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  • in reply to: About the new "Shapes and Colors" survey #14781
    Jennifer
    Jennifer
    Participant

    Thanks Kathleen. I guess I may change my answer re 3) then, because Luna definitely has sable tipping showing in her body patches, I just wasn’t sure whether that “counted” or not.

    Re 9) it’s definitely not common, but I’ve volunteered with our local public shelter for a couple decades, where we get tons of pit mixes, and I’ve seen it maybe a few times in bluenose pits (not puppies). Usually they turn that yellowish-greenish-amberish color but apparently not quite 100% of the time.

    in reply to: What info do I get from my dog's sequence? #14727
    Jennifer
    Jennifer
    Participant

    It seems like most of the genetic tests commercially available nowadays, whether from UC Davis or Embark or whatever, will at least give you a rundown of your dog’s genotype for several of the genes presently known to be associated with certain physical traits–coat pattern and texture, overall body size (numerous genes involved in that) etc., in addition to level of inbreeding. And Darwin’s Ark is looking at much more of the genome than any of those tests, so I’d imagine(?) all of that info and more would be available. How “useful” that info is would depend on your interests–like, I’d be curious to know if my dog might be merle (she has very little black coat pigment, so I can’t reliably tell by looking) because if she were it might explain some odd quirks about her coat patterning and eye color, but I don’t know that that’d really be “useful” info so much as personally interesting to me. But what’s really exciting to me about this study is not so much anything I’d learn about Luna specifically–I already know her behavioral quirks, and as far as it goes no DNA test is going to help me manage those–but rather the opportunity to contribute in some small way to furthering scientists’ understanding of the genetic bases of dog behavior, which in the long run could be very helpful for breeders too.

    in reply to: Different results? #8153
    Jennifer
    Jennifer
    Participant

    Do Bee’s Embark “Family Tree” results correspond fully to her “Summary” bar graph? I.e., does the tree show 4 great-grandparents labeled “Golden Retriever” and 4 labeled “Bloodhound?” Or is one or more of them possibly labeled “Golden Retriever mix” or “Bloodhound mix?” Because sometimes Embark tweaks those Summary bar graph numbers a bit to make them add up to 100, even when the family tree suggests otherwise. This happened with my dog, actually–the Embark breed %s I’m quoting for her are taken from her Summary, but her Summary actually just says “9.1% Shetland Sheepdog,” whereas on her family tree, one great-grandparent is labeled “Shetland Sheepdog mix,” which confused me because all the other breeds they’d called were already represented on her tree as purebred GGs, and the Summary numbers added up to 100, implying that all DNA had been accounted for. I emailed them and they said her family tree was more accurate in that respect, that in fact they were seeing some too-mixed-to-call DNA in association with her Sheltie DNA.

    If that’s not the case for Bee though, then I got nuthin’.

    in reply to: Different results? #7636
    Jennifer
    Jennifer
    Participant

    My mutt has been tested with WP, Embark, and DA.

    WP:

    ~ 50% Australian Cattle Dog
    ~ 25% Boxer
    ~ 12.5% Australian Shepherd (asterisked, indicating uncertainty as to whether the predicted % is really accurate)
    ~ 12.5% too mixed to call/unknown, with Sighthound and Herding groups listed as possibilities

    Embark:

    34.9% ACD
    25.1% Boxer
    15.8% Australian Shepherd
    15.1% Border Collie
    9.1% too mixed to call/unknown, with Sheltie specifically predicted to be in the mix

    DA:

    35.6% ACD
    26.7% unknown
    21.2% Boxer
    6.2% Border Collie
    3.8% Collie
    3.6% Sheltie
    2.9% Australian Shepherd

    In my dog’s case, I’m guessing(?) the main reason for the differences may be that she really is roughly 75% assorted herders (as WP and Embark found), but that without both a very large number of markers and a very robust reference panel, it becomes difficult to accurately assign all her non-Boxer DNA to one-or-another herding breed, since all the herding breeds detected in her to date are thought to be members of the extended collie/UK sheepdog family (Parker et al. 2017), and therefore pretty closely related. So I’ll be interested to see how much of her current 26.7% unknown winds up getting reassigned to already-called herding breeds. Would be just as ready to believe there’s a splash of something that hasn’t been called yet knocking around in there, though! The ACD and Boxer have been pretty obvious in her from the beginning (nip nip nip, boing boing boing) so I’m not surprised those two findings have held fairly constant across all three tests.

