Chimp & See Talk

Genetic questions

  • Orohena by Orohena

    Hello !
    Sooo big questions that I have since a while (but wanted to look around here to make sure there was not the answer) is about genetic studies.
    I think I saw that few of scientist here study how to get non-invasive genetic sample and also study these samples. I also saw on PanAf (in the PanAf field methods) that you get faecal, urine samples for genetic and pathogen studies.
    And saw somewhere that you make endocrinological analyses.

    So my questions are:

    • What are you looking in the faecal samples ? and in the urine samples ?
    • Do you sometimes find blood samples ? or hair ?
    • About the genetic samples : I think I read that you almost never can relate sample to an individual chimp, but what are you looking for ? Do you try to get the full sequence of the DNA ? Do you have target genes ? What kind of genes are you looking for and why ? What are you looking for in endocrinology ? Is it just to look for diseases ?
    • About the pathogen : Is it always about pathogen ? I read that you can differentiate people by their microbiome (which I think you can find in faeces sample) so are you looking for that too ?
    • Do you make only genetic and pathogen studies or do you do also proteomics ?

    I also read, in the PanAf field methods, that you can find and collect "wadges" and then it says "Wadges look like dentist imprint
    of your mouth and teeth" so my question is : do you try to identify chimp or at least individual with these imprints ? Do you try to find DNA or any other genetic material in it ?

    You have 4 hours ! Haha, I'm kidding. 😄

    I know it's a lot of question, maybe there are answer somewhere on PanAf or here...
    Also, I know that if it is not published you can't say everything but in that case, stay evasive, I understand saying everything is not possible.
    I hope it's not too much asking ! 😃

    Posted

  • yshish by yshish moderator in response to Orohena's comment.

    Really interesting questions! I am curious about the answers myself 😃

    Posted

  • lauraklynn by lauraklynn moderator

    I am also curious what data is being obtained from samples at PanAf. At my zoo we have helped collect fecal samples from our apes to look at cortisol and immunoglobulin-A levels and we are currently collecting urine samples for a study looking at oxytocin.

    Posted

  • Orohena by Orohena in response to lauraklynn's comment.

    Do you have any idea why they were looking at cortisol, immunoglobulin-A and what they will study with oxytocin ? What are they trying to deduce/conclude from that ?

    Posted

  • MimiA by MimiA scientist, moderator

    Hi @Orohena - I'll do my best 😃

    What are you looking in the faecal samples ? and in the urine samples ?

    *For feces we are using them in 3 ways, for diet analysis (looking at the seeds, insects, bones, and other things in the feces), for genetic analysis and for pathogen analysis., The urine samples have been much harder to obtain, so that project is on hold now.

    Do you sometimes find blood samples ? or hair ?

    Yes! We sometimes get blood if there has been a fight, but it is very rare. Hair is collected from nests for isotope analyses to look at diet composition as well

    About the genetic samples : I think I read that you almost never can relate sample to an individual chimp, but what are you looking for ?

    I am not totally sure what you mean here 😃 Every feces samples that contains DNA will provide us with a 'DNA fingerprint' (also known as a microsatellite genotype) for the individual it came from. From this we we can estimate population size, grouping patterns, possible movement between groups, group associations and relatedness. We will also sequence large portions of the chimp genome from a subset of samples to look at selection at certain genes and population histories.

    Do you try to get the full sequence of the DNA ?

    No, that would be very expensive as fecal DNA is highly degraded.

    Do you have target genes ?

    Yes

    What kind of genes are you looking for and why ?
    We'll be looking at genomic sequences that can tell is about the population histories of our study populations and to try to evaluate if there have been different selection pressures on different populations.

    What are you looking for in endocrinology ?

    indicators of stress would be the main goal

    Is it just to look for diseases ?

    Diseases are detected using fecal samples

    About the pathogen : Is it always about pathogen ? I read that you can differentiate people by their microbiome (which I think you can find in faeces sample) so are you looking for that too ?

    yes we are

    Do you make only genetic and pathogen studies or do you do also proteomics ?

    we do not have any proteomics in the plan

    I also read, in the PanAf field methods, that you can find and collect "wadges" and then it says "Wadges look like dentist imprint of your mouth and teeth" so my question is : do you try to identify chimp or at least individual with these imprints ?

    No, that would be tricky since we dont have dental casts from the study indivduals

    Do you try to find DNA or any other genetic material in it ?

    yes we do 😃

    Happy to answer more if you have any ore questions 😃

    Posted

  • Orohena by Orohena

    Thank you very much @MimiA for your answers ! It is very interesting !

    I had guess that you would not sequence the full DNA but I didn't thought about microsatellite 😃
    So if I well understand, the genetic studies are mainly related to the individual in the group and the populations histories.
    You don't look for particular genetic diseases that chimps can have. I guess for most of the heavy genetic diseases, the individuals have no chances to survive but is there some genetic diseases that are known in chimps ?

    I think that all your answer satisfied my curiosity for now 😃 My brain will process that now maybe more question will come later, haha! But I can't wait to see articles about that in the future to know more !
    We see a lot of the field team in the videos but it seems to be a lot of lab work with the samples that you collect too!

    Great job to the lab team !

    Posted

  • MimiA by MimiA scientist, moderator

    Not a ton is known about chimp genetic diseases though we would predict a lot of similarities with human diseases and will look for signals of this.

    For what is known in chimps, I have to admit I am not totally sure, the only thing that pops into my mind is: https://link.springer.com/article/10.1007%2Fs10329-017-0597-8 (there have been suspected cases in the wild as well based on how the animals looked and acted but nothing published I think).

    There are certainly some heart conditions known in captive apes too but I do not know if the genetic roots are known of this or if its an issue with captivity.

    We also have the "issue" of not having phenotypes to match our genotypes. Meaning, even if we pick up something in the genome that seems interesting, since we can't relate it to a given chimp on a camera trap (and we never really see individuals directly), we don't know if this genetic anomaly has any actual effect on the individual.

    Posted