Evolution: the Facts.

[Dinwar]

Not really--morphology and DNA are pretty close, far as I've seen. Of course, that only gets us back to the mid-Pleistocene or so. The real issue is that the fossil record isn't always in agreement with DNA, but given that the fossil record is more holes than rock it's not surprising that we'd find differences--they're an artifact of the lack of data (the missing taxa in DNA analysis, and the missing specimens in the fossil record).

 

[dgilman]

I wish I could participate more often here because you guys can teach me stuff. However current work pressure is interfering. I'll get back to you all when the current hectic schedule subsides.

One major problem I am having is that I also disagree with tons of the stuff being proposed by the "creationists". They are so embarrassingly illogical and contradictory that I refuse to be referred as a "creationist". The other problem is that Prof. Behe is a lousy debater. I read his stuff, his arguments are weak.

The biggest problem I have though is every time I criticize the evolution theory, somebody says that I'm arguing that God did it. If the theory is wrong, that does not prove that God did it, it only means that the evidence and the theory don't match as well as they should. It also means that they really don't know how we now have this awe-inspiring great variety of live. Ignorance of how they came about does not prove that God did it.

They don't know how life even arose on this planet, not only because of the results of those experiments, but also because of the confirmed time lines. Every peer-reviewed paper on the subjects that I have read shows that life arose on this planet almost as soon as it got an ocean. That time span makes it unreasonable to conclude that it happened spontaneously. Does that prove God did it? No! That fact, plus the Robert Shapiro's thesis shows that science will most likely never be able to find out how.

None of the papers I have read on how multi-cellular life evolved have any confirmable hypothesis. They are all logical, they all use observations of what occurs around us today. The observations show what the possible pathways might be, but scientists will most likely never be able to confirm any of those pathways.

 

[Dinwar]

Every peer-reviewed paper on the subjects that I have read shows that life arose on this planet almost as soon as it got an ocean.

Right--with error bars the span of the Phanerozoic.

You keep mentioning papers. Got any examples?

 

[Lukraak_Sisser]

I wish I could participate more often here because you guys can teach me stuff. However current work pressure is interfering. I'll get back to you all when the current hectic schedule subsides.

One major problem I am having is that I also disagree with tons of the stuff being proposed by the "creationists". They are so embarrassingly illogical and contradictory that I refuse to be referred as a "creationist". The other problem is that Prof. Behe is a lousy debater. I read his stuff, his arguments are weak.

The biggest problem I have though is every time I criticize the evolution theory, somebody says that I'm arguing that God did it. If the theory is wrong, that does not prove that God did it, it only means that the evidence and the theory don't match as well as they should. It also means that they really don't know how we now have this awe-inspiring great variety of live. Ignorance of how they came about does not prove that God did it.

They don't know how life even arose on this planet, not only because of the results of those experiments, but also because of the confirmed time lines. Every peer-reviewed paper on the subjects that I have read shows that life arose on this planet almost as soon as it got an ocean. That time span makes it unreasonable to conclude that it happened spontaneously. Does that prove God did it? No! That fact, plus the Robert Shapiro's thesis shows that science will most likely never be able to find out how.

None of the papers I have read on how multi-cellular life evolved have any confirmable hypothesis. They are all logical, they all use observations of what occurs around us today. The observations show what the possible pathways might be, but scientists will most likely never be able to confirm any of those pathways.

But determining how things can happen by looking at what we see now IS the way we have to work. As you say, it is impossible to actually see in the past, but science is working on the assumption that the laws of physics (and by extension chemistry) do work the same now as they did then.
If we can create self replicating molecules based on our best estimate of a pre-biotic earth than that is a possible way how such a thing might have happened then.
There are theories that life did indeed come from interstellar space, but that just pushed the chemistry back further. At some point it did have to appear spontaneously.


'as soon as an ocean' geologically is still a LOT of time. look at all the things that have happened to earth in a lot shorter time span (say from the appearance of the first land life to now)

As for multicellular life, the fact that we can still find lifeforms that conceivably go multicellular from their current unicellular cooperative state, combined with genetic evidence there IS no real debate about how it happened. But the knowledge to fully understand these papers would take several years of study.

