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    Jennifer
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    Hi Lindsay — I think(?) you meant to reply to me. My question was why they didn’t break down longevity for blacks and yellows separately, as opposed to averaging them together under “non-chocolate.” Especially since the implication is that chocolate being a recessive may have something to do with the longevity difference, when in fact yellow is a recessive too.

    It may be that there’s simply no statistically significant difference in longevity between blacks and yellows–that would perhaps fit with what I was speculating might be a breed history in which chocolates (but not yellows) were once quite uncommon, and only recently experienced a dramatic increase in numbers due to color-driven show/pet market breeding. I don’t know enough abut Lab breeding to know how common it is for breeders to concertedly select for yellow vs. freely breeding yellows and blacks together based on other criteria (working ability, conformation etc.) and just letting the chips fall where they may in terms of color.

    Still, as far as I can see, the study doesn’t actually say one way or another whether there was, in fact, any statistically significant longevity difference between blacks and yellows.

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    Jennifer
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    One thing that puzzled me about this study…yellow is recessive too, and at least in the population studied, not that much more common than chocolate (27.8% yellow vs. 23.8% chocolate), so it’s not particularly obvious to me why they only report two median longevity figures–one for chocolates and one for “non-chocolates”–rather than breaking down blacks and yellows separately? They do suggest that “[t]he significantly shorter lifespan of chocolate dogs compared with non-chocolate dogs may reflect differences in lifetime burden of disease, notably disorders of the integument…that may create differences in accumulated immune response,” for which they cite as evidence that chocolates had the highest rates of one specific ear disease and one specific skin disease. Okay, but…why can’t you tell me first what the longevity difference between blacks and yellows is? lol. Maybe I’m missing something here?

    Anyway, while I know little about Labs personally, I do know a few people who are active in various sports with field-bred Labs (blacks and yellows), and am told by them that you “never” see chocolates among the high-ranking field or sport dogs, and only rarely in service work. I find it hard to believe that serious field, sport and service breeders (as opposed to show breeders) would avoid chocolates simply because they don’t want that “Dudley look,” IF there were lots of chocolates with great working potential available for them to use in their breeding programs. (Although maybe I’m being naive there!) So…I’m also wondering if perhaps chocolate (but not yellow) was originally a highly uncommon color in the breed, and only later became (relatively) popularized, through the show ring? or, perhaps was subject from a very early stage in the breed’s development to some (now-forgotten?) prejudice a bit more insidious than fear of the Dudley look??

    in reply to: Should I update information? #6117
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    Jennifer
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    A couple more questions about updating. My dog was 1.5 y.o. when I filled out the surveys (she’s 3 y.o. now). She already showed some noise sensitivities at the time, but that problem definitely seems to have worsened as she’s gotten older. I could’ve sworn there was a question or two pertaining to noise sensitivity in the surveys but, looking over the 12 surveys I’m able to see and access in the sidebar after clicking “Surveys,” I’m not seeing anything like that. Am I remembering incorrectly, or was there in fact a question or two about noise sensitivity in there somewhere? And also, weren’t there more than 12 surveys?

    in reply to: Black Mouth Cur “purebred” or no #6171
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    Jennifer
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    Not that it matters with regard to Darwin’s Dogs, but FWIW, Black Mouths are recognized by the UKC, and I know that Embark, at least, does test for at least some of the UKC-only Cur types, such as the Mountain Cur and the Catahoula–I’ve seen both those breeds repeatedly turn up in individual dogs’ Embark breed ancestry results. Not sure whether Embark presently has enough Black Mouth DNA on file to reliably test for Black Mouth ancestry, but if nothing else, the fact that they’ve successfully tested for other Curs demonstrates that just because a breed isn’t AKC-recognized doesn’t mean it doesn’t still constitute a genetically distinct population. Even if it’s the case that working Black Mouth breeders might be a bit loosey-goosey in the sense that maybe sometimes they’ll use a great working dog in their breeding program even if they know that individual isn’t pure Black Mouth, occasional occurrences of that type probably wouldn’t significantly affect the genetic distinctiveness of the breed. Just as an example, all the commercial dog DNA ancestry tests are able to recognize working (ABCA-registered only) Border Collies as Border Collies, even though it’s well known that the ABCA sometimes “ROMs” (registers on merit) dogs whom they know fully well aren’t purebred BC by ancestry, so long as those dogs have proven themselves as great sheepdogs who work in the BC style. So something like that might well be true of Black Mouths, too. “Cur” in contemporary American English actually more often refers to that specific group of Southern-origin, multipurpose farm dogs who are especially known for their treeing skills, rather than to its older meaning of “any old mixed-breed dog.”

