# zoological systematics evolutionary research



## John (Mar 18, 2011)

a rather lengthy and vrry scientific journal was put out in jan 2010 there is far too much info too type here so i will just put out the final conclusion for comment."hence, we conclude it is best to return to the situation before s.p.babcocki was revalidated:the usage of subspecies within s. pardalis should be abandoned".


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## Yvonne G (Mar 18, 2011)

Yes, a lot of people feel that way. The fellow who is in partnership with me on my turtles/tortoises argues that there are no subspecies of leopard tortoises. He's quite adamant. But the folks who believe they should be two different subspecies are also quite adamant. Just the fact that they have different looks as hatchlings tells me that they are different.


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## Robert (Mar 18, 2011)

squamata said:


> a rather lengthy and vrry scientific journal was put out in jan 2010 there is far too much info too type here so i will just put out the final conclusion for comment."hence, we conclude it is best to return to the situation before s.p.babcocki was revalidated:the usage of subspecies within s. pardalis should be abandoned".



Can you post a link to the article? Sounds pretty interesting. I'd like to read it. Thanks.


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## John (Mar 18, 2011)

actually the link was sent too me,have not seen danny hear in some time so i'll see what i can do to find it



emysemys said:


> Yes, a lot of people feel that way. The fellow who is in partnership with me on my turtles/tortoises argues that there are no subspecies of leopard tortoises. He's quite adamant. But the folks who believe they should be two different subspecies are also quite adamant. Just the fact that they have different looks as hatchlings tells me that they are different.


actually yvonne this journal is the findings of extensive dna testing it has nothing too do with range or apeasrances


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## Balboa (Mar 18, 2011)

The abstract for the article that Squamata is referring to can be found here:

http://onlinelibrary.wiley.com/doi/10.1111/j.1439-0469.2010.00565.x/abstract

Unfortunately its copyrighted material, so technically one needs to pay to view the entire article (or be a member of an organization with access, etc.)

The title for the article is "Mitochondrial phylogeography and subspecies of the wide-ranging sub-Saharan leopard tortoise Stigmochelys pardalis (Testudines: Testudinidae) â€“ a case study for the pitfalls of pseudogenes and GenBank sequences"

The article was really meant more as a critique of some of the methods currently utilized in genetic research. They point out the flaw in the previous study that had substantiated breaking the leopards into pardalis and babcocki.

There's fuel enough in this article for both sides of the debate.

Personally my take on it is somewhat as follows:
IF we are going to break down leopards by sub-species, there is much more work to be done. It would appear that there are more than two "sub-species". As it is currently set-up, pardalis is one (plus maybe a couple more) haplotypes, and babcocki is a waste-basket of everything else.

A more reasonable approach is to view all Leopards as one species, but recognize the distinctive Geographic Phenotypes that exist in the wild. More study needs to be done here as well. The Haplotype range map presented in the article correlates to some geographic differences in Africa over the range studied. This implies that some of the haplotypes may represent phenotypes adapted to differing environments. These animals may in fact require mildly different cares in captive conditions.

In other words at present Leopards from SE Africa and NE Africa are both considered "Babcockers", when in fact they have different genetics and different environments.


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## dmmj (Mar 18, 2011)

I wonder if the same could be applied to the 3 sub species of russians?


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## John (Mar 18, 2011)

Balboa said:


> The abstract for the article that Squamata is referring to can be found here:
> 
> http://onlinelibrary.wiley.com/doi/10.1111/j.1439-0469.2010.00565.x/abstract
> 
> ...



thanks for the help on this one brett.


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## Yvonne G (Mar 18, 2011)

dmmj said:


> I wonder if the same could be applied to the 3 sub species of russians?



I was thinking the exact same thing!! You know what they say...great minds, etc, etc!!


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## Kristina (Mar 18, 2011)

What about Redfoots too?


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## dmmj (Mar 18, 2011)

kyryah said:


> What about Redfoots too?


Are you talking about RF VS Cherry head? or NA and SA?


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## Kristina (Mar 18, 2011)

All of them. I have always found it odd that Redfoots are delineated into "locales" while Russians have ssp. I guess the same could be true for Leos. If Redfoots don't have ssp., then it makes sense that Leos could just vary according to "locale" as well.