 

[Kotatsu]

Paleontologists (not sure if biologists joined them or not) have been pushing to switch from taxonomy to cladistics for decades. What's held them back is that the cladistic system is so cumbersome that it becomes unusable.

I don't understand this part. What is the difference between "cladistics" and "taxonomy" in the quote above? Taxonomy is simply and entirely the system we employ for naming terminal branches and a small group of internal nodes, nothing else. There is no version of cladistics that I am aware of that does the same, and thus I cannot see how you could possibly replace taxonomy with cladistics, as that would leave all the terminal branches nameless.

Part of the issue is that classical taxonomy is more stable than cladistics or phylogeny--a new species can be added without upsetting the whole structure. Cladistics and phylogeny, on the other hand, change with each added species because they generate hypotheses about the ancestry of KNOWN taxa. That said, most paleontology papers dealing with species and inter-relationships among them include cladistic analyses.

A good case can be made for the proposition that any phylogeny that could potentially change with the addition of a new taxon is not a good phylogeny. In a good phylogeny, the relationships between the included clades should be the same as in the "true tree", regardless of if all relevant taxa are included or not. The only thing that should change with the addition of a new taxon, if you have made a good initial sampling, is support values and branch lengths.

A good taxonomy can certainly change, especially if it is a "classical" taxonomy, in which the paradigm of "bridgeable gaps" is applied. The addition of a single, previously unknown, specimen series could provide the impetus in a purely morphology-based systematics to combine two species, two genera, or even, theoretically, two species. This is because a taxonomy is flat, whereas a systematic is two-dimensional and if the new taxon "bridges the gap" between two presumably closely related genera, they may be judged to be the same genus. This happens all the time in lice, but has of course fallen out of favour now that we have more refined (genetic) data sets).

Well that's just a problem with taxonomy. I think cladistics works better, but what it will come down to is ignoring what a species is as we know it and instead use gene pools from populations. It's more informative this way.

Again, cladistics does not work better than taxonomy at the things taxonomy actually does. Cladistics does not include any set of rules for how species are to be names or how stability is to be achieved once they are named. That is the realm of taxonomy and systematics, and even so, cladistics does not in any way supplant these field. Cladistics is just another tool to use to arrive as a classification, and still requires both a systematic and a taxonomy to be useful in any way whatsoever. Otherwise you have a nameless tree, about which nothing useful can be said.

Simply put, we assume that there is a true tree. This tree is approximated by phylogenetics, delimited by cladistics, described by systematics, and named by taxonomy. A single worker may thereby arrive at a specific classification. None of these four disciplines really do the work that any of the other fields do, so it is manifestly wrong to state that one will come to supplant another. If you are dissatisfied with code-based taxonomy, you need a new taxonomy, nothing else.

From my perspective I would think ultimately to be helpful to the user of the data.

This is precisely the aim an use of taxonomy, classification, and systematics. Cladistics and phylogenetics, whether based on morphology, genetics, behaviour, or any other set of characters, is the tools we use to arrive at a specific systematic, which is then arranged according to a classification of its constituent parts, which in turn are named through the process of taxonomy.

I often provoke ecologists by saying that without taxonomy and systematics, they are collecting nonsense data, and might as well be making things up. When they -- very rarely -- protest, I simply point to the sort of ecological studies that I used to read when I worked with works, which had to do with faunal surveys. As I worked with aquatic worms, and wanted to establish a world distribution of a few species from the literature, I frequently got frustrated by ecologists simply reporting "Oligochaeta sp." or "Lumbricidae sp." as if that is information of any sort.

Anyway, I just came back from handing my thesis (380 pages!) to the print office, and am off to celebrate, so have a nice evening, all!

 

[sphenisc]

Anyway, I just came back from handing my thesis (380 pages!) to the print office, and am off to celebrate, so have a nice evening, all!

Congratulations on your final submission! I'm sure it's one of the lousiest theses ever written.

