[jesse mcclure]

**Eric**, including the overnight time sounds right. The *average* time spent in a crate is under 2 hours, but the average (as arithmetic mean) is not the best representation of these data as they do not follow a normal “bell curve” distribution. Many dogs have more than 8 hours per day in a crate for that question – and there is a very large overlap with these dogs and those dogs who are said to sleep in a crate. It just turns out that only about 10% of our dogs sleep in a crate overnight, so those ~8 hours for all those dogs doesn’t have a huge impact on the overall average. In otherwords the “average” is about 2 hours, but this is because around 10% of our dogs spend 10 or so hours a day in a crate because they sleep there, while many others are rarely or never crated at all.

On a related metric, a vast majority of dogs listed as sleeping in a crate overnight also have 8 or more hours per day in a crate – so most of our participants are answering that question in the same way you did. There do seem to be some exceptions, but that should not matter in the long run.

**Andrea**, I think that could just as well be counted as crate time or not as crate time. So it should be fine as is.

[jesse mcclure]

Thanks Allison, we are really interested in the potential for North Amercan “village dogs”. It’s unclear, and a bit controversial, as to whether there are any remaining “just dog” dogs in the US. A majority of our mixed breed dogs in the US are just that **mixed**. They are a remixture of a variety of purebred dogs. But it’s possible that some of them are – or at least include some ancestry of – dogs that never went through a breed-creation bottleneck.

Detecting that, however, may be pretty difficult. There is a subtle but hugely important difference in saying we can’t confidently assign a block of DNA to a specific breed ancestry and saying we can confidently say is not from a breed ancestry. There are some genetic metrics that can get at this in principle, but in practice it depends on the resolution of data we can get.

[jesse mcclure]

I’ve just revised the “not genotyped” note to say “not yet genotyped” as that is the meaning.

If we were to learn there was a problem with your sample, we’d let you know and potentially send a new kit.

[jesse mcclure]

Hunting itself is not one of the recommended activities. It could have been – it was in our initial pool of items, but perhaps it is because there are so many component behaviors in being a good gun dog that the personality surveys didn’t align well with being an effective gun dog. In otherwords, there may be a wide range of dog “personalities” that can make great gun dogs. While I’m not a hunter myself, this would make sense to me: does your hunting dog need to track, or to retrieve, or to point, or all of the above? Each of these components are in the activity list.

Or it could just as well be that there is a behavioral dimension relating to being motivated for the actual hunt (retrieving a real duck) but having less interest in the dog-sport components of hunting. But this behavioral trait may not have been captured by the personality portion of our questionairres so we didn’t find good correlations on which to recommend hunting itself for a given dog.

Also, when you look at the activity recommendation page, every activity is listed for every dog regardless of their survey responses. This is because we generally want to encourage people to be active with their dogs. *All* of the activites are good/healthy for dogs in general and if we can introduce people to dog activities they’ve never thought of or heard of before, that itself is a win in my book. We just take the 9 categories of activities and sort them (and give them a “paw” rating) based on which one looks like it would be best for your dog.

[jesse mcclure]

Becky, that sounds right to me. For that checkbox in the dog profile we are really looking for whether the pup is an officially registered purebred. Any major kennel club would be fine (AKC, CKC, etc). There are certainly many purebred dogs who have never been officially registered, and that’s fine. We’ll be able to figure that out from the DNA anyways. But getting a check for registered purebreds serves two related purposes.

First, some background – one of the things many of our participants want to know is what breed mix their dog is (if they are mixed). While this is not a goal of our research, we’d very much like to provide our participants with feedback that they most want, so we are working on getting some ancestry reconstruction up and running. One of the major hurdles for this is having an ample reference panel of **known** purebred dogs of as many breeds as possible. We don’t need all that many representatives of each breed, but we do need many many breeds. For these analyses, failing to include additional representatives of a given breed will not really have any negative impact (except perhaps for very rare breeds) – but including a incorrectly identified purebred could really mess up the analysis. So we’d prefer to be overly cautious and any dog that is “supposedly” a purebred is not worth including (especially for an already well represented breed like pugs).

So in short, we want to include only dogs that we can be absolutely sure are purebred. Still, one might be absolutely sure that their dog is a purebred but they’ve just never bothered with the registration process. Here still using only officially registered dogs is good for less-scientific but more practical reasons: as our reference data will become a shared resource for the scientific community, and our results will be published (and peer reviewed) it is cleaner to define our purebred references as “registered” purebred as opposed to “either registered, or otherwise asserted by the owner”, The official registration through the AKC, CKC, or other breed clubs just adds an impartial confirmation which can ensure confidence in our purebred reference set.

[jesse mcclure]

William, we don’t use the breed in generating the recommendations. It’s based only off of the survey answers you’ve provided for your dog. There certainly can be dogs of a breed typically used for hunting that may not love huntng. But for now there could also be a simpler explanation: we don’t yet have sufficient data to make the best recommendations. This should be changing quickly though, so check back to see the changes to your pup’s recommendations.

All we know for now is that based on our currently limited data set, your dog’s personality survey was most similar to dogs that did not love hunting (if hunting was not highly rated for your dog). This could be a real pattern, or it may be an oddity of the limited data which will get cleared up as more answers come in.

