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2010-09-08
Individuating Species
There is an idea that species should be individuated by common descent. For example, the phylogenetic species concept (P weak) holds that a species consists of all of the descendants of any member, up until a speciation event. According to a stronger version (P strong), a species consists of all of the descendants of a single individual.

I wonder how people's intuitions respond to the following (empirically plausible) counter-examples.

1. Reproductive isolation A group G of organisms of species S gets separated from the others. G faces different ecological conditions than the remainder of S, and speciates. (That is, members of G cease naturally to interbreed with members of S.)

a. This is straightforwardly a counter-example to P strong, since there are several founders of species G -- their common ancestor belongs to S, or perhaps even to a predecessor of S.

b. This is potentially also a counter-example to P weak, since a founder member of G may have left offspring behind in S. Thus, not all of its descendants are members of G.

2. Parallel speciation Anadromous (ocean living, stream spawning) sticklebacks A sometimes leave offspring behind in streams. These don't return to the ocean, but live in streams, and thus speciate. But here's the thing: this happens many times so that A sticklebacks have descendant species S1, S2, S3 etc in different streams and lakes. Further, each of the Si daughter species mates assortatively by size so that in each stream/lake there is an SiLarge and an SiSmall.

a. Does A cease to exist every time a new Si comes into exist? (Implausible!) If it does not, P weak is violated, since members of A have descendants in A after speciation.

b. It turns out that for all i, j, members of the SiLarge species can interbreed with members of the SjLarge species, but not with members of the SjSmall species. So by an interbreeding conception, the SiLarge species are the same. But this contradicts P weak (and a fortiori, P strong).

My intuition is that the individuation-by-descent criterion falls to these examples. Is there anybody else out there who has intuitions about this?  (I am not expecting a horde, I admit!)

2010-09-09
Individuating Species
Reply to Mohan Matthen
Dear Mohan, I am very puzzled by this. The idea that a species should be defined by descent from an individual seems plain silly, and P strong is obviously wrong across the board, unless you are a creationist. Who is putting forward such 'ideas' I wonder? 

Species is a rough and ready biological term that has been defined in various ways over time. Nobody in biology believes (I hope) that there is actually a 'true natural referent' of the word, although the Wikipedia entry might lead one to doubt this:

'In biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring. While in many cases this definition is adequate, more precise or differing measures are often used, such as similarity of DNA, morphology or ecological niche.'


This begs the question of what 'adequate' means. As far as I am concerned there is no criterion of adequacy to have. If I want to discuss groups that are cross-infertile and call those species then the term species is adequate to discuss cross-infertile groups, that's all. If I want to discuss groups that naturally segregate for reasons of migratory instinct, like eastern and western Bonelli's warblers, but are cross-fertile in a cage, then I can use 'species' to deal with that idea if I want to unless a committee has decided we all have to use the word one way. There is a whiff of cart before horse here.


I doubt that there is a useful definition of species that goes back in evolutionary time. All life forms are cross-infertile with their dead forbears. Whether a life form that has been monospecific at all times over the last 10 million years (maybe the gharial) is the same species now as it was 10 million years ago is a meaningless question unless you have a particular similarity or dissimilarity you have in mind. I think it would be more useful simply to state whether or not the gharial has changed in this regard rather than bother with the species question - which adds no heuristic value.


Best 


Jo

2010-09-09
Individuating Species
Dear Jo,

I'll just give you some quotes to substantiate my characterization of this species concept. We can continue the discussion with these in mind.

Here is a paragraph from Marc Ereshefsky's Stanford Encyclopedia entry on species. He characterizes three different species concepts; the one I am concerned with is the second.

"Biologists offer various definitions of the term ‘species’ (Claridge, Dawah, and Wilson 1997). Biologists call these different definitions ‘species concepts.’ The Biological Species Concept defines a species as a group of organisms that can successfully interbreed and produce fertile offspring. The Phylogenetic Species Concept (which itself has multiple versions) defines a species as a group of organisms bound by a unique ancestry. The Ecological Species Concept defines a species as a group of organisms that share a distinct ecological niche. These species concepts are just three among over a dozen prominent species concepts in the biological literature."

Here, from some unsigned class notes from the University of Washington's Biology 354 is a fuller statement of that concept:

"The Phylogenetic Species Concept
Monophyly is the centerpiece of the PSC. In other words, the populations of each species should share a common ancestor."

and the Wikipedia entry you quote from offers (for the PSC):

"A group of organisms that shares an ancestor; a lineage that maintains its integrity with respect to other lineages through both time and space."

