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what makes a species?


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#21 Guest_fundulus_*

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Posted 26 February 2011 - 09:19 AM

Of interest to the discussion. Gray tree frog Vs. Cope's gray tree frog. http://en.wikipedia..../Gray_tree_frog Visually identical,different calls, cannot interbreed due to differing number of chromosomes.

Yeah, that would be a classic prezygotic reproductive isolating barrier, a "gametic" barrier to reproduction.

#22 Guest_mikez_*

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Posted 26 February 2011 - 02:38 PM

No, I'd say that species are real and exist in nature. But they don't arise, and remain separate, the same way(s).


Right, I agree with that, which does not contadict what I said earlier. The problem is finding a definition that includes all the ways they arise and remain separate without contradicting itself.

Where I get confused is where you hear people say a certain wide spread group that is considered a species but displays profound variation both regionally and locally is actually a "group" of species.
And then you get into defining a sub-species which gets even uglier.
I've seen the multi-page flame wars go on and on about whether sub-species even should be recognized at all. :tongue:

#23 Guest_fundulus_*

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Posted 26 February 2011 - 03:53 PM

Mike, we're looking at the same thing really. There are at least 23 well-defined species concepts, which reflects the diversity of life and what kind of evidence is available for us as humans to interpret what's going on. The species question is the central question in biology; if we don't know what we're looking at, what the use is something like ecology or biodiversity, because what are comparing to what?

#24 Guest_mywan_*

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Posted 27 February 2011 - 12:13 AM

The problem is finding a definition that includes all the ways they arise and remain separate without contradicting itself.

It is my contention that this is logically impossible, even in principle. It does not destroy the utility of the species concept, but self contradiction of any possible choice of definitions remains. It may even be worthwhile to formulate this mathematically to prove the impossibility.

So long as you expect the species concept to have the logical property that if set {A} is a member of the set {B} and set {B} is a member of set {C} then set {A} must be a member of set {C}, principle of bivalence, then any possible definition of species MUST violate this property. This is a direct result of the common descent of all species.

The species concept technically qualifies as a "fuzzy set". Fuzzy sets are allowed the "grades of membership", x ∈ A, m(x), required to deal, at least in part, with the ring species example but still maintains a fatal flaw with respect to species. That is that ANY predefined grade of membership will result both in differing species being grouped together and the same species being designated as differing species. The non-linearities in the differing speciation mechanisms insures that "grades of membership" must be a variable (not constant) with respect to the grade of membership designating a differing species. Hence no predefined definition of species will ever avoid self contradiction.

The search for a species definition as quoted above is as pointless as perpetual motion.

#25 Guest_mywan_*

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Posted 27 February 2011 - 02:21 AM

The species question is the central question in biology; if we don't know what we're looking at, what the use is something like ecology or biodiversity, because what are comparing to what?

The impossibility of a non-contradictory definition of species does not limit our capacity to know what we are comparing. When we consider a single specimen we can only determine its identity relative to the rest of its species withing certain error bars. The human genome project did not map a genetic sequence that is valid for any living human. Rather it took an average over many individuals. Hence any given individual is going to deviate from that norm, and even the average will vary over time. It also happens that differing species can genetically differ by less than the differences between members of a singular species. Yet this does not prevent us from knowing what we are looking at, because when this happens we know for a fact that these species are very closely related.

It is not the particular species that tells use, except very generally, what we are looking at. Rather it is a progression of deviations (error bars of individuals from the norm) over time. The norm never stays completely put from generation to generation. Speciation is the most general sense defines a bifurcation point in which th gene flow between two groups is essentially stopped. Yet whether speciation has occurred or not has no bearing on our capacity to see by what degree two groups has diverged. Whether or not speciation of the Ensatina salamander had occurred at the south end of the valley yet or not has no bearing on our capacity to see how closely related they are. They could have diverged more without speciation or less with speciation, it makes no difference. We still know how closely related they are, and essentially how much time they have been diverging with or without a speciation event. We still know exactly where they are on the tree of life with or without a species label. The labels just allows us to quickly zero in on the neighborhood of the tree of life some specimen is on. Differing species does not always designate a variance in a group membership greater than the variance between members of a single species. But it does 'always' tell use where in the progression of the tree of life it belongs with minimal error bars.

