion (a gene implicated in starch
digestion).
Findings
Prior to the onset of dog domestication, the wolf-dog ancestral population had
substantially more genetic diversity than modern wolf populations. Dogs and wolves
separated, each forming distinct clades, from that common ancestral population (Figure
2) approximately 15,000 years ago indicating a single origin population prior to the
adoption of widespread agriculture by humans. There are no representatives of the
wolf-dog ancestral population today. The modern wolf is derived from wolf populations
that diverged from the wolf-dog ancestral population at about the same time as the
earliest dogs. Their divergence corresponds with the late Pleistocene period of
environmental change which could have impacted availability of prey species.

Figure 2. Stone age painting of a canid in the Font de Gaume Cave, in southwest France illustrating the
3
pre-domestication population of Canini , the clade that includes domestic dogs and wolves. The paintings
date from around 16,000-14,000 BC.

In this study, the Basenji and the Dingo genome sequences showed considerably lower
mean heterozygosity rates (meaning that they had less genetic variability or gene
3

In the Canidae family, the Canini group is related to wolves and the Vulpini is related foxes.

diversity) than any of the three wolf genomes. This finding suggested a dramatically
reduced effective population size for dogs, compared with modern wolf populations.
The Dingo's (Figure 3) heterozygosity rate was about the same as most domestic dogs
(Lindblad-Toh et. al., 2005), while the Basenji's (Figure 4) rate was somewhat lower.
Both dog and wolf populations experienced population bottlenecks after they separated.
However, the bottleneck for dogs was severe, in the order of 1500% decrease in
effective population size. Over the past 50,000 years, the Basenji effective population
size dropped from an estimated 35,000 individuals at the divergence point to 1,6401,980 individuals 4,000 years ago (Figure 4).

Figure 3. A female dingo in the forest of Fraser Island, off the coast of Queensland, Australia. Fraser
Island is a popular tourist destination and one of the only places in Australia to get close with wild
dingoes. Unfortunately there are problems with human-dingo interactions. Dingoes are given ear tags to
help identify individuals. Photo credit/property: Bradley Smith/howlingdingo.com.au

Figure 4. The Basenji as it is today and through time, still found in isolated and inaccessible areas where
it is used as a traditional hunting tool by forest-dependent people; Luenga Village, Democratic Republic of
Congo. Photo credit/property: Dr. Jo Thompson, Lukuru Foundation.

Geographic origin of dog domestication could not be inferred but the study concluded
that none of the modern wolves correspond to the location of the ancestral wolf-dog
population because none of the sampled wolves is more closely related to domestic
dogs than any of the others. The study found evidence that dogs diverged from the
ancestral wolf-dog population at approximately the same time the three wolf populations
diverged from each other. Therefore, domestic dogs and modern wolves evolved from
a now-extinct, common ancestral population, supporting the theory that dogs and
wolves are in fact "sister clades" (Figure 5).

Figure 5. Based on this study, the best fit for the data suggests that domestic dogs diverged from the
common ancestral wolf population at about the same time that the sampled wolf populations diverged
from each other as the most plausible scenario of their evolution.

Comparing the seven genome sequences for evidence of inbreeding between dogs and
wolves, the study noted significant evidence of admixture between (a) the Israeli Wolf
and the Basenji, (b) the Chinese wolf and the Dingo, and (c) the Israeli Wolf and the
Boxer. Since Basenjis are geographically isolated from any modern wolf populations,
the authors believe this is a result of gene flow between a population ancestral to

Basenjis and Boxers that inbred with a population ancestral to Israeli wolves in western
Eurasia.
Findings from an earlier study (Axelsson et.al., 2013) were interpreted to suggest that
the AMY2B gene (implicated in starch digestion) rapidly increased in the earliest dog
populations and that this was a critical part of the domestication process facilitating the
ability of dogs to feed on agricultural garbage around human agrarian settlements
(Figure 6). However, the current study found that the AMY2B gene had not reached
100% frequency / spread through the early dog population. In fact, all of the wolves in
the study, the Dingo, and the Siberian Husky (historically associated with nomadic
hunter gatherers of the Artic) had low frequencies of genes for processing starches,
while the Basenji and other breeds with histories of long association with humans in
agrarian societies had higher numbers of starch-processing genes. Based on this
evidence, the study concludes it is likely that domestication of dogs occurred prior to the
adoption of agriculture by humans.

Figure 6. A village dog sniffing a pot of rice, the dietary staple in Vadgaon, near Chowk, Raigad District,
Konkan Coast area in Maharashtra state, Western India. Photo credit/property: Kiran Khalap.

References:
1) Axelsson E, Ratnakumar A, Arendt M-J, Maqbool K, Webster Mt, et. at. (2013)
The genomic signature of dog domestication reveals adaptation to a starch-rich
diet. Nature 495: 360-364.
2) Durand EY, Patterson N, Reich D, Slatkin M (2011) Testing for Ancient
Admixture between Closely Related Populations. Mol Biol Evol 28: 2239-2252.

3) Freedman AH, Gronau I, Schweizer RM, Ortega-Del Vecchyo D, Han E, et al.

(2014) Genome Sequencing Highlights the Dynamic Early History of Dogs.
PLoS Genet 10(1): e1004016.doi:10.1371/journal.pgen.1004016
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ancient human demography from individual genome sequences. Nat Genet 43:
1031-1034.
5) Li H and Durbin R (2011) Inference of human population history from individual
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6) Lindblad-Toh K, Wade CM, Mikkelsen TS, Karlsson EK, Jaffe DB, et al. (2005)
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