    OTOH, shelter-adopted dogs who were labeled at shelter as “Black Mouths” based on nothing more than happening to have several physical features of that breed are another story, and no reputable commercial ancestry test would use such dogs in their reference sample pool. I know a dog that was sold at shelter as a “Black Mouth Cur” but tested as a GSD/Boxer mix, which I don’t doubt, since while the dog does look a fair amount like a Black Mouth in pics (as you might expect from a GSD/Boxer mix), in real life it’s improbably huge compared to one (over 70 lbs.), bounces clownishly around like a Boxer, and shows no hunting instincts whatsoever. That kind of thing happens a lot–shelters labeling a mutt as some improbably rare breed because it helps them sell faster “and besides, it just *looks* like one…”

    in reply to: Mutt Project #6143
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    Jennifer
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    That’s a lot of questions! ** 🙂 ** I don’t know whether you saw the MuttMix project’s [FAQs](https://iaabcprojects.org/faq/) page–it actually does have answers to several of them, such as how were the reference panel breeds chosen and where did that data come from, how do the genotyping and low-coverage sequencing work, how accurate is the breed-calling algorithm and how was that determined, what happens if one of the breeds in a dog isn’t included in the reference panel, etc. Not as much detail as you’re looking for in some cases, but there are answers there.

    I know your post wasn’t in response to me, but I’m maybe a little puzzled as to what your intended line of questioning is? Those are good questions about the diversity of the reference panel, but at some points it almost comes across as if you’re making a kind of all-or-nothing argument, where either the reference panel must include all possible genetic signature variants across all regional strains and all recognized subtypes of every known breed, or else the results will be gibberish. But there’s an awful lot of middle ground between those things. If a test dog happens to be, say, 50/50 McNab/Dutch Shepherd (highly unlikely since both are rare, but just as an example), and neither breed were in the reference panel, then the results won’t be right-on-the-money accurate, but that doesn’t mean they could come out as any old random hodgepodge. The dog might for example get called as BC/GSD (very close relatives with extensive haplotype sharing), or as those two + some % “No Call,” or as those two + some % [other closely related breeds] + some % “No Call,” or simply as “No Call,” depending not only on the diversity of the reference panel, but also on the algorithm’s probabilistic modeling and the quantity and ancestry-informative value of the markers queried for the genotyping/sequencing. But the dog certainly wouldn’t get called as equal parts Poodle, Dal and Pug (no matter which currently available breed test you’re talking about); no way is there going to be sufficient matching for calls like that. If instead it were a megamutt, and Poodle, Dal and Pug were just calls on single-digit-percentages’ worth of its DNA, then in that case way-off-base false positives become significantly more possible, since with distant purebred ancestors like that you’re reduced to making inferences from tiny portions of DNA.

    With Embark and Wisdom Panel results, off the top of my head, I’ve seen ABCA Border Collies test as purebred Border Collies, NSDR-registered ACDs test as purebred ACDs (no NSDR dogs were in the reference panels), UKC-registered APBTs test as AmStaffs (both tests have since added APBT to their reference panels), and an FCI-registered Saluki from Bahrain test as high-content Saluki with some “mixed”/indeterminate. (Embark also has the nice feature of including village/pariah dogs from several international locations in their reference panel, which in some cases has enabled them to ID imported street dogs from Asia and Europe that had came back 100% “mixed”/indeterminate with Wisdom Panel.) These are all just anecdotes, but the point is, while there’s no one-size-fits-all answer to “What would happen if…,” neither does any testing service’s algorithm default to eeny-meeny-miny-moe when slam-dunk matches are lacking.

    Regarding using BYB dogs in a reference panel, I’d imagine that would be highly inadvisable in most breeds’ cases, due to increased risk that some of your samples won’t really be purebred.

