[jesse mcclure]

Kristen,

We currently have 3,724 dogs enrolled whose owners have indicated that they are registered purebreds. There are about twice that number of our enrolled dogs that have only one breed listed by the owner.

[jesse mcclure]

Becky & Casey,

Perhaps we should be more detailed with that “location” description. It is accurate in that your dogs’ samples have moved from spit in a tube, through purified DNA in a smaller tube, and then through a sequencing machine to be turned into computerized data. However, that data, in it’s initial form isn’t particularly meaningful. The “analysis underway” is a bit of an understatement.

There are several stages that data goes through. One of the earliest stages of the data that comes off the sequencers is a file full of “reads”. These are short chunks of DNA in the range of hundreds of “letters” long. As your dogs’ dna is made up of several *billion* letters, these are really tiny bits of the genome. These individual ‘reads’ are initially in no particular order, we just know that a given list of letters appeared somewhere in your dog’s DNA: so this is basically the worlds worst jigsaw puzzle to put together tens of millions of these ‘reads’ to make a full picture of your dogs DNA (this is called ‘aligning’ to a reference in genomic terms if you want to read further).

From there we do actually have a sequence of letters representing your dog’s DNA, but at each of those there is also a fair bit of uncertainty – or a margin of error. The good news is the sequencing machine tells us how sure it is about each letter. When we take this information from your dog, and put it side-by-side with *many* other dog samples, we can make good inferences about which letters we should really believe and which ones might have been an error (this would be ‘variant calling’ in genomics).

After these steps, we have the first type of data that would be meaningful … to a geneticist. But it would still just look like gibberish to most normal people. But we can turn this data into something more meaningful for you. We can infer who your dog may share ancestry with (this turns out to be what most of our participants are interested in: what breeds is their dog related to). We can also see which coat color genes your dog has (of course you already know what color your dog is!)

Each of these stages take a fair bit of work. Lots of big computers sure help us do it in a more practical time-frame, but we still have to get all the data running through all the right computers. The last stage, of turning the genetic data into something useful for dog owners, may be the most challenging and time consuming.

Our goal, of course, is to see what variants your dog has and pair this with what you tell us about your dog. For example, we might find little differences in the DNA of all the dogs that are most playful, or most social, or most anxious, or those prone to allergies, etc. But *those* answers will only come out once we have looked at the DNA of a *whole lot* of dogs.

[jesse mcclure]

The criteria vary widely as we have some primary funding sources, and continue to supplement these with numerous small projects targetting specific discrete questions. For each target question we seek dogs that may be both high and low for that trait: for example, only getting lots of dogs that may have food allergies would not be that useful for asking questions about the genetics of food allergies, we also include lots of dogs who do not show any signs of allergies as a comparison group. Currently targeted groups include dogs that are high or low in each of anxiety, impulsivity, retrieving and/or toy focus, food-allergy related symptoms, tendency to over-eat or eat quickly, and sociability.

**Contributions:** Yes, there have been some changes in the option for participants to contribute. We are not taking such donations just yet, but previously this was something we were hoping to do and/or brainstorming about. Now we have a consultant working with us setting up the accounts and getting everything in order to have a secure system to accept contributions. I hope to have a blog entry in the near future detailing the progress and timeline for this, but it is no longer just a hoped for plan, but it is an imminent change which will be coming to our webste.

—
*note: I see you had this posted on another thread, it seems better on it’s own here, so I’ll remove your other post*

[jesse mcclure]

Thanks Robert. I editted your post to make that link a little nicer looking. This also just came up on our Twitter feed.

It’s definitely interesting. Personally I’m skeptical about whether there is any signal value to the sneeze. Maybe the dogs just sneeze when they are about to leave for the hunt because they’re excited, or because it clears out their sniffers to get ready.

I think the original authors were appropriately cautious about these possibilities. Of course the popular version hypes the most interesting interpretation to draw us in.

That said, many communicative signals do emerge as the result some other process that originally is just coincidental or functional for some non-communicative purpose. If sneezing consistently predicts the hunt it could take on meaning as a signal.

[jesse mcclure]

Mary-claire, yes that was a new addition to the ‘personalized feedback’ page for each dog. It’s not at all polished or pretty, but I wanted to at least be more transparent. We’ve recently added greater sample tracking to our database – so I’ve modified that page to give a summary of the tracking of your dog’s sample. Dates before several months ago may be fairly vague (anything before 2017 just says “2016”). And at the moment there isn’t much explanation for the different locations.