As Ereshefsky rightly points out, there are other versions of PSC, but I was querying this version.

all best,

Mohan

2010-09-09
Individuating Species
Reply to Mohan Matthen
Dear Mohan, A lifetime in biomedical science has taught me that there are a lot of dumb people in biology and that includes review writers who cannot tell (or prefer not to upset grant reviewers) which of the ideas they are reviewing are coherent and which dumb. You started out by pointing out that the 'phylogenetic species concept' is leaky. My point was that it is plain silly. All life forms share lots of common ancestors (even if just a billion preCambrian protocells) and lots of non-common ones. The definition is hopeless. The weak version just introduces a circular and self-destruct caveat - when speciation has occurred there are new species - admitting the original definition was wrong! And what the heck is a lineage that maintains its integrity with respect to other lineages? This is just the Bishop of Oxford's supernatural pseudodynamics replaced by a more trendy atheist version: an idea generated by people who think science is about confirming what you think ought to be the case when in fact it is about discovering where things are not what you thought they ought to be. The result is a classic pseudoconcept, which, like free will, does not even begin to make sense. The fact that thousands of papers may have been written about it and it gets into encyclopaedias cuts no ice with me I am afraid. I have learnt that one the long way. This is, to borrow from Richard Feynman, evo-flapdoodlery and nothing more.

The human mind's inability to understand its own shortcomings becomes ever more fascinating as one gets older. 

Best wishes

Jo

2010-09-09
Individuating Species
Dear Jo,

Just to test the false v silly dichotomy, let me offer you a couple of ideas and you can tell me whether you think they have any merit.

First, cladistic theory (at least in its historical version) does taxonomy by descent. Let A be a species, and suppose that B and C broke off from it. Now suppose that D and E break off from B. E could be more similar to C than it is to D. Nevertheless, cladistics will classify D and E together. The rank of a grouping will depend on how far back you have to go to get a common ancestor. The closest common ancestor of E and C is A, while the closest one for D and E is B, which is a descendant of A. Thus D and E belong in a group of a lower rank than E and C. (You might want to draw a family tree.)

Second, cladistic theory proposed that proper classifications of rank higher than species should be monophyletic, i.e., that they should include all and only the descendants of some node. In practice, though, they will be paraphyletic -- they'll include only but not all descendants of some node. Dinosaur is not monophyletic because it doesn't include aves, but it is paraphyletic.

Now, somebody got the bright idea that they might extend the idea to species. But species is the smallest grouping. It is just a node. So where the previous idea had the ancestor-descendant relation among taxa or classes, these people thought to use the ancestor-descendant relation among individual organisms. This is where it starts getting silly in my mind.

Obviously species cannot be monophyletic, for the reason you give -- namely that if they were we would all belong to weird preCambrian species. So there's the idea that species should include all indviduals up to speciation. Speciation is defined by the evolution of reproductive isolation. Nor are they paraphyletic (for the reasons I gave in my original post).

Ok, let's just say that extending the idea to species in this way is silly. I am particularly happy to say this so because I was once attacked by a crazed biologist because I didn't buy this notion of species. (Not a bad man, but a silly one. Rattled me though.)

Going back to my example, though, I was talking about descent among classes -- populations or even species -- not individuals. In my example, the anadromous stickleback speciates several times, i.e., it leaves individuals behind in freshwater lakes or streams, and these evolve reproductive isolation. So here are a bunch of stream stickleback classes the members of which do not naturally mate with the anadromous stickleback from which they speciated. But by the cladistic criterion of species -- smallest group -- they can't belong to the same species as each other. However -- surprise, surprise -- they are not reproductively isolated from one another. When put into the same fish tank, they spawn.

This last bit was what made me say 'false' or 'leaky' or 'problematic'. But it isn't in the same camp as the clearly silly version of the phylogenetic species concept. It's classification by descent, but descent of groups not individuals.

best,

Mohan

2010-09-10
Individuating Species
Reply to Mohan Matthen
Dear Mohan, As far as I can see none of this is of any real interest since it is just a quibble about classification. Cladists seem to suffer from Ralph Waldo Emerson's 'a certain foolish consistency is the hobgoblin...'. Since cross fertility, hybrid fertility (even self-fertility in hermaphrodites, which fish can be serially) and behavioural isolation mechanisms operate in quite different ways in various groups of plants and simple and complex animals there will by definition be no 'smallest group' species concept that is useful for all purposes. 