Biodiversity is as important within species as it is to the range of species. The toxin resistant tomcod in a recent thread here was the result of a gene that less than 10% of the initial tomcod population possessed, and fewer still that expressed this gene sufficiently to offer any significant toxin resistance. It would be a mistake of the first order to conflate species diversity with biodiversity. Biodiversity within species is paramount to the survival of species. So to say that the species concept is required to know what you are looking at overlooks the most important variables to the long term survival of any given species, and to life in general.

The reason species is a vitally important concept is that it defines the bifurcation points at which the biodiversity within a species can be multiplied out into multiple groups, ecological niches, survival strategies, etc. Two closely related species lacking biodiversity within the species is less diverse that one species with a healthy in-group biodiversity. If for no other reason this is sound reason to accept the limitations of the species concept, and not place undue importance in defining species as the sole determinant of biodiversity or specimen identity.

Not only is species not requires to know what we are looking at, placing that kind of importance on the species concept undermines the understanding of the long term survival needs of any given species.

#26 Guest_fundulus_*

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Posted 27 February 2011 - 11:08 AM

OK, you're pushing for the equivalent of voodoo economics in biology. That's all I can really say. Peace, out.

#27 Guest_mywan_*

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Posted 27 February 2011 - 02:55 PM

I am starting to feel like I might survive again after a bout with a virus, so I will use microbiology as an example.

I will explain exactly why not only is it not voodoo biology, but the converse is, in the same way Sci-Fi movie mutations are. It would be useful to consider the situation in microbiology. With most species there is an extremely high degree of constancy over our lifetime, or even since the development of science itself. Speciation in microbiology effectively mirrors the rest of biology, except over time spans we can actually observe. So, unlike the rare instances of ring species and other such species concept issues, we can actually watch the entire progression in microbes and these rare event become ubiquitous. This makes it far more common for microbiologist to deny the usefulness of the species concept. So what are the rules of thumb for defining species that have developed in microbiology?

It basically comes down to: if the similarity between gene sequences are closer than about 97% then they are checked by DNA-DNA hybridization to see if they are the same species or not. Note how this approach applied universally would define lions and tigers as the same species. The 3% deviation corresponds to the "grade of membership" I described previously as defined by "fuzzy sets" (wiki link), (original paper link). Yet this DNA-DNA hybridization test is due to the very fact that species cannot be determined by grades of membership.

Hence far from being "voodoo biology", it is an 'empirical' fact of biology. Speciation events are almost never defined by singular mutation events or as any set of events defined at even a roughly singular point in time.

Some (condensed) history of the species concept:
The binomial classification we now use was developed well before Darwin's Origin of Species. The definition in use at the time was outlined by John Ray, which was an extension to biblical "kinds". It was characterized by the idea that species always produced the same species and these species were permanently fixed. So when Darwin published On the Origin of Species it immediately lead to a crisis in the validity of the species concept. Because in any transition from one species to another there must be some period of time in which there is no objective fact of the matter whether there was one or more species. This continued till the modern synthesis of Mendel's inheritance theory was combined with Darwin's, from which a more modern view of species began to develop. Most strongly with the Biological Species Concept (BCS) as outlined by Ernst Mayr.

Now note how Ernst Mayr's BCS was geared around groups (sets) that reproduce with each other and are reproductively isolated from other groups. Hence there was no specification of how divergent two groups must be by any quantitative measure. Reproductive isolation, such that the two groups evolved independently, was the determining factor. This is very effective in almost all cases over the lifetime of our observations. Only a few special cases relative to the total are problematic, unless you look at it over many millennia or dealing with very short generations as in bacteria. Then that random variability in defining where in the 3% deviation speciation occurs becomes problematic, except by case by case testing.