 

[Dinwar]

I don't understand this part. What is the difference between "cladistics" and "taxonomy" in the quote above? Taxonomy is simply and entirely the system we employ for naming terminal branches and a small group of internal nodes, nothing else.

I probably used the term impropperly--I meant Linnean classification. It's not the terminal branches that are the problem, it's the nodes and clades.

A good case can be made for the proposition that any phylogeny that could potentially change with the addition of a new taxon is not a good phylogeny.

To some extent, yes. However, when you add the dimension of time to the equation things get a bit more weird. You're right, any phylogeny should be merely a subset of the true phylogeny for life--however, in practice what we get are working hypotheses about interrelaltionships between organisms, and sometimes paleontologists find things that say "Nope, that hypothesis is wrong". The recent Mesozoic bird finds are an example of this. And perhaps "wrong" isn't the right term--the subset we were dealing with was much more "sub" than "set"; the data was too incomplete to give us an accurate picture, and our best hypothesis turned out to need tweeking (not major tweeking, mind you--but tweeking none the less).

Part of the issue is that modern phylogenetic methods treat every taxa as an end-node on the diagram. When you go back in time, you start dealing with the central nodes, and the system has a tendancy to react poorly to that.

Simply put, we assume that there is a true tree. This tree is approximated by phylogenetics, delimited by cladistics, described by systematics, and named by taxonomy.

Very well said. I'm going to have to steal this. This is the most succinct, accurate, and witty way to describe this system I've ever heard. Thank you.

And congrats on your submission of your thesis! Now stop wasting time on message boards and go have a beer!

 

[Acleron]

...
Anyway, I just came back from handing my thesis (380 pages!) to the print office, and am off to celebrate, so have a nice evening, all!

Well done

 

[Lowpro]

Anyway, I just came back from handing my thesis (380 pages!) to the print office, and am off to celebrate, so have a nice evening, all!

Thanks for adding to our pool of knowledge

 

[Sideroxylon]

Congratulations, Kotatsu.

 

[Kotatsu]

I probably used the term impropperly--I meant Linnean classification. It's not the terminal branches that are the problem, it's the nodes and clades.

Well, you may remember that I don't think that cladistics and phylogenetics is in any way incompatible with Linnaean systematics, either. With the specific classification Linnaeus used, certainly, but not with the method he built. There is no requirement in the Code (which is the modern incarnation f this systematic method) to give a specific rank-name to every level in a phylogenetic tree, merely to the classical ones: species, genus, family, order, class, and kingdom, with phylum and domain added later and variety taken away (for animals). The ridiculous bloating of ranks in the 1900s that gave us, between order and family, parvorder, infraorder, suborder, superfamily, and many others, and which added tribus and a whole range of suggestions for what to call subspecific taxa is exactly that -- ridiculous. But also entirely unnecessary.

Any phylogenetic tree can unambiguously be described by the Linnaean method. Certainly, you don't capture all the variation and all the structure of the tree with a linear model such as the Linnaean, but depending on your systematics and your taxonomy, you may capture much of it, and it is up to the responsible scientist to construct a classification that is as informative as possible, given a limited sets of ranks.

However, I hear you ask, what about using one of those so-called "phylogenetic taxonomies" instead? Surely a method that is designed precisely for dealing with phylogenetic trees and the naming of their parts should be superior? It may seem superior in some respects, yes, but it is essentially -- at least to the extent that I understand it, having attended a workshop on it and read most of the early papers on the PhyloCode, but by no means being an expert -- more useless than the Linnaean method.

There are many reasons that I say so, but the most fundamental is the useage of terms. I will readily admit that I like family, order, tribus, class and so on. These are familiar terms that have been used since the 1700s, and within a given group of (at least extant) organisms, they generally give a basic idea of the degree of complexity and variety they are meant to convey. Sure, this degree is not transferrable to most other groups of organisms, but as long as that is understood -- and it sadly isn't by ecologists, who may gladly compare the amount of different families in two areas without referring to a specific classification as if this was an understandable metric in any way whatsoever -- I don't see how this fact should cause any problem.

