Reptile & Amphibian Forums

Does anyone know if it is feasible and/or practical to do DNA analysis of scat to determine ranges?
Thanks
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www.phrynosoma.com

wow! the things you must sit up at night thinking of Cable!

I would think certainly feasable, if you mean scientifically possible. but economically feasable, or, practicality is another story. imagine the man hours involved to search for enough scat to put together such a distribution map of any large scale! not to mention the lab cost to test so many samples!

I'm afraid not practical until the pocket field DNA test kit is perfected and mass produced affordably.

but then again...I smell a possible government research grant!
your tax dollars at work?

Yeah, I guess I spend a bit of time thinking about these guys. They fascinate me no end.

Just trying to come up with better ways to track than gluing a radio transmitter onto their backs. This way would be the least intrusive method I can think of. But you are probably right, cost prohibitive. I don't know much about DNA analysis and the related equipment. Collecting samples in my neck of the woods (or cacti) is no difficult task.

One of these days maybe I'll get the education necessary for that grant. By then they'll have the pocket DNA kit at Walmart for $9.95 LOL.
Cheers!
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www.phrynosoma.com

DNA analysis from scat would not be a viable test or indicator of home range. DNA from scat would not yield mDNA necessary for PCR replication. DNA would be so fragmented, if available at all, from the digestive process.

The only process that is reliable is CMRR, capture-mark-release-recapture, and radio-tracking for home range study and analysis. CMRR and radio tracking requires point intensive data gathering on a regular schedule basis. A minimum of at least 70 tracking points is required for even a base line of home range. Home range also has to be analyzed as to time of year, sex, habitat quality, and age. It is not a simple process and is very labor intensive. Predator-Prey analysis is also very important in the analysis.

Lester G. Milroy III
Consevation Biologist

What is considered the proper way to "mark" a horned toad these days? Right now I'm dabbing a wee bit of nail polish on the horns of my babies, taking note of the pattern of marking. This works fine in my home, but sheding the scales tends to force me to re-mark periodically. So I have to assume this doesn't work for field studies.

Thanks,
Roger

Hi Roger,
I am sure Lester can give you the lowdown on approved techniques but I'll throw you out some food for thought.
Joe Collet has a paper on using unique spot patters from HL's to identify individuals. I have used this on my hatchlings since birth (or shortly thereafter) and it seems to be holding true.
It amounts to a scan or photo of the underside of each HL as the photos below show. I assign a unique number to each and date stamp the scans for refference.
As you can see, two months and a shedding later the spot pattern is not changed.

This one is from the same group and illustrates the uniqueness of each individual.

I want to put this to the test in the field this spring.
Cheers!
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www.phrynosoma.com

There are several ways to mark HLs. It depends on the study requirement needs. If it is a short term study for Lincoln-Petterson CMRR, a simple marker number on the belly will do just fine. If you are doing long term tracking, there are several ways to mark the HLs involved. One way is toe-clipping, which I do not like or practice. Another way is beading, which works well, but has some drawbacks. The third way is to use PIT tags that work very well and require no remarking or other maintenance. To use PIT tags, you must have a Reader-scanner to read the tags once the HLs have been marked. (I tag all of my field study and captive study animals and have had no problems with the tag use).

The use of a scanner, to photocopy individual HLs belly markings works well, but is very labor intensive and material intensive. Once the scans are accomplished, you must maintain a book containing all of the scans and carry it with you. This is not usable in field research.

Lester G. Milroy III
Conservation Biologist

Thank you Lester,
I had a feeling. I was thinking that maybe the cloaca lining might provide some usable DNA on the way out. But again, I have no special knowledge of DNA analysis.

Do you happen to have a template or paper I might use as a guide to range study by chance?
I have a very viable population of Solare within a mile or so of my house and I do tend to spend quite a bit of time in the field there as it is. It would be great if I could produce some valuable data for study.
Thanks again.
Cable
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www.phrynosoma.com

not trying to argue Les... I'm no lab tech, but I've seen CSI a few times . maybe this applies to this question of HL's as well and maybe it doesn't. but I know mitochondrial is the easiest to get and can norrow you down to at least species if there is a control sample. it can tell you about ancestry from maternal side. generally nuclear DNA is needed for individual specific identification, but I don't think that's what Cable was suggesting. I think he meant it would be good enough to identify samples as species specific.