The exceptions in higher order animals, although rare relative to the total, still constitutes a large group of exceptions. Consider the Ensatina salamanders. Although the two groups at the south end cannot interbreed they are not strictly speaking reproductively isolated, as given sufficient time offspring from one group can through several generations have offspring that breeds with the other group. So under the BCS model the two non-interbreeding groups of salamanders are still the same species. This also violates the legitimacy of the species rules used in microbiology, as intermediaries are by definition removed by the testing procedure in that case.

Why species are important, even without the possibility of a non-contradictory definition:
Species defines a bifurcation point where reproductive isolation allows the divergence or biodiversity to exceed what is possible for a singular species, in which the variability is limited by gene transfers and the need to remain mutually compatible reproductively. Hence speciation is of paramount importance to the diversity of all life. Something this important cannot be ignored by biologist, regardless of how fuzzy the definition is. Yet it must be recognized even a singular speciation event is a plural of events. Speciation often depends as much on the lack of an intermediary, such as the lack of a geographical connection, behavioral exclusions, or intermediary species (as in ring species), as it does on any quantitative deviation from a norm population. We can pretend that because species is not controversial in the vast majority of cases, where deviations exceed some threshold, that the straggler cases within this threshold region can be fixed by more careful definitions. But the fact is it simply is not so. The plethora of mechanisms are simply too pluralistic for any given definition to not contradict itself. We are applying the law of the excluded middle to a situation that by definition (common descent) requires a middle ground.

#28 Guest_mywan_*

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Posted 27 February 2011 - 08:16 PM

As I think about it I expect some disagreement or debate over the details or claims as I have stated them. However, it seems strange to simply label the notion voodoo biology when not a single empirically valid example of a species concept lacking subjective judgment has ever been posited, historical or otherwise. I guess I need to leave this alone here and find ways to challenge myself on these claims.

#29 Guest_CATfishTONY_*

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Posted 27 February 2011 - 08:24 PM

As I think about it I expect some disagreement or debate over the details or claims as I have stated them. However, it seems strange to simply label the notion voodoo biology when not a single empirically valid example of a species concept lacking subjective judgment has ever been posited, historical or otherwise. I guess I need to leave this alone here and find ways to challenge myself on these claims.


Please don't stop, threads like this keep the forum alive!

#30 Guest_mywan_*

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Posted 27 February 2011 - 10:41 PM

Well, I was studying my objection to the over-emphasis of the species concept. Such emphasis is on the grounds of evolutionarily significant unit. Which is defined as "a population of organisms that is considered distinct for purposes of conservation". Now let use compare the practices of many fish hatcheries, in which the distinct units being conserved is a species of trout, and consider the potential effects on toxin resistant tomcod in another thread here if they had received the same conservation treatment.

The toxin resistance of these tomcod resulted from a single gene which existed in fewer than 10% of the original tomcod population. A gene which in no way represents a distinct unit for purposes of conservation. The loss of that gene in the original population would not even had a significant statistical effect on the genome of the population as a whole. Had these tomcod been subjected to the same external pressures on genetic diversity as we subject many trout populations to the odds of that gene remaining would be limited. Yet this one, non-unit with respect to conservation, was the single defining factor between life and death of the tomcod in that region.

This is why genetic diversity should not be defined by species count alone, nor designated the sole unit for purposes of conservation. Species are paramount, in that they multiply the potential genetic diversity, but do not themselves define genetic diversity.

The definition of species is simply too course grained to be an effective proxy for genetic diversity, except in an equally course grained estimation. The genetic variability (genetic distance) between various gorilla populations is as great as the genetic distance between chimpanzees and bonobos. Yet for two equal spreads in genetic distance we have two units of conservation in one spread and only one unit of conservation in the other. In fact this equality in genetic distance between gorillas in one group and chimpanzees and bonobos in the other is the main argument for subdividing the gorillas into subspecies. Yet at what point is anybody questioning the logic of species being a distinct unit for purposes of conservation? The relative diversity spread here makes the tomcods look like identical clones of each other by comparison.