But even setting that apart, there is the matter of the inanity of sweeping away these terms which, notwithstanding what I wrote above, do give an approximate suggestion of hierarchy and variation, and replace them with the, for systematic purposes, contentless word "clade", while retaining some of the specific names for individual clades.

Which of these are the most informative (the numbers are made up):
"The class Aves contains 27 orders, the largest of which is the Passeriformes with approximately 75 families and over 700 genera"
"The clade Aves contains 27 clades, the largest of which is the Passeriformes with approximately 26 clades and over 700 smaller clades"

I would argue that the former, of course with proper references to the classification you are using, is more useful, simply because it uses different names for clades on different levels -- because that is what Linnaean ranks are -- and because there is a history behind those terms. "Clade" is a worthwhile term for divisions which exist in a given phylogenetic tree, but which fall between those divisions representing e.g. family and genus. They do not all have to be named (as is the case in amphibian classification...), and the ranks themselves need not be named, but the Linnaean ranks certainly have an immense value as being benchmarks so that the level of diversity can be approximated. "Eukaryota" is a clade, but so is "Cygnus" (swans). However, no one would ever claim that Eukaryota is a genus or that Cygnus is a domain.

(I am here ignoring the abominable way the PhyloCode, or at least early incarnations of it, are actively working against having taxonomy reflecting relationships by fixating genus names in the name of stability, so that a Carduelis will be named Carduelis even if we find that it is more closely realted to Carpodacus. Stability is good, but the flexible stability of the Linnaeus-based Code is far superior.)

Part of the issue is that modern phylogenetic methods treat every taxa as an end-node on the diagram. When you go back in time, you start dealing with the central nodes, and the system has a tendancy to react poorly to that.

This is mainly a funding problem and an incapacity of many modern workers to understand that morphological data is as useful as genetic data. As the vast majority of phylogenies are constructed solely from molecular data, you can necessarily only use extant or recently extinct organisms. I started preparing a morphological data set for the lice I was working with and wanted to analyse that, but my supervisor simply said that "No one does that any longer" and I never finished the data set, nor used it for anything other than a set of notes when I did some species descriptions.

Also, again, there are no fossil lice of the group I'm working on (suborder Ischnocera), and I am still waiting for a mail from you saying, "Hey, Kotatsu, I was out doing fieldwork and uncovered this vast horde of one million fossil lice, do you want them?" I find it cruel of you to keep these lice from me.

Congratulations on your final submission! I'm sure it's one of the lousiest theses ever written.

And congrats on your submission of your thesis! Now stop wasting time on message boards and go have a beer!

Well done

Thanks for adding to our pool of knowledge

Congratulations, Kotatsu.

Thank you, all. I think that by the end of the week (or next week?) the electronic version of the 130-page introduction will be online, if anyone's interested. Learn all about the history of parasite classification!

 

[Kotatsu]

I wish I could participate more often here because you guys can teach me stuff. However current work pressure is interfering. I'll get back to you all when the current hectic schedule subsides.

I am perfectly willing to believe you, but to me, this reads as "I have no examples or arguments to back up my assertions with now that actual scientists are questioning me". If your work schedule is so full, try getting your PhD friend form whom you have got your information in the first place to come here. If he/she makes the claims you say he/she makes, then he/she should be equally, or better placed, to answer the questions put to you. In other words, if we can get to discuss this with the source of your nonsense, your continued participation becomes less essential.

 

[Kotatsu]

Would love a link or summary if you do locate it.

Just to reconnect: I have the PDFs of the papers I was thinking of now, so if you want them, please PM me some way to send them to you. Some may be available through Google scholar and so on, but I figure it is easier for me to just send your the PDFs now that I have them.

 

[Kotatsu]

They're the same population if they're both part of the group that actually interbreeds (this sentence is very sloppy, but I think it gets my point across). There's have to be some limit, and some other rules--a single member of a population breeding with a single member of another population does not mean that those two are the same population, and ring species play merry havoc with pretty much any definition of anything--but it would remove some of the more silly consequences of the term "species".