    Having been a shelter volunteer for 23 years, my own experience is that shelter mix guesses are more often than not based on the crudest, most seat-of-the-pants visual assessments–and we don’t, of course, make any attempt whatsoever to seriously consider the possibility that Happy might have 4+ breeds in him when formulating guesses; there’s no way the human brain can simultaneously evaluate the likelihood of that many theoretically possible combinations for producing a dog with the cumulative assortment of separately inherited physical and behavioral traits that you see in front of you. In reality, even just a basic knowledge of coat genetics alone will immediately make evident how many of the breed mixes you’ll see ascribed on e.g. Petfinder are at best incomplete, if even partially correct. (To turn your line of questioning around: Does the average shelter worker know what other patterns and colors BCs come in besides dominant black with Irish spotting–or even that those two are separately inherited traits, which are in turn masking other heritable colors? Does s/he know the difference between a field-bred Lab and a bench-bred Lab in conformation? Does s/he realize that 1st gen Lab mixes are almost always black regardless of the Lab parent’s color, that 1st-gen Poodle mixes usually have wire coats that can make them dead ringers for terrier mixes, that the unique Dalmatian spotting pattern is recessive so a 1st gen Dal mix can’t express it, that a 1st gen Pug mix can’t be black-and-tan? No to every one of those, at least in every shelter I’ve ever volunteered at–and if s/he doesn’t know those things, what are the odds that s/he has any meaningful idea at all what other potential mixes of “Top 50” breeds might produce a dog that looks like Happy?) I’d love to think that years of working with assorted shelter mutts and purebreds has made me an expert at ID’ing mixes by looks alone, but in reality it’s only driven home for me how hopeless that endeavor is, unless *maybe* we’re talking picking up on something with a really extreme phenotype being in the mix (sighthound, Chow, Pug, to some degree pit types)–and even then, at best that only tells me one breed or type.in there. And mutts can only beget mutts, so yes, it’s entirely plausible that the statistically typical US shelter mutt would be a multimix, even when it does happen to have one purebred parent.

    IMO, one really cool thing about this study is the wealth of new ancestry-informative data the purebreds in it will contribute to future reference panels, due to the low-coverage sequencing.

    in reply to: Mutt Project #6140
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    Jennifer
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    I loved seeing some of the results you’ve shared so far on Twitter. Is the formatting on those a “sneak peek” of sorts at what the results eventually to be shared with those whose dogs were genotyped might look like?

    I regularly browse a subreddit where people post the results of their dogs’ breed ancestry DNA tests, so I wasn’t too surprised to see how complex some of the mixes shared so far seem to be, nor how little some of those dogs resemble much of anything detected in them. It’s unfortunate how marketing pressures tend to result in shelters feeling a need to ascribe a simple “A x B”-type mix guess to mutts put up for adoption–as in, “We think handsome Happy is a Lab/Border Collie mix!” Among other issues, that can tend to create a false expectation in people’s minds that if Happy looks kinda sorta like a Lab, well then he must be largely Lab, when in reality he might have no Lab in him at all. That in turn could lead to some pretty off-base expectations about what kind of energy level, interests, and social behavior your newly adopted mutt will turn out to have, especially if it hasn’t spent a good amount of time with a foster who’s had opportunities to observe some of those qualities in a variety of situations.

    Just out of curiosity, are you able to say at this point whether reported results might include any info about the dog’s genotype for various physical traits whose genetic bases are known? For example, whether a dog is merle, or whether it’s a dominant (Agouti locus) red vs. a recessive (Extension locus) red, etc.? I realize such findings are unlikely to be of much interest from your end, given the study’s emphases, but was just curious as to what range of “translated into plain English” genotype info you were thinking of providing.

    in reply to: How comprehensive is your canine DNA database? #5815
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    Jennifer
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    Is she an AKC-registered Shih Tzu with a pedigree? I would imagine (but don’t actually know) that Wisdom Panel probably only uses pedigreed AKC- (and possibly some UKC-) registered purebreds for their reference database, and might well employ additional quality controls beyond that, such as always working closely with breed club officials to procure reference samples. If they *were* including (supposed) purebreds sourced from puppy mills and BYBs in their sampling, I’d think that would be a bad idea–it’d dramatically increase the likelihood of non-purebreds winding up in their reference pool, and therefore compromise their overall accuracy at picking out the breed in question in a mix. And since the Shih Tzu breed club [considers](http://americanshihtzuclub.org/imperial) “imperial” Shih Tzus to be a disreputable scam in which undesirably nonstandard dogs are marketed as “exotic” and desirable, it seems unlikely to me that Wisdom Panel would see fit to intentionally include “imperial” Shih Tzus in their reference database–by definition, no reputable Shih Tzu breeders are deliberately producing these dogs.

