# Population genetics of the Amazonian tortoises, Chelonoidis



## N2TORTS (Aug 22, 2013)

Abstract. 
We conducted a population genetic analysis of the two Amazonian tortoises, Chelonoidis denticulata (n = 40)and Chelonoidis carbonaria (n = 39) in a region of sympatry within the XingÃº River basin. High levels of gene flow among sampled localities indicated lack of population structure for both species.



http://eco.ib.usp.br/labvert/population-genetics-chelonoidis.pdf


*Results
Population genetics analysis
A total of 40 individuals of C. denticulata from
four locations, and 39 individuals of C. carbonaria
from three locations (all except S1)
were analyzed. The 433 base pairs of the 5
end of the cytochrome b (cyt-b) sequences were
used for population level studies of the two Chelonoidis
species; *this region contained a total of
47 variable positions (table 1). A total of eight
haplotypes was found in C. carbonaria samples
and five in C. denticulata samples.*

Hummm........


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## Madkins007 (Aug 22, 2013)

Oh boy! Dueling studies!

Vargas-Ramirez, Mario and Jerome Maran, Uwe Fritz. "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?" Organisms, Diversity and Evolution, 2010.
http://www.fundacionbiodiversa.org/pdf/Mario/Vargas_2010_Chelonoidis.pdf

"Despite incomplete locality sampling, our results provide evidence for a subdivision of Chelonoidis carbonaria in genetically distinct, geographically vicariant populations, while C. denticulata seems to represent a more or less homogenous species. This suggests a marked correlation between habitat preference and phylogeographic differentiation."

In other words, there are at least five distinct variations between red-footed populations based on the DNA, which almost exactly matches up with Pritchard's and others field observations, as well as comments made by CDMay, etc. (Pritchard, Peter C. H. and Pedro Trebbau. Turtles of Venezuela (Contributions to Herpetology). SSAR, 1984. ISBN 0916984117.) 

Further- "It is obvious that the genetic structuring of C. carbonaria revealed in the present study not only calls for further research on geographic and taxonomic variation, but also for a reassessment of the conservation status of the distinct genetic units." 

Or... based on the DNA results, red-footeds should probably be broken into 2 to 5 different species, and that some of these species are in potential trouble.

Both studies mention the lack of good research on these species and this region, which is truly tragic considering the importance of regions like this to the entire world.


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## Baoh (Aug 22, 2013)

I would not make conclusions regarding validity of speciation via mitochondrial DNA analyses. Lineage and flow of mitochondrial DNA, sure, it has some value, but this is typically done because it is cheap, fast, and easy. Not because it is most thorough. Then there are SNPs, which also have their limitations as research tools (which is why one should not hang one's hat too heavily on services such as 23andme). Then there are whole chromosomes and entire genomes and these are slow and expensive processes by comparison, often requiring massive collaborative efforts despite the improvements in efficiency


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## Madkins007 (Aug 22, 2013)

Oh, come on Baoh! Split'em up! Split'em Up! Chant it with me!


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## N2TORTS (Aug 22, 2013)

Yupâ€¦.
To occupy a broad area with great environmental variations, the species present a great variation in morphological characteristics (Pritchard and Trebbau, 1984). According to Guix et al. (2001), apparently the variation in the scutelation pattern can be caused due to environmental changes. Breeding in captivity can lead C. carbonaria to the development of morphological, behavioral, and reproductive abnormalities when hatchlings originating from a region grow in other areas, environmentally diverse from the one where they were born, and it leads to the masculinization of females (Guix et al. 2001).