Out of curiosity, do you hunt with your dog? Does she enjoy it and/or do well at it? In other words, do you expect she’d like hunting based on her breed, or do you know she does based on experience?

[jesse mcclure]

**Rebecca**, we did spend a bit of time and effort figuring out how to best group activities into meaningful groups. We had a good bit of preliminary data to find which activities tended to group together – but trends are just trends, there are always exceptions. A great example is the Tracking category where some of the specific activites are really only good for small dogs and some others may be best for large dogs. But the temperaments or personalities of dogs that benefit most from tracking activities have some similarities despite their body sizes being completely different. So we don’t expect that *all* the activities in a highly rated category will be great for the dog they are recommended for – but it’s likely that one of them could be.

There is always a bit of a balancing act between binning and splitting this type of data. If we bin too much we get activities that really might not be similar at all grouped together. On the flip side, if we split out each individual activity, we’d not be able to make useful inferences: you’d tell us your dog likes Fly Ball, and we’d be able to say “Your dog may like Fly Ball” – not so helpful. But by finding clusters of activities that have grouped together in many dogs (we did a cluster/factor analysis on preliminary data) we can make inferences that many dogs that like Fly Ball also like Agility – and we can also see what temperament or personality traits from the surveys correlate with that sport preference.

—

**Lindsay**, you’re absolutely right: for the moment the recommendations may be pretty bad. Help us improve them. As noted on the sports page:

> Please note that the scores for these recommendations (the number of “paws”) will change as we gather more data on which to base the recommendations. For now these are quite preliminary

But even with an expansive data set, we’ll still be wrong from time to time. Life would be boring if it could be so easily reduced to a handful of numbers. But that doesn’t mean the numbers aren’t useful. These sports recommendations work a lot like career recommendations based on personality tests for people. We may know that *on average* personality types like an INTJ on the Myers Briggs scale may be well suited to carreers in the scienes. So all else being equal, and INTJ should think whether the sciences may be right for them. But there are countless INTJs who would be miserable as scientists, and many phenomenal scientists who have Myers Briggs types that are not common in the field.

I’ve also written up an article all about these sports recommendations for our November newsletter which unfortunately has been delayed. But that should be out soon.

[jesse mcclure]

Rebecca, that should be no problem at all. There are undoubtedly going to be skin cells and all sorts of other stuff in *all* the samples. The instructions are really just to distinguish this from other collection kits where the goal is to get skin cells. These kits get the best DNA from saliva itself, not the dead skin cells – so the goal is to soak up saliva.

We’ve used these kits well on small pups:


[jesse mcclure]

Thanks for the question – 10 seconds should be fine. 30 seconds is what the swab manufacturer recommends and doing our best to meet this goal is good, but we’ve tested the swabs with less time in the mouth, less time after eating, etc, and they are surprisingly reliable. So I’m not worried at all about 10 seconds.

But if any sample cannot be used, you will be put back in the list to receive a new kit (eventually). As for social media: by all means, post about us everywhere! Brittney might be able to chime in here on how to best “tag” us or whatever it may be called on all those sites. There’s a reason she coordinates our social media: I have no idea how that all works, but Darwin’s Dogs is on Facebook, Twitter, Instagram, and probably several others I don’t even remember (I manage our github, that’s my flavor of social media).

[jesse mcclure]

Barbara, if you follow the “Enter here” link which is the same one in the current dogs of the month listing. That should take you to your first dogs profile, scrolled down to the checkbox you need to click on, and even have it highlighted in blue text.

[jesse mcclure]

The *species* is fine. Our current breeds are where the question lies.

Most people have heard of village dogs: those free living domesticated dogs around the world. What many of us in developed nations don’t realize is that these village dogs greatly out number our pet dogs … greatly. If breeds can be maintained, wonderful. If they can’t, it will not faze the species: even in the worst case breed-doomsday scenarios, the rise and fall of “breeds” could end up being just tiny blip in the history of the domestic dog that would leave little to no effect on the species as a whole.

I am in no position to speculate on the future of German Shepherd Dogs, or Irish Wolfhounds, or … But *dogs* have a pretty secure future. I hope for the best for the breeds, but the future of domestic dogs doesn’t rely on any particular outcome for any particular breeds.

[jesse mcclure]

In response to the original question, there is a good argument to be made that carefully chosing parents within a breed may be able to do better at avoiding disease risk variants than random “oops” pups as in both cases natural selection has effectively been removed. But the important difference between purebreds and mixed breeds is lack of genetic diversity in most pure breeds.

Note that a large portion of genetic variants that may predispose a dog to disease are recessive: a dog can carry one copy of the variant and not be impacted – or at least not impacted nearly as much as a dog with two copies (one from mom, one from dad). The odds of a mixed breed dog having both parents be carriers of the *same* harmful variant and getting the harmful variant from each parent is exceedingly small. Within a breed, in contrast, there is much less genetic diversity, so if a potentially harmful variant exists, it exists in a lot of the dogs in that breed. So the odds of both parents each being a carier of such a variant is much higher.

Breed clubs can make good choices on which dogs should be used for further breed and which may not be suitable. But even under the best of circumstances, this leads to a diminishing gene pool, so eventually even if only the best possible pairings are being bred, there are simply so few possible pairings to chose from that “the best” may not be as good as we’d want it to be.

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