Jo

2010-09-12
Individuating Species
Reply to Mohan Matthen
I am appalled that the concept of "species" is so problematic. I always felt it was a bit shifty, but I assumed that this is because I don't know a great deal about biology.

You both seem to be saying that one of the key words in today's political debate about "the environment" has no clear and agreed-upon definition! So the environmentalist's concern about the infamous snail darter and the spotted owl was ill-defined...perhaps even deceptive? This is no trivial issue; in the case of the spotted owl, an entire industry (logging in the state of Oregon) was pretty much shut down, and many people were put out of work. For what? We were led to believe that this action was necessary because some unique group of animals was in danger of being wiped out, and that this loss was something horribly disastrous.

But now I wonder precisely what makes these owls so special; other than they apparently have spots, and happen to live in trees that are sometimes cut down. Perhaps other owls who are not quite so fragile might have moved in. So what if they don't have spots? Or perhaps the spotted owls would have changed their nesting habits, and lodged in scrubby trees that are not subject to logging. (Would that count as a "speciation event"? In that case, I suppose one could still say that the spotted owl "species" was wiped out, and replaced by the "scrub nesting spotted owl".)

Also, this question occurs to me: what sense does the government's "endangered species" list make, when we do not even know how to define the groups of animals or plants that go on the list?

I suppose that I am not surprised that my government has lied to me. However, there must be a great many dishonest biologists--those who collaborate with the government in drawing up these specious lists, and those who do not raise the question of exactly how "species" is defined in the course of public debate about such "environmental" issues. I suppose that such openness might cost them their government grants.

2010-09-12
Individuating Species
Reply to Mohan Matthen
Hi Mohan,

Regarding (1): I suspect that, by the time speciation was complete, the population would have a common ancestor postdating its geographical isolation.

I'm assuming here that (a) speciation generally requires at least one new mutation to appear in the population; and (b) new mutations originally appear in a single individual. 

If (b) is right, then, when a new mutation spreads through the population and goes to fixation, all the remaining individuals will be descendants of the individual who introduced the trait. And if (a) is right, this process will have to occur at least once before speciation occurs.

Best wishes

Jonathan.

2010-09-13
Individuating Species
Reply to Mohan Matthen
If I can point you at Alan Templeton's work, this should go some distance to removing the "species are specious" claim (a line which I shall use for a paper title soon). In particular he discusses the evolutionary history as defining, or at least being the target of operational investigation into, the species.

Templeton, Alan R. 2001. Using phylogeographic analyses of gene trees to test species status and processes. Molecular Ecology 10:779--791.


In this, he defines a species quite naturally as a group of organisms that are an evolutionary lineage whose boundaries arise from the genetic and ecological forces that create cohesive reproductive communities:
The cohesion concept is made operational by testing two null hypotheses:
1 the organisms sampled are derived from a single evolutionary lineage, and
2 the lineages identified by rejecting hypothesis 1 are genetically exchangeable and/or ecologically interchangeable.
Only when both null hypotheses are rejected can a sample of organisms be split into two or more cohesion species. Otherwise, the organisms are regarded as members of a single cohesion species until future data or analyses allow the rejection of the null hypotheses.
This view, that an organism is demographically or genetically exchangeable in effect sets up the equivalence class in quite natural ways.


As to "the" phylogenetic concept, there is no such beast. Either cladists already know what the species is (so as to exclude haplotype groups and other coalescent lineages), or they are using an arbitrary demarcation (the Hennig criterion which extinguishes at speciation, and which may be taken as a hypothesis about names, not taxa), or they have no conception at all. There are at least three if not more things that are called PSCs, but I think (and argue in my book) they are illusory.

2010-09-13
Individuating Species
Reply to Mohan Matthen
Apologies for not responding sooner. I have been away from Toronto.

Hi Jonathan (Birch): nice to hear from you.

I think that PSC strong is indeed motivated by your condition that speciation takes place through mutation. This is not an uncommon assumption: it is also made, for instance, by Roy Sorenson. And you are right: if a species is initiated by a mutation in a single individual, then it will consist of all of the descendants of a single individual (up to a speciation event).