VHL is one contractor we tried out for extracting the DNA from the swabs. A vast majority of the samples that went through VHL are currently being genotyped, as these come back (over the next couple of weeks) they’ll be added to the sample tracking data that you will see on that page. So while I can’t make any promises, there is a good chance we’ll have Boomer’s data very soon. Two big caveats on that though: 1) not every sample that went through VHL is being genotyped currently, but any that aren’t are still high in the queue to be run next. 2) if Boomer’s is in this incoming batch, we’ll have the *raw* data very soon. While this raw data is what I’m excited to get (as my primary job is to do the analyses of batches of such raw data) such raw data will not mean much to you.

We will turn this raw data into various nice reports for you, but that report preparation will take a good bit longer.

[jesse mcclure]

Hi Greg,

That work came out of Elaine Ostrander’s group. Hers is one of the other big dog-research groups, but at present we each have our own data sets.

We do plan on releasing our (anonymized) database as a public resource for the dog community. Right now we just need to get some more of the infrastructure in place for that to work smoothly, but any research groups that can benefit from more dog data are free to contact us. We’ve also been able to benefit from some of the genetic data for purebreds published by Elaine’s group.

[jesse mcclure]

Randy, you are quite right. Brittney has answered the same question over and over again, right here in this thread. I believe she has demonstrated remarkable patience in doing so. We have over 12 *thousand* dogs enrolled, and we do value each and every one of them – however Brittney will not publicly answer the same question 12 thousand times when the answer is readily available directly above.

Such expectations are disrespectful not only of Brittney, but also of fellow dog owners here. Does the third person to ask the same question think they are deserving of a different answer than the first?

If anything is unclear in an existing answer, feel free to seek clarification. If you’d like to learn more about our process, please check out our newsletters and blog posts which we create to do our best to keep you all informed. Then also look at the About Us page and see the number of people working on this research. That even overesitmates the number. Brittney and I are the only two for whom Darwin’s Dogs is our primary responsibility.

We have invested money, time, effort, and expertise into creating Darwin’s Dogs. We have asked participants only to invest a little time in answering surveys, and a fair bit of patience as we fine tune methods to get reliable data from DNA samples. This is research – we are pioneering new ground finding new ways to get information out of dog DNA that no one has done before. This is not a product that you purchased. If what you have invested in this seems too much, and does not feel equitable to you, then I’d be sorry to lose you as a contributor to this great opportunity.

Feel free to send questions, comments, suggestions, or any other feedback to the info@darwinsdogs.org which Michele answers, or on the forums here which Brittney keeps a close eye on. If you have harsher critiques or complaints those need not be vented on the forums to Brittney or via an email to Michele – but feel free to send them directly to me at jmcclure@darwinsdogs.org.

[jesse mcclure]

In my experience working alongside people of a wide variety of backgrounds in the dog world, there are few questions that get such variation in the claims made. I’ve heard anecdotal accounts from those who swear neutering has one affect or another (many accounts even claiming opposite effects), or that doing so at certain ages has certain affects, as well as others who quite confidently claim there is no affect on behavior. Sadly, the scientific studies that have tried to address this get just as varied of results.

To me, personally, this leads to a great deal of doubt that there is any *consistent* effect. I don’t necessarily doubt that some individuals may have some changes, but I doubt there is any meaningful pattern that can be inferred. And as such I’d suggest that concerns about behavior (one way or the other) should not influence ones choice on whether or not, or when, to spay/neuter.

There is better data, however, on potential impacts on the dog’s long term health. I’ll leave recommendations based on the pet’s health in the hands of the veterinarian, but suggest that the veterinarian’s recommendation on what the best approach for the dogs health should be the deciding factor of when to spay or neuter.

Don’t get me wrong – I’m all for sharing any experiences anyone has here on this thread. I’d just like to suggest that anyone still deciding on when to spay or neuter their dog perhaps should not be swayed by very limited information about how it *might* affect their behavior when there may be more concrete information on how it *will* impact their health.

[jesse mcclure]

Al, you’re right the reference set will be the biggest limitation in any breed analysis we might do as described in our [FAQ](https://darwinsdogs.org/?pg=faq#will-you-tell-me-about-my-dogs-breed-ancestry).

To elaborate, let me start by reiterating that we are not a breed test. That is not our purpose, and it is not our goal. Ancestry information will be a likely by-product of our analyses and we will share any such information that we find on your dog – but we are not offering breed testing as a product.

