I had my RTs' DNA tested to determine their subspecies!

biochemnerd808

Well-Known Member
10 Year Member!
Joined
Nov 3, 2012
Messages
1,463
Location (City and/or State)
Central Arkansas (we moved!)
I know there has been some talk about genetic testing of the more 'fancy' tortoise breeds. Well, since Russian tortoises are my jam, I decided to have my Russian tortoises genetically tested, too (the results are at the very end, if you don't want to read the long story). And since it is my hope that other tortoise breeders will jump on the band-wagon and have theirs tested, I decided to write down the info here.

When I built my original founder group (from Craigslist tortoises!), I visually matched the adults, based on shell shape, coloration, and the configuration of their plastron scutes. I was fairly sure that they were all the same subspecies, but I wasn't confident WHICH one (I thought either T.h.horsfieldii or T.h.kazachstanica).
I lost a few of my founder group to a raccoon in WA a year before we moved to AR. I also decided that I didn't want the remaining wild-caught adults to have to adjust to yet another climate. So before moving, I rehomed the remaining WC adults and only moved with the CB group (one or two babies from each of my females, all the same father, plus 2 little CB males I got from trusted breeder friends).

Here is a photo of my little CB group. They range from 10 years old to 5years, except for the one at the bottom right, which is a 2-year-old CB2.
IMG_20230708_161128.jpg

I wanted to know the subspecies of my tortoises for sure so that I can produce subspecies-pure progeny. We all know how e.g. leopard tortoises were imported to the US and interbred willy-nilly, and now we have a schmorgas of leopard mutts. The same thing is happening with Russian tortoises.

I produce about 9-15 baby Russian tortoises per year, with three more young CB females coming up to breeding size in the next year or two. Knowing the subspecies of my Russian tortoises allows me to breed with conservation of the species in mind.
KatieTTPG1.jpg

I learned about the GENDIKA laboratory in the Netherlands from my tortoise buddy, Matthew Hills. They do genetic testing of many animals. (GENDIKA) (set it to 'English' in your browser or use Google translate). I reached out to them and inquired whether they are able to determine the subspecies of Russian tortoises.
As it turns out, YES, they are able to, and they were able to tell me the subspecies, the clade, and the specific locality my tortoises originated from! It cost me EUR60 (about $55 at the time) per tortoise, plus $25 for USPS priority mail. I had 7 of them tested, since of my 8 adults, two are full siblings.

Some notes:
Gendika needs buccal swabs for the genetic sequencing and subspecies determination. A buccal swab is a non invasive way to get a tissue sample from the inside of the tortoise's cheek.
PS: If you don't have experience (man)handling tortoises, you should have a vet do the buccal swab. A lot can go wrong if you don't know how. To do this yourself, you need to know how to safely hold the tortoise's head out, and how to safely open their mouth.
I am lucky to have over a decade of experience doing beak maintenance on tortoises for a rescue, so I was confident I could do it without harming the tortoises.
It takes 2 people. One holds the tortoise like a burger. The other (me) catches the tortoise's neck on either side (NOT top and bottom) between thumb and pointer, right behind the jaw. The tortoise gets mad and pees all over the person holding them. If you're lucky, the tortoise opens its mouth at you and you can pop that swab right into their mouth (5 of the 7 did this). If you are not lucky, the tortoise clamps its mouth shut (2 of the 7 did this). I used a plastic dental tool to carefully pry the mouth open, and held it open by keeping the tool in its mouth like a bit on a horse. You will feel like you don't have enough hands and will probably be
💩
on. A 3rd person might be useful, if only to video your swearing.
😆

Once the swab is within the V of the tortoise's jaw, you can let the head go. Keep the swab IN the tortoise's mouth when it retracts its head. You swipe the swab on the inside of its cheeks and on its tongue with a twirling motion, about 10-15 seconds of swab and swirl.

You have to leave the tubes slightly open for a few days to let the sample dry. It's illegal to ship wet samples.
PS: I have since learned that it would have been BETTER to go through a local veterinary school or animal biology department at our local university, since they have specific export permits. There are some strict laws about exporting animal tissues. So while (as seen below) there are codes etc. you put on the shipping envelope, it could have still been stopped by customs. Let's keep things legal!

I talked to AR Fish and Wildlife, and to the lead clerk at USPS about how to ship the samples. I was told: The sample tubes have to be inside a bag inside the envelope, and everything is properly labeled "UN3373 Biological Substance Category B" (label from Gendika) and "Research sample for vet" and "No commercial value" on the outside, plus signed customs form with value $1. You need to include an HS Tariff code. Based on my research, 3001.20.00 (tissue sample from animal) is the closest approximation. My package still sat in customs in the Netherlands for three weeks, but then it moved along to Gendika. I paid for the order AFTER Gendika sent me an email confirming that they received the samples.