The problem almost always comes back to "what to do with asexual organisms". The approach that would give the most stable understanding of what a species or a population may be would, to my mind, be one that starts with asexual organisms and then tries to find a way to include also sexual ones, because it seems to be way too hard to do it the other way around.

I'd say they are new species once the separation exists in the first place because "species" makes more sense when you recognize that the gene flow is what determines it. Although this is contentious of course, and impossible to determine for ancient animals to a great degree, but it makes sense.

It is also impossible to determine for extant animals, as you cannot know a priori that two populations that live on separate islands will not in the near future come in contact with each other due to land rising or a bridge being built or something, and then be able to recommence gene flow between themselves again. Fish living upstream and downstream of a recently constructed dam could be said to be separated, and should then be different species, but once the dam breaks down due to poor engineering ten years later? Are they still different species?

Incidentally, I downloaded a paper on "Parallel speciation, despeciation and respeciation: implications for species definition" (G. F. Turner, Fish and Fisheries, 2002, 3, 225-229) which I am aching to read, and now I finally have time!

If you cut the middle populations out, the living members would clearly be two separate speceis; however, until that happens, what do you call them?

In practice this is very simple:
For all organisms except birds: different subspecies or different populations of the same species.
For birds: different species.

Despite being a birdwatcher, I have never liked the national taxonomic committees that exist for birds, and especially not the way some of them seem to want to treat anything that is slightly different and identifiable in the field under good conditions as a separate species, regardless of if there is any actual supporting evidence or not (see: Redpolls, Common and Pallid Swift). Bird taxonomy as understood by the amateurs who argue about these things on the internet is a world apart from actual taxonomy.

You are quite correct, perhaps a range.

The main problem I see with allowing the use of averages and means to delimit any section of life is that it seems to inevitably give rise to the poor taxonomy that considers a different in the average measurement of X to be sufficient difference between two series of specimens for the to be different species. Zlotorzycka described over a dozen new subspecies of Anatoecus dentatus and Anatoecus icterodes, one from each host (ducks) in Central Europe (= Poland) alone, because they differed slightly in their average width and so on. There will always be people like that, who see an average difference of 0.0001mm between two groups of specimens as highly significant, because that fits into their preconceived notions of where the lines ought to be drawn.

Give me any definition for species and I can poke holes in it. I'm sure Kotatsu can do more.

Like I said, the ideas of de Queiroz on this (I will post references when I get to work) is virtually unassailable, but only (essentially) by making "species" very vague.

 

[Kotatsu]

Incidentally, a paper on water beetle taxonomy was hanging on my door when I came to work this morning. It contains gems such as these:

It should be noted that the fierce competitor, the neo-nazi Manfred Jäch from the Naturhistorisches Museum Wien, Wien, Austria is one of the editors (read "controllers") of the Baltic Journal of Coleopterology.

In the present and future papers we want to show that the Makhan genera are valid and that Makhan is not the "rogue taxonomist" that many of the international scientific Gestapo have incorrectly and illegally portrayed.

They do not even know how to rear larvae from the adults! can they show us a Hydrochus larva? This answer is no! Are they scientists or stooges! We believe they are stooges!

Manfred Jäch has shown himself to be a pompous, arrogant, ignorant and highly jealous individual who is greatly frustrated about getting funds for his own research and lives solely from tax-payer funded money (he cannot make money by any other means because he is unemployable for mainstream labouring work like most academics, and unsuitable for jobs where one has to follow orders).

No further material will ever be sent to this person. Jach's [sic] neonazi behaviour makes him a world laughing stock and is so typical of the country he resides in.

The whole article is available from here ("The genera Hydrochus..." by Makhan, Khani and Exxetpanah), a small purportedly scientific journal which has no peer-review apart from the editor -- who seems to write most of the articles -- also reading it. His publications may or may not be worthwhile -- I am no coleopterologist -- but he includes in his publication also letters he has written to various governmental bodies in Australia and researchers and editors, complaining about the oppression and suppression of his work. The foreword to one of his books -- on Australian beetles -- was written by him and signed by a "prominent salesman" in Brisbane, but later retracted when he was sued for having stolen the text from a scientist he contacted earlier on (this part of one of his papers is very unclear).