"Mitochondrial DNA (mtDNA) provides a valuable locus for forensic DNA typing in certain circumstances. The high number of nucleotide polymorphisms or sequence variants in the two hypervariable portions of the non-coding control region can allow discrimination among individuals and/or biological samples. The likelihood of recovering mtDNA in small or degraded biological samples is greater than for nuclear DNA because mtDNA molecules are present in hundreds to thousands of copies per cell compared to the nuclear complement of two copies per cell. Therefore, muscle, bone, hair, skin, blood and other body fluids, even if degraded by environmental insult or time, may provide enough material for typing the mtDNA locus."

( source ) http://www.mitotyping.com/dna.htm

would there not be sufficient cells from digestive enzymes present in scat, given prevalence of mitochondrial within cells, as stated above, to do this analysis? without regards
at this point as to whether it is otherwise practical?

Mick Palermo
fireside3@hotmail.com

Thank you Mick for the refresher course on DNA and mDNA. The question was could scat be used for home range analysis. The answer is no, it cannot be used for home range analysis for an individual. Samples from scat may be possible, but cost analysis would be very prohibitive. You would still have to have a base line DNA sample from an individual for mapping and comparison.

you're welcome, and thank you Lester for your pithy reply.
Cable's question was actually:

"Does anyone know if it is feasible and/or practical to do DNA analysis of scat to determine ranges?
Thanks"

whether it was species range, or, individual "home" range was not specified.

I was advocating the question of it's use in determining species range, not an individual, for the obvious reasons of difficulty in tracking an individual by this method.

one would only need to take a baseline from any individual of the species concerned.

apparently addressing Cable's question you responded, in part;

"The answer is no, it cannot be used for home range analysis for an individual. Samples from scat may be possible, but cost analysis would be very prohibitive. You would still have to have a base line DNA sample from an individual for mapping and comparison."

you definitively stated "no" at the beginning of this statement, however, continued by using the words "possible" and "prohibitive", finishing up with the requirement for a baseline. this does not reflect a definitive "no" on the matter. it only reflects difficulty.

again, my question was;

"would there not be sufficient cells from digestive enzymes present in scat, given prevalence of mitochondrial within cells, as stated above, to do this analysis? without
regards at this point as to whether it is otherwise practical?"

I think we are all in agreement, thus far, about the financial nature of such an undertaking. but your reply is far short of my question.

assuming you had adequate budget requirements at your disposal, and, access to a lab with which to conduct the analyses, it is still your contention that scientifically the requirements could not be met by way of any residual in the sample? if you still believe the answer to be "no", as a conservation biologist, could you elaborate on the specific _scientific_ reason why it is not viable?

Mick Palermo
fireside3@hotmail.com

To get more specific, I had in mind the tracking of individuals in a given area vs range of species. It would be far to cost and time intensive for me to try and determine the range of the species.

But thanks for the DNA enlightenment. Maybe in time it will be cheaper and more feasible.

Regarding the type of DNA available, I was extrapolating the use of a cotton swab in the mouth to determine DNA of humans and was thinking as scat passed through the mucus membranes of the cloaca it might leave similar traces.

Lester,
I found a home range study on Phrynosoma Solare (oddly enough conducted within a few miles of my home in the same area I have been observing Solare). I was fairly amazed to see the range is quite small for an individual. Given this and the density of populations in a given area I still think it feasible to use the camera/scanner method for visual ID of unique spot patterns ventrally. You are right in concluding the scanner too cumbersome for field use. But a camera would make quick work of this process. The resulting photos could be categorized by sex, field study site, and possibly other criteria to reduce time spent looking for particular records on recapture. Only a small portion of the HL vent area need be photographed for ID purposes as this photo shows. The patterns are quite unique, even among siblings.

I think it would be a simple matter to print these and laminate for easy field identification.
Are you implanting or gluing the PIT tags?

Cheers!
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www.phrynosoma.com

As Cable was intimating, those who have the right camera and knowlege can put an f in the photo or m for sex. One could put in a co-ordinate the date, and still not impinge on enough of the picture to have a good record.
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Phrynosoma.com

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