However, in (1) I am thinking of speciation by an isolation event -- when a group of individuals gets isolated by a barrier, and then evolves on its own. In many cases, post-isolation evolution may be driven by post-isolation mutations. But first of all, there may be no crucial mutation that constitutes speciation: evolution is driven by variation in the group. Secondly, this variation may be a remnant of pre-isolation mutations.

In sum: I don't think that the assumption of a single crucial mutation (or polyploidy) is necessary.

Jo, I do agree with you about that notorious hobgoblin infecting cladists. But I don't agree with you about "quibble about classification". Species are classes that support generalizations of various sorts. Some think that phylogeny preserves a lot of structure -- all fitness-neutral characteristics are preserved in reproduction. So these people think that a history based taxonomy is probably the thickest basis for generalizations. Others (myself included) think that species are groups of individuals that have a shared evolutionary trajectory because of various interactions with each other and with their environment -- I don't mean this to exclude phylogenetic considerations. It may be true, as you say, that no one group concept will cover all of the interactions that organisms have with one another. So there may be several ways of drawing species boundaries. But this is compatible with the demand that boundary conceptions be true to some ontologically valid criterion (such as the two offered just now).

Peter, I think you're being unduly pessimistic. It may be that we cannot agree how best to define species. But there may nonetheless be broad agreement that e.g. the spotted owl (or whatever) is a species. In fact, any debate about species concepts proceeds against a background of agreed species classifications. Species classifications don't await a definitive species concept.

This said, it must indeed be acknowledged that the shape of the argument for preserving a particular species is unclear (at least to me). (To make my position explicit: I feel strongly that many such species should be preserved, but I am not sure what the rational basis of this feeling is.) The biodiversity folks want lots of species, and I can understand the force of their argument -- environmental homeostasis depends on high biodiversity. But why is it important to preserve a single species -- the spotted own, for example? Without wishing to comment on that particular case (about which I know next to nothing) -- I think that the reason is that if you destroy a species that is relatively high up the food chain, you disturb environmental balance and reduce biodiversity.

By the way, E. O. Wilson argued that if you treat species as individuals (as collections of interacting organisms, for example), then you have a reason for not destroying individual species that parallels the reason for not killing individual organisms. (I am not entirely convinced, but I'll put this out there.)

John: I agree, of course, that there is no one phylogenetic species concept (in fact, I offered two, and each of those comes in many varieties). However, I do want to say, though I won't try and argue this in detail, I think that if you take breakdown of gene-flow as a speciation event, then the cohesion species concept as you define it is equivalent to my P strong: "a species consists of all of the descendants of a single individual" (up until a speciation event).

I look forward to seeing your book on the history of species concepts.

all the best to all of you,

Mohan

2010-09-13
Individuating Species
Reply to Mohan Matthen
Dear Mohan, If the 'species problem' is not just a quibble about definition then I fear it is something much worse - a reflection of bad thinking likely to lead to non-sequitur generalisation. How you define your terms should have absolutely no effect on the scientific explanatory power, or ethical or aesthetic implications of an argument. The problem (of Peter's sort) comes when people tag words to hold-alls full of associated ideas - unfortunately the norm in science but something one can at least strive to avoid. (For my part the arguments for protecting spotted owls are the same for all common usages of the term species, but they do not necessarily generalise to blue whales, smallpox, or the Hood Island mockingbird.) If someone wants a heavily theory laden category that will often match up with the morphological 'species' groups we start off with as data then I would have thought the best thing was to introduce a new word. Muddling up definition qua explanandum with definition qua explanans is always a recipe for trouble is it not? In immunology we had antibodies and then when we had some biochemical theory we invented a new word, immmunoglobulins, so as not to get muddled when we need to be clear. I suspect evolutionary theory would benefit from something similar!

Best wishes

Jo

2010-09-13
Individuating Species
Dear Jo,

It's not a matter of defining words, but of identifying kinds.  There is a long literature that holds that it is difficult to understand what a gene is. Similarly, there is a long literature about how to understand what a species is. It may well be that that genes and species are not unitary kinds. And if so, it would be helpful to define different kinds of species, and assign biological taxa previously lumped together to these different kinds. People in the literature do say things like this: such and so species satisfies the biological species concept quite well, but so and so other species is best captured by the cohesion species concept (or some other species concept).  If they are right, one might want to say, as you do: well why not split species up? Marc Ereshefsy does say exactly this 1992. Or one may want to say: no let's try harder to find a unitary kind of grouping.

