Barking up the wrong species tree: How gene flow shaped canine evolution

Complex patterns of gene flow in the family Canidae.

Hybridization between wolves and dogs is relatively common. A recent study in Spain, for example, reported a wolf with about one‐third dog-DNA. But what about other members of the canine family? A large team of international scientists sequenced the genomes of all members of the genus Canis. Comparing the genetic code of these animals revealed a complex evolutionary history shaped by gene flow. The results appeared in the journal Current Biology.

 

From Trees to Networks

The analyses revealed gene flow among numerous species. The figure below summarizes the findings. Solid arrows indicate known admixture events, dashed arrows refer to newly discovered patterns of gene flow. This widespread exchange of genetic material indicates that capturing canine evolution in a bifurcating tree is difficult (if not impossible). A network approach might be a better here. This is in line with recent studies on other animals, such as bats, baboons, whales, mammoths and – of course – birds. Scientists that try to force such evolutionary histories into a single species tree are probably barking up the wrong tree.

Dog network.jpg

The complex evolutionary history of Canidae. Solid arrows indicate known admixture events, dashed arrows refer to newly discovered patterns of gene flow (from Gopalakrishnan et al. 2018 Current Biology).

 

Dogs and Dholes

Let’s have a look at some admixture events. The analyses provided strong evidence for gene flow between African hunting dog (Lycaon pictus) and dhole (Cuon alpinus). This finding is a bit surprising, because these species currently do not overlap. African hunting dogs roam the plains of – you guessed it- Africa while dholes live in Asia. Perhaps dholes used to occur in the Middle East and interbred with African hunting dog from North Africa. Clearly, more research is needed to determine the timing and location of admixture.

dog_and_dhole

African hunting dogs (© Derek Keats | Wikimedia Commons) and dholes (© Raju Venkatesha Murthy | Wikimedia Commons) exchanged genes.

 

A Hybrid Species?

Apart from the expected dog introgression into gray wolves (Canis lupus), gene flow was also uncovered between gray wolves, golden jackals (Canis aureus) and African golden wolves (Canis anthus). In addition, the African golden wolf also received genetic material from the Ethiopian wolf (Canis simensis). This complex web of interactions prompted the researchers to have a closer look at the African golden wolf. Detailed analyses indicated that this wolf is probably a hybrid species between Ethiopian wolf and gray wolf, which contributed 28% and 72% of the genetic material, respectively.

Canis_anthus_bea_Ngorongoro_Crater.jpg

The African golden wolf (© xorge | Wikimedia Commons) is probably a hybrid species.

 

Spooky Introgression

Finally, the genomes of gray wolf and coyote (Canis latrans) contain a fraction of DNA that cannot be attributed to any extant species. The researchers suggest that this is the outcome of hybridization with an as-yet-unidentified species, a so-called ghost lineage. A similar scenario has recently been proposed in human evolution, based on deep learning analyses. I wouldn’t be surprised if more “spooky introgression in the distant past” will be uncovered in other systems. Stay tuned!

1024px-Trickster_goddess_(1134461130).jpg

Coyote probably received genetic material from a now extinct lineage (© matt knoth | Wikimedia Commons).

 

References

Gopalakrishnan, S., Sinding, M.S., Ramos-Madrigal, J., Niemann, J., Samaniego Castruita, J.A., Vieira, F.G.,Carøe, C., Montero, M., Kuderna, L., Serres, A., González-Basallote, V.M., Liu, Y., Wang, G., Marques-Bonet, T., Mirarab, S., Fernandes, C., Gaubert, P., Koepfli, K., Budd, J., Rueness, E.K., Heide-Jørgensen, M.P., Petersen, B., Sicheritz-Ponten, T., Bachmann, L., Wiig, Ø., Hansen, A.J. & Gilbert, M.T.P. (2018) Interspecific Gene Flow Shaped the Evolution of the Genus Canis. Current Biology, 28(21):3441-3449.

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