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Author Topic:   How do you tell one species of turtle from another?
Percy
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Posts: 22391
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 1 of 16 (771197)
10-22-2015 9:08 AM


It was reported today that a New Tortoise Species In The Galapagos Islands Went Unidentified For More Than A Century, based upon the recently published paper Description of a New Galapagos Giant Tortoise Species (Chelonoidis; Testudines: Testudinidae) from Cerro Fatal on Santa Cruz Island. What was thought to be a single species of turtle is actually two different species.
The species identification was performed using DNA analysis, but I'd like to understand how they were able to tell from DNA samples alone that they were different species. Yes, they identified different evolutionary lineages, but do they actually know that this new species of turtle does not and perhaps cannot breed with the old? I mean, even if one turtles' DNA was made of ooblick, if they could freely interbreed it would mean they're the same species, but I could not find in the paper where they ever address this issue ( I did not carefully read the paper - I confess to scanning it and doing a number of searches for word fragments like "inter", "breed", "egg", "fertil", etc. -). Or are they perhaps using some DNA bookkeeping criteria for determining species that ignores interfertility of populations?
I put this here in Coffee House because it isn't related to creation/evolution, and because it's really just a question, though probably not a simple one.
--Percy

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 Message 5 by Blue Jay, posted 10-22-2015 11:29 AM Percy has replied
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NosyNed
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Posts: 8996
From: Canada
Joined: 04-04-2003


Message 2 of 16 (771201)
10-22-2015 9:26 AM
Reply to: Message 1 by Percy
10-22-2015 9:08 AM


Wild Ass Guess
I gots no real clue. But I was a consultant and had to be good at making up plausible sounding answers .
I'm guessing that by looking at the genomes they decided that there was no gene flow between the two populations.

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NoNukes
Inactive Member


Message 3 of 16 (771202)
10-22-2015 10:02 AM
Reply to: Message 1 by Percy
10-22-2015 9:08 AM


Yes, they identified different evolutionary lineages, but do they actually know that this new species of turtle does not and perhaps cannot breed with the old?
The paper gives a discussion of the reasons for the classification by DNA of the turtles as different species. The rationale does not include any consideration of interbreeding. The idea expressed in the article is that the different species have had little to no gene flow between them, and the time of divergence is expressed in millions of years in the past as opposed to being of recent vintage.
quote:
Each of the two taxa have numerous private alleles, implying very little recent gene flow, and they are as genetically divergent from each other as the other named species are from one another [11, 13, 20]. Previous studies have also revealed the existence of a limited amount of introgression between the two taxa [11, 13, 20], which is not unexpected given their geographical proximity.
I take this sentence to mean that the two taxa can interbreed, but that they have genetic divergence on the order/magnitude that we find between species under the current classification system.
Or are they perhaps using some DNA bookkeeping criteria for determining species that ignores interfertility of populations?
Yeah, that seems to be what is going on. I would add though that the kind of genetic separation involved probably would not exist if there were unrestricted interbreeding.
Edited by NoNukes, : No reason given.
Edited by NoNukes, : No reason given.

Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)
History will have to record that the greatest tragedy of this period of social transition was not the strident clamor of the bad people, but the appalling silence of the good people. Martin Luther King
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Percy
Member
Posts: 22391
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 4 of 16 (771204)
10-22-2015 11:02 AM
Reply to: Message 3 by NoNukes
10-22-2015 10:02 AM


NoNukes writes:
quote:
Each of the two taxa have numerous private alleles, implying very little recent gene flow, and they are as genetically divergent from each other as the other named species are from one another [11, 13, 20]. Previous studies have also revealed the existence of a limited amount of introgression between the two taxa [11, 13, 20], which is not unexpected given their geographical proximity.
I take this sentence to mean that the two taxa can interbreed, but that they have genetic divergence on the order/magnitude that we find between species under the current classification system.
This is very interesting. It tells me that at least in some realms of biology they might not know the degree of genetic interfertility when they make the determination of different species. These two turtle species could, as far as the scientists know, be 100% genetically interfertile, with the low introgression due to other factors like geography, behaviors, etc.
I expected that genetic interfertility would have counted for more. I'm a little surprised. But maybe it makes sense. It must be hard to measure objectively and accurately. And whether the DNA molecules of two separate populations continue to play nicely together must include large elements of chance, so maybe it's reasonable that genetic interfertility not play a significant role.
Thanks.
--Percy