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## dolfanjack (Mar 18, 2011)

The problem with scientist is they want to group things into neat little packages and nature just doesn't give a hoot about such things. Hear in the PNW some biologest want to seperate salmon not only by species but by individual river systems. A species might be abundent in many river systems but with declining salmon numbers in another river system so scientist want to close all the fishing for that species. Just my inflated two pennies. Jack


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## Balboa (Mar 18, 2011)

Good points on redfoots and russians.

The whole concept of sub-species is a major headache, just look at greeks, which is why I think a large part of science wants to abandon the whole practice. We're trying to differentiate critters and put nature in our clean little black and white organizational system when nature just doesn't play by those rules.

The "old-fashioned" defining practice of species has a much stronger test. If two critters can mate and produce viable off-spring (able to reproduce itself) its a species. If the off-spring is non-viable (sterile) they're a common genus. Nice and simple and substantiable. Beyond that you get into gray areas that you're trying to polarize.

I've had an innate resistance to the cherry-head are a sub-species so need to be maintained as such idea. Its similar to the western hermans and pardalis deal. Identifying these as sub-species gives scientific credibilty to maintaining them as "pure" lines, which creates a market for them due to rarity. This tends to de-value the "waste-basket" of all other members of the species, some of which may represent unique populations as well.

Scientifically they're all the same; a hermans is a hermans, redfoot is a redfoot, russian is a russian.

If the benefactors of a species wish to promote the maintenance of breeds representing geographical variation in the species, all the power to them. Preserve the diversity of nature. Just realize this may well fall more into the realm of human vanity than reality. A tortoise could likely care less where its parents came from, just as I could care less that I'm a mutt, with blended lines from all over Europe and outside as well. I appreciate that genetic diversity embodied in me.


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## dmmj (Mar 18, 2011)

Regarding russians I seem to recall egyptiandan saying the different subspecies can't breed with each other, I could be wrong. Regarding RF's don't the cherry heads come from regular RF's or am I mistaken on that?


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## Balboa (Mar 18, 2011)

HAHA, Jack beat me to the punch and put it better.

Dave, the cherryheads actually do come from a different region than "the redfoots". Cherryheads are primarily south of the Amazon Rainforest, the redfoots to the north of it. The western edge is a whole 'nother bag of arguments.


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## Madkins007 (Mar 18, 2011)

A few points of clarification.

Human labels on animals do not change the nature of the animals. It is just an attempt by us to better understand the relationship of animals- what is related to what and how closely. It is not the relationships that are changing as we make things into species, sub-species, etc.- it is our understanding of that relationship.

The idea is indeed that all members of a species can freely and successfully interbreed- whether it is a subspecies of the species, or a race, breed, etc. If two subspecies CANNOT successfully breed, then one of them is in the wrong species category.

Appearance or even behavior is not enough to make a species or subspecies- ALL pet dogs are the same species and there are no subspecies, but breeds breed true, and freely interbreed with every other pet dog. You can tell a dog's breed by looking at it even as a baby.

In Red-foots, the DNA evidence STRONGLY suggests that all Yellow-foots are one species (just had to say that to get it out in the open.) Then, Red-foots show 5 different DNA groups, similar to but not exactly like the sticky note about the Races of Red-foots...
- NORTHERN (PANAMANIAN)- from Panama to the Andes in Venezuela
- NORTH-EASTERN (COLUMBIAN)- Obviously in Columbia. This one surprised me- I don't think anyone had previously suggested this group before.
- NORTH-WESTERN (GUYANAN)- Venezuela to Brazil along the northern coast. This is the 'typical Red-foot'
- EASTERN (BRAZILIAN)- Eastern Brazil, home of the Cherry-head, but there are also yellow-headed tortoises in this group that are otherwise just like the Cherry's
- SOUTHERN (GRAN CHACO)- Paraguay and Bolivia

(Info from "VARGAS-RAMIREZ, Mario; Maran, Jerome; Fritz, Uwe. "Red- and yellow-footed tortoises, Chelonoidis carbonaria
and C. denticulata (Reptilia: Testudines: Testudinidae), in South American savannahs and forests: do their phylogeographies reflect distinct habitats?" which can be found at http://www.fundacionbiodiversa.org/pdf/Mario/Vargas_2010_Chelonoidis.pdf. GROUP NAMES are from his paper. (NAMES IN PARENTHESIS) are the ones I use in the Tortoise Library. There is a map at http://www.tortoiselibrary.com/range.html)

This paper and others on Red-foot DNA also point out some other interesting elements, like the DNA of Red-foots does not really enter the forested regions that Yellow-foots prefer- in other words, there is one big blob of Yellow-foot DNA, but 5 'islands' of Red-foot DNA that do not mix naturally because they don't enter the forest to visit other islands.