    There are some breeds that are notorious for not breeding true to size–Chihuahuas and Italian Greyhounds come to mind; I don’t know enough about Shih Tzus or Miniature Poodles to know whether that might be true of them as well, let alone “imperial” Shih Tzus who obviously aren’t well-studied or well-documented. There are numerous genes involved in determining size; some have yet to be identified, and also some forms of inherited “shortness” may be recessive or polygenic recessive, and therefore will express only occasionally in a given population. And then there are environmental factors like poor maternal nutrition that can result in permanent non-heritable stunting, too. Not trying to argue WP’s findings are correct–they could very well be wrong; no breed test is infallible, but OTOH stranger things have happened than a 5-pounder and a (presumably) 10+-ish pounder producing a 4-pounder.

    in reply to: those pesky unwanted mutations #6029
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    Jennifer
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    The study (linked in the article) says that 100% of the albino Dobies examined displayed photophobia (light sensitivity); they had no other vision problems. I don’t know whether dogs with piebald-linked blue eyes, e.g. some white Boxers and some Dalmatians, commonly show light sensitivity, or for that matter whether dogs with blue eyes due to other causes commonly do either (merles, Huskies etc.). I haven’t noticed my dog squinting her one blue eye in sunlight, but it might be I just haven’t been paying attention, or it might be that she has protective factors that albinos don’t (e.g. her eyelids are black, and her eye doesn’t seem to be quite as icy-pale as an albino’s, which might have to do with different extent of pigment loss in the iris).

    The link between being a high-white piebald and going deaf early in puppyhood isn’t fully understood, but it has something to do with the fact that pigment cells participate in ion exchange in the vascular networks around them, including helping stabilize potassium in the vascular networks supplying the cochlea. And certain forms of piebald mutations (there are several, with high-white piebalds tending to carry multiple mutations at once in the gene involved) can delay or block the migration to and/or establishment of pigment cells within the inner ear during fetal development. If no pigment cells are present in the inner ear by early puppyhood, when the cochlea is completing development, then ion exchange doesn’t happen properly, and the cochlea winds up effectively wasting away due to neuron death, rather than maturing to allow normal hearing by the time the ear canals open (around 3 weeks after birth). There are no really large-scale studies on this AFAIK, but by most estimates to date, the rates of deafness in high-white piebalds average around 10-20%, varying by breed. Albino dogs, by contrast, do have a normal distribution of pigment cells–they’re just not able to make pigment with them–so they’re spared this increased risk of deafness.

    White GSDs aren’t piebald, though; they’re carrying a recessive mutation on a different gene (the same one that causes most GSDs to have black face masks) which in effect turns off their ability to produce black pigment in their fur (but not in their skin and eyes). For reasons that aren’t yet fully clear, dogs with this mutation also tend to have much paler red pigment than other dogs of their breed or type, so that they often appear white, cream, or yellow (other examples of this include American Eskimos, Maltese, yellow Labs, etc.). This particular mutation is not known to have any health effects. It’s possible that early GSD breeders mistook the white of white GSDs for piebald white, which dog breeders in general had long recognized was linked to an increased risk of deafness in puppyhood. Other claims I’ve heard are that white was considered unfavorable in a guard breed (too visible at night), or that it was simply an article of Nazi pseudoscience that white-furred animals are “weaker” in some ill-defined way (the effective “ban” on white GSDs happened only after breeding came under control of the Nazi regime). At any rate, the “ban” never wound up getting lifted after WWII. The UK Kennel Club did recently announce plans to recognize the White Swiss Shepherd, specifically, as a separate breed, so it’s likely the AKC will eventually follow suit–though if so that won’t help white GSDs who don’t descend from FCI-registered White Swiss Shepherd lines, which I’m pretty sure most US white GSDs don’t. The thing is, due to their many decades of isolation, US white GSDs will almost inevitably have fallen so far behind the mainstream GSD population in terms of the rigors of selection undergone, that they probably really are de facto an “inferior” population at this point, at least from the POV of a good working-line or show-line breeder.

    in reply to: those pesky unwanted mutations #6027
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    Jennifer
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    I wonder how the rates of skin tumors and vision disturbances (light sensitivity) in dogs with this mutation compare to those of the high-white piebald dogs commonly found in numerous breeds (and mixes, including mine at left). Many piebald dogs do have spotted skin even in areas where their fur is white, which might have limited protective effect, but not all of them do; and in certain breeds piebaldism can also cause blue eyes, presumably the cause of the light sensitivity in these Dobermans (you can see the ones pictured in the article squinting). And whereas this type of albinism doesn’t result in increased risk of deafness in puppies, being high-white piebald does. It’s interesting how such health risks are treated as unacceptable and therefore to be rigorously selected against in some breeds, but as a can’t-be-helped inevitability in others. Then again, in Dobies the overwhelming majority of dogs have always been solid-colored so it’s very doable to select against albinism, whereas you can’t very well have Dalmatian or Cattle Dog spotting or “flash pattern” Boxer white markings without piebald mutations…

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