But if you are looking for a breed test, there are a few metrics you should be interested in to determine how well breeds can be assigned:

### 1. how is the variation in your dog’s DNA captured

Note that virtually no method of analyzing a DNA sample tells us *everything* about that DNA. There is always a trade-off between how much data we can get and the cost and complexity of the analysis. Whole genome sequencing at a depth of 30x can get pretty close to getting all the information in a DNA sample. But whole genome sequencing is orders of magnitude more expensive than most other approaches. No currently available breed test is doing whole genome sequencing.

All comercially available breed tests that I am aware of use genotyping. This is a much cheaper, easier, and much more efficient analysis that samples a number of positions within the DNA that are known to vary among dogs. To put this in context, there are about 18 million positions in the dog genome that are known to be different between dogs. Until recently, genotyping tools for dogs only checked ~170 thousand of those positions. That’s *less than 1%* of the actual variation. To be fair, if those 170 thousand spots are well chosen, good inferences can be made about many more because of linkage as I recently described in the [IAABC journal](http://iaabcjournal.org/2016/10/01/spell-behavior-darwins-dogs-use-gs-cs-ts/). But even under the best of conditions, those genotyping tools are only getting a portion of the variation. Very recently a new genotyping tool for dogs was made available that samples ~650 thousand different positions. This is better than the 170 thousand tool, but still has limitations *especially* for mixed breed dogs.

Here at Darwin’s Dogs we are not sure that new genotyping tool will be good enough for our study of behavioral variation. So we are experimenting with a new approach called low coverage sequencing. This works a lot like the whole genome sequencing mentioned at the start, but rather than getting high confidence measures of nearly every bit of the DNA we get just *some* measure of almost every bit of the DNA, and by comparing across a large number of dogs we can make good inferences about which measures are reliable and which may be false positives or misses.

So here’s a summary of relevant analysis techniques. Full sequencing gets high quality measures of nearly every spot in the DNA but it is prohibitively expensive – no breed test uses this technique. Genotyping gets high quality measures of a small subset of the DNA – this is what most breed tests use. Low coverage sequencing gets moderate quality measures of nearly every spot in the DNA.

### 2. How extensive is the reference data set

This is the question you are asking. To do proper breed assignment, one does need an extensive database of dogs from as many breeds as possible. Here at Darwin’s Dogs we do have access to some published and publicly availble genomes of purebred dogs, but it’s really not enough. But we also have something else: we have 12000 dogs currently a fair portion of which are registered purebreds. I just did a quick count of how many distinct registered purebred dogs we have and it looks to be about 400 breeds.

### 3. What algorithm is used to assign breed ancestry to various parts of your dogs DNA

This may be the most “mysterious” part of the process for two reasons. First, most comercially available breed-tests consider this to be a proprietary secret recipe. They will not likely share their method. In contrast, we will absolutely share all the details to any ancestry mapping we do once it is up and running. But the second reason this is a bit “mysterious” is the algoritms used are far from easy reading. Anyone with an advanced math degree would likely find it digestable, but for most of us it’s pretty tricky. Most approaches to breed assignment work much like ancestry reconstruction in humans. A google scholar search for these topics will give lots of examples.

—

So, overall, how will our ancestry reconstruction compare to breed tests? First and most importantly, this is not our goal and we don’t promise any results – so if you really want a breed test, we don’t compare: send your dog’s sample into one of the comercial services. But for the depth of information we get out of your dog’s DNA, we will be getting much more. For the number of reference purebreds used, comercial tests that have been in business for a while probably have quite a bit more than we do – but we are growing quickly. For the algoritm used for the analysis … I can’t compare as I don’t know what the breed-tests use.

[jesse mcclure]

Those are wonderful questions Linda. I hope to be able to have a thorough response soon but for now a few previews: we are casting a wide net of gathering genetic variation relevant to a wide range of behaviors including fear and anxiety. We do hope that any contributions we can make to basic science will aid in applied fields in both veterinary and human medicine.

But the direct motivation of adding the newest survey was to aid in another project we have headed up by the newest member of or research team [Kathryn Lord](https://darwinsdogs.org/?pg=about). This is also a great excuse to drag her on to the forums to say a few words. Unfortunately while we’ve been plowing through the snow in Massachusetts, she just headed out to Hawaii! When she get’s back I’ll see if she wants to chime in here about her work with wolves and wolf hybrids. In a very small nutshell, she has been exploring the differences in behavioral development in wolves and dogs and she has joined our group to study potential genetic / epigenetic regulation of early developmental periods in dogs and wolves. As part of her work, she wanted a bit more detail on the range of social behavior we see in pet dogs so she assembled these additional survey questions on socialization with humans.