Anyway, I found this hilarious, and traced the dispute with Jäch back to a paper the latter wrote in Koleopterologische Rundschau in 2006, entitled "Taxonomy and Nomenclature threatened by D. Makhan" (available from their homepage for the price of 0.1 euros). This text, if accurate, seem to be very enlightening, claiming for instance that Makhan demands 120,000 euros from anyone who wishes to see his collection, lying about his academic position to be able to borrow specimens, and does not shy away from publishing the same article twice.

I like this sort of dispute very much. There are a lot of papers like this, and whenever I need to do something entirely else, I start searching for this kind of thing, and enjoy it immensely. Only very rarely do I get to see authors that actually call other authors neonazis. In a different paper by Hawkeswood, he compares a taxonomist at a museum in Australia with Stalin, though I lost the exact reference.

 

[Lowpro]

It is also impossible to determine for extant animals, as you cannot know a priori that two populations that live on separate islands will not in the near future come in contact with each other due to land rising or a bridge being built or something, and then be able to recommence gene flow between themselves again. Fish living upstream and downstream of a recently constructed dam could be said to be separated, and should then be different species, but once the dam breaks down due to poor engineering ten years later? Are they still different species?

According to my definition yes the two populations would be the same species again, but understand that I'm also trying to describe gene flow/restriction now, not classification; I'd rather not use the term species due to preconceptions.

And as for extant animals, yea we cannot answer for that, I really am referring to answering for what we have now. I am not saying we should only consider species as a classification, but consider species as a snapshot of gene flow. We are able to do this for current species, not so muh for unknown (undiscovered) organisms or fossils.

Interestingly though Kotatsu, if that damn broke in ten years, there's a possibility that those two fish may never have gene flow. In ten years who knows, there could be a deviation of mating habits and the females don't lay the eggs properly (slow water versus fast riffles determine how a female may be conditioned to lay her eggs, and the new species from a slow river may not adapt, nor may the males either...). In Alabama we've seen a LOT of this from Darter populations. There may also be morphology changes too that cause a sexual selection that further restrict interbreeding and restrict gene flow.

 

[Kotatsu]

According to my definition yes the two populations would be the same species again, but understand that I'm also trying to describe gene flow/restriction now, not classification; I'd rather not use the term species due to preconceptions.

I would say that generally, such a division has no practical use unless it is shown to be durable. Gene flow cannot be meaningfully measured over such short durations, I think, because the lower time limit would necessarily be arbitrary.

My ex-girlfriend broke up with me when we were on a trip to Berlin, and she went back to Würzburg where she was studying, and I went back to my hometown. What may prudently be called gene flow between the two of us ceased instantly. If this happened en masse, that would still not mean that the population in Würzburg and the population in Gothenburg suddenly from that moment on became separate "species" or whatever you want to call them.

Physical separation introduces only a formal and perhaps an actual restriction to gene flow, but not necessarily a persistent restriction, and you will have to persuade me that such separation that is not known to be, or at least has not been shown to be, of any significant duration is a biologically meaningful separation.

Interestingly though Kotatsu, if that damn broke in ten years, there's a possibility that those two fish may never have gene flow. In ten years who knows, there could be a deviation of mating habits and the females don't lay the eggs properly (slow water versus fast riffles determine how a female may be conditioned to lay her eggs, and the new species from a slow river may not adapt, nor may the males either...). In Alabama we've seen a LOT of this from Darter populations. There may also be morphology changes too that cause a sexual selection that further restrict interbreeding and restrict gene flow.

This is certainly a possibility, but it is not enough data to determine unambiguously whether gene flow has stopped between the two populations in any manner that will prove to be significant under a longer time period. It may certainly be possible to show this for some specific cases, but I do not believe these cases will lend themselves to generalizations of organisms in general. If the bell curve-ends of both populations still overlap sufficiently, that may be sufficient to permit gene flow in a future, mixed, population.