    in reply to: American pit bull #7411
    Jennifer
    Jennifer
    Participant

    I think you might be somewhat confusing the American Bully with the APBT? The APBT, AmStaff, Staffy Bull, Bull Terrier, and Mini Bull Terrier all originate from the same early-19th-century crosses in the UK (old English Bulldog x assorted terriers, likely with a pinch of Whippet as well). Over time, different strains of that basic “Bull-and-Terrier” type developed. The BT and MBT were the first to split off from the rest, in the mid-19th century (this is all still happening in the UK). Then the Staffy Bull and APBT diverged in the late 19th century, due to the lines which became the APBT having been taken to the US by immigrants. The AmStaff was developed later (in the US, early 20th century) out of various APBT strains, and is registered through the AKC whereas APBTs are registered through the UKC. (While AmStaffs and APBTs remain very closely related, AmStaffs tend to be somewhat taller, stockier, mellower, and less athletic–sort of like a show-line version of the APBT, whereas the APBT remains well-suited for sports, farm work such as hog-catching, and, unfortunately, underground dog-fighting as well.) Finally, the American Bully was developed in the late 20th century by crossing AmStaffs, APBTs, and assorted smaller bully-ish breeds–it’s not really clear which smaller breeds were used, but Frenchies and Staffy Bulls were almost certainly among them. (In fact, this is thought to be how Bostons originated as well, excpet they’ve been around since the late 19th century.) The AmBull was the last of these breeds to be recognized by a major kennel club (UKC, 2013).

    However, the vast majority of “pit bulls,” including many who are marketed as supposed purebreds of one of the above breeds, are non-pedigreed dogs who very often have several of the above breeds, as well as pinches of various other breeds, in them (e.g., mastiff types for a bigger and tougher-looking “pit bull,” Bostons for a smaller and cuter-looking one, etc.). While there’s no way for a DNA test to tell which crosses in a mutt’s background were deliberate vs. which ones were “oopsies,” Lola’s results to date could fit well with her having either American Bully, or else some generic “pit bull” meant to mimic an American Bully, in the near reaches of her family tree. As for the Mini Schnauzer x probable(?)-multi-bully-mix at the parent level, that would almost certainly have been an “oops”–I doubt anyone is breeding that mix deliberately, as there wouldn’t seem to be much of a market for it.

    in reply to: Genetic Diversity vs Gene Quality #7394
    Jennifer
    Jennifer
    Participant

    My mutt’s reported genetic diversity is 22%; is that unremarkable for a multimix with completely unrelated parents? Embark reported her CoI as 0%, fwiw. She does have some rather closely related herding breeds between the two sides of her family, so I could see there being some increased overlap because of that.

    in reply to: Low Percentage Traits in DNA #7392
    Jennifer
    Jennifer
    Participant

    One thing I’ve noticed, in browsing a subreddit where people share their dogs’ DNA breed test results, is that people can sometimes be quite resistant to accepting a finding that their mutt contains only a very small percentage of “Breed X,” when said mutt happens to have inherited some particularly dramatically visible trait associated with “Breed X.” For example, a dog who has a merle coat pattern, or whose coat texture is wiry-scruffy with facial bearding. Both those traits are dominant or co-dominant and caused by just one gene, so even a tiny amount of ancestry from a merle or wiry-coated breed could be sufficient to cause them if the portion of DNA inherited from that ancestor happened to include that gene. But they’re also both very “loud” traits visually, and that loudness can trick us into assuming that there must be “a lot” of some merle or wiry-coated breed in there. And once you’ve gotten that idea into your head, it can be easy to then proceed to convince yourself that your mutt “clearly” also shows other, more vaguely defined and/or multi-gene traits associated with that breed, like “high energy” or “feisty” or “fast” or “leggy”–these are all pretty relative terms, and someone with years of experience in a breed commonly described as having them may understand them quite differently than the average person.