[jesse mcclure]

Randy,

Sorry for the slow responses during the Holidays. I did see this thread, but it seemed like you had done the right thing so all seemed well. You are right that the question does seem to be missing a valuable option for light brown or tan. Selecting black and white, and optionally the chocolate brown color with a comment that there is tan and/or tricolor ensures all the information is there.

We can revise questions, but that would make the data inconsistent as many people will have answered the old version of the question, and new members will get the revised version. That makes analysis virtually impossible. Instead what we are doing is keeping track of questions that do not work well (there are quite a few!) and we will include a revised version of these questions – as needed – in future surveys. Another good example is “Dog sits frog style.” A lot of people have been very confused by that question having no idea what it was referring to – so the answers to that question will not be particularly meaningful. We do have an upcoming survey on “Resting Styles” that includes frog-style and many other lounging positions with good example photos and descriptions.

We really take a bit of the pasta chef approach to the surveys: we throw it all against the wall and see what sticks. We certainly don’t want to waste anyone’s time with questions that are obviously no good, but often we don’t know which questions will be useful until we get lots of responses and comments.

[jesse mcclure]

Brittney is correct. But if you are able, please feel free to pass on our information to anyone who adopts the dogs. We’d love to have those dogs enrolled once they are with their family.

[jesse mcclure]

I had to look up Hamiltonsovare too. Good looking dogs.

Our ancestry mapping does depend on good reference data for each breed – but as we have many purebred dogs signed up to this project we’ll be able to use them as a reference panel. Some or preliminary tests are looking promising suggesting that a reference panel of a dozen or so representatives of each breed may suffice. Of course, these should ideally be as unrelated as possible. A dozen purebreds from the same parents, or even the same breeder, may be problematic.

Out of curiosity, I just checked our data, Asley, yours are the only Hamiltonsovares (I also checked for anything starting with “Hamilton” as wikipedia suggests they have other names including Hamilton Hound).

Of course a vast majority of genetic variants that one might be concerned about for health reasons would be shared among many breeds. So if there are genetic variants associated with any medical issues we may be able to find them just as well in these dogs as any others (notwithstanding any breed-unique issues). If you have a veterinarian or kenel club that can work with that genetic data it will be all yours if/when your dog’s DNA is analyzed. We will also be working on giving nice summaries or reports for the genetic data, but this will not include giving any medical advice or diagnostics.

[jesse mcclure]

That’s one of the remaining big limitations of our photo uploads – or at least that is the generous way of phrasing it. Really this is a problem with certain mobile devices. So far I’ve only seen this problem with photos coming from a certain popular brand of electronics.

The digital information in a photo is saved in a specific orientation which corresponds to the physical camera hardware. But many mobile devices can be held in many orientations, and thanks to their accelerometer (or similar hardware) they can store some meta-data with the image essentially noting that “the camera was upside down when this was taken”. In reality the meta data is just an orientation or rotation, but that’s what it’s meant to convey.

That way when you view that image in an image program on your computer, the image program can see that note and rotate the image before it displays it. This is all done with a (nearly) universally aggreed upon meta data called [EXIF](https://en.wikipedia.org/wiki/Exchangeable_image_file_format). Our image handling now properly orients any image that has embeded EXIF metadata saying how it should be displayed.

Unfortunately one manufacturer has decided that they don’t want to play nicely with the rest of the digital world, so they don’t use the same notation for image orientation that the rest of the world does. If you take a photo with one of their devices, it may only display properly oriented on other devices from that same manufacturer. Sometimes image viewers not from that manufacturer do jump through extra hoops to placate the eccentricities of this one tech company – but that is not always trivial to do.

So in short, images uploaded to our site will be properly oriented if they follow the (essentially) universal standard notation of keeping track of image orientation. If they do it differently, though, you will need to rotate them before uploading. Or, on a case-by-case basis, I am able to rotate them for you if you let me know it’s needed.

**EDIT:** Dan, I’ve rotated your two dogs’ images, so they should be set for now.

[jesse mcclure]

As long as the swab was put back in the blue liquid (a stabilizing solution) and closed up it will be perfectly fine. These samples are perfectly shelf-stable at a range on normal room temperatures for a long time.

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