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Blue Jay
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Posts: 2843
From: You couldn't pronounce it with your mouthparts
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(2)
Message 5 of 16 (771206)
10-22-2015 11:29 AM
Reply to: Message 1 by Percy
10-22-2015 9:08 AM


Hi, Percy.
Percy writes:
Or are they perhaps using some DNA bookkeeping criteria for determining species that ignores interfertility of populations?
It's basically this. If you look at Fig. 2A, you can see that the two populations from Santa Cruz island (the orange and red blocks) resolve at very different locations on the phylogenetic tree.
They're apparently not even sister groups: the Cerro Fatal population's is most closely related to a population from Cristobal Island, which is considered a separate species (Chelonoidis chathamensis); and the La Reserva population is most closely related to a population from Fernandina Island, which is also considered a separate species (C. phantastica).
When you classify species by genetic analysis, the only real criterion is consistency: if the Cristobal and Fernandina populations are considered separate species, then, to be consistent, these two Santa Cruz populations should also be considered separate species. The alternative is to reshuffle all the currently-accepted species into an alternative arrangement (for example, looking at Fig 2A, you could argue that there are really only 3-4 different "primary" lineages), but elevating one population to a new species is less work and less confusion than trying to reassign everything.

-Blue Jay, Ph.D.*
*Yeah, it's real
Darwin loves you.

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Percy
Member
Posts: 22391
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 6 of 16 (771215)
10-22-2015 12:57 PM
Reply to: Message 5 by Blue Jay
10-22-2015 11:29 AM


Thanks. That's even more detailed and makes it more clear.
This is still sort of beside the point, but it still doesn't feel right to me to ignore genetic interfertility. Say we had some standard measure of genetic interfertility. Say we took 100 sperm of one species and 100 eggs of another. Then we mixed one sperm and one egg and see if we achieved fertilization. We repeat this for the remaining 99 sperm and eggs. Then we do the same again, but this time with 100 sperm of the other species and 100 eggs of the other other species. From this we get a measure of genetic interfertility. Or imagine any other way you like of obtaining this number, the point is that we develop a way of measuring the genetic interfertility between two different species.
So we've classified C. chathamensis and C. phantastica as two different species, but if we don't know to what degree they're genetically interfertile, how much sense does it make to say that?
--Percy

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Blue Jay
Member (Idle past 2697 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 7 of 16 (771228)
10-22-2015 2:52 PM
Reply to: Message 6 by Percy
10-22-2015 12:57 PM


Hi, Percy.
Percy writes:
So we've classified C. chathamensis and C. phantastica as two different species, but if we don't know to what degree they're genetically interfertile, how much sense does it make to say that?
It's just a matter of deciding whether the product you get from using rigorous, experimentally-derived standards like interfertility would be substantially more useful and informative than a product based on something less intellectually pure but more logistically viable.
Ultimately, a species designation is a hypothesis about the population's evolutionary history and genetic isolatoin. Experimentation to test those hypotheses would be the intellectually pure thing to do, but when you consider how resource-intensive it would be, and the high likelihood that it will only be really useful to a very narrow range of academics, you can kind of guess that it's a low priority.

-Blue Jay, Ph.D.*
*Yeah, it's real
Darwin loves you.

This message is a reply to:
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NoNukes
Inactive Member


Message 8 of 16 (771232)
10-22-2015 3:26 PM
Reply to: Message 6 by Percy
10-22-2015 12:57 PM


So we've classified C. chathamensis and C. phantastica as two different species, but if we don't know to what degree they're genetically interfertile, how much sense does it make to say that?
Is the lack of sense because you are trying to force fertility into the definition? Perhaps your definition is not flexible enough to capture actual usage of the term.
From the wikipedia article on species.
quote:
in biology, a species (abbreviated sp., with the plural form species abbreviated spp.) is one of the basic units of biological classification and a taxonomic rank. A species is often defined as the largest group of organisms where two hybrids are capable of reproducing fertile offspring, typically using sexual reproduction. While in many cases this definition is adequate, the difficulty of defining species is known as the species problem. Differing measures are often used, such as similarity of DNA, morphology, or ecological niche.
If inter-fertility is not a hard and fast part of the definition, then that would seem to address the question you ask about making sense.

Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)
History will have to record that the greatest tragedy of this period of social transition was not the strident clamor of the bad people, but the appalling silence of the good people. Martin Luther King
If there are no stupid questions, then what kind of questions do stupid people ask? Do they get smart just in time to ask questions? Scott Adams

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RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(3)
Message 9 of 16 (771239)
10-22-2015 4:42 PM
Reply to: Message 8 by NoNukes
10-22-2015 3:26 PM


Functional isolation is all that is needed for evolution
Is the lack of sense because you are trying to force fertility into the definition? Perhaps your definition is not flexible enough to capture actual usage of the term.
Curiously I find I am moving away from a strict infertility definition to one of functional non-breeding, especially where behavior (bird song) or timing (morning vs evening) or breeding location (return to different locations) isolates members of one group from the other reproductively.
Certainly we see things like lama and camel hybrids being possible, so they are not reproductively isolated, it is just rather impractical to consider that they would find a way to interbreed.
Functional isolation -- whatever causes the loss of gene flow -- is all you need for independent natural selection of different mutations to occur and cause differentiation between populations; the groups that don't interbreed won't care whether they are or are not interfertile.
"Species" is a human contrived artificial concept, so if the definition is not as useful in one situation as in another, then we should review the definition.
Enjoy

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Rrhain
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Posts: 6351
From: San Diego, CA, USA
Joined: 05-03-2003


(2)
Message 10 of 16 (771260)
10-22-2015 9:57 PM
Reply to: Message 1 by Percy
10-22-2015 9:08 AM


Percy writes:
quote:
I mean, even if one turtles' DNA was made of ooblick, if they could freely interbreed it would mean they're the same species
No, it wouldn't. Ring species show that the concept of species is more complicated. Indeed, the inability to breed is a sign of being different species, but just because you can breed doesn't mean you're the same species. Reproductive isolation can also include breeding processes that isolate populations.
I'm not saying that your concerns aren't valid, but I'm assuming that the authors know about this and thus their genetic analysis would be made with that knowledge.

Rrhain

Thank you for your submission to Science. Your paper was reviewed by a jury of seventh graders so that they could look for balance and to allow them to make up their own minds. We are sorry to say that they found your paper "bogus," specifically describing the section on the laboratory work "boring." We regret that we will be unable to publish your work at this time.

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Percy
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Posts: 22391
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 11 of 16 (771290)
10-23-2015 4:12 PM
Reply to: Message 7 by Blue Jay
10-22-2015 2:52 PM


Blue Jay writes:
It's just a matter of deciding whether the product you get from using rigorous, experimentally-derived standards like interfertility would be substantially more useful and informative than a product based on something less intellectually pure but more logistically viable.
Sure, the species problem, as NoNukes reminds us.
So interfertility is one way of looking at species, as in a population. A population, a group of mutually interbreeding organisms, is all the same species. And the overalll population of tortoises on Santa Cruz island is mutually interbreeding (unfortunately, to some unknown extent), and therefore they're all the same species. By that way of looking at it.
But by the genetic way of looking at it, they're different species.
These two ways (and more) of defining species have been discussed here before, but that article seemed to be saying, "They *are* two different species," and hence my question, which I might rephrase like this: When did genetics win out as *the* determining factor in determining species?
It didn't, of course, and even though they're geneticists writing from a genetics perspective it still doesn't seem right that they should completely ignore interfertility.
--Percy

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NoNukes
Inactive Member


(1)
Message 12 of 16 (771291)
10-23-2015 8:20 PM
Reply to: Message 11 by Percy
10-23-2015 4:12 PM


These two ways (and more) of defining species have been discussed here before, but that article seemed to be saying, "They *are* two different species,"
To be completely fair to the article authors, the rationale for saying that the turtles are of different species is given in the article. The rationale given boils down to saying that the genetic differences are greater than the differences between other groupings of turtles which are already designated as different species.
The other thing to note is that regardless of the degree of certainty expressed in the article, what is written is the opinion of the authors. My inclination is to agree with their rationale, but the designation of species and sub species is somewhat in the eye of the beholder.
ABE:
I took a look at the wikipedia classification on birds, not only are there interfertile species of birds, there are bird hybrids formed from pairs of birds that are classified as different genii and different families although the latter is described as rare.
Edited by NoNukes, : No reason given.

Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)
History will have to record that the greatest tragedy of this period of social transition was not the strident clamor of the bad people, but the appalling silence of the good people. Martin Luther King
If there are no stupid questions, then what kind of questions do stupid people ask? Do they get smart just in time to ask questions? Scott Adams

This message is a reply to:
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RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


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Message 13 of 16 (771310)
10-24-2015 8:52 AM
Reply to: Message 11 by Percy
10-23-2015 4:12 PM


It didn't, of course, and even though they're geneticists writing from a genetics perspective it still doesn't seem right that they should completely ignore interfertility.
Is there a selection benefit to infertility?
Is there a reason\cause that would always end in infertility over generations of isolation?
Does infertility play a role in mate selection? Species mate recognition?
If the answers to these questions are no, then perhaps we need to look at the definition rather than try to force it in all situations.
Sure if two populations cannot interbreed we can be sure they are different species, but if two populations consistently fail to mate due to mate preferences doesn't that result in the same gene isolation?
If infertility only occurs through random mutations that are selected for other purposes and not to cause infertility between groups, then actual infertility is a random process, while mate selection preferences are a consistent selection process, ongoing in every generation.
So I would say that lack of gene flow is sufficient to define species as a separately, independently evolving group -- which is what is the critical point for macroevolution to proceed.
Birds are a great example of how mate selection can cause gene isolation via behavior (mental incompatibility) versus physical incompatibility, but we also have lions and tigers and other examples that have been classically defined as different species even though it is possible to interbreed them.
There are also cases of cryptic species that appear similar but don't interbreed. The mosquito that carries malaria has a cryptic sister species that doesn't. They look alike but one population breeds in the morning and the other breeds in the evening, and thereby became genetically separate.
Now we could nitpick and say that behavioral isolation just means we have an incipient species and that they aren't fully a new species until we have infertility; but we can also say that we have speciation for all intents and purposes, as the result is the same as far as evolution is concerned.
Enjoy
Edited by RAZD, : ..

we are limited in our ability to understand
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This message is a reply to:
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Percy
Member
Posts: 22391
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


(1)
Message 14 of 16 (771315)
10-24-2015 11:13 AM


Replying to everyone...
I guess the conclusion to draw from this short thread is that one must keep clearly in mind how vague a term is species. Not only is there the species problem where science attempts to describe the real and messy world, but many of our discussions focus on an idealized conception of species where we concoct scenarios that evolve them in unambiguous directions of our own invention. The reality is very messy. Moving back and forth between threads discussing hypothetical scenarios and threads discussing the real world can result in a cognitive whiplash.
But beyond that, even after I read through all the details of genetic differences in the paper about the Santa Cruz tortoises (again, in the interest of full disclosure, I've only skimmed through much of it) I'm still left wondering what threshold of degree of difference in the two turtle populations was surpassed? We get diagrams like this chock full of information:
These provide a strong impression of how different the proposed species are, but what are the objective criteria for the amount of difference that makes a different species? Looking at the paper's Discussion section, a key part of their rationale for the Santa Cruz tortoises being two different species involves genetic distance, but they qualify that approach by saying, "Using genetic distance values for species delimitation is not a practice we ascribe to because of its several flaws." But they use it anyway because "the two Santa Cruz taxa are as divergent for both types of genetic markers as other named Giant Galapagos tortoise species." Well, okay, but how good is the scientific support for the classification as separate species for those other Giant Galapagos tortoise populations?
--Percy

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AZPaul3
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Message 15 of 16 (771343)
10-24-2015 7:45 PM


All you need do is turn the turtles over and look at the bottom side. Those that say "Producto de Mexico" are a different species from the ones that say "Febrique en Indonesia".

  
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