Perhaps by making this case clearer the case I made with respect to the other limits of the species concept will be easier to understand. In principle a well defined speciation event can occur in which genetic variability between species lacks very much statistically significant genetic distance at all. While other cases involve huge genetic spreads lumped together. Not to mention the presents of statistically insignificant genes within a single species with limited genetic spread, which could define the difference between extinction or not for that species.

I am far more concerned about the potential effects of these gross over-simplification, entailed by the species concept and units of conservation, than I am about a bunch of hobbyist releasing their captives to native environments. At least in the case of released captives natural selection will very quickly erase the detrimental gene flow. Not that I am suggesting it. That cannot be said of a concerted year after year industrial scale release. Effectively placing a constant artificial forcing effect on the system as a whole. To what degree is the species concept as a unit of conservation used to justify this behavior?

#31 Guest_Newt_*

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Posted 28 February 2011 - 09:55 AM

To what degree is the species concept as a unit of conservation used to justify this behavior?



You could say this has been an issue in cases of stocking into areas of sympatry. Northern muskellunge have been stocked in areas once inhabited by distinct southern musky, and Florida bass in the range of northern largemouth, etc., perhaps on the theory that a musky is a musky and it doesn't matter what the source population is.

However, I would say that far more important than species concepts or limited appreciation of genetic diversity within recognized species is the basically agricultural mindset of many fisheries managers. You could convince such a manager that southern musky are quite genetically divergent from northerns, perhaps even at the species level, and he would not change his stocking strategy. After all, he already has a convenient source of northern musky, rearing techniques are well-established, and he knows they will grow well in the cold reservoirs where they are stocked. Why confuse the situation with unknown variables?

As an addendum to the species concept vs. reality issue, I would say that a lot of folks seem to get hung up on the idea that variation is discrete OR it is continuous, with no room for a middle path, which seems to be what we actually see in nature.

As a further addendum, I would point out that microbes are not a good microcosm for speciation in, say, fishes. Sexual vs. asexual reproduction, horizontal gene flow in bacteria, sexual selection in vertebrates, and the utter inapplicability of the BCS to bacteria are some pretty serious hindrances to direct comparison.


#32 Guest_fundulus_*

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Posted 28 February 2011 - 10:28 AM


As a further addendum, I would point out that microbes are not a good microcosm for speciation in, say, fishes. Sexual vs. asexual reproduction, horizontal gene flow in bacteria, sexual selection in vertebrates, and the utter inapplicability of the BCS to bacteria are some pretty serious hindrances to direct comparison.

Which is why there are so many species concepts, because it varies; no sex, no BSC.

#33 Guest_mywan_*

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Posted 28 February 2011 - 12:11 PM

OK, these at first glance appear to be valid issues with respect to bacteria and BCS. But the same sex issues exist in higher animals. Some doing both sexual and asexual reproduction. Some switching sex with age or environmental conditions. So what about horizontal gene flow in bacteria, how much of your genome was placed there by viruses? The 8% you will see quoted pertains to endogenous retroviruses, which are like tiny scars which have no selective pressures due to active evolutionary functions. We use them to date species divergence exactly because they are subject only to genetic drift. If you could trace the source of all functional genes it is likely that you are mostly made of genes which at some point was planted there by viruses. In fact gene therapy is a technique of inserting functional genes into our genome most often by way of a virus, which existed for bacteria long before there even was multicellular life. Those subjected to strong selective evolutionary pressure enough years in the past may not even be identifiable to there source. So in the strictest sense your genetic makeup may be 100% a viral product. Even being more conservative you are primarily a product of viral inputs which continue to this day.