I think, in general, that a good place to divide populations into taxa is when multiple (at least two) independent species concepts suggest they are different taxa. I will have to reread the de Queiroz papers (and will send them to you, Sideroxylon, today) on this, though.

 

[Venom]

You'll note that I keep saying "...by the biological species concept". There's a reason for that: we really don't have a good definition of the term "species". The biological species concept is the idea that any actually OR POTENTIALLY interbreeding populations are the same species. Problem is, it's not really meaningful in many cases. I mean, if the population doesn't actually interbreed, does it make sense to talk about potentialities? For example, if you have fish in small pools, all more or less isolated and carried by birds from one lake to another, does it make sense to talk about the same species of fish in all those issolated lakes? Or, conversely, there are insects that lay their eggs on fruit. If they lay their eggs on apples they mate at one time of the year; if they lay their eggs on pears they mate at another time (not really clear why). Are they separate species? How far do you go with this? I know a lot of women who refuse to sleep with tall, lanky guys with extremely curly hair and a penchant for talking about rocks for hours on end. Are tall, lanky geologists a different species from those girls?

Other species concepts do exist. Paleontology uses the morphospecies concept--when it looks different enough, we call it a new species. As you can imagine, all kinds of fun problems arise--for example, it took a long time to realize that ammonites are sexually dimorphic. There are also species concepts defined by genetic similarities, and I believe one or two more that I'm not thinking of just now.

But yeah, that's the basics of allopatric speciation (the idea you're talking about).

How do taxonomists recognize subspecies? All the relevant populations can interbreed and the differences are subtle.

I notice that many historic subspecies assignments get reassigned often.

ex. Panthera leo atrox ===> P. leo atrox ===> P. atrox

Is this just because of sloppy/outdated work? Or is it always that way today.

 

[Dinwar]

How do taxonomists recognize subspecies?

It really depends on the taxonomist. Some don't like the idea. Some like it too much. I believe the Code deals with this issue to some extent, but like the rest of the Code those sections deal with proper nomenclature. Recognition is another world entirely, and is somewhat subjective. I mean, there are actual tests you can run to determine if something is the same species as something else or not--a subspecies level can be considered a biologically meaningless ranking. That said, the real-world answer is that they study the taxa hard enough to be able to differentiate, to their satisfaction and the satisfaction of other experts, between various populations of the same species.

The question does get pretty profound, however. The issue is, how do you determine what's significant from what's not? It's not AS hard with modern organisms, as you can usually grab some DNA and relatively easily get an answer (anything coded by DNA is going to be heritable); however there are complications, such as things NOT in the DNA that are heritable. And this is only easy compared to doing something similar with the fossil record, where it's usually impossible. Shared, derived traits are the standard for paleontologcial taxonomy (with the caveat that "derived" merely means "different from the somewhat arbitrarily defined archaeic form").

I notice that many historic subspecies assignments get reassigned often.

ex. Panthera leo atrox ===> P. leo atrox ===> P. atrox

Is this just because of sloppy/outdated work? Or is it always that way today.

ETA: Never mind--didn't see the strike-through on the second P. leo atrox.

As for the rest of it, taxonomy is always going to be doing this. Different researchers emphasize different aspects of the organism, and new techniques lead to new (and, one hopes, better) ways to determine how organisms are related to one another. I know that the entire genus Titanocarcinus (a type of very small crab) was revised about 6 years ago--I actually got to see the page proofs of it, because one of my professors did the revising. A friend of mine is also revising the Galatheid family. The discovery of more basal birds than Archaeopteryx necessitated some nomenclatural shuffling as well. We've also recently been finding some facinating examples of dinosaurs previously classified as different species, which have recently been shown to merely be different stages of growth. So as long as there are new discoveries to be made in biology and paleontology taxonomists will argue about what to call things.

 

[six7s]

It really depends on the taxonomist. Some don't like the idea. Some like it too much

I quite like aronra's 5-part youTube series on Falsifying Phylogeny cos - even though he talks at a gazillion miles per hour - it's easy to understand

ETA: part 1: