I’m not sure why you think I don’t understand the basics of taxonomy. Yes, I am well aware that all arctic wolves are grey wolves. That is not at issue. I am going to try one last time to explain.The difference here is that there's no animal in PZ that's a "generic mammal" with a listed scientific name as (Mammalia). All the animals in PZ are much more specific than that, and for good reason. By contrast, having a specific species means you include everything else from bellow. All Arctic wolves are grey wolves, but not all grey wolves are Arctic wolves. So by having all grey wolves, you not only include the Arctic subspecies but every other subspecies too. You don't get to pick and chose which subspecies are or aren't included in the whole species.
Here's a visual that might help illustrate things. The red group includes everything in the other coloured groups as a fundamental of how taxonomy operates.
a) the setup
A zoo obtains several wolves captured in turkey. The zoo places them on display and adds a sign saying: Canis lupus
q1: is the sign incorrect?
q2: does the enclosure have arctic wolves in it?
The paper is very good and interesting. It does not, however, show that Grey Wolves (excluding domestic dogs) are not paraphyletic. All the grey wolves in the study are Eurasian wolves. The authors note that their data suggest (not demonstrate) that wolves from the three sampled sites (all Eurasian wolves) are more closely related to each other than to domestic dogs. This suggests:The most recent literature supports grey wolfs existing as a monophyletic clade without dogs.
A) that domestic dogs are monophyletic
B) that (the 3 sampled populations of) Eurasian wolves are monophyletic in relation to domestic dogs (not necessarily also true in relation to new world wolves, since there could have been multiple invasions of NA from NE Asia).
Reading further, in fact, the dates given for the divergence between wolves and dogs makes it very unlikely that dogs and Eurasian wolves are not more closely related to each other than to at least some new world wolves, unless all new world wolves descend from a single source population info Eurasian wolves less than 16 thousand years ago (when domestication occurred). Noting though that the paper does not look at new world wolves at all.
Edit: For a more recent paper showing just how messy relationships among wolves actually are, see This paper, which does compare old and new world populations, though it does not include domestic dogs.
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