So the only difference between the lateral gene flows effecting us and other higher animals, with sexual reproduction only, verses bacteria, even to this day is simply a matter of time scale, period. In a sense your body is a group of bacteria that evolved to work together. Not to mention the range of separable host bacteria in and on us which function symbiotically, which we could not survive without.

So the exceptions list to separate the relevance of bacteria to the species question fails as any exception to the mechanisms in play for any and all species on earth, in the past and to this very day. So just because (most of the time) you can presently ignore the issue over the short run does not mean that many examples do not exist that cannot be ignored now and none can be ignored over a sufficient period of time. Bits of viral DNA you receive during your life is often inherited by your offspring, making viral DNA a direct player in the evolution of your family, as with all life.

Interesting off topic curiosity:
Bacteria 'speak' two languages, called quorum sensing like in ants. One language is geared to speaking to members of its own species only. The other is geared toward speaking to other species of bacteria. This quorum sensing is used in various ways to, as a group, defeat antibiotic treatments and signal stages of infections. So given the microbiologist testing procedure for determining speciation in bacteria: what role(s) does quorum sensing play and how much (in)dependence does speciation have on the quorum sensing mechanism?

#34 Guest_mywan_*

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Posted 28 February 2011 - 02:29 PM

In picking on the issue of lateral gene flow in bacteria the most important specific mechanism implied is conjugation. Certainly not, as some may analogize, a form of sexual reproduction in bacteria. In a more limited sense the analogy has a few functional elements, though we can ignore that. What is more interesting is explicit examples of inter-kingdom conjugation. This is relevant because it more directly articulates examples that cannot be ignored in the present involving explicitly the same mechanism that is responsible for the majority of lateral gene flow in bacteria. Thus it is complementary to the viral DNA implant issues in the previous post, involving fully functional genes to boot.

Agrobacterium is a bacterium that uses horizontal gene transfers into plants to induce tumors. This induce the production of opines, used as an energy source by the bacteria. Oh, by the way, in lab culture this bacterium can genetically transforms several types of human cells and has been known to infect people with suppressed immune systems. Almost looks like the precursor to many Sci-Fi movies.

Evidence of recent interkingdom horizontal gene transfer between bacteria and Candida parapsilosis

Phylogenetic and syntenic information infer that two C. parapsilosis genes originate from bacterial sources. One encodes a putative proline racemase (PR). Phylogenetic analysis also infers that there were independent transfers of bacterial PR enzymes into members of the Pezizomycotina, and protists. The second HGT gene in C. parapsilosis belongs to the phenazine F (PhzF) superfamily. Most CTG species also contain a fungal PhzF homolog. Our phylogeny suggests that the CTG homolog originated from an ancient HGT event, from a member of the proteobacteria. An analysis of synteny suggests that C. parapsilosis has lost the endogenous fungal form of PhzF, and subsequently reacquired it from a proteobacterial source. There is evidence that Schizosaccharomyces pombe and Basidiomycotina also obtained a PhzF homolog through HGT.
[...]
Until recently, the process of gene transfer has been assumed to be of limited significance to eukaryotes [7]. The availability of diverse eukaryotic genome sequence data is dramatically changing our views on the important role gene transfer can play in eukaryotic evolution.



Bacterial Conjugation in the Cytoplasm of Mouse Cells

Intracellular pathogenic organisms such as salmonellae and shigellae are able to evade the effects of many antibiotics because the drugs are not able to penetrate the plasma membrane. In addition, these bacteria may be able to transfer genes within cells while protected from the action of drugs. The primary mode by which virulence and antibiotic resistance genes are spread is bacterial conjugation. Salmonellae have been shown to be competent for conjugation in the vacuoles of cultured mammalian cells. We now show that the conjugation machinery is also functional in the mammalian cytosol. Specially constructed Escherichia coli strains expressing Shigella flexneri plasmid and chromosomal virulence factors for escape from vacuoles and synthesizing the invasin protein from Yersinia pseudotuberculosis to enhance cellular entry were able to enter 3T3 cells and escape from the phagocytic vacuole. One bacterial strain (the donor) of each pair to be introduced sequentially into mammalian cells had a conjugative plasmid. We found that this plasmid could be transferred at high frequency. Conjugation in the cytoplasm of cells may well be a general phenomenon.