But this is not a matter of using different words, so much as it is a matter of distinguishing kinds of species, or eliminating a unitary species concept in favour of a plurality of other less extensive concepts.  (This doesn't quite parallel what you describe happening in immunology, where a functionally defined term 'antibody' was replaced by a biochemical term 'immunoglobulin'.)

About spotted owls, I agree with you . . .

best,

Mohan

2010-09-14
Individuating Species
Reply to Mohan Matthen
My book is out now:

2009. Species: a history of the idea, Species and Systematics. Berkeley: University of California Press.

Also I have a short target article:

2010. What is a species? Essences and generation. Theory in Biosciences 129:141–148.



As to your P strong, in asexual species it follows logically. But in sexual species, and in particular in species that are "paraphyletic" or respeciated, it doesn't follow. There are several known species (some cichlids, I think, see Turner 2002) where species have occurred more than once but are able to interbreed with previously speciated populations. This is because they both primitively share developmental and genetic systems, and because they have locally adapted to ecological conditions. Of all the species conceptions I know (about 25 in the current literature) only Templeton's seems to cover these examples.

The notion that a species must be monophyletic (that is, have a universally shared ancestor not shared with any other species) is unwarranted in my view. There will almost always be a coalescent in a sexual species, but it is at best a sufficient condition, and not a necessary one, and I'm not even sure it is sufficient.

Richard Richard's recent book looks to deal with these questions well, but I only got my review copy about three days ago.

Richards, Richard A. 2010. The species problem: a philosophical analysis. Cambridge: Cambridge University Press.



2010-09-14
Individuating Species
Reply to Mohan Matthen
Dear Mohan, We seem to have a habit of agreeing extensively on practicalities but not on metaphysics. To me there are no 'kinds' in science to identify. The idea that there are kinds to find, like genes, is one of the main obstacles to progress in science. It stimulates enquiry initially but then generates empty bandwagons. The real progress is usually made by people who have no truck for kinds, just for observations and dynamics, in my experience. So the problem is of making sure we have clear terms for each of our useful sets of observations and for each of our theoretical (explanatory, dynamic...) ideas. Or, since observation is always to some extent interpretation, or theory, laden, it is often more a question of the level of theoretical loading. Antibody and immunoglobulin are loaded in different ways.

So what I am arguing for is not assigning lumped taxa to different kinds or 'splitting species up', it is using a different term each time you want to talk about a different idea, as clear scientific argument requires. There are lots of ideas about, useful in different contexts, so we need several terms. An insistence that there is some 'real kind' called a species is to me closer to the Bishop of Oxford (without the creation bit) than it is to Darwin. If I were a modern day geneticist I think I would consider 'species' as no more than a convenient title for a chapter in an undergraduate textbook (just as I do for 'rheumatoid arthritis' or 'autoimmunity'), not as a serious scientific tool. 

Best 

Jo

 

2010-09-14
Individuating Species
Dear Jo,

Since you are a distinguished scientist, I take it as a good sign that we agree about "practicalities".

I won't take up too much more space with this. But I have a "nearly final" draft on this site 2013 which expands on the following argument:

1. That Leo is tawny is explained by Leo being a lion.
2. Therefore, lion is an explanatory kind.

However, this doesn't tell us much about what kind of explanatory kind lion is. Devitt 2008 argues that it is an "intrinsic" essence. But consider 3.

3. That Leo has a mane is explained by Leo being a lion.
4. However, not all lions have a mane: Lizzie, a female lion, does not.
5. Therefore, lion is a kind that supports explanations of sub-kinds.

Intrinsic essences can only explain the characteristics of things that share the essence. So 5 argues against a Devitt-style explanation.

How can 5 be true? Leo has a mane because of sexual selection. 3 is true in virtue of relations among the males and females of the lion-class.

Thus, lion is an explanatory kind because its explanatory force derives in part from the nature of relations among characteristic sub-classes of lions.

Generalizing (perhaps too hastily): interactive species are classes of organisms, the ecological interactions of which (historically) explain properties of some individual members. (But perhaps there are other kinds of species, and they should receive designations of their own. John can be informative about this, I think.)

 If you agree with the above, it is all I really want.  The so-called phylogenetic species concept goes by the boards.

best,

Mohan