These are the sterile, individually wrapped sample swabs I used: Swabs
They worked well, the tip did not lose any pieces or fibers into the tortoise's mouth.

Ok, so after all this TLDR, you're probably wondering what the subspecies of my tortoises are? Here you go:
Screenshot_20240530_113721_Adobe Acrobat.jpg
I was so pleased to find out that they are all of the same subspecies (Testudo h. kazachstanica) and clade (red). And it was cool to look at a world map and see exactly where their parents originated from. My husband's reaction: "WHAT? We have Iranians in our house?" My answer: "They were born in the US. That's good enough for me."

I hope more Russian tortoise breeders (and breeders of other species, too!) will have their tortoises' DNA sequenced so we can produce more subspecies-pure progeny.

KatieTTPG4.jpg
 

SinLA

Well-Known Member
Tortoise Club
Joined
Apr 19, 2022
Messages
2,292
Location (City and/or State)
Los Angeles
This is very interesting. Can you share pictures side by side of the two different subspecies?
 

Yvonne G

Old Timer
TFO Admin
10 Year Member!
Platinum Tortoise Club
Joined
Jan 23, 2008
Messages
93,558
Location (City and/or State)
Clovis, CA
I know there has been some talk about genetic testing of the more 'fancy' tortoise breeds. Well, since Russian tortoises are my jam, I decided to have my Russian tortoises genetically tested, too (the results are at the very end, if you don't want to read the long story). And since it is my hope that other tortoise breeders will jump on the band-wagon and have theirs tested, I decided to write down the info here.

When I built my original founder group (from Craigslist tortoises!), I visually matched the adults, based on shell shape, coloration, and the configuration of their plastron scutes. I was fairly sure that they were all the same subspecies, but I wasn't confident WHICH one (I thought either T.h.horsfieldii or T.h.kazachstanica).
I lost a few of my founder group to a raccoon in WA a year before we moved to AR. I also decided that I didn't want the remaining wild-caught adults to have to adjust to yet another climate. So before moving, I rehomed the remaining WC adults and only moved with the CB group (one or two babies from each of my females, all the same father, plus 2 little CB males I got from trusted breeder friends).

Here is a photo of my little CB group. They range from 10 years old to 5years, except for the one at the bottom right, which is a 2-year-old CB2.
View attachment 373231

I wanted to know the subspecies of my tortoises for sure so that I can produce subspecies-pure progeny. We all know how e.g. leopard tortoises were imported to the US and interbred willy-nilly, and now we have a schmorgas of leopard mutts. The same thing is happening with Russian tortoises.

I produce about 9-15 baby Russian tortoises per year, with three more young CB females coming up to breeding size in the next year or two. Knowing the subspecies of my Russian tortoises allows me to breed with conservation of the species in mind.
View attachment 373234

I learned about the GENDIKA laboratory in the Netherlands from my tortoise buddy, Matthew Hills. They do genetic testing of many animals. (GENDIKA) (set it to 'English' in your browser or use Google translate). I reached out to them and inquired whether they are able to determine the subspecies of Russian tortoises.
As it turns out, YES, they are able to, and they were able to tell me the subspecies, the clade, and the specific locality my tortoises originated from! It cost me EUR60 (about $55 at the time) per tortoise, plus $25 for USPS priority mail. I had 7 of them tested, since of my 8 adults, two are full siblings.

Some notes:
Gendika needs buccal swabs for the genetic sequencing and subspecies determination. A buccal swab is a non invasive way to get a tissue sample from the inside of the tortoise's cheek.
PS: If you don't have experience (man)handling tortoises, you should have a vet do the buccal swab. A lot can go wrong if you don't know how. To do this yourself, you need to know how to safely hold the tortoise's head out, and how to safely open their mouth.
I am lucky to have over a decade of experience doing beak maintenance on tortoises for a rescue, so I was confident I could do it without harming the tortoises.
It takes 2 people. One holds the tortoise like a burger. The other (me) catches the tortoise's neck on either side (NOT top and bottom) between thumb and pointer, right behind the jaw. The tortoise gets mad and pees all over the person holding them. If you're lucky, the tortoise opens its mouth at you and you can pop that swab right into their mouth (5 of the 7 did this). If you are not lucky, the tortoise clamps its mouth shut (2 of the 7 did this). I used a plastic dental tool to carefully pry the mouth open, and held it open by keeping the tool in its mouth like a bit on a horse. You will feel like you don't have enough hands and will probably be
💩
on. A 3rd person might be useful, if only to video your swearing.
😆

Once the swab is within the V of the tortoise's jaw, you can let the head go. Keep the swab IN the tortoise's mouth when it retracts its head. You swipe the swab on the inside of its cheeks and on its tongue with a twirling motion, about 10-15 seconds of swab and swirl.