Here is an essay on the debate about the importance of horizontal gene transfer to evolution (pdf):
http://www.compgen.u...-essay-2003.pdf

So how much I am overstating the case here is easily debated. In a sense you could say these gene transfers merely provided fodder, a junk pile from which sexual evolution acted on. Even with the most conservative position possible with the available empirical data, it still has to qualify as another item on an exceptions list, however rare.

There is more, that blurs the line even further. Where rather than direct microbial interference with gene sequences it produces exquisitely targeted interference with the survival strategies, behavioral characteristics, etc., of eukaryotes. Thus the potential for bacterial induced speciation, as a survival strategy of the bacteria itself, becomes essentially unavoidable.

#35 Guest_mikez_*

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Posted 28 February 2011 - 05:38 PM



You could say this has been an issue in cases of stocking into areas of sympatry. Northern muskellunge have been stocked in areas once inhabited by distinct southern musky, and Florida bass in the range of northern largemouth, etc., perhaps on the theory that a musky is a musky and it doesn't matter what the source population is.



I'm not sure if I'm still following carefully enough [somebody mentioned MATH and my brain shut down - just like school :-$ ], But I submit these examples typify where some of the confusion comes in. I would have said the examples given represent subspecies but I know there's some flip flopping on some of these re species vs subspecies vs strain, morph, type etc.
Besides the examples given, I would add domestic strains of rainbow and brook trout stocked in areas where isolated "strains" are found. They're clearly not the same animal as nature provided, despite being "native", yet often nothing but DNA testing can reliably set them apart.

Perhaps that is the answer - DNA gets the final say on what a species is.

#36 Guest_CATfishTONY_*

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Posted 28 February 2011 - 05:56 PM

I was wanting to know what makes a speice?


baker46947, thank you for this thread.
winter was lagging on and you my fellow NANFA friend found away to get the ball rolling!!!
i am new to fish but as i see it.
we have small groups of special fish in isolated situations like the pupfish named devil's hole pupfish.
they were left alone for some time and a new species came from it.
and large groups of fish like the esox. large as in (wide spread) for a genus.
isolated yes, yet a pike is a pike here or there some small some large.
just like people we all have changed. from our original form.
climate,time and breeding, with it's never ending mutations has morphed us into the subspecies we are today around the globe.
bottom line as i see it a species is able to breed and have offspring that does the same.
anything else is just a longer drawn out way to catalog more stuff and and more name.


#37 Guest_farmertodd_*

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Posted 28 February 2011 - 09:56 PM

Perhaps that is the answer - DNA gets the final say on what a species is.


And even with DNA/molecular evidence supporting a hypothesis... it's still only a supported hypothesis ;)

As I tell my students: If you want the Truth, talk to a preacher. If you want Proof, talk to a lawyer. For the rest of us, there's Evidence - and the best we can hope for is that the filter we've passed our test across tells us something meaningful about evolutionary relationships in the natural world.

Todd

#38 Guest_mywan_*

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Posted 28 February 2011 - 11:35 PM

I have Spring Peepers (Pseudacris crucifer) doing their deeds in the pool outside my front door :tongue:

I'm not sure if I'm still following carefully enough [somebody mentioned MATH and my brain shut down - just like school :-$ ], But I submit these examples typify where some of the confusion comes in. I would have said the examples given represent subspecies but I know there's some flip flopping on some of these re species vs subspecies vs strain, morph, type etc.
Besides the examples given, I would add domestic strains of rainbow and brook trout stocked in areas where isolated "strains" are found. They're clearly not the same animal as nature provided, despite being "native", yet often nothing but DNA testing can reliably set them apart.