A considerable morphological variation in the tortoise population is commonly observed, although the quantification of this variation and the establishment of the evolutive processes that have shaped it are a very difficult task due to the complex interactions between the phenotype, locomotor development, and behavior (Delmas et al., 2007). These morphological variations may be caused by selection pressure or by ecological habits, such as predation. Additionally, the availability of food resources and even reproductive behaviors also seem to influence morphology (Morafka, 1982; Germano, 1993; Willemsen and Hailey, 2003). In this scenario, biometric analysis is important as it may provide information on the degree of divergence between species and populations (Leary et al., 2003; FernÃ¡ndez and Rivera, 2003; Lindeman, 2003; Boone and Holt, 2001).

http://www.scielo.br/scielo.php?pid=S1519-69842012000100018&script=sci_arttext


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## Madkins007 (Aug 22, 2013)

From what I can tell, this last paper (http://www.scielo.br/scielo.php?pid=S1519-69842012000100018&script=sci_arttext) focused on telling reds from yellows, not variation within reds. The tortoises they got were from a Brazilian zoo, and were likely mostly the Eastern/Brazilian forms (from Vargas-Rameriz's paper). The mention of Guix's paper (Guix, Juan Carlos, Daniel L. Fedullo and Flavio B. Molina. "Masculinization of captive females of Chelonoidis carbonaria (Testudinidae)" Rev. Esp. Herp. #15, 2001.) sort of reinforces that since his research was done on the Easterns as well. (Its been a while since I read this one, so I don't remember if I based that on the internal descriptions of the tortoises or where they came from.)

The score so far...
1. There is probably at least some hybridization between reds and yellows along the edges of the overlap territories. One possibility is that this allows them to better deal with changing conditions or exploit territories. The offspring usually do not show any special characteristics.
2. There seems to be one type of yellow-footed tortoise.
3. There may be as many as 5 kinds of red-footed tortoise.
4. DNA and physical characteristics can distinguish between reds and yellows... most of the time.
5. Reds show a lot of variation, some of which seems to be tied to locality.

As a person who has no special understanding of genetics or the terminology of that field, is this a decent summation of the papers so far as they apply to this discussion?


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## N2TORTS (Aug 22, 2013)

Sounds Perfect! 


Mark is this the Vargas paper? 
...............phylogeographies reflect distinct habitats?
http://www.iucn-tftsg.org/wp-content/uploads/file/Articles/Vargas-Ramirez_etal_2010a.pdf


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## Bryan (Aug 23, 2013)

I have a hard time believing that the Yellowfoots at the St. Louis Zoo are the exact same genetically as much smaller adults of different geographic populations. If this were the case then why don't we see 100+ lb. Carbonaria?


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## Yvonne G (Aug 23, 2013)

I moved the RF discussion off the Galap thread over to here:

http://www.tortoiseforum.org/thread-77833.html

I wasn't sure if THIS thread that you started, JD, continued the same discussion or not, so I didn't merge them. Should I put the other thread over here into this one?


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## Baoh (Aug 23, 2013)

Madkins007 said:


> Oh, come on Baoh! Split'em up! Split'em Up! Chant it with me!



I believe a thorough analysis would reveal aspects of what you are looking for (subspeciation, but not so much full speciation, for example), but I will wait for such work to be done (if it is ever done) and would prefer not to pre-conclude on this sort of topic.


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## Madkins007 (Aug 23, 2013)

In all honesty, I suspect that IF they split carbonaria, it will be into Northern and Southern, along habitat, plastron pattern, shell shape, and behavioral lines, then MAYBE sub-species a few of them out. 

A few years ago I was in low-level contact with a scientist from France who felt that there was already sufficient justification for at least two species, and had published along those lines. It appeared at the time that at least some academic circles, mostly in France, etc., were going that direction. I don't have enough contact with that sort of thing to know if it is still going on, or has faded out some.

But you are absolutely correct- this is all speculation and basically just messing around at this point.


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## cdmay (Aug 26, 2013)

Agree with both Madkins and BOAH. While it is tempting to pronounce that species or sub-species exist it is probably best to wait on the academics. When one examines what little passes for identifiable speciation in other taxa, it makes it all the more probable that these things exist within the genus _Chelonoidis._ I of course have my own beliefs.

Like Madkins though I have had discussions with notable people in the field (Pritchard, Buskirk, Harding, Vinkes, etc) and they uniformly agree that there are at least a couple of sub-species and possibly even a full species that can be identified--if only someone would do the work. The problem is that there are so many taxonomic issues to be dealt with in Herpetology and so very few people to do that work.


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