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Texas A&M DNA test & the fun results

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    #21
    samhorse, thank you for the insightful information! When I talked to the person at Texas A&M, he told me her fourth "hit" was Andalusian. I did look at the phylogenetic tree and tried to research why the results did not make sense. I also looked into what is being bred on reservations and locally. Your analysis makes lots of sense and I'm going to enjoy reading your summary page. I'm curious and really interested about how you came to do this research.

    FYI,I have seen some gorgeous mustangs from the Warm Springs Reservation and other places and it would be really fantastic if my mare did have Barb blood. To give you an idea of her phenotype, here is a photo.

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      #22
      sparkygrace No DNA test needed, your mare is 100% lovely.

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        #23
        Thank you, Gamma. She has a twin brother who was on the feed lot with her. He has the same markings, but is more refined. I believe being a twin is why she ended up being small (14.1). A trainer with a good eye picked them up before they were shipped off to the slaughter house. She will likely be the best horse I've owned. I've owned many, most way more expensive than she. Until the fires hit, we were schooling 2nd level. A few BNT's have been super impressed with her attitude and movement. She is a big puppy dog.

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          #24
          Just wanted to stop by and say-- all of these horses are TERRIBLE, USELESS, you'd better load all of them up and send them to ME!

          Really, all of them are beautiful and you should be proud of them.
          I loff my Quarter horse clique

          I kill threads dead!

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            #25
            OP-what an adorable horse, regardless of breed.

            These tests are not based on good science. Testing for a "breed" requires alleles that are at 100 frequency within a breed, and 0% in others. These markers just do not exist in horses, period. It's fine for fun, but the fact that they take money in exchange for "results" is pretty unethical, IMO (as a geneticist, all be it a microbial geneticist).

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              #26
              It’s not meant to be a breed test though. It a test for ancestral DNA associated with some breeds that is compared by a computer algorithm. That is what is advertised, but many people misinterpret their results.

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                #27
                Originally posted by SMK View Post
                OP-what an adorable horse, regardless of breed.

                These tests are not based on good science. Testing for a "breed" requires alleles that are at 100 frequency within a breed, and 0% in others. These markers just do not exist in horses, period. It's fine for fun, but the fact that they take money in exchange for "results" is pretty unethical, IMO (as a geneticist, all be it a microbial geneticist).
                As a biochemist, I dont think the above is actually quite accurate. The test is just suggestive for an individual horse, most certainly, and should be evaluated thoughtfully based upon the horses location, phenotype and just what makes sense, as a fun way to tell the horses story.

                However with respect to breeds, there are a plethora of breed to breed comparative peer-reviewed studies using these markers to determine how breeds are related. In these studies they evaluate 50-100s of horses from each breed, so develop statistical data on the frequency of the alleles within various breeds. Its not just is a marker present or absent, but rather which markers whos up in which breeds at which frequencies. They are a pretty interesting and very scientifically valid tool for use in population genetic studies of whole breeds.

                I also think the revenue is used to do research on horse genetics. Dr Cothren has done a huge amount of analysis on breeds all over the world and on our mustangs here in the US, for which Im very grateful. Id be hesitant though if it was a for-profit company for sure.

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                  #28
                  Originally posted by samhorse View Post

                  As a biochemist, I dont think the above is actually quite accurate. The test is just suggestive for an individual horse, most certainly, and should be evaluated thoughtfully based upon the horses location, phenotype and just what makes sense, as a fun way to tell the horses story.

                  However with respect to breeds, there are a plethora of breed to breed comparative peer-reviewed studies using these markers to determine how breeds are related. In these studies they evaluate 50-100s of horses from each breed, so develop statistical data on the frequency of the alleles within various breeds. It's not just is a marker present or absent, but rather which markers whos up in which breeds at which frequencies. They are a pretty interesting and very scientifically valid tool for use in population genetic studies of whole breeds.

                  I also think the revenue is used to do research on horse genetics. Dr Cothren has done a huge amount of analysis on breeds all over the world and on our mustangs here in the US, for which Im very grateful. Id be hesitant though if it was a for-profit company for sure.
                  Even looking at genome wide SNPs, which is a far, far more accurate way determine relationships, the data are unimpressive. Check out Peterson et al., 2013, in PLoS ONE. Let's just say that there's a reason it's in PLoS ONE and not a quality journal. And sadly, that's the best journal that this sort of research is published in. Additionally, the majority of this literature is describing diversity within a breed, not establishing markers for breed identification.

                  Your second to last sentence the the second paragraph is exactly the problem. They are not picking good markers, likely because they don't exist. It's basically MLST. A=allele 1 B=allele 3 C=allele 2 would equal a QH. A=allele 4 B=allele 3 C=allele 5 would equal a Morgan. There is no validation. And I totally get that. I do a lot of bioinformatics and genome sequencing; it's difficult and time consuming. And expensive. I'm totally fine with not having quality research that can ID horse breeds, because I'd just as soon that money be spent on IDing causes for equine genetic diseases.

                  And it totally makes sense that there are no good markers strongly associated with breeds. Horse breeds aren't monophyletic groups. And clearly the PCA from the 2013 paper shows that the older, purer breeds are far more distinct than most breeds. It's laughable to me that they include breeds like QHs and WBs. It's hard to ID an Oldenburg when one parent is a Hanoverian and the other is a Holsteiner. I like to think that Lauries Crusador XX and Prince Thatch XX are somewhere laughing at the idea of Hanoverians being a genetically distinct breed.

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                    #29
                    Originally posted by samhorse View Post
                    The dna analysis being used in these tests is very precise and the exact same type of data used to verify parentage.

                    This is a really great article that describes how it works: https://vgl.ucdavis.edu/services/parentage

                    This is a NIST standard of what the information you see on the second page of the report "K, L" etc actually means: https://strbase.nist.gov/horseSTRs.htm

                    From here they feed the info to a computer and it tries to figure how what the most likely breed could be, based upon the markers it sees. This is where imprecision arises, given the overlaps across breeds like the Thoroughbred family. They explicitly say that you will see the breeds overlap in the families when you place the order but dont reiterate it on the results form and folks forget.

                    Our mustangs are like 100 different landraces since each HMA has its own local horses, so can be quite interesting. I created this summary page describing the "Families" and reasons why they may show up in a given mustang's heritage here. https://farmymcfarmplace.weebly.com/dna-testing.html The idea is to use the test results, the BREED FAMILIES not individual breeds, think about your horse's phenotype, think about the history of the horse's HMA and build a story from all information that seems reasonable.
                    Thanks for the link. My little Nevada Mustang is very Barb looking so it would be fun to see how much Spanish type influence she has (Lava Beds HMA) and if there are any surprises. Any Mustangs near Rock Springs Wyoming might have a bit of TB, according to a story from a very old cowboy I knew when I was a kid...

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