Perhaps that is the answer - DNA gets the final say on what a species is.

I tried very hard to maintain an intuitive description so it could be followed without the math. My mind does not work in either math or language, both are merely translations. Though math is quiet superior in many cases, I am still trying to set the problem up for a better quantitative outline.

The problems with species verses genetics is more endemic than it appears. Here is why. The wildcard in the species definition is more or less in-group fertility. Suppose, for arguments sake, a single 'letter' mutation occurs in one member of a species which provides it with a previously unavailable environment and makes the original environment unavailable. I do not know such is possible on such an insignificant variance, but neither does anybody else. Nor even asked. Yet this situation would rightly define a separable species in spite of an effectively zero genetic difference. A member of one of those species could differ by over a million times that and still not constitute another species, or even an significantly divergent member of that species. These two groups even deserve their own conservation status, as the two environments are not mutually compatible and both are needed to broaden the total diversity. Being separated this way and given time the divergence between the two will grow.

In other cases members of a single species may inhabit a range with some variable habitats. Some have slightly better adaptations to some parts of the environment, others for other parts of the environment. So this begs the question: what level of genetic difference do you require before they receive separate conservation status, 0.01%, 1%, 2%, ...? What if they clearly are divergent in behavior, survival strategy, etc., but genetically they are different by less than the difference between members with the same behavior, survival strategy, etc.?

Genetic distance is non-linear in effect this way. A large genetic different can mean nothing concerning morphology, survival strategy, habitat, etc., but a tiny genetic difference can make the apparent differences as plain as day in multiple ways. Consider the locally adapted trout that we are stocking its habitat with the same species but from a different local. Suppose testing shows the divergence between them to fall below some threshold, justifying external stock. If we continue with this stocking indefinitely then the divergence between the two groups will never increase when in fact it should have.

Yes, we need to conserve species, and the diversity within species. While not insuring, through our heavy handed species centric tactics, the prevention of divergences that should have occurred. If we conserve the changes out of nature it dies. We need to bring to bear our genetic tools, but the non-static nature of nature puts us in danger of removing the changes nature requires in order to conserve what it no longer should be. The environment makes a better unit of conservation than the species it contains. Introductions should be very limited and primarily for recovery from complete at fault losses. Introductions most certainly should not be given huge industrial size advantages in numbers, swamping better adapted populations by shear force of artificial numbers. If we worked out our issues with effluents problems and impervious drainage systems we could multiply the diversity of life by an untold amount without any species specific conservation. Good solutions to these problems would themselves qualify as awesome wildlife sanctuaries.

#39 Guest_mywan_*

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Posted 01 March 2011 - 05:44 PM

In physics the limits of a problem are often the first thing to define. It is these limits that define the state of the problem. In the biological/ecological sciences not only is the species concept problem not resolve it is not even defined. Meanwhile each author will publish with implicit assumptions about what kind of assumptions define the issue, which are often incongruent with each other. This lack of limits is like asking a physicist about the speed of light and getting the response: well.. umm.. that's just how fast light goes. I have been trying to work out exactly what math is needed. Not that I am going to provide it here but simply explain what numbers are needed and some of the information it would provide. First the most general possible definition of species, as the OP asked for, to work with.

Species - A division where a reproductive set or group can be subdivided into separate groups and evolve independently.

Many expect this division to correspond to some set genetic difference to delineate between the groups, but this is not always the case. Though in all cases a separate species will, given enough time, continue to genetically diverge from closely related species. This is why we cannot water down or remove conditions for species as defined by BSC, in an attempt to make such definitions non-contradictory, as the separate evolution allows a the genetic diversity to exponentially increase over what is possible in a single species.