    Also, even within most pure breeds, there’s sufficient diversity present in the collective gene pool to yield individuals who may be quite far off the norm or ideal for that breed (as epitomized by show or field champions) in both looks and behavior. Sometimes this gets read simply as that individual being a “faulty” example of the breed, other times it may lead to accusations or suspicions that the individual isn’t really purebred. There can be characteristic variations within lines, too; for example, German Shepherds bred for police work are as a group likely to display a somewhat different balance of behavioral and perhaps physical traits than those bred for seeing eye dog work, which in turn will look and act somewhat different than GSDs bred for show ring success. Backyard-bred and puppy mill dogs of a given breed, who generally haven’t been bred according to any selection criteria at all–just “whatever two dogs of this breed I happened to already own”–are especially likely to display variation from the breed standard, because standards are meant to define an ideal that breeders must keep continuously and rigorously selecting for; they aren’t meant to summarize all possible individuals that could result from the genetic diversity naturally present in the breed.

    in reply to: Is there a link to see an example #7302
    Jennifer
    Jennifer
    Participant

    For the morphological predictions, since that’s not a focus of the study per se, would that basically take the form of noting which alleles the dog is carrying at genes already known to affect physical phenotype? (e.g. curly hair, brachycephaly, merle) Or do you also have ambitions to identify previously unknown causative mutations, or to share data with researchers who are studying physical phenotype? For example, I have a purely armchair interest in color and coat pattern genetics, and I know that even in that one small and admittedly-not-too-important-in-the-big-picture area, there are still so many unanswered questions despite the relative simplicity of identifying good candidates for study, probably largely due to a shortage of funding for research into the topic.

    in reply to: Different testing than Wisdom Panel? #7291
    Jennifer
    Jennifer
    Participant

    The breed testing process, including number of markers used, was discussed in the FAQs for the MuttMix project, a collaboration between Darwin’s Ark and IAABC:

    http://iaabcprojects.org/faq/

    “Our reference panel of dog breeds has information for about 200,000 markers in each dog, so these are the markers we currently use in our breeds test. Our technology, however, tests at least 1 million markers in each dog. For some dogs, we have information on all 2.4 billion nucleotides in their DNA. Over time, our breed calling algorithm will perform better and better as we change over to a reference panel that includes just as much information for each dog.”

    For comparison, here’s Wisdom Panel’s summary of their process:

    https://help.wisdompanel.com/s/article/How-does-Wisdom-Panel-work

    “Once your sample is received at our lab it is scanned into our system and assigned to a batch for testing. It then undergoes processing to extract the DNA from your dog’s cells, which is examined for the 1800+ markers that are used in the tests. The results of these markers are sent to a computer that evaluates them using a proprietary algorithm designed to consider all of the pedigree trees that are possible in the last three generations of your dog’s ancestry. Our computer algorithm uses samples from our extensive breed database to analyze these potential pedigrees and calculate which one is the best match.”

    …and Embark’s summary of their process:

    [link deleted, because it created a huge obnoxious Embark logo…lol…but, this is from the FAQs on their website]

    “At the lab we extract your pup’s DNA and run it on our custom-built genetics chip, which is a proprietary DNA microarray with over 200,000 markers…Ultimately, we use several proprietary algorithms to build the story of your dog and his or her DNA one chromosomal segment at a time. If numbers are your thing, we test about 256 quadrillion (that’s 500 million times 500 million) different possible genetic ancestry combinations for your dog using the latest and greatest science.”

    So, Darwin’s Ark’s breed testing process is different from both WP’s and Embark’s in that they’re using low-coverage sequencing, which does test many more markers, but their reference panel of purebred DNA is still in the process of being built up, simultaneous with the DNA testing of dogs they’re already doing. (Initially, their reference panel contained only whatever breed-specific DNA information was publically available, as alluded to above.) So, owners of dogs who’ve already received their initial breed test results will most likely see those results update over time, with an increasingly lower % of “Unknown” ancestry as the reference panel becomes more robust.

    All three tests use algorithms to analyze each dog’s results for their chosen markers against the purebred dogs in their reference panel. Wisdom Panel’s and Embark’s algorithms also produce three-generation predicted “family trees” for each dog, whereas Darwin’s Ark reports their breed calls as a simple bar chart ordering the detected breeds from lowest to highest percentage of ancestry.

    But probably the biggest difference is that Wisdom Panel and Embark are for-profit companies focused specifically on breed analysis (Embark does also publish some research based on their findings), whereas Darwin’s Ark is a “citizen science” study focused on the genetic bases of dog behavior, with breed analysis effectively being a side benefit of your dog’s being selected for one-or-another phase of the ongoing study. And participating is free (unless you choose to donate, as explained in the FAQs, under “About” at the top of this page).

    in reply to: "Carolina dogs" in reference panel? #7274
    Jennifer
    Jennifer
    Participant

    How do researchers handle this when sampling village/pariah dogs? For example, if you’re collecting DNA from, say, Indian Pariah Dogs, how do you “ensure” you’re only sampling “pure” ones, and not mixes of IPD with recently arrived strays of foreign ancestry, or even just plain ol’ mutts?

    I gather from articles I’ve read that Brisbin at least sometimes approves dogs for the CD studbook based solely on looking at photos and completed questionnaires from owners who mailed in that information, and at some other times, based solely on meeting and observing a dog someone adopted from a shelter somewhere. Maybe not the most scientific way to do it, especially in a time when, as Stephanie mentioned, there’s an increasing amount of romanticized public interest in these dogs. (For awhile there, there was an eyebrow-raisingly improbable number of “Carolina Dogs” and “Carolina Dog mixes” being posted to Petfinder–basically, “Well, it’s tawny, prick-eared and shorthaired, so let’s call it a CD”–but I notice they’ve recently quietly dropped CDs from their breeds list altogether, which makes me wonder if someone of influence complained.) But what else is Brisbin supposed to do? He knows better than anyone else what the real thing can look like, they need genetic diversity to build a breed, and wild-caught CDs are hard to come by and could even themselves turn out to be mutts anyway.

    in reply to: "Carolina dogs" in reference panel? #7271
    Jennifer
    Jennifer
    Participant

    It may be that there already are some Darwin’s Ark participants with registered CDs, I don’t know–this is, after all, a citizen science project designed to draw upon dog owners’ personal knowledge of their own dogs’ everyday behaviors. Currently, the UKC is the only registry for Carolina Dogs, and Brisbin himself is the keeper of the UKC Carolina Dog studbook, so to own a registered CD is by definition to own a dog Brisbin approved for addition to the studbook (or whose immediate ancestors had all already been thus approved and registered). I mention registration because I gather from previous statements by members of the Darwin’s Ark team that proof of registration is a prerequisite for their using a participant’s dog’s DNA as a breed reference sample. Which would make sense, since that’s how it’s usually done by any researchers or testing companies whose work requires verifying the purebred status of dogs who are specifically being studied as examples of that breed, or whose DNA will be used as a reference in breed mix analysis of other dogs.

    in reply to: "Carolina dogs" in reference panel? #7219
    Jennifer
    Jennifer
    Participant

    Have you seen the studies from Shannon et al (2015) and Ni Leathlobhair et al (2018)? Those are the two most recent genetic studies to include Carolina Dogs, and both concluded that all CDs tested were of predominantly European ancestry, with a range of 0-35% pre-Columbian/Asian ancestry at the level of individuals. Which is still a high average of pre-Columbian/Asian ancestry for an American dog type from outside the Arctic/Alaska region, but nonetheless paints a pretty different picture from what Brisbin had originally speculated, back in the days before this kind of testing was possible. AFAIK, the only other studies relevant to the CD are a couple earlier, more tentative ones that had looked only at mitochondrial DNA.

    Shannon et al: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4640804/
    Ni Leathlobhair et al: https://www.researchgate.net/publication/326211519_The_evolutionary_history_of_dogs_in_the_Americas

    I know Embark tests for Carolina Dog, FTR. They are fairly generic-looking dogs even when pure, in the sense that any number of mixes with a good dose of spitz and/or herding type in them could wind up looking quite a lot like one.

    in reply to: looks #7184
    Jennifer
    Jennifer
    Participant

    I guess(?) in principle you could, if your image hosting service wouldn’t consider that hotlinking and you’re using the correct HTML tags and attributes. A simpler way would be to just cut and paste the “Direct Link” for your picture(s) or album, which on most image hosting services will be in the form “https://NameOfImageHostingService/IndividualPhotoOrAlbumCode” or something like that. That would just appear as ordinary text on this forum, but any reader could then cut and paste it into their browser’s address bar to view the picture(s).

    in reply to: looks #7177
    Jennifer
    Jennifer
    Participant

    Which test? What was the exact breakdown of the results? And do you have a link to any photos of the dog? It’s hard to know what to picture when someone says a dog “looks just like a pit bull.”

    in reply to: results seem to be spot on #7168
    Jennifer
    Jennifer
    Participant

    Boxer mixes are often very fast, if they inherit the breed’s sprinter’s legs and fast-twitch : slow-twitch muscle ratio without its impeding top-heaviness. Like Corsos and Danes, Boxers descend from coursing mastiffs used to hunt wild boar, which required both lots of speed and lots of brute strength (boars fight back), so their build had to strike a balance between two opposing needs. A mix, though, could potentially wind up inheriting the speed traits but not so much the strength ones. Of course, her speed could also come from something else in her ancestry–it’s just a thought.

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