You have to leave the tubes slightly open for a few days to let the sample dry. It's illegal to ship wet samples.
PS: I have since learned that it would have been BETTER to go through a local veterinary school or animal biology department at our local university, since they have specific export permits. There are some strict laws about exporting animal tissues. So while (as seen below) there are codes etc. you put on the shipping envelope, it could have still been stopped by customs. Let's keep things legal!

I talked to AR Fish and Wildlife, and to the lead clerk at USPS about how to ship the samples. I was told: The sample tubes have to be inside a bag inside the envelope, and everything is properly labeled "UN3373 Biological Substance Category B" (label from Gendika) and "Research sample for vet" and "No commercial value" on the outside, plus signed customs form with value $1. You need to include an HS Tariff code. Based on my research, 3001.20.00 (tissue sample from animal) is the closest approximation. My package still sat in customs in the Netherlands for three weeks, but then it moved along to Gendika. I paid for the order AFTER Gendika sent me an email confirming that they received the samples.

These are the sterile, individually wrapped sample swabs I used: Swabs
They worked well, the tip did not lose any pieces or fibers into the tortoise's mouth.

Ok, so after all this TLDR, you're probably wondering what the subspecies of my tortoises are? Here you go:
View attachment 373232
I was so pleased to find out that they are all of the same subspecies (Testudo h. kazachstanica) and clade (red). And it was cool to look at a world map and see exactly where their parents originated from. My husband's reaction: "WHAT? We have Iranians in our house?" My answer: "They were born in the US. That's good enough for me."

I hope more Russian tortoise breeders (and breeders of other species, too!) will have their tortoises' DNA sequenced so we can produce more subspecies-pure progeny.

View attachment 373233
Kudos to you for doing this!!!!! Many years ago I had EgypyianDan look at my group of Russians (I had quite a few from being turned in to my rescue) and I kept only the Kazachstanica, adopting out all the others.
 

SinLA

Well-Known Member
Tortoise Club
Joined
Apr 19, 2022
Messages
2,292
Location (City and/or State)
Los Angeles
Two subspecies? Where did you get she had two?
Not that she HAS two, but she said she was trying to see if they were one or the other, so since all of hers are one, I'm curious what the other looks like... I would assume mine is the same as hers, but I don't know what is different about them (if anything) in terms of morphology...
 

Yvonne G

Old Timer
TFO Admin
10 Year Member!
Platinum Tortoise Club
Joined
Jan 23, 2008
Messages
93,558
Location (City and/or State)
Clovis, CA
@SinLA Under our Russian section look in the stickies for a thread by egyptiandan titled "Russian Subspecies." Because he used Photobucket some of the details are hard to see, but maybe you can get satisfaction from that thread.
 

SinLA

Well-Known Member
Tortoise Club
Joined
Apr 19, 2022
Messages
2,292
Location (City and/or State)
Los Angeles
@SinLA Under our Russian section look in the stickies for a thread by egyptiandan titled "Russian Subspecies." Because he used Photobucket some of the details are hard to see, but maybe you can get satisfaction from that thread.
found it!


Thanks!
 

wellington

Well-Known Member
Moderator
10 Year Member!
Tortoise Club
Joined
Sep 6, 2011
Messages
50,728
Location (City and/or State)
Chicago, Illinois, USA
Not that she HAS two, but she said she was trying to see if they were one or the other, so since all of hers are one, I'm curious what the other looks like... I would assume mine is the same as hers, but I don't know what is different about them (if anything) in terms of morphology...
Okay I see. I thought I missed something, that's why I questioned it.
I skim over long posts and sometimes miss things.
 

biochemnerd808

Well-Known Member
10 Year Member!
Joined
Nov 3, 2012
Messages
1,463
Location (City and/or State)
Central Arkansas (we moved!)
I thought maybe it was the parents that were the 100% and the offspring would be the 99%
So, here is roughly how the PhD at the lab explained it to me (and it made sense to my somewhat rusty biochem degree brain). I asked if the 99% meant that there was some other subspecies mixed in. She said no, they are all 100% the T.h.kazachstani, but that within the subspecies, there are different clades, and within the clades, there are different haplotypes (noted in the case of my animals as D, E and F).