In order to quantify how fuzzy the lines between species is it must be done statistically. To do this as individual variables, which can later be combined, we need to provisionally place undue restrictions on what defines a speciation event. In the previous post I assumed a speciation event resulted from a single point-like letter mutation (substitution). The odds against this is so exceedingly small as to nearly be pointless. Even if we knew this value as a non-zero probability this one data point is generally useless. So provisionally we will limit the speciation to sexual fertility, irrespective of any environmental constraints, intermediaries as in ring species, etc. Conversely this becomes DNA-DNA hybridization in microbiology, used as a proxy for fertility in asexual bacteria.

To give this meaning we graph the known genetic distance 'd' to the empirical probability that a speciation event 's' has occurred. This defines a function d(s) which returns the probability of a speciation event from a given genetic distance. Now, instead of a simple ad hoc denial of the self contradictions, we can quantitatively define statistically where and how much the variability defining a species overlaps the variability within a species. This would give us a huge amount of information, and define the limits of desperately needed to characterize to problem. Once information about population dynamics and other variables are included our understanding of the long term evolution of the system can grow exponentially.

I do not know what this function looks like, I only that these parameters overlap and result in statistical variances in what defines a species. Variances which result in self contradiction if you want species to be purely objective. This way the probability is purely objective, even if a given case instance is not. Obtaining the necessary empirical information may be easier in microbiology, but I suspect speciation in bacteria is tied almost excursively to quorum sensing rather than any actual incompatibilities in conjugation. This would also explain why it happens in a much narrower range of genetic distances than in sexual reproduction. Anybody know any good databases of genetic distances between closely related species and/or good databases on the genetic variability within various species?

Final note:
I am against removing or artificially limiting conditions defined by BSC to make the species concept non-contradictory. As anything restrictive enough to do so would deny the separability of two groups are under independent evolutionary paths. Even if the genetic distance is essentially nil. It is far better to simply define the situation for what it is, rather than pretending that maybe somebody someday will make the contradictions go away without invalidating implicit assumptions.

Edited by mywan, 01 March 2011 - 05:49 PM.


#40 Guest_daveneely_*

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Posted 04 March 2011 - 07:23 AM

I'll keep this short.

The shortcomings of the BSC are many and have been discussed at length elsewhere. Mywan's application of set theory above is inappropriate in this context, given that species have characteristics more similar to that of individuals (as first siggested by Ghiselin, M. 1974. A radical solution to the species problem. Systematic Zoology 23: 536–544) rather than classes: individuals are spatio-temporally bounded, they are composed of parts rather than members [why your use of set theory isn't relevant], and cannot be defined, only described. I find it somewhat amusing how many times you've used the term definition above! This isn't some recent hare-brained idea; taxonomists have long recognized this by diagnosing and describing species, not defining them. Think about the ontogenetic trajectory that other individuals (like for example, human individuals) go through, from infant to adult; the same individual might scarcely resemble itself at a different point along that arc. Lineages and species behave in the same way.

In this regard, a case can be made for using a plurality of species concepts. Different concepts vary widely in their utility and the proportion of diversity that they recognize. Folk concepts (like the redneck "if'n it's got scales it's a carp, if'n it don't it's a catfish") are widely used by the vast majority of humans, and are often remarkably accurate (or at least congruent with other concepts) for larger animals and plants or organisms of some direct human utility. The BSC fails miserably for asexual species, fossils, and anywhere where allopatric speciation is prevalent (which appears to be most of Earth). The Paterson's mate recognition concept fails for many of the same reasons. The various incarnations of phylogenetic species concepts may overlook some organisms because they're data-dependent. All operational concepts have some issues, but not using them is throwing the baby out with the bathwater. The ESC isn't operational, but is extremely useful as a theoretical concept that we can approach by using other concepts as proxies.

As for microbiologists or bar-coding ecologists using some arbitrary distance criterion for species, that's been demonstrated to NOT be a good approach as it tells you nothing about the relationship of a group to its sister taxon, and can in fact be positively misleading. You might want to look into how poorly DNA-DNA hybridization fared when applied to birds... ;) As for using statistics to come up with some estimate of species "boundaries," that's missing the whole point...

Perhaps nothing else in biology is as important as species...



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