It is likely that when the Red-foot DNA comes up for peer reviews and discussion by the proper committees, that there will end up being at least a couple new species out of it- maybe 2 species and 2-3 subs for each. More likely, however, given the current trend to eliminate official subspecies- 5 different species.


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## onarock (Mar 18, 2011)

Mark, do they know the % of genetic difference between the 5?


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## dolfanjack (Mar 18, 2011)

And then you have seperate but closely related species that can breed with one another creating (fertile) hybrids that can then reproduce with each other or back to their parents. Botanist had a heck of a time in the 1800's naming North American pitcher plants there was so much back crossing.


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## egyptiandan (Mar 18, 2011)

It's available free  http://www.iucn-tftsg.org/wp-content/uploads/file/Articles/Fritz_etal_2010a.pdf

Some neat tidbits  There is nothing scientific about genus'. They are just a convient place to put like species. Our understanding of "species" goes out the window with the lower vertebrates. The Asian turtles are a prime example. Almost every asian species will hybridize with any other and 99 percent of the time they are fertile. I'm not talking animals of the same genus, but different genus. So our neat packaged idea about a species doesn't seem to fit the lower vertebrates. 

Danny


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## Saloli (Mar 18, 2011)

if they look different, do their mating rituals differ? if so chances are they are different. which paper are we refering to? can you please send me a copy i'd like to read it


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## egyptiandan (Mar 18, 2011)

Click on the link in post #19 

Danny


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## John (Mar 19, 2011)

I don't think you can really judge by looks of these animals,the paper is based on dna analysis,it is not uncommon in the reptile world for one species too adapt itself too a slightly different environment,be it either appearence or behaviour,but if all the different animals throughout the range can be linked back than it is one species.

I don't see this nothion as being far fetched.look at for example the eastern box turtle,it has a very large range and it my state alone it lives in several different habitats,its shell colorations and patterns can differ throughout its range,i find them in dry areas,swampy meadowlands,dense woodlands,open grasslands,bogs.and several can look very unique when compared too other specimens.so are they different subspecies?or is it one species adapted too live in different habitats?


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## John (Mar 19, 2011)

I guess this should be moved from the debate section too the general section.hey mods can ya do it?


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## Madkins007 (Mar 19, 2011)

squamata said:


> I don't think you can really judge by looks of these animals,the paper is based on dna analysis,it is not uncommon in the reptile world for one species too adapt itself too a slightly different environment,be it either appearence or behaviour,but if all the different animals throughout the range can be linked back than it is one species.
> 
> I don't see this nothion as being far fetched.look at for example the eastern box turtle,it has a very large range and it my state alone it lives in several different habitats,its shell colorations and patterns can differ throughout its range,i find them in dry areas,swampy meadowlands,dense woodlands,open grasslands,bogs.and several can look very unique when compared too other specimens.so are they different subspecies?or is it one species adapted too live in different habitats?





So far, almost all true Eastern Box Turtles tested have the same basic DNA, although there is some interesting stuff going on in that group, with the larger Gulf Coast Box being considered as a separate species. (Based on a program given by Joseph Collins.) 

Taxonomy is a really odd science. It is really interesting, but can get really confusing.


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## Saloli (Mar 19, 2011)

yeah i agree about taxonomy. it can be confusing. many species are seperated not by major genetic or physical differences but behavioral differences take for example the Lake Malawi Cichlids or some of the Chorus Frogs some of which are so simalar genetically and physically yet don't normally breed because females don't recognize male's calls. then there are the parthenogenic species like some of the race runner lizards or the Amazon Mollies. from what i've read the gulf coasts are being considered not a seperate species but a intragrade between carolina and putnami at least those in florida panhandle which would mean no subspecieces status but would mean that they are descended from the oldest known lineage of carolina. here is an article if you want to read it it can be baught "Morphological and molecular evidence indicates that the Gulf Coast box turtle (Terrapene carolina major) is not a distinct evolutionary lineage in the Florida Panhandle"
JASON M. BUTLER1, C. KENNETH DODD jr1, MATT ARESCO2, JAMES D. AUSTIN1,*Article first published online: 14 MAR 2011

here is a book (herpetological) on Terrapene North American Box Turtles: A Natural History C. Kenneth Dodd
p.s. i know a little of topic

if you can direct me to the info from Collins if not a contact for him thanks


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## John (Mar 20, 2011)

onarock said:


> Mark, do they know the % of genetic difference between the 5?



hey paul thats it iremember now. pitcher plants


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## Terry Allan Hall (Mar 20, 2011)

Balboa said:


> Good points on redfoots and russians.
> 
> The whole concept of sub-species is a major headache, just look at greeks, which is why I think a large part of science wants to abandon the whole practice. We're trying to differentiate critters and put nature in our clean little black and white organizational system when nature just doesn't play by those rules.
> 
> ...



I tend to agree w/ your observations, but remember that controversy recently over the concept of "Designer tort6oises"?


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## John (Mar 20, 2011)

i also found it very interesting that throughout the range fecal samples tested showed that although the same food was available for the most part,specimens from different regions seemed too be consuming different diets.


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## Balboa (Mar 20, 2011)

Terry Allan Hall said:


> I tend to agree w/ your observations, but remember that controversy recently over the concept of "Designer tort6oises"?



Trust me, that was keenly on my mind and has been ever since.


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## Madkins007 (Mar 20, 2011)

Saloli said:


> if you can direct me to the info from Collins if not a contact for him thanks



It was during a talk at the local herp club about a year or so ago. I don't recall his exact words, and most of the program was on snake taxonomy, but part of the conversation was about how unusually big this group is compared to most _T. carolina_. 

However, he is one of the heads of the Center for North American Herpetology- http://www.cnah.org/ 

Joseph T. Collins
Kansas Biological Survey
2101 Constant Avenue
The University of Kansas
Lawrence, Kansas 66047
(785) 393-4757 (cell)
[email protected]


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## Terry Allan Hall (Mar 20, 2011)

Balboa said:


> Terry Allan Hall said:
> 
> 
> > I tend to agree w/ your observations, but remember that controversy recently over the concept of "Designer tort6oises"?
> ...


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## HLogic (Mar 20, 2011)

Something to consider... The DNA testing performed most often is on mitochondrial DNA. mtDNA provides a convenient mechanism to determine relationships among relatively closely related specimens due to its mechanism of transmission, the stability of the tranfer and its relative instability subsequently. This reduces to having a nice neat little package of DNA that can easily be traced and compared to show the 'distance' between one specimen and another.

Nuclear DNA is far more complex. Its transfer (half from each parent), subsequent recombination (shuffling) and it's relative stability make for a much more difficult analysis and initially less indicative of the 'distance' under investigation.

With that said, DNA research, at the level of interest, is a rather young science (DNA was only discovered in the late 1800's and its function was unknown until the early 1950's). Only in the last 30 years or so have we had the technology to test it in any usable way. Fruitflies are well known, many bacterial pathogens have been mapped, the human genome was finally mapped in 2003 but most other species have not been touched. It takes considerable time, determination and of course, money, to perform these analyses. Additionally, reptiles are not the top priority of most researchers, universities, pharmacological manufacturers or anyone else but us...

So, using a relatively new technique to perform a partial analysis of a relatively small percentage of the genetic material available is certain to leave many gaps in the determination of what is and what isn't. Also, little thought is given to processes in flux (e.g. perhaps babcocki & pardalis are in the process of subspeciation). 

We have a tendancy as humans in most cultures to want to identify, categorize and separate one thing from another. Scientists are insanely bent on that pursuit (for the most part). Until the techniques, methods and understanding of the processes of speciation are better known and perhaps a redefinition or refinement of taxonomy; we will continue to have a questionable division of taxonomic structure and many changes forthcoming. Putting things in boxes is not a bad concept but we really don't know how many boxes there are, what belongs in which box or where each box belongs in the big stack of boxes known as taxonomy.


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## Saloli (Mar 21, 2011)

yeah i know who he is. thanks for the contact.

you have to keep in mind which type of classification is being used Linnean or Cladistic because there are differences.


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