The "hybridization to the haplotype" means that for the one that is 99% D, there might be 1% of E in there, due to Bob the Russian tortoise's great great great great grandfather wandering a little further over to Judy's territory and mating with her. A haplotype is a cluster of genes that are inherited together.

If I were to break it down into a flow chart there would be:
Testudo horsfieldii (species)

Testudo horsfieldii kazachstani (subspecies)

Testudo horsfieldii kazachstani red clade (clade within subspecies)

Testudo horsfieldii kazachstani, red clade, haplotype D (or E, F, etc... I assume there are also A, B, C, but I don't have those) - so the possible variation that is being seen is HERE at this level. But all are 100% both in the same clade and subspecies.

Hard to show in text only, lol. Hope this makes sense. All really good questions!
 

wellington

Well-Known Member
Moderator
10 Year Member!
Tortoise Club
Joined
Sep 6, 2011
Messages
50,728
Location (City and/or State)
Chicago, Illinois, USA
So, here is roughly how the PhD at the lab explained it to me (and it made sense to my somewhat rusty biochem degree brain). I asked if the 99% meant that there was some other subspecies mixed in. She said no, they are all 100% the T.h.kazachstani, but that within the subspecies, there are different clades, and within the clades, there are different haplotypes (noted in the case of my animals as D, E and F).

The "hybridization to the haplotype" means that for the one that is 99% D, there might be 1% of E in there, due to Bob the Russian tortoise's great great great great grandfather wandering a little further over to Judy's territory and mating with her. A haplotype is a cluster of genes that are inherited together.

If I were to break it down into a flow chart there would be:
Testudo horsfieldii (species)

Testudo horsfieldii kazachstani (subspecies)

Testudo horsfieldii kazachstani red clade (clade within subspecies)

Testudo horsfieldii kazachstani, red clade, haplotype D (or E, F, etc... I assume there are also A, B, C, but I don't have those) - so the possible variation that is being seen is HERE at this level. But all are 100% both in the same clade and subspecies.

Hard to show in text only, lol. Hope this makes sense. All really good questions!
Good explanation. Does make it more clear, thanks.
 

turtlesteve

Well-Known Member
10 Year Member!
Joined
Sep 23, 2012
Messages
727
The likely issue is that the lab is not getting a complete and perfect sequence, there are likely sequencing errors or gaps, etc. due to either the sample quality or the raw data. In other words, the most likely explanation is that 100% reflects a higher quality sample and better data. 98% is a lower quality sample / data. It doesn't necessarily reflect hybridization.

Was mentioned earlier but since mtDNA is maternal only, it is unaffected by hybridization. It will show the maternal lineage only.

Steve P.
 

biochemnerd808

Well-Known Member
10 Year Member!
Joined
Nov 3, 2012
Messages
1,463
Location (City and/or State)
Central Arkansas (we moved!)
The likely issue is that the lab is not getting a complete and perfect sequence, there are likely sequencing errors or gaps, etc. due to either the sample quality or the raw data. In other words, the most likely explanation is that 100% reflects a higher quality sample and better data. 98% is a lower quality sample / data. It doesn't necessarily reflect hybridization.

Was mentioned earlier but since mtDNA is maternal only, it is unaffected by hybridization. It will show the maternal lineage only.

Steve P.
Yes, very good point/clarification. Thanks for bringing this up, Steve. It was mentioned in the TTPG FB group, but not yet on here.

The lab uses mitochondrial DNA because it is very stable.

Important detail to note: Ideally, folks should have their wild-caught founder animals tested, then pair them up by subspecies, and keep good notes.

And I'll cast an eye at the postal system if the sample quality is blamed. It took over a month from when I collected the swabs until they isolated the DNA and sequenced it... thanks to sitting in customs for more than 3 weeks. Still, even 99% is conclusive. Thankfully, I don't plan to publish any big papers on this, so I'm content with the findings. :)
 

S2G

Active Member
Joined
Feb 21, 2021
Messages
118
Location (City and/or State)
AL
You know i don't think Ive ever seen a domed russian. I think every single one ive ever seen atleast in my part of the southeast have all been T.h.kazachstanica. There's ALOT around here. I dont feel comfortable doing the swab, but i definitely want to get the testing on my group. Now im curious about the shops near to see if they have any different subspecies.
 

jaizei

Unknown Member
Moderator
10 Year Member!
Joined
Feb 5, 2011
Messages
9,190
Location (City and/or State)
Earth
found it!


Thanks!

If you haven't discovered this yet, clicking the image and opening in a new tab removes photobuckets watermark. I think that's just there when the image is hot linked.
 

New Posts

Top