I wonder with “American Village Dogs” to what extent it will ever be possible to confidently say whether trace matches with existing breeds truly might represent a purebred ancestor of that breed at some point further back in the line, or whether they might represent a shared ancestor with that breed much, much further back. Embark’s description of the “American Village Dog” does mention that “these dogs are almost completely descended from European dogs imported during the Colonial Era.” It looks like Darwin’s Ark also found trace amounts of several other breeds not detected by Embark in Zoe–some European, some Amerasian, some mixes of both.
There was a study published last year examining genetic relationships between 161 breeds: Parker et al. 2017. One of the surprises from that study was that the GSD, in particular, showed significant genetic relationships with many distinctly American breeds, including breeds like the Xolo and Peruvian Hairless which hadn’t previously been supposed to have any such ancestry. The researchers weren’t sure whether this finding reflected unrecorded outcrossings to actual registered purebred GSDs in more recent times, or colonial-era interbreeding between truly indigenous American dogs and imported Southern European cousins of the German landrace herding dogs which were